Je Voudrais

MD Jérôme Honnorat
email: jerome.honnorat@chu-lyon.fr

TCR T-cell receptor VGCC voltage-gated calcium channels

DNA deoxyribonucleic acid GAD65 glutamic acid decarboxylase 65 GWAS genome-wide association studies HLA human leukocyte antigen IgLON5 immunoglobulin-like cell adhesion molecule 5 KIR killer cell immunoglobulin-like receptor LD linkage disequilibrium LE limbic encephalitis LEMS Lambert-Eaton myasthenic syndrome

LGI1 leucine-rich glioma

Introduction

The major histocompatibility complex Pour explorer cette hypothèse, nous avons mené une étude basée sur des entretiens des patients pour rapporter les antécédents familiaux d'auto-immunité chez 68% des 65 patients inclus. Les maladies auto-immunes et les modèles potentiels d'hérédité étaient très divers, suggérant une prédisposition génétique hétérogène qui implique probablement des gènes différents.

Dans un deuxième travail, nous avons cherché à mieux caractériser l'association entre l'allèle HLA DRB1*11:01 et les maladies à anticorps anti-CASPR2 en utilisant une classification clinique précise de 56 patients grâce à une analyse en cluster. Nous avons donc obtenu quatre sousensembles différents de patients (EL isolée, EL combinée à d'autres symptômes, syndrome de Morvan, et neuromyotonie acquise). Les deux groupes d´EL semblaient indistincts lorsque nous avons étudié leurs caractéristiques biologiques (titres d'auto-anticorps, présence ou non dans le LCR, association d'un cancer…). A l'opposé, les syndromes de Morvan et les neuromyotonies avaient des caractéristiques très différentes des EL, permettant de séparer trois groupes ayant des attributs bien distincts. Nous avons ensuite effectué un génotypage HLA par NGS chez 30 patients, et trouvé que DRB1*11:01 était surreprésenté uniquement chez les patients ayant une EL (94% de porteurs), tandis que les patients atteints de syndrome de Morvan et de neuromyotonie acquise présentaient des fréquences de porteurs similaires à celles du groupe témoin. Ces résultats soutiennent l´existence de mécanismes pathogènes différents, en particulier entre l´EL non paranéoplasique et le syndrome de Morvan généralement associé au thymome malin. De plus, nous avons utilisé une analyse in silico pour comparer l'affinité des différentes molécules HLA présentes dans notre cohorte EL pour les peptides dérivés de CASPR2, trouvant un chevauchement modeste dans leur spectre de liaison.

L'objectif de notre troisième étude était de déterminer s'il existe des différences entre les patients avec une EL à anticorps anti-LGI1 portant DRB1*07:01 et ceux ne portant pas cet allèle.

Nous avons constaté que les non-porteurs (9/72, 12%) étaient plus fréquemment de jeunes femmes, présentant donc un profil démographique atypique pour cette maladie. De plus, dans la même étude, nous avons étudié la valeur clinique et pronostique de la positivité du liquide céphalo-rachidien (LCR) pour les anticorps LGI1 dans une cohorte étendue de 134 patients. Nous avons observé que les patients avec (105/134, 78%) et sans (29/134, 22%) anticorps détectables dans le LCR étaient cliniquement indiscernables, bien que certaines différences dans les tests complémentaires et les résultats du pronostique à long terme suggèrent que la positivité du LCR traduit une réponse immunitaire plus intense. Cependant, il n'y avait aucune association entre la positivité du LCR et l´HLA. Finalement, lorsque nous avons comparé le spectre de liaison aux peptides de DRB1*07:01 à celui des molécules DRB1 trouvées dans les non-porteurs de DRB1*07:01, nous avons obtenu un grand chevauchement, comprenant principalement des peptides dans le domaine riche en leucine.

Au contraire, les affinités de liaison des hétérodimères DQ associés à ces DRB1 étaient très diverses, ce qui suggère que les molécules DRB1 sont très probablement impliquées dans une présentation altérée des peptides dérivé de LGI1.

La quatrième et dernière étude visait à élargir nos connaissances concernant la présentation clinique et la pathogenèse de l'EL à anticorps anti-AK5. Nous avons examiné 10 nouveaux patients ainsi que 16 cas de la littérature, fournissant une description plus détaillée de leur présentation clinique, qui était caractérisée par une amnésie sévère (100%), une dépression (68%), une perte de poids/asthénie/anorexie (44%), et l'absence de crises convulsives au début de la maladie, mais ultérieurement présentes chez 16% des patients. Tous les patients présentaient des anomalies du LCR, l'IgG1 était la sous-classe prédominante dans le LCR et le sérum, et des hyper-intensités du lobe temporal évoluant vers une atrophie sévère étaient observées dans près de 90% des cas. Nous avons également génotypé 11 patients à l'aide de NGS et trouvé une association avec l'haplotype de classe II DQA1*05:01-DQB1*02:01-DRB1*03:01 (73% de porteurs). Enfin, nous avons pu observer l'infiltrat massif de lymphocytes T CD4+ et CD8+ avec une expression intense de granzyme B dans une biopsie du lobe temporal d'un patient. Corrélé à l'analyse protéomique du LCR montrant que les voies de l'apoptose et des réponses immunitaires innées/adaptatives étaient enrichies par rapport aux patients à anticorps anti-LGI1/CASPR2/Yo/Ma2, nos résultats permettent de montrer que l´EL à anticorps anti-AK5 a une pathogenèse très distincte dominée par les lymphocytes T et conduisant à une réponse cytotoxique agressive.

Nos résultats mettent en évidence plusieurs point importants. Premièrement, il existe dans certains sous-groupes une forte association entre un allèle HLA spécifique et une EL nonparanéoplasique (LGI1 et CASPR2). Ces patients ont des anticorps de sous-type IgG4.

Deuxièmement, une association plus faible avec l´haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01 est observée dans d'autres cas (GAD65 et AK5). Chez ces patients, les troubles neurologiques ne sont pas liés au cancer, les patients ont des anticorps de sous-type IgG1, et les lymphocytes T semblent jouer un rôle majeur dans la pathogenèse des syndromes neurologiques.

Troisièmement, l´implication du système HLA dans la prédisposition génétique aux syndromes neurologiques paranéoplasiques semble faible. En conclusion, les résultats de cette thèse soutiennent un rôle significatif de l´HLA dans la pathogenèse des encéphalites auto-immunes. Notre travail a permis une meilleure caractérisation des associations précédemment rapportées ainsi que la description de nouveaux haplotypes, soulignant l'importance d'une classification clinique et biologique précise des encéphalites autoimmunes pour mieux comprendre les mécanismes pathogéniques qui semblent être différents suivant les entités étudiées. combined with other features, Morvan syndrome, and acquired neuromyotonia), which showed different immunological characteristics, except for the two LE groups that appeared to be indistinct in terms of autoantibody titers and spectrum. We then performed HLA genotyping by NGS in 30 patients with available DNA, and found an overrepresentation of DRB1*11:01 only in the LE group (94% carriers), while patients with Morvan syndrome and acquired neuromyotonia presented carrier frequencies similar to those of the control cohort. These results support different pathogenic mechanisms, particularly between non-paraneoplastic LE and Morvan syndrome that is usually associated with malignant thymoma. Additionally, we used an in silico analysis to compare the CASPR2-derived peptides affinity of the different HLA molecules present in our LE cohort, finding a modest overlap in their binding spectrum.

The objective of our third study was to determine whether differences exist between patients with anti-LGI1 LE carrying DRB1*07:01 and those not carrying these allele. We found that noncarriers (9/72, 12%) were more frequently young women, therefore showing an atypical demographic profile for this disease. Moreover, in the same study, we investigated the clinical and prognostic value of cerebrospinal fluid (CSF) positivity for LGI1 antibodies in an extended cohort of 134 patients. We observed that patients with (105/134, 78%) and without (29/134, 22%) detectable antibodies in the CSF were clinically indistinguishable, though some differences in paraclinical tests and long-term outcome suggested that those with positive CSF have a more intense immune response. However, there was no association between HLA carrier status and anti-

LGI1 CSF positivity. Interestingly, when we compared the peptide-binding spectrum of DRB1*07:01 to that of the DRB1 molecules found in non-DRB1*07:01 carriers, we obtained a large overlap, mostly including peptides in the leucine-rich domain. To the contrary, the binding affinities of the DQ heterodimers associated with these DRB1 were highly diverse, suggesting that DRB1 molecules are those involved in an altered LGI1-derived peptides presentation.

The fourth and last study aimed to expand our knowledge regarding the clinical presentation and pathogenesis of anti-AK5 LE. We reported 10 new cases and reviewed 16 from the literature, providing a more detailed description of their clinical presentation, which was characterized by severe amnesia (100%), depression (68%), weight loss/asthenia/anorexia (44%), and typically no seizures at onset but lately present in 16% of the patients. Moreover, all patients presented CSF abnormalities, IgG1 was the predominant subclass in both CSF and serum, and temporal lobe hyper-intensities evolving into severe atrophy were observed in nearly 90% of the patients. We also genotyped 11 patients using NGS and found an association with the class II haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01 (73% carriers). Furthermore, the massive infiltrate of CD4+ and CD8+ T-cells with intense granzyme B expression observed in a temporal brain biopsy of one patient, and the CSF proteomic analysis showing that apoptosis and innate/adaptive immune pathways were enriched compared to patients with LGI1/CASPR2/Yo/Ma2 antibodies, suggest a very distinct pathogenesis in anti-AK5 LE mediated by T-cells leading to an aggressive cytotoxic response.

Our results sustain the existence of a strong association between specific HLA alleles and non-paraneoplastic LE with IgG4 antibodies (LGI1 and CASPR2), while a weaker association is observed between the haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01 and other types of encephalitis with IgG1 antibodies (GAD65 and AK5). In this second group, the neurological disorders are not associated with cancer and T-cells seem to play a major role in the pathophysiology. Finally, there is likely an absence of HLA involvement in the genetic predisposition to paraneoplastic neurological syndromes. In conclusion, the results of this PhD project support a significant role of HLA in the pathogenesis of autoimmune encephalitis and related disorders, based on a better characterization of previously reported associations as well as the description of new ones, highlighting the importance of precise clinical and biological classifications of autoimmune encephalitides to better understand the mechanisms of these diseases that seem to be different according to the subgroups.

INTRODUCTION

The discovery of antibodies against neuroglial antigens of the peripheral and/or central nervous system (CNS) has greatly expanded the field of neuroimmunology and revolutionized neurological practice. Among these antibodies, those targeting surface receptors and synaptic proteins, such as antibodies against N-methyl-D-aspartate receptor (NMDAR) and others related to autoimmune encephalitis [START_REF] Dalmau | Paraneoplastic Anti-N-methyl-D-aspartate Receptor Encephalitis Associated with Ovarian Teratoma[END_REF][START_REF] Dalmau | Autoantibodies to Synaptic Receptors and Neuronal Cell Surface Proteins in Autoimmune Diseases of the Central Nervous System[END_REF], have particularly contributed to this development, not only for its value as diagnostic biomarkers but also due to its pathogenic role.

However, the primary trigger of the immune tolerance breakdown is still unknown for the majority of autoimmune encephalitides.

Genetics is likely to play a major role in the pathogenesis of autoimmune encephalitides.

First, as mentioned before, the absence of obvious environmental triggers for most of these disorders suggests that the underlying mechanisms could be related to inherent, genetic characteristics of the patients. Second, some acquired factors such as cancer may lead to the development of a paraneoplastic neurological syndrome (PNS) in some subjects, while not in others, probably reflecting the interaction with a high-risk genotype. Third, the same antibody may appear in association with different phenotypes and notably with and without a tumor, suggesting the existence of distinct pathogenic pathways, some of them likely genetics-dependent. Finally, it is frequent that patients presenting with some types of autoimmune encephalitis and related disorders have other systemic autoimmune diseases, suggesting a shared predisposition to self-tolerance loss.

Thus, genetic investigations in autoimmune encephalitis may provide important insights regarding the pathogenesis and nosological classification of these disorders.

The Major Histocompatibility complex

The major histocompatibility complex (MHC), and more specifically the human leukocyte antigen (HLA), is the main genetic factor related to autoimmune diseases, accounting for a half of known genetic predisposition [START_REF] Seldin | The genetics of human autoimmune disease: A perspective on progress in the field and future directions[END_REF]. Although more than 200 associations between HLA and diseases (immune-mediated or not) have been described, the underlying pathogenic mechanisms remain poorly defined [START_REF] Simmonds | The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF]. Initially, the particular genetic characteristics of HLA, and the complex interaction with other genes and environment have prevented further clinically-meaningful developments in this field [START_REF] Seldin | The genetics of human autoimmune disease: A perspective on progress in the field and future directions[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF]. However, in recent years technological advances and increasing knowledge about peptide-HLA interactions has enabled to further understand the role of HLA in disease susceptibility [START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF].

Genetic characteristics of the MHC

The MHC is located on chromosome 6p21.3 and represents the most dense and polymorphic region of the human genome, comprising nearly 270 genes with more than 30000 alleles [START_REF] Klein | The HLA System[END_REF][START_REF] Vandiedonck | The human Major Histocompatibility Complex as a paradigm in genomics research[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF][START_REF] Robinson | IPD-IMGT/HLA Database[END_REF].

The MHC is divided in three regions: class I, II, and III (Figure 1) [START_REF] Klein | The HLA System[END_REF][START_REF] Vandiedonck | The human Major Histocompatibility Complex as a paradigm in genomics research[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. MHC class III differs from class I and II as it only contains genes encoding non-HLA molecules, being either relevant to the innate immune responses such as the complement or the tumor necrosis factor, or completely unrelated to the immune system [START_REF] Vandiedonck | The human Major Histocompatibility Complex as a paradigm in genomics research[END_REF][START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. Classic HLA class I includes HLA-A, B, and C, while the main class II genes are DP, DQ, and DR [START_REF] Klein | The HLA System[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. Class I genes encode the alpha chain of the HLA class I molecule, which includes the peptide-binding groove; the beta-chain is the β2-microglobulin, which is encoded by a gene outside of the MHC on chromosome 15 [START_REF] Klein | The HLA System[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. HLA class II genes code for alpha (i.e. DPA) or beta (i.e. DPB) chains, both of them form the peptide-binding groove [START_REF] Klein | The HLA System[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF].

The degrees of genetic density and polymorphism are not uniform across the MHC: class III is particularly dense and moreover it harbors almost no pseudogenes, while HLA-B is the most polymorphic locus, and class II genes encoding beta-chains show a notably greater allelic diversity than those encoding alpha-chains (Table 1) [START_REF] Vandiedonck | The human Major Histocompatibility Complex as a paradigm in genomics research[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. Furthermore, much of the variability of classical HLA concentrates in the exons that encode the amino acids of the peptide-binding groove [START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. The extreme variation of HLA is thought to have been evolutionarily favored since a greater diversity of HLA molecules and their repertoires are associated with a broader and therefore more efficient immune reaction against infections [START_REF] Vandiedonck | The human Major Histocompatibility Complex as a paradigm in genomics research[END_REF]. HLA alleles follow a nomenclature based on different digit-levels. The first two digits represent the allele group, which usually corresponds to the serological antigen. The two following digits describe the allelic subtype that encodes a given protein and therefore determine the peptidebinding affinities. Further digits are used to distinguish DNA variants (synonymous substitutions in exons or polymorphisms in introns) that do not change the amino acid sequence. Finally, several suffixes may also be added to indicate particular expression characteristics, such as N and L for alleles with respectively null or low expression (Figure 2) [START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF]. in the genome, meaning that alleles from closely located loci are found (and inherited) in a nonrandom distribution [START_REF] Vandiedonck | The human Major Histocompatibility Complex as a paradigm in genomics research[END_REF][START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. Haplotypes composition and frequency varies greatly between populations, and moreover LD is not uniform across the MHC [START_REF] Vandiedonck | The human Major Histocompatibility Complex as a paradigm in genomics research[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF]. Besides, LD sometimes makes it difficult to establish the causal locus in diseaseassociation studies, but conversely it allows to infer HLA by imputation methods in large samples and population studies [START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF].

Classic HLA molecules: structure and function

HLA class I and II molecules are glycoproteins with some shared and differential characteristics. The heavy, alpha chain of HLA class I includes two domains forming the peptide binding groove (α1 and α2), an immunoglobulin-like domain (α3), a transmembrane region, and a cytoplasmic tail. However, the light chain of HLA class I, the β2-microglobulin, does not form part of the peptide-binding groove and is indeed encoded by a gene located outside the MHC.

Conversely, HLA class II molecules comprise two heavy chains (alpha and beta) with the same structure (a binding domain, α1/β1; an immunoglobulin-like domain, α2/β2; a transmembrane region, and a cytoplasmic tail) (Figure 3) [START_REF] Klein | The HLA System[END_REF][START_REF] Rudolph | How TCRs bind MHCs, peptides, and coreceptors[END_REF][START_REF] Blum | Pathways of antigen processing[END_REF]. peptides up to 24 amino acids in length or even longer; in this case, the N-and C-termini are more accessible to the TCR (Figure 4) [START_REF] Klein | The HLA System[END_REF][START_REF] Marsh | HLA facts book[END_REF][START_REF] Rudolph | How TCRs bind MHCs, peptides, and coreceptors[END_REF]. neutral, green [START_REF] Rapin | The MHC motif viewer: a visualization tool for MHC binding motifs[END_REF] The floor of the peptide-binding groove has several "pockets" where the interaction between the HLA and the so-called binding core of the peptide, which is usually 9 amino acids long, takes place. Some of these pockets are key to determining the HLA repertoire, since they are particularly important for the bound between the peptide and the HLA (Figure 4). Indeed, the residues that define these pockets differ from one allele to another and are the most polymorphic of the HLA amino acid sequence [START_REF] Klein | The HLA System[END_REF][START_REF] Marsh | HLA facts book[END_REF]. However, the aforementioned affinity is not absolutely specific, and a given HLA molecule is able to bind thousands or even more than a million of peptides, while a single peptide might be presented by different HLA that therefore share, at least partially, their repertoire (Figure 5) [START_REF] Rapin | MHC motif viewer[END_REF][START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF].

HLA class I molecules are expressed by all nucleated cells and generally, but not exclusively, present endogenous peptides generated by proteosomal proteolysis to CD8+ T-cells;

additionally, HLA class I can be recognized by killer cell immunoglobulin-like receptors (KIR) and leukocyte immunoglobulin-like receptors (LILR) [START_REF] Klein | The HLA System[END_REF][START_REF] Blum | Pathways of antigen processing[END_REF][START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF]. Conversely, HLA class II is only expressed by professional antigen presenting cells that interact with CD4+ T-cells, and present peptides (traditionally considered of mainly exogenous origin) obtained by lysosomal proteolysis after endocytosis and phagocytosis [START_REF] Klein | The HLA System[END_REF][START_REF] Blum | Pathways of antigen processing[END_REF][START_REF] Jurewicz | Class II MHC antigen processing in immune tolerance and inflammation[END_REF]. In order to interact correctly with the HLA-peptide complex, the TCR must be placed diagonally with the less polymorphic loops of the variable domain, CDR1 and CDR2, binding the walls, and the highly variable loop CDR3 interacting with the peptide (Figure 6) [START_REF] Klein | The HLA System[END_REF][START_REF] Rudolph | How TCRs bind MHCs, peptides, and coreceptors[END_REF]. The process also needs the involvement of several co-receptors such as CD4 and CD8 [START_REF] Klein | The HLA System[END_REF][START_REF] Rudolph | How TCRs bind MHCs, peptides, and coreceptors[END_REF]. [START_REF] Klein | The HLA System[END_REF]. Once in the thymic medulla, a large amount of self-peptides are again presented by HLA on medullary thymic epithelial cells, macrophages, and dendritic cells, which also express several co-stimulatory molecules that allow the establishment of stronger interactions [START_REF] Klein | The HLA System[END_REF]. The expression of this wide array of self-peptides is controlled by the AIRE (autoimmune regulator) gene [START_REF] Anderson | Projection of an immunological self shadow within the thymus by the aire protein[END_REF].

However, in this phase, thymocytes showing high-affinity interactions receive a signal leading to apoptosis in order to suppress auto-reactivity and promote self-tolerance; in contrast, those with lower affinities become naïve T-cells that leave the thymus (Figure 7) [START_REF] Klein | The HLA System[END_REF].

Additionally, some thymocytes with an intermediate affinity against the peptide-HLA complexes constitute a special subpopulation of T-lymphocytes known as T regulatory (Treg) cells, which contribute to peripheral immune tolerance by inhibiting auto-reactive T-cells [START_REF] Jurewicz | Class II MHC antigen processing in immune tolerance and inflammation[END_REF].

Mechanisms of the association between HLA and autoimmune diseases

Although more than 200 associations between HLA and autoimmune diseases have been described, the underlying mechanisms involved are yet unknown for almost all of them, mainly due to the particular genetic characteristics of MHC described above, the limited knowledge regarding the interaction between HLA and the targeted self-peptide, and the additional role that other non-HLA genes as well as environmental factors likely play (Caillat-Zucman, 2017). However, interesting advances have recently been made in both the TCR-peptide-HLA interaction and the modifications in genetic expression (Table 2) [START_REF] Simmonds | The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF]. [START_REF] Illing | Immune self-reactivity triggered by drug-modified HLA-peptide repertoire[END_REF] Increased HLA expression C allotypes Crohn´s disease [START_REF] Kulkarni | Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease[END_REF] Epistatic interaction with ERAP1 B27 Ankylosing spondylitis [START_REF] Evans | Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility[END_REF] B51 Behçet disease [START_REF] Kirino | Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1[END_REF] Many of the mechanisms proposed to be involved in the association between HLA and autoimmunity imply the escape of thymic negative selection because of disturbances in the TCRpeptide-HLA interaction, such as alternate docking (i.e. the TCR binds the peptide-HLA complex with an abnormal geometry) or TCR stabilization of weak peptide-HLA complexes; in both scenarios the affinity of the TCR-peptide-HLA bound is sufficiently low to prevent apoptosis in the thymus but strong enough to initiate an immune response in the periphery [START_REF] Simmonds | The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF]. Moreover, an alternate docking can provoke that the TCR only interacts with a small area of the peptide, which increases the probability for this TCR to be activated in the periphery by different peptides sharing the few residues recognized (hotspot molecular mimicry) [START_REF] Dendrou | HLA variation and disease[END_REF]. Besides, a given peptide may bind several HLA using distinct residues, which in turn modify the amino acids that interact with the TCR (altered register), explaining the diverse effects mediated by different HLA (i.e. risk and protective alleles) [START_REF] Simmonds | The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF]. Furthermore, post-translational modifications of both self and foreign peptides may create neo-antigens in the periphery, activating auto-reactive T-cell populations that were not eliminated in the thymus since they were not exposed to those peptides [START_REF] Sollid | Molecular mechanisms for contribution of MHC molecules to autoimmune diseases[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF][START_REF] Jurewicz | Class II MHC antigen processing in immune tolerance and inflammation[END_REF]. Interestingly, it has been shown that small molecules such as certain drugs (abacavir, carbamazepine) are also able to bind HLA altering the conformation of the peptide-binding groove, therefore modifying its repertoire and generating neo-epitopes [START_REF] Sollid | Molecular mechanisms for contribution of MHC molecules to autoimmune diseases[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF].

In addition, altered expression of HLA molecules has recently been associated with autoimmunity, including polymorphisms in non-coding regions such as promoters, and epigenetic modifications, particularly DNA methylation (Caillat-Zucman, 2017). Epistatic interactions with non-HLA genes is another mechanism that might modify the levels of HLA expression, as it has been described between the locus ERAP1, encoding an aminopeptidase involved in peptide processing, and several HLA class I [START_REF] Sollid | Molecular mechanisms for contribution of MHC molecules to autoimmune diseases[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF]. Finally, future research should address the identification of polymorphims that modify genetic expression using eQTL (expression quantitative trait loci) mapping, the evolution of TCR repertoires, and the definition of HLA immunopeptidomes [START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF].

HLA and autoimmune neurological diseases with autoantibodies

In the following section, we will review the current knowledge regarding the associations between HLA and neurological diseases with autoantibodies, principally autoimmune encephalitides, as well as their clinical relevance and pathogenic implications. This section is largely based on a published review that can be found in the Annex (Muñiz-Castrillo et al., 2020c);

this article was also used to a lesser extent for the previous section. Despite the scarcity and also sometimes recent description of many of these diseases, which hindered the inclusion of large samples and even the reproduction of the results in different populations and by distinct research laboratories, some findings are promising as they suggest the existence of a strong genetic predisposition and raise the possibility of future research on the immune tolerance breakdown.

Interestingly, two different patterns have been observed in several autoimmune neurological diseases. On the one hand, IgG4-mediated neurological diseases have a strong association with specific class II haplotypes (Table 3), as it has also been shown in other uncommon nonneurological entities with IgG4 antibodies [START_REF] Huijbers | The expanding field of IgG4-mediated neurological autoimmune disorders[END_REF], Muñiz-Castrillo et al., 2020c). On the other hand, T-cell mediated disorders or with autoantibodies of IgG1 subclass are mainly related to the ancestral haplotype 8.1 (Table 4), which is known to be associated with many other systemic autoimmune diseases (Muñiz-Castrillo et al., 2020c).

Paraneoplastic neurological syndromes with Hu antibodies

Antibodies against Hu proteins are the most common onconeural antibody and show a wide clinical spectrum, ranging from peripheral manifestations, e.g. sensory neuronopathy, to CNS syndromes, e.g. limbic encephalitis (LE) [START_REF] Graus | Anti-Hu-associated paraneoplastic encephalomyelitis: analysis of 200 patients[END_REF][START_REF] Giometto | Paraneoplastic neurologic syndrome in the PNS Euronetwork database: a European study from 20 centers[END_REF]. Since the targeted antigens of Hu antibodies are RNA-binding proteins located in the nucleus of neurons and cells of small-cell lung cancer (SCLC), these antibodies are not believed to be pathogenic [START_REF] Graus | Anti-Hu-associated paraneoplastic encephalomyelitis: analysis of 200 patients[END_REF]. Conversely, the presence of specific anti-Hu CD8+ T-cells has been demonstrated in PNS patients with Hu antibodies, suggesting a cell-mediated pathogenesis [START_REF] Roberts | Patients with lung cancer and paraneoplastic Hu syndrome harbor HuD-specific type 2 CD8+ T cells[END_REF].

Nevertheless, Hu antibodies are reliable markers of SCLC, which is present in more than 80% of the patients [START_REF] Graus | Anti-Hu-associated paraneoplastic encephalomyelitis: analysis of 200 patients[END_REF]. However, non-paraneoplastic cases have been reported in children and adolescents, suggesting that anti-Hu autoimmunity may also appear as a pure dysimmune condition [START_REF] Honnorat | Autoimmune limbic encephalopathy and anti-Hu antibodies in children without cancer[END_REF]. In addition, Hu antibodies may be detected in 15% of neurologically asymptomatic patients with SCLC [START_REF] Graus | Recommended diagnostic criteria for paraneoplastic neurological syndromes[END_REF]. Thus, this heterogeneity of clinical presentations and onco-immunological associations might reflect complex interactions between the immunogenetic profiles of patients and tumors.

Initially, two small studies with incomplete HLA genotyping, including only 22 patients in total, found no association between HLA and PNS with Hu antibodies [START_REF] Uchuya | Lack of association between human leukocyte antigens and the anti-Hu syndrome in patients with small-cell lung cancer[END_REF][START_REF] Tanaka | Lack of association between human leukocyte antigens and anti-Hu syndrome in patients with small-cell lung cancer[END_REF]. However, an association with the HLA B*7 supertype was later reported in a small series of seven patients; additionally, CD8+ T-cell reactivity against Hu peptides was shown in only three patients from the same study [START_REF] Tanaka | Cytotoxic T cell activity against peptides of Hu protein in anti-Hu syndrome[END_REF] SCLC should be further investigated, since they might provide some clues regarding the initiation of the anti-Hu immune response, as well as the potential implications of HLA in the presentation of neoantigens derived from Hu proteins and its interaction with anti-Hu CD8+/CD4+ T-cells.

Paraneoplastic cerebellar degeneration with Yo antibodies

Antibodies against the Yo antigens, also known as Purkinje cell antibody 1 (PCA-1), are the second most common onconeural antibody and are strongly associated with paraneoplastic cerebellar degeneration (PCD) in women with breast or ovarian cancers [START_REF] Giometto | Paraneoplastic neurologic syndrome in the PNS Euronetwork database: a European study from 20 centers[END_REF][START_REF] Mckeon | Purkinje cell cytoplasmic autoantibody type 1 accompaniments: the cerebellum and beyond[END_REF]. However, due to the cytoplasmic location of Yo antigens (CDR2 and CDR2L), and based on neuropathological studies and animal models, the pathogenesis of anti-Yo PCD is thought to be mainly mediated by CD8+ T-cells [START_REF] Mckeon | Purkinje cell cytoplasmic autoantibody type 1 accompaniments: the cerebellum and beyond[END_REF][START_REF] Yshii | CTLA4 blockade elicits paraneoplastic neurological disease in a mouse model[END_REF].

Nevertheless, humoral response seems to be also important since B-cells were abundant in the inflammatory infiltrates of ovarian tumors [START_REF] Small | Genetic alterations and tumor immune attack in Yo paraneoplastic cerebellar degeneration[END_REF]. Besides, despite Yo antigens being widely expressed in ovarian cancers, it has been shown that only those tumors associated with PCD carry several genetic alterations in CDR2 and/or CDR2L loci, suggesting that these particular genetic abnormalities are needed to trigger the immune tolerance breakdown [START_REF] Small | Genetic alterations and tumor immune attack in Yo paraneoplastic cerebellar degeneration[END_REF].

The first studies investigating HLA in PCD with Yo antibodies reinforced the cell-mediated pathogenesis hypothesis, describing an association with A*24, and cytotoxic T-cell reactivity against Yo-derived peptides in A*24 carriers [START_REF] Tanaka | HLA A24 in paraneoplastic cerebellar degeneration with anti-Yo antibody[END_REF][START_REF] Tanaka | Cytotoxic T cell activity against the peptide, AYRARALEL, from Yo protein of patients with the HLA A24 or B27 supertype and paraneoplastic cerebellar degeneration[END_REF].

Nevertheless, only class I genotyping was performed and sample size was small (n=9) [START_REF] Tanaka | HLA A24 in paraneoplastic cerebellar degeneration with anti-Yo antibody[END_REF][START_REF] Tanaka | Cytotoxic T cell activity against the peptide, AYRARALEL, from Yo protein of patients with the HLA A24 or B27 supertype and paraneoplastic cerebellar degeneration[END_REF] 9% of the control group (p<0.05, OR=8.87), while no association was observed in patients with PCD and breast cancer [START_REF] Hillary | Complex HLA association in paraneoplastic cerebellar ataxia with anti-Yo antibodies[END_REF].

The complex associations between HLA and anti-Yo PCD reinforce the hypothesis of involvement of both cellular and humoral immune responses. Additionally, it is possible that neoepitopes appearing due to the aforementioned genetic alterations in Yo loci are more immunogenic when presented by certain HLA. Thus, further studies are necessary to investigate the HLA profiles of patients with PCD and Yo antibodies in larger samples, including all types of associated tumors, taking into account their histological and genetic characteristics, and analyzing the interactions between HLA, Yo-derived peptides, and TCR.

Lambert-Eaton myasthenic syndrome

Lambert-Eaton myasthenic syndrome (LEMS) is a neuromuscular junction disorder that can be either non-paraneoplastic or appear in association with SCLC (approximately 50% each).

However, both forms do not differ in their clinical presentation and often have antibodies against P/Q-type voltage-gated calcium channels (VGCC), which are present in nearly 90% of all LEMS cases [START_REF] Wirtz | Differences in clinical features between the Lambert-Eaton myasthenic syndrome with and without cancer: an analysis of 227 published cases[END_REF][START_REF] Titulaer | Lambert-Eaton myasthenic syndrome: from clinical characteristics to therapeutic strategies[END_REF]. The pathogenic role of VGCC antibodies has been proven, as well as the expression of VGCC by SCLC cells that might act as a trigger for the paraneoplastic cases [START_REF] Titulaer | Lambert-Eaton myasthenic syndrome: from clinical characteristics to therapeutic strategies[END_REF]. In contrast to VGCC antibodies, which are not useful to distinguish between paraneoplastic and non-paraneoplastic LEMS [START_REF] Titulaer | Lambert-Eaton myasthenic syndrome: from clinical characteristics to therapeutic strategies[END_REF], anti-glial nuclear antibodies (AGNA or SOX1) are strongly associated with SCLC and can be used to suspect an underlying cancer [START_REF] Graus | Anti-glial nuclear antibody: Marker of lung cancer-related paraneoplastic neurological syndromes[END_REF].

In addition, HLA differences between paraneoplastic and idiopathic LEMS have been reported in a few studies [START_REF] Willcox | Increased frequency of IgG heavy chain marker Glm(2) and of HLA-B8 in Lambert-Eaton myasthenic syndrome with and without associated lung carcinoma[END_REF][START_REF] Parsons | Increased frequency of HLA class II alleles DRB1 * 0301 and DQB1 * 0201 in Lambert-Eaton myasthenic syndrome without associated cancer[END_REF][START_REF] Wirtz | HLA class I and II in Lambert-Eaton myasthenic syndrome without associated tumor[END_REF][START_REF] Wirtz | HLA-B8 in patients with the Lambert-Eaton myasthenic syndrome reduces likelihood of associated small cell lung carcinoma[END_REF][START_REF] Wirtz | HLA and smoking in prediction and prognosis of small cell lung cancer in autoimmune Lambert-Eaton myasthenic syndrome[END_REF]; the largest among these included 26 paraneoplastic and 51 idiopathic patients [START_REF] Wirtz | HLA and smoking in prediction and prognosis of small cell lung cancer in autoimmune Lambert-Eaton myasthenic syndrome[END_REF].

The extended, highly conserved, haplotype 8.1 (A*01:01-B*08:01-DQB1*02:01-DRB1*03:01) or its components have been found to be more frequent in non-paraneoplastic LEMS of Caucasianorigin than in healthy controls or paraneoplastic LEMS [START_REF] Willcox | Increased frequency of IgG heavy chain marker Glm(2) and of HLA-B8 in Lambert-Eaton myasthenic syndrome with and without associated lung carcinoma[END_REF][START_REF] Parsons | Increased frequency of HLA class II alleles DRB1 * 0301 and DQB1 * 0201 in Lambert-Eaton myasthenic syndrome without associated cancer[END_REF][START_REF] Wirtz | HLA class I and II in Lambert-Eaton myasthenic syndrome without associated tumor[END_REF][START_REF] Wirtz | HLA-B8 in patients with the Lambert-Eaton myasthenic syndrome reduces likelihood of associated small cell lung carcinoma[END_REF][START_REF] Wirtz | HLA and smoking in prediction and prognosis of small cell lung cancer in autoimmune Lambert-Eaton myasthenic syndrome[END_REF]. Furthermore, B*08:01 was the allele with the strongest association:

in the largest series with complete genotyping, it was carried by 69% of idiopathic LEMS vs. 23%

of the control group (p<0.001), and 12% of paraneoplastic LEMS (p<0.001) [START_REF] Wirtz | HLA class I and II in Lambert-Eaton myasthenic syndrome without associated tumor[END_REF][START_REF] Wirtz | HLA and smoking in prediction and prognosis of small cell lung cancer in autoimmune Lambert-Eaton myasthenic syndrome[END_REF]. Moreover, idiopathic LEMS cases involved more frequently younger patients, commonly women, non-smokers, and with coexisting autoimmune diseases [START_REF] Wirtz | HLA class I and II in Lambert-Eaton myasthenic syndrome without associated tumor[END_REF]. Besides, it has also been suggested that HLA-B*08:01 could improve the immune surveillance against SCLC, as only 21% of LEMS smokers carrying this allele developed SCLC compared to 69% of non-carriers (p<0.005, OR=0.16, 95% CI [0.04-0.62]) [START_REF] Wirtz | HLA and smoking in prediction and prognosis of small cell lung cancer in autoimmune Lambert-Eaton myasthenic syndrome[END_REF].

In conclusion, two different pathogenic pathways may lead to LEMS: one HLA-dependent and unassociated with cancer, which is likely a common substrate of other autoimmune diseases;

and another triggered by the aberrant expression of VGCC by SCLC cells. Nevertheless, more studies with a greater number of patients are needed to confirm this hypothesis, including different ethnic origins, and considering the positivity for VGCC and other antibodies.

Myasthenia gravis

Myasthenia gravis (MG) is an immune-mediated and highly heterogeneous neuromuscular junction disorder that can be classified according to the distribution of the characteristic fatigable weakness in ocular MG, exclusively involving the oculo-motor system, and generalized MG, which involves axial and proximal limb muscles as well. Additionally, MG can also be classified according to the presence or absence of antibodies against the acetylcholine receptor (AchR), which are detected in nearly 80% of generalized MG and 50% of ocular MG [START_REF] Querol | Myasthenia gravis and the neuromuscular junction[END_REF][START_REF] Cetin | Pathogenic Mechanisms and Clinical Correlations in Autoimmune Myasthenic Syndromes[END_REF]). However, it has been shown that a considerable proportion of patients previously considered as "seronegative" have other antibodies directed to different proteins located at the postsynaptic membrane of the neuromuscular junction. Among them, muscle-specific tyrosine kinase (MusK) antibodies are the most common, accounting for 40-70% of AchR antibody-negative patients [START_REF] Querol | Myasthenia gravis and the neuromuscular junction[END_REF][START_REF] Cetin | Pathogenic Mechanisms and Clinical Correlations in Autoimmune Myasthenic Syndromes[END_REF]. Interestingly, Musk antibodies are principally of IgG4 subclass, in contrast to AchR antibodies that are mainly IgG1 [START_REF] Querol | Myasthenia gravis and the neuromuscular junction[END_REF][START_REF] Cetin | Pathogenic Mechanisms and Clinical Correlations in Autoimmune Myasthenic Syndromes[END_REF]. Moreover, anti-MusK MG is characterized by prominent bulbar involvement, poor response to usual treatments, and lack of associated thymus pathology [START_REF] Querol | Myasthenia gravis and the neuromuscular junction[END_REF][START_REF] Cetin | Pathogenic Mechanisms and Clinical Correlations in Autoimmune Myasthenic Syndromes[END_REF]. Indeed, MG may rarely appear as a paraneoplastic disease, with a malignant thymoma being diagnosed in nearly 10-15% of patients; in such cases MG is almost always generalized and associated with AchR antibodies [START_REF] Sharp | Paraneoplastic neuromuscular disorders[END_REF]. Furthermore, non-thymomatous MG is divided into early-onset MG (EOMG) and late-onset MG (LOMG). The age boundary between the two is usually set at 50 years, but it is not uniformly accepted and other authors have also recognized an intermediate-onset MG, between 40 and 60 years of age [START_REF] Maniaol | Late Onset Myasthenia Gravis Is Associated with HLA DRB1*15:01 in the Norwegian Population[END_REF][START_REF] Cetin | Pathogenic Mechanisms and Clinical Correlations in Autoimmune Myasthenic Syndromes[END_REF]). EOMG appears typically in women with AchR antibodies and thymus hyperplasia, while LOMG is more common in men, AchR antibody-positivity is less frequent, and thymus is normal or atrophic [START_REF] Querol | Myasthenia gravis and the neuromuscular junction[END_REF][START_REF] Cetin | Pathogenic Mechanisms and Clinical Correlations in Autoimmune Myasthenic Syndromes[END_REF]. Finally, juvenile-onset MG (JOMG) is a form of patients younger than 18 years of age, usually with pure ocular involvement, without AchR antibodies, and more prevalent in East Asia than in Caucasian populations [START_REF] Popperud | Juvenile myasthenia gravis in Norway: HLA-DRB1*04:04 is positively associated with prepubertal onset[END_REF][START_REF] Feng | HLA typing using next-generation sequencing for Chinese juvenile-and adult-onset myasthenia gravis patients[END_REF].

EOMG has typically been associated with the ancestral haplotype 8.1 in Caucasian populations [START_REF] Machens | Correlation of Thymic Pathology with HLA in Myasthenia Gravis[END_REF][START_REF] Giraud | Linkage of HLA to myasthenia gravis and genetic heterogeneity depending on anti-titin antibodies[END_REF][START_REF] Saruhan-Direskeneli | HLA-DQ Polymorphism in Turkish Patients With Myasthenia Gravis[END_REF], 2016;[START_REF] Maniaol | Late Onset Myasthenia Gravis Is Associated with HLA DRB1*15:01 in the Norwegian Population[END_REF][START_REF] Santos | HLA and age of onset in myasthenia gravis[END_REF]. However, it has been shown in large series that the allele B*08:01 is the one truly associated with EOMG, with a reported allele frequency of 33% (vs. 13%

in healthy bone marrow donors, p<0.001, OR=3.12, 95% CI [2.3-4.2]) in one of these studies [START_REF] Maniaol | Late Onset Myasthenia Gravis Is Associated with HLA DRB1*15:01 in the Norwegian Population[END_REF]; the remaining alleles of the haplotype were explained by LD [START_REF] Maniaol | Late Onset Myasthenia Gravis Is Associated with HLA DRB1*15:01 in the Norwegian Population[END_REF][START_REF] Saruhan-Direskeneli | Genetic heterogeneity within the HLA region in three distinct clinical subgroups of myasthenia gravis[END_REF][START_REF] Varade | Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis[END_REF]. Interestingly, this finding is the same as that of non-paraneoplastic LEMS [START_REF] Wirtz | HLA and smoking in prediction and prognosis of small cell lung cancer in autoimmune Lambert-Eaton myasthenic syndrome[END_REF]. Nevertheless, several different weak associations have been described in non-Western European Caucasian, American, and Asian populations [START_REF] Deitiker | Association with HLA DQ of early onset myasthenia gravis in Southeast Texas region of the United States: HLA DQ risk factors for myasthenia gravis in Southeast Texas[END_REF][START_REF] Xie | Association between HLA-DRB1 and myasthenia gravis in a northern Han Chinese population[END_REF][START_REF] Ehsan | Association of HLA class II (DRB1, DQA1, DQB1) alleles and haplotypes with myasthenia gravis and its subgroups in the Iranian population[END_REF].

In contrast, there are slightly more homogeneous results for LOMG across populations of Caucasian and Asian-origin. DQB1*05:02 and DRB1*16 have been reported with allele frequencies of approximately 15% (vs. less than 6% in healthy controls; p<0.005, OR ranging from 2.95 to 5.51); however, no carrier frequencies were provided [START_REF] Testi | Association of HLA-DQB1*05:02 and DRB1*16 Alleles with Late-Onset, Nonthymomatous, AChR-Ab-Positive Myasthenia Gravis[END_REF][START_REF] Massa | Thymomatous myasthenia gravis: novel association with HLA DQB1*05:01 and strengthened evidence of high clinical and serological severity[END_REF].

In addition, DRB1*15:01 has been described with an allele frequency of 26% (vs. 13% in healthy controls; p<0.001, OR=2.38, 95% ) and carried by 42% of LOMG patients (vs. 22%

of EOMG, p<0.05; OR=2.5, 95% CI [1.4-4.6]), in two different studies from Japan and Norway [START_REF] Suzuki | Clinical and immunological differences between early and late-onset myasthenia gravis in Japan[END_REF][START_REF] Maniaol | Late Onset Myasthenia Gravis Is Associated with HLA DRB1*15:01 in the Norwegian Population[END_REF].

The association between HLA and JOMG has principally been studied in East Asia, where this form is more common. A Japanese study on 87 patients found that the main haplotypes were DQA1*03:01-DQB1*03:03-DRB1*09:01 (68% vs. 28% in the control group; p<0.001, RR=5.4), and DQA1*01:02-DQB1*06:04-DRB1*13:02 (45% vs. 9%; p<0.001; RR=8.6) [START_REF] Shinomiya | A variant of childhood-onset myasthenia gravis: HLA typing and clinical characteristics in Japan[END_REF]. Moreover, DRB1*09:01 was also frequently observed (50% of the alleles; usually in LD with B*46:01-DQA1*01:01-DQB1*03:03) in a Chinese series of 41 patients with JOMG, but carrier frequencies were not provided and p values were uncorrected [START_REF] Feng | HLA typing using next-generation sequencing for Chinese juvenile-and adult-onset myasthenia gravis patients[END_REF].

Interestingly, a Norwegian study distinguished two clinical and genetic groups in JOMG [START_REF] Popperud | Juvenile myasthenia gravis in Norway: HLA-DRB1*04:04 is positively associated with prepubertal onset[END_REF]. On the one hand, post-pubertal patients (n=26) had characteristics more closely related to EOMG, since 40.4% carried B*08:01, 85% were AchR antibody-positive, and 65% had thymus hyperplasia [START_REF] Popperud | Juvenile myasthenia gravis in Norway: HLA-DRB1*04:04 is positively associated with prepubertal onset[END_REF]. On the other hand, pre-pubertal patients (n=17) were typical JOMG cases, presenting with pure ocular involvement, lower rates of AchR antibody-positivity, and carrying more frequently DRB1*04:04 (26% vs. 7.7% of post-pubertal patients; p=0.01, OR=3.27, 95% CI [2.00-5.36]) [START_REF] Popperud | Juvenile myasthenia gravis in Norway: HLA-DRB1*04:04 is positively associated with prepubertal onset[END_REF].

Similarly to LOMG, anti-MusK MG shows approximately the same HLA associations through very different populations [START_REF] Niks | Strong association of MuSK antibody-positive myasthenia gravis and HLA-DR14-DQ5[END_REF][START_REF] Bartoccioni | HLA class II allele analysis in MuSK-positive myasthenia gravis suggests a role for DQ5[END_REF][START_REF] Alahgholi-Hajibehzad | Association of HLA-DRB1 * 14, -DRB1 * 16 and -DQB1 * 05 with MuSK-myasthenia gravis in patients from Turkey[END_REF][START_REF] Ehsan | Association of HLA class II (DRB1, DQA1, DQB1) alleles and haplotypes with myasthenia gravis and its subgroups in the Iranian population[END_REF][START_REF] Nikolic | High frequency of DQB1*05 and absolute absence of DRB1*13 in muscle-specific tyrosine kinase positive myasthenia gravis[END_REF][START_REF] Kanai | HLA-DRB1*14 and DQB1*05 are associated with Japanese anti-MuSK antibody-positive myasthenia gravis patients[END_REF]. Moreover, in a meta-analysis including 177 patients with anti-MusK MG, DQB1*05-DRB1*16 (26% vs. 9% in healthy controls; OR=4.37, p<0.001) and DQB1*05-DRB1*14 (19% vs. 5%; OR=3.36, p<0.001)

were the main reported haplotypes [START_REF] Hong | HLA and MuSK-positive myasthenia gravis: A systemic review and meta-analysis[END_REF]. However, at allele level, DQB1*05 was carried by 78% of the patients (vs. 37%; p<0.001, OR=5.39), while only 39% carried DRB1*14 (v.

8%; p<0.001, OR=5.32) and 34% DRB1*16 (vs. 10%; p<0.001, OR=4.98), suggesting a primary DQ effect in the association between HLA and anti-MusK MG [START_REF] Hong | HLA and MuSK-positive myasthenia gravis: A systemic review and meta-analysis[END_REF]. Nevertheless, DRB1 locus might influence the immune response as well, since differences in IgG4 titers and cytokine production have been reported according to the DRB1 alleles (DRB1*14 and/or DRB1*16) (Çebi et al., 2019).

Conversely, no consistent positive association has so far been described between HLA and thymomatous MG [START_REF] Giraud | Linkage of HLA to myasthenia gravis and genetic heterogeneity depending on anti-titin antibodies[END_REF][START_REF] Suzuki | Clinical and immunological differences between early and late-onset myasthenia gravis in Japan[END_REF][START_REF] Xie | Association between HLA-DRB1 and myasthenia gravis in a northern Han Chinese population[END_REF][START_REF] Maniaol | Late Onset Myasthenia Gravis Is Associated with HLA DRB1*15:01 in the Norwegian Population[END_REF][START_REF] Ehsan | Association of HLA class II (DRB1, DQA1, DQB1) alleles and haplotypes with myasthenia gravis and its subgroups in the Iranian population[END_REF]. Although several studies have reported different associations with both HLA class I (A*24, A*25) and class II (DRB1*10, DQA1*04, DQB1*06) alleles, these results have never been reproduced, statistical analyses were not corrected for multiple comparisons, histological types of the thymomas were heterogeneous, and genotyping was often incomplete [START_REF] Machens | Correlation of Thymic Pathology with HLA in Myasthenia Gravis[END_REF]Vandiedonck et al., 2009;[START_REF] Yang | The association of HLA-DQA1*0401 and DQB1*0604 with thymomatous myasthenia gravis in northern Chinese patients[END_REF][START_REF] Santos | HLA and age of onset in myasthenia gravis[END_REF][START_REF] Massa | Thymomatous myasthenia gravis: novel association with HLA DQB1*05:01 and strengthened evidence of high clinical and serological severity[END_REF].

In summary, associations between HLA and MG are highly diverse, likely reflecting its own clinical and immunological heterogeneity. Thus, future studies should establish uniform diagnostic criteria for each subtype of MG, especially regarding age of onset and thymus pathology, in order to better define particular HLA profiles.

Chronic inflammatory demyelinating polyradiculoneuropathy with neurofascin-155 antibodies

Neurofascin-155 (NF155) is a cell-adhesion protein expressed at the paranodal loops of Schwann cells and recognized by IgG4 subclass antibodies defining an uncommon type of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP). The clinical phenotype of CIDP with NF155 antibodies is characterized by severe distal weakness with sensory ataxia, and disabling postural and intentional tremor [START_REF] Querol | Neurofascin IgG4 antibodies in CIDP associate with disabling tremor and poor response to IVIg[END_REF][START_REF] Ogata | Characterization of IgG4 anti-neurofascin 155 antibody-positive polyneuropathy[END_REF][START_REF] Devaux | Neurofascin-155 IgG4 in chronic inflammatory demyelinating polyneuropathy[END_REF].

Moreover, clear cerebellar ataxia and CNS demyelinating lesions have also been reported in a few cases [START_REF] Ogata | Characterization of IgG4 anti-neurofascin 155 antibody-positive polyneuropathy[END_REF][START_REF] Devaux | Neurofascin-155 IgG4 in chronic inflammatory demyelinating polyneuropathy[END_REF], and it has been shown that NF155 antibodies from CIDP patients are able to bind the hippocampus and cerebellum in rat brain slides [START_REF] Querol | Neurofascin IgG4 antibodies in CIDP associate with disabling tremor and poor response to IVIg[END_REF][START_REF] Devaux | Neurofascin-155 IgG4 in chronic inflammatory demyelinating polyneuropathy[END_REF]. Unlike other types of CIDP, response to IVIG is usually poor, but rituximab may be useful in these cases [START_REF] Querol | Rituximab in treatment-resistant CIDP with antibodies against paranodal proteins[END_REF].

Due to its scarcity and recent description, only two studies have thus far focused on the association between HLA and CIDP with NF155 antibodies. ) is likely to be a consequence of a small sample size [START_REF] Ogata | Unique HLA haplotype associations in IgG4 anti-neurofascin 155 antibody-positive chronic inflammatory demyelinating polyneuropathy[END_REF]. Besides confirming the overlapping peptide-binding spectrums of DRB1*15:01 and DRB1*15:02, Ogata and colleagues described that the associated DQ heterodimers also shared a very similar peptide repertoire [START_REF] Ogata | Characterization of IgG4 anti-neurofascin 155 antibody-positive polyneuropathy[END_REF]. In conclusion, although the aforementioned association between HLA class II and CIDP with NF155 antibodies is consistent with an antibody-mediated pathogenesis, future investigations should first include larger cohorts in order to increase the statistical power and, secondly, address the pathogenic mechanisms underlying this association.

Anti-IgLON5 disease

The disease associated with IgLON5 (immunoglobulin-like cell adhesion molecule 5)

antibodies is characterized by a wide clinical spectrum, including complex sleep disorder (non-REM and REM parasomnias, obstructive sleep apnea, central hypoventilation), bulbar dysfunction, gait disturbances, dysautonomia, ocular abnormalities, movement disorders, and cognitive impairment [START_REF] Sabater | A novel non-rapid-eye movement and rapid-eye-movement parasomnia with sleep breathing disorder associated with antibodies to IgLON5: a case series, characterisation of the antigen, and post-mortem study[END_REF][START_REF] Gaig | Clinical manifestations of the anti-IgLON5 disease[END_REF][START_REF] Honorat | IgLON5 antibody: Neurological accompaniments and outcomes in 20 patients[END_REF]. It is an enigmatic condition lying between autoimmune encephalitis and neurodegenerative diseases. On the one hand, supporting an immune-mediated pathogenesis, patients have IgG4 antibodies against the neuronal cell adhesion molecule IgLON5, usually in both serum and CSF, and some positive responses to immunotherapy have been reported [START_REF] Bonello | IgLON5 disease responsive to immunotherapy[END_REF][START_REF] Gaig | Clinical manifestations of the anti-IgLON5 disease[END_REF][START_REF] Honorat | IgLON5 antibody: Neurological accompaniments and outcomes in 20 patients[END_REF][START_REF] Moreno-Estébanez | Anti-IgLON5 Disease Responsive to Immunotherapy: A Case Report with an Abnormal MRI[END_REF][START_REF] Logmin | Intravenous immunoglobulins as firstline therapy for IgLON5 encephalopathy[END_REF]. On the other hand, initial pathological studies revealed tau protein deposits in the hypothalamus and brainstem without inflammatory changes [START_REF] Sabater | A novel non-rapid-eye movement and rapid-eye-movement parasomnia with sleep breathing disorder associated with antibodies to IgLON5: a case series, characterisation of the antigen, and post-mortem study[END_REF]. However, more recent reports lacking taupathy in early stages of the disease [START_REF] Erro | Anti-IGLON5 disease: A new case without neuropathologic evidence of brainstem tauopathy[END_REF], as well as evidence of cytoskeleton disruption caused by IgLON5 antibodies [START_REF] Landa | Effects of IgLON5 Antibodies on Neuronal Cytoskeleton: A Link between Autoimmunity and Neurodegeneration[END_REF], seem to reinforce the hypothesis of an autoimmune disorder leading to a neurodegenerative process.

Furthermore, a strong association with HLA class II, as in other IgG4-mediated diseases, also suggests an autoimmune pathogenesis. An association with DQB1*05:01-DRB1*10:01 has been described in several case reports and small series [START_REF] Sabater | A novel non-rapid-eye movement and rapid-eye-movement parasomnia with sleep breathing disorder associated with antibodies to IgLON5: a case series, characterisation of the antigen, and post-mortem study[END_REF][START_REF] Simabukuro | Sleep disorder, chorea, and dementia associated with IgLON5 antibodies[END_REF][START_REF] Bonello | IgLON5 disease responsive to immunotherapy[END_REF][START_REF] Moreno-Estébanez | Anti-IgLON5 Disease Responsive to Immunotherapy: A Case Report with an Abnormal MRI[END_REF][START_REF] Logmin | Intravenous immunoglobulins as firstline therapy for IgLON5 encephalopathy[END_REF]. Moreover, DQB1*05:01-DRB1*10:01 was carried by 13/15 (86.6% vs. 1.6% in the general population;

OR=36, 95% CI [19.5-67.0]) and 20/35 (57.1% vs. 2.4%; p<0.001, OR=54.5, 95% CI [22.2-133.9]) patients in the largest cohorts [START_REF] Gaig | Clinical manifestations of the anti-IgLON5 disease[END_REF][START_REF] Gaig | HLA and microtubule-associated protein tau H1 haplotype associations in anti-IgLON5 disease[END_REF]. In addition, DQA1*01-DQB1*05 were carried by more than 90% of the patients, often but not always linked to DRB1*10:01 [START_REF] Gaig | HLA and microtubule-associated protein tau H1 haplotype associations in anti-IgLON5 disease[END_REF]. However, an in silico analysis predicted two IgLON5-derived peptides as strong binders for DRB1*10:01, but no peptide was predicted as a strong binder for the DQA1*01-DQB1*05 heterodimer [START_REF] Gaig | HLA and microtubule-associated protein tau H1 haplotype associations in anti-IgLON5 disease[END_REF]. Conversely, those two peptides, belonging to the signal peptide and the Ig-like 2 domain, were also predicted as strong binders for another DRB1 molecule frequent in the cohort, DRB1*01:01, which was carried by 20% of the patients, although not at a higher frequency than controls [START_REF] Gaig | HLA and microtubule-associated protein tau H1 haplotype associations in anti-IgLON5 disease[END_REF]. Thus, the two main DRB1 molecules associated with anti-IgLON5 disease seem to be able to bind the same IgLON5-derived peptides with high affinity [START_REF] Gaig | HLA and microtubule-associated protein tau H1 haplotype associations in anti-IgLON5 disease[END_REF].

Interestingly, some clinical and immunological differences related to the HLA carrier status have been described in anti-IgLON5 disease, since patients lacking DRB1*10:01 presented more commonly with a PSP-like phenotype or cognitive decline, while DRB1*10:01-carriers usually displayed the typical sleep or bulbar features at disease onset and showed less frequently IgG4 subclass predominance [START_REF] Gaig | HLA and microtubule-associated protein tau H1 haplotype associations in anti-IgLON5 disease[END_REF]. It is therefore possible to distinguish two distinct subgroups of anti-IgLON5 disease based on different immunological, clinical, and genetic features.

However, whether pathogenic differences exist between DRB1*10:01 carriers and non-carriers is still far from being elucidated, as well as which are the triggers that lead to the development of the immune response against IgLON5.

Encephalitis with leucine-rich glioma-inactivated 1 antibodies

Leucine-rich glioma-inactivated 1 (LGI1) is a secreted protein that forms a trans-synaptic complex between ADAM23 (a disintegrin and metalloproteinase 23) and ADAM22, which respectively interact with presynaptic voltage-gated potassium channels (VGKC) and postsynaptic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPAR) [START_REF] Irani | Antibodies to Kv1 potassium channel-complex proteins leucine-rich, glioma inactivated 1 protein and contactinassociated protein-2 in limbic encephalitis, Morvan's syndrome and acquired neuromyotonia[END_REF]. Antibodies against LGI1 characterize a frequent type of LE, are mainly of IgG4 subclass, and recognize different epitopes in the epitempin and leucine-rich repeat domains [START_REF] Ariño | Anti-LGI1-associated cognitive impairment: Presentation and long-term outcome[END_REF], van Sonderen et al., 2016b;[START_REF] Petit-Pedrol | LGI1 antibodies alter Kv1.1 and AMPA receptors changing synaptic excitability, plasticity and memory[END_REF].

Since anti-LGI1 LE is usually a non-paraneoplastic disorder with no other identified triggers [START_REF] Ariño | Anti-LGI1-associated cognitive impairment: Presentation and long-term outcome[END_REF], van Sonderen et al., 2016b), a genetic predisposition was investigated independently in a Korean (n=11) and a Dutch (n=25) cohort. Both groups simultaneously described a strong association with DRB1*07:01, which was carried by nearly 90% of patients (for the Korean series 91% vs. 13% in controls, p<0.001, OR=65.8, 95% ]; for the Dutch series, 88% vs. 19.6% in controls, p<0.001, OR=26.37, 95% CI [8.54-81.49]) [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Van Sonderen | Anti-LGI1 encephalitis is strongly associated with HLA-DR7 and HLA-DRB4: Anti-LGI1 Encephalitis[END_REF]. In addition, other alleles were found to be more frequent in patients than in controls due to their LD with DRB1*07:01, such as B*44:03, C*07:06, DQB1*02:02, and DRB4 [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Van Sonderen | Anti-LGI1 encephalitis is strongly associated with HLA-DR7 and HLA-DRB4: Anti-LGI1 Encephalitis[END_REF]. More recently, the haplotypes DQA1*02:01-DQB1*02:02-DRB1*07:01 and DQA1*02:01-DQB1*03:03-DRB1*07:01 were further confirmed to be associated with LGI1 LE in two larger cohorts [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF][START_REF] Mueller | Genetic predisposition in anti-LGI1 and anti-NMDA receptor encephalitis: GWAS Autoimmune Encephalitis[END_REF].

The first in silico study found that DRB1*07:01 had the highest affinity for LGI1-derived peptides among all HLA class II, although DQB1*02:02 was not analyzed [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF].

Moreover, the core FLFTPSLQL, located in the leucine-rich repeated domain, showed the highest affinity as well as an elevated docking score for the heterodimer DRA1*01:01-DRB1*07:01 [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF]. By contrast, this peptide and others were also predicted as strong binders for the HLA associated with anti-CASPR2 (contactin-associated protein-like 2) disorders, which was interpreted as a lack of disease-specificity [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF].

Regarding the clinical correlation, it was initially suggested that paraneoplastic anti-LGI1

LE was not associated with DRB1*07:01 (2/4 patients with tumors did not carry this allele) [START_REF] Van Sonderen | Anti-LGI1 encephalitis is strongly associated with HLA-DR7 and HLA-DRB4: Anti-LGI1 Encephalitis[END_REF]. Conversely, the English group did not find differences between patients with (n=9) and without cancer (n=59) [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF]. However, the tumors included were very prevalent, such as basal cell carcinoma, whose pathogenic relationship with anti-LGI1 LE is controversial. Interestingly, the alleles B*57:01 and C*06:02, which are known to be linked respectively to antibiotic-induced rash and psoriasis, were detected in patients presenting these comorbidities [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF].

Thus, although it seems clear that anti-LGI1 LE is strongly associated with DRB1*07:01 across distinct populations, it remains unknown whether clinical differences exist between carriers and noncarriers, as well as the role of this HLA association in the pathogenesis.

Diseases with contactin-associated protein-like 2 antibodies

Contactin-associated protein-like 2 (CASPR2) plays an important role in the clustering of VGKC at the juxtaparanodes in the peripheral nervous system, but it is also expressed by CNS inhibitory neurons. Antibodies against CASPR2 are associated with three different clinical phenotypes: LE, Isaac´s syndrome/acquired neuromyotonia, and Morvan syndrome [START_REF] Irani | Antibodies to Kv1 potassium channel-complex proteins leucine-rich, glioma inactivated 1 protein and contactinassociated protein-2 in limbic encephalitis, Morvan's syndrome and acquired neuromyotonia[END_REF][START_REF] Lancaster | Investigations of caspr2, an autoantigen of encephalitis and neuromyotonia[END_REF]. Despite the existence of some degree of clinical overlap, which has been sometimes interpreted as a continuum (van Sonderen et al., 2016a;[START_REF] Gadoth | Expanded phenotypes and outcomes among 256 LGI1/CASPR2-IgG-positive patients: LGI1/CASPR2-IgG + Patients[END_REF], certain manifestations seem to be disease-specific and, moreover, there are different immunological characteristics and oncological associations that likely reflect distinct underlying pathogeneses. For instance, Morvan syndrome is often a paraneoplastic disorder associated with malignant thymoma, and co-occurring myasthenia gravis and serum LGI1 antibodies are also common in these cases [START_REF] Irani | Morvan syndrome: Clinical and serological observations in 29 cases[END_REF][START_REF] Joubert | Characterization of a Subtype of Autoimmune Encephalitis With Anti-Contactin-Associated Protein-like 2 Antibodies in the Cerebrospinal Fluid, Prominent Limbic Symptoms, and Seizures[END_REF]. Conversely, LE patients do not present with these comorbidities, but they have been reported to have higher rates of CSF positivity for CASPR2

antibodies and more IgG4 than IgG1 subclass [START_REF] Joubert | Characterization of a Subtype of Autoimmune Encephalitis With Anti-Contactin-Associated Protein-like 2 Antibodies in the Cerebrospinal Fluid, Prominent Limbic Symptoms, and Seizures[END_REF]. However, the epitopes recognized by CASPR2 antibodies, mainly located in the laminin G1 and discoidin domains, did not differ between clinical phenotypes [START_REF] Olsen | Caspr2 autoantibodies target multiple epitopes[END_REF][START_REF] Joubert | Characterization of a Subtype of Autoimmune Encephalitis With Anti-Contactin-Associated Protein-like 2 Antibodies in the Cerebrospinal Fluid, Prominent Limbic Symptoms, and Seizures[END_REF].

There is so far a single study investigating the HLA profile of patients with CASPR2

antibodies, describing an association with the allele DRB1*11:01, carried by 48% of 31 patients compared to 9% of healthy controls (p<0.001, OR=9.4, 95% ) [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF]. In addition, DRB1*11:01 was usually detected in LD with DQA1*05:01-DQB1*03:01 (41.9% vs.

8.9%, p<0.001, OR= 7.4, 95% CI [3.5-15.2]). Indeed, the in silico analysis found a more specific peptide-binding spectrum for the heterodimer DQA1*05:01-DQB1*03:01 than for DRB1*11:01 when compared to the HLA associated with anti-LGI1 LE [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF]. Despite these interesting findings, no clinical correlation was reported, likely due to the low number of patients included with Morvan syndrome (n=3, none of them with malignant thymoma) and acquired neuromyotonia (n=2). Moreover, nearly 20% of patients had atypical presentations [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF]. Thus, further studies are needed to clarify whether the aforementioned HLA association is shared by all diseases with CASPR2 antibodies as well as its pathogenic implications.

Anti-N-methyl-D-aspartate receptor encephalitis

Anti-NMDAR encephalitis is the most common autoimmune encephalitis [START_REF] Hébert | Epidemiology of paraneoplastic neurologic syndromes and autoimmune encephalitides in France[END_REF]. Antibodies are of IgG1 subclass and target the GluN1 subunit leading to crosslink, internalization, and finally reducing the number of NMDAR at the synapsis [START_REF] Dalmau | Anti-NMDA-receptor encephalitis: case series and analysis of the effects of antibodies[END_REF].

Although anti-NMDAR encephalitis may appear in almost every type of patient, the frequency and nature of tumor associations vary with age, sex, and ethnic origin: nearly 40% of young women have an underlying ovarian teratoma, which are moreover more common in non-Caucasian patients, while children and young men usually present with a non-paraneoplastic disease, and malignant tumors, mostly carcinomas, are almost exclusively observed in elderly patients [START_REF] Titulaer | Treatment and prognostic factors for long-term outcome in patients with anti-NMDA receptor encephalitis: an observational cohort study[END_REF][START_REF] Bost | Malignant tumors in autoimmune encephalitis with anti-NMDA receptor antibodies[END_REF]. Ovarian teratomas associated with anti-NMDAR encephalitis have some particular characteristics strongly suggesting that they act as triggers of the immune response, such as high rates of neuroglial tissue and glial expression of GluN1, as well as prominent and wellorganized inflammatory infiltrates [START_REF] Chefdeville | Immunopathological characterization of ovarian teratomas associated with anti-N-methyl-D-aspartate receptor encephalitis[END_REF]. In addition, another potential trigger are CNS infections, mostly herpes-simplex virus encephalitis [START_REF] Armangue | Frequency, symptoms, risk factors, and outcomes of autoimmune encephalitis after herpes simplex encephalitis: a prospective observational study and retrospective analysis[END_REF], but many other agents have also been described [START_REF] Cavaliere | Anti-NMDAR encephalitis preceded by non-herpetic central nervous system infection: Systematic literature review and first case of tick-borne encephalitis triggering anti-NMDAR encephalitis[END_REF]. Although it has been proposed that neural destruction provoked by CNS infections leads to NMDAR release and immunization, additional mechanisms such as molecular mimicry might be involved [START_REF] Armangue | Frequency, symptoms, risk factors, and outcomes of autoimmune encephalitis after herpes simplex encephalitis: a prospective observational study and retrospective analysis[END_REF][START_REF] Cavaliere | Anti-NMDAR encephalitis preceded by non-herpetic central nervous system infection: Systematic literature review and first case of tick-borne encephalitis triggering anti-NMDAR encephalitis[END_REF]. Furthermore, other yet unrecognized triggering infections may exist, since prodromal symptoms resembling mild viral processes have been reported in up to 70% of the patients [START_REF] Dalmau | Clinical experience and laboratory investigations in patients with anti-NMDAR encephalitis[END_REF], and recently non-encephalitic herpes-simplex infection has also been associated with anti-NMDAR encephalitis [START_REF] Salovin | Anti-NMDA receptor encephalitis and nonencephalitic HSV-1 infection[END_REF].

The aforementioned variety of etiopathogenic contexts may also be influenced by a different genetic predisposition. However, a first attempt to identify an association between HLA and anti-NMDAR encephalitis found no positive results, though sample size was very small, just including 17 cases from Korea [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF]. Later, a study performed in a much larger German cohort (n=96) reported a weak association with B*07:02 exclusively for adult patients (n=49, allele frequency 21% vs. 13% in the control group; p<0.05, OR=2.32, 95% CI [1.34-4.00]) [START_REF] Mueller | Genetic predisposition in anti-LGI1 and anti-NMDA receptor encephalitis: GWAS Autoimmune Encephalitis[END_REF]. More recently, DRB1*16:02 was found to be more frequent in Chinese patients than in controls, but it accounted for less than 15% of the alleles of a series including 61 patients (vs. less than 5% in the control group; p<0.05, OR=3.41, 95% CI [1.81-6.17]) [START_REF] Shu | HLA class II allele DRB1*16:02 is associated with anti-NMDAR encephalitis[END_REF]. Moreover, carrier frequencies between paraneoplastic (mostly ovarian teratomas) and non-paraneoplastic cases were similar, and the only observed clinical difference was a possible worse treatment response in DRB1*16:02 carriers [START_REF] Shu | HLA class II allele DRB1*16:02 is associated with anti-NMDAR encephalitis[END_REF]. Although the authors suggested that DRB1*16:02 could play a pathogenic role based on in silico binding and docking predictions for one NMDAR-derived peptide [START_REF] Shu | HLA class II allele DRB1*16:02 is associated with anti-NMDAR encephalitis[END_REF], these findings are inconclusive due to the natural HLA promiscuity.

Thus, it seems that anti-NMDAR encephalitis have a less clear association with HLA than IgG4-mediated encephalitides. However, this hypothesis should be confirmed by studies performed in yet larger samples, also aiming to identify other non-HLA loci that might be relevant in the genetic predisposition to anti-NMDAR encephalitis.

Neurological disorders with glutamic acid decarboxylase antibodies

Antibodies against glutamic acid decarboxylase 65 (GAD65), the limiting enzyme in the synthesis of gamma-aminobutyric acid (GABA), have mainly been described in three neurological disorders that are generally non-paraneoplastic: LE, stiff-person syndrome (SPS), and cerebellar ataxia, but mild or partial forms of all of these have also been reported, such as temporal lobe epilepsy, stiff-leg syndrome, or isolated nystagmus [START_REF] Saiz | Spectrum of neurological syndromes associated with glutamic acid decarboxylase antibodies: diagnostic clues for this association[END_REF][START_REF] Gresa-Arribas | Antibodies to Inhibitory Synaptic Proteins in Neurological Syndromes Associated with Glutamic Acid Decarboxylase Autoimmunity[END_REF]Muñoz-Lopetegi et al., 2020). GAD65 antibodies are mainly of IgG1 subclass and its pathogenic role remains controversial, principally due to the intracellular location of the antigen and lack of consistent evidence of internalization by neurons [START_REF] Gresa-Arribas | Antibodies to Inhibitory Synaptic Proteins in Neurological Syndromes Associated with Glutamic Acid Decarboxylase Autoimmunity[END_REF]. Conversely, T-cells seem to play a major role based on pathological findings and T-lymphocyte proliferation after GAD65-antigenic stimulation [START_REF] Costa | T-cell reactivity to glutamic acid decarboxylase in stiff-man syndrome and cerebellar ataxia associated with polyendocrine autoimmunity[END_REF][START_REF] Bien | Immunopathology of autoantibody-associated encephalitides: clues for pathogenesis[END_REF]. Moreover, serum GAD65

antibodies are also present in patients with other systemic organ-specific autoimmune diseases, especially type 1 diabetes mellitus, although neurological patients have also CSF antibodies and much higher serum titers [START_REF] Honnorat | Cerebellar Ataxia With Anti-Glutamic Acid Decarboxylase Antibodies: Study of 14 Patients[END_REF][START_REF] Saiz | Spectrum of neurological syndromes associated with glutamic acid decarboxylase antibodies: diagnostic clues for this association[END_REF]Muñoz-Lopetegi et al., 2020).

Despite these immunological differences, systemic organ-specific autoimmune diseases are often diagnosed in patients and their relatives, suggesting a shared genetic predisposition that has so far been poorly investigated [START_REF] Honnorat | Cerebellar Ataxia With Anti-Glutamic Acid Decarboxylase Antibodies: Study of 14 Patients[END_REF][START_REF] Burns | Clinically disparate stiffperson syndrome with GAD65 autoantibody in a father and daughter[END_REF][START_REF] Saiz | Spectrum of neurological syndromes associated with glutamic acid decarboxylase antibodies: diagnostic clues for this association[END_REF]. the former being part of the extended haplotype 8.1 and also related to many other autoimmune diseases, such as thyroiditis and celiac disease [START_REF] Simmonds | The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action[END_REF]. Due to this association with other autoimmune diseases, DQB1*02:01 and DRB1*03:01 were independently investigated in two series of SPS, describing carrier frequencies of 44% (n=18) and 72% (n=18), respectively; however, genotyping only included HLA class II and the p values provided were uncorrected [START_REF] Pugliese | Association of HLA-DQB1*0201 with stiff-man syndrome[END_REF][START_REF] Dalakas | The clinical spectrum of anti-GAD antibody-positive patients with stiff-person syndrome[END_REF]. Likewise, DQ2-DR3 was also reported in 4/5 patients with SPS and 2/6 with cerebellar ataxia [START_REF] Costa | T-cell reactivity to glutamic acid decarboxylase in stiff-man syndrome and cerebellar ataxia associated with polyendocrine autoimmunity[END_REF]. In addition, other uncommon haplotypes, such as DQA1*01:02-DQB1*05:02-DRB1*15:01, have been found in familial cases of neurological disorders with GAD65 antibodies [START_REF] Burns | Clinically disparate stiffperson syndrome with GAD65 autoantibody in a father and daughter[END_REF][START_REF] Belbezier | Multiplex family with GAD65-Abs neurologic syndromes[END_REF]. Furthermore, other pedigrees with several neurological patients but without HLA genotyping have been reported [START_REF] Kuchling | GAD Antibody-Associated Late-Onset Cerebellar Ataxia in Two Female Siblings[END_REF][START_REF] Xiao | Familial case reports of stiff-person syndrome[END_REF], reinforcing the hypothesis of a strong genetic predisposition to neurological disorders with GAD65 antibodies.

Despite being one of the first neurological diseases with autoantibodies in which HLA was

analyzed, what we know about the immunogenetic characteristics of neurological patients with GAD65 antibodies remains superficial. Larger studies comprising all clinical presentations, with complete genotyping, and ideally also including important non-HLA loci, should enable to confirm whether these diseases have a shared genetic predisposition between them and with systemic organspecific autoimmune diseases.

Demyelinating CNS disorders with autoantibodies

Once considered as a severe variant of multiple sclerosis (MS), neuromyelitis optica (NMO) is now a well-differentiated disease after the discovery of serum antibodies of the IgG1 subclass against aquaporin-4 (AQP4, a water channel expressed by astrocytes) [START_REF] Lennon | A serum autoantibody marker of neuromyelitis optica: distinction from multiple sclerosis[END_REF][START_REF] Lennon | IgG marker of optic-spinal multiple sclerosis binds to the aquaporin-4 water channel[END_REF].

In addition, clinical phenotypes associated with AQP4 antibodies have been shown to be more diverse than initially reported, and the so labeled neuromyelitis optica spectrum disorders (NMOSD) currently include longitudinally extensive transverse myelitis and optic neuritis, as well as cerebral syndromes involving area postrema, brainstem, and diencephalon [START_REF] Wingerchuk | International consensus diagnostic criteria for neuromyelitis optica spectrum disorders[END_REF]. Furthermore, reinforcing its clinical and immunological distinctness compared to MS, NMO also shows a different epidemiology, being more frequent in African, East Asian, and Latin American populations, while MS is more common in Caucasian ones [START_REF] Alonso | Neuromyelitis Optica (NMO IgG+) and Genetic Susceptibility, Potential Ethnic Influences[END_REF]. This particular geographical distribution likely reflects a diverse genetic predisposition and is obviously also accompanied by different associations with HLA.

Several studies have reported an association between NMO and DRB1*03:01 in Caucasian or mixed-origin patients [START_REF] Zéphir | Is neuromyelitis optica associated with human leukocyte antigen?[END_REF][START_REF] Brum | HLA-DRB association in neuromyelitis optica is different from that observed in multiple sclerosis[END_REF][START_REF] Blanco Morgado | HLA-DRB1 en pacientes caucásicos con neuromielitis óptica[END_REF][START_REF] Deschamps | Different HLA class II (DRB1 and DQB1) alleles determine either susceptibility or resistance to NMO and multiple sclerosis among the French Afro-Caribbean population[END_REF][START_REF] Pandit | Human leukocyte antigen association with neuromyelitis optica in a south Indian population[END_REF][START_REF] Alvarenga | The HLA DRB1*03:01 allele is associated with NMO regardless of the NMO-IgG status in Brazilian patients from Rio de Janeiro[END_REF][START_REF] Alonso | Neuromyelitis Optica (NMO IgG+) and Genetic Susceptibility, Potential Ethnic Influences[END_REF], although these results have not been consistently found [START_REF] Asgari | HLA, PTPN22 and PD-1 associations as markers of autoimmunity in neuromyelitis optica[END_REF][START_REF] Brill | Increased occurrence of anti-AQP4 seropositivity and unique HLA Class II associations with neuromyelitis optica (NMO), among Muslim Arabs in Israel[END_REF]. The main limitation of most of these studies was the inclusion of patients positive and negative for AQP4 antibodies, which likely do not share the same pathogenesis and might therefore have a different genetic profile. Indeed, several sub-analyses, and a recent study including 132 patients with NMO and AQP4 antibodies, showed that the DRB1*03:01 association depended on anti-AQP4 positivity (p<0.001, OR=4.09, 95% CI [2.91-5.74]) [START_REF] Zéphir | Is neuromyelitis optica associated with human leukocyte antigen?[END_REF][START_REF] Blanco Morgado | HLA-DRB1 en pacientes caucásicos con neuromielitis óptica[END_REF][START_REF] Pandit | Human leukocyte antigen association with neuromyelitis optica in a south Indian population[END_REF][START_REF] Estrada | A whole-genome sequence study identifies genetic risk factors for neuromyelitis optica[END_REF]. This association with DRB1*03:01 is concordant with the common co-occurrence of autoimmune systemic diseases in NMO patients [START_REF] Pittock | Neuromyelitis optica and non organ-specific autoimmunity[END_REF]. Additionally, there is another minor association with DRB1*10:01 described in the same populations across several studies; however, all of them provided uncorrected p values so this finding needs further confirmation (Guimaraães [START_REF] Brum | HLA-DRB association in neuromyelitis optica is different from that observed in multiple sclerosis[END_REF][START_REF] Blanco Morgado | HLA-DRB1 en pacientes caucásicos con neuromielitis óptica[END_REF][START_REF] Pandit | Human leukocyte antigen association with neuromyelitis optica in a south Indian population[END_REF][START_REF] Alvarenga | The HLA DRB1*03:01 allele is associated with NMO regardless of the NMO-IgG status in Brazilian patients from Rio de Janeiro[END_REF][START_REF] Alonso | Neuromyelitis Optica (NMO IgG+) and Genetic Susceptibility, Potential Ethnic Influences[END_REF].

Associations between HLA and NMO in patients from East Asia were initially even more difficult to interpret, partially due to the analysis of opticospinal MS (now considered as a synonym of NMO) along with "conventional" MS [START_REF] Matsushita | Association of the HLA-DPB1*0501 allele with anti-aquaporin-4 antibody positivity in Japanese patients with idiopathic central nervous system demyelinating disorders[END_REF][START_REF] Isobe | Influence of HLA-DRB1 alleles on the susceptibility and resistance to multiple sclerosis in Japanese patients with respect to anti-aquaporin 4 antibody status[END_REF]. Nowadays, the most important alleles that have been specifically linked to anti-AQP4 positive NMO are DRB1*16:02 (carried by 9% vs. 0.8% in the healthy controls; p<0.01), and DPB1*05:01 (85% vs.

nearly 65% in healthy controls; p<0.01) [START_REF] Matsushita | Association of the HLA-DPB1*0501 allele with anti-aquaporin-4 antibody positivity in Japanese patients with idiopathic central nervous system demyelinating disorders[END_REF][START_REF] Wang | HLA-DPB1*0501 is associated with susceptibility to anti-aquaporin-4 antibodies positive neuromyelitis optica in Southern Han Chinese[END_REF][START_REF] Yoshimura | Distinct genetic and infectious profiles in Japanese neuromyelitis optica patients according to anti-aquaporin 4 antibody status[END_REF]. In addition, a negative association has also been reported with DRB1*09:01 (6% vs.

27.5% in healthy controls; p<0.01, OR=0.16, 95% CI 0.07-0.37), regardless of the AQP4 antibody status [START_REF] Yoshimura | Distinct genetic and infectious profiles in Japanese neuromyelitis optica patients according to anti-aquaporin 4 antibody status[END_REF]. Interestingly, a recent familial case report from Taiwan described a NMO female patient that inherited DRB1*03:01 from her also NMO-affected mother (who was heterozygote for DRB1*03:01/16:02), and DPB1*05:01 from her healthy father [START_REF] Lee | Intra-family phenotype variations in familial neuromyelitis optica spectrum disorders[END_REF];

this case represents therefore a good example of the complex interactions among risk HLA alleles at the same or different loci that might be involved in the genetic predisposition to NMO.

Thus, two major associations have been described between HLA and NMO depending on the population origin, and in all cases the association seems to be more solid for anti-AQP4 positive cases. Recently, it was shown that some adults patients with reportedly seronegative NMO had actually autoantibodies of IgG1 subclass against the myelin oligodencrocyte glycoprotein (MOG) [START_REF] Kitley | Myelin-oligodendrocyte glycoprotein antibodies in adults with a neuromyelitis optica phenotype[END_REF][START_REF] Jarius | MOG-IgG in NMO and related disorders: a multicenter study of 50 patients. Part 1: Frequency, syndrome specificity, influence of disease activity, long-term course, association with AQP4-IgG, and origin[END_REF], configuring a clinically heterogeneous entity called MOGassociated disorders (MOGAD), since pediatric patients, which are much more frequent than in NMO, usually present with acute disseminated encephalomyelitis (ADEM) [START_REF] Cobo-Calvo | Clinical Features and Risk of Relapse in Children and Adults with Myelin Oligodendrocyte Glycoprotein Antibody-Associated Disease[END_REF]. Despite some clinical overlap with NMO, the particular demographic and immunological MOGAD characteristics reflect distinct underlying mechanisms. In this way, no association between HLA and MOGAD was found in a recent Dutch cohort, including sub-analyses according to age and clinical presentation, while anti-AQP4 positive NMO patients presented significantly higher carrier frequencies than controls of DRB1*03:01 and other alleles of the haplotype 8.1 [START_REF] Bruijstens | HLA association in MOG-IgG-and AQP4-IgG-related disorders of the CNS in the Dutch population[END_REF]. To the contrary, it has been reported a modest association between DQB1*05:02 and MOGAD in Chinese patients (allele frequency of 18.9% vs. 10.7% in healthy controls, p=0.002, OR=1.95, 95% CI 1.25-3.0), which was stronger when only pediatric cases were analyzed (p=0.015, OR=2.43, 95% CI 1.39-4.11), and also accompanied by an association with the linked allele DRB1*16:02 (p=0.001, OR=3.28, 95% CI 1.55-6.25) (Sun et al., 2020b). However, adult patients showed no association with HLA (Sun et al., 2020b), and the association with DRB1*16:02 is likely to be ethnically biased since it has been also reported with NMO, anti-NMDAR encephalitis, and many other autoimmune diseases in Asiatic populations, always with low carrier frequencies [START_REF] Chen | Comprehensive meta-analysis reveals an association of the HLA-DRB1*1602 allele with autoimmune diseases mediated predominantly by autoantibodies[END_REF]. Moreover, although Sun at al. tried to established a link between T-and B-cell epitopes using in silico and in vitro analyses, the selection of the peptide binding the heterodimer DQA1*01:01-DQB1*05:02 was already based on a previously reported Bepitope, and the difference observed in antibody recognition for the mutated peptide between DQB1*05:02-carriers and non-carriers was barely significant (p=0.047) (Sun et al., 2020b).

In conclusion, future studies on associations between HLA and CNS demyelinating diseases should rely on well-defined clinical phenotypes accompanied by specific autoantibodies in order to perform genotyping on uniform populations. This will allow us to obtain more consistent results that may lead to a better understanding of the pathogenesis of these diseases.

OBJECTIVES OF THE PhD PROJECT

As illustrated in our introduction, genetics likely plays an important role in the pathogenesis of autoimmune encephalitis and related disorders, interacting with known and yet undefined environmental factors. Classical HLA are the main loci related to autoimmune diseases, partially due to their particular genetic structure but especially because of their major role in antigen presentation and T-cell selection in the thymus. There is already some evidence, described in detail in the introduction, regarding the association between HLA and several types of autoimmune encephalitis. However, many questions remain unsolved and warrant further investigation. First, genetic studies for many autoimmune encephalitides are either absent or performed with incomplete HLA genotyping, in small samples, or included only some of their clinical phenotypes. Second, though it seems that HLA profiles correlate with certain clinical and immunological features in some autoimmune neurological diseases with autoantibodies, whether this also occurs in autoimmune encephalitides whose association with HLA has recently been described is still unclear. Finally, even for those autoimmune encephalitides that present a well-defined association with HLA, its precise role in the pathogenesis is far from being elucidated.

Thus, this PhD project aims to provide new insights regarding the role of HLA in autoimmune encephalitis and related disorders, by addressing three main objectives:

1. To establish the weight of HLA in the genetic predisposition to autoimmune encephalitis and related disorders.

2. To determine its correlation with clinical phenotypes and immunological characteristics, trying to identify particular subsets of patients.

3. To study potential pathogenic mechanisms underlying the association between HLA and autoimmune encephalitis, using an in silico approach to predict peptide-binding affinities.

In order to answer these questions, we selected four groups of autoimmune encephalitis and related disorders defined by the presence of antibodies against the following antigens:

1. Glutamic acid decarboxylase 65 (GAD65).

2. Contactin-associated protein-like 2 (CASPR2).

3. Leucine-rich glioma-inactivated 1 (LGI1).

Adenylate kinase 5 (AK5).

The structure of the PhD is therefore based on the investigations performed in these four types of autoimmune encephalitis, with both published clinic-genetic studies as well as some additional unpublished analyses. Secondly, and based on the primary DQ2 effect described previously, we aimed to determine whether GAD65-derived peptides preferentially bind DQ heterodimers rather than DR ones. Using an in silico approach, we confirm this hypothesis and, moreover, we also predict that one of the T-epitope partially co-localize with a B-epitope. However, these results must be demonstrated experimentally and, additionally, the diversity of HLA observed in the previous study should be taken into consideration.

STUDIES OF THE ROLE

Finally, since nearly 60% of the patients carried different HLA haplotypes, and there was no association between DQ2 and clinical phenotype, we hypothesized that other non-HLA loci might be involved. To explore this possibility, we conducted an interview-based study to describe the autoimmune comorbidities of patients and their relatives, as well as their potential patterns of inheritance. We found that nearly 70% of the patients reported family history of autoimmunity, which was highly heterogeneous and often resembling autoimmune polyendocrine syndromes.

These results strongly suggest a diverse genetic predisposition probably including several non-HLA genes, and will allow performing broader genetic studies such as GWAS on appropriately selected pedigrees. In silico analysis supports a primary DQ effect in the association between HLA and GAD65 antibodies

Introduction

In our first study on immunogenetics of neurological syndromes with GAD65 antibodies, the haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01, which is known to be associated with type 1 diabetes mellitus and other organ-specific autoimmune diseases, was the most common in a cohort of 32 unrelated patients. Nevertheless, at allele level, only DQB1*02:01 was significantly more frequent compared to controls, and there was also a strong trend for DQA1*05:01; we therefore suggested a primary DQ effect in the association between HLA and neurological syndromes with GAD65 antibodies (Muñiz-Castrillo et al., 2020a). Consequently, we then aimed to explore, using an in silico approach, whether GAD65-derived peptides bind preferentially the DQA1*05:01-DQB1*02:01 heterodimer, or DRB1*03:01, which forms heterodimers with the almost invariable DRA.

Methods

The NetMHCIIpan 3.2 server was used to predict HLA class II binding affinities for 15amino acid-long consecutive overlapping peptides from the full-length sequence of GAD65, obtained in FASTA format from the database UniProt (accession number Q05329). The NetMHCIIpan 3.2 server provides the prediction value for each peptide as a percentile rank after comparing its score to that of 200000 random natural peptides of the same length [START_REF] Jensen | Improved methods for predicting peptide binding affinity to MHC class II molecules[END_REF]. A peptide was considered as a strong binder when it had a rank value ≤1%, meaning that its predicted affinity is among the top 1%; we therefore considered intermediate binders those with a rank value <3%. In addition, we also investigated whether the peptides predicted as potential Tepitopes (strong and intermediate binders) could also be targets of B-cells using the BepiPred-2.0 server to predict sequential B-epitopes with the epitope threshold recommended by default (0.5).

BepiPred-2.0 is based on a random forest algorithm that is trained using, for each residue, its computed volume, hydrophobicity, polarity, and the relative surface accessibility (exposed/buried) and secondary structure (helix/sheet/coil) that are simultaneously predicted by NetSurfP if the advanced output is selected [START_REF] Jespersen | BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes[END_REF].

Results

Five 15-amino acid long peptides were predicted to be intermediate binders to DRB1*03:01 (Table ). Four of them shared the same 9-amino acid core IKCDERGKM, which was below the Bepitope threshold using BepiPred-2.0. The fifth peptide GYEMVFDGKPQHTNV (core MVFDGKPQH) was found to be above the B-epitope threshold, its central part exposed and located within a coil (Figure). No strong binders were predicted to DRB1*03:01. Twenty-one 15-amino acid long peptides were predicted to bind DQA1*05:01-DQB1*02:01, seven as strong binders and 14 as intermediate binders (Table). Seven core peptides were identified; among them, FLIEEIERL and FTYEIAPVF were the sole strong binders. Only FLIEEIERL was predicted to form part of a Bepitope, lying between a coil and a helix (Figure). No other core peptides were predicted as sequential B-epitopes.

Discussion

We show herein that GAD65-derived peptides were predicted to bind with higher affinity DQA1*05:01-DQB1*02:01 than DRB1*03:01, supporting our previous hypothesis that the association between HLA and neurological diseases with GAD65 antibodies is mostly DQdependent (Muñiz-Castrillo et al., 2020a).

Besides, one of the strong binding core peptides to DQA1*05:01-DQB1*02:01 was also predicted to be a B-cell linear epitope located in the C-terminal domain. In contrast to antibodies against GAD65 from patients with type 1 diabetes mellitus that principally recognize conformational epitopes in the C-terminal and central (catalytic) domains [START_REF] Richter | Autoreactive epitopes defined by diabetes-associated human monoclonal antibodies are localized in the middle and C-terminal domains of the smaller form of glutamate decarboxylase[END_REF]Fenalti et al., 2008), those from neurological patients mainly target linear epitopes in the three domains but especially the central one [START_REF] Kim | Higher autoantibody levels and recognition of a linear NH2-terminal epitope in the autoantigen GAD65, distinguish stiff-man syndrome from insulin-dependent diabetes mellitus[END_REF][START_REF] Raju | Analysis of GAD65 autoantibodies in Stiff-Person syndrome patients[END_REF][START_REF] Fouka | GAD65 epitope mapping and search for novel autoantibodies in GAD-associated neurological disorders[END_REF][START_REF] Gresa-Arribas | Antibodies to Inhibitory Synaptic Proteins in Neurological Syndromes Associated with Glutamic Acid Decarboxylase Autoimmunity[END_REF]. In addition, conformational epitopes have also been reported in patients with SPS [START_REF] Butler | Identification of a dominant epitope of glutamic acid decarboxylase (GAD-65) recognized by autoantibodies in stiff-man syndrome[END_REF][START_REF] Daw | Glutamic acid decarboxylase autoantibodies in stiffman syndrome and insulin-dependent diabetes mellitus exhibit similarities and differences in epitope recognition[END_REF].

Importantly, the co-localization of GAD65 B-epitopes and DRB1*04:01-restricted Tepitopes has already been reported in type 1 diabetes mellitus (Fenalti et al., 2008). Moreover, one of these CD4+ T-epitopes also co-localized with one of the main CD8+ T-epitopes [START_REF] Panina-Bordignon | Cytotoxic T cells specific for glutamic acid decarboxylase in autoimmune diabetes[END_REF]Fenalti et al., 2008), which is particularly relevant as cytotoxic T-cells are thought to be the principal effectors of the immune damage in type 1 diabetes mellitus.

Furthermore, an initially MHC class II-restricted C-terminal T-cell response in a mouse model of type 1 diabetes mellitus was later followed by antigen spreading [START_REF] Fenalti | GAD65 as a prototypic autoantigen[END_REF]. Taken together, these findings support an important role of B-cells in the modulation of T-cell responses against GAD65 in type 1 diabetes mellitus [START_REF] Fenalti | GAD65 as a prototypic autoantigen[END_REF].

Similarly to type 1 diabetes mellitus, neurological syndromes with GAD65 antibodies are thought to be mainly T-cell mediated, while the pathogenic role of the antibodies remains controversial [START_REF] Baizabal-Carvallo | The neurological syndromes associated with glutamic acid decarboxylase antibodies[END_REF][START_REF] Graus | GAD antibodies in neurological disorders -insights and challenges[END_REF]. However, only a few studies in SPS have so far investigated T-epitopes, which were located in the three domains of GAD65 [START_REF] Schloot | GAD65-Reactive T cells in a non-diabetic stiff-man syndrome patient[END_REF][START_REF] Lohmann | Immune reactivity to glutamic acid decarboxylase 65 in stiffman syndrome and type 1 diabetes mellitus[END_REF][START_REF] Skorstad | Cerebrospinal fluid T cell responses against glutamic acid decarboxylase 65 in patients with stiff person syndrome[END_REF]. Interestingly, SPS patients had different Tepitopes compared to those observed in type 1 diabetes mellitus [START_REF] Schloot | GAD65-Reactive T cells in a non-diabetic stiff-man syndrome patient[END_REF], and clones isolated from CSF were shown to be more GAD65-specific than those from the blood [START_REF] Skorstad | Cerebrospinal fluid T cell responses against glutamic acid decarboxylase 65 in patients with stiff person syndrome[END_REF]. Besides, most of these T-epitopes were HLA-DR restricted [START_REF] Schloot | GAD65-Reactive T cells in a non-diabetic stiff-man syndrome patient[END_REF][START_REF] Skorstad | Cerebrospinal fluid T cell responses against glutamic acid decarboxylase 65 in patients with stiff person syndrome[END_REF], although diverse DR alleles were reported, few patients carried DQ2-DR3, and in another study no relationship was observed between T-epitopes and HLA [START_REF] Lohmann | Immune reactivity to glutamic acid decarboxylase 65 in stiffman syndrome and type 1 diabetes mellitus[END_REF].

Thus, the interactions between B-and T-epitopes and the role of HLA are yet obscure in neurological syndromes with GAD65 antibodies, and should be further investigated. Moreover, since B-epitopes recognized by GAD65 antibodies [START_REF] Fouka | GAD65 epitope mapping and search for novel autoantibodies in GAD-associated neurological disorders[END_REF][START_REF] Gresa-Arribas | Antibodies to Inhibitory Synaptic Proteins in Neurological Syndromes Associated with Glutamic Acid Decarboxylase Autoimmunity[END_REF] and HLA profiles (Muñiz-Castrillo et al., 2020a) do not differ between neurological phenotypes, other immunological and genetic factors are likely to be involved in the pathogenic pathways leading to different clinical presentations.

Study I. Conclusions

The first study provides several, though rather indefinite, answers regarding the role of HLA in neurological disorders with GAD65 antibodies. First, the class II haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01, the most frequently found in our cohort, clearly establishes a link with many autoimmune systemic diseases that are associated with the same haplotype. Moreover, these autoimmune organ-specific diseases were commonly reported in patients and their relatives in our interview-based study. Furthermore, the association seemed to be dependent on a DQ effect, and, accordingly, a higher affinity of GAD65-derived peptides was predicted for the DQ heterodimer of this haplotype.

Nevertheless, the overall low DQ2-DR3 carrier frequency as well as the variable patterns of familial autoimmunity found likely reflect that neurological disorders with GAD65 antibodies are highly heterogeneous regarding their genetic predisposition, which could be in turn partially related to the ethnic variety observed. This genetic heterogeneity might also be responsible for the own clinical diversity of neurological disorders with GAD65 antibodies. Thus, in order to precisely identify the weight of HLA in the genetic predisposition, larger and more homogeneous subgroups of patients should be analyzed.

In addition to HLA, it seems that other genes might be particularly important for the pathogenesis of neurological disorders with GAD65 antibodies, especially for those cases with strong familial aggregation of autoimmune diseases. Once again, building homogeneous clinical cohorts of patients will improve the power and accuracy of the genetic analysis investigating these non-HLA genes. Conversely, for the familial studies, an extensive sampling and biological confirmation of the autoimmune comorbidities is of capital importance. These non-HLA loci should ideally be investigated using GWAS or whole exome sequencing (WES) rather than by small predefined selections of genes that might offer a restricted view of the actual genetic landscape of neurological disorders with GAD65 antibodies.

Commentary

Antibodies targeting CASPR2 may appear in patients with three main clinical phenotypes (Morvan syndrome, acquired neuromyotonia, and LE), which have been frequently treated as a continuum. Indeed, this consideration hindered the identification of a strong HLA association in a first study addressing this aspect in patients with CASPR2 antibodies, since they were analyzed altogether and, moreover, a considerable proportion of atypical phenotypes were included. Thus, in order to clearly define whether patients with CASPR2 antibodies have a shared or phenotypespecific association with HLA, we first conducted a cluster analysis of 56 patients to get a more accurate clinical classification. We therefore obtained four groups: isolated LE, LE co-occurring with other CNS symptoms such as cerebellar ataxia, acquired neuromyotonia, and Morvan syndrome.

Then, HLA genotyping using NGS was performed in 30 patients with available DNA.

Despite confirming the association with DRB1*11:01-DQA1*05:01-DQB1*03:01 with anti-CASPR2 autoimmunity as a whole, when the groups were compared to controls separately, only LE had a significantly higher DRB1*11:01-carrier frequency (94.1% versus 18.3%). To the contrary, DRB1*11:01 was not statistically more frequent in patients with neuromyotonia and Morvan syndrome than in controls. The differences in HLA profiles, along with the other clinical and immunological findings, strongly suggest different pathogenic pathways, at least for LE with CASPR2 antibodies and paraneoplastic Morvan syndrome.

Finally, given the strong association between non-paraneoplastic LE and DRB1*11:01-DQA1*05:01-DQB1*03:01, we aimed to investigate their binding affinity for CASPR2-derived peptides, as well as that of the other HLA present in the non-DRB1*11:01carriers. Hence, using an in silico approach, we found a modest overlap in the spectrums of these HLA molecules.

Peptide-binding spectrum of HLA associated with anti-CASPR2 encephalitis

Introduction

After discovering that the association between the haplotype DQA1*05:01-DQB1*03:01-DRB1*11:01 and diseases with CASPR2 antibodies was exclusively present in patients with nonparaneoplastic LE, and therefore absent in Morvan syndrome co-occurring with malignant thymoma, we hypothesized that the origin of the former could be a dysfunction in the presentation of CASPR2-derived peptides, which could eventually lead to a loss of central and/or peripheral selftolerance (Muñiz-Castrillo et al., 2020b). Accordingly, we compared the peptide-binding spectrum of the most frequent haplotype to that of others more uncommonly carried by patients with anti-CASPR2 LE, since we expected a similar repertoire supporting our hypothesis. In addition, we aimed to determine whether the predicted T-epitopes co-localize with B-epitopes, which were principally located in the discoidin (Disc, 35-181 amino acids) and laminin G1 (Lam1, 216-368 amino acids) domains [START_REF] Olsen | Caspr2 autoantibodies target multiple epitopes[END_REF][START_REF] Pinatel | Inhibitory axons are targeted in hippocampal cell culture by anti-Caspr2 autoantibodies associated with limbic encephalitis[END_REF][START_REF] Joubert | Characterization of a Subtype of Autoimmune Encephalitis With Anti-Contactin-Associated Protein-like 2 Antibodies in the Cerebrospinal Fluid, Prominent Limbic Symptoms, and Seizures[END_REF].

Methods

Subjects and HLA haplotyping

Patients with anti-CASPR2 LE were selected from our previous study, in which HLA genotyping at a four-digit level was performed using NGS technology and the most likely

Peptide binding prediction

The full-length sequence of CASPR2 was obtained in FASTA format from the database UniProt (accession number Q9UHC6). We used the NetMHCIIpan 3.2 server with the offset correction to predict HLA class II binding affinities for 15-amino acid-long consecutive overlapping CASPR2-derived peptides. The server provides the prediction value for each peptide as a percentile rank obtained by comparing its score to those of 200000 random natural peptides that are the same length as the query peptide. We considered a peptide as a strong binder when it had a rank value ≤3%, meaning that its predicted affinity is among the top 3% for the protein of interest [START_REF] Jensen | Improved methods for predicting peptide binding affinity to MHC class II molecules[END_REF].

The peptide-binding spectrum of DRB1*11:01 was compared to that of the DRB1 detected in the patient non-carrying DRB1*11:01. The DQ heterodimers were exclusively investigated in cis form. Thus, the peptide-binding spectrum of DQA1*05:01-DQB1*03:01, which appeared combined with DRB1*11:01, was compared to that of the two DQ heterodimers carried by the patient negative for DRB1*11:01.

Results

CASPR2-derived peptide-binding prediction for DRB1

Twenty-six 15-amino acid-long CASPR2-derived peptides were predicted as strong binders for DRB1*11:01, encompassing 7 core-peptides, none of them located within the Disc or the Lam1 domains. Conversely, they belonged to the C-terminal region of CASPR2 (Fibrinogen C, Laminin G3, and Laminin G4 domains). Additionally, among those 26 peptides, 7 and 4 peptides were respectively predicted as strong binders for DRB1*15:01 and DRB1*04:01. Three peptides were predicted as strong binders for the three DRB1 analyzed: RVQFNQIAPLKAALR (position 1181)

and VQFNQIAPLKAALRQ (position 1182), which shared the core FNQIAPLKA; and the adjacent QFNQIAPLKAALRQT (position 1183, core IAPLKAALR; Table 1).

Thirteen peptides were predicted as strong binders for DRB1*15:01, all of them in the Cterminal region of CASPR2. Thirty-one peptides were predicted as strong binders for DRB1*04:01, including 9 peptides in the Disc domain and 2 peptides in the Lam1 domain, though those presenting the highest affinity were in the C-terminal region of CASPR2 (Table 2).

CASPR2-derived peptide-binding prediction for DQ heterodimers

Seventy-nine 15-amino acid-long CASPR2-derived peptides, encompassing 24 cores, were 3).

Forty-four peptides were predicted as strong binders for DQA1*01:02-DQB1*06:02, but only 5 of them were located in the Lam1 domain. Fifty-four peptides were predicted as strong binders for DQA1*03:01-DQB1*03:02, 5 of them in the Lam1 domain, and only 1 in the Disc domain. Thus, most of the strong binders were in the C-terminal region of CASPR2 (Table 4).

Discussion

The in silico analysis presented herein showed that DRB1*11:01 peptide-binding spectrum is closer to that of DRB1*15:01 than that of DRB1*04:01, although the degree of overlap between these three DRB1 was indeed modest. Regarding the analysis for the DQ heterodimers, there was a slightly wider shared spectrum between them than that observed for DRB1. Despite the obvious limitation of having only one patient not carrying DQA1*05:01-DQB1*03:01-DRB1*11:01, these peptides in common are the best candidates to be explored in experimental assays for T-cell response characterization.

So far, there is only one in silico analysis in anti-CASPR2 disorders reported in the literature, which was mainly focused on the comparison between the binding properties of the HLA associated with anti-LGI1 LE and that of anti-CASPR2 disorders. The authors argued against disease-specificity since many LGI1-and CASPR2-derived peptides could potentially bind both HLA [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF]. However, this might be a misinterpretation given the natural promiscuity of the peptide-HLA interactions [START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF][START_REF] Sidney | Epitope prediction and identification-adaptive T cell responses in humans[END_REF].

Intriguingly, none of the CASPR2-derived peptides predicted as strong binders for DRB1*11:01 were in the Disc and Lam1 domains that include the major B-epitopes [START_REF] Olsen | Caspr2 autoantibodies target multiple epitopes[END_REF][START_REF] Pinatel | Inhibitory axons are targeted in hippocampal cell culture by anti-Caspr2 autoantibodies associated with limbic encephalitis[END_REF][START_REF] Joubert | Characterization of a Subtype of Autoimmune Encephalitis With Anti-Contactin-Associated Protein-like 2 Antibodies in the Cerebrospinal Fluid, Prominent Limbic Symptoms, and Seizures[END_REF]. Conversely, they were preferentially in the Cterminal region, and this was also the case for most of the predicted peptides for the DQ heterodimers, although a few strong binders for the latter were in the Disc and Lam1 domains.

However, epitope spreading as well as post-translational modifications of the peptides in the Disc and Lam1 domains could explain the apparent lack of co-localization between B-and T-epitopes [START_REF] Doyle | Autoantigens: novel forms and presentation to the immune system[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF].

Study II. Conclusions

The second study addressing the neurological disorders with CASPR2 antibodies constitutes the best example of how an accurate clinical classification can clarify the association with HLA.

The extremely high DRB1*11:01 carrier frequency in patients with LE contrasts with that observed in the other phenotypes. This difference is particularly relevant between non-paraneoplastic LE and Morvan syndrome, which is often associated with malignant thymoma, as it likely reflects two very distinct pathogenic mechanisms. On the one hand, it is tempting to hypothesize that an abnormal CASPR2-derived peptides presentation by DRB1*11:01 occurs in patients with LE, either in the thymus leading to the escape of auto-reactive T-cells from negative selection, or in the periphery causing a dysfunction of Treg lymphocytes. On the other hand, the broad biological (CASPR2,

LGI1, AchR antibodies) and clinical (Morvan syndrome, myasthenia gravis) autoimmune spectrum associated with malignant thymoma strongly suggest an unspecific loss of central self-tolerance.

However, the overall cohort of our study was rather small, especially concerning patients with acquired neuromyotonia that are therefore difficult to place in the picture described above. In addition, little or even no evidence exists supporting the two proposed pathogeneses. Thus Commentary HLA-DRB1*07:01 has been strongly associated with anti-LGI1 LE, but so far no differences have been reported between carriers and noncarriers of this allele. Moreover, in contrast to other types of autoimmune encephalitis with antibodies targeting surface or synaptic antigens, CSF testing is less sensitive than serum. However, it is unclear whether patients with positive and negative CSF are clinically, immunologically, or genetically different.

We therefore studied the clinical and immunological characteristics of a cohort of 134 patients with anti-LGI1 LE, including 29 without CSF antibodies. We found no significant difference between these two subsets of patients for most of the variables analyzed, although CSF positivity was associated with shorter diagnosis delay, hyponatremia, and inflammatory abnormalities in the CSF and magnetic resonance imaging (MRI), suggesting a more intense CNS immune reaction that was further supported by a poorer long-term outcome of patients with detectable antibodies in the CSF.

We also obtained the HLA genotypes of 72 patients with available DNA using NGS.

Importantly, when we compared patients according to their DRB1*07:01 carrier status, we found that noncarriers (9/72, 12%) were more frequently young women. Thus, this group of patients shows particular genetic and demographic characteristics that might reflect also a distinct pathogenesis.

However, it has not been studied whether patients with different HLA are able to present

LGI1-derived peptides with a similar affinity. Hence, we performed an in silico analysis comparing the peptide-binding spectrum of DRB1 and DQ heterodimers. We found a large overlap in the spectrums of DRB1 molecules, while the opposite was observed for the DQ heterodimers. These results suggest that the different DRB1 molecules might be similarly involved in an altered LGI1derived peptide presentation.

Peptide-binding spectrum of HLA associated with anti-LGI1 encephalitis

Introduction

Anti-LGI1 LE has been strongly associated with the allele DRB1*07:01, which is carried by nearly 90% of the patients, usually in linkage disequilibrium with DQA1*02:01-DQB1*02:02 [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Van Sonderen | Anti-LGI1 encephalitis is strongly associated with HLA-DR7 and HLA-DRB4: Anti-LGI1 Encephalitis[END_REF][START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF]. A strong association with class II haplotypes suggests that the pathogenesis of anti-LGI1 LE may be related to an altered peptide presentation to CD4+ T-cells. In silico studies concerning peptide-binding properties in anti-LGI1 LE are very scare and so far inconclusive [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF]. Thus, after the identification of some demographic differences between DRB1*07:01 carriers and noncarriers (Muñiz-Castrillo et al., 2021a), we aimed to investigate whether the HLA molecules found in the noncarriers are able to present the same peptides as DRB1*07:01 with high affinity.

Additionally, we verified the position of the predicted peptides in the leucine-rich repeat (LRR, 1-223 amino acids) and the epitempin (ETP, 224-557 amino acids) domains, where the epitopes recognized by LGI1 antibodies are located [START_REF] Ohkawa | Autoantibodies to epilepsy-related LGI1 in limbic encephalitis neutralize LGI1-ADAM22 interaction and reduce synaptic AMPA receptors[END_REF][START_REF] Petit-Pedrol | LGI1 antibodies alter Kv1.1 and AMPA receptors changing synaptic excitability, plasticity and memory[END_REF][START_REF] Ramberger | Distinctive binding properties of human monoclonal LGI1 autoantibodies determine pathogenic mechanisms[END_REF].

Methods

Subjects and HLA haplotyping

Patients with anti-LGI1 LE were selected from our previous study, for which HLA genotyping at a four-digit level was performed using NGS and the most likely haplotypes according to ethnical origin were selected based on the public database HaploStats of the National Marrow Donor Program (NMDP).

A total of 63/72 (87.5%) patients carried DRB1*07:01, 53/63 (84.1%) along with DQA1*02:01-DQB1*02:02. The remaining 10 patients had other DQ heterodimers, mainly DQA1*02:01-DQB1*03:03 (Table 1). The 9 non-DRB1*07:01 carriers had very variable DRB1 and DQ alleles (Table 2), all of them were also investigated for peptide-binding prediction.

Peptide binding prediction

The full-length sequence of LGI1 was obtained in FASTA format from the database UniProt (accession number, O95970). We used the NetMHCIIpan 3.2 server with the offset correction to predict HLA class II binding affinities for 15-amino acid-long consecutive overlapping LGI1derived peptides. The server provides the prediction value for each peptide as a percentile rank obtained by comparing its score to those of 200000 random natural peptides that are the same length as the query peptide. A peptide was considered as a strong binder when it had a rank value ≤3%, meaning that its predicted affinity is among the top 3% for the protein of interest [START_REF] Jensen | Improved methods for predicting peptide binding affinity to MHC class II molecules[END_REF]. The peptide-binding spectrum of DRB1*07:01 was compared to that of the DRB1 detected in the noncarriers of this allele. Similarly, we compared the peptide-binding spectrum of the most frequent DQ heterodimer, DQA1*02:01-DQB1*02:02, to that of the remaining DQ heterodimers (only in cis form).

Results

LGI1-derived peptide-binding prediction for DRB1 Twenty-seven 15-amino acid-long LGI1-derived peptides were predicted as strong binders for DRB1*07:01, including 9 core-peptides located in both the LRR and the ETP domains. The (1 peptide). The peptide RHTFRGLKSLIHLSL (position 132, core FRGLKSLIH, LRR domain) was the only one predicted as a strong binder for all the DRB1 (Table 3). Seven out of 9 (77.8%) non-DRB1*07:01 carriers had at least one DRB1 with a large (>50%) overlap with DRB1*07:01 (Table 2) 4); these three DRB1 were among those with a lesser overlap with DRB1*07:01. As it occurred with DRB1*07:01, the peptides showing the highest affinity were in the LRR domain (Tables 3 and4).

LGI1-derived peptide-binding prediction for DQ heterodimers

Seventeen 15-amino acid-long LGI1-derived peptides were predicted as strong binders for DQA1*02:01-DQB1*02:02, comprising 7 core-peptides in both the LRR and the ETP domains. 5). All the patients not carrying DQA1*02:01-DQB1*02:02 had at least one DQ heterodimer with a slight overlap with DQA1*02:01-DQB1*02:02 (Tables 1 and2). 6).

Discussion

This in silico analysis found a wider overlap in their strong binding LGI1-derived peptidesspectrum for DRB1 than for DQ heterodimers. Indeed, most of the 9 non-DRB1*07:01 carriers had at least one DRB1 with a large shared spectrum with DRB1*07:01. These results, along with the generally stronger genetic association with DRB1*07:01 than with DQ alleles [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Van Sonderen | Anti-LGI1 encephalitis is strongly associated with HLA-DR7 and HLA-DRB4: Anti-LGI1 Encephalitis[END_REF][START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF][START_REF] Mueller | Genetic predisposition in anti-LGI1 and anti-NMDA receptor encephalitis: GWAS Autoimmune Encephalitis[END_REF], Muñiz-Castrillo et al., 2021a), suggest that DRB1 and not DQ might be involved in an altered LGI1-derived peptide presentation.

Interestingly, strong binders for DRB1 molecules were located within both the LRR and ETP domains, but the peptides with the highest affinity were in the LRR domain. Moreover, one peptide within this domain was predicted as a strong binder for all the DRB1 analyzed. Conversely, the strong binders for DQA1*02:01-DQB1*02:02 were more uniformly distributed, and, furthermore, those for the rest of DQ heterodimers were preferentially in the ETP domain. Taken together, these results could suggest a dominant T-cell immune response against DRB1*07:01restricted LRR epitopes that is followed by epitope spreading towards the ETP domain. Recently, it has been shown that the antibodies had different in vitro and in vivo effects according to their targeted domain [START_REF] Ramberger | Distinctive binding properties of human monoclonal LGI1 autoantibodies determine pathogenic mechanisms[END_REF]. Those that recognized LRR were able to bind already docked LGI1 provoking its internalization, whereas anti-ETP antibodies inhibited the binding between free LGI1 and its partners. In addition, anti-LRR antibodies showed a stronger bound to brain tissue and more prominent in vivo effects. However, both subpopulations of antibodies cooccurred and, moreover, remained stable over time, although the samples used for epitope evolution assessment belonged to patients already treated and it is noteworthy that only IgG4 antibodies were evaluated [START_REF] Ramberger | Distinctive binding properties of human monoclonal LGI1 autoantibodies determine pathogenic mechanisms[END_REF]. Since there is some evidence of epitope spreading and switching of IgG subclass showing different pathogenic mechanisms in other autoimmune diseases with mainly IgG4 antibodies and strong HLA association, such as anti-MusK MG and pemphigus vulgaris [START_REF] Huijbers | The expanding field of IgG4-mediated neurological autoimmune disorders[END_REF][START_REF] Koneczny | Update on IgG4-mediated autoimmune diseases: New insights and new family members[END_REF], further studies in anti-LGI1 LE should address the potential functional differences between IgG4 and IgG1 LGI1 antibodies, the temporal evolution of epitopes and IgG subclasses, as well as the vitro characterization of T-cell epitopes and its relationship with the B-cell response. Compared to neurological disorders with GAD65 or CASPR2 antibodies, anti-LGI1 LE is a much more uniform disease and this is reflected in its association with HLA. Yet, we found that non-DRB1*07:01 carriers were younger and more commonly women than carriers; whether other HLA alleles are overrepresented in this small subset of patients should be investigated in larger cohorts. Moreover, HLA genotyping could be helpful to clarify the nature of paraneoplastic anti-

LGI1 LE, always controversial, although its rarity has so far made it difficult to evaluate. In addition, other non-HLA loci might modulate the effect of DRB1*07:01 or other HLA alleles yet to be described in the non-DR7 carriers. These non-HLA genes could eventually have an influence over the clinical presentation or the prognosis, which was not observed for DRB1*07:01. Thus, a better characterization of the HLA profile of non-DR7 carriers and paraneoplastic cases, as well as broader genetic studies such as GWAS, will expand our understanding of the genetic predisposition to anti-LGI1 encephalitis.

The precise role of HLA in the initiation of the T-cell response against LGI1 is still unknown. The in silico analysis performed strongly suggests that DRB1 molecules, and not DQ heterodimers, are involved in the LGI1-derived peptide presentation. Moreover, it seems that the Tepitopes are preferentially located in the LRR domain, being tempting to hypothesize that an initial T-cell reaction against this domain is followed by epitope spreading towards the ETP domain.

Moreover, this phenomenon could occur in parallel with the B-cell response that has recently been shown to be characterized by, at least, two different populations of IgG4 antibodies against the LRR and ETP domains. Future research should focus on the in vitro characterization of the anti-LGI1

specific T-cells and a more precise correlation with the B-cell response.

Commentary

Anti-AK5 LE is a rare autoimmune encephalitis characterized by a prominent limbic involvement, although seizures have been reported to be absent in most patients and other clinical features remain poorly described. Moreover, its pathogenesis is largely unknown compared to that of other non-paraneoplastic LE, and to date no genetic study has been performed.

We therefore conducted a study describing the clinical characteristics of 10 new patients as well as reviewing those of the 16 previously reported. We found that patients with AK5 antibodies have a particular demographic profile that resembles that of anti-LGI1 and anti-CASPR2 LE, but they are clinically distinct. In addition, CSF and MRI inflammatory abnormalities were extremely frequent. Most patients did not respond to immunotherapy and developed severe medial temporal atrophy.

In order to investigate the pathogenic mechanisms underlying these clinical specificities, we analyzed the neuropathology from the temporal biopsy of one patient, as well as the CSF proteomic profile of a series of patients compared to that of non-paraneoplastic (LGI1/CASPR2) and paraneoplastic (Yo/Ma2) neurological disorders.

Study IV. Conclusions

Based on the findings of the fourth study, anti-AK5 LE appears as a very distinct nonparaneoplastic encephalitis. Some clinical characteristics of anti-AK5 encephalitis are especially intriguing, such as the absence of seizures in early phases of the diseases that likely reflect a different structural immune-mediated damage of the temporal lobe compared to that occurring in other LE with antibodies targeting intracellular and cell surface antigens. Indeed, the HLA, proteomic, and tissue analyses pointed out a T-cell mediated pathogenesis with a major involvement of cytotoxic T-cells, but also CD4+ T-cells and innate immunity. However, the primary trigger of this immune reaction as well as the exact role of the HLA in the pathogenesis requires further investigation. Larger cohorts would enable to precisely determine the allele responsible for the HLA association, which could in turn be useful to establish whether HLArestricted AK5-specific T-cells exist. Additionally, GWAS could also be helpful for a better characterization of the association with HLA, as well as to explore other predisposing genes, although the rarity of the disease likely constitutes an obstacle for its use in anti-AK5 LE.

GENERAL DISCUSSION

Relevant results

This PhD project aimed to investigate the role of HLA in autoimmune encephalitis and related disorders by determining its importance in the genetic predisposition to these diseases, describing phenotype-genotype correlations, and predicting peptide-binding affinities.

First, we found that the associations with HLA are very diverse in both their type and strength according to the clinical subgroups. The extended haplotype 8.1 or some of their components were associated with GAD65 neurological disorders, as well as with anti-AK5 LE.

However, the carrier frequencies were particularly modest for the former (41%) (Muñiz-Castrillo et al., 2020a), while, depending on the allele considered, those for anti-AK5 LE ranged from 64% to 73% (Muñiz-Castrillo et al., 2021b). In addition to the low DQ2-carrier frequency in neurological disorders with GAD65 antibodies, the results of our exploratory study regarding the familial history of autoimmunity in these patients suggest that other non-HLA loci are involved in their genetic predisposition (Muñiz-Castrillo et al., 2021c). Interestingly, neurological disorders with GAD65

antibodies and anti-AK5 LE have in common a predominance of IgG1 subclass and a likely T-cell mediated pathogenesis [START_REF] Gresa-Arribas | Antibodies to Inhibitory Synaptic Proteins in Neurological Syndromes Associated with Glutamic Acid Decarboxylase Autoimmunity[END_REF][START_REF] Ng | Clinico-pathological correlation in adenylate kinase 5 autoimmune limbic encephalitis[END_REF][START_REF] Graus | GAD antibodies in neurological disorders -insights and challenges[END_REF], Muñiz-Castrillo et al., 2021b). Conversely, LE with antibodies targeting LGI1 and CASPR2, which are possibly pathogenic and mainly of IgG4 subclass [START_REF] Pinatel | Inhibitory axons are targeted in hippocampal cell culture by anti-Caspr2 autoantibodies associated with limbic encephalitis[END_REF][START_REF] Ariño | Anti-LGI1-associated cognitive impairment: Presentation and long-term outcome[END_REF][START_REF] Joubert | Characterization of a Subtype of Autoimmune Encephalitis With Anti-Contactin-Associated Protein-like 2 Antibodies in the Cerebrospinal Fluid, Prominent Limbic Symptoms, and Seizures[END_REF], van Sonderen et al., 2016a;[START_REF] Petit-Pedrol | LGI1 antibodies alter Kv1.1 and AMPA receptors changing synaptic excitability, plasticity and memory[END_REF], showed particular and very strong associations with a specific HLA allele, DRB1*07:01 in anti-LGI1 patients (88% carriers) and DRB1*11:01 (94%) in patients with anti-CASPR2 LE (Muñiz-Castrillo et al., 2021a, b). These well-differentiated HLA profiles suggest a major role of HLA in the pathogenesis of anti-LGI1 and anti-CASPR2 LE. Nevertheless, whether an altered HLA-peptide-TCR interaction takes place in the thymus allowing the escape of auto-reactive CD4+ T-cells, or in the periphery activating lymphocytes not previously exposed to those antigens is still unknown. Furthermore, although Bcells expansion, class-switching, and maturation occurring in the germinal centers often require the interaction with CD4+ T-cells, the exact mechanisms involved and especially the role of HLA on these processes remain obscure [START_REF] Rawlings | Altered B cell signalling in autoimmunity[END_REF], Sun et al., 2020a). So far, only an integrative hypothesis, based on shared but scare knowledge regarding other autoimmune diseases with IgG4 antibodies and strong HLA associations, has been proposed and will be discussed in the following section.

Secondly, we highlighted how important an accurate clinical classification is in order to identify HLA associations, as it has already been pointed out in other autoimmune diseases such as MG [START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Zhong | HLA in myasthenia gravis: From superficial correlation to underlying mechanism[END_REF]. Using a cluster analysis of patients with CASPR2

antibodies, we obtained well-defined groups with homogeneous clinical presentations that notably correlate with immunological and genetic features. We were therefore able to demonstrate that the association with DRB1*11:01, previously reported with a rather low carrier frequency in a heterogeneous cohort [START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF], was exclusively present in patients with anti-CASPR2 LE, and absent in Morvan syndrome and acquired neuromyotonia, which in turn supports the existence of different pathogeneses (Muñiz-Castrillo et al., 2020b). The absence of an association with HLA in patients with Morvan syndrome is probably linked to the high frequency of malignant thymoma in these cases. Similarly, we tried to determine whether patients with LGI1 antibodies differed in their clinical or immunological characteristics according to their DRB1*07:01-carrier status, and found that noncarriers were more frequently young women (Muñiz-Castrillo et al., 2021a), likely reflecting a complex interaction between HLA, sex, and age. Interestingly, the two types of MG defined by the age of onset (EOMG and LOMG) also differ in their sex predominance and HLA associations [START_REF] Zhong | HLA in myasthenia gravis: From superficial correlation to underlying mechanism[END_REF]. Conversely, no difference was observed between DQ2carriers and noncarriers with GAD65 neurological disorders (Muñiz-Castrillo et al., 2020a), and our sample of anti-AK5 LE was too small to make such type of comparisons (Muñiz-Castrillo et al., 2021b).

Finally, the in silico analyses for peptide-binding prediction will be particularly useful to

Perspectives

Expanding HLA associations

Although the association with a given HLA has already been well established for some autoimmune encephalitides, such as DRB1*07:01 in anti-LGI1 LE [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Van Sonderen | Anti-LGI1 encephalitis is strongly associated with HLA-DR7 and HLA-DRB4: Anti-LGI1 Encephalitis[END_REF][START_REF] Binks | Distinct HLA associations of LGI1 and CASPR2-antibody diseases[END_REF], whether secondary associations are present in the noncarriers or other alleles or loci modulate the risk is yet unknown. A good example of these complex interactions is narcolepsy, in which nearly 90% of the patients carry DQB1*06:02, but different DQA1 and DPB1 alleles may either increase risk or be protective, while DQB1*03:01 is associated with younger age at onset [START_REF] Bonvalet | Autoimmunity in narcolepsy[END_REF]. Thus, it is possible that the non-DRB1*07:01 young women with anti-LGI1 LE carry other risk alleles yet to be described.

In addition, there are still many autoimmune encephalitides whose HLA associations have not been investigated, although the low prevalence of these diseases likely will require large and collaborative international studies in order to be adequately powered. The HLA genotyping in these disorders will provide important insights into their pathogenesis, which might be particularly relevant for those without a known trigger. Moreover, the study of HLA in non-paraneoplastic autoimmune encephalitis and related disorders has so far yielded more positive results than that of PNS [START_REF] Wirtz | HLA and smoking in prediction and prognosis of small cell lung cancer in autoimmune Lambert-Eaton myasthenic syndrome[END_REF][START_REF] De Graaf | HLA-DQ2+ individuals are susceptible to Hu-Ab associated paraneoplastic neurological syndromes[END_REF][START_REF] Hillary | Complex HLA association in paraneoplastic cerebellar ataxia with anti-Yo antibodies[END_REF], Muñiz-Castrillo et al., 2020c). In contrast, somatic genetic alterations of tumors represent a promising research field, as already reported for PCD with Yo antibodies [START_REF] Small | Genetic alterations and tumor immune attack in Yo paraneoplastic cerebellar degeneration[END_REF]. Notably, mutations in tumors may also involve HLA loci, decreasing its expression or variability, which facilitates the evasion from the anti-tumor immune response [START_REF] Dendrou | HLA variation and disease[END_REF]. Furthermore, malignant thymomas, which are associated with several PNS including Morvan syndrome and MG, showed different immunological abnormalities, such as decreased number of Treg cells and lack of expression of AIRE and HLA class II, explaining their association with autoimmunity [START_REF] Weksler | Alterations of the immune system in thymic malignancies[END_REF]. Finally, the recent introduction of immune checkpoint inhibitors as treatment of some cancers has led to the description of multiple and often severe immunological toxicities, which can also affect the nervous system and resemble classical PNS [START_REF] Vogrig | Central nervous system complications associated with immune checkpoint inhibitors[END_REF][START_REF] Vogrig | Cranial Nerve Disorders Associated With Immune Checkpoint Inhibitors[END_REF][START_REF] Marini | Neurologic Adverse Events of Immune Checkpoint Inhibitors: A Systematic Review[END_REF]. Interestingly, some attempts have been made to describe associations between HLA and ICI-induced (neurological and systemic) side effects, though the results are inconclusive mainly due to a small sample size (Hasan [START_REF] Ali | Human leukocyte antigen variation is associated with adverse events of checkpoint inhibitors[END_REF][START_REF] Chang | HLA-B27 association of autoimmune encephalitis induced by PD-L1 inhibitor[END_REF].

Deciphering the role of HLA in TCR repertoires

The identification of an association between HLA and autoimmune encephalitis is the first step to characterize the T-cell responses in these disorders, including the peptides acting as Tepitopes and the TCR recognizing them [START_REF] Dendrou | HLA variation and disease[END_REF]. Currently, the most widely used procedures to predict T-epitopes are bioinformatics algorithms based on experimental data obtained by binding assays (a receptor-ligand inhibition reaction with purified HLA molecules and synthetic peptides) and/or immunopeptidomes (eluted, natural ligands detected by mass spectrometry), as well as on the description of the HLA binding-motifs [START_REF] Peters | T Cell Epitope Predictions[END_REF][START_REF] Sidney | Epitope prediction and identification-adaptive T cell responses in humans[END_REF]. In general, in silico predictions for HLA class II are less reliable than those for HLA class I due to the different structure of their peptide-binding grooves, which determines that the optimal and minimal sizes are poorly defined for T-epitopes presented by HLA class II [START_REF] Peters | T Cell Epitope Predictions[END_REF][START_REF] Sidney | Epitope prediction and identification-adaptive T cell responses in humans[END_REF]. However, these algorithms have been shown to be very accurate, especially the NetMHCbased method [START_REF] Peters | T Cell Epitope Predictions[END_REF], which is the one used in this PhD project. Furthermore, prediction methods have recently been developed even for those HLA molecules without experimental data [START_REF] Peters | T Cell Epitope Predictions[END_REF][START_REF] Reynisson | NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data[END_REF]. Nevertheless, the actual usefulness of these bioinformatics algorithms is to reduce the amount of peptides to be tested in experimental assays, since not all predicted binders for HLA molecules are necessarily immunogenic and recognized by TCR [START_REF] Sidney | Epitope prediction and identification-adaptive T cell responses in humans[END_REF]. Accordingly, peptides predicted as strong binders for several HLA found in patients with the same disease are the best candidates, as promiscuous peptides are often immunodominant, and should therefore be selected to determine HLA-restricted responses [START_REF] Peters | T Cell Epitope Predictions[END_REF][START_REF] Sidney | Epitope prediction and identification-adaptive T cell responses in humans[END_REF]. In addition, post-translational modifications altering the peptide-HLA affinity should be considered [START_REF] Sollid | Molecular mechanisms for contribution of MHC molecules to autoimmune diseases[END_REF][START_REF] Caillat-Zucman | New insights into the understanding of MHC associations with immunemediated disorders: MHC-associated immune diseases[END_REF][START_REF] Dendrou | HLA variation and disease[END_REF], and they can also be predicted using several computational tools [START_REF] Audagnotto | Protein post-translational modifications: In silico prediction tools and molecular modeling[END_REF].

The HLA restriction of T-cell responses can be investigated using either transfected cell lines/transgenic mice expressing a single HLA molecule, or HLA tetramers, which are usually preferred because they are technically easier to develop [START_REF] Sidney | Epitope prediction and identification-adaptive T cell responses in humans[END_REF]. In these HLA tetramers assays, four peptide-HLA complexes are linked by streptavidin. The HLA molecules are generally synthesized by bacteria (class I) or eukaryotic cell lines (class II), and the peptide loading may take place at different stages of the HLA-tetramer production process [START_REF] Bakker | MHC multimer technology: current status and future prospects[END_REF][START_REF] Christophersen | Peptide-MHC class I and class II tetramers: From flow to mass cytometry[END_REF]. Additionally, higher-order multimers (i.e. pentamers) may increase the stability and affinity of the TCR-peptide-HLA complexes, and therefore facilitate the detection of auto-reactive, especially CD4+, T-cells [START_REF] Bakker | MHC multimer technology: current status and future prospects[END_REF][START_REF] Christophersen | Peptide-MHC class I and class II tetramers: From flow to mass cytometry[END_REF]. Besides, the streptavidin is coupled to a fluorophore for visualization by flow cytometry, and more recently to metals for mass cytometry; these techniques allow the quantification and phenotypic characterization of the T-cells selected by their HLA-peptide repertoire [START_REF] Dendrou | HLA variation and disease[END_REF][START_REF] Christophersen | Peptide-MHC class I and class II tetramers: From flow to mass cytometry[END_REF]. Moreover, TCR sequencing at single-cell level may further define the particular features of antigen-specific auto-reactive T-cells, including selective VDJ usage [START_REF] Dendrou | HLA variation and disease[END_REF]. A good example of the potential utility of these technological advances is represented by recent studies on narcolepsy [START_REF] Luo | Autoimmunity to hypocretin and molecular mimicry to flu in type 1 narcolepsy[END_REF][START_REF] Luo | T cell reactivity to regulatory factor X4 in type 1 narcolepsy[END_REF].

Several peptides (derived from hypocretin, Influenza H1N1 virus/vaccine, or regulatory X factor 4), HLA-DQB1*06:02 tetramers, and peripheral blood mononuclear cells (PBMC) from patients were used to expand CD4+ T-cells reactive to those peptides. In these experiments, peptides were selected based on previous competition binding assays and tetramers were stained with fluorophores. The dominant T-epitopes, including post-translationally modified hypocretin-derived peptides, were subsequently identified, as well as peptide-specific CD4+ T-cells subpopulations, for which single-cell TCR sequencing revealed selective VDJ repertoires [START_REF] Luo | Autoimmunity to hypocretin and molecular mimicry to flu in type 1 narcolepsy[END_REF][START_REF] Luo | T cell reactivity to regulatory factor X4 in type 1 narcolepsy[END_REF].

Autoimmune encephalitides and other neurological and systemic autoimmune diseases with IgG4 antibodies show associations with HLA as strong as that observed in narcolepsy [START_REF] Huijbers | The expanding field of IgG4-mediated neurological autoimmune disorders[END_REF][START_REF] Koneczny | Common Denominators in the Immunobiology of IgG4 Autoimmune Diseases: What Do Glomerulonephritis, Pemphigus Vulgaris, Myasthenia Gravis, Thrombotic Thrombocytopenic Purpura and Autoimmune Encephalitis Have in Common?[END_REF]. However, the presence of known infectious triggers, the absence of well characterized autoantibodies, and the specific death of hypocretin producing neurons induced by cytotoxic T-cells distinguish narcolepsy from autoimmune diseases with IgG4 antibodies [START_REF] Bonvalet | Autoimmunity in narcolepsy[END_REF], and suggest a very different physiopathology. Indeed, the underlying mechanism of the association between HLA and IgG4-mediated diseases is unknown and especially intriguing, since IgG4 is produced after chronic and intense antigen stimulation, usually having anti-inflammatory effects [START_REF] Huijbers | The expanding field of IgG4-mediated neurological autoimmune disorders[END_REF][START_REF] Koneczny | Update on IgG4-mediated autoimmune diseases: New insights and new family members[END_REF]. Furthermore, IgG4 antibodies are generally considered unable to activate the complement and cytotoxic cells due to the particular characteristics of their Fc region, and their effects principally depend on blocking protein-protein interactions [START_REF] Koneczny | Common Denominators in the Immunobiology of IgG4 Autoimmune Diseases: What Do Glomerulonephritis, Pemphigus Vulgaris, Myasthenia Gravis, Thrombotic Thrombocytopenic Purpura and Autoimmune Encephalitis Have in Common?[END_REF]. Hence, given the strong HLA associations that autoimmune diseases with IgG4 antibodies show, it has been hypothesized that particular peptide-DRB1 complexes favor the differentiation of auto-reactive CD4+ T-cells into Treg cells in the thymus. After antigen exposition in the periphery, these Treg cells would stimulate auto-reactive Bcells to switch IgG subclass and differentiate into IgG4-producing plasma cells, probably in the germinal centers, in order to limit the autoimmune response [START_REF] Koneczny | Common Denominators in the Immunobiology of IgG4 Autoimmune Diseases: What Do Glomerulonephritis, Pemphigus Vulgaris, Myasthenia Gravis, Thrombotic Thrombocytopenic Purpura and Autoimmune Encephalitis Have in Common?[END_REF], Sun et al., 2020a). However, when the location of the B-epitope unfortunately determines that the antibody blocks the protein function, these IgG4 have a pathogenic and deleterious effect [START_REF] Koneczny | Common Denominators in the Immunobiology of IgG4 Autoimmune Diseases: What Do Glomerulonephritis, Pemphigus Vulgaris, Myasthenia Gravis, Thrombotic Thrombocytopenic Purpura and Autoimmune Encephalitis Have in Common?[END_REF]. To date, there is little evidence supporting this hypothesis, with some contradictory results regarding the levels of several interleukins involved in IgG4 switching (mainly IL-10) and Treg cells in anti-Musk MG and pemphigus vulgaris [START_REF] Koneczny | Common Denominators in the Immunobiology of IgG4 Autoimmune Diseases: What Do Glomerulonephritis, Pemphigus Vulgaris, Myasthenia Gravis, Thrombotic Thrombocytopenic Purpura and Autoimmune Encephalitis Have in Common?[END_REF]. Furthermore, HLA tetramers have preliminarily been used only in pemphigus vulgaris [START_REF] Veldman | Detection of low avidity desmoglein 3-reactive T cells in pemphigus vulgaris using HLA-DR beta 1*0402 tetramers[END_REF], although T-response characterization has been approached using other more traditional techniques such as Tcell culture proliferation assays, cytokine secretion measurements, and conventional TCR sequencing [START_REF] Lin | Development and characterization of desmoglein-3 specific T cells from patients with pemphigus vulgaris[END_REF][START_REF] Hacker-Foegen | T cell receptor gene usage in desmoglein-3-specific T lymphocytes from patients with pemphigus vulgaris[END_REF][START_REF] Marino | T cell repertoire in DQ5-positive MuSK-positive myasthenia gravis patients[END_REF][START_REF] Yi | Characterization of CD4 and CD8 T cell responses in MuSK myasthenia gravis[END_REF].

Thus, according to the possibilities offered by the methodology exposed above and the results of this PhD project, the HLA-restricted T-cell responses using HLA tetramers along with TCR sequencing should be investigated in anti-LGI1 and anti-CASPR2 LE, since they both show strong associations with a particular DRB1 allele supporting an important pathogenic role of CD4+ T-cells.

Beyond HLA: GWAS and non-HLA genes

Despite HLA loci being the most frequently associated with autoimmune diseases, some autoimmune encephalitides show relatively weak or even no association with HLA, such as neurological disorders with GAD65 antibodies or anti-NMDAR encephalitis [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Mueller | Genetic predisposition in anti-LGI1 and anti-NMDA receptor encephalitis: GWAS Autoimmune Encephalitis[END_REF][START_REF] Shu | HLA class II allele DRB1*16:02 is associated with anti-NMDAR encephalitis[END_REF], Muñiz-Castrillo et al., 2020a). These findings have shifted attention to non-HLA genes, but studies investigating these loci have until now been limited by methodological issues and small samples sizes.

So far, there is only one study that analyzed non-HLA loci in 19 patients (2 related) with neurological disorders and GAD65 antibodies [START_REF] Thaler | Possible link of genetic variants to autoimmunity in GAD-antibody-associated neurological disorders[END_REF]. However, one patient presented an atypical phenotype (demyelinating CNS disease), another with cerebellar ataxia also had cooccurring Yo antibodies, and, notably, the presence of GAD65 antibodies in serum and CSF was highly heterogeneous and their titers were low. Moreover, the authors selected 33 immune systemrelated genes based on unreported criteria and used published data to compare, though no statistical analysis was performed. Several variants were observed, mainly at the genes encoding cytotoxic Tlymphocyte-associated protein 4 (CTLA4), caspase 10, and protein tyrosin phosphatase nonreceptor type 22 (PTPN22) [START_REF] Thaler | Possible link of genetic variants to autoimmunity in GAD-antibody-associated neurological disorders[END_REF]. Some of these loci have already been found to be associated with autoimmune polyglandular/polyendocrine syndrome (APS) type 2 in GWAS [START_REF] Michels | Autoimmune polyglandular syndromes[END_REF]. Additionally, a patient with type 1 APS and anti-GAD65 LE has been reported [START_REF] Kopczak | GAD antibodyassociated limbic encephalitis in a young woman with APECED[END_REF], suggesting that mutations in the AIRE gene (the cause of type 1 APS) could also be associated with GAD65 neurological disorders. Furthermore, we reported family history of autoimmune diseases in two thirds of patients with neurological disorders and GAD65 antibodies, and nearly 90% of them showed patterns very similar to APS (Muñiz-Castrillo et al., 2021c). Hence, the next step will be to perform GWAS/WES in these pedigrees to identify potentially associated non-HLA genes.

Several studies have unsuccessfully tried to find a solid association between HLA and anti-NMDAR encephalitis [START_REF] Kim | Anti-LGI1 encephalitis is associated with unique HLA subtypes: HLA Subtypes in Anti-LGI1 Encephalitis[END_REF][START_REF] Mueller | Genetic predisposition in anti-LGI1 and anti-NMDA receptor encephalitis: GWAS Autoimmune Encephalitis[END_REF][START_REF] Shu | HLA class II allele DRB1*16:02 is associated with anti-NMDAR encephalitis[END_REF]. Consequently, non-HLA genes have gained interest. However, the single study using GWAS in anti-NMDAR encephalitis failed to discover any significant association, although the sample was relatively small (96 patients) [START_REF] Mueller | Genetic predisposition in anti-LGI1 and anti-NMDA receptor encephalitis: GWAS Autoimmune Encephalitis[END_REF]. More recently, 28 immunity-related pre-selected genes were genotyped in two Chinese cohorts (176 patients in total), finding polymorphisms in the genes BANK1 (B-cell scaffold protein with ankyrin repeats), TBX21 (T-box transcription factor TBX21), and IRF7 (interferon regulatory factor 7) [START_REF] Shu | Anti-NMDAR encephalitis is associated with IRF7, BANK1 and TBX21 polymorphisms in two populations[END_REF]. Interestingly, IRF7 and TBX21 are related to the immune response against viral infections, which might be linked to the fact that approximately one third of patients with herpes simplex virus 1 encephalitis subsequently develop an autoimmune encephalitis, mainly with NMDAR antibodies [START_REF] Armangue | Frequency, symptoms, risk factors, and outcomes of autoimmune encephalitis after herpes simplex encephalitis: a prospective observational study and retrospective analysis[END_REF]. In addition, a missense mutation of the toll-like receptor 3 gene, which predisposes to herpes simplex virus 1 encephalitis, has been reported in a case of post-herpetic autoimmune encephalitis [START_REF] Armangue | Tolllike receptor 3 deficiency in autoimmune encephalitis post-herpes simplex encephalitis[END_REF]. Therefore, GWAS in larger cohorts of anti-NMDAR encephalitis will clarify the association with genes involved in adaptive and innate anti-viral immune responses, as well as whether patients with post-herpetic forms have the same genetic background than the idiopathic or teratoma-related ones.

Two groups of non-HLA genes related to innate immunity are increasingly being associated with autoimmune disorders: MHC class III and the leukocyte receptor complex [START_REF] Horton | Gene map of the extended human MHC[END_REF][START_REF] Agrawal | Significance of KIR like natural killer cell receptors in autoimmune disorders[END_REF]. MHC class III shows an extremely high gene density and the functions of these genes are very diverse, although many of them mediate inflammatory and immune responses [START_REF] Horton | Gene map of the extended human MHC[END_REF][START_REF] Trowsdale | Major Histocompatibility Complex Genomics and Human Disease[END_REF][START_REF] Lokki | The complexity and diversity of major histocompatibility complex challenge disease association studies[END_REF].

Moreover, some loci show a strong linkage disequilibrium with HLA class I and II, and are therefore inherited together as haplotypes. For instance, variants in the complement (BF, C2, C4A/B) and tumor necrosis factor (TNF) genes form part of the extended haplotype 8.1, and may contribute to its association with several autoimmune systemic diseases [START_REF] Simmonds | The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action[END_REF][START_REF] Gambino | Autoimmune diseases and 8.1 ancestral haplotype: An update[END_REF]. Likewise, these MHC III genes might be involved in the pathogenesis of autoimmune encephalitides associated with the aforementioned haplotype, i.e. neurological disorders with GAD65 antibodies and anti-AK5 LE (Muñiz-Castrillo et al., 2020a, 2021b).

Furthermore, our neuropathological and proteomic data in anti-AK5 LE points at the innate immune system, which fits with the involvement of MHC III (Muñiz-Castrillo et al., 2021b).

The leukocyte receptor complex (LRC) is located on chromosome 19q13.4 and includes several genes belonging to the immunoglobulin superfamily, such as the leukocyte immunoglobulin-like receptors (LILRs) and the killer-cell immunoglobulin-like receptors (KIRs) [START_REF] Trowsdale | The genomic context of natural killer receptor extended gene families[END_REF]. The LILRs are preferentially expressed by neutrophils and monocytes/macrophages, representing one of the first line defenses against infections, but they also modulate inflammatory responses. Most of the LILRs are membrane receptors that can be classified as activating or inhibitory according to the tyrosine-based motif in their cytoplasmic tail, and a subset of them recognize HLA class I molecules (Lewis [START_REF] Marffy | Leukocyte Immunoglobulin-Like Receptors (LILRs) on Human Neutrophils: Modulators of Infection and Immunity[END_REF]. In general, LILRs genes show limited variability as they interact with either the β2-microglobulin or conserved sequences of the heavy alpha chain [START_REF] Saunders | A bird's eye view of NK cell receptor interactions with their MHC class I ligands[END_REF][START_REF] Marffy | Leukocyte Immunoglobulin-Like Receptors (LILRs) on Human Neutrophils: Modulators of Infection and Immunity[END_REF].

Conversely, polymorphism and copy number variation are extremely diverse in KIRs loci, likely reflecting a coevolution with HLA [START_REF] Trowsdale | The genomic context of natural killer receptor extended gene families[END_REF][START_REF] Vilches | KIR: diverse, rapidly evolving receptors of innate and adaptive immunity[END_REF][START_REF] Saunders | A bird's eye view of NK cell receptor interactions with their MHC class I ligands[END_REF]. The structure of KIRs resembles that of LILR, with a variable number of immunoglobulin-like domains and a tyrosine-based motif that may be activating or inhibitory.

However, KIRs recognize variable regions of the peptide-binding groove of HLA class I, mainly HLA-C [START_REF] Vilches | KIR: diverse, rapidly evolving receptors of innate and adaptive immunity[END_REF][START_REF] Saunders | A bird's eye view of NK cell receptor interactions with their MHC class I ligands[END_REF]. Inhibitory KIRs serve to scan HLA expression on cellular surface, which is down-regulated in virally infected and tumor cells, with the recognition of HLA normally expressed by healthy cells leading to the inhibition of natural killer cells cytotoxicity. To the contrary, the ligands and therefore the function of some activating KIRs remain to be defined [START_REF] Vilches | KIR: diverse, rapidly evolving receptors of innate and adaptive immunity[END_REF][START_REF] Saunders | A bird's eye view of NK cell receptor interactions with their MHC class I ligands[END_REF]. Interestingly, an imbalance between inhibitory and activating KIRs in favor of the latter has been related with autoimmunity [START_REF] Parham | MHC class I molecules and KIRs in human history, health and survival[END_REF]. In addition to KIRs, natural killer cells also express non-polymorphic receptors of the C-type lectin-like superfamily, which are encoded by the natural killer complex (NKC) on chromosome 12p13.1 and recognize HLA-E, a non-classical HLA class I [START_REF] Vilches | KIR: diverse, rapidly evolving receptors of innate and adaptive immunity[END_REF][START_REF] Saunders | A bird's eye view of NK cell receptor interactions with their MHC class I ligands[END_REF]. In summary, LRC/NKC could contribute to the genetic predisposition to autoimmune encephalitis, given their role in the innate immune responses against already known environmental triggers (i.e. virus and cancer), and the fact that HLA is the major ligand for most of these receptors. Moreover, the independent inheritance of LRC/NKC and MHC leads to a wide range of possible combinations and interactions, especially between the polymorphic loci of KIR and HLA, warranting further investigations regarding their roles in the pathogenesis of autoimmune encephalitis.

Conclusions

The results of this PhD project support an important role of HLA in the pathogenesis of some types of autoimmune encephalitis, thanks to a better characterization of previously reported associations and the description of new ones. In this way, we confirmed the association between the ancestral haplotype 8.1 and neurological disorders with GAD65 antibodies. However, the low carrier frequency and the strong and diverse familial aggregation of systemic autoimmune diseases suggest that other non-HLA genes are potentially involved. Similarly, we reported a new association between anti-AK5 LE and the aforementioned haplotype, which along with our proteomic and histological data suggest a pathogenesis mainly mediated by CD8+ T-cells but also involving CD4+ T-cells and innate responses.

Importantly, we showed that accurate clinical classifications are essential to establish precise associations, demonstrating that the allele DRB1*11:01 is exclusively overrepresented in patients with CASPR2 antibodies and non-paraneoplastic LE, but not with other phenotypes including Morvan syndrome with malignant thymoma, therefore supporting a different physiopathology.

Likewise, the analysis of subgroups provided interesting although yet intriguing findings, such as the particular demographic characteristics of non-DRB1*07:01 carriers in anti-LGI1 LE. To the contrary, no genotype-phenotype correlation was observed in neurological disorders with GAD65 antibodies; whether this reflects the absence of association between HLA and neurological presentation should be investigated in larger cohorts with precise clinical classifications.

Additionally, we performed in silico binding predictions that will contribute to deeper investigations of the T-cell responses in autoimmune encephalitides, especially in those with IgG4 antibodies given their particularly strong association with HLA. Future research should focus on the identification of T-epitopes and the characterization of TCR repertoires, which could eventually be performed using recent technical advances such as HLA tetramers and single cell TCR sequencing.

Notably, we also highlighted the differences in the strength of the HLA associations according to the type of autoimmune encephalitis. Hence, broader genetic analysis such as GWAS should be performed in order to identify potentially relevant non-HLA loci, especially for those autoimmune encephalitides with weak or no association with HLA. However, even in those encephalitides with strong and now well-established HLA associations, other genes may modulate its effects and warrant further studies.

We can therefore summarize our results regarding the association between HLA and autoimmune encephalitis as follows: specific HLA alleles are strongly associated with nonparaneoplastic LE characterized by IgG4 antibodies (DRB1*07:01 in LGI1 and DRB1*11:01 in CASPR2), the ancestral haplotype 8.1 is frequent in non-paraneoplastic disorders that are primarily T-cell mediated and have IgG1 antibodies (GAD65 and AK5), and, finally, PNS seem to lack HLA associations. In conclusion, this PhD project provides new findings that constitute a first step into the immunogenetic characterization of autoimmune encephalitis and related disorders.

  Genetic characteristics of the MHC Classic HLA molecules: structure and function Mechanisms of the association between HLA and autoimmune diseases HLA and autoimmune neurological diseases with autoantibodies Paraneoplastic neurological syndromes with Hu antibodies Paraneoplastic cerebellar degeneration with Yo antibodies Lambert-Eaton myasthenic syndrome Myasthenia gravis Chronic inflammatory demyelinating polyradiculoneuropathy with neurofascin-155 antibodies Anti-IgLON5 disease Encephalitis with leucine-rich glioma-inactivated 1 antibodies Diseases with contactin-associated protein-like 2 antibodies Anti-N-methyl-D-aspartate receptor encephalitis Neurological disorders with glutamic acid decarboxylase antibodies Demyelinating CNS disorders with autoantibodies Objectives Studies of the role of HLA in autoimmune encephalitis and related disorders Study I. Neurological disorders with glutamic acid decarboxylase antibodies Primary DQ effect in the association between HLA and neurological syndromes with anti-GAD65 antibodies In silico analysis supports a primary DQ effect in the association between HLA and GAD65 antibodies Familial autoimmunity in neurological patients with GAD65 antibodies: an interview-based study Study II. Diseases with contactin-associated protein-like 2 antibodies Anti-CASPR2 clinical phenotypes correlate with HLA and immunological features Peptide-binding spectrum of HLA associated with anti-CASPR2 encephalitis Study III. Encephalitis with leucine-rich glioma-inactivated 1 antibodies Clinical and prognostic value of immunogenetic characteristics in anti-LGI1 encephalitis Peptide-binding spectrum of HLA associated with anti-LGI1 encephalitis Study IV. Encephalitis with adenylate kinase 5 antibodies Distinctive clinical presentation and pathogenic specificities of anti-Deciphering the role of HLA in TCR repertoires Beyond HLA: GWAS and non-HLA genes Conclusions References Annex Associations between HLA and autoimmune neurological diseases with autoantibodies RÉSUMÉ Récemment, plusieurs types d´encéphalites auto-immunes et d´autres maladies associés ont été décrites grâce à la découverte d'autoanticorps ciblant différents antigènes neurogliaux du système nerveux central et périphérique. Bien que la découverte de ces anticorps ait permis des diagnostics plus précis et une meilleure compréhension de certains mécanismes pathogéniques sous-jacents, les processus exacts menant à la rupture de tolérance immune sont encore inconnus. Ceux-ci sont probablement le résultat d'une interaction complexe entre des facteurs environnementaux et des caractéristiques génétiques. L'antigène leucocytaire humain (human leukocyte antigen, HLA) est le principal facteur génétique lié à l'auto-immunité. De nombreuses associations avec différentes maladies autoimmunes ont été décrites et dans certains cas, un rôle dans la pathogenèse a été démontré. Cependant, peu d'études ont été menées à ce jour sur les encéphalites auto-immunes et plusieurs questions restent en suspens. Notre travail visait à étudier l'importance du système HLA dans la prédisposition génétique des encéphalites auto-immunes, la corrélation génotype-phénotype, et les affinités de liaison aux peptides des HLA qui sont associés à ces encéphalites. Nous avons sélectionné quatre sous-types d'encéphalites autoimmunes définies par la présence d'anticorps contre glutamic acid decarboxylase 65 (GAD65), contactin-associated protein-like 2 (CASPR2), leucine-rich glioma-inactivated 1 (LGI1), et adenylate kinase 5 (AK5). Dans une première étude, nous avons étudié l'association entre l´HLA et les troubles neurologiques à anticorps anti-GAD65. Trois types de troubles peuvent être retrouvés : encéphalite limbique (EL), ataxie cérébelleuse, et syndrome de la personne raide. Nous avons obtenu les génotypes HLA de 32 patients non apparentés avec des présentations neurologiques différentes et des anticorps anti-GAD65, en utilisant à la fois le séquençage de nouvelle génération (nextgeneration sequencing, NGS) et l'inférence basée sur des données de GWAS (genome-wide association studies). Nous avons constaté que l'haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01 était le plus fréquent (41% des patients), bien qu'au niveau allélique seul DQB1*02:01 était statistiquement significatif. Aucune association n'a été observée entre le statut de porteur DQ2 et les caractéristiques démographiques, les comorbidités auto-immunes ou le phénotype neurologique. Nous avons également étudié les propriétés de liaison des molécules HLA de l'haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01 aux peptides dérivés de GAD65 en utilisant une approche in silico. Nous avons constaté que les hétérodimères DQ avaient une affinité plus élevée que DRB1*03:01. Enfin, puisque l'haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01 était porté par moins de la moitié des patients, nous émettons l'hypothèse que d'autres gènes non-HLA pourraient être impliqués dans la prédisposition génétique aux troubles neurologiques à anticorps anti-GAD65.

Figure 1 .

 1 Figure 1. The MHC showing the main HLA genes (top), and the schematic structure of HLA class I (note that the β2microglobulin is not encoded by HLA genes) and class II molecules (bottom) (Muñiz-Castrillo et al., 2020c)

Figure 2 .

 2 Figure 2. Nomenclature of HLA alleles (adapted from the IMGT database)

Figure 3 .

 3 Figure 3. Three-dimensional structures of the entire molecule and the peptide-binding groove of HLA class I (A, B) and class II (C, D). A bound peptide is represented in red. Polymorphic residues delimitating the peptide-binding groove are marked in yellow[START_REF] Blum | Pathways of antigen processing[END_REF]

Figure 4 .Figure 5 .

 45 Figure 4. Schematic representation illustrating the different conformation of the peptide-binding groove of HLA class I and II, showing also the residues that interact with the anchoring pockets

Figure 6 .

 6 Figure 6. Schematic representation illustrating the geometry of the TCR-peptide-HLA interaction

Figure 7 .

 7 Figure 7. HLA and selection in the thymus

  Type 1 diabetes mellitus is strongly associated with HLA class II haplotypes DQA1*05:01-DQB1*02:01-DRB1*03:01 (DQ2-DR3) and DQA1*03:01-DQB1*03:02-DRB1*04 (DQ3-DR4),

  OF HLA IN AUTOIMMUNE ENCEPHALITIS AND RELATED DISORDERS STUDY I. NEUROLOGICAL DISORDERS WITH GLUTAMIC ACID DECARBOXYLASE ANTIBODIES Primary DQ effect in the association between HLA and neurological syndromes with anti-GAD65 antibodies. Muñiz-Castrillo S, Ambati A, Dubois V, Vogrig A, Joubert B, Rogemond V, Picard V, Lin L, Fabien N, Mignot E, Honnorat J (J Neurol 2020 Jul;267(7):1906-1911. doi: 10.1007/s00415-020-09782-8) In silico analysis supports a primary DQ effect in the association between HLA and GAD65 antibodies (unpublished) Familial autoimmunity in neurological patients with GAD65 antibodies: an interview-based study. Muñiz-Castrillo S, Vogrig A, Montagnac C, Joubert B, Benaiteau M, Casez O, Chaumont H, Hopes L, Lanoiselée HM, Navarro V, Thomas B, Ursu R, Gonçalves D, Fabien N, Ducray F, Julier C, Honnorat J (J Neurol 2021 Feb 5. doi: 10.1007/s00415-021-10424-w)CommentaryDespite being one of the first antibodies described in CNS autoimmunity, GAD65 antibodies and their associated neurological disorders remain enigmatic. Similarly, the association between HLA and GAD65 neurological disorders was first reported almost 30 years ago, but very few studies have since then investigated the role of HLA in these diseases. Moreover, given the controversy around the pathogenic role of GAD65 antibodies, the study of T-cell responses could provide important and new insights into their pathogenesis. Furthermore, autoimmune comorbidities have often been reported in patients with GAD65 neurological disorders, but the frequency of these systemic autoimmune diseases among the relatives of the patients and their patterns of inheritance are yet unknown.In a first study, we aimed to deeper investigate the potential association between HLA and GAD65 neurological disorders. We therefore performed HLA genotyping in 32 unrelated patients presenting with the three main GAD65 clinical phenotypes (i.e. SPS, LE, and cerebellar ataxia), using both next-generation sequencing (NGS) and imputation based on genome-wide association studies (GWAS) data. The haplotype DQA1*05:01-DQB1*02:01-DRB1*03:01 was the most frequent, though it was carried by only 41% of the patients. However, at allele level, only DQB1*02:01 was statistically significant. Moreover, we also compared the demographic and clinical characteristics of the patients according to their DQ2-carrier status, but no difference was found.

Figure .

 . Figure. B-cell epitope prediction using BepiPred-2.0 shows co-localization with T-cell epitopes. An extract of the results obtained by BepiPred-2.0 is shown for the core peptides MVFDGKPQH (493-501), which is an intermediate binder to DRB1*03:01; and FLIEEIERL (573-581), which was predicted as a strong binder to DQA1*05:01-DQB1*02:01. Residues scoring above the threshold for B-epitope prediction are colored in orange. Structural prediction is represented in the second line (H, helix; C, coil; E, sheet); while surface accessibility (E, exposed; B, buried) is shown below

  haplotypes according to ethnical origin were selected based on the public database HaploStats of the National Marrow Donor Program (NMDP). Sixteen out of 17 (94.1%) patients with anti-CASPR2 LE carried DRB1*11:01, all of them along with DQA1*05:01-DQB1*03:01, except the only one carrying DRB1*11:01:02 instead of DRB1*11:01:01, whose DQ alleles were not successfully genotyped at four-digit level and therefore were not included in the analysis. The haplotypes of the remaining patient of the series, who did not carry DRB1*11:01, were DRB1*15:01-DQA1*01:02-DQB1*06:02 and DRB1*04:01-DQA1*03:02-DQB1*03:02.

  predicted as strong binders for DQA1*05:01-DQB1*03:01. Only 8 and 15 peptides were respectively located within the Disc and the Lam1 domains. Conversely, the majority of the peptides were in the C-terminal region of CASPR2. The spectrum of strong binders was partially shared with the heterodimers DQA1*01:02-DQB1*06:02 (15 peptides) and DQA1*03:01-DQB1*03:02 (23 peptides). Eight peptides were predicted as strong binders for the three DQ heterodimers analyzed: TNEAKGAESAESADA (position 1295) and HTNEAKGAESAESAD (position 1294), which shared the core AKGAESAES; DRNYWNAASFPNPSS (position 794, core YWNAASFPN); DHHWHSVVIERQGRS (position 273), DDHHWHSVVIERQGR (position 272), and LDDHHWHSVVIERQG (position 271), which shared the core WHSVVIERQ (located within the Lam1 domain); RNVKQASLQVDRLPQ (position 889) and ERNVKQASLQVDRLP (position 888), which had the same core QASLQVDRL (Table

  , larger cohorts accurately clustered to obtain homogeneous subgroups are needed to confirm the distinctness of the association between DRB1*11:01 and LE compared to Morvan syndrome, as well as to better defined the precise position of acquired neuromyotonia. Furthermore, the identification of non-DRB1*11:01 carriers in the LE group could improve the in silico analysis and therefore facilitate the in vitro characterization of the T-cell responses. Finally, the understanding of the pathogenesis of Morvan syndrome will surely require the histological and genetic analysis of malignant thymomas, although the participation of non-HLA loci cannot be ruled out. STUDY III. ENCEPHALITIS WITH LEUCINE-RICH GLIOMA-INACTIVATED 1 ANTIBODIES Clinical and Prognostic Value of Immunogenetic Characteristics in Anti-LGI1 Encephalitis. Muñiz-Castrillo S, Haesebaert J, Thomas L, Vogrig A, Pinto AL, Picard G, Blanc C, Do LD, Joubert B, Berzero G, Psimaras D, Alentorn A, Rogemond V, Dubois V, Ambati A, Tamouza R, Mignot E, Honnorat J (Neurol Neuroimmunol Neuroinflamm 2021 Mar 5;8(3):e974. doi: 10.1212/NXI.0000000000000974) Peptide-binding spectrum of HLA associated with anti-LGI1 encephalitis (unpublished)

  strong binding peptide-spectrum was widely shared (>50%) with DRB1*01:01 (20 peptides), DRB1*04:01 (20 peptides), DRB1*04:08 (20 peptides), DRB1*16:01 (17 peptides), and DRB1*15:01 (14 peptides); moderately with DRB1*04:03 (11 peptides), DRB1*04:02 (9 peptides), DRB1*13:03 (9 peptides), and DRB1*11:01 (8 peptides); and presented only a minor overlap with DRB1*08:06 (4 peptides), DRB1*11:04 (4 peptides), DRB1*12:01 (2 peptides), and DRB1*13:01

.

  Regarding the strong binders for the DRB1 other than DRB1*07:01, the largest spectrum was predicted for DRB1*04:01 (50 peptides), DRB1*04:08 (45 peptides), DRB1*04:03 (30 peptides), and DRB1*01:01 (30 peptides). A smaller spectrum was predicted for DRB1*16:01 (22 peptides), DRB1*04:02 (17 peptides), DRB1*13:03 (17 peptides), DRB1*15:01 (16 peptides), DRB1*12:01 (14 peptides), DRB1*11:01 (13 peptides), DRB1*11:04 (9 peptides), DRB1*08:06 (7 peptides), and DRB1*13:01 (3 peptides). The predicted peptides were in both the LRR and the ETP domains, excepting for DRB1*08:06, DRB1*11:04, and DRB1*13:01, whose peptides were only in the LRR domain (Table

  There was only a slight overlap in the strong binders-spectrum with the heterodimers DQA1*02:01-DQB1*03:03 (2 peptides), DQA1*01:02-DQB1*05:02 (2 peptides), DQA1*02:01-DQB1*03:02 (2 peptides), DQA1*03:01-DQB1*03:02 (1 peptide), DQA1*05:05-DQB1*03:01 (1 peptide), DQA1*03:03-DQB1*03:01 (1 peptide), and DQA1*03:03-DQB1*03:03 (1 peptide). The remaining three DQ heterodimers did not share their spectrums (Table

  The DQ heterodimers, other than DQA1*02:01-DQB1*02:02, showing a highest number of predicted strong binders were DQA1*01:01-DQB1*05:01 (28 peptides) and DQA1*01:02-DQB1*05:02 (21 peptides). Lower numbers of strong binders were predicted for DQA1*01:02-DQB1*06:02 (11 peptides), DQA1*02:01-DQB1*03:03 (10 peptides), DQA1*03:03-DQB1*03:03 (10 peptides), DQA1*02:01-DQB1*03:02 (9 peptides), DQA1*03:01-DQB1*03:02 (9 peptides), DQA1*03:03-DQB1*03:01 (6 peptides), DQA1*01:03-DQB1*06:03 (6 peptides), and DQA1*05:05-DQB1*03:01 (5 peptides). The strong binders predicted for these ten DQ heterodimers were preferentially in the ETP domain (Table

  LGI1-derived peptides predicted as strong binders for DRB1*07:01 (% rank ≤3), and their % rank predicted for the DRB1 present in non-DRB1*07‡Core peptides predicted for DRB1*07:01 Peptides in the LRR domain are colored in orange, those in the ETP domain in green Peptides predicted as strong binders for DRB1*07:01 and also for other DRB1 are colored in yellow

  the LRR domain are colored in orange, those in the ETP domain in green

  Finally, we studied the HLA genotypes of 11 patients with available DNA. The presence of extensive infiltrates of CD4+ and CD8+ T-cells with an intense granzyme B expression, the up-regulation of CSF proteins involved in apoptosis and innate/adaptive immune responses, and the association with the extended haplotype 8.1 points to a distinct T-cell mediated pathogenesis, which does not respond to conventional immunotherapy and consequently provokes an extremely severe neuronal loss.

158

  Supplementary Table3. AK5-derived peptides predicted as strong binders for HLA class II molecules

  further investigate the T-cell responses in anti-LGI1 LE, selecting the strong binders shared by DRB1*07:01 and the DRB1 found in the non-DRB1*07:01 carriers. To the contrary, the analyses in the remaining autoimmune encephalitides were highly limited due to different reasons, including the extreme diversity of HLA in GAD65 neurological disorders, the presence of only a single non-DRB1*11:01 carrier in anti-CASPR2 LE, and the lack of a large enough sample to allow the identification of the truly associated locus in anti-AK5 LE.

Table 1 .

 1 HLA class I and main class II genes with their number of alleles and proteins (IMGT database 3.44)

		Gene	Alleles	Proteins
	HLA class I	A	6766	4064
		B	7967	4962
		C	6621	3831
		E	271	110
		F	45	6
		G	82	22
	HLA class II	DPA1	258	107
		DPA2	5	0
		DPB1	1749	1106
		DPB2	6	0
		DQA1	306	143
		DQA2	40	11
		DQB1	1997	1303
		DRA	29	2
		DRB1	2949	2015

Table 2 .

 2 Some examples of molecular mechanisms identified in the association between HLA and autoimmune diseases

	Molecular mechanism	HLA	Autoimmune disease
	Alternate docking	DRB1*15:01	Multiple sclerosis (Hahn et al., 2005)
	TCR stabilization of weak peptide-	DRB1*04:01	Multiple sclerosis (Quandt et al., 2004)
	HLA complexes
	Altered register	DQ2 & DQ8	Type 1 diabetes mellitus (Stadinski et al., 2010)
		DR15 (risk) & DR1	Goodpasture disease (Ooi et al., 2017)
		(protection)
	Hotspot molecular mimicry	DRB1*15:01	Multiple sclerosis (Epstein-Barr virus) (Lang et al.,
			2002)
	Post-translational modifications	DQ2 & DQ8	Coeliac disease (deaminated gliadins) (Molberg et
			al., 1998)
		DRB1*04:01 &	Rheumatoid arthritis (citrullination) (Scally et al.,
		DRB1*04:04	2013)
	Small molecules modifying the TCR	B*57:01	Abacavir hypersensitivity (Illing et al., 2012)
	repertoire	B*15:02	Carbamazepine induced Stevens-Johnson
			syndrome

Table 3 .

 3 Associations

	between HLA and IgG4-mediated neurological diseases (Muñiz-Castrillo et al., 2020c)
	Antibody	HLA	Carriers
	Musk	DQB1*05	78%
		DQB1*05-DRB1*14	26%
		DQB1*05-DRB1*16	20%
	NF155	DRB1*15	77%
	IgLON5	DQB1*05:01-DRB1*10:01	57-90%
		DQA1*01-DQB1*05	90%
	LGI1	DRB1*07:01	90%
	CASPR2	DRB1*11:01	48%

Table 4 .

 4 Associations between HLA and neurological diseases with IgG1 antibodies(Muñiz-Castrillo et al., 2020c)

	Antibody	HLA

  The first one included 13 patients (92% of Caucasian origin) that were compared to 35 NF155-negative CIDP, finding that DRB1*15

alleles (mostly DRB1*15:01 but also DRB1*15:02) were carried by 77% of the patients with NF155 antibodies, usually in LD with DQB1*06. In contrast, DRB1*15 was detected in only 14% of the NF155-negative CIDP patients (OR=20, 95%

) and 17% of the healthy population (OR=16.9, 95%

)

[START_REF] Martinez-Martinez | Anti-NF155 chronic inflammatory demyelinating polyradiculoneuropathy strongly associates to HLA-DRB15[END_REF]

. Additionally, in silico analyses showed that the repertoire of NF155-derived peptides predicted as binders for DRB1*15:01 and DRB1*15:02 highly overlapped, therefore suggesting that both DRB1*15 molecules may present the same peptides in a very similar way

[START_REF] Martinez-Martinez | Anti-NF155 chronic inflammatory demyelinating polyradiculoneuropathy strongly associates to HLA-DRB15[END_REF]

. Furthermore, all these results were confirmed in a second series of 22 Japanese patients, in which all patients carried the haplotypes DRB1*15:01-DQA1*01:02-DQB1*06:02 (13/22, 31.8% vs. 7.8% in healthy controls, OR=5.54, 95% CI [2.80-10.96], corrected p<0.001) or DRB1*15:02-DQA1*01:03-DQB1*06:01

(9/22, 20.5% vs. 8.4%, OR=2.81,

.09], corrected p>0.05), though the latter was not significant after multiple comparison correction

[START_REF] Ogata | Unique HLA haplotype associations in IgG4 anti-neurofascin 155 antibody-positive chronic inflammatory demyelinating polyneuropathy[END_REF]

. Similarly, at allele level, only DRB1*15:01 remained significantly more frequent in NF155positive patients than in healthy controls (31.8% vs. 8.0%, OR=5.36, 95% CI [2.71-10.59], corrected p<0.001), although the loss of significance for DRB1*15:02 (20.5% vs. 8.4% in controls, OR=2.81, 95% CI [1.30-6.09], corrected p>0.05

  Supplementary table.HLA allele carrier frequencies in patients with GAD65-Ab neurological diseases (cases)

	B*35:08 C*16:02 DQB1*06:04	1 (3) 0 (0) 1 (3)	0 (0) 3 (2) 10 (7)	0.18 1 0.69	1
	compared to controls B*37:01 C*16:04 DQB1*06:09	0 (0) 1 (3) 3 (9)	1 (1) 0 (0) 6 (4)	1 0.18 0.37	1
	Allele B*38:01 C*17:01 DRB1*01:01 A*01:01 B*39:01 C*18:01 DRB1*01:02 A*02:01 B*39:06 DPB1*01:01 DRB1*01:03 A*02:02 B*39:09 DPB1*02:01 DRB1*03:01 A*02:05 B*40:01 DPB1*02:02 DRB1*03:02 A*02:11 B*40:02 DPB1*03:01 DRB1*04:01 A*03:01 B*40:06 DPB1*04:01 DRB1*04:02 A*11:01 B*41:01 DPB1*04:02 DRB1*04:04 A*23:01 B*41:02 DPB1*05:01 DRB1*04:05 A*24:02 B*42:01 DPB1*06:02 DRB1*04:08 A*25:01 B*42:02 DPB1*09:01 DRB1*07:01 A*26:01 B*44:02 DPB1*09:02 DRB1*08:01 A*29:01 B*44:03 DPB1*10:01 DRB1*08:02 A*29:02 B*44:05 DPB1*104:01 DRB1*08:03 A*30:01 B*45:01 DPB1*11:01 DRB1*08:04 A*30:02 B*47:01 DPB1*13:01 DRB1*08:06 A*30:04 B*49:01 DPB1*14:01 DRB1*09:01 A*31:01 B*50:01 DPB1*15:01 DRB1*10:01 A*32:01 B*51:01 DPB1*16:01 DRB1*11:01 A*33:01 B*52:01 DPB1*17:01 DRB1*11:02 A*33:03 B*53:01 DPB1*18:01 DRB1*11:04 A*34:02 B*55:01 DQA1*01:01 DRB1*12:01 A*36:01 B*56:01 DQA1*01:02 DRB1*12:02 A*66:01 B*57:01 DQA1*01:03 DRB1*13:01 A*66:02 B*57:03 DQA1*01:04 DRB1*13:02 A*68:01 B*58:01 DQA1*01:05 DRB1*13:03 A*68:02 B*58:02 DQA1*02:01 DRB1*13:12 A*68:17 B*67:01 DQA1*03:01 DRB1*14:01 A*69:01 B*73:01 DQA1*03:02 DRB1*14:02 A*74:01 B*81:01 DQA1*03:03 DRB1*14:04 B*07:02 C*01:02 DQA1*04:01 DRB1*15:01 B*08:01 C*02:02 DQA1*05:01 DRB1*15:02 B*13:01 C*02:10 DQA1*05:03 DRB1*15:03 B*13:02 C*03:02 DQA1*05:05 DRB1*16:01 B*14:01 B*14:02 B*15:01 B*15:03 B*15:10 B*15:16 B*15:17 B*18:01 B*27:02 B*27:03 B*27:05 B*35:01 B*35:02 B*35:03 B*35:05 C*16:01 DQB1*06:03 C*15:05 DQB1*06:02 C*15:02 DQB1*06:01 C*14:02 DQB1*05:03 C*12:03 DQB1*05:02 C*12:02 DQB1*05:01 C*08:04 DQB1*04:02 C*08:02 DQB1*03:19 C*07:02 DQB1*03:03 C*07:01 DQB1*03:02 C*06:02 DQB1*03:01 C*05:01 DQB1*02:02 C*04:01 DQB1*02:01 C*03:04 DQA1*06:01 C*03:03 DQA1*05:09 DRB1*16:02	Patients, n=32 (%) 3 (9) 3 (9) 2 (6) 5 (16) 4 (12) 1 (3) 1 (3) 10 (31) 1 (3) 9 (28) 0 (0) 1 (3) 0 (0) 10 (31) 13 (41) 1 (3) 2 (6) 0 (0) 0 (0) 1 (3) 0 (0) 4 (12) 0 (0) 4 (12) 1 (3) 10 (31) 0 (0) 2 (6) 1 (3) 2 (6) 3 (9) 5 (16) 1 (3) 2 (6) 1 (3) 6 (19) 1 (3) 3 (9) 0 (0) 0 (0) 0 (0) 0 (0) 7 (22) 3 (9) 3 (9) 0 (0) 1 (3) 1 (3) 3 (9) 2 (6) 1 (3) 1 (3) 1 (3) 6 (19) 2 (6) 0 (0) 2 (6) 1 (3) 0 (0) 3 (9) 0 (0) 5 (16) 0 (0) 1 (3) 2 (6) 0 (0) 1 (3) 1 (3) 1 (3) 1 (3) 0 (0) 2 (6) 0 (0) 0 (0) 1 (3) 0 (0) 1 (3) 0 (0) 0 (0) 0 (0) 2 (6) 1 (3) 0 (0) 4 (12) 1 (3) 3 (9) 0 (0) 2 (6) 0 (0) 21 (66) 0 (0) 0 (0) 0 (0) 5 (16) 4 (12) 2 (6) 1 (3) 1 (3) 5 (16) 1 (3) 2 (6) 0 (0) 1 (3) 3 (9) 0 (0) 6 (19) 0 (0) 0 (0) 0 (0) 3 (9) 0 (0) 1 (3) 1 (3) 0 (0) 0 (0) 1 (3) 0 (0) 3 (9) 1 (3) 3 (9) 2 (6) 2 (6) 7 (22) 10 (31) 2 (6) 13 (41) 0 (0) 1 (3) 2 (6) 0 (0) 4 (12) 2 (6) 0 (0) 2 (6) 5 (16) 1 (3) 0 (0) 2 (6) 2 (6) 0 (0) 0 (0) 0 (0) 2 (6) 1 (3) 0 (0) 0 (0) 3 (9) 0 (0) 0 (0) 1 (3) 1 (3) 2 (6) 1 (3) 8 (25) 1 (3) 3 (9) 0 (0) 1 (3) 6 (19) 6 (19) 0 (0) 6 (19) 0 (0) 2 (6) 1 (3) 0 (0) 8 (25) 0 (0) 12 (38) 4 (12) 5 (16) 2 (6) 3 (9) 8 (25) 7 (22) 13 (41) 1 (3) 0 (0) 1 (3) 0 (0) 0 (0)	Controls, n=137 (%) 5 (4) 8 (6) 14 (10) 21 (15) 4 (3) 4 (3) 11 (8) 61 (45) 1 (1) 34 (25) 1 (1) 0 (0) 2 (1) 36 (26) 20 (15) 7 (5) 7 (5) 1 (1) 5 (4) 0 (0) 1 (1) 17 (12) 18 (13) 23 (17) 0 (0) 62 (45) 3 (2) 14 (10) 0 (0) 20 (15) 3 (2) 23 (17) 3 (2) 10 (7) 3 (2) 23 (17) 5 (4) 8 (6) 1 (1) 5 (4) 1 (1) 4 (3) 40 (29) 6 (4) 22 (16) 1 (1) 2 (1) 0 (0) 8 (6) 3 (2) 4 (3) 6 (4) 1 (1) 5 (4) 0 (0) 8 (6) 3 (2) 10 (7) 4 (3) 8 (6) 2 (1) 12 (9) 1 (1) 1 (1) 9 (7) 5 (4) 5 (4) 6 (4) 5 (4) 5 (4) 2 (1) 4 (3) 16 (12) 1 (1) 23 (17) 6 (4) 1 (1) 4 (3) 1 (1) 7 (5) 13 (9) 9 (7) 2 (1) 2 (1) 1 (1) 23 (17) 13 (9) 3 (2) 2 (1) 57 (42) 1 (1) 3 (2) 4 (3) 19 (14) 20 (15) 0 (0) 4 (3) 3 (2) 21 (15) 5 (4) 6 (4) 8 (6) 2 (1) 7 (10) 1 (1) 39 (28) 1 (1) 1 (1) 1 (1) 15 (11) 3 (2) 0 (0) 0 (0) 2 (1) 2 (1) 5 (4) 4 (3) 18 (13) 0 (0) 22 (16) 8 (6) 14 (10) 21 (15) 19 (14) 15 (11) 22 (16) 1 (1) 3 (2) 7 (5) 2 (1) 5 (4) 3 (2) 2 (1) 35 (26) 7 (5) 3 (2) 9 (7) 12 (9) 11 (8) 5 (4) 3 (2) 3 (2) 15 (11) 0 (0) 2 (1) 8 (6) 14 (10) 2 (1) 3 (2) 0 (0) 5 (4) 19 (14) 0 (0) 33 (24) 8 (6) 1 (1) 5 (4) 3 (2) 17 (12) 9 (7) 1 (1) 32 (23) 3 (2) 12 (9) 11 (8) 6 (4) 29 (21) 6 (4) 35 (26) 17 (12) 18 (13) 42 (31) 26 (19) 39 (28) 36 (26) 20 (15) 14 (10) 1 (1) 9 (7) 1 (1) 3 (2)	0.17 0.43 0.73 Uncorrected P value Corrected P value 1 0.04 1 1 0.46 1 0.34 0.66 1 1 0.23 1 0,65 1 0.002 0.07 0.18 0.67 1 1 0.58 1 1 1 1 0.02 0.90 0.18 0.18 0.16 1 1 0.78 0.18 0.25 1 0.08 0.73 0.57 1 1 0.57 1 1 0.43 1 1 0.79 1 1 1 0.51 0.58 0.41 1 1 0.46 0.37 0.43 0.23 1 1 0.18 0.34 0.006 0.12 0.03 1 0.23 0.69 1 1 0.35 1 0.32 1 1 0.43 1 0.58 1 1 0.34 1 1 1 1 1 0.04 1 1 0.05 0.31 0.34 1 1 1 0.59 0.73 0.68 1 1 0.34 0.01 0.34 0.41 1 0.13 0.35 1 0.01 0.26 1 0.23 1 0.78 1 1 1 1 0.57 1 1 0.03 0.64 0.35 1 0.46 1 1 0.37 1 1 0.71 1 1 1 1 1 0.18 1 1 1 0.18 1 0.76 1 0.18 1 1 0.73 1 0.42 0.41 0.74 0.003 0.05 1 0.03 0.67 1 1 0.06 0.57 1 0.01 0.25 0.05 0.23 0.18 1 0.37 1 1 0.18 1 1 1 1 0.02 0.32 1 0.58 0.57 1 0.35 0.39 0.04 0.60 1 1 0.64 1 0.18 1 1 1 0.74 0.46 0.59 1 1 0.63 0.59 1 1 0.19 1 1 0.58 0.77 0.003 0.05 1 0.29 0.82 1 1 0.82 0.002 0.03 0.21 0.30 1 1 0.57 0.68 1 1 1
			50

Table 1 .

 1 CASPR2-derived peptides predicted as strong binders for DRB1*11:01 (% rank ≤3), and their % rank

	predicted for DRB1*15:01 and DRB1*04:01
	Position	Peptide	Core ‡	11:01	DRB1 15:01	04:01
		VFLIRYMFRHKGTYH	IRYMFRHKG	0.17	2.5	37
		FLIRYMFRHKGTYHT	IRYMFRHKG	0.17	2.5	27
		LVFLIRYMFRHKGTY	IRYMFRHKG	0.2	3	41
		TLVFLIRYMFRHKGT	IRYMFRHKG	0.3	4	46
		LIRYMFRHKGTYHTN	IRYMFRHKG	0.4	5	26
		CTLVFLIRYMFRHKG	IRYMFRHKG	0.8	6	55
	685	YVSYFCKMSRLLNTP	FCKMSRLLN	0.9	12	17
	684	QYVSYFCKMSRLLNT	FCKMSRLLN	1	8.5	16
		RVQFNQIAPLKAALR	FNQIAPLKA	1.1	1.8	0.4
		VQFNQIAPLKAALRQ	FNQIAPLKA	1.3	1.9	0.8
	686	VSYFCKMSRLLNTPD	FCKMSRLLN	1.3	20	17
		QFNQIAPLKAALRQT	IAPLKAALR	1.5	2.5	1.4
		IRYMFRHKGTYHTNE	IRYMFRHKG	1.6	11	30
	683	EQYVSYFCKMSRLLN	FCKMSRLLN	1.6	9	19
	687	SYFCKMSRLLNTPDG	FCKMSRLLN	1.8	25	16
	931	QGFLGCIRSLRMNGV	FLGCIRSLR	1.9	4	11
	930	QQGFLGCIRSLRMNG	FLGCIRSLR	2.5	8.5	16
	932	GFLGCIRSLRMNGVT	FLGCIRSLR	2.5	3	10
		TTDFLAVLVKPTGSL	FLAVLVKPT	2.5	15	7
		TDFLAVLVKPTGSLQ	LAVLVKPTG	2.5	16	8
		FNQIAPLKAALRQTN	IAPLKAALR	2.5	4	4.5
	688	YFCKMSRLLNTPDGS	FCKMSRLLN	3	33	16
	929	GQQGFLGCIRSLRMN	FLGCIRSLR	3	8.5	16
		FTTDFLAVLVKPTGS	FNQIAPLKA	3	19	7.5
		DFLAVLVKPTGSLQI	LAVLVKPTG	3	15	10
		SRVQFNQIAPLKAAL	FCKMSRLLN	3	4.5	0.5
	‡Core predicted for DRB1*11:01
	Peptides predicted as strong binders for DRB1*11:01 and also for DRB1*15:01 and/or DRB1*04:01 are colored in
	yellow
	No peptide was located in the Disc or Lam1 domains

Table 2 .

 2 Position of CASPR2-derived peptides predicted as strong binders (% rank ≤3) for DRB1*15:01 and

	DRB1*04:01
		DRB1
	15:01		04:01
	Position	Rank	Position	Rank
	933	1.7	497	0.08
	1181	1.8	498	0.08
	1182	1.9	496	0.12
	1280	2.5	499	0.15
	1281	2.5	1181	0.4
	1183	2.5	495	0.4
	1061	2.5	1180	0.5
	823	2.5	500	0.5
	1279	3	1182	0.8
	932	3	823	0.8
	1063	3	1179	0.8
	1062	3	824	1
	1060	3	822	1
			110	1
			111	1.3
			1183	1.4
			109	1.4
			45	1.6
			108	1.8
			44	1.8
			821	1.9
			825	2
			1063	2.5
			1062	2.5
			1178	2.5
			112	2.5
			46	2.5
			241	3
			242	3
			1064	3
			43	3
	Peptides in the Disc domain are colored in blue, those in the Lam1 domain in red

Table 4 .

 4 Position of CASPR2-derived peptides predicted as strong binders (% rank ≤3) for DQA1*01:02-DQB1*06:02

	and DQA1*03:01-DQB1*03:02
	DQA1*01:02-DQB1*06:02		DQA1*03:01-DQB1*03:02
	Position	Rank	Position	Rank
	1195	0.03	273	0
	1194	0.03	272	0
	1295	0.1	1155	0.02
	1193	0.1	271	0.04
	1196	0.14	1154	0.07
	1294	0.17	879	0.14
	1255	0.25	1153	0.26
	505	0.31	274	0.27
	1296	0.33	878	0.29
	1254	0.33	1156	0.32
	1253	0.49	667	0.37
	504	0.51	888	0.43
	1293	0.52	270	0.46
	218	0.71	669	0.54
	888	0.79	767	0.6
	1192	0.79	466	0.64
	1256	0.82	889	0.8
	506	0.91	465	0.83
	217	1	939	0.85
	795	1.04	668	0.92
	1197	1.07	890	0.94
	503	1.07	666	1
	796	1.19	938	1.11
	273	1.33	768	1.14
	887	1.43	794	1.17
	272	1.53	1301	1.2
	473	1.53	1289	1.21
	474	1.59	877	1.23
	886	1.72	1295	1.26
	482	1.75	1290	1.35
	794	1.84	670	1.35
	1303	1.95	793	1.48

Table e

 e

	-1. Definition of the clinical features
	Clinical feature	Definition
	Amnesia	Clinical description and/or evidence of episodic memory disturbances in
		neuropsychological evaluation
	FBDS	Clinical description of brief dystonic movements involving the face, upper limb,
		and/or lower limb
	Other seizures	Clinical description of stereotyped episodes compatible with focal seizures or
		generalized tonic-clonic seizures (FBDS excluded)
	Status epilepticus	Clinical description with compatible EEG
	Psychiatric symptoms	Clinical description of depression, anxiety, psychosis, hallucinations, irritability,
		hetero-aggressiveness, abnormal behavior
	Frontal syndrome	Clinical description of dorsolateral frontal syndrome (i.e. apathy, abulia), orbitofrontal
		syndrome (i.e. disinhibition, impulsiveness), frontal-release signs (i.e. grasping),
		and/or executive dysfunction detected in neuropsychological evaluation
	Sleep disturbances	Insomnia or hypersomnolence, inversion of circadian rhythm, suspicion of REM sleep
		behavioral disorder
	Apraxia	Ideomotor, ideational, constructional apraxia based on clinical description and/or
		neuropsychological evaluation
	Aphasia	Alteration in language production based on clinical description and/or
		neuropsychological evaluation
	Dysautonomia	Sweating or thermoregulatory abnormalities, orthostatic hypotension, cardiac
		dysrhythmias, gastrointestinal dysmotility
	Abbreviations: FBDS, faciobrachial dystonic seizures

Table e -

 e 2. HLA allele carrier frequencies in patients with anti-LGI1 LE compared to controls

	B*38:01 DRB1*04:02 Table e-3. Univariate analysis of prognostic factors 13 (4.3) 7 (2.3)	5 (6.9) 9 (12.5)	0.36 0.001	1 0.03
	Allele A*01:01 A*01:83 A*02:01 A*02:03 A*02:05 A*02:06 A*02:07 A*02:20 A*03:01 A*03:02 A*11:01 B*39:01 B*39:05 B*39:06 B*39:10 B*39:24 B*40:01 B*40:02 B*41:02 B*44:02 B*44:03 B*44:05 B*44:15 DRB1*04:03 DRB1*04:04 DRB1*04:05 Age DRB1*04:06 18-54 DRB1*04:07 55-64 DRB1*07:01 65-74 DRB1*07:05 75 DRB1*08:01 Men DRB1*08:02 Diagnostic delay DRB1*08:03 <3 months DRB1*08:06 3 to <6 months DRB1*09:01 6 to <9 months A*23:01 B*45:01 DRB1*10:01 9 months A*24:02 B*47:01 DRB1*11:01 First symptom A*24:58 B*49:01 DRB1*11:02 Amnesia A*25:01 B*50:01 DRB1*11:03 Other seizures A*26:01 B*50:02 DRB1*11:04 FBDS A*26:08 B*51:01 DRB1*12:01 Psychiatric symptoms Controls, n=300 (%) 65 (21.7) 0 (0.0) 138 (46.0) 1 (0.3) 4 (1.3) 1 (0.3) 1 (0.3) 1 (0.3) 58 (19.3) 1 (0.3) 40 (13.3) 9 (3.0) 1 (0.3) 1 (0.3) 2 (0.7) 1 (0.3) 17 (5.7) 17 (5.7) 0 (0.0) 42 (14.0) 56 (18.7) 3 (1.0) 1 (0.3) 6 (2.0) 16 (5.3) 8 (2.7) 3 (1.0) 6 (2.0) 86 (28.7) 1 (0.3) 11 (3.7) 1 (0.3) 1 (0.3) 0 (0.0) 4 (1.3) 24 (8.0) 2 (0.7) 9 (3.0) 55 (18.3) 0 (0.0) 55 (18.3) 1 (0.3) 19 (6.3) 3 (1.0) 5 81.7) 5 (1.7) 5 (1.7) 21 (7.0) 0 (0.0) 16 (5.3) 2 (0.7) 47 (15.7) 2 (0.7) A*29:01 3 (1.0) B*51:02 1 (0.3) DRB1*13:01 39 (13.0) mRS at onset A*29:02 29 (9.7) B*51:07 1 (0.3) DRB1*13:02 20 (6.7) mRS=1 A*30:01 7 (2.3) B*51:08 1 (0.3) DRB1*13:03 4 (1.3) mRS=2 A*30:02 15 (5.0) B*52:01 7 (2.3) DRB1*13:07 1 (0.3) mRS=3 A*30:04 2 (0.7) B*55:01 4 (1.3) DRB1*14:01 2 (0.7) mRS=4 A*31:01 14 (4.7) B*56:01 1 (0.3) DRB1*14:04 1 (0.3) mRS=5 A*32:01 24 (8.0) B*57:01 14 (4.7) DRB1*14:38 1 (0.3) Amnesia A*32:07 1 (0.3) B*57:02 1 (0.3) DRB1*14:54 17 (5.7) Other seizures A*33:01 6 (2.0) B*58:01 9 (3.0) DRB1*15:01 51 (17.0) FBDS A*33:03 4 81.3) B*82:01 1 (0.3) DRB1*15:02 5 (1.7) Psychiatric symptoms A*34:02 0 (0.0) C*01:02 29 (9.7) DRB1*15:03 3 (1.0) Sleep disorders A*43:01 0 (0.0) C*02:02 40 (13.3) DRB1*16:01 17 (5.7) Frontal syndrome A*66:01 6 (2.0) C*02:10 2 (0.7) DRB1*16:02 1 (0.3) Aphasia A*66:02 1 (0.3) C*03:02 4 (1.3) DQB1*02:01 73 (24.3) Apraxia A*68:01 24 (8.0) C*03:03 26 (8.7) DQB1*02:02 78 (26.0) Dysautonomia A*68:02 5 (1.7) C*03:04 26 (8.7) DQB1*03:01 100 (33.3) ICU admission A*68:03 1 (0.3) C*04:01 61 (20.3) DQB1*03:02 48 (16.0) Status epilepticus A*74:03 1 (0.3) C*05:01 58 (19.3) DQB1*03:03 18 (6.0) Hyponatremia A*74:06 1 (0.3) C*06:02 36 (12.0) DQB1*03:19 3 (1.0) Abnormal MRI B*07:02 49 (16.3) C*07:01 79 (26.3) DQB1*04:02 19 (6.3) Inflammatory CSF B*07:05 2 (0.7) C*07:02 56 (18.7) DQB1*05:01 62 (20.7) LGI-Abs in CSF B*07:06 1 (0.3) C*07:04 7 (2.3) DQB1*05:02 22 (7.3) IgG1 in serum B*08:01 44 (14.7) C*07:18 6 (2.0) DQB1*05:03 19 (6.3) IgG4 in serum B*13:02 9 (3.0) C*07:41 1 (0.3) DQB1*05:04 2 (0.7) IgG1 in CSF B*14:01 11 (3.7) C*08:02 25 (8.3) DQB1*06:01 48 (16.0) IgG4 in CSF B*14:02 16 (5.3) C*12:02 7 (2.3) DQB1*06:02 48 (16.0) HLA DRB1*07:01 B*15:01 31 (10.3) C*12:03 27 (9.0) DQB1*06:03 41 (13.7) First line treatment B*15:03 2 (0.7) C*14:02 13 (4.3) DQB1*06:04 17 (5.7) Second line treatment B*15:10 0 (0.0) C*14:03 4 (1.3) DQB1*06:09 4 (1.3) Chronic immunotherapy B*15:17 2 (0.7) C*15:02 20 (6.7) Abbreviations: FBDS, faciobrachial dystonic seizures; ICU, intensive care unit; LGI1-Abs, antibodies against leucine-Patients, n=72 (%) Uncorrected p value Corrected p value 16 (22.2) 1 1 (1.4) 0.19 25 (34.7) 0.08 0 (0.0) 1 3 (4.2) 0.13 0 (0.0) 1 0 (0.0) 1 0 (0.0) 1 12 (16.7) 0.73 0 (0.0) 1 8 (11.1) 2 (2.8) 1 1 0 (0.0) 1 1 1 (1.4) 0.35 1 0 (0.0) 1 1 0 (0.0) 1 1 3 (4.2) 0.77 1 2 (2.8) 0.54 1 1 (1.4) 0.19 1 9 (12.5) 0.85 1 24 (33.3) 0.01 0.54 0 (0.0) 1 1 0 (0.0) 1 1 1 (1.4) 1 1 1 (1.4) 0.21 mRS 2, n (%) mRS>2, n (%) P value 1 1 (1.4) 1 0.03 1 1 (1.4) 0.57 18 (17) 1 (4) 1 0 (0.0) 0.60 28 (26) 4 (15) 1 63 (87.5) 2.1 10 -20 41 (38) 11 (41) 8.1 10 -19 0 (0.0) 1 20 (19) 11 (41) 1 1 (1.4) 0.47 68 (63) 16 (59) 0.68 1 0 (0.0) 1 0.90 1 0 (0.0) 1 40 (38) 11 (41) 1 1 (1.4) 0.19 36 (34) 10 (37) 1 3 (4.2) 0.13 1 12 (11) 3 (11) 0.69 6 (8.3) 1 (1.4) 0.47 1 0 (0.0) 0.21 1 18 (17) 3 (11) 1 8 (11.1) 1 (1.4) 0.19 1 4 (5.6) 0.006 0.22 0.26 0.16 0 (0.0) 2 (2.8) 0.39 1 0 (0.0) 1 1 34 (31) 14 (52) 1 3 (4.2) 3 (4.2) 0.18 1 1 (1.4) 1 1 33 (31) 5 (19) 0.18 6 (8.3) 1 (1.4) 0.19 1 1 (1.4) 0.21 1 27 (25) 5 (19) 0.62 0 (0.0) 6 (8.3) 0.13 1 2 (2.8) 0.17 1 13 (12) 3 (11) 1 0 (0.0) 0 (0.0) 1 1 2 (2.8) 0.01 0.41 <0.001 1 14 (19.4) 0.02 0 (0.0) 1 1 0 (0.0) 0.01 0.68 9 (8) 0 (0) 0.92 10 (13.9) 0.0003 0 (0.0) 1 1 1 (1.4) 1 1 25 (23) 0 (0) 0.009 0 (0.0) 0 (0.0) 0.35 1 0 (0.0) 1 1 52 (49) 12 (44) 0.08 0 (0.0) 0 (0.0) 1 1 0 (0.0) 1 1 16 (15) 8 (30) 1 3 (4.2) 1 (1.4) 0.35 1 0 (0.0) 1 1 5 (5) 7 (26) 1 8 (11.1) 12 (16.7) 0.001 0.05 0 (0.0) 1 1 90 (84) 26 (96) 0.09 0.48 0 (0.0) 0 (0.0) 1 1 0 (0.0) 0.05 1 79 (74) 19 (70) 0.41 1 0 (0.0) 3 (4.2) 0.70 1 6 (8.3) 0.07 1 59 (55) 12 (44) 0.31 0.60 2 (2.8) 0 (0.0) 1 1 1 (1.4) 1 1 65 (61) 18 (67) 0.57 0.32 1 (1.4) 7 (9.7) 1 1 1 (1.4) 0.57 1 42 (39) 6 (22) 0.09 0.19 1 (1.4) 6 (8.3) 0.32 1 4 (5.6) 1 1 50 (47) 14 (52) 0.63 0.19 1 (1.4) 1 (1.4) 0.47 1 0 (0.0) 1 1 7 (7) 4 (15) 0.23 1 0 (0.0) 0 (0.0) 1 1 5 (6.9) 0.0006 0.01 12 (11) 5 (19) 0.33 1 3 (4.2) 5 (6.9) 0.81 1 53 (73.6) 1.3 10 -13 2.2 10 -12 4 (4) 2 (7) 0.41 0.32 0 (0.0) 5 (6.9) 0.81 1 11 (15.3) 0.002 0.03 7 (7) 5 (19) 0.05 0.58 0 (0.0) 17 (23.6) 0.52 1 16 (22.2) 0.22 1 5 (4.7) 5 (19) 0.02 1 0 (0.0) 9 (12.5) 0.23 1 12 (16.7) 0.006 0.10 54 (51) 17 (63) 0.24 1 0 (0.0) 25 (34.7) 0.00002 0.0007 0 (0.0) 1 1 70 (67) 15 (57) 0.25 1 7 (9.7) 18 (25.0) 0.88 1 2 (2.8) 0.39 1 52 (54) 15 (57) 0.85 0.19 0 (0.0) 8 (11.1) 0.16 1 19 (26.4) 0.34 1 82 (77) 23 (85) 0.33 1 0 (0.0) 0 (0.0) 0.35 1 4 (5.6) 0.79 1 64 (84) 13 (100) 0.20 1 9 (12.5) 0 (0.0) 0.60 1 0 (0.0) 0.03 0.54 60 (79) 12 (92) 0.44 0.71 8 (11.1) 0.007 0 (0.0) 1 1 0 (0.0) 1 1 18 (56) 6 (75) 0.43 0.37 3 (4.2) 5 (6.9) 0.81 1 1 (1.4) 0.0003 0.005 30 (94) 7 (88) 0.49 0.73 2 (2.8) 0 (0.0) 0.35 1 8 (11.1) 0.36 1 53 (85) 10 (100) 0.34 0.54 8 (11.1) 6 (8.3) 1 1 2 (2.8) 0.007 0.11 104 (97) 26 (96) 1 0.83 1 (1.4) 3 (4.2) 1 1 0 (0.0) 0.05 1 49 (46) 15 (56) 0.36 0.47 1 (1.4) 0 (0.0) 1 1 0 (0.0) 1 1 17 (16) 2 (7) 0.36 0.19 0 (0.0) 2 (2.8) 0.27 1 1 B*15:18 3 (1.0) 0 (0.0) B*15:24 0 (0.0) 1 (1.4) B*18:01 43 (14.3) 2 (2.8) 0.004 B*18:03 1 (0.3) 0 (0.0) B*27:02 2 (0.7) 1 (1.4) B*27:05 20 (6.7) 7 (9.7) B*27:12 1 (0.3) 0 (0.0) B*35:01 24 (8.0) 7 (9.7) B*35:02 7 (2.3) 2 (2.8) B*35:03 11 (3.7) 1 (1.4) B*35:08 5 (1.7) 0 (0.0) B*37:01 3 (1.0) 1 (1.4) B*37:02 3 (1.0) 0 (0.0) DRB1*04:01 36 (12.0) 7 (9.7) 0.68 1 1 DRB1*03:01 74 (24.7) 5 (6.9) 0.001 0.03 0.57 DRB1*01:03 3 (1.0) 0 (0.0) 1 1 0.58 DRB1*01:02 11 (3.7) 0 (0.0) 0.13 1 0.47 DRB1*01:01 45 (15.0) 18 (25.0) 0.05 1 0.68 C*18:02 1 (0.3) 0 (0.0) 1 1 0.63 C*17:38 2 (0.7) 0 (0.0) 1 1 1 C*17:03 3 (1.0) 0 (0.0) 1 1 0.44 C*17:01 2 (0.7) 1 (1.4) 0.47 1 0.47 C*16:02 1 (0.3) 1 (1.4) 0.35 1 1 C*16:01 41 (13.7) 17 (23.6) 0.04 1 0.21 C*15:13 1 (0.3) 1 (1.4) 0.35 1 0.19 C*15:06 1 (0.3) 0 (0.0) 1 1 1 C*15:05 3 (1.0) 0 (0.0) 1 1 rich glioma-inactivated 1; mRS, modified Rankin scale
		110

Table 1 .

 1 DQ haplotypes other than DQA1*02:01-DQB1*02:02 in DRB1*07:01 carriers with anti-LGI1 LE

	Haplotype/1		Haplotype/2
	DQA1	DQB1	DQA1	DQB1
	02:01	03:03	03:03	03:03
	02:01	03:03	01:02	05:02
	02:01	03:03	05:05	03:01
	02:01	03:03	01:01	05:01
	02:01	03:03	03:01	03:02
	02:01	03:03	03:03	03:01
	03:01	03:02	02:01	03:02
	02:01	03:03	01:01	05:01
	02:01	03:03	01:01	05:01
	02:01	03:03	01:01	05:01

Table 2 .

 2 Class II haplotypes of non-DRB1*07:01 carriers with anti-LGI1 LE

		Haplotype/1			Haplotype/2
	DRB1	DQA1	DQB1	DRB1	DQA1	DQB1
	08:06	01:02	06:02	13:03	05:05	03:01
	04:01	03:01	03:02	13:01	01:03	06:03
	01:01	01:01	05:01	04:02	03:01	03:02
	04:02	03:01	03:02	12:01	05:05	03:01
	16:01	01:02	05:02	16:01	01:02	05:02
	04:08	03:03	03:01	11:04	05:05	03:01
	11:01	05:05	03:01	15:01	01:02	06:02
	01:01	01:01	05:01	16:01	01:02	05:02
	04:03	03:01	03:02	15:01	01:02	06:02

Table 3 .

 3

Table 4 .

 4 Position of LGI1-derived peptides predicted as strong binders (% rank ≤3) for DRB1 other than DRB1*07:01

	DRB1

Table 5 .

 5 LGI1-derived peptides predicted as strong binders for DQA1*02:01-DQB1*02:02 (% rank ≤3), and their % rank predicted for the DQ heterodimers (cis form) present in the

		DQA1	*02:01	DQB1	*03:02	3.82	4.72	4.36	8.63	8.38	7.29	11.36	6.44	4.58	6.69	14.37	13.78	1.22	7.39	0.56	6.34	12.1
		DQA1*	03:03	DQB1*	03:03	10.29	11.93	11.18	21.3	15.12	12.33	24.4	12.77	17.97	13.72	25.02	22.09	6.18	22.84	0.39	25.27	21.16
		DQA1*	01:03	DQB1*	06:03	38.54	39.65	36.65	31.31	36.13	32.38	52.51	32.87	16.91	38.32	33.66	51.16	10.51	27.53	5.57	26.78	18.45
		DQA1*	01:02	DQB1*	06:02	70.93	80.07	78.64	62.37	10.05	44.56	73.06	40.17	53.9	39.91	65.5	85.72	27.97	71.8	5.22	60.16	47.63
	non-DQA1*02:01-DQB1*02:02 carriers	DQA1* DQA1* DQA1* DQA1* DQA1* DQA1* DQA1*	Positi Peptide on Core ‡ 02:01 02:01 03:01 05:05 01:01 01:02 03:03 DQB1* DQB1* DQB1* DQB1* DQB1* DQB1* DQB1*	02:02 03:03 03:02 03:01 05:01 05:02 03:01	11.52 57 NARSIPRTVPPDVIS PRTVPPDVI 0.54 5.71 6.4 6.91 47.67 35.45	12.29 58 ARSIPRTVPPDVISL PRTVPPDVI 0.65 6.87 7.86 7.87 48.47 42.66	11.66 59 RSIPRTVPPDVISLS PRTVPPDVI 0.65 6.01 8.06 7.6 45.55 42.34	27.57 230 QDLPYQSLSIDTFSY YQSLSIDTF 1.03 13.5 12.79 10.27 33.45 38.2	15.48 56 ENARSIPRTVPPDVI PRTVPPDVI 1.2 11.68 11.37 10.67 62.91 37.74	15.45 372 SLHAWYRDTDVEYLE YRDTDVEYL 1.26 10.1 8.69 8.18 3.21 17.39	31.67 229 SQDLPYQSLSIDTFS YQSLSIDTF 1.29 16.9 15.64 11.83 35.94 42.59	15.18 373 LHAWYRDTDVEYLEI YRDTDVEYL 1.29 8.25 9.19 7.84 4.6 29.89	19.94 99 TSNSFDVISDDAFIG FDVISDDAF 1.56 16.56 3.49 11.15 5.35 5.92	17.33 374 HAWYRDTDVEYLEIV YRDTDVEYL 1.65 8.39 11.83 8.49 8.42 44.55	37.58 231 DLPYQSLSIDTFSYL YQSLSIDTF 1.92 20.9 19.45 14.38 37.01 46.39	23.02 60 SIPRTVPPDVISLSF PRTVPPDVI 2.03 16.37 19.03 15.02 71.94 71.67	11.92 329 IRKPNDIETFKIENN PNDIETFKI 2.32 2.3 4.13 10.46 6.37 2.45	26.75 100 SNSFDVISDDAFIGL FDVISDDAF 2.36 22.06 5.4 13.62 7.66 12.04	1.03 341 ENNWYFVVADSSKAG WYFVVADSS 2.45 0.54 0.84 2.82 3.71 1.86	26.34 101 NSFDVISDDAFIGLP VISDDAFIG 2.84 16.23 5.96 12.59 15.8 21.99	31.52 98 FTSNSFDVISDDAFI FDVISDDAF 3 29.36 4.54 18.3 9 5.44	‡Core peptides predicted for DQA1*02:01-DQB1*02:02	Peptides in the LRR domain are colored in orange, those in the ETP domain in green	Peptides predicted as strong binders for DQA1*02:01-DQB1*02:02 and also for other DQ heterodimers are colored in yellow

Table 1 .

 1 Allele carrier frequencies of anti-AK5 LE patients compared to controls

	Supplementary Allele	Controls, n=442 (%)	Patients, n=11 (%)	Uncorrected p value	Corrected p value
	A*01:01	92 (20.8)	7 (63.6)	0.002995	0.12579
	A*01:23	1 (0.2)	0 (0.0)	1
	A*02:01	161 (36.4)	4 (36.4)	1
	A*02:02	11 (2.5)	0 (0.0)	1
	A*02:03	2 (0.5)	0 (0.0)	1
	A*02:05	12 (2.7)	0 (0.0)	1
	A*02:06	3 (0.7)	0 (0.0)	1
	A*02:17	2 (0.5)	0 (0.0)	1
	A*02:38	1 (0.2)	0 (0.0)	1
	A*03:01	88 (19.9)	0 (0.0)	0.133190
	A*03:02	3 (0.7)	0 (0.0)	1
	A*11:01	41 (9.3)	1 (9.1)	1
	A*11:02	1 (0.2)	0 (0.0)	1
	A*23:01	33 (7.5)	1 (9.1)	0.580313
	A*23:17	2 (0.5)	0 (0.0)	1
	A*24:02	78 (17.6)	1 (9.1)	0.698098
	A*24:03	6 (1.4)	0 (0.0)	1
	A*24:10	1 (0.2)	0 (0.0)	1
	A*25:01	12 (2.7)	0 (0.0)	1
	A*26:01	37 (8.4)	1 (9.1)	1
	A*26:08	1 (0.2)	0 (0.0)	1
	A*29:01	6 (1.4)	0 (0.0)	1
	A*29:02	41 (9.3)	0 (0.0)	0.609694
	A*30:01	16 (3.6)	0 (0.0)	1
	A*30:02	11 (2.5)	0 (0.0)	1
	A*30:04	7 (1.6)	0 (0.0)	1
	A*31:01	24 (5.4)	1 (9.1)	0.468294
	A*31:04	1 (0.2)	0 (0.0)	1
	A*32:01	57 (12.9)	1 (9.1)	1
	A*32:26	1 (0.2)	0 (0.0)	1
	A*33:01	13 (2.9)	1 (9.1)	0.294786
	A*33:03	10 (2.3)	1 (9.1)	0.239268
	A*33:05	1 (0.2)	0 (0.0)	1
	A*34:02	5 (1.1)	0 (0.0)	1
	A*36:01	4 (0.9)	0 (0.0)	1
	A*66:01	4 (0.9)	0 (0.0)	1
	A*66:02	1 (0.2)	0 (0.0)	1
	A*66:03	1 (0.2)	0 (0.0)	1
	A*68:01	25 (5.7)	0 (0.0)	1
	A*68:02	18 (4.1)	1 (9.1)	0.379186
	A*74:01	3 (0.7)	0 (0.0)	1
	A*80:01	1 (0.2)	0 (0.0)	1
	B*07:02	74 (16.7)	0 (0.0)	0.224724
	B*07:05	3 (0.7)	0 (0.0)	1
	B*07:06	3 (0.7)	0 (0.0)	1
	B*08:01	51 (11.5)	7 (63.6)	0.000088	0.005808
	B*13:02	13 (2.9)	2 (18.2)	0.047399
	B*14:01	21 (4.8)	0 (0.0)	1
	B*14:02	36 (8.1)	2 (18.2)	0.233546
	B*15:01	29 (6.6)	0 (0.0)	1
	B*15:03	13 (2.9)	0 (0.0)	1
	B*15:09	1 (0.2)	0 (0.0)	1
	B*15:10	2 (0.5)	0 (0.0)	1
	B*15:16	1 (0.2)	0 (0.0)	1
	B*15:17	6 (1.4)	1 (9.1)	0.159065
	B*15:18	5 (1.1)	0 (0.0)	1
	B*15:24	1 (0.2)	0 (0.0)	1
	B*15:25	1 (0.2)	0 (0.0)	1
	B*18:01	52 (11.8)	0 (0.0)	0.623491
	B*18:02	1 (0.2)	0 (0.0)	1

Table 2 .

 2 AK5-derived peptides predicted as strong binders for HLA class I molecules

	Peptide	Position (AK5-1)	Position (AK5-2)	Position (AK5-3)	A*01:01	Rank % a B*08:01	C*07:01
	LARREIPQL	10				0.4167
	ARREIPQLF	11					0.01
	SKPEDPVEY	29		3			0.2572
	SCLQKVKEL	40		14		0.2183
	SRRSFLRNV	75		49			0.2908
	RRSFLRNVM	76		50			0.1216
	NSNFPYRRY	87		61	0.3328
	FPYRRYDRL	90		64		0.0247
	RRYDRLPPI	93		67			0.0843
	DRLPPIHQF	96		70			0.0306
	LPPIHQFSI	98		72		0.4884
	ETAELIEEY	114		88	0.0649
	TRPRPKIIL	128		102			0.1409
	RPRPKIILV	129		103		0.0738
	QSLKIAERY	148		122	0.2671
	IAERYGFQY	152		126	0.0703
	LLRKKIHST	166		140		0.0956
	TSSNRKWSL	174		148		0.1764
	EIKQKLMQI	201		175		0.0157
	FPRDVAQAL	220		194		0.048
	NQRLKERLL	247		221		0.1629
	NAAPLVKYF	281		255			0.2465
	YFQEKGLIM	288		262		0.2436	0.3075
	QCEKLVEKY	392	27	366	0.3852
	RRIGDPQLV	475	110	449			0.0799
	LLQRSRSSL	497	132	471		0.2989
	YYRASIPVI	521	156	495			0.4896
	YRASIPVIA	522	157	496			0.2965
	RASIPVIAY	523	158	497			0.331
	ASIPVIAYY	524	159	498	0.1899		0.1448
	AYYETKTQL	530	165	504			0.0961
	a Rank value is only provided for the strong binders for each HLA

Table 4 .

 4 Statistically significant up-regulated CSF proteins in anti-AK5 LE compared to anti-LGI1/CASPR2 and anti-Yo/Ma2 patients Abbreviation

	vs. Yo/Ma2 a	logFold Corrected P	Change value	3.84 0.0007		0.76 0.02				0.71 0.005				1.07 0.03			3.04 0.0007					0.85 0.04
	vs. LGI1/CASPR2	logFold Corrected P	Change value	5.85 0.005	2.11 0.03	1.00 0.03	1.42 0.03	1.13 0.04	3.27 0.01	1.28 0.001	1.04 0.01	1.42 0.03	1.32 0.003	1.20 0.04	1.74 0.001	1.10 0.03	3.44 0.003	1.14 0.03	0.84 0.04	1.73 0.008	0.50 0.03	0.68 0.03	1.88 0.04	0.81 0.04	0.68 0.04	0.91 0.04	2.48 0.003		1.11 0.01	1.18 0.01
	vs. Controls	logFold Corrected P	Change value	0.31 0.02	0.25 0.005	0.13 0.004	0.11 0.002	0.25 0.007	0.25 0.0002	0.06 0.0001	0.14 0.003	0.16 0.0003	0.10 0.0008	0.13 0.0007	0.23 0.0004	0.09 0.0009	0.22 0.002	0.08 0.01	0.03 0.04	0.26 0.0009	0.05 0.0001	0.15 0.0002	0.39 0.004	0.09 0.04	0.12 0.0005	0.09 0.01	0.19 0.0004		0.08 0.003	0.07 0.002
		Protein		Carbonic anhydrase 3	Macrophage-capping protein	CD 209 antigen	CMRF35-like molecule 6	Granulocyte colony-stimulating factor	Complement 1r	Complement c4-a/c4-b	Protein FAM3B	Glial fibrillary acidic protein	Progranulin	Hepatitis A virus cellular receptor 2	Ubiquitin-like protein 15	Lysozyme C	Myoglobin	Macrophage mannose receptor 1	Phosphatidylethanolamine-binding protein 1	Phosphoglycerate mutase 1	Peptidyl-prolyl cis-trans isomerase A	Proteasome activator complex subunit 1	SLAM family member 7	Protein S100-A4	SUMO-conjugating enzyme UBC9	Ubiquitin-fold modifier-conjugating enzyme 1	Protein 14-3-3 (beta/alpha, epsilon, eta, gamma, theta,	zeta/delta, sigma)	Protein 14-3-3 beta/alpha	Protein 14-3-3 zeta/delta
				CA3	CAPG	CD209	CD300C	CSF3	C1R	C4A/C4B	FAM3B	GFAP	GRN	HAVCR2	ISG15	LYZ	MB	MRC1	PEBP1	PGAM1	PPIA	PSME1	SLAMF7	S100A4	UBE2I	UFC1	YWHAB/E/G/H/Q/Z & SFN		YWHAB	YWHAZ

a Blank spaces correspond to non-significant differences in CSF protein expression between anti-AK5 and anti-Yo/Ma2 patients

Un grand merci à toute l´équipe du Centre de

Supplementary Figure . The first two (C1 and C2) genetic principal components (PC) scatter plot. PC analysis is a statistical tool that reduces data dimension, describing a large amount of data as new, un-correlated variables, labeled PC. Genotypes of patients (GAD) and controls were converted in 9 PC based on single nucleotide polymorphisms.

Comparing PC by scatter plot enabled to guide case-control ethnical matching

Supplementary File

Familial autoimmunity in neurological patients with GAD65 antibodies: an interview-based study

Sergio Muñiz-Castrillo, MD 1,2 ; Alberto Vogrig, MD 1,2 ; Clémentine Montagnac, MD 1,2 ; Bastien Joubert, MD PhD 1,2 ; Marie Benaiteau, MD 3 ; Olivier Casez, MD 4 ; Hugo Chaumont, MD 5 ; Lucie Hopes, MD 6 ; Hélène-Marie Lanoiselée, MD 7 ; Vincent Navarro, MD PhD 8 ; Benjamin Thomas, MD 9 ; Renata Ursu, MD 10 ; David Gonçalves, PharmD 11 ; Nicole Fabien, PhD 11 ; François Ducray, MD PhD 1,2 ; Cécile Julier, PhD 12 ; Jérôme Honnorat, MD PhD 1,2 . Positive regulation of transport 4.90x10 -6 GO:0002376

STUDY II. DISEASES WITH

Immune system process 7.50x10 -6 GO:0048584

Positive regulation of response to stimulus 8.04x10 -6 GO:0006955

Immune response 1.75x10 -5 GO:0048583

Regulation of response to stimulus 3.01x10 -5 GO:0002252

Immune effector process 5.28x10 -5 GO:0051707

Response to other organism 5.28x10 -5 GO:0006950

Response to stress 6.67x10 -5 GO:0051704

Multi-organism process 7.30x10 -5 GO:0010638

Positive regulation of organelle organization 7.65x10