L. Bourhis, L. Guerri, L. Dusseaux, M. Martin, E. Soudais et al., Mucosal-associated invariant T cells: unconventional development and function, Trends in Immunology, vol.32, issue.5, pp.212-218, 2011.
DOI : 10.1016/j.it.2011.02.005

L. Bourhis, L. Mburu, Y. Lantz, and O. , MAIT cells, surveyors of a new class of antigen: development and functions, Current Opinion in Immunology, vol.25, issue.2, pp.174-180, 2013.
DOI : 10.1016/j.coi.2013.01.005

E. Treiner, Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1, Nature, vol.107, issue.6928, pp.164-169, 2003.
DOI : 10.1126/SCIENCE.1069639

E. Treiner, L. Duban, I. Moura, T. Hansen, S. Gilfillan et al., Mucosal-associated invariant T (MAIT) cells: an evolutionarily conserved T cell subset, Microbes and Infection, vol.7, issue.3, pp.552-559, 2005.
DOI : 10.1016/j.micinf.2004.12.013

M. Gold, Human Mucosal Associated Invariant T Cells Detect Bacterially Infected Cells, PLoS Biology, vol.177, issue.6, p.1000407, 2010.
DOI : 10.1371/journal.pbio.1000407.t003
URL : https://hal.archives-ouvertes.fr/inserm-00707307

L. Bourhis and L. , Antimicrobial activity of mucosal-associated invariant T cells, Nature Immunology, vol.201, issue.8, pp.701-708, 2010.
DOI : 10.1177/09680519060120050601
URL : https://hal.archives-ouvertes.fr/hal-00550333

P. Georgel, M. Radosavljevic, C. Macquin, and S. Bahram, The non-conventional MHC class I MR1 molecule controls infection by Klebsiella pneumoniae in mice, Molecular Immunology, vol.48, issue.5, pp.769-775, 2011.
DOI : 10.1016/j.molimm.2010.12.002

A. Meierovics, W. Yankelevich, and S. Cowley, MAIT cells are critical for optimal mucosal immune responses during in vivo pulmonary bacterial infection, Proceedings of the National Academy of Sciences, vol.2, issue.2, pp.3119-3128, 2013.
DOI : 10.3389/fmicb.2011.00026
URL : http://www.pnas.org/content/110/33/E3119.full.pdf

L. Kjer-nielsen, MR1 presents microbial vitamin B metabolites to MAIT cells, Nature, vol.8, issue.7426, pp.717-723, 2012.
DOI : 10.1038/ni1432

A. Corbett, T-cell activation by transitory neo-antigens derived from distinct microbial pathways, Nature, vol.60, issue.7500, pp.361-365, 2014.
DOI : 10.1107/S0907444904019158

D. Grimaldi, Specific MAIT cell behaviour among innate-like T lymphocytes in critically ill patients with severe infections, Intensive Care Medicine, vol.32, issue.1, pp.192-201, 2014.
DOI : 10.1097/01.CCM.0000145999.42971.4B

S. Abrahamsson, Non-myeloablative autologous haematopoietic stem cell transplantation expands regulatory cells and depletes IL-17 producing mucosal-associated invariant T cells in multiple sclerosis, Brain, vol.136, issue.9, pp.2888-2903, 2013.
DOI : 10.1093/brain/awt182

V. Annibali, CD161highCD8+T cells bear pathogenetic potential in multiple sclerosis, Brain, vol.134, issue.2, pp.542-554, 2010.
DOI : 10.1093/brain/awq354
URL : https://academic.oup.com/brain/article-pdf/134/2/542/17346767/awq354.pdf

I. Magalhaes, Mucosal-associated invariant T cell alterations in obese and type 2 diabetic patients, Journal of Clinical Investigation, vol.125, issue.4, pp.1752-1762, 2015.
DOI : 10.1172/JCI78941DS1
URL : http://www.jci.org/articles/view/78941/files/pdf

N. Serriari, Innate mucosal-associated invariant T (MAIT) cells are activated in inflammatory bowel diseases, Clinical & Experimental Immunology, vol.17, issue.Suppl. 1, pp.266-274, 2014.
DOI : 10.1002/ibd.21355
URL : http://onlinelibrary.wiley.com/doi/10.1111/cei.12277/pdf

C. Cosgrove, Early and nonreversible decrease of CD161++/MAIT cells in HIV infection, Blood, vol.121, issue.6, pp.951-961, 2013.
DOI : 10.1182/blood-2012-06-436436

E. Leeansyah, Activation, exhaustion, and persistent decline of the antimicrobial MR1-restricted MAIT-cell population in chronic HIV-1 infection, Blood, vol.121, issue.7, pp.1124-1135, 2013.
DOI : 10.1182/blood-2012-07-445429

E. Wong, Low Levels of Peripheral CD161++CD8+ Mucosal Associated Invariant T (MAIT) Cells Are Found in HIV and HIV/TB Co-Infection, PLoS ONE, vol.176, issue.12, p.83474, 2013.
DOI : 10.1371/journal.pone.0083474.t002

C. Fernandez, A. Kelleher, R. Finlayson, D. Godfrey, and S. Kent, NKT cell depletion in humans during early HIV infection, Immunology and Cell Biology, vol.92, issue.7, pp.578-590, 2014.
DOI : 10.1128/JVI.00605-08

F. Tilloy, An Invariant T Cell Receptor ?? Chain Defines a Novel TAP-independent Major Histocompatibility Complex Class Ib???restricted ??/?? T Cell Subpopulation in Mammals, The Journal of Experimental Medicine, vol.156, issue.12, pp.1907-1921, 1999.
DOI : 10.1016/S0171-2985(11)80244-5

M. Dusseaux, Human MAIT cells are xenobiotic-resistant, tissue-targeted, CD161hi IL-17-secreting T cells, Blood, vol.117, issue.4, pp.1250-1259, 2011.
DOI : 10.1182/blood-2010-08-303339
URL : http://www.bloodjournal.org/content/bloodjournal/117/4/1250.full.pdf

L. Walker, Human MAIT and CD8???? cells develop from a pool of type-17 precommitted CD8+ T cells, Blood, vol.119, issue.2, pp.422-433, 2012.
DOI : 10.1182/blood-2011-05-353789

S. Huang, MR1 antigen presentation to mucosal-associated invariant T cells was highly conserved in evolution, Proceedings of the National Academy of Sciences, vol.70, issue.3, pp.8290-8295, 2009.
DOI : 10.1002/prot.21688

E. Billerbeck, Analysis of CD161 expression on human CD8+ T cells defines a distinct functional subset with tissue-homing properties, Proceedings of the National Academy of Sciences, vol.81, issue.9, pp.3006-3011, 2010.
DOI : 10.1128/JVI.02144-06

J. Ussher, T cells, including the MAIT cell subset, are specifically activated by IL-12+IL-18 in a TCR-independent manner, European Journal of Immunology, vol.23, issue.1, pp.195-203, 2014.
DOI : 10.1093/intimm/dxr047

X. Tang, IL-7 Licenses Activation of Human Liver Intrasinusoidal Mucosal-Associated Invariant T Cells, The Journal of Immunology, vol.190, issue.7, pp.3142-3152, 2013.
DOI : 10.4049/jimmunol.1203218
URL : http://www.jimmunol.org/content/jimmunol/190/7/3142.full.pdf

S. Havenith, Analysis of stem-cell-like properties of human CD161++IL-18R??+ memory CD8+ T cells, International Immunology, vol.24, issue.10, pp.625-636, 2012.
DOI : 10.1093/intimm/dxs069

L. Bourhis and L. , MAIT Cells Detect and Efficiently Lyse Bacterially-Infected Epithelial Cells, PLoS Pathogens, vol.26, issue.10, p.1003681, 2013.
DOI : 10.1371/journal.ppat.1003681.s007

A. Kurioka, MAIT cells are licensed through granzyme exchange to kill bacterially sensitized targets, Mucosal Immunology, vol.156, issue.2, pp.429-440, 2015.
DOI : 10.1002/cyto.a.21015
URL : http://doi.org/10.1038/mi.2014.81

C. Turtle, Innate signals overcome acquired TCR signaling pathway regulation and govern the fate of human CD161hi CD8??+ semi-invariant T cells, Blood, vol.118, issue.10, pp.2752-2762, 2011.
DOI : 10.1182/blood-2011-02-334698

A. Savage, The Transcription Factor PLZF Directs the Effector Program of the NKT Cell Lineage, Immunity, vol.29, issue.3, pp.391-403, 2008.
DOI : 10.1016/j.immuni.2008.07.011

E. Martin, Stepwise Development of MAIT Cells in Mouse and Human, PLoS Biology, vol.1, issue.3, p.54, 2009.
DOI : 10.1371/journal.pbio.1000054.sd001
URL : https://hal.archives-ouvertes.fr/inserm-00707793

M. Lepore, Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCR? repertoire, Nat Commun, vol.5, p.3866, 2014.
DOI : 10.1038/ncomms4866
URL : http://www.nature.com/articles/ncomms4866.pdf

C. Turtle, H. Swanson, N. Fujii, E. Estey, and S. Riddell, A Distinct Subset of Self-Renewing Human Memory CD8+ T Cells Survives Cytotoxic Chemotherapy, Immunity, vol.31, issue.5, pp.834-844, 2009.
DOI : 10.1016/j.immuni.2009.09.015

J. Croxford, S. Miyake, Y. Huang, M. Shimamura, and T. Yamamura, Invariant V??19i T cells regulate autoimmune inflammation, Nature Immunology, vol.172, issue.9, pp.987-994, 2006.
DOI : 10.4049/jimmunol.172.5.3034

I. Kawachi, J. Maldonado, C. Strader, and S. Gilfillan, MR1-restricted V? 19i mucosal-associated invariant T cells are innate T cells in the gut lamina propria that provide a rapid and diverse cytokine jci, 2015.

M. Shimamura, Y. Huang, R. Migishima, M. Yokoyama, T. Saitoh et al., Localization of NK1.1+ invariant V??19 TCR+ cells in the liver with potential to promptly respond to TCR stimulation, Immunology Letters, vol.121, issue.1, pp.38-44, 2008.
DOI : 10.1016/j.imlet.2008.08.002

R. Reantragoon, Antigen-loaded MR1 tetramers define T cell receptor heterogeneity in mucosal-associated invariant T cells, The Journal of Experimental Medicine, vol.24, issue.11, pp.2305-2320, 2013.
DOI : 10.1007/978-1-60327-058-8_28
URL : http://jem.rupress.org/content/jem/210/11/2305.full.pdf

W. Chua, S. Truscott, C. Eickhoff, A. Blazevic, D. Hoft et al., ABSTRACT, Infection and Immunity, vol.80, issue.9, pp.3256-3267, 2012.
DOI : 10.1128/IAI.00279-12

I. Sakala, Functional Heterogeneity and Antimycobacterial Effects of Mouse Mucosal-Associated Invariant T Cells Specific for Riboflavin Metabolites, The Journal of Immunology, vol.195, issue.2, pp.587-601, 2015.
DOI : 10.4049/jimmunol.1402545

K. Terrence, C. Pavlovich, E. Matechak, and B. Fowlkes, Premature Expression of T Cell Receptor (Tcr)???? Suppresses Tcr???? Gene Rearrangement but Permits Development of ???? Lineage T Cells, The Journal of Experimental Medicine, vol.157, issue.4, pp.537-548, 2000.
DOI : 10.1002/eji.1830191030

G. Vera, Cernunnos Deficiency Reduces Thymocyte Life Span and Alters the T Cell Repertoire in Mice and Humans, Molecular and Cellular Biology, vol.33, issue.4, pp.701-711, 2013.
DOI : 10.1128/MCB.01057-12

N. Bosc and M. Lefranc, The mouse (Mus musculus) T cell receptor alpha (TRA) and delta (TRD) variable genes, Developmental & Comparative Immunology, vol.27, issue.6-7, pp.6-7465, 2003.
DOI : 10.1016/S0145-305X(03)00027-2

J. Guo, Regulation of the TCR?? repertoire by the survival window of CD4+CD8+ thymocytes, Nature Immunology, vol.3, issue.5, pp.469-476, 2002.
DOI : 10.1038/ni791

T. Keane, Mouse genomic variation and its effect on phenotypes and gene regulation, Nature, vol.5, issue.7364, pp.289-294, 2011.
DOI : 10.1371/journal.pgen.1000729
URL : http://www.nature.com/nature/journal/v477/n7364/pdf/nature10413.pdf

M. Lochner, T cells, The Journal of Experimental Medicine, vol.205, issue.6, pp.1381-1393, 2008.
DOI : 10.1084/jem.20071451
URL : https://hal.archives-ouvertes.fr/pasteur-01402753

J. Bautista, Intraclonal competition limits the fate determination of regulatory T cells in the thymus, Nature Immunology, vol.101, issue.6, pp.610-617, 2009.
DOI : 10.4049/jimmunol.175.9.5751

A. Rahimpour, Identification of phenotypically and functionally heterogeneous mouse mucosal-associated invariant T cells using MR1 tetramers, The Journal of Experimental Medicine, vol.212, issue.7, pp.1095-1108, 2015.
DOI : 10.1038/nprot.2007.315

C. Soudais, In Vitro and In Vivo Analysis of the Gram-Negative Bacteria???Derived Riboflavin Precursor Derivatives Activating Mouse MAIT Cells, The Journal of Immunology, vol.194, issue.10, pp.4641-4649, 2015.
DOI : 10.4049/jimmunol.1403224
URL : https://hal.archives-ouvertes.fr/hal-01433111

S. Huang, MR1 uses an endocytic pathway to activate mucosal-associated invariant T cells, The Journal of Experimental Medicine, vol.162, issue.5, pp.1201-1211, 2008.
DOI : 10.1016/j.cell.2005.08.018
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373850/pdf

M. Mulvey, J. Schilling, and S. Hultgren, Establishment of a Persistent Escherichia coli Reservoir during the Acute Phase of a Bladder Infection, Infection and Immunity, vol.69, issue.7, pp.4572-4579, 2001.
DOI : 10.1128/IAI.69.7.4572-4579.2001

F. Legoux, E. Debeaupuis, K. Echasserieau, D. L. Salle, H. Saulquin et al., Impact of TCR Reactivity and HLA Phenotype on Naive CD8 T Cell Frequency in Humans, The Journal of Immunology, vol.184, issue.12, pp.6731-6738, 2010.
DOI : 10.4049/jimmunol.1000295

P. Dellabona, E. Padovan, G. Casorati, M. Brockhaus, and A. Lanzavecchia, An invariant V?24

J. Fergusson, CD161 Defines a Transcriptional and Functional Phenotype across Distinct Human T Cell Lineages, Cell Reports, vol.9, issue.3, pp.1075-1088, 2014.
DOI : 10.1016/j.celrep.2014.09.045
URL : https://doi.org/10.1016/j.celrep.2014.09.045

N. Seach, Double Positive Thymocytes Select Mucosal-Associated Invariant T Cells, The Journal of Immunology, vol.191, issue.12, pp.6002-6009, 2013.
DOI : 10.4049/jimmunol.1301212
URL : http://www.jimmunol.org/content/jimmunol/191/12/6002.full.pdf

E. Leeansyah, L. Loh, D. Nixon, and J. Sandberg, Acquisition of innate-like microbial reactivity in mucosal tissues during human fetal MAIT-cell development, Nature Communications, vol.101, p.3143, 2014.
DOI : 10.1073/pnas.0305986101

C. Biot, Preexisting BCG-Specific T Cells Improve Intravesical Immunotherapy for Bladder Cancer, Science Translational Medicine, vol.147, issue.12, pp.137-72, 2012.
DOI : 10.4049/jimmunol.0803974
URL : https://hal.archives-ouvertes.fr/pasteur-01402032

T. Arstila, Identical T Cell Clones Are Located within the Mouse Gut Epithelium and Lamina Propria and Circulate in the Thoracic Duct Lymph, The Journal of Experimental Medicine, vol.3, issue.5, pp.823-834, 2000.
DOI : 10.1084/jem.189.10.1591

T. Magoc and S. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, issue.21, pp.2957-2963, 2011.
DOI : 10.1093/bioinformatics/btr507
URL : https://academic.oup.com/bioinformatics/article-pdf/27/21/2957/576912/btr507.pdf

S. Li, IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling, Nature Communications, vol.175, p.2333, 2013.
DOI : 10.1172/JCI28277
URL : https://hal.archives-ouvertes.fr/hal-00875260

S. Huang, Evidence for MR1 Antigen Presentation to Mucosal-associated Invariant T Cells, Journal of Biological Chemistry, vol.160, issue.22, pp.21183-21193, 2005.
DOI : 10.1073/pnas.92.7.2479
URL : http://www.jbc.org/content/280/22/21183.full.pdf

C. Hung, K. Dodson, and S. Hultgren, A murine model of urinary tract infection, Nature Protocols, vol.67, issue.8, pp.1230-1243, 2009.
DOI : 10.1128/IAI.70.12.7042-7049.2002