 Introduction History and geographical location of the unit

The CEA-CNRS URA 2210 unit (CEA unit associated to CNRS) is located at MIRCen (Molecular Imaging Research Centre, Fontenay aux roses), a Service of the Biomedical Imaging Institute (I²BM) of the CEA. URA 2210 also depends on CNRS (commission 28,INSB).

The URA 2210 is the continuation of the URA CEA-CNRS 1285 originally created and directed by Mr André SYROTA at the Service Hospitalier Frédéric Joliot (SHFJ, CEA, Orsay) as an interface between cellular and molecular neurobiology and brain imaging. The URA 2210 unit was created in 2004 with Mr Philippe HANTRAYE as its director. In 2011, the URA 2210 was renewed after its first AERES evaluation with Mr Emmanuel BROUILLET as its director.

At the beginning of 2009, the majority of the members of the URA 2210 unit moved to MIRCen, a Preclinical Research Centre jointly financed and built by CEA and INSERM (CRC CEA-INSERM) at Fontenay-aux-Roses. At this time, all preclinical research activities of the URA 2210 were concentrated in MIRCen whereas the clinical activities of the unit remained located at Henri Mondor Hospital and at SHFJ for the PET/MRI imaging of the patients.

In addition to its affiliation to CNRS and CEA, URA 2210 asks for its affiliation to Paris 11 (Université Paris-Saclay in 2015) in order to contractually reinforce its long standing links with this south Paris University.

Because the research activities of URA 2210 are clearly oriented towards medical applications, the URA 2210 also asks for its affiliation to INSERM.

Management team

The (URA 2210) neurodegenerative disease laboratory is headed by Mr Emmanuel BROUILLET (Research director at CNRS) since 2010. He will be the director of the unit for the next five years.

The lab is constituted of 3 research teams. Team 1 which focuses its research on the role of "Cell-cell interactions in neurodegeneration" is directed by Mr Gilles BONVENTO (Research director at Inserm). Team 2 which focuses its research on "Preclinical and clinical therapeutics for neurodegenerative diseases", is directed by Mr Philippe HANTRAYE (Research director at CNRS). Team 3, is focused on "Multimodal imaging of neurodegenerative diseases", and is directed by Mr Marc DHENAIN (Research Director at CNRS). 2  Assessment of the unit

Unit workforce

Strengths and opportunities related to the context

The URA 2210 is internationally acknowledged as a unit using translational approaches from basic science to clinical applications in the field of neurodegenerative diseases including Parkinson's, Huntington's and Alzheimer's diseases. The strength of the unit relies on its unique gathering of scientists experts in different fields using multidisciplinary methodologies. Members of the unit are experts in:

-the development of methodologies such as gene transfer, image processing, PET (Positron Emission Tomography), MRI (Magnetic Resonance Imaging), and NMR (Nuclear Magnetic Resonance spectroscopy) brain imaging; -the development of animal models using gene transfer in rodent and non-human primates, which contributes to better understanding the pathophysiology of disease progression. The unit is organized in such way that scientific equipments are accessible to all the teams. These include MIRCen platforms (brain imaging, image processing, vectorology, behaviour and histology). The URA 2210 is hosted at MIRCen and several technicians and engineers of the unit are part-time dedicated to platform activities. The clinical group has access to brain imaging PET facilities at Service Hospitalier Frédéric Joliot (CEA). These platforms are also dedicated to national and international collaborations.

Members of the unit have developed very strong relationship with pharma industry (IPSEN-BEAUFOUR, OXFORD BIOMEDICA, SANOFI-AVENTIS, SERVIER, ROCHE, ELI LILLY, etc).

Scientists gather their expertise in taskforces to synergistically work on transversal programs. The unit members are involved in clinical trials in collaboration with clinicians at Henri Mondor Hospital (Creteil).

Weaknesses and threats related to the context

Disequilibrium in the size of the teams, including the technical staff, and the small size of one team makes the feasibility of the projects vulnerable.

A lack of focus in overall direction and broad range of some projects that merit a more in-depth attention. The coherence of overall goals is not clear for some projects.

The experts committee noted that the lack of in depth study of mechanistic limits the teams to publish in high IF journals.

Recommendations

The teams should streamline their research plans and focus on projects with highest interest and feasibility.

It is recommended to the small team (team 3) to define a clear strategy to attract new researchers.

It is recommended to encourage young researchers (in particular in team 2) to lead some of the team's projects.

 Detailed assessments

Assessment of scientific quality and outputs

The teams of URA 2210 unit have focused their research on neurodegenerative diseases, especially Huntington's, Parkinson's and Alzheimer's diseases. They developed a translational research strategy allowing the transfer of findings from basic research in animal models of these diseases to clinical trials in patients. They developed animal models using lentiviral and AAVs vectors mimicking disease progression in which they developed innovative brain imaging methods to assess progression of neurodegeneration and therapeutic efficacy.

The major findings of the unit during last 5 years are:

1) the defect in energy metabolism at the level of neuron-astrocyte interactions in pathogenic mechanisms of Huntington's disease;

2) the efficacy of gene transfer using siRNA for the treatment of Huntington's disease;

3) the efficacy of gene transfer using viral vectors targeting the replacement of dopamine in MPTP-treated non-human primate. This approach was successfully transferred to parkinsonian patients (The Lancet paper); 4) the realization of new animal (rodent and non-human primate) models of Alzheimer's disease; 5) the development of innovative brain imaging methods.

Given the medium size of the unit, the scientific output is of excellent quality. The unit has published more than 110 papers in peer-reviewed journals since 2008. Among the most important papers that were led by researchers from the unit (as first and/or last author) are:

-Sci. Translational Med ( 2009 -Human Molecular Genetics (2008, 2010x2, 2013x2); -Journal of Neuroscience (2009Neuroscience ( , 2011, 2012x2);, 2012x2);-Neuroimage (2008-Neuroimage ( , 2010x2, 2011-Neuroimage ( , 2013)); -Neurobiology of Aging (2009Aging ( , 2011, 2012x2, 2013x2), 2012x2, 2013x2) -The Lancet (in collaboration, 2 members of the unit have contributed as co-authors, but not 1 st /last/corresponding author).

Considering the individual achievements of each team, a discrepancy of productivity in terms of peer-reviewed publications between the teams can be noted.

In addition to the overall quality and volume of original publications, the URA 2210 members obtained three licenced patents, one for radiolabels PBR/TSPO [AD0628: EP 08291013.4 -SHFJ et MIRCen], one on siRNA strategy [AD0618: EP07290751.2 -MIRCen] and one on « silencing » specific astrocytes [AD13019: EP12305588.1. -MIRCen].

Assessment of the unit's academic reputation and appeal

Researchers of the URA 2210 are involved in a large number of national and international collaborations, as well as pharma industry partnership attesting of their excellent visibility. The fact that the lab is hosted in the MIRcen with several platforms (managed by the staff of the three teams) plays an important role in the unit's visibility.

The excellent quality of the UMR 2210 is attested by the numerous grants from public institutions, patient's foundations and pharma industry they have received. The committee noted the award of a junior ERC grant to one of the researchers and the "Grand prix de la Fondation de France & Fondation Alzheimer" to one of the team leaders.

Scientists of the URA 2210 are frequently invited to give lectures at national and international institutes and meetings.

Scientists are involved in scientific advisory boards (ANR, Dim biotherapy, Dim neurosciences, ITMO Neurosciences, ENP, JPND, NeurATRIS, etc) and editorial activities.

Assessment of the unit's interaction with the social, economic and cultural environment One of the most important interactions of the teams of the unit is with pharma industry (Oxford BioMedica, SANOFI, ROCHE, Servier, Eli Lilly, etc).

The team 2 leader is member of the strategic management of MEDICEN PARIS REGION.

Scientists of the URA 2210 are engaged in public activities.

Assessment of the unit's organisation and life

Because URA 2210 is hosted at MIRCen and URA 2210's researchers, engineers and technicians are deeply implicated in the running/managment of the MIRCen equipments and platforms, the teams benefit from all these equipments and platforms. The lab is organized in such a way that scientists use common resources and share facilities that allow submitting joint applications involving 2 or 3 teams. The strategy to apply to different calls is orchestrated during lab meetings to avoid internal competition and maximize chances of obtaining grants.

There are many ongoing interactions between the 3 research teams generating collaborations, which are productive. 30 % of the unit's publications include co-authors from at least two different teams of the URA 2210 unit.

The unit as a whole brings together all of the elements that are essential for the identification of novel therapeutic strategies in neurodegenerative diseases and translate these from the laboratory to the clinic.

All three teams have regular team meetings, as well as cross-cutting steering committees, in which representatives of the three teams are involved. This approach allows for a unified approach across the entire unit, and enhances the potential for inter-team collaboration.

Committee members met with the technicians and engineers of the center. They expressed their total approval of the proposed project. They have been involved in the AERES evaluation proposal. Indeed, they all have read the AERES document before it was submitted and attended the presentation preparations by the team leaders. Although many technical staff are involved in the platform activities of MIRCen (up to 50 % of their activity), all attested that they feel very well implicated in the different research projects. They are informed of the main aims to achieve and the progress of the project. They seem to interact very efficiently with researchers and PhD students, and are often associated to publications, if not to acknowledgments. Many of them have already attended scientific meetings including international ones and even had the occasion to present posters. The unit leader and the team leaders seem to have achieved a very good management of the technical staff providing them with the means to fulfil their duties in a very productive, efficient and comfortable manner.

Committee members met with PhD students and post-docs of the unit. They expressed strong enthusiasm and happiness in regard to the technical facilities (numerous skills and strong facilities offered by the platforms) notably. The unit is successful in attracting PhD students from abroad (one PhD student from Canada) and the national CEA grant application plays a key role in this attractiveness. PhD students and post-docs of the unit regularly attend national and international meetings and actively participate to local meetings.

Assessment of the unit's involvement in training through research

The URA 2210 unit is involved in training of all categories of permanent and non-permanent personnel (technicians, students, engineers/researchers). During the last 5 years 16 PhDs defended their thesis and 20 Master 2 students were trained.

The team leaders are involved in teaching and organizing courses for Paris area's Universities. Scientists are actively involved in the steering committees of different Master 2 programs and PhD programs ("École Doctorale"). The lab has an active strategy to favour the hosting of students for their Master 2 rotations and PhD training.

Assessment of the strategy and the five-year plan

During the last five years, the unit was composed of 4 teams and recently it was decided to reorganize the teams into 3 teams only according to the scientific affinities and complementarities. The candidate director is Mr Emmanuel BROUILLET.

The scientific aims of the URA 2210 for the next 5 years are envisioned in the continuity of the past and current projects focusing on three major neurodegenerative diseases (Parkinson's, Huntington's and Alzheimer's) to:

1) better understand the pathophysiological mechanisms of cell death and dysfunction;

2) develop and validate new therapeutic strategies at a preclinical stage using new rodent and non-human primate models. The researchers will evaluate novel bio-therapies based on the utilization of viral vector-based gene delivery such as CNTF (Ciliary Neurotrophic Factor), siRNA, dopamine enzyme replenishment;

3) develop and validate new brain imaging methods that could be applied for the quantitative in vivo followup of neurodegeneration and the evaluation of therapeutic efficacy in animal models first and then in patients.

The projects are considered important for biomedical research as they involve various complementary aspects using different techniques and approaches and many points of convergence on topics. The committee considers that the proposed projects are in general of excellent quality, and led by scientists with solid reputations and good visibility in their respective fields. However, some of the projects are too ambitious and not focused enough (See specific comments in team-by-team analysis).  Detailed assessments

 Team-by-team analysis

Assessment of scientific quality and outputs

Cell-cell interactions are widely recognised as an important component of many neurodegenerative diseases. However, the role of metabolism and metabolic pathways in these interactions is less clear and growing only now in importance and interest. Team 1 has identified these processes as central to Huntington's disease (HD) and plan to extend this premise to both Alzheimer's and Parkinson's disease over the next 5 years. The team employs an impressive array of state-of-the-art methods ranging from genetic screening to in vivo imaging, and span from in vitro cell based studies to in vivo disease models and, ultimately, to man. As such, they are very well placed to undertake the proposed work, and this is innovative both in direction and approach.

The progress made over the last 5 years is excellent, as evidenced from the substantial number of publications, including several in high impact journals such as PNAS, Human Molecular Genetics, Journal of Neuroscience and Neuroimage. The team collaborates widely both nationally and internationally, in order to extend their expertise and impact.

The work of team 1 is highly interdisciplinary not least by virtue of the wide range of methodologies employed. Over the last 5 years there has clearly been some close interactions between the original team 1 (cell-cell interactions) and team 3 (in vivo imaging), and these have now been merged in the forthcoming proposal. Such interactions are no doubt facilitated by the movement of all research teams into the same location, and more recently through the introduction of combined regular group meetings.

The approaches being used within the field of neurodegenerative disease are cutting-edge and, in some cases, have not been reported elsewhere in this context. At the same time the focus on metabolic processes and in particular neuron-astrocyte interactions in the context of reactive astrogliosis, as underlying disease progression is an interesting concept that has not been widely considered previously.

Another aspect of the work from Team 1 is the focus on the development of new viral vectors, which provide both strong research tools for dissecting out causal relationships both in vitro and in vivo, and also potential new therapeutic strategies. Notably work with the CNTF-expressing lentivirus has led to a clinical trial in HD (Huntington disease) patients.

Assessment of the unit's academic reputation and appeal

Several members of Team 1 have already secured research funding from a variety of sources, including Industrial partners, which is indicative of their standing in the scientific community and their fundability. As mentioned above, they have numerous collaborations both nationally and internationally and also host a number of foreign students and postdoctoral scientists.

The high quality of the team members is attested by the numerous grants and awards they have received during the past five years. These include 1 junior ERC grant to one of the researchers within the team and 1 prestigious award "Grand prix de la Fondation de France & Fondation Alzheimer" to the team leader.

Members of the team have been involved in a number of activities at the publishing level, including acting as a Topic Editor for Frontiers in Cellular Neuroscience and writing insightful and well-positioned review articles (e.g. Escartin and Rouach, 2013, Astroglial networking contributes to neurometabolic coupling. Frontiers in Neuroenergetics).

Assessment of the unit's interaction with the social, economic and cultural environment Many of the methods and approaches developed by team 1 are novel and original, including viral-based gene transfer models, microMRI and molecularly-targeted MRI. The team plans to use these techniques to measure early metabolic dysfunctions in ND (Neurodegenerative disease) in humans. The projects have a strong biomedical focus and the close interactions of team 1 members with the more clinical teams and also the Henri Mondor Hospital, undoubtedly facilitates translation of promising methods (biological and imaging) from bench to clinic. Although team 1's activity is mainly academic, they have a number of industrial collaborations (e.g. Servier, Eli Lilly). These collaborations will place the Team in a good position to exemplify findings in the lab into potential clinical products.

The participation in a range of public engagement activities by several members of Team 1 is excellent. They have participated in a number of activities directed at increasing public awareness and understanding of the research conducted by URA 2210.

Assessment of the unit's organisation and life

Team 1 plays an essential role in providing basic science projects and the preclinical imaging development for the identification of novel therapeutic strategies in neurodegenerative disease. The cross-cutting themes of the unit facilitate integration of Team 1's activities into the unit as a whole.

Representatives of Team 1 are involved in regular team meetings, as well as cross-cutting steering committees.

Assessment of the unit's involvement in training through research

The unit has a strong student population, and team 1 in particular has trained a considerable number of students over the past 5 years; 5 completed and 6 currently in progress. The attractiveness of the team is high, as assessed by PhD students applying from abroad (Canada). They also attracted 5 over the fifteen national CEA grants for PhD. Given the successful completion of several students, guidance and quality of supervision is likely high. Both PhD students and post-docs have gone on to continue with scientific careers on leaving MIRCen, whilst previous Masters students in the lab have gone on to PhD studentships either at MIRCen or elsewhere. Several of Team 1 members are involved in co-ordination of the Masters teaching modules.

Assessment of the strategy and the five-year plan

The proposed programme will build on previous work, around the central hypothesis that the convergence of damage developed within multiple cell types, including glial cells, is crucial to the selective neuronal dysfunction occurring in neurodegenerative diseases. The work will focus particularly on metabolic interactions between cells, and will use a variety of tools including viral vectors, cell sorting, animal models, in vivo cell and animal imaging. The team plans to extend their previous findings and methods in HD to both AD and PD over the coming years.

The proposal describes a number of imaging and spectroscopy approaches that will be implemented or developed to address biological questions. Several of these methods reflect new developments and are quite challenging -for example, the developments in diffusion weighted MRS (Magnetic Resonance Spectroscopy) will push the boundaries of what is possible with this method, which by necessity carries some risk. Nevertheless, the potential benefits could be substantial if it is indeed possible to obtain information at the cellular scale in models of neurodegeneration. The 13C MRS methods are well established by Mr Julien VALETTE and the collaboration with Mr Pierre-Gilles HENRY in Minnesota will further strengthen this element of the proposal. The use of both FRET (Fluorescence Resonance Energy Transfer) metabolic nanosensors and 17O imaging have potential for yielding very interesting data, and will complement existing metabolic measurements.

The work describing the consequences of reactive astrogliosis and astrocyte function per se in neurodegenerative disease is both novel and timely, and few other groups are working in similar areas. Increasing interest has focussed in recent years on the role of astrocytes in mediating and modulating neuronal function and associated vascular and metabolic responses. The natural, but currently understudied, extension of these concepts is the impact of the astrocyte inflammatory response during disease on normal functioning of these processes. Understanding how astrocytes contribute to neurodegenerative diseases, both directly and indirectly, may be critical to effective treatment. Moreover, extending this idea into the regional vulnerability projects and the possibility that different astrocyte populations respond differentially is an exciting concept -it is not clear whether the team also plans to look at different reactive astrocyte phenotypes, rather than just reactivity per se in different regions, but this is also an emerging concept and may be important in this context.

During the site visit, the Team members clarified the interactions between methodological and biological aspects of this programme, and on the basis of previous experience and output, all elements of the programme are very likely to be achievable. The only significant concern on the part of the reviewer's was the breadth of proposed projects, and the likelihood that the team might be overstretching themselves. Nevertheless, it was recognised that translating their previous developments and findings in HT into other neurodegenerative diseases was a logical progression of their work.

Conclusion

Overall, the opinion of this team is excellent. It is clear that work within this part of the unit into the pathophysiological mechanisms of cell death and dysfunction will underpin many of the downstream clinical studies, and provide important insight into the biology underlying the imaging biomarkers. The research proposed by the team is likely to attract further funding and industrial partnerships.

 Strengths and opportunities:

Multi-level approach from cells, through animal models to man (in collaboration with other teams).

Multiple techniques allowing understanding of molecular, cellular and whole organism level biology.

Development of new imaging methods that have potential for clinical translation and validation in preclinical models.

 Weaknesses and threats:

Slight lack of focus in overall direction broad range of projects.

 Recommendations:

Prioritise projects to develop clearer overall focus and avoid over-stretching the team.  Detailed assessments

Assessment of scientific quality and outputs

The main activities of team 2 are focused on developing, assessing and validating innovative strategies for neurodegenerative diseases (ND) including Huntington's (HD), Parkinson's (PD) and Alzheimer's (AD). One particularity and originality of this team is modelling ND in large animals using gene transfer techniques. Hence, these models can be used to develop new PET imaging tracers for early stage neurodegenerative events and develop new cell-based and gene-based therapeutic strategies, in particular for the treatment of PD and HD.

In the past 4 years the team developed mainly two animal models: 1) a genetic primate model of HD based on gene transfer (first with a lentivirus and more recently with AAV5 serotype) of a mutated form of the Huntingtin gene (171 a.a. N-terminal fragment of Htt with 82 glutamines stretch) in the caudate-putamen;

2) two models of tauopathy based on the somatic gene transfer of a mutated form (P301L) form of the human tau gene in the hippocampus of adult rat of non-human primates.

These models constitute an important translational output since they allow the development of more pertinent and more predictive animal models of these ND, and can provide the opportunity to characterize early biomarkers along with the possibilities to test new therapeutic strategies.

In this way, the CEA environment provides a unique opportunity for developing and validating, besides classical pharmacological tracers, new PET tracers, based on non-conventional targets (amyloid plaques, neurofibrillary tangles, huntingtin aggregates, Lewi Bodies) that are in a R&D pipeline under patent. The team has an excellent involvement in MIRCen's platforms (pre-clinical Imaging Platform for Gene and cell therapy).

The team has a good publication record with 77 published papers during the past five years, an average citation per item of 12 (PNAS, J. cerebral blood flow Metab, Neurobiol Aging, Neuroimage, Lancet, Plos One, Human mol Genet, J Neurosc, etc).

The Impact factor of main publication journals is of good level. In addition, the team had a very recent publication in the Lancet journal in which four team members are co-authors. This study concerns a clinical trial in PD patients using ProSavin, a new gene transfer approach aimed at restoring DA synthesis and release in the striatum. The authors participated significantly to the pre-clinical studies in non-human primates, and brain imaging in human. Although several papers are signed in first author position by team members the committee noted that only few publications are signed as last authors by the team members (including the team leader) and the large majority are in collaboration. It appeared that a major part of the activity of the team was devoted to platform activities in the field of ND research.

Assessment of the unit's academic reputation and appeal

The team leader has numerous national and international academic collaborations, and also industrial collaborations (3). The team members are very active in European networks (8 EU grant applications). The team leader is the coordinator of NeurATRIS that gathers five nodes (MIRCen, ICM/IHU Salpétrière, Henri Mondor Hospital, Kermlin Bicêtre and B.I.R.D.) and is the French part of the large European translational consortium EATRIS. Thus, the team appears to have a large international and national visibility being at the centre of several major projects and scientific programs. This is in contrast with the apparent fact that, during the 5 past years, the team leader participated to only two international conferences (one of them as a chair), which is surprising when considering his unique expertise and reputation in the field of gene therapy for ND in non-human primates and brain imaging.

Assessment of the unit's interaction with the social, economic and cultural environment

The team's interaction with the social economic and cultural environment is outstanding, with translational activities built upon strong collaboration with clinical investigation, pharmaceutical companies and international networks. A collaboration in continuity with the initial experiments performed in non-human primates, a phase 1/II trial of ProSavin®, a dopamine replacement gene therapy strategy for the treatment of PD in Europe has been published very recently in The Lancet journal and has received a wide media coverage. Translational activities also concern new cell and gene therapy approaches in HD (cell grafts and lentiviral CNTF transfert).

Three patents have been recently licenced by the team, with eight industrial collaborations (Ipsen; Servier; Oxford Biomedica ; Hoffman-LaRoche; Braingene), and long lasting collaborations with Big pharmas (Sanofi, Servier).

The team leader has exceptional public engagement activities by participating in scientific committees (ANR, Scientific board of Dim biotherapy and Dim neurosciences, ITMO Neurosciences, ENP, JPND, PI of NeurATRIS; Arc, etc). He is also member of the strategic management of MEDICEN PARIS REGION (responsible for the imaging area). The team leader and several team members are strongly involved, as heads for example, in MIRcen's platforms.

The team members participate actively to lay ("grand public") manifestations, including writing articles for lay audience or participating to press conferences.

Assessment of the unit's organisation and life

Excellent involvement in MIRCen's platforms.

Team 2 members are involved in regular team meetings as well as cross-cutting steering committees

Assessment of the unit's involvement in training through research

The team is not very much actively involved in training through research as only few PhD thesis were recently defended and few PhD students are currently present within this team. A post-doc fellow from the team was recruited as the head of the rodent behavioural platform in MIRCen. Another post-doc was recruited in 2013 as a Research Scientist at Servier. (Only 1 PhD student completed his PhD).

Assessment of the strategy and the five-year plan

For the coming period, the main activities of team 2 will focus on animal modelling, PET imaging and experimental therapeutics, following a continuum of translational research ultimately aiming at clinical phase I/II trials.

Three main topics will be pursued:

1) translational research in HD, owing to the transfer of AAV5 gene overexpressing the N-terminal part of the mutant Htt in the caudate putamen of non-human primates. Characterization of this new animal model will be performed at different time points with a study of relationships between striatal territories injected and the behavioural impairments. The PET imaging will be used to study the progression rate of striatal neuronal loss, presynaptic loss of function and the neuroinflammation/astrocytic reaction;

2) translational research in AD: development of the rat and primate models of Tauopathy. The preliminary results have allowed to assess the biodistribution and neuronal specificity of AAV9) CBA construct overexpressing the wild type or tau gene in the hippocampus and projection areas, like the cingulate cortex. Imaging and behavioural analysis will be performed in a large cohort of primates. Proteomic analysis will be performed in collaboration with Lille in order to measure peripheral biomarkers of the progression of tauopathy, with the final goal to follow up patients for the evaluation of new therapies and specificity of existing and novel PET tracers to be used in the clinic to follow disease progression;

3) New PET tracers for ND: owing to financial support obtained through NeurATRIS initiative, implementation of a cyclotron and laboratories for the production and radiochemical labelling of compounds with carbon 11 and Fluorine 18. These tools will allow PET imaging of the parkinsonian state, proteopathies (synucleopathies, tauopathies and AD).

These ambitious projects clearly represent translational activities in which the team has a recognized expertise. However, a lack of in depth study of mechanistics is to be noted. Nevertheless, the projects present significant interest, for optimizing gene therapy, imaging, identifying biomarkers in ND.

In HD, some innovative projects were presented with the grafting of iPS cells in the HD primate model for example. However, there was little information about the advancement of the projects (are the iPS cells really differentiated into striatal neurons apart from DARPP32 expression?).

The transplicing therapeutic strategy is proposed in order to selectively silence the mutated Htt. In this project, gene reprogramming at mRNA level is proposed using a strategy based on spliceosome-mediated RNA transplicing (SmaRT). Although challenging, and requiring innovative cellular models, this project is highly innovative and promising. It clearly demands for driving forces, for example PhD or post-doc, in addition to the researcher in charge.

Preclinical innovative therapeutic strategies in PD with an adjustment of the gene transfer approach to individual's needs, and the use of "regulatable" constructs are not convincing as previous published studies in rodent and especially in non-human primates proved that the method was not efficient and without benefit.

 Weaknesses and threats:

Too many projects, some of them (the more fundamental ones) merit a more in-depth attention, and/or forces (students, Post-docs).

 Recommendations:

Prioritisation of projects to avoid becoming solely a technical platform.

Several young researchers/engineers were recently recruited with a CEA position within this team. They have the potential to become in time quite independent and perhaps leading some of the projects that were presented. These researchers should be encouraged to supervise PhD students, seek for independent fundings specifically aimed at young researchers early in their career, and become, when ready, project leaders within this team. The "Multimodal Imaging of Neurodegenerative Diseases" team led by Mr Marc DHENAIN has recently been founded as part of the re-organization of the URA 2210 unit. In the previous 5 years, Mr Marc DHENAIN and his current team members were part of the "Preclinical Brain Imaging" team led by Mr Vincent LEBON. Overall, the "Multimodal Imaging of Neurodegenerative Diseases" team is smaller than the original "Preclinical Brain Imaging" team, as several team members and their research projects have now been incorporated into a different team (Cell-Cell interaction in neurodegeneration).

Over the last 5 years, the members of the newly-constituted Multimodal Imaging of Neurodegenerative Diseases team have successfully implemented MR microscopic imaging methods to detect and monitor progression of amyloid plaques in several animal models of AD. They have also put a significant effort into the development of post mortem imaging in primates and rodents and brain imaging protocols to co-register MRI and PET images with 3D post mortem data. Finally, using in vivo and post mortem imaging techniques, the group has contributed to identify several biomarkers of aging in the mouse lemur primate and to assess the effect of anti-amyloid therapies and other therapies in preclinical models of AD. This research effort resulted in an excellent number of methodological and preclinical publications in peerreviewed journals with a very good impact factor including PNAS, Plos One, Neuroimage, Neurobiology of Aging, Journal of Neuroscience, etc (41 papers, Average Citations per Item: 5.61, h-index: 10).

Compared to the other teams, the group has not published any very high impact paper. However, the committee acknowledges that the nature of their work, although crucial for preclinical research, is too specialist and technical to target journals with very high impact factor.

Assessment of the unit's academic reputation and appeal

The development of post mortem imaging and imaging protocols to co-register in vivo and post mortem imaging findings has given to the team an incontestably international recognition. Results of their studies have been presented at several international Conferences/Congresses. Mr Marc DHENAIN has been invited to give lectures at several national and international conferences.

There are very strong industrial collaborations with several pharma companies and the team has already attracted a considerable level of both pharma and public funding in several areas of their proposed programme of work.

Assessment of the unit's interaction with the social, economic and cultural environment

Similarly to the other two teams, the main research focus of the "Multimodal Imaging of Neurodegenerative Diseases" team is on Neurodegenerative diseases. These chronic and progressive conditions represent one of the leading medical and societal challenges faced by our society.

The team has many internal and external collaborations including the Institut Pasteur, the ICM (Institut du Cerveau et de la Moelle épinière) and the Hoffmann-LaRoche laboratories. As mentioned before there is a strong connection with industry.

Mr Marc DHENAIN has given many general presentations on ongoing research and therapies of Alzheimer's disease.

Assessment of the unit's organisation and life

The team seems to be perfectly integrated into the URA 2210 unit. There is a clear synergistic collaboration between the three teams. There are regular team, project and platform meetings which will ensure integration across teams and increase strength of approach. Team 3 is an essential component of the unit as a whole in establishing links between the preclinical and clinical efforts, particularly with respect to image analysis and development of imaging biomarkers.

Assessment of the unit's involvement in training through research

The original "Preclinical Brain Imaging" team had a significant role in academic research and student training. The newly-constituted Multimodal Imaging of Neurodegenerative Disease trained 6 PhD students (5 defended), 12 masters, and 4 engineers/post-doctoral fellows. This represents ~40 % of the total number of supervised students in the lab. We notice that Mr Marc DHENAIN is involved in the coordination of Paris area Doctorate Schools (ED n°419, ED n°158, ED n°425) and University Diploma (since 2013), Kremlin-Bicêtre, "Translational Research in Neurological disorders". He also serves in thesis and HDR committees.

Assessment of the strategy and the five-year plan

Over the next five years the team intend to continue and extend their previous work on methodological developments in brain imaging at the preclinical level. Studies in AD patients will also be started.

The main focus will be on the cross correlation between different imaging modalities and the development of appropriate imaging biomarkers of neurodegeneration. This structure will provide greater interaction between the preclinical and clinical elements of the unit and pull together the imaging strategy across the whole.

The proposed work on amyloid plaque imaging is well-funded, and although there are few specific details of the methods to be used, or hypotheses to be tested the level of current funding indicates that this aspect of the proposal is competitive and novel.

Another important aspect of their work will be the co-registration and correlation of in vivo imaging findings with post mortem histology. This is a very novel and intriguing field. It should be noticed that other groups are also working in this area. Nevertheless, application to the neurodegenerative diseases in question is novel and important.

The section on animal models and therapies seems a little fragmented and the overall goals or direction less clear. Nevertheless, there are some interesting and novel concepts. In particular, the role of mast cells in AD pathology is a new and interesting avenue, as is identifying the mechanisms by which immunotherapy reduces amyloid load -both questions could lead to more or improved therapies in this area.

Conclusion

Overall, the opinion on this team is very positive. Development of multimodal Imaging protocols and identification of sensitive imaging biomarkers of the neurodegenerative process are crucial steps for both preclinical and clinical research in this field. The research proposed by the team could lead to significant advancements in brain imaging techniques, which will also benefit the other two teams and attract pharma/industrial patterns.

 Strengths and opportunities:

-strong and long-standing collaboration with scientists of the other teams; -unique expertise in 3D analysis of tissue sections; -strong training record; -strong clinical element. This will allow translation of other programmes into clinic; -great potential for developing and validating imaging techniques with clinical and industrial applications.

 Weaknesses and threats:

The team is relatively small, particularly considering that the proposed programme is complex and covers different aspects including methodological developments, preclinical and clinical research. The team also intend to extend their focus to the degenerative process in Huntington's disease and Parkinson's disease. There is a plan to recruit a young researcher on a permanent position.

Coherence of overall goals is unclear.

 Recommendations:

The proposed programme would very much benefit from the recruitment of 1 or 2 additional researchers.

Neurodegenerative Diseases Lab URA CEA-CNRS 2210 Life Science Division Molecular Imaging Research Center

C o m m i s s a r i a t à l ' é n e r g i e a t o m i q u e e t a u x é n e r g i e s a l t e r n a t i v e s URA CEA-CNRS 2210 18 Route du Panorama -BP 6 92265 Fontenay aux Roses Cedex Tél : (33) 01.46.54.83.72 / 96 22 Fax : (33) The director of the research Unit, on behalf of all the researchers of the Unit, is grateful to the AERES committee and his chairman for his in depth and detailed analysis of our research activities and projects and his very positive comments.

The committee acknowledged the excellence of the Unit's productivity in terms of publications, patents, and services at the preclinical and clinical levels. The committee also noted our strong interaction with the environment through national and international collaborations and partnerships, especially with pharmaceutical industries. The key role played by the researchers of the Neurodegenerative Diseases Laboratory in teaching and supervising young scientists has been also underlined. The committee also emphasized that the state-of-the-art equipment whose the Unit is in charge in the different platforms of MIRCen is a key strength in our project.

The committee pointed out that the wide diversity of research projects of our three teams may be overstretching considering the workforce in presence. This reflects the ambition of our research program and the high enthusiasm and motivation of our researchers. The director of the Unit and the team leaders will make their utmost efforts, with the help of our institutions, to secure the feasibility of the envisioned projects through different actions, including the recruitment of young researchers.

Emmanuel Brouillet, PhD Head, Neurodegenerative Diseases Laboratory, Molecular Imaging Research Center (MIRCen) Institute for BioMedical Imaging (I 2 BM) Life Science Division, CEA

N3:N4:

  Permanent professors and similar positions N2: Permanent EPST or EPIC researchers and similar positions 5 5 Other permanent staff (without research duties) 1 1 Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers (DREM, Postdoctoral students, visitors

  spent at least 12 months in the unit 3 Number of Research Supervisor Qualifications (HDR) taken Qualified research supervisors (with an HDR) or similar positions 2 3

Conclusion

  Strengths and opportunities:-development of non-human primate models; -original gene therapy approaches; -new tools for PET imaging; -strong environment; -unique expertise for brain imaging in primates; -strong potential for translational activities; -significant national and european visibility.

  Other professors (PREM, ECC, etc.) N5: Other EPST or EPIC researchers (DREM, Postdoctoral students, visitors, etc.

Fontenay

  -aux-roses, le 3 mars 2014 Objet : Rapport AERES E2015-EV-0912281K-S2PUR150007648-006570-RT, Neurodegenerative Disease Laboratory -Answer from the Director Dear Colleagues,

Unit workforce Number as at 30/06/2013 Number as at 01/01/2015

	N1: Permanent professors and similar positions	1	1
	N2: Permanent researchers from Institutions and similar positions	12	12
	N3: Other permanent staff (without research duties)	16	17
	N4: Other professors (Emeritus Professor, on-contract Professor, etc.)	1	1
	N5: Other researchers from Institutions (Emeritus Research Director, Postdoctoral students, visitors, etc.)	5	4
	N6: Other contractual staff (without research duties)	6	4
	TOTAL N1 to N6	41	39

Unit workforce Number as at 30/06/2013 Number as at 01/01/2015

	Doctoral students	7
	Theses defended	12
	Postdoctoral students having spent at least 12 months in the unit*	11
	Number of Research Supervisor Qualifications (HDR) taken	1
	Qualified research supervisors (with an HDR) or similar positions	5	7

  01.46.54.91.16 Etablissement public à caractère industriel et commercial R.C.S. PARIS B 775 685 019

 Supervising bodies general comments


Dr Sylvie Bouttier
email: sylvie.bouttier@u-psud.fr

Dr Thomas Candela
email: thomas.candela@u-psud.fr

Dr Cécile

Dr Jean-Christophe Marvaud
email: jean-christophe.marvaud@u-psud.fr

Dr Séverine Péchiné
email: severine.pechine@u-psud.fr

1 Introduction History and geographical location of the unit

The unit is located in the Chatenay-Malabry Pharmacy campus, Faculty of Pharmacy, University Paris-Sud. The EA 4043 exists since 1993 with various projects on the study of the microbial digestive ecosystem, and with INRA contract (MICALIS unit).

Management team

Ms Anne COLLIGNON (PU PH), was the head of the unit "Ecosystème microbien digestif et Santé" since 2001 and is responsible for the first axis of research "Clostridium difficile and its interactions with the host and the microbial digestive ecosystem" and will retire during the next contract. Ms Claire JANOIR, who is a member of the team since 1999, is applying as the next Director for the new contract (2015-2019) and will take the lead of the first axis of research. A PI (PU PH) will be responsible for the second axis of research "Antibiotic resistance in staphylococci". 2  Overall assessment of the interdisciplinary unit

The team is a nationally and internationally well recognized research group in the study of Clostridium difficile infection and in the antibiotic resistance in clostridia. The research projects concern a medically important field, since C. difficile is the most frequent cause of nosocomial diarrhea worldwide and was responsible for recent severe outbreaks. The team is in particular well known for the investigation of C. difficile surface components and intestinal colonization by this pathogen based on gnotoxenic animal models and analysis of microbiota. The team has multiple national and international collaborations, and it is competitive and attractive for recruiting professors, assistantprofessors and PhD students as well as for obtaining financial funding.

 Strengths and opportunities related to the context

-the team has a long standing and unique expertise in the study of the interactions of C. difficile with microbial digestive eco-system, including the use of gnotobiotic animals.

-the team has a long experience and competence in the investigation of C. difficile surface components and characterization of transposons and antimicrobial resistance in Clostridia.

-in its current organization, this is a multidisciplinary team with 6 HDR (4 HDR + 2 équivalents, Doctorats d'État en Sciences Pharmaceutiques) and 3 additional supervisors (bacteriologists, microbiological clinicians, molecular and cellular biologists, biochemists) with a strong expertise in gnotobiotic animal models.

-the rapidly evolving knowledge based on the intestinal flora, in particular due to advances in DNA sequencing techniques, should provide interesting opportunities for collaboration in the near future, in particular in the framework of existing collaborations with INRA.

-the attractiveness of the team for hiring and promoting assistant professors and professors is effective since, during the last 5 year contract, 1 professor (PU-PH) 1 assistant professor (MCU) and 2 assistant hospitalo-universitaires (AHU) were recruited.

-the team has collaborations with multiple national and international partners, notably the Center for Molecular Microbiology, (Imperial College London, UK), the Institute of Infection, Immunity, and Inflammation (University of Nottingham, UK), the Instituto of Technologia Quimica e Biologica (Universida de Nova de Lisboa, Portugal), the Veterinary Science and Microbiology team, (University of Arizona, USA); the INRA group under contract (Unit MICALIS), the Laboratory "Pathogénèse des bactéries anaérobies", (Institut Pasteur, Paris), the team "Ecosystème intestinal, probiotiques, antibiotiques" (Université Paris Descartes, Paris) and also with local teams, technical platforms, Institut Galien (UMR CNRS 8612) for the development of the mucosal vaccination against C. difficile infections and with EA401 "Matériaux et Santé" for chemical analysis of polysaccharides.

-a significant number (10 in total) of PhD students have been or are currently formed.

-the team has easy access to facilities and technical resources, such as the axenic animal care facilities of EA 4043 and the "Institut Fédératif de Recherche -Institut Paris-Sud Innovation Thérapeutique" ("IFR-IPSIT"), technical platforms at the Faculty, the L2 laboratory of the INSERM unit UMR-S 984, close to their unit, for the cellular microbiology studies.

the team has been quite successful for fund raising fropm various sources such as Ministry funds, 2 grants from ANR, one European grant (FP7 HEALTH-2007-B-223585 HYPERDIF, 2008-2010) and 5 industrial projects.

 Weaknesses and threats related to the context all members of the team have important teaching and hospital duties, including the future team leader for the next contract.

-the committee found that there is a relatively large number of research axes in a very competitive area, in particular for the S. aureus project.

-the field of C. difficile is highly competitive at international level.

-there are no post-doctoral fellows and a limited number of projects financed by external funds can be used for postdoctoral fellows.

moving to "Plateau de Saclay" in the framework of the UPSay operation, scheduled for 2017-2018, constitutes an opportunity but also a threat particularly regarding the distance to hospitals that may result in great disturbances in the research activities.

 Recommendations

-the leader and the senior scientists should carefully identify the research projects that will allow the team to be competitive and to improve the impact of their publications.

-the team should concentrate the efforts to participate in EU-funded consortiums (Horizon 2020, Marie Curie etc,.), and in Joint ventures with pharmaceutical companies. Many current activities both on S. aureus and C. difficile focus on mechanisms of resistance to antibiotics or mucosal vaccine development. Thus, the topics should be very attractive for raising external funds recruiting post doctoral fellows.

 Detailed assessments Assessment of scientific quality and outputs

The level of publications was found to be very good. 29 publications are directly related to the research projects of the team during the previous 5 year contract and mostly with IF ranking between 3 and 5 that correspond to the best journals of the C. difficile discipline and 3 with IF comprised between 5 and 10. Among the 29 publications, 23 have scientists of the team act as main authors (first and/or last position).The publications cover the two axes of research of the team including C. difficile colonization and C. difficile surface components, as well as antibiotic resistance in Clostridia. Two publications are breakthroughs in the knowledge of C. difficile and intestinal ecology, and microbiota investigation in newborns in relation with the risk of colonization by C. difficile. In addition, the team has participated to 51 publications in collaboration with other teams and to 9 book chapters.

Assessment of the unit's academic reputation and appeal

The academic reputation of the team is considered excellent based on its international notoriety. Indeed, the team is an internationally recognized leadership on specific topics like C. difficile surface components, microbial ecology of the gastrointestinal tract and risk factors of C. difficile colonization as illustrated by 11 invited conferences in the domain and 39 oral or poster presentations in national and international meetings.

The team is attractive for Master and PhD students (14 Master 2 and 10 PhD students during the 2009-2013 period including 4 foreigner students). However, no post-doctoral fellow has been recruited during the period. One student received a thesis award 2009. The team has excellent and fruitful collaborations at national and international levels. The team succeeded in obtaining two ANR grants, one as coordinator and one as partner, as well as an EU FP7 project as partner, and 4 industrial grants including 4 as coordinator. Members of the team participated to scientific committees of 3 international meetings and have organized 3 national meetings. Members of the team have been invited to give conferences in national, European, and international meetings (22 in total). It is noteworthy that the team provided its expertise in C. difficile animal models to several national and international teams.

Assessment of the unit's interaction with the social, economic and cultural environment

The team obtained 3 academic and 4 industrial grants including participation to clinical research projects (Noninterventional biomedical research ICD-MATER (2011-2012), Clinical multicentric research project SERODIFF (2013)(2014)(2015), Biomedical multicentric research project PORTADIFF (2013)(2014), Clinical multicentric research project Microbs (2012Microbs ( -2013)), 1 international epidemiological group (EUCLID, European study group Clostridium difficile of European Society of Clinical Microbiology and Infectious Diseases). The team participated to clinical networks (members of the team participate to the national antibiotic resistance committee, a member of the team presides a clinical research group "Groupe de Microbiologie Clinique", and another member is part of the "Conseil d'administration de l'association OutcomeRea reseau microbiologique associé" and member of the "College de Bactériologie Virologie des Hopitaux Généraux"). However, no patent has been submitted.

Assesment of the unit's organisation and life

The organization of the team is well structured. Each project is driven by a researcher in charge and participants including PhD students and collaborators are well identified. The Assistant Professors share different responsibilities such as the laboratory meeting organization and website management (http://www.emds.u-psud.fr/), Animal care facilities (authorization, N°A9201991), Hygiene and security.

The team is dynamic with an excellent communication between all the members. The quality and friendly communication with the supervisors were appreciated by all students. Weekly laboratory meetings and regular scientific meetings with other teams from the University reinforce the interactions between all the members of the team and with other scientists in the campus. A weekly laboratory meeting concerning technical difficulties, planned experiments and bibliography is organized. A monthly meeting is organized regarding strategy for research and publication. The PhD and Master students as well as Assistant Professors present their work and participate actively to the general discussion. A monthly meeting of the IPSIT (Institut Paris-Sud Innovation Thérapeutique) is scheduled with external invited speakers that allow to broaden the formation of young researchers through a multidisciplinary approach (a team member is part of the organization board of the IPSIT scientific meetings).

Additionally,participation, according to the subject, to the MICALIS scientific meetings is effective at the INRA in Jouy en Josas. Permanent staff, PhD and Master students actively participate to national and international scientific meetings to present their work and discuss with other colleagues. There is a permanent formation policy including continuous training of technical staff and researchers. The management is well organized with responsibility shared between all the professors and assistant professors.

Assessment of the unit's involvement in training through research

Numerous PhD and Master students have been supervised by the team (7 PhD during the last period, 3 in progress, 14 Master 2 students). Two former PhD students are currently in post-doctoral fellow training at Pasteur Institute (Paris) and University of Sherbrooke (Canada). Two other former PhD students have been recruited as Assistant Professors (in the team unit after a 3 year-post-doctoral training and at the "Université Paris Descartes"). One former PhD student has been recruited as microbiologist in the industry. Three PhD students are currently working in the unit. Furthermore, 2 AHU will be recruited in November 2013, and will be registered as PhD student. Members of the team are involved in the management of Master "Médicaments et autres produits de santé". The team leader is responsible for the Microbiology pole including Master 1 and Master 2. Additionally, team members are deeply involved in Master 1 or Master 2 trainings as exemplified by the facts that: a) at the M1 level, the team leader is responsible for the Master1 module "Interactions hôtes-microorganismes" UE95B, b) a team leader is responsible for the module "Exploitation des genomes pour le diagnostic et le traitement des maladies infectieuses" EU95C, c) a team professor is responsible for the Master 1 module "Microbiologie Générale" ,d) at the M2 level, the team leader is responsible for the course UE1 (UE, Unité d'enseignement) "Mécanismes cellulaires et moléculaires de la pathogénie de microorganismes", e) a team professor is responsible for the course UE2 "Antiinfectieux, mécanismes d'action et résistance des microorganismes".

The team belongs to the doctoral school "Innovation thérapeutique: du fondamental à l'appliqué" ED425, and the team leader is responsible for the Microbiology pole and for the corresponding PhD students. A team professor is responsible for the international relation and student exchange in the framework Erasmus project. 3 team members are in progress for HDR. It is noteworthy that supervision of PhD and Master students is well equilibrated between all the professors and assistant professors of the team. The research projects of the team, C. difficile infection and development of vaccine as well as antibio-resistance, are in the scope of the Doctoral School facilitating the recruitment of PhD students by the team.

Assessment of the strategy and the five-year plan

The EA 4043 unit will undergo major restructuration, during the next five-year contract. The team will have a new leader. In addition, this new team will join UPSay and since the INRA group from Jouy en Josas will also become a member of UPSay, it has been decided that the contract with INRA would not be renewed. Nonetheless, the collaborations with the INRA Partners belonging to the TGU MICALIS will continue. The five year plan is based on two distinct axes of research: (i) C. difficile pathogenesis including 4 sub-axes (immune response to surface proteins, characterization of surface proteins involved in colonization, mucosal vaccine strategy, and biofilm formation), and (ii) antibiotic resistance in Staphylococcus aureus and other Gram-positive bacteria.

The first axis "C. difficile and its interaction with the host" is mostly a continuation of previous research activities and will be coordinated by the new team leader. The first specific objective is to decipher the role of several surface components of C. difficile vegetative cells and spores in colonization. These components include "Clostridial wall proteins", peptidoglycan, "Moonlighting" proteins, and spore proteins. The second specific objective is to characterize the innate and immune response to these bacterial surface components. This will involve use of cellular and animal models as well as analysis of human samples. The third objective is to develop a mucosal vaccine strategy based on identification of protective antigen combinations in animal models. They also propose to develop vectorization strategies and passive immunization. The fourth objective is to evaluate the role of biofilm in bacterialhost interactions based on in vitro and animal studies. Together, these objectives form an ambitious and coherent research project. Drawbacks include the very large number of surface structures and questions that will be addressed by members of the team. It seems that the project is excellent in identifying relevant research areas to further elucidate understanding of the basis for C. difficile colonization and infection. However, several aspects do not appear to be based on hypotheses and the number of objectives appears rather important with respect to the number of manpower that will be devoted to each of these objectives.

The second axis will concern the mechanism of resistance to antibiotics acting on translation in staphylococci. This axis will be coordinated by a professor, who has been recently recruited by the team. A first specific objective is to analyze the genetic environment of cfr gene in clinical isolates. This gene encodes a ribosomal RNA methyltransferase conferring resistance to linezolid, streptogramins A, lincomycin and pleuromutilin antibiotics. Transfer of cfr gene to various bacterial species will be tested in vitro and in gnotobiotic mice. A second objective concerns the characterization of a new mechanism of resistance to mupirocin, a leucyl-tRNA synthetase inhibitor, which has been identified by the investigator in coagulase negative staphylococci. This will be based on whole genome sequencing but the rationale for using this technique has not been provided. As a third objective, it is mentioned that analyses will be performed to establish correlations between virulence factors and colonization fitness in S. aureus. These specific objectives are interesting but the long term strategy and the relationships with the first research axis are not sufficiently described.

The two axes of research will benefit from the animal models developed in the previous contract. All the axes and sub-axes of research are pertinent and promising at the fundamental level with perspectives of translation to the medical level. However, priorities should be defined among the numerous research sub-axes, in adequacy with the limited human resources of the team. It is essential to identify the most promising projects for future successes in competitive funding, attractiveness for post-doctoral fellows, and design of successful strategies for publications in higher ranked journals.

 Theme-by-theme analysis

Detailed assessments

Three different axes have been conducted during the last five year period, which involved colonization factors, analysis of interactions with intestinal microbiota and development of a vaccinal strategy. Regarding the first axis, among the main results that should be mentioned are: a) the role of Cwp84 in the pathogenic process of C. difficile, b) the fact that colonization factors are regulated by environmental conditions (hyperosmolarity, iron depletion and sub-inhibitory concentrations of antibiotics) demonstrated using in vitro transcriptomic studies, c) the obtention of surface proteins mutants in C. difficile, thanks to the development of ClosTron by the team of Nottingham (European contract FP7-HEALTH-2007-B-223585 HYPERDIFF), their study to ascertain their functions, the in vivo transcriptomic studies in their monoxenic mouse model on the 630 strain (first sequenced strain) and the epidemic hypervirulent strain 027 R20291 in collaboration with the Laboratory of Pathogenesis of anaerobic bacteria "Institut Pasteur". The second axis was focussed on the study of the intestinal microbiota of young infants according to C. difficile colonization (Press release by the American Society for Microbiology). Results show that the presence of C. difficile was associated with changes in the ecosystem's composition, especially with absence of bifidobacteria and that toxigenic strains responsible for adult infections circulate in healthy infants who represent a potential reservoir of infectious bacteria. The third axis provided evidence that mucosal immunization with surface proteins could at least partially inhibit colonization by C. difficile and protect the hamster against C. difficile infection.

Overall opinion of the theme

The theme of C. difficile colonization is of great importance since C. difficile infections are the most frequent cause of nosocomial diarrhea and colitis worldwide and are one of the main side effects of antibiotherapy. A better understanding of (i) the development of C. difficile in the intestinal tract, (ii) the role of microbiota, and (iii) the perturbation of the microbiota by antibiotics is critical to develop efficient prevention strategies of C. difficile infections and for a better adaptation to antibiotic treatment. The axes investigated by the team which are C. difficile factors involved in intestinal colonization, sequences of C. difficile colonization in the intestinal tract, influence of the microbiota are pertinent and crucial for a better knowledge of C. difficile infections. Relevant results have been obtained by the team during the previous period as illustrated by the publications, invited conferences, attractiveness for PhD students, obtention of academic and industrial grants.



Strengths and opportunities:

The team is pionner in the investigation of C. difficile surface components and has obtained original results in the analysis of the intestinal colonization by C. difficile (two publications are breakthroughs in this domain). A main part of the originality of this research axis is based on the team expertise in gnotoxenic animal models. The team has national and international collaborations sharing their expertise in animal models and has benefited from the experience of external teams in bacterial genetics. In addition, investigations in the human host in natural conditions are performed through clinical research projects. This research axis has important translational potential in the medical field regarding the development of vaccine.



Weakness and threats:

-the C. difficile axis is increasingly competitive.

-there is absence of team members involved in full time research.

no post doctoral fellow support is currently supporting the competiveness of this research axis.



Recommendations:

-the leader and the senior scientists should carefully identify the research subaxes that will allow the team to be competitive and to improve the impact of their publications.

-the team would concentrate the efforts to participate to external grants allowing the recruitment of post doctoral fellows.

-the most pertinent research axis concerns the innate and adaptive immune host responses to C. difficile, which will allow to better understand the factors involved in the colonization of the digestive tract by this pathogen. The team has already characterized cell surface components which are the most appropriate candidates to elicit the immune response, and has the experience in animal models to investigate the intestinal colonization by C. difficile. This part would be reinforced including the participation and/or collaboration of cellular biologists and immunologists.

Detailed assessments

Overall opinion of the theme Antibiotic resistance is a major problem in the control of infectious diseases. Antibiotic resistance is more prevalent in some groups of pathogens like S. aureus. Clostridia which are inhabitants of the digestive tract represent a reservoir of resistance genes. Genetic transfer of antibiotic resistance determinants is a crucial mechanism in theevolution of emergent pathogens.

Relevant results have been obtained in the axis of antibiotic resistance in clostridia and genetic analysis of transfer by conjugative transposons. The new second axis on investigation of new mechanisms of resistance, horizontal transfer of resistance, and correlation between virulence factors and colonization is promising. Of note, antibiotic resistance to two antibiotics acting on protein synthesis, linezolid and mupirocin, will be investigated in gram positive bacteria (Staphylococcus aureus).



Strengths and opportunities:

The team has the experience and competency in genetic analysis of antibiotic resistance. The gnotoxenic animal model is a valuable tool to analyze gene transfer in the intestinal tract in vivo and to investigate the virulence factors. The development of studies of axis 2 will benefit animal models developed by EA 4043. The involvement of team members in clinical activities or responsibilities is an excellent opportunity for investigation of variant clinical isolates and translation of research projects to medical application.

The work is also part of a translational approach with funding already obtained MICROBS (multicentric study). The sequencing of the genome of S. aureus strains having a specific antibiotic resistance profile will bring a new technical expertise in genomics and bioinformatics within the team.



Weaknesses and threats:

The S. aureus research field is competitive. Axis 2 shows no link with the first axis as resistance mechanisms studied will be specific to S. aureus. There is an absence of team members involved in full time research as well as no post doctoral fellow on this axis.



Recommendations:

A better definition of the specific aims of the project regarding the virulence factors of S. aureus and a better interaction between the two research axes of the team are recommended.

English version Our Response to the AERES Expert Committee Report

The entire team thanks the AERES Committee of Experts for their work and the constructive remarks outlined in their evaluation report. We very much appreciate the recognition of our expertise, our national and international recognition and our attractivity.

We are aware of some weaknesses, especially the absence of fulltime researchers and post-doctoral fellows. Consequently, one of our first objectives in the future contract will be to find funding in order to recruit one or two post-doctoral fellows. The ongoing proposals are already written in that direction.

Regarding our strategy for the future contract, we will take into account the Committee's recommendations. However, we would like to clarify some points concerning the suggestions which have been made to concentrate our forces on a few sub-axes of axis 1, and the necessity to reinforce the links between the two axes.

During the next contract, the themes of the unit will be centered on two axes concerning two key nosocomial pathogens: Clostridium difficile and Staphylococci. These fields are highly competitive, however, their medical importance can favor obtaining funding based on institutional and industrial calls. In addition, the two axes projects are linked to the skills and the expertise of the team members.

The first axis entitled, "Clostridium difficile pathogenesis: role of surface components " has been one of our unit's major project and one which has gained our unit international recognition. We will continue studying the colonization process of the digestive tract with: 1) a fundamental sub-axis regarding surface proteins and their role in colonization and biofilm formation; and 2) a translational sub-axis regarding the host immune response against these proteins (study in animal models and in human clinical trials) as well as pursue the development of the vaccinal strategy by mucosal route in animal models.

The Committee has recommended that we should concentrate our efforts on the study of the immune response and the development of vaccinal strategy, since these topics are attractive for raising industrial funding (some of our projects have already received industrial funding). We are fully aware of the possibilities of the valorisation of these studies, however, we think that it is also crucial to continue to develop more fundamental research and to characterize new surface antigens involved : 01.46.83.55.29 anne.collignon@u-psud.fr in colonization in order to improve the efficiency of our mucosal vaccine strategy by combining several vaccine antigens. Several surface components have already been identified and have been presented in our project, whereas only the more promising will be further characterized. To avoid dispersion and according to technological evolution, the thematic intestinal microbiota analysis will be stopped but occasional collaborations with INRA teams (belonging to future University Paris Saclay) will be done to answer specific questions.

The second axis entitled, "Antibiotic resistance in Staphylococci" is going to be developed by a professor with hospital functions (PU-PH) recruited during the ongoing contract. This axis is in adequation with her expertise and her hospital functions. The project, which will be developed and have priority, concerns antibiotic resistance targeting the ribosome in staphylococci. As presented during the oral presentation of our project, one of the resistance mechanisms to linezolid is shared between clostridia and staphylococci. Studies on these bacteria will be performed in parallel, thus promoting the development of technical and thematic interactions between the unit's two research axes. In addition, in vivo transfer studies will be performed in gnotobiotic animal models using the expertise of the team members.

Finally, all the members of the unit with hospital functions will participate to clinical studies concerning the two axes, C. difficile and staphylococci.

Version française Objet : Réponse au rapport du Comité d'experts de l'AERES

Toute l'équipe remercie le comité d'experts pour son évaluation de l'unité EA4043 et pour les remarques constructives formulées dans le rapport concernant le projet de recherche pour le contrat quinquennal 2015-2019. Nous apprécions la reconnaissance par le comité d'une part, des expertises de l'unité et, d'autre part, de sa notoriété nationale et internationale. Nous sommes conscients de certaines faiblesses, en particulier l'absence de chercheurs temps plein et de post-doctorants. Aussi, l'un des objectifs du prochain contrat quinquennal est de réussir à trouver des financements pour l'accueil d'au moins un à deux post-doctorants. Les projets en cours sont d'ores et déjà rédigés en ce sens. Concernant la stratégie pour le contrat à venir, nous tiendrons compte des recommandations du comité. Nous souhaitons cependant apporter quelques précisions concernant la suggestion de concentrer les forces de l'équipe sur quelques thématiques de l'axe 1, et le renforcement nécessaire des liens entre les deux axes de recherche développés dans les prochaines années. L'unité existante est organisée autour de deux axes, et cette organisation sera similaire dans le prochain quinquennal, bien que les thématiques évoluent. Les thématiques seront centrées sur deux pathogènes nosocomiaux de grande importance, Clostridium difficile et les staphylocoques. La recherche sur ces bactéries est certes très compétitive, mais leur importance médicale favorise l'obtention de financements sur projets institutionnels et industriels. D'autre part, les projets de recherche des deux axes sont fondés sur les compétences et expertises des membres de l'équipe.

Le premier Axe intitulé "Physiopathologie des infections à Clostridium difficile : rôle des composants de surface" est la suite d'un de nos axe de recherche développé dans le laboratoire depuis plusieurs années pour lequel nous sommes reconnus. Nous poursuivrons l'étude du processus de colonisation du tube digestif avec : 1) un volet fondamental sur l'étude des protéines de surface et leur rôle dans la colonisation et la formation d'un biofilm ; et 2) un volet translationnel comportant l'étude de la réponse de l'hôte vis à vis de ces protéines (étude en modèle animal et chez l'homme par des essais cliniques) et la poursuite du développement d'une stratégie vaccinale par voie muqueuse en modèle animal. Compte-tenu de la taille de l'équipe, le comité suggère de nous focaliser sur l'étude de la réponse immunitaire et le développement de la stratégie vaccinale, soulignant que ces thématiques sont favorables à l'obtention de contrats industriels (certains projets bénéficiant déjà d'un financement industriel). Nous sommes effectivement conscients de la valorisation possible à moyen terme de ces études mais il nous semble aussi important de continuer à développer en amont une recherche plus fondamentale pour caractériser de nouveaux antigènes de surface jouant un rôle dans la colonisation afin d'améliorer l'efficacité de notre stratégie vaccinale en combinant plusieurs antigènes d'intérêt. Plusieurs composants de surface ont été identifiés et présentés dans le projet de l'unité, mais le travail de caractérisation ne sera poursuivi que sur les plus intéressants d'entre eux dans la perspective de la stratégie vaccinale. Par ailleurs, pour éviter de diversifier trop nos axes de recherche, et compte-tenu des évolutions technologiques, la thématique sur l'analyse du microbiote intestinal ne sera pas reconduite. Cependant des collaborations avec des équipes INRA (qui seront membres de la future Université Paris Saclay) seront maintenues sur des projets précis et permettront, en fonction de l'évolution des travaux, de répondre à des questions ponctuelles.

Le deuxième axe intitulé "Résistance aux antibiotiques chez les Staphylocoques" va être développée par un PU-PH recruté au cours du contrat actuel. Cette thématique est en adéquation avec son expertise et ses fonctions hospitalières. Le projet de cet axe qui sera développé en priorité concerne la résistance aux antibiotiques ciblant le ribosome chez les staphylocoques. Comme exposé lors de la présentation orale du projet, un des mécanismes de résistance au linézolide est commun chez les staphylocoques et les clostridies et des études seront menées en parallèle dans les deux genres, favorisant ainsi le développement de liens techniques et thématiques entre les deux axes. Par ailleurs, l'expertise de l'équipe dans les modèles animaux gnotoxéniques sera valorisée par les études in vivo de transfert génétique.

Enfin, tous les membres hospitalo-universitaires de l'équipe seront impliqués dans les études cliniques développées sur les deux thématiques, C. difficile et les staphylocoques.

Professeur Anne COLLIGNON

Professeur Claire JANOIR

N5:

  Permanent researchers from Institutions and similar positions N3: Other permanent staff (without research duties) N4: Other professors (Emeritus Professor, on-contract Professor, etc.) 1 2 Other researchers from Institutions (Emeritus Research Director, Postdoctoral students, visitors, etc.) spent at least 12 months in the unit Number of Research Supervisor Qualifications (HDR) taken 3 Qualified research supervisors (with an HDR) or similar positions 6 4

FTE

  Antibiotic resistance gene transfer in the microbial digestive ecosystem: role of clostridial conjugative transposons Manager's name: Mr Thierry LAMBERT (until 2015) After January 2015, modification of theme n°2 : "Antibiotic resistance andvirulence for permanent EPST or EPIC researchers FTE of other permanent staff without research duties (IR, IE, PRAG, etc.) FTE for other professors (PREM, ECC, etc.) 0,25 FTE for postdoctoral students having spent at least 12 months in the unit FTE for other EPST or EPIC researchers (DREM, etc.) excluding postdoctoral students FTE for other contractual staff without research duties

  Conduct or programme of visit:9h-9h15Presentation of AERES visit philosophy and of expert committee by the AERES

Theme 1 :

 1 Clostridium difficile and its interactions with the host and the microbial digestive ecosystem

	Manager's name:	Ms Anne COLLIGNON and Ms Claire JANOIR
	Workforce
	Theme workforce in Full Time Equivalents	As at 30/06/2013	As at 01/01/2015
	FTE for permanent professors		2,5	4,25
	FTE for permanent EPST or EPIC researchers
	FTE of other permanent staff without research duties
	(IR, IE, PRAG, etc.)
	FTE for other professors (PREM, ECC, etc.)	0,5	0,25
	FTE for postdoctoral students having spent at least 12 months in the unit
	FTE for other EPST or EPIC researchers (DREM, etc.) excluding postdoctoral students
	FTE for other contractual staff without research duties
	FTE for doctoral students		2
	TOTAL		5	4,5