L. Abeler-dö-rner, M. Swamy, G. Williams, A. C. Hayday, and A. Bas, , 2012.

, Butyrophilins: an emerging family of immune regulators, Trends Immunol, vol.33, pp.34-41

E. J. Adams, S. Gu, and A. M. Luoma, Human gamma delta T cells: Evolution and ligand recognition, Cell. Immunol, vol.296, pp.31-40, 2015.

H. Afrache, P. Gouret, S. Ainouche, P. Pontarotti, and D. Olive, The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response, Immunogenetics, vol.64, pp.781-794, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00831095

J. P. Allison and W. L. Havran, The immunobiology of T cells with invariant gamma delta antigen receptors, Annu. Rev. Immunol, vol.9, pp.679-705, 1991.

B. Arden, S. P. Clark, D. Kabelitz, and T. W. Mak, Human T-cell receptor variable gene segment families, Immunogenetics, vol.42, pp.455-500, 1995.

D. M. Asarnow, W. A. Kuziel, M. Bonyhadi, R. E. Tigelaar, P. W. Tucker et al., Limited diversity of gamma delta antigen receptor genes of Thy-1+ dendritic epidermal cells, Cell, vol.55, pp.837-847, 1988.

S. D. Barbee, M. J. Woodward, G. Turchinovich, J. J. Mention, J. M. Lewis et al., Skint-1 is a highly specific, unique selecting component for epidermal T cells, Proc. Natl. Acad. Sci. USA, vol.108, pp.3330-3335, 2011.

A. Bas, M. Swamy, L. Abeler-dö-rner, G. Williams, D. J. Pang et al., Butyrophilin-like 1 encodes an enterocyte protein that selectively regulates functional interactions with T lymphocytes, Proc. Natl. Acad. Sci. USA, vol.108, pp.4376-4381, 2011.

M. Bigby, J. S. Markowitz, P. A. Bleicher, M. J. Grusby, S. Simha et al., Most gamma delta T cells develop normally in the absence of MHC class II molecules, 1993.

, J. Immunol, vol.151, pp.4465-4475

L. M. Boyden, J. M. Lewis, S. D. Barbee, A. Bas, M. Girardi et al., Skint1, the prototype of a newly identified immunoglobulin superfamily gene cluster, positively selects epidermal gammadelta T cells, Nat. Genet, vol.40, pp.656-662, 2008.

M. Girardi, J. Lewis, E. Glusac, R. B. Filler, L. Geng et al., Resident skin-specific gammadelta T cells provide local, nonredundant regulation of cutaneous inflammation, J. Exp. Med, vol.195, pp.855-867, 2002.

D. Guy-grand, P. Vassalli, G. Eberl, P. Pereira, O. Burlen-defranoux et al., , 2013.

, Origin, trafficking, and intraepithelial fate of gut-tropic T cells, J. Exp. Med, vol.210, pp.1839-1854

T. Hanke, R. Mitnacht, R. Boyd, and T. Hü-nig, Induction of interleukin 2 receptor beta chain expression by self-recognition in the thymus, J. Exp, 1994.

. Med, , vol.180, pp.1629-1636

C. Harly, Y. Guillaume, S. Nedellec, C. M. Peigné, H. Mö-nkkö-nen et al., , pp.2269-2279, 2012120.

A. C. Hayday, Annu. Rev. Immunol, vol.18, pp.975-1026, 2000.

A. Hayday and R. Tigelaar, Immunoregulation in the tissues by gammadelta T cells, Nat. Rev. Immunol, vol.3, pp.233-242, 2003.

A. Hayday and P. Vantourout, A long-playing CD about the gd TCR repertoire, Immunity, vol.39, pp.994-996, 2013.

M. Hirano, P. Guo, N. Mccurley, M. Schorpp, S. Das et al., Evolutionary implications of a third lymphocyte lineage in lampreys, Nature, vol.501, pp.435-438, 2013.

K. Hochedlinger, Y. Yamada, C. Beard, J. , and R. , , 2005.

S. Itohara, A. G. Farr, J. J. Lafaille, M. Bonneville, Y. Takagaki et al., Homing of a gamma delta thymocyte subset with homogeneous T-cell receptors to mucosal epithelia, Nature, vol.343, pp.754-757, 1990.

J. Jameson, K. Ugarte, N. Chen, P. Yachi, E. Fuchs et al., A role for skin gammadelta T cells in wound repair, Science, vol.296, pp.747-749, 2002.

J. C. Janeway, P. Travers, M. Walport, and M. J. Shlomchik, Immunobiology: The Immune System in Health and Disease, 2001.

M. K. Jenkins and R. H. Schwartz, Antigen presentation by chemically modified splenocytes induces antigen-specific T cell unresponsiveness in vitro and in vivo, J. Exp. Med, vol.165, pp.302-319, 1987.

K. D. Jensen, X. Su, S. Shin, L. Li, S. Youssef et al., Thymic selection determines gammadelta T cell effector fate: antigen-naive cells make interleukin-17 and antigen-experienced cells make interferon gamma, Immunity, vol.29, pp.90-100, 2008.

M. S. Jordan, M. P. Riley, H. Boehmer, and A. J. Caton, Anergy and suppression regulate CD4(+) T cell responses to a self peptide, Eur. J. Immunol, vol.30, pp.136-144, 2000.

J. Kaufman, J. Jacob, I. Shaw, B. Walker, S. Milne et al., Gene organisation determines evolution of function in the chicken MHC, Immunol. Rev, vol.167, pp.101-117, 1999.

A. R. Kazen, A. , and E. J. , Evolution of the V, D, and J gene segdiversity, Proc. Natl. Acad. Sci. USA, vol.108, pp.332-340, 2011.

H. P. Kim and W. J. Leonard, The basis for TCR-mediated regulation of the IL-2 receptor alpha chain gene: role of widely separated regulatory elements, EMBO J, vol.21, pp.3051-3059, 2002.

H. Komano, Y. Fujiura, M. Kawaguchi, S. Matsumoto, Y. Hashimoto et al.,

, Homeostatic regulation of intestinal epithelia by intraepithelial gamma delta T cells, Proc. Natl. Acad. Sci. USA, vol.92, pp.6147-6151

W. A. Kuziel, A. Takashima, M. Bonyhadi, P. R. Bergstresser, J. P. Allison et al., Regulation of T-cell receptor gammachain RNA expression in murine Thy-1+ dendritic epidermal cells, Nature, vol.328, pp.263-266, 1987.

S. Kyes, E. Carew, S. R. Carding, C. A. Janeway, . Jr et al., , 1989.

, Diversity in T-cell receptor gamma gene usage in intestinal epithelium, Proc. Natl. Acad. Sci. USA, vol.86, pp.5527-5531

Y. G. Lai, M. S. Hou, Y. W. Hsu, C. L. Chang, Y. H. Liou et al., IL-15 does not affect IEL development in the thymus but regulates homeostasis of putative precursors and mature CD8 alpha alpha+ IELs in the intestine, J. Immunol, vol.180, pp.3757-3765, 2008.

S. B. Landau, W. I. Aziz, J. Woodcock-mitchell, and R. Melamede, V gamma (I) expression in human intestinal lymphocytes is restricted, Immunol. Invest, vol.24, pp.947-955, 1995.

C. Lebrero-ferná-ndez, J. H. Bergströ-m, T. Pelaseyed, and A. Bas-forsberg, Murine Butyrophilin-like (Btnl) 1 and Btnl6 form heteromeric complexes in small intestinal epithelial cells and promote proliferation of local T lymphocytes. Front, Immunol. Today, vol.12, pp.436-438, 1991.

L. Lefrancois and T. Goodman, In vivo modulation of cytolytic activity and Thy-1 expression in TCR-gamma delta+ intraepithelial lymphocytes, Science, vol.243, pp.1716-1718, 1989.

L. Lefrancois, R. Lecorre, J. Mayo, J. A. Bluestone, and T. Goodman, , 1990.

, Extrathymic selection of TCR gamma delta + T cells by class II major histocompatibility complex molecules, Cell, vol.63, pp.333-340

B. Li and C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, vol.12, p.323, 2011.

J. P. Lodolce, D. L. Boone, S. Chai, R. E. Swain, T. Dassopoulos et al., IL-15 receptor maintains lymphoid homeostasis by supporting lymphocyte homing and proliferation, Immunity, vol.9, pp.669-676, 1998.

M. I. Love, W. Huber, A. , and S. , Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

A. E. Moran, K. L. Holzapfel, Y. Xing, N. R. Cunningham, J. S. Maltzman et al., T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse, J. Exp. Med, vol.208, pp.1279-1289, 2011.

D. E. Oppenheim, S. J. Roberts, S. L. Clarke, R. Filler, J. M. Lewis et al., Sustained localized expression of ligand for the activating NKG2D receptor impairs natural cytotoxicity in vivo and reduces tumor immunosurveillance, Nat. Immunol, vol.6, pp.928-937, 2005.

A. Palakodeti, A. Sandstrom, L. Sundaresan, C. Harly, S. Nedellec et al., The molecular basis for modulation of human Vg9Vd2 T cell responses by CD277/butyrophilin-3 (BTN3A)-specific antibodies, J. Biol. Chem, vol.287, pp.32780-32790, 2012.

P. Pereira, J. J. Lafaille, D. Gerber, and S. Tonegawa, The T cell receptor repertoire of intestinal intraepithelial gammadelta T lymphocytes is influenced by genes linked to the major histocompatibility complex and to the T cell receptor loci, Proc. Natl. Acad. Sci. USA, vol.94, pp.5761-5766, 1997.

T. Pertel, S. Hausmann, D. Morger, S. Zuger, J. Guerra et al., TRIM5 is an innate immune sensor for the retrovirus capsid lattice, Nature, vol.472, pp.361-365, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01402086

P. Poussier, J. , and M. , Thymus independent T cell development and selection in the intestinal epithelium, Annu. Rev. Immunol, vol.12, pp.521-553, 1994.

N. J. Prescott, B. Lehne, K. Stone, J. C. Lee, K. Taylor et al., Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes, UK IBD Genetics Consortium, vol.11, p.1004955, 2015.

D. A. Rhodes, M. Stammers, G. Malcherek, S. Beck, and J. Trowsdale, The cluster of BTN genes in the extended major histocompatibility complex, Genomics, vol.71, pp.351-362, 2001.

, Animal experiments were undertaken in full compliance with UK Home Office regulations and under a

, Flow Cytometry Flow cytometry was performed using the following antibodies, coupled to the indicated fluorochromes

, Antibodies for mouse: CD3 APC Cy7 (17A2)

. Cd3-percpcy5, , vol.5, pp.145-147

, TCRb Brilliant Violet, vol.421, pp.57-597

A. Tcrb, , p.57

. Cd122-pe,

, CD122 Brilliant Violet, p.421

. Cd122-apc,

. Tigit-pe, , vol.7

, CD45RB APC Cy7, pp.363-379

, Lag3 PerCP-efluor, vol.9, issue.7, p.710

, CD24 FITC (M1/69)

F. Tcr-vd4,

P. E. Tcr-vd4,

. Ccr9-pecy7,

. Cd44-pecy7, , vol.7

, TCRVg7 (F2.67) was provided by Pablo Pereira, Institut Pasteur

A. Tcrvg4, , pp.3-10

B. Tcrd,

, Ki67 FITC (B56/ MOPC-21)

, CD45 Qdot 605, pp.30-41

, CD5 Brilliant Violet, vol.510, pp.53-60

T. Pecy7,

, CD161/NK1.1 Brilliant Violet, vol.136, p.650

, CD8a AlexaFluor, vol.700, pp.53-59

. Cd25-apc,

. Gitr-pe, DTA-1)

. Cd44-fitc, , vol.7

, CD62L PerCP-Cy5, vol.5, p.14

. Klrg1-bv421, , vol.2

B. Cd11c,

B. Cd11b,

A. Ly6g, , vol.1

, Ly6C AlexaFluor, vol.700, p.21

. Cd103-pe, , vol.290

, CD317 Brilliant Violet, vol.927, p.650

. Mhcii/ia/ie and . Fitc,

, CD86 Pe-Cy7 (GL1)

, CD3 Brilliant Violet, vol.421, pp.145-147

, CD19 Brilliant Violet, p.421

, CD161/NK1.1 (lin) Brilliant Violet, p.421

P. E. Igg1, , pp.85-86

, B220 (CD45R) AlexaFluor, vol.700, pp.3-6

, IgM Brilliant Violet, vol.786

, IgD PerCPCy5.5 (11-26c.2a)

. Cd95-pecy7,

, CD138 Brilliant Violet, vol.650, pp.281-283

, Antibodies for human: CD25 Brilliant Violet 421 (BC96), CD23 Brilliant Violet, vol.421

. Cd25-pe, , vol.96

, CD3 Brilliant Violet, p.510

, BUV (UCHT, vol.1

, EpCAM eFlour, issue.1B7, p.660

A. Streptavidin,

, Streptavidin Brilliant Violet 421; TCRgd PeCy7 (IMMU510)

P. Vg9, , vol.360

P. E. Vg9, , vol.3

A. Vd1,

, Vd2 PerCP (B6)

, Vg3/5 biotin (56.3) and Vg8 biotin (R4.5.1) were provided by

. Dykddddk-apc,

, Viability dyes (near IR or Blue) were from Invitrogen. Anti TCRVg7 (F2.67) was purified from hybridoma supernatant using the mouse TCS purification system (Abcam) and conjugated to biotin or AF647, HA-DyLight, vol.650

, Purified anti-TCRVg7 was conjugated to biotin (EZ-Link Sulfo-NHS-LC Biotinylation Kit, Thermo Fisher Scientific) or to AF647 (labeling kit, Thermo Fisher Scientific). Anti-human Vg2/3/4 (23D12, biotinylated), Vg5/3 (56.3, biotinylated) and Vg8 (R4.5.1, biotinylated) were provided by, Ki-67 staining was performed on cells fixed and permeabilised using the Foxp3 staining buffer set (eBioscience), vol.67

, RNAscope RNAscope was performed on paraffin embedded sections using probes and kits obtained from Advanced Cell Diagnostics using the RNAscope 2.0 HD Reagent Kit-BROWN. Reference sequences are as follows: Btnl1, GenBank:NM_001111094, vol.1, pp.576-1723

G. Btnl4, , pp.560-968

G. Btnl6, , pp.30747-30748

. Wencker, Isolation of Murine Intestinal Intra-epithelial Lymphocytes (IEL) IEL were isolated from mouse small intestine as previously described, p.10, 2014.

, 20/40/80% Percoll density gradient at 700 g for 30min. IEL were harvested from the 40 to 80% Percoll interface. Spleen and Mesenteric Lymph Node Immunophenotyping Comprehensive immunophenotyping of Btnl1-/-mice was performed using a platform developed by the Wellcome Trust Infection and Immunity Immunophenotyping (3i) consortium (www.immunophenotyping.org). In brief, Spleen and MLN were digested with collagenase (1mg/ml)/DNAse (0.1 mg/ml) in 2% FCS PBS (+ Ca/Mg) for 20 minutes at 37 C and filtered through 30mm cell strainers. Cells were plated on 96 well V-bottom plates, washed in PBS and stained with Zombie Near-IR (Biolegend) for live/dead discrimination, Antibody stains were performed at 4 C for 20mins. Full details regarding phenotyping panels are included in Table S3. Samples were acquired on a BD LSR Fortessa X-20

. Mode-k-co-culture-assays, Pen/Strep, 2.5% HEPES, 1% Glutamine, 1% non-essential amino acids, 1% sodium pyruvate, 0.2% b-mercapto-ethanol (GIBCO) and cytokines including IL-2 (10U/ml), IL-15 (10 ng/ml) (Immunotools), RPMI 1640 supplemented with 10% FCS, p.10

, MODE-K were seeded in 48-well plates 24h prior to the addition of 10 5 unsorted or (where indicated) positively FACS-sorted (CD45+Vg7+) IEL and incubated for 16-18h in 10% CO 2 unless indicated otherwise. For transwell assays, 2x10 5 MODE-K cells were seeded onto 24-well transwell plates (3 mm pore size -Corning)

, either in direct contact (below), sequestered from (above), or split 50:50 with MODE-K cells (above and below the transwell), IEL

, IEL Stimulation 96-well U bottom plates were coated overnight with 10 mg/ml LEAF-Purified anti-mouse CD3-? or Hamster IgG Isotype control (Biolegend) at 4 C and washed once with PBS 1x before seeding IEL. 100,000 IEL were seeded per well, p.37

, Confocal Imaging Proximal small intestine (SI) samples were fixed in Zamboni's fixative, blocked with normal goat serum and stained with antibodies against TCRb, TCRd, TCRVd4 (encoded by TRDV2-2) (GL2), CD3 and Vg7. Z-Sections were acquired on a confocal-LSM-710 microscope (Zeiss) and processed and analyzed using Imaris Software

, Bone Marrow Chimeras and Adoptive IEL Transfers later. IEL harvested from 4 week-old WT mice were column-purified using CD45 microbeads (MACS Miltenyi biotec) and IV-injected into

, RNA libraries were generated using the KAPA Stranded RNA-seq Kit with RiboErase (HMR) (KAPA BIOSYSTEMS). Paired-end sequencing on HiSeq 2500 (illumina) using rapid run chemistry, lo IEL were sorted from from pooled D14-17 pups directly into RLT buffer

. Clark, Excess resected skin discarded at the time of cutaneous or reconstructive surgery was obtained from adult donors after informed consent and in compliance with local ethical approval (REC number 06/Q0704/18). This study was conducted adhering to the principles of the Declaration of Helsinki. Primary gut lymphocytes were obtained using an adaptation of the method of Kupper and Clarke, 2006.

. Clark, Skin lymphocytes were isolated using the method as originally described, 2006.

, Longitudinal RNAscope analysis of Btnl1 expression during gut development. (H) Gene expression by qRT.PCR along the length of the gut in WT mice (n R 3). (I) Gene expression by qRT.PCR in the thymus of WT and Btnl1À/À animals compared to the proximal small intestine. (J) Organization of WT and targeted loci for Btnl1À/À, Btnl1 indel/indel and Btnl4À/À mice, WT versus alymphoplasia (aly/aly) mice. (G)

, Probes targeting the indicated regions were generated to detect the WT and targeted alleles. Data are representative of R 1 (A,K) or R 2 (C,E,G,H,I) independent experiments. Some panels include data pooled from 2 (F), > 3 (D) or > 6 (B) independent experiments. All error bars represent mean ± SD, orange: inserted targeting cassette. Knockout ES cell clones were obtained from the international mouse consortium IKMC-ID 67994 (Btnl1) and 81524 (Btnl4). (K)

, Conventional RT-PCR analysis of BTN3A2, BTNL3 and BTNL8 expression in the indicated tissues. (D) Conventional RT-PCR analysis of BTN3A1, BTNL3, BTNL8, EPCAM and TCR Vg2/3/4 expression in the indicated samples. (E) Cell surface expression of FLAG-BTNL3, FLAG-BTNL8S or FLAG-BTNL8 co-transfected in HEK293 cells with the indicated constructs. Histogram overlays show the expression of each BTNL after gating on GFP+ cells (numbers in brackets indicate geometric mean fluorescence intensity, gMFI). (F) Schematic illustrating the method of human intestinal tissue-resident lymphocytes isolation and co-culture with HEK293 transductants. (1) Endoscopic biopsies recovered from ascending colon of healthy donors. (2) Washed in complete media supplemented with antibiotic. (3) 1 biopsy applied to each matrix. (4) Culture for 5-7 days in complete medium supplemented with antibiotics, IL-2 and IL-15. (5) Co-culture with HEK293 cell lines transduced with EV, L3, L8 or L3+8. (G) Cell surface CD25 expression on indicated subsets of human gut-derived lymphocytes after co-culture with EV versus L3+8-transduced HEK293 cells. (H) Gating parameters for sorting of Btnl3+8-responsive human gut-derived lymphocytes. (I) TCRVg chain usage (left) and cell surface TCRgd expression (right, FACS-sorted gd T cells harvested from human intestinal tissue were analyzed by deep sequencing for TCR Vg chain usage. (B) Schematic illustrating the murine and human Btnl2/BTNL2 and Btnl9/BTNL9 loci, adapted from the NCBI gene viewer. (C)