, Bibliography, issue.1

J. Anaya, C. Ramirez-santana, M. Alzate, N. Molano-gonzalez, and A. Rojas-villarraga, The Autoimmune Ecology, Frontiers in immunology, vol.7, pp.139-2016

E. Generali, A. Ceribelli, M. Stazi, and C. Selmi, Lessons learned from twins in autoimmune and chronic inflammatory diseases, Journal of Autoimmunity, vol.83, pp.51-612017
DOI : 10.1016/j.jaut.2017.04.005

L. Panse, R. Cizeron-clairac, G. Bismuth, J. Berrih-aknin, and S. , Microarrays Reveal Distinct Gene Signatures in the Thymus of Seropositive and Seronegative Myasthenia Gravis Patients and the Role of CC Chemokine Ligand 21 in Thymic Hyperplasia, The Journal of Immunology, vol.177, issue.11, pp.7868-79, 2006.
DOI : 10.4049/jimmunol.177.11.7868

F. Truffault, V. De-montpreville, B. Eymard, T. Sharshar, L. Panse et al., Thymic Germinal Centers and Corticosteroids in Myasthenia Gravis: an Immunopathological Study in 1035 Cases and a Critical Review Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Berrih-Aknin S. Myasthenia Gravis: paradox versus paradigm in autoimmunity Both Treg cells and Tconv cells are defective in the Myasthenia gravis thymus: roles of IL-17 and TNF-alpha, Clin Rev Allergy Immunol Nat Protoc; Journal of autoimmunity Journal of autoimmunity, vol.524652528, pp.108-2444, 2009.

N. Avidan, L. Panse, R. Berrih-aknin, S. Miller, and A. , Genetic basis of myasthenia gravis ??? A comprehensive review, Journal of Autoimmunity, vol.52, issue.9, pp.146-532014
DOI : 10.1016/j.jaut.2013.12.001

K. Ishigaki, Y. Kochi, A. Suzuki, Y. Tsuchida, H. Tsuchiya et al., Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis, Nature Genetics, vol.5, issue.7, pp.1120-1125, 2017.
DOI : 10.1038/nature12873

I. Gabrielsen, S. Amundsen, H. Helgeland, S. Flam, N. Hatinoor et al., Genetic risk variants for autoimmune diseases that influence gene expression in thymus, Human Molecular Genetics, vol.42, pp.3117-3141, 2016.
DOI : 10.1093/nar/gkr917

E. Boyle, Y. Li, and J. Pritchard, An Expanded View of Complex Traits: From Polygenic to Omnigenic, Cell, vol.169, issue.7, pp.1177-86, 2017.
DOI : 10.1016/j.cell.2017.05.038

J. Zheng, S. Ibrahim, F. Petersen, and X. Yu, Meta-analysis reveals an association of PTPN22 C1858T with autoimmune diseases, which depends on the localization of the affected tissue, Genes & Immunity, vol.22, issue.8, pp.641-52, 2012.
DOI : 10.1002/1521-4141(2002010)32:10<2737::AID-IMMU2737>3.0.CO;2-0

A. Lefvert, Y. Zhao, R. Ramanujam, S. Yu, R. Pirskanen et al., PTPN22 R620W promotes production of anti-AChR autoantibodies and IL-2 in myasthenia gravis, Journal of Neuroimmunology, vol.197, issue.2, pp.110-113, 2008.
DOI : 10.1016/j.jneuroim.2008.04.004

A. Gjorloff-wingren, M. Saxena, S. Williams, D. Hammi, and T. Mustelin, Characterization of TCR-induced receptor-proximal signaling events negatively regulated by the protein tyrosine phosphatase PEP, European Journal of Immunology, vol.272, issue.12, pp.3845-54, 1999.
DOI : 10.1074/jbc.272.22.14483

K. Hasegawa, F. Martin, G. Huang, D. Tumas, L. Diehl et al., PEST Domain-Enriched Tyrosine Phosphatase (PEP) Regulation of Effector/Memory T Cells, Science, vol.303, issue.5658, pp.685-694, 2004.
DOI : 10.1126/science.1092138

G. Burn, L. Svensson, C. Sanchez-blanco, M. Saini, and A. Cope, a good candidate susceptibility gene for autoimmune disease?, FEBS Letters, vol.303, issue.23, pp.3689-98, 2011.
DOI : 10.1126/science.1092138

L. Menard, D. Saadoun, I. Isnardi, Y. Ng, G. Meyers et al., The PTPN22 allele encoding an R620W variant interferes with the removal of developing autoreactive B cells in humans, Journal of Clinical Investigation, vol.121, issue.9, pp.3635-3679, 2011.
DOI : 10.1172/JCI45790DS1

C. Maine, K. Marquardt, J. Cheung, and S. La, PTPN22 Controls the Germinal Center by Influencing the Numbers and Activity of T Follicular Helper Cells, The Journal of Immunology, vol.192, issue.4, pp.1415-1439, 1950.
DOI : 10.4049/jimmunol.1302418

Y. Natkunam, The Biology of the Germinal Center, Hematology, vol.2007, issue.1, pp.210-215, 2007.
DOI : 10.1182/asheducation-2007.1.210

F. Aloisi and R. Pujol-borrell, Lymphoid neogenesis in chronic inflammatory diseases, Nature Reviews Immunology, vol.68, issue.3, pp.205-222, 2006.
DOI : 10.1128/IAI.68.1.100-106.2000

S. Berrih-aknin, S. Ragheb, L. Panse, R. Lisak, and R. , Ectopic germinal centers, BAFF and anti-B-cell therapy in myasthenia gravis, Autoimmunity Reviews, vol.12, issue.9, pp.885-93, 2013.
DOI : 10.1016/j.autrev.2013.03.011

M. Leite, P. Strobel, M. Jones, K. Micklem, R. Moritz et al., Fewer thymic changes in MuSK antibody-positive than in MuSK antibody-negative MG, Annals of Neurology, vol.32, issue.3, pp.444-452, 2005.
DOI : 10.1053/hupa.2001.27106

L. Panse, R. Bismuth, J. Cizeron-clairac, G. Weiss, J. Cufi et al., Thymic remodeling associated with hyperplasia in myasthenia gravis, Autoimmunity, vol.175, issue.8, pp.401-413, 2010.
DOI : 10.4049/jimmunol.175.8.5115

J. Weiss, P. Cufi, L. Panse, R. Berrih-aknin, and S. , The thymus in autoimmune Myasthenia Gravis: Paradigm for a tertiary lymphoid organ, Revue Neurologique, vol.169, issue.8-9, pp.640-649, 2013.
DOI : 10.1016/j.neurol.2013.02.005

S. Berrih-aknin, N. Ruhlmann, J. Bismuth, G. Cizeron-clairac, E. Zelman et al., CCL21 overexpressed on lymphatic vessels drives thymic hyperplasia in myasthenia, Annals of Neurology, vol.6, issue.4, pp.521-552, 2009.
DOI : 10.4049/jimmunol.173.8.4791

J. Weiss, P. Cufi, J. Bismuth, B. Eymard, E. Fadel et al., SDF- 1/CXCL12 recruits B cells and antigen-presenting cells to the thymus of autoimmune myasthenia gravis patients. Immunobiology, pp.373-81, 2013.

W. Ma, C. Chang, M. Gershwin, and Z. Lian, Development of autoantibodies precedes clinical manifestations of autoimmune diseases: A comprehensive review, Journal of Autoimmunity, vol.83, pp.95-112, 2017.
DOI : 10.1016/j.jaut.2017.07.003

N. Zuckerman, W. Howard, J. Bismuth, K. Gibson, H. Edelman et al., Ectopic GC in the thymus of myasthenia gravis patients show characteristics of normal GC, European Journal of Immunology, vol.57, issue.4, pp.1150-61, 2010.
DOI : 10.1002/0470867302.ch14

C. Leprince, S. Cohen-kaminsky, S. Berrih-aknin, B. Vernet-der-garabedian, D. Treton et al., Thymic B cells from myasthenia gravis patients are activated B cells. Phenotypic and functional analysis, Journal of immunology, vol.145, pp.2115-2137, 1990.

S. Schonbeck, F. Padberg, R. Hohlfeld, and H. Wekerle, Transplantation of thymic autoimmune microenvironment to severe combined immunodeficiency mice. A new model of myasthenia gravis., Journal of Clinical Investigation, vol.90, issue.1, pp.245-50, 1992.
DOI : 10.1172/JCI115843

A. Aissaoui, I. Klingel-schmitt, J. Couderc, D. Chateau, F. Romagne et al., Prevention of autoimmune attack by targeting specific T-cell receptors in a severe combined immunodeficiency mouse model of myasthenia gravis, Annals of Neurology, vol.23, issue.4, pp.559-67, 1999.
DOI : 10.1172/JCI118741

M. Sudres, M. Maurer, R. M. Bismuth, J. Truffault, F. Girard et al., Preconditioned mesenchymal stem cells treat myasthenia gravis in a humanized preclinical model, JCI Insight, vol.2, issue.7, pp.89665-2017
DOI : 10.1172/jci.insight.89665DS1

URL : https://hal.archives-ouvertes.fr/hal-01510169

P. Cufi, N. Dragin, N. Ruhlmann, J. Weiss, E. Fadel et al., Central role of interferon-beta in thymic events leading to myasthenia gravis, Journal of Autoimmunity, vol.52, pp.44-52, 2014.
DOI : 10.1016/j.jaut.2013.12.016

URL : https://hal.archives-ouvertes.fr/hal-01514459

J. Kim, Y. Yang, J. Moon, E. Lee, S. So et al., Serum BAFF expression in patients with myasthenia gravis, Journal of Neuroimmunology, vol.199, issue.1-2, pp.151-155, 2008.
DOI : 10.1016/j.jneuroim.2008.05.010

F. Mackay, S. Woodcock, P. Lawton, C. Ambrose, M. Baetscher et al., Mice Transgenic for Baff Develop Lymphocytic Disorders along with Autoimmune Manifestations, The Journal of Experimental Medicine, vol.51, issue.11, pp.1697-710, 1999.
DOI : 10.1038/32588

A. Davidson and . Targeting, Targeting BAFF in autoimmunity, Current Opinion in Immunology, vol.22, issue.6, pp.732-741, 2010.
DOI : 10.1016/j.coi.2010.09.010

T. Torgerson and H. Ochs, Immune dysregulation, polyendocrinopathy, enteropathy, X-linked: forkhead box protein 3 mutations and lack of regulatory T cells. The Journal of allergy and clinical immunology, pp.744-50, 2007.

S. Gertel-lapter, K. Mizrachi, S. Berrih-aknin, S. Fuchs, and M. Souroujon, Impairment of regulatory T cells in myasthenia gravis: Studies in an experimental model, Autoimmunity Reviews, vol.12, issue.9, pp.894-903, 2013.
DOI : 10.1016/j.autrev.2013.03.009

J. Buckner, Mechanisms of impaired regulation by CD4+CD25+FOXP3+ regulatory T cells in human autoimmune diseases, Nature Reviews Immunology, vol.3, issue.12, pp.849-59, 2010.
DOI : 10.4049/jimmunol.172.6.3580

E. Wehrens, G. Mijnheer, C. Duurland, M. Klein, J. Meerding et al., Functional human regulatory T cells fail to control autoimmune inflammation due to PKB/c-akt hyperactivation in effector cells, Blood, vol.118, issue.13, pp.3538-3586, 2011.
DOI : 10.1182/blood-2010-12-328187

E. Wehrens, B. Prakken, and F. Van-wijk, T cells out of control???impaired immune regulation in the inflamed joint, Nature Reviews Rheumatology, vol.10, issue.1, pp.34-42, 2013.
DOI : 10.1016/j.autrev.2011.04.015

Y. Hu, W. Tian, L. Zhang, H. Liu, G. Yin et al., Function of regulatory T-cells improved by dexamethasone in Graves' disease, European Journal of Endocrinology, vol.161, issue.1, pp.641-647, 2012.
DOI : 10.1016/S0002-9440(10)64171-5

C. Zhang, J. Shan, L. Feng, J. Lu, Z. Xiao et al., The effects of immunosuppressive drugs on CD4+CD25+ regulatory T cells: a systematic review of clinical and basic research, Journal of Evidence-Based Medicine, vol.20, issue.4, pp.117-146, 2010.
DOI : 10.1016/j.trim.2008.01.005

A. Suarez, P. Lopez, J. Gomez, and C. Gutierrez, Enrichment of CD4+ CD25high T cell population in patients with systemic lupus erythematosus treated with glucocorticoids, Annals of the Rheumatic Diseases, vol.65, issue.11, pp.1512-1519, 2006.
DOI : 10.1136/ard.2005.049924

C. Luther, E. Adamopoulou, C. Stoeckle, V. Brucklacher-waldert, D. Rosenkranz et al., Prednisolone Treatment Induces Tolerogenic Dendritic Cells and a Regulatory Milieu in Myasthenia Gravis Patients, The Journal of Immunology, vol.183, issue.2, pp.841-849, 2009.
DOI : 10.4049/jimmunol.0802046

A. Alunno, M. Manetti, S. Caterbi, L. Ibba-manneschi, O. Bistoni et al., Altered Immunoregulation in Rheumatoid Arthritis: The Role of Regulatory T Cells and Proinflammatory Th17 Cells and Therapeutic Implications, Mediators of Inflammation, vol.9, issue.8, p.751793, 2015.
DOI : 10.1038/nrrheum.2014.105

M. Maddur, S. Othy, P. Hegde, J. Vani, S. Lacroix-desmazes et al., Immunomodulation by Intravenous Immunoglobulin: Role of Regulatory T Cells, Journal of Clinical Immunology, vol.112, issue.S1, pp.4-8, 2010.
DOI : 10.4049/jimmunol.179.8.5571

D. Gur-wahnon, T. Mizrachi, S. Wald-altman, A. Higazi, A. Brenner et al., Tissue plasminogen activator involvement in experimental autoimmune myasthenia gravis: Aggravation and therapeutic potential, Journal of Autoimmunity, vol.52, 2014.
DOI : 10.1016/j.jaut.2013.12.017

M. Thiruppathi, J. Sheng, L. Li, B. Prabhakar, and M. Meriggioli, Recombinant IgG2a Fc (M045) multimers effectively suppress experimental autoimmune myasthenia gravis, Journal of Autoimmunity, vol.52, 2014.
DOI : 10.1016/j.jaut.2013.12.014

URL : http://europepmc.org/articles/pmc4518541?pdf=render

T. Delong, T. Wiles, R. Baker, B. Bradley, G. Barbour et al., Pathogenic CD4 T cells in type 1 diabetes recognize epitopes formed by peptide fusion, Science, vol.298, issue.1-2, pp.711-715, 2016.
DOI : 10.1016/j.jim.2005.01.001

A. Marshak-rothstein, Toll-like receptors in systemic autoimmune disease, Nature Reviews Immunology, vol.308, issue.11, pp.823-858, 2006.
DOI : 10.1126/science.1109893

T. Vatanen, A. Kostic, E. Hennezel, H. Siljander, E. Franzosa et al., Variation in Microbiome LPS Immunogenicity Contributes to, Autoimmunity in Humans. Cell, vol.165, pp.1551-2016

P. Cufi, N. Dragin, J. Weiss, P. Martinez-martinez, D. Baets et al., Implication of double-stranded RNA signaling in the etiology of autoimmune myasthenia gravis, Annals of Neurology, vol.29, issue.suppl, pp.281-93, 2013.
DOI : 10.1016/j.vaccine.2010.08.002

D. Zhernakova, P. Deelen, M. Vermaat, M. Van-iterson, M. Van-galen et al., Identification of context-dependent expression quantitative trait loci in whole blood, Nature Genetics, vol.14, issue.1, pp.139-184, 2017.
DOI : 10.1093/bioinformatics/btr406

G. Consortium, The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans, Science, vol.55, issue.4, pp.648-60, 2015.
DOI : 10.1016/j.biopsych.2003.10.013

C. Chang and M. Gershwin, Drugs and autoimmunity ??? A contemporary review and mechanistic approach, Journal of Autoimmunity, vol.34, issue.3, pp.266-75, 2010.
DOI : 10.1016/j.jaut.2009.11.012

X. Xiao and C. Chang, Diagnosis and classification of drug-induced autoimmunity (DIA), Journal of Autoimmunity, vol.48, issue.49, pp.48-4966, 2014.
DOI : 10.1016/j.jaut.2014.01.005

A. Wakkach, S. Poea, E. Chastre, C. Gespach, F. Lecerf et al., Establishment of a Human Thymic Myoid Cell Line, The American Journal of Pathology, vol.155, issue.4, pp.1229-1269, 1999.
DOI : 10.1016/S0002-9440(10)65225-X

A. Wakkach, T. Guyon, C. Bruand, S. Tzartos, S. Cohen-kaminsky et al., Expression of acetylcholine receptor genes in human thymic epithelial cells: implications for myasthenia gravis, Journal of immunology, vol.157, pp.3752-60, 1996.

N. Wittenbrink, A. Klein, A. Weiser, J. Schuchhardt, and M. Or-guil, Is There a Typical Germinal Center? A Large-Scale Immunohistological Study on the Cellular Composition of Germinal Centers during the Hapten-Carrier-Driven Primary Immune Response in Mice, The Journal of Immunology, vol.187, issue.12, pp.6185-96, 2011.
DOI : 10.4049/jimmunol.1101440

H. Shiono, Y. Fujii, M. Okumura, Y. Takeuchi, M. Inoue et al., Failure to down-regulate Bcl-2 protein in thymic germinal center B cells in myasthenia gravis, European Journal of Immunology, vol.184, issue.4, pp.805-814, 1997.
DOI : 10.1212/WNL.34.9.1182

J. Fullerton and D. Gilroy, Resolution of inflammation: a new therapeutic frontier, Nature Reviews Drug Discovery, vol.182, issue.8, pp.551-67, 2016.
DOI : 10.4049/jimmunol.0801739

G. Fredman and I. Tabas, Boosting Inflammation Resolution in Atherosclerosis, The American Journal of Pathology, vol.187, issue.6, pp.1211-1232, 2017.
DOI : 10.1016/j.ajpath.2017.01.018

M. Chan and A. Moore, Resolution of Inflammation in Murine Autoimmune Arthritis Is Disrupted by Cyclooxygenase-2 Inhibition and Restored by Prostaglandin E2-Mediated Lipoxin A4 Production, The Journal of Immunology, vol.184, issue.11, pp.6418-6444, 2010.
DOI : 10.4049/jimmunol.0903816

URL : http://www.jimmunol.org/content/jimmunol/184/11/6418.full.pdf

L. Norling, S. Headland, J. Dalli, H. Arnardottir, O. Haworth et al., Proresolving and cartilage-protective actions of resolvin D1 in inflammatory arthritis, JCI Insight, vol.1, issue.5, pp.85922-2016
DOI : 10.1172/jci.insight.85922DS1

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4855303

T. Lawrence and D. Gilroy, Chronic inflammation: a failure of resolution? International journal of experimental pathology, pp.85-94, 2007.

M. Zamani, S. Aslani, A. Salmaninejad, M. Javan, and N. Rezaei, PD-1/PD-L and autoimmunity: A growing relationship, Cellular Immunology, vol.310, pp.27-41, 2016.
DOI : 10.1016/j.cellimm.2016.09.009

H. Nishimura, M. Nose, H. Hiai, N. Minato, and T. Honjo, Development of Lupus-like Autoimmune Diseases by Disruption of the PD-1 Gene Encoding an ITIM Motif-Carrying Immunoreceptor, Immunity, vol.11, issue.2, pp.141-51, 1999.
DOI : 10.1016/S1074-7613(00)80089-8

H. Nishimura, T. Okazaki, Y. Tanaka, K. Nakatani, M. Hara et al., Autoimmune Dilated Cardiomyopathy in PD-1 Receptor-Deficient Mice, Science, vol.291, issue.5502
DOI : 10.1126/science.291.5502.319

, Science, vol.291, pp.319-341, 2001.

D. Makarious, K. Horwood, and J. Coward, Myasthenia gravis: An emerging toxicity of immune checkpoint inhibitors, European Journal of Cancer, vol.82, pp.128-164, 1990.
DOI : 10.1016/j.ejca.2017.05.041

A. Renton, H. Pliner, C. Provenzano, A. Evoli, R. Ricciardi et al., A Genome-Wide Association Study of Myasthenia Gravis, JAMA Neurology, vol.72, issue.4, pp.396-404, 2015.
DOI : 10.1001/jamaneurol.2014.4103

H. Ueda, J. Howson, L. Esposito, J. Heward, H. Snook et al., Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease, Nature, vol.52, issue.6939, pp.506-517, 2003.
DOI : 10.1093/nar/gnf052

D. Schubert, C. Bode, R. Kenefeck, T. Hou, J. Wing et al., Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations, Nature Medicine, vol.17, issue.12, pp.1410-1416, 2014.
DOI : 10.1038/sj.leu.2403202

N. Komatsu, K. Okamoto, S. Sawa, T. Nakashima, M. Oh-hora et al., Pathogenic conversion of Foxp3+ T cells into TH17 cells in autoimmune arthritis, Nature Medicine, vol.20, issue.1, pp.62-70, 2014.
DOI : 10.1016/S1534-5807(02)00369-6

N. Gagliani, A. Vesely, M. Iseppon, A. Brockmann, L. Xu et al., Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation, Nature, vol.31, issue.7559, pp.221-226, 2015.
DOI : 10.1093/bioinformatics/btu638