Team presentation and main achievements
GENERAL INTERESTS
Our main interests in immunology are
- The molecular pathways that underlie differentiation, migration and activation of immune effectors and
- How genetic or acquired modifications in these pathways may lead to immune deficits or to autoimmune reactions.
Our main cellular model is the Natural Killer (NK) cell, but we also study B/T cells or monocytes in some contexts. We use a wide range of experimental models, often-transgenic mice that we create by inserting new epitopes or mutations. We also apply systems biology methods, taking advantage of the full range of omics-approaches. Finally, we perform translational research, whose secondary goal is to find novel ways to manipulate immune function in various diseases.
Lab organization
The common interest of the four subgroups is lymphocyte activation and signaling, studied under different but complementary angles. The groups 1 and 2 study how NK cells develop, migrate and are activated during immune responses, and in particular during anti-tumor or antiviral responses. Group 2 has a special interest for immunometabolism. Group 3 studies how mutations in genes involved in lymphocyte activation may cause inflammation or autoimmunity. Group 4 is delocalized at the Lyon-Sud hospital and performs immune monitoring in patients in the context of different team projects, and with the help from the SIRIC Lyrican (collaboration with the CRCL). Although the questions addressed may appear different, these four topics benefit prominently from the complementarity in models, expertises, perspectives and methodologies within the team. The efficiency of our strategy is evidenced by the important scientific production outlined below
RECENT ACHIEVEMENTS
- Group 1 (TW): S1P receptors in NK and T cells (TW)
More recently, we decided to test the relevance of our findings on S1P5 in human. This led us to start two important collaborations 1) with local clinicians who provided us with pediatric tonsils or adult lymph nodes and 2) with Biogen, who provided us with newly designed S1P5 antagonists. We found that similar to mouse, human NK cells acquire S1P5 expression upon maturation and that this receptor is essential for their responsiveness to S1P, and presumably their exit from lymphoid organs2. In the course of these experiments, we also made the original observation that human memory T cells are repulsed by S1P, which contradicted current views on the role of S1P in T cell trafficking. This repulsion is mediated by S1P2, a receptor whose role in the immune system hasn’t been fully elucidated3 (Figure 1).
- Group 1 (TW): Sequential actions of Eomes and T-bet promote stepwise maturation of NK cells
Eomes and T-bet are T-box transcription factors (TFs) essential for type-1 cellular immunity. The homology of their DNA binding domain suggest redundancy in their transcriptional activity. However, we found that Eomes and T-bet have complementary roles in NK cells with sequential actions promoting stepwise maturation through the regulation of largely distinct gene sets (Figure 2). Eomes acted more often as an activator of transcription inducing proliferation and the expression of many NK cell signature genes at the immature stage, while T-bet acted more frequently as a repressor decreasing the expression of many lineage genes at the mature stage, the latter being linked to its ability to induce transcriptional repressors such as Zeb2 or Blimp1. We generated novel transgenic mouse strains facilitating T-bet and Eomes chromatin immunoprecipitation. Analysis of genomic binding in NK cells revealed a strong overlap between Eomes and T-bet and pointed to Runx3 as cofactor of transcriptional regulation. Yet, each TF specifically induced key target genes endowing NK cells with specific functions such as cytotoxicity for Eomes and responsiveness to IL-12 for T-bet. Moreover, analyses of chromatin revealed that the accessibility of NK cell signature genes and maturation-acquired properties are largely associated with Eomes and T-bet binding. Finally, our integrated genomic and transcriptomic analysis points to many novel genes and pathways that deserve further investigation in NK cells. Submitted to Nat. Immunol.
Figure 2 : Eomes and T-bet are sequentially required for NK cell maturation. (A) Image stream X (ISX) analysis of T-bet and Eomes expression in gated NK cells. Representative images are shown for the three NK cell subsets. CD122 staining was used to visualize the membrane. (B) Eomes and T-bet control different transitions during NK cell maturation. They also have complementary roles in the control of gene expression upon maturation as T-bet and Eomes regulate mostly distinct gene sets and at different maturation stages both transcriptionally and epigenetically.
- Group 2 (AM): Regulation of mTOR in NK cells (AM, TW)
IL-15 has long been known to be essential for NK cell development and homeostasis6. Moreover, high concentrations of this cytokine enhance NK cell proliferation and cytotoxicity7. The molecular basis of this dual activity remained obscure until we found that low IL-15 concentrations were sufficient to induce STAT5 phosphorylation while high IL-15 concentrations are required to induce mTOR phosphorylation and activation. mTOR is a S/T kinase that regulates translation and metabolic activity in response to a wide variety of signals. Increasing evidence show that the control of mTOR activity is key to regulate effector functions of a wide variety of immune cells8. Using a specific deletion of mTOR in mouse NK cells, we showed that mTOR was required for proper NK cell development and also for their activation in vitro and in vivo in antiviral settings. Mechanistically, mTOR regulates NK cell metabolic activity (glycolysis and mitochondrial function) to sustain proliferation, and also increases IL-15 receptor levels in a positive feedback-signaling loop. mTOR is also essential for up regulation of granzyme B and the cytolytic machinery. Treatment of mice with rapamycin inhibits NK cell capacity to kill MHC-I deficient cells in vivo. As this drug is currently used in several clinical conditions, our work has important implications (see “projects”). More recently, we also found that mTOR activity is tightly regulated by inhibitory and activating receptors during NK cell “education”. High mTOR activity is favored by chronic engagement of inhibitory receptors and is required to maintain NK cell responsiveness. Upon stimulation, the mTOR/Akt pathway amplifies signaling through activating NK cell receptors by enhancing calcium flux and LFA-1 integrin activation9.
- Group 2 (AM): Long-term treatment with rapamycin impairs NK cell maturation and function in women with metastatic breast cancer (AM, TW)
Building up on our discovery that mTOR is a central rheostat of NK cell reactivity we sought to study its role in human NK cells. We collaborated with oncologists from the Centre Léon Bérard, in the context of the “Lyrican” network, to monitor NK cell phenotype and function in women treated with everolimus (rapamycin) as monotherapy for metastatic breast cancer. We monitored peripheral NK cell activity at T0, 1 month, 3 months and 9 months after the start of treatment. We found that rapamycin profoundly impaired NK cell response to IL-15, which led to a progressive block in their maturation and a decrease in their effector functions (especially IFNg secretion) in response to ex vivo stimulation with tumor or antibody-coated cells. These results highlight the essential role of mTOR in human NK cell homeostasis and function and also suggest that long-term treatment with mTOR inhibitors impair anti-tumor immune function.
- Group 3 (AB): Identification of novel genetic causes of early-onset autoimmunity
The contribution of genetic mutations in the development of autoimmune or autoinflammatory diseases is believed to be more important for pediatric-onset than for adult-onset cases. Based on this, Alexandre Belot constituted a cohort of pediatric cases, in the context of a newly created national reference center (centre de reference des rhumatismes inflammatoires et maladies autoimmunes de l’enfant, RAISE, plan national maladies rares, >400 patients) that he coordinates. Exome sequencing is performed on all familial cases, so as to identify potential genetic causes and mouse models are sometimes produced to test the causality of the gene variants identified. This work led to the discovery of several novel monogenic or oligogenic causes of autoimmune or autoinflammatory diseases (mutations in Prkdc10, Socs1, Def6, Lyn). Moreover, we contributed to collaborative efforts for a better diagnosis of autoinflammatory disorders (Interferon signature, with Yanick Crow for lupus patients, inflammasome activation for FMF patients, with Thomas Henry, CIRI) and for personalized treatments of patients (collaboration Imagine Institute, Paris, patients with mutations in Tmem173 (STING), treated with Ruxolitinib). Recently, we generated a mouse model of PKCd deficiency that recapitulates lupus features found in patients. We perform biochemical studies to try to understand how PKCd regulates B cell proliferation and activation.
- Group 3-4: (SV, AB) Type I IFN immunoprofiling in COVID-19 patients
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which causes coronavirus disease 2019 (COVID-19), is characterized by a wide spectrum of disease encompassing asymptomatic carriage, mild to severe upper respiratory tract illness that can evolve into respiratory failure, or rapidly progressing severe viral pneumonia with acute respiratory distress syndrome. We assessed the kinetics of plasma IFN-I in a cohort of 26 patients with COVID from the intensive care unit at Hospices Civils de Lyon. Our data demonstrate a heterogeneous pattern of IFN-α response in patients with COVID-19, with IFN-I response being impaired in about 20% of critically ill patients. Patients with an impaired IFN-I response had on average a poorer outcome, suggesting that defective innate immunity could contribute to disease exacerbation11.
SPONSORS
Inserm, erc, university, anr, league, finovi