Team presentation and main research themes

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 RESEARCH THEMES

• Group 1 (TW): NK cell differenciation and reactivity

Natural Killer (NK) cells are innate lymphocytes displaying several effector functions, including granule-dependent cytotoxicity, secretion of inflammatory cytokines (TNF-α and IFN-γ) and chemokines (CCL3-5) that are thought to have complementary roles during immune responses. NK cells have important roles in anti-viral immune responses and in immunosurveillance of cancers, especially hematological malignancies. Target cell recognition by NK cells is finely regulated through a wide range of activating and inhibitory receptors. Group 1 interests include the following:

NK cells acquire their reactivity against tumor and other target cells during a differentiation process called maturation. Immature NK cells reside mostly in the bone marrow and lymph nodes where they develop from progenitors, while mature NK cells patrol in the blood circulation. NK cells undergo major transcriptional changes during maturation, and one of our goals is to identify the transcription factors (TF) involved, the associated epigenetic mechanisms and the effector pathways that are regulated. Our pioneer work in this field included the discovery of the role of Zeb2 in terminal maturation, and the role of the Eomes-to-T-bet balance during this process. Current projects involve the study of the role of different TF downstream of Eomes and T-bet in regulating NK cell reactivity and effector functions.

NK cell reactivity is dynamically regulated through the interaction of activating and inhibitory receptors with their ligands. Upon chronic stimulation of activating receptors, NK cells become dysfunctional, a process that remains poorly understood at the molecular level. We set up mouse models of lymphoma with controlled expression of activating/inhibitory ligands. Using these models, we found that NK cells become rapidly dysfunctional, within 24h of contact with immunogenic tumors, in a way that is independent of immune checkpoint proteins. Our current projects include the study of the molecular mechanism of NK dysfunctions using Omics and metabolic analysis.

Figure 1 : Chronic stimulation induced NK cell dysfunction is temporally dissociated from Immune Checkpoints (ICPs) expression and is reversible upon exposure to high IL-15 concentration or chronic stimulation discontinuation

Group 2 (AM): NK cell immunometabolism (AM, TW)

Natural Killer (NK) cells are innate lymphocytes with anti-tumor and anti-viral abilities. These functions are controlled by the engagement of inhibitory and activating receptors and are modulated by the environment, in particular by immune factors such as cytokines. Among them, IL-15 and IL-18 are strong positive NK cell regulators.

NK cell activation depends on the integration of a large set of intracellular and extracellular cues, in order to ensure a proper cellular response in line with the cell environment. We and others showed the importance of the mechanistic Target Of the Rapamycin (mTOR) in this process.

The importance of both biosynthetic and bioenergetic metabolism to sustain immune responses is increasingly recognized. A major question in the field is to identify the environmental nutrients that conditions the response of particular cell types and the metabolic configuration they allow.

In this context, our objectives are to dissect the reciprocal links between mTOR, the bioenergetic metabolism and NK cell reactivity through :

• Deciphering the relations between mTOR, glycolysis and reactivity.
• Identifying what impedes mTOR activation in exhausted NK cells.

Figure 2 : Overview of the mTORC1 pathway

• 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. We also recently identified 6 novel variants in the gene coding for the phosphatase PTPN2, a negative regulator of JAK/STATs signaling pathway, in patients with pediatric-onset systemic lupus or Evans syndrome (Figure 3).

Figure 3 : Haploinsufficiency in PTPN2 leads to JAK/STATs pathway hyper activation and systemic autoimmunity

• Group 3-4: (SV) Innovative cell and gene therapy

This group aims to develop innovative cell and gene therapy products structured around two main axes (Figure 4):

1.            Development of Immunotherapies Based on Activated NK Cells: Various strategies are being explored to harness NK cells' natural properties for therapeutic purposes, including the use of cytokine-induced memory-like (CIML) NK cells, genetically modified CAR-NK cells expressing specific antigen receptors, and engineered NK cells expressing high-affinity antibody receptors. In line with the expertise of the LYACTS team in Natural Killer (NK) cell biology, we aim to contribute to the field of immunotherapies, particularly focusing on the therapeutic role of activated and gene modified NK cells in infectious diseases and cancer.

2.            Genetic Correction of Monogenic Autoimmune/Inflammatory Diseases by Crispr-Cas9: The Crispr/Cas9 tool enables precise genome editing with unprecedented ease. CRISPR/Cas9 platform offer advantages over traditional gene therapy approaches by preserving endogenous gene regulation and expression levels and avoiding uncontrolled transgene integration. Clinical trials utilizing CRISPR-Cas9-based therapies are underway for various genetic disorders, including hemoglobinopathies and primary immunodeficiencies. In line with the expertise of the LYACTS team in monogenic immune disorders, we aim to expand the application of gene editing strategies in this field.

Our goal is to advance translational research and facilitate the clinical application of innovative immunotherapies and gene editing approaches. Our affiliation with a hospital-based unit for the production of Advanced Therapy Medicinal Products will streamline the transition of these therapeutic interventions to clinical practice in a GMP-compliant production facility.

Figure 4 : Two main approaches for innovative cell and gene therapy

SPONSORS

Inserm, erc, university, anr, league, finovi