president Didier Houssin

Evaluation report

This report is the result of the evaluation by the experts committee, the composition of which is specified below.

The assessments contained herein are the expression of an independent and collegial deliberation of the committee. The Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) is located at the INSA site in Toulouse and has existed in its current state since 2007, following the fusion of two independent laboratories dedicated to Biotechnology-Bioprocesses and Environmental Process Engineering. The LISBP is composed of 11 teams and 5 platforms. The scientific objectives are to offer a basic research input for an integrated approach to modern industrial biotechnology with wide applications in energy (biofuels), synthons, biomaterials, pharmaceuticals, food and feed as well as water resources. The platforms cover the areas Transcriptome -Biopuces (GeT); Engineering and Screening for Original Enzyme (ICEO); Métabolomics and Fluxomics (MetaToul) and the technical platform for quantitative and functional ecology. 2  Overall assessment of the interdisciplinary unit

Unit name:

Management team

Global assessment of the unit LISBP was created based on the vision of combining applied microbiology and biochemical engineering with process engineering, as to enable the integrated development of biotechnological applications. LISBP is bridging cutting edge research in synthetic biology with applications in process engineering. The philosophy is to bring engineering concepts into biology. To that end, two different laboratories were merged into one, which now houses a broad range of complementary expertise. Such a multidisciplinary organization is unique in France and has made LISBP one of the leading centers for industrial biotechnology in the country. Their activities are supported by the joint technology platform 'MetaToul', while interactions with the industry are promoted by the demonstrator project 'Toulouse White Biotechnology'.' Overall, this set-up is very attractive and forms an excellent basis for cutting-edge research. Both units together developed into one of the leading centers for science, research and application on industrial biotechnology in Europe.

However, some organizational challenges still need to be resolved with respect to the overlapping competencies and diverging sizes of the teams. This situation has been exaggerated by the recent growth of LISBP, due to its remarkable success in attracting project funding. The key challenge still is to integrate engineering projects and (synthetic) biology of various kinds in a scientific way. Nevertheless, a clear structure has been put in place to handle these issues and to ensure a smooth transition into a unified laboratory with a common research goal. In that way, LISBP should be able to position itself at the forefront of science, not only in France but also worldwide.

Strengths and opportunities in relation to the context

LISBP houses a broad range of complementary expertise in (synthetic) biology and process engineering, which is rather unique in France.

All required tools are available, also through the joint technology platform MetaToul.

The connections with industry are facilitated by the demonstrator project Toulouse White Biotechnology (TWB).

The laboratory has been very successful in attracting funding from public and private sources.

The scientific output of the different teams is excellent and is even still increasing.

Weaknesses and threats related to the context

Multidisciplinary collaborations (engineering integrated in biology) have not been fully established, which carries a risk of dispersion.

The international visibility of LISBP as a center for industrial biotechnology is rather low. Industrial biology and synthetic biology are very competitive domains at the international stage.

In some teams, technical support lacks critical mass and renewal of staff is uncertain.

The planned change in management causes uncertainty over future directions in a time of transition.

Recommendations

Organize the teams to maximize complementarity and coherence in their structure with the objective of scientific excellence.

Enable multidisciplinary collaborations by focusing on specific targets and rewarding ambitious projects.

Increase international visibility by applying for European projects and by attracting foreign scientists.

  Ms Pascale DARAN-LAPUJADE, Delft University of Technology, The Netherlands (representative of the CSS INRA) Mr Pascal DHULSTER, Polytech'Lille (representative of the CNU) Ms Francine FAYOLLE, GEPEA Nantes Mr Jean-Luc GALZI, University of Strasbourg, (representative of the CoNRS) Ms Marie-Thérèse GUIDICI-ORTICONI, Aix-Marseille University Mr Robbert KLEEREBEZEM, Delft University of Technology, The Netherlands Ms Laurence MUHR, LRPG, University of Lorraine Scientific delegate representing the HCERES: Ms Catherine SCHUSTER Representatives of the unit's supervising institutions and bodies: Ms Catherine AZZARO (representative of the Doctoral School N°468) Mr Eric JUSTES (representative of the Doctoral School N°458) Ms Emmanuelle MAGUIN, INRA Ms Isabelle MAILLET, INRA Ms Marie-Yvonne PERRIN, CNRS Mr Bertrand RAQUET, INSA 1  Introduction History and geographical location of the unit

241 (190,2) Unit workforce Number as at 30/06/2014 Number as at 01/01/2016

	Head: Mr Nicholas LINDLEY Deputy head: Mr Pascal GUIRAUD Deputy head: Mr Pierre MONSAN HCERES nomenclature SVE2_LS9 Biotechnologies, sciences environnementales, biologie synthétique, agronomie ST5 Sciences pour l'ingénieur Unit workforce Unit workforce Number as at 30/06/2014 N1: Permanent professors and similar positions 43 (19.85) N2: Permanent researchers from Institutions and similar positions 30 (28.7) N3: Other permanent staff (without research duties) 64 (54.15) N4: Other professors (Emeritus Professor, on-contract Professor, etc.) 6 (2) N5: Other researchers (Emeritus Research Director, Postdoctoral students, visitors, etc.) 89 (76.2) N6: Other contractual staff (without research duties) 6 (5.5) TOTAL N1 to N6 71 Theses defended 107 Postdoctoral students having spent at least 12 months in the unit 33 Number of Research Supervisor Qualifications (HDR) taken 9 238 (186,4) Doctoral students Qualified research supervisors (with an HDR) or similar positions 46	Number as at 01/01/2016 44 (21.35) 33 (31.7) 62 (52.15) 5 (1.5) 88 (75) 9 (8.5) 49

signed by their chairman.by the chairman of the expert committee".


Matthew L Mr

Albert

Matthew L Mr

Arturo Mr

Zychlinsky

Jonathan Mr

David Braun

Simon Mr

Fillatreau

Morgan Mr

Huse

Mr Ludger Klein

Paul Mr

Klenerman

Ms Nadine Lemaitre

This report is the result of the evaluation by the experts committee, the composition of which is specified below.

The Department composed of 14 research units and 2 associated technical platforms is headed by Mr Matthew L. ALBERT since 2009, he will also be the head of the department for the next period. With in the Department 170 scientists share interest in exploring the fundamental processes of immunity and the hope that their contributions will provide new insight into disease pathogenesis, inspire novel vaccines and support the design of unique therapeutic strategies. During the last five years the department recruited 4 new team leaders. 2  Overall assessment of the unit

Management team

Head

Global assessment of the unit

The Department of Immunology at the Institute Pasteur comprises both basic and disease focused research in immune responses. It is comprised of 14 teams of different seniority and covers a wide range of topics that include innate immunity, acquired immunity, vaccinology and infectious diseases and goes from cellular biology, physiology and clinical trials in terms of approaches. The department has a growing focus on human immunology which is in accordance with its interest in human health. The Department includes two core facilities that are available to teams in the whole Pasteur campus and even to extramural investigators. These facilities are the Cytometry and the Human Immunology Platforms. They are both an excellent resource for the investigators in the department. There are at least seven outstanding groups that are doing cutting edge research as detailed later in this document. The other teams were considered excellent. All the investigators publish consistently in top journals and are frequent guests in international meetings. Further support in the areas of animal husbandry and bioinformatics support were thought to be required to ensure the high quality of the research done in the Depatment.

Strengths and opportunities in relation to the context

The clear strength of the Department is the inclusion of outstanding scientists that are doing highly original research. The move to include human immunology and close links to the clinics is an opportunity to understand Immunology in a global way and use the information for diagnostics, treatment and vaccinology.

Weaknesses and threats related to the context

The Department will experience the retirement of two senior and internationally recognized Immunologists. Immunology, which is at the core of the interest of the Institut Pasteur requires a minimal core of scientist to maintain diversity and scientific excellence. Therefore the Department will be well served by recruiting in areas of Immunology not covered now in their portfolio, myeloid cells come to mind, to ensure their further growth.

Recommendations

Given the excellence of the deparment the committee recommends further funding and support. The committee would be happy to encourage the further competitive recruitment of principal investigators, preferably and as stated above in the areas of Immunology that are not currently covered.

The interest in human biology requires a large organization and availability of technology that the Deparment requires and needs to have a succesful future. In particular, the Department requires a dedicated unit dedicated to solve the Bioinformatic questions raised by their research. This appears to be suboptimal in the current status. Another area of improvement is the capacity to raise different mouse lines and use them experimentally.

The committee would also like to encourage, in the spirit of the origins of the Institute Pasteur to further the current efforts to understand immunity to infections and, if possible, taking advantage of the expertise in Infectiology available on campus.

  Mr Tom MACDONALD, Centre for Immunology and Infectious Disease, Blizard Institute, London, UK Mr Richard MOXON, Department of Paediatrics, University of Oxford, UK (Representative of the Pasteur Institute Scientific Council) Mr Christian MÜNZ, Institute of Experimental Immunology, University of Zurich, Switzerland Mr Tom H.M. OTTENHOFF, Leiden University Medical Center, Leiden, The Netherlands Mr Frédéric RIEUX-LAUCAT, Fondation Imagine, Institut des Maladies Génétiques, Paris Scientific delegate representing the HCERES: Ms Catherine SCHUSTER Representative(s) of the unit's supervising institutions and bodies: Ms Pascale COSSART, Institut Pasteur Ms Isabelle CREMER, (representative of the Doctoral School N°394) Mr Alain ISRAEL, Institut Pasteur Ms Catherine MONNOT (representative of the Doctoral School N°394) Mr Antonino NICOLETTI (representative of the Doctoral School N°157) Ms Stéphanie POMMIER, Inserm Ms Geneviève dE SAINT BALMAIN (representative of the Doctoral School N°157) 1  Introduction History and geographical location of the unit The Department of Immunology at Pasteur follows on the long tradition initiated by the recruitment of Mr Eli METSCHINKOFF by Louis Pasteur. The Department is located in the center of Paris and has attractive and modern labs.

78) Unit workforce Number as at 30/06/2014 Number as at 01/01/2016

  : Mr Matthew L. ALBERT

	Deputy head : Mr Philippe BOUSSO HCERES nomenclature SVE1_LS6 Immunologie, microbiologie, virologie, parasitologie SVE1_LS1 Biologie moléculaire et structurale, biochimie Unit workforce Unit workforce N1: Permanent professors and similar positions N2: Permanent researchers from Institutions and similar positions N3: Other permanent staff (without research duties) N4: Other professors (Emeritus Professor, on-contract Professor, etc.) N5: Other researchers (Emeritus Research Director, Postdoctoral students, visitors, etc.) N6: Other contractual staff (without research duties) TOTAL N1 to N6 Theses defended Postdoctoral students having spent at least 12 months in the unit Number of Research Supervisor Qualifications (HDR) taken (132.Doctoral students Number as at 30/06/2014 Number as at 01/01/2016 8 7 31 36 54 (38.78) 55 (39.78) 1 (0.25) 40 45 5 5 139 (123.03) 148 30 37 68 9 Qualified research supervisors (with an HDR) or similar positions 28 30


 Introduction History and geographical location of the unit

The research entity "Immunogénétique Moléculaire" is headed by the same unit Director since 1988. Initial research programs focused on the comparative analysis of antigens and blood group genes of humans and primates. In the late 90s, a new theme has been developed focusing on the polymorphism of the major histocompatibility complex of macaques.

The research entity was transferred in 2003 to the site of the Faculty of Medicine of Rangueil, where it is still located. A new relocation to the site of Purpan Hospital is planned for 2016.

The laboratory and the hospital laboratory are located on the same campus but they are separated geographically.

Management team

The research entity is composed of a single team of 4 teachers/researchers and 2 technicians. The research entity is managed by its director with the help of the researchers. The general policy of the laboratory is regularly discussed among researchers. Priority is always given to the areas of research funded by private or institutional contracts. Credit applications are managed collegially in response to invitations to tender. Priority is given to principal aims of the research team. For the next contract, the management will be in continuity with this strategy. 2  Overall assessment of the unit

Global assessment of the unit

The unit has developped a unique knowhow in immunogenetics of non-human primates. It is involved in a number of collaborative programs and it is supporting through these collaborations high quality research. The expertise of the unit and its recognition within the community has allowed its integration in several national and international networks. The unit renown in immunogenetics, which has been built in the field of macaque polymorphisms, leads to the development of ambitious new reseach theme on the immunogenetics of human immune system. This reseach area is of major interest for the scientific community from a basic research as well as a clinical point of view. Overall, the unit is producing innovative reseach of very good quality.

Strengths and opportunities in relation to the context

-The expertise of the research entity lies in the immunogenetics of non-human primates and it is nationally and internationally recognized for its expertise in the knowledge of major histocompatibility complex of cynomolgus macaques.

-The presence of clinical reseachers in the research entity should have a strong impact on the development of the study on the exploration of inter-individual variability on the immune response in humans. It should favor the access to clinical samples and the constitution of patient cohorts.

-The research entity is involved in translational research with contacts with the industry.

Weaknesses and threats related to the context -The research program on immunogenetics of macaques is mainly driven by the unit Director with low input of the other researchers, whereas it is highly competitive at the international level.

-The two main programs of the research entity are only loosely linked.

-The infrastructure of the research entity is physicaly seperated leading to weak interactions.

-The implication of the the three teacher/researchers in the development of the research programs is limited by the hospital responsabilities.

Recommendations

-The research laboratory and the hospital laboratory should be geographically closer in order to maintain the unit of this small size team.

-The workforce dedicated to the immunogenetics of macaques should be further strengthened with the recruitment of a PhD student and/or a postdoc fellow.

-The data collected for the study on the exploration of inter-individual variability on the immune response in humans will require integrated analysis which should not be underestimated.

-The research entity should strive to link both main programs by gradually implementing the same functional assays in macaque blood samples.

N4:N6

  Other permanent staff (without research duties) 2 2 Other professors (Emeritus Professor, on-contract Professor, etc.) N5: Other researchers (Emeritus Research Director, Postdoctoral students, visitors, etc.) 1 spent at least 12 months in the unit Number of Research Supervisor Qualifications (HDR) taken Qualified research supervisors (with an HDR) or similar positions 1 1


Evaluation report

This report is the result of the evaluation by the experts committee, the composition of which is specified below.

The assessments contained herein are the expression of an independent and collegial deliberation of the committee.

Unit name:

Pathophysiology and biotherapies of mucosal infections The unit is a major actor of UJM that federates a coherent and original research at cross-roads between mucosal immunology, inflammation and infection led by seventeen UJM professors and one EFS director of research.

Since 2010, the research of this mono-thematic unit has been organized in two major scientific projects:

 Project 1 that aims to understand the mechanisms of infection by HIV at mucosal surfaces and to develop therapeutic approaches to block mucosal transmission of HIV;

 Project 2 dedidacted to several aspects of mucosal and endothelial inflammation and comprising several basic and translational projects including studies about i) the contribution of platelets in acute and chronic inflammation due to infection or transfusion, ii) the signalling pathways involved in the differentiation of B lymphocytes of IgA isotype in response to infectious stimuli, iii) the role and pronostic value of IgA immunoglobulins in IgA nephropathy, iv) gut and respiratory tract chronic inflammation induced by bacterial pathogens.

Within the continuity of the research developed during the past five years, a restructuration of research activities is proposed for the period 2016-2020, this aims at reinforcing transversal interactions between main projects. The research program will be organized in three workpackages : 1) Study of the molecular interactions between different mucosal pathogens and mucosal surfaces; 2) Mucosal vaccination and therapeutic strategies against infections; 3) Mucosal and endothelial inflammation.

The unit is part of the federative research structure IFRESIS composed of the research units of the Faculty of Medicine, of Ecole Nationale Supérieure des Mines, of St Étienne CHU and of Loire Cancerology Institute -Lucien Neuwirth.

Management team

The current director of the GIMAP is Mr Bruno POZZETTO. The proposed director for the next period (2016-2020) is Mr Thomas BOURLET, if validated by the unit council. The unit council is composed of all the permanent members of the unit. The research unit is headed by the director assisted by an executive board composed of the full professors (PU-PH) of the unit. 2  Overall assessment of the unit

HCERES

Global assessment of the unit

The GIMAP unit is a major actor of UJM that federates a coherent and original research at cross-roads between mucosal immunology, inflammation and infection led by seventeen UJM professors and one EFS director of Research.

The research is organized in two main axes: Axis 1, headed by Mr Bruno POZZETTO, is focused on the analysis of mucosal immunity and, in particular, on the study of the interactions between HIV and the female genital mucosae. It includes both a basic science arm in which viral variants and reservoirs are analyzed and the mucosal immune response to HIV infection is dissected, as well as a preclinical arm dealing with microbicides and vaccinal approaches. Researchers within this axis have developed a number of national and international collaborations, have obtained some important results (in particular the very promising monoclonal neutralizing antibody -H7-against HIV-1 envelope), and have published several original papers in scientific journals of an overall higher than average quality during the last five years.

The second axis, directed by Mr Olivier GARRAUD, is related to basic and translational research on mucosal and endothelial inflammation and comprises different topics. They include a few interesting and original projects (e.g. molecular interaction between thrombocytes and pathogens). Several projects are clinically highly relevant (e.g. links and interactions between blood transfusion and inflammation). Researchers have obtained results of major importance particularly in transfusion medicine, and have published original papers of good scientific quality in specialized peer-reviewed journals.

Strengths and opportunities in relation to the context



Interesting and promising field of research in a highly competitive context.



Relatively few complex research units focus on mucosal immunity.



Good quality of publications (233 original publications between January 2009 and December 2014 among which 51 with an impact factor >5).



Excellent training program with 17 PhD theses defended during the last 4 years.



Strong combination of basic and translational research for both axes.



Very good level of local recruitment (students, researchers).

Weaknesses and threats related to the context  International collaborations should be extended.



Financial support stems from local or national agencies. Competition for international grants is recommended.

 International visibility could be improved.



Publications are of good, but not outstanding quality.



Research of axis 1 is limited to HIV infection. The research could be widened to include other infectious agents.



Research of axis 2 is a mix of different groups and research perspectives. Link with clinical research (clinical trials initiated at this site) could be improved. Although inter-disciplinarity and transdisciplinarity are the keys of the success of axis 2, this benefit is associated with a risk of dispersion and heterogeneity.

Recommendations

The unit coordination of the various projects is effective and coherent and provides a global efficiency in spite of the diversity of the topics covered by members of the unit. The recommendation is to continue the effort engaged to increase the coherence between projects, to recruit several full-time experienced researchers, including postdoctoral fellows, to reinforce tasking forces on main projects and to join efforts to compete for EU-funded grants and other international grants. The reorganization of the research in workpachages for the next period could be taken as an opportunity to concentrate tasking forces on most promising basic and translational projects (host-pathogen interactions at mucosal surface, mucosal vaccination and immunotherapy, platelets and inflammation) and to initiate controlled clinical trials at this site.

  Mr Mario CLERICI, Milan University, Italy Mr Stephan HARBARTH, Geneva University Hospitals, Switzerland Mr Jean-Daniel TISSOT, University of Lausanne, Switzerland Mr Philippe VAN DE PERRE, Montpellier University (representative of CNU) Scientific delegate representing the HCERES: Mr Kamel BENLAGHA Representatives of the unit's supervising institutions and bodies: Mr Christophe DESRAYAUD (director of the Doctorale School SIS n°488) Mr Youcef OUERDANE, University of Saint-Étienne Mr Pierre TIBERGHIEN, EFS 1  Introduction History and geographical location of the unit GIMAP was created in 1991 as a group of Jean Monnet University (UJM) located in the Faculty of Medicine Jacques Lisfranc of Saint Étienne (France) to develop a research on mucosal immunology related to genital infection by HIV.

Unit workforce Number as at 30/06/2014 Number as at 01/01/2016

	Unit workforce
	N1: Permanent professors and similar positions	17 [8,5]	16 [8]
	N2: Permanent researchers from Institutions and similar positions	2	2
	N3: Other permanent staff (without research duties)	9 [8,5]	9 [8,5]
	N4: Other professors (Emeritus Professor, on-contract Professor, etc.)	1	1
	N5: Other researchers (Emeritus Research Director, Postdoctoral students, visitors, etc.)	1	1
	N6: Other contractual staff
	(without research duties)
	TOTAL N1 to N6	30	29
	Unit workforce	Number as at 30/06/2014	Number as at 01/01/2016
	Doctoral students	18
	Theses defended	17
	Postdoctoral students having spent at least 12 months in the unit	2
	Number of Research Supervisor Qualifications (HDR) taken	4
	Qualified research supervisors (with an HDR) or similar positions	15	15
	nomenclature
	SVE1_LS6 Immunologie, microbiologie, virologie, parasitologie