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Genome-wide association studies identifying hundreds of susceptibility loci for autoimmune diseases indicate that genes active in immune cells predominantly mediate risk. However, identification and functional characterization of causal variants remain challenging. Here, we focused on the immunomodulatory role of a protective variant of histone deacetylase 7 (HDAC7). This variant (rs148755202, HDAC7.p.R166H) was identified in a study of low-frequency coding variation in multiple sclerosis (MS). Through transcriptomic analyses, we demonstrate that wild-type HDAC7 regulates genes essential for the function of Foxp3 + regulatory T cells (T regs ), an immunosuppressive subset of CD4 T cells that is generally dysfunctional in patients with MS. Moreover, T reg -specific conditional hemizygous deletion of HDAC7 increased the severity of experimental autoimmune encephalitis (EAE), a mouse model of neuroinflammation. In contrast, T regs transduced with the protective HDAC7 R166H variant exhibited higher suppressive capacity in an in vitro functional assay, mirroring phenotypes previously observed in patient samples. In vivo modeling of the human HDAC7 R166H variant by generation of a knock-in mouse model bearing an orthologous R150H substitution demonstrated decreased EAE severity linked to transcriptomic alterations of brain-infiltrating T regs , as assessed by single-cell RNA sequencing. Our data suggest that dysregulation of epigenetic modifiers, a distinct molecular class associated with disease risk, may influence disease onset. Last, our approach provides a template for the translation of genetic susceptibility loci to detailed functional characterization, using in vitro and in vivo modeling.

The T cell immune synapse is a site of intense vesicular trafficking. Here we show that the golgin GMAP210, known to capture vesicles and organize membrane traffic at the Golgi, is involved in the vesicular transport of LAT to the immune synapse. Upon activation, more GMAP210 interact with LAT-containing vesicles and go together with LAT to the immune synapse. Regulating LAT recruitment and LAT-dependent signaling, GMAP210 controls T cell activation. Using a rerouting and capture assay, we show that GMAP210 captures VAMP7-decorated vesicles. Overexpressing different domains of GMAP210, we also show that GMAP210 allows their specific delivery to the immune synapse by tethering LAT-vesicles to the Golgi. Finally, in a model of ectopic expression of LAT in ciliated cells, we show that GMAP210 tethering activity controls the delivery of LAT to the cilium. Hence, our results reveal a function for the golgin GMAP210 conveying specific vesicles to the immune synapse., P. Le Baccon from PICT-IBiSA@Pasteur microscopy facility (Institut Curie, Paris), the PICT-IBiSA, member of the France-BioImaging National Research infrastructure, supported by French National Research Agency through the Investments for the Future program (France-BioImaging, ANR-10-INSB-04) and the CelTisPhyBio Labex (No. ANR-10-LBX-0038) part of the IDEX PSL (No. ANR-10-IDEX-0001-02 PSL), L. Sengmanivong and all the staff from the Nikon Imaging Center (Institut Curie-CNRS, Paris), Damarys Loew, Florent Dingli et Guillaume Arras from the Institut Curie Mass Spectrometry, and Proteomics facility (LSMP), S. Moutel from Antibody platform (Institut Curie, Paris), B. Malissen, and R. Roncagalli (CIML, Marseille, France) for giving us the LAT-TST constructs. Alexandre Benmerah (INSERM UMR-1163, Laboratory of Inherited Kidney Diseases, Institut Imagine, Paris, France) for discussion and protocols, Ana-Maria Lennon-Duménil and Michel Bornens (Institut Curie, Paris) for critical reading of our manuscript. Bertsy GOIC for the graphic design and scientific discussions. A.E.Z. received a grant from l’Association pour la Recherche contre le Cancer (ARC), J.- M.C. received grants from La Ligue Nationale Contre le Cancer and Fondation pour la Recherche Médicale. C.T.B. received a grant from Fondazione Telethon—Italy (Grant GGP1102). Work was supported by funds from Institut Curie, INSERM, ANR (ANR-13- BSV2-0018 NeuroImmunoSynapse, ANR-10-IDEX-0001-02 PSL* and ANR-11-LABX0043), the Fondation pour la Recherche Médicale (FRM, FRM DEQ20140329513”).

Significance CD4 T cells are major regulators of immune responses against both self and pathogens. Understanding pathways that govern CD4 T cell differentiation and regulation are thus key for the discovery of new immunoregulatory drug targets. Here, we have identified an epigenetic pathway that regulates the expression of a set of proteins that determine T cell responsiveness. By silencing enhancers distal to a set of genes known to be involved in regulatory T cell function, the epigenetic modifiers TRIM28 and HP1β/γ regulate T cell receptor signaling. This leads to defective metabolic reprograming and inefficient effector differentiation of naive T cells. This mechanism provides an exciting opportunity to regulate T cell responsivity in both autoimmunity and T cell-based immunodeficiencies., Naive CD4+ T lymphocytes differentiate into different effector types, including helper and regulatory cells (Th and Treg, respectively). Heritable gene expression programs that define these effector types are established during differentiation, but little is known about the epigenetic mechanisms that install and maintain these programs. Here, we use mice defective for different components of heterochromatin-dependent gene silencing to investigate the epigenetic control of CD4+ T cell plasticity. We show that, upon T cell receptor (TCR) engagement, naive and regulatory T cells defective for TRIM28 (an epigenetic adaptor for histone binding modules) or for heterochromatin protein 1 β and γ isoforms (HP1β/γ, 2 histone-binding factors involved in gene silencing) fail to effectively signal through the PI3K–AKT–mTOR axis and switch to glycolysis. While differentiation of naive TRIM28−/− T cells into cytokine-producing effector T cells is impaired, resulting in reduced induction of autoimmune colitis, TRIM28−/− regulatory T cells also fail to expand in vivo and to suppress autoimmunity effectively. Using a combination of transcriptome and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses for H3K9me3, H3K9Ac, and RNA polymerase II, we show that reduced effector differentiation correlates with impaired transcriptional silencing at distal regulatory regions of a defined set of Treg-associated genes, including, for example, NRP1 or Snai3. We conclude that TRIM28 and HP1β/γ control metabolic reprograming through epigenetic silencing of a defined set of Treg-characteristic genes, thus allowing effective T cell expansion and differentiation into helper and regulatory phenotypes.

Carpier et al. show that LAT trafficking to the immune synapse depends on endosome-to-Golgi/TGN retrograde transport and is controlled by Rab6 and Syntaxin-16. Moreover, they show that this retrograde pathway controls the TCR-induced activation of T lymphocytes., The adapter molecule linker for activation of T cells (LAT) orchestrates the formation of signalosomes upon T cell receptor (TCR) stimulation. LAT is present in different intracellular pools and is dynamically recruited to the immune synapse upon stimulation. However, the intracellular traffic of LAT and its function in T lymphocyte activation are ill defined. We show herein that LAT, once internalized, transits through the Golgi–trans-Golgi network (TGN), where it is repolarized to the immune synapse. This retrograde transport of LAT depends on the small GTPase Rab6 and the target soluble N-ethylmaleimide-sensitive factor attachment protein receptor (t-SNARE) Syntaxin-16, two regulators of the endosome-to-Golgi/TGN retrograde transport. We also show in vitro in Syntaxin-16– or Rab6-silenced human cells and in vivo in CD4+ T lymphocytes of the Rab6 knockout mouse that this retrograde traffic controls TCR stimulation. These results establish that the retrograde traffic of LAT from the plasma membrane to the Golgi-TGN controls the polarized delivery of LAT at the immune synapse and T lymphocyte activation., Graphical Abstract

Activated PI3Kδ Syndrome (APDS) is an inherited immune disorder caused by heterozygous, gain-of-function mutations in the genes encoding the phosphoinositide 3-kinase delta (PI3Kδ) subunits p110δ or p85δ. This recently described primary immunodeficiency disease (PID) is characterized by recurrent sinopulmonary infections, lymphoproliferation, and susceptibility to herpesviruses, with Epstein-Barr virus (EBV) infection being most notable. A broad range of PIDs having disparate, molecularly defined genetic etiology can cause susceptibility to EBV, lymphoproliferative disease, and lymphoma. Historically, PID patients with loss-of-function mutations causing defective cell-mediated cytotoxicity or antigen receptor signaling were found to be highly susceptible to pathological EBV infection. By contrast, the gain of function in PI3K signaling observed in APDS patients paradoxically renders these patients susceptible to EBV, though the underlying mechanisms are incompletely understood. At a cellular level, APDS patients exhibit deranged B lymphocyte development and defects in class switch recombination, which generally lead to defective immunoglobulin production. Moreover, APDS patients also demonstrate an abnormal skewing of T cells toward terminal effectors with short telomeres and senescence markers. Here, we review APDS with a particular focus on how the altered lymphocyte biology in these patients may confer EBV susceptibility.

The authors regret that in the original version of their paper, they mistakenly used the phrase OVA-expressing cells instead of OVA-secreting cells in parts of the text and cited reference Boissonnas et al. (2007. http://dx.doi.org/10.1084/jem.20061890) instead of Zeelenberg et al. (2008. http://dx.doi.org/10.1158/0008-5472.CAN-07-3163) and Sedlik et al. (2014. http://dx.doi.org/10.3402/jev.v3.24646). The Results and discussion paragraph containing the corrected references and full bibliographic information appear below. Fil: Alloatti, Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina Fil: Rookhuizen, Derek C.. Institute Curie. U-932 Immunity And Cancer; Francia Fil: Joannas, Leonel. Institute Curie. U-932 Immunity And Cancer; Francia Fil: Carpier, Jean-Marie. Institute Curie. U-932 Immunity And Cancer; Francia Fil: Iborra, Salvador. Institute Curie. U-932 Immunity And Cancer; Francia Fil: Magalhaes, Joao G.. Institute Curie. U-932 Immunity And Cancer; Francia Fil: Yatim, Nader. Institut Pasteur, Paris; Francia Fil: Kozik, Patrycja. Institute Curie. U-932 Immunity And Cancer; Francia Fil: Sancho, David. Institute Curie. U-932 Immunity And Cancer; Francia Fil: Albert, Matthew L.. Institut Pasteur, Paris; Francia Fil: Amigorena, Sebastian. Institute Curie. U-932 Immunity And Cancer; Francia

Biogenesis of the immune synapse at the interface between antigen-presenting cells and T cells assembles and organizes a large number of membrane proteins required for effective signaling through the T-cell receptor. We showed previously that the intraflagellar transport protein 20 (IFT20), a component of the intraflagellar transport system, controls polarized traffic during immune synapse assembly. To investigate the role of IFT20 in primary CD4(+) T cells in vitro and in vivo, we generated mice bearing a conditional defect of IFT20 expression in T cells. We show that in the absence of IFT20, although cell spreading and the polarization of the centrosome were unaffected, T-cell receptor (TCR)-mediated signaling and recruitment of the signaling adaptor LAT (linker for activation of T cells) at the immune synapse were reduced. As a consequence, CD4(+) T-cell activation and proliferation were also defective. In vivo, conditional IFT20-deficient mice failed to mount effective antigen-specific T-cell responses, and their T cells failed to induce colitis after adoptive transfer to Rag(-/-) mice. IFT20 is therefore required for the delivery of the intracellular pool of LAT to the immune synapse in naive primary T lymphocytes and for effective T-cell responses in vivo.

The initiation of cytotoxic immune responses by dendritic cells (DCs) requires the presentation of antigenic peptides derived from phagocytosed microbes and infected or dead cells to CD8(+) T cells, a process called cross-presentation. Antigen cross-presentation by non-activated DCs, however, is not sufficient for the effective induction of immune responses. Additionally, DCs need to be activated through innate receptors, like Toll-like receptors (TLRs). During DC maturation, cross-presentation efficiency is first upregulated and then turned off. Here we show that during this transient phase of enhanced cross-presentation, phago-lysosome fusion was blocked by the topological re-organization of lysosomes into perinuclear clusters. LPS-induced lysosomal clustering, inhibition of phago-lysosome fusion and enhanced cross-presentation, all required expression of the GTPase Rab34. We conclude that TLR4 engagement induces a Rab34-dependent re-organization of lysosomal distribution that delays antigen degradation to transiently enhance cross-presentation, thereby optimizing the priming of CD8(+) T cell responses against pathogens. Fil: Alloatti, Andrés. Inserm; Francia. Institute Curie; Francia Fil: Kotsias, Fiorella. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario; Argentina. Institute Curie; Francia. Inserm; Francia. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Departamento Virologia; Argentina Fil: Pauwels, Anne Marie. University of Ghent; Bélgica Fil: Carpier, Jean Marie. Institute Curie; Francia. Inserm; Francia Fil: Jouve, Mabel. Institute Curie; Francia Fil: Timmerman, Evy. University of Ghent; Bélgica Fil: Pace, Luigia. Institute Curie; Francia. Inserm; Francia Fil: Vargas, Pablo. Institute Curie; Francia. Inserm; Francia. Centre National de la Recherche Scientifique; Francia Fil: Maurin, Mathieu. Institute Curie; Francia. Inserm; Francia Fil: Gehrmann, Ulf. Institute Curie; Francia. Inserm; Francia Fil: Joannas, Leonel. Institute Curie; Francia. Inserm; Francia Fil: Vivar, Omar I.. Institute Curie; Francia. Inserm; Francia Fil: Lennon Duménil, Ana Maria. Institute Curie; Francia. Inserm; Francia Fil: Savina, Ariel. Institute Curie; Francia. Inserm; Francia. Roche SAS; Francia Fil: Gevaert, Kris. University of Ghent; Bélgica Fil: Beyaert, Rudi. University of Ghent; Bélgica Fil: Hoffmann, Eik. Inserm; Francia. Institute Curie; Francia. University of Ghent; Bélgica Fil: Amigorena, Sebastian. Inserm; Francia. Institute Curie; Francia

The mechanisms by which Lat (a key adaptor in the T cell antigen receptor (TCR) signaling pathway) and the TCR come together after TCR triggering are not well understood. We investigate here the role of SNARE proteins, which are part of protein complexes involved in the docking, priming and fusion of vesicles with opposing membranes, in this process. Here we found, by silencing approaches and genetically modified mice, that the vesicular SNARE VAMP7 was required for the recruitment of Lat-containing vesicles to TCR-activation sites. Our results indicated that this did not involve fusion of Lat-containing vesicles with the plasma membrane. VAMP7, which localized together with Lat on the subsynaptic vesicles, controlled the phosphorylation of Lat, formation of the TCR-Lat-signaling complex and, ultimately, activation of T cells. Our findings suggest that the transport and docking of Lat-containing vesicles with target membranes containing TCRs regulates TCR-induced signaling.