Team 08 - J. Izopet / B. Lagane - Institut Toulousain des Maladies Infectieuses et Inflammatoires

Viral infection : persistence, host response and pathophysiology

Coordinators : J. Izopet, B. Lagane

Scientific Objectives

The main objective of our team is to improve the understanding of the pathophysiology of HIV-1 and Hepatitis E virus (HEV) infections, two important public health concerns worldwide. We focus on how viral and host determinants, and their interplay, shape the outcome of both infections. Important issues we are interested in include viral replication, transmission, dissemination and persistence in cells and tissues and pathogenesis. We also investigate the setting up of immune responses in the context of these infections, and conversely how dysregulation of their homeostasis contributes to pathogenesis. Finally, our activities extend to the study of the mechanisms of action of antiviral compounds and viral escape from treatments. Our proximity to the University Hospital, combined with our skills in basic and clinical research, enable us to carry out translational research and to adapt our activities to deal with health emergencies (e.g. SARS-CoV2 pandemic). We are committed to maintaining cutting-edge research implying investments in technological development. We are involved in student/post-doc teaching/training, hence contributing to the formation of future scientists.

Our projects

AXIS 1: HIV

Our areas of interest are virus transmission, cell tropism, viral dissemination and persistence in tissues, and the mechanisms of pathogenesis (CD4 T cell depletion and immune system dysregulation). Basic research on these themes is carried out by two closely complementary and interconnected groups: (i) HIV-1 cellular and tissue tropism (head: B. Lagane) and (ii) HIV-1 reservoirs and immune reconstitution in the gut mucosa of people living with HIV-1 (PLWH) on antiretroviral therapy (ART) (head: P. Delobel). We are also involved in translational research through development of two HIV immunotherapy clinical trials promoted and funded by ANRS-MIE and led by P. Delobel.

HIV-1 cellular and tissue tropisms

PI: B. Lagane; Participants: H. Chamma, D. Martres, T. Montagné, B. Puissant, S. Raymond, C Vellas

Our team has long been involved in characterizing the tropism of viral quasispecies in PLWH (Bioinformatics, 2020). More recently, we have also investigated the determinants of HIV-1 transmission, through characterization of the genotypic/phenotypic properties of CXCR4-using HIV-1 envelope glycoproteins (Env) in recently infected individuals. Our studies have also aimed at better understanding the molecular details of Env/receptor interactions and their role in HIV-1 cellular tropism and pathogenesis. We have described how HIV-1 Envs influence CCR5 conformation (PLoS Pathog., 2018; Viruses, 2021) and functions (eLife, 2022), the mechanisms of the increased pathogenicity of CXCR4-using viruses (PLoS Pathog., 2021) and of macrophage infection (PLoS Pathog., 2022; J. Cell. Biol., 2023) and the mode of action of HIV-1 inhibitors (Molecules, 2023; Sci.Adv., 2023). Building on these findings, our studies are now divided into three research axes fully funded by ANRS-MIE and Sidaction:

(i) CCR5 signaling – role of the CCR5’s PDZ-domain binding motif (PBM) during HIV-1 infection. This work deals with CCR5 signaling and its role in health and disease. We aim to explore the role of novel PDZ-domain containing proteins we have recently identified as CCR5 interactors, in particular in HIV-1 entry, replication and dissemination (Participants: H. Chamma; Coll. C. Caillet-Saguy, Institut Pasteur).

(ii) Mapping of HIV-1 target CD4+ T cell subsets in secondary lymphoid organs (SLO). CD4+ T lymphocytes in secondary lymphoid organs (SLO) are sites of HIV-1 replication and reservoirs from the earliest stages of infection and undergo HIV-1-induced death, leading to AIDS. Using tonsils as a SLO model, we study both on isolated cells and in the tissue context the phenotype of CD4 T lymphocytes targeted by viruses isolated from recently infected individuals, and the consequences in viral replication, CD4 T cell depletion, the nature/size of reservoirs and latency-reversing strategies. (Participants: B. Puissant-Lubrano, S. Raymond, D. Martres and T. Montagné).

(iii) Mechanisms of HIV-1 infection of intestinal macrophages: role in viral persistence and rebound. We have identified compartmentalized HIV-1 reservoirs in myeloid cells in the intestinal mucosa of PLWH on ART, raising the questions of their origin, nature and role upon treatment interruption. We seek to characterize the cellular tropism of HIV-1 Envs from intestinal macrophages or CD4 T cells, the phenotype of intestinal macrophages through multiplexed confocal microscopy, the mechanisms of their infection and the biological properties of macrophage-derived viruses, in particular after reactivation of latently infected cells (Participants: C. Vellas, hiring of a post-doc in progress).

HIV-1 persistence in the gut and failure to reconstitute mucosal immunity under antiretroviral therapy

PI: Prof. P. Delobel; Participants: N. Collercandy, C. Vellas, M. Quaranta, M. Requena.

For several years, our group has been interested in better understanding the persistence of HIV-1 and the reconstitution of immunity in the intestinal mucosa under antiretroviral (ARV) treatment. Our work has focused on in vivo pathophysiological studies in people living with HIV-1 (PLWH) and the development of ex vivo models.
Reconstitution of CD4+ T lymphocytes in the intestinal mucosa of PLWH remains incomplete despite effective ARV treatment, and this is dissociated from the blood compartment and lymphoid organs. This lack of intestinal immune reconstitution is responsible for the persistence of impaired epithelial integrity, microbial translocation, and deleterious chronic mucosal and systemic inflammation.
Our work is mainly based on cohorts of PLWH on ARVs, and HIV-negative controls, recruited at the University Hospital of Toulouse, who underwent intestinal endoscopic biopsies at different levels of the intestinal tract (duodenum, ileum and colon) in the ANRS EP44 and EP61 GALT studies (PI: Prof. P. Delobel). A new study (GALT-2) is in preparation in which new colon biopsies will be collected.
We have also developed an ex vivo culture model of primary human enterocytes differentiated on transwells, which allow us to reproduce a polarized intestinal epithelium, as well as a histoculture model to study HIV infection in the microenvironment of intestinal tissue.
Key findings:

A disruption of chemotactic axes is involved in the failure to reconstitute the intestinal immune barrier in PLHIV on ARVs: We have shown that a defect in CD4+ T cell recruitment is involved in the incomplete immune reconstitution of the duodenal mucosa of PLWH on ARVs, due to an alteration of the CCL25-CCR9 axis (Mavigner et al. J Clin Invest 2012). We have also described an alteration in the CCL20-CCR6 axis, associated with a defect in the recruitment of CCR6+ T cells, particularly Th17, contributing to the Th17/Treg imbalance (Loiseau et al. Mucosal Immunol 2016). In contrast to Th17, we have shown that intestinal Th22s are normally reconstituted under ARV, with recruitment via the CCL28-CCR10 axis remaining functional, as an alternative to the deficient CCL20-CCR6 axis (Nayrac et al. Mucosal Immunol, 2021). We have also shown that pro-inflammatory CXCR3+ Th1 and CD8+ T memory effector lymphocytes are increased in the intestinal mucosa of PLWH on ARVs, and that these lymphocytes contribute to the defect in the production of CCL20, ligand of CCR6, and to the production of CXCL9/10/11, ligands of CXCR3, through an effect of IFN- and IL-18 on enterocytes, inducing a vicious cycle of pro-inflammatory cell recruitment (Loiseau et al. J Infect Dis 2019).
Molecular characterization of the HIV-1 reservoir in the intestinal compartment of PLWH on ARVs: In the ANRS EP61 GALT study, we demonstrated that the HIV-1 reservoir was enriched in intact proviral DNA in the colon compared to the blood. This intact proviral reservoir is associated with colonic CD4+ PD-1+TIGIT- T lymphocytes and low genetic diversity of viral quasispecies, suggesting clonal amplification of proviruses (Vellas et al. eBioMedicine 2024).
We have also characterized the HIV reservoir in intestinal monocytes/macrophages, showing a low frequency of infection of these myeloid cells compared to CD4+ T lymphocytes. Nevertheless, intact proviruses and non-integrated HIV-1 DNA can be detected in intestinal monocytes/macrophages. Compartmentalization of viral quasispecies between monocytes/macrophages and CD4+ T cells was also observed. The tropism of viral envelopes isolated from macrophages remained T-tropic, suggesting a mechanism of macrophage infection involving CD4+ T cells (Vellas et al. J Infect Dis 2024).

Ongoing work and projects:

Intestinal and blood translocated microbiota in PLWH on ARVs: A characterization of the intestinal microbiota, studied in stages at the duodenal, ileal and colonic levels, as well as blood translocated microbiota, has been performed in participants of the ANRS EP61 GALT study. Metabolomic studies in blood and intestinal tissue are also underway (coll. M. Serino, IRSD). We are studying the interactions between the microbiota and intestinal mucosal immunity in PLWH.
T V1 lymphocytes in the blood and intestine of PLWH on ARV: In a substudy of the ANRS EP61 GALT study, we characterized the phenotype, transcriptome, functional profile and TCR repertoire of V1 T lymphocytes in the blood and duodenum of PLWH and HIV-negative controls. We demonstrated a clonal expansion of V1 cells with TEMRA CX3CR1+ phenotype and cytotoxic profile in PLWH. Triggers for this expansion include CMV and changes in the gut and blood microbiota translocated in PLWH. The frequency of cytotoxic V1 CX3CR1+ T cells in the blood and duodenum appears to be negatively correlated with residual cell-associated HIV-1 RNA in these two compartments, suggesting a possible role for cytotoxic V1 T cells in controlling residual viral replication (Collercandy et al. submitted).
Phenotype, functions and trafficking of CX3CR1+ effector lymphocytes between blood and gut compartments in PLWH on ARVs: Following on from the work on T cells V1, we also set out to analyze CD8+ and NK T cells, which also express CX3CR1. These CX3CR1+ lymphocytes share a cytotoxic effector phenotype that is associated with the antitumor response in oncology, and may therefore also have an antiviral role in the elimination of HIV-infected cells. This ongoing work includes phenotypic and functional analysis of blood and intestinal CX3CR1+ lymphocytes from participants in the ANRS EP61 GALT study, as well as exploration of the CX3CL1-CX3CR1 chemotactic axis, including factors in the intestinal microenvironment (cytokines, microbiota) associated with CX3CL1 expression by enterocytes, and its cleavage into soluble form (Collercandy et al. in prep).
Intestinal resident memory T lymphocytes (TRM) during HIV-1 infection: mechanisms involved in their depletion and role in viral persistence under ARVs: The homeostasis of intestinal TRM seems to be particularly disturbed during HIV-1 infection, with our preliminary results showing a more pronounced depletion of TRM compared to non-TRM, and incomplete reconstitution under ARVs involving both CD4+ and CD8+ TRM, particularly in the colon. CD4+ TRM may be particularly susceptible to HIV-1 infection during the replicative phases of infection and may constitute a viral reservoir, including intact proviruses, in long-lived cells. Chronic inflammation of the intestinal mucosa in PLWH on ARVs could also reduce the effector functions of CD8+ TRM and their tissue retention, and favor the recirculation of ex-TRM cells. We plan to characterize intestinal TRM in PLWH, including the mechanisms involved in their reduction, their possible recirculation, and their role in HIV-1 persistence on ARVs.

AXIS 2: HEV

Pathogenesis of HEV infection

In collaboration with N. Blanchard, we will be implicated in the projet MOTIF : iMpact of chrOnic infections on cogniTIve and motor Functions during aging (Participant: F. Abravanel).

HEV life cycle in hepatocytes and enterocytes

Role of autophagy regulators and endoplasmic reticulum quality proteins in HEV release from hepatocytes

PI: S Chapuy-Regaud, Participants: S Lhomme; J Izopet, a post-doc to be hired

The hepatitis e virus uses cell membranes to support replication and assembly, and to leaves the cell in the form of lipid-associated, quasi-enveloped particles. Our recent work shows the role of autophagy-associated proteins in the viral cycle. The expression of these proteins may be triggered by endoplasmic reticulum (ER) stress involving ERAD (endoplasmic reticulum-associated degradation). We aim to identify the regulators of autophagy and ER quality involved in the viral cycle and leading to the preferential release of viral particles at the apical pole of polarized epithelial cells.

Study of the molecular motifs conferring a replicative advantage to the virus-host recombinant variants of the hepatitis E virus.

PI: S Lhomme; Participants: J Izopet, S Chapuy-Regaud, N Jeanne, O Paronetto, a post-doc to be hired

Hepatitis E virus (HEV) is a leading cause of viral hepatitis. It can cause chronic hepatitis E, defined by the persistence of the virus for more than 3 months, in immunocompromised patients. Virus-host recombinant viruses (VHRVs) that have incorporated human gene fragments into the proline-rich region (PPR) of their genome have been described in chronically infected patients (Lhomme, JVI, 2014; Lhomme, Front Microbiol, 2020). These human gene fragments had various origins: ribosomal protein S17, S19, tyrosine aminotransferase, inter-alpha trypsin inhibitor and promoted HEV replication in vitro. Our most recent work showed that 5 recombinant variants had a replicative advantage: RNF19A, ZNF787, KIF1B, RPS17 and EEF1A1, while 2 had not : RNA18 and RPL6 (Paronetto et al., JVI, 2024). The mechanisms leading to this replicative advantage over viruses lacking the human gene fragment are currently unknown. With different approaches, we aim to identify these mechanisms.

Other details

Publications

2025

Kamar, N.; Marion, O.; Abravanel, F.; Esposito, L.; Bello, A. Del; Izopet, J.

Porcine-derived pancreatic enzyme replacement therapy: a cause of hepatitis E virus transmission? Journal Article

In: Gut, vol. 74, no. 2, pp. 331-332, 2025, ISSN: 1468-3288 (Electronic) 0017-5749 (Linking).

Viral infection : persistence, host response and pathophysiology

Scientific Objectives

Our projects

AXIS 1: HIV

AXIS 2: HEV

Pathogenesis of HEV infection

HEV life cycle in hepatocytes and enterocytes

Other details

Our team

Publications

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

Social impact

Knowledge of the biology of RNA viruses and pathophysiological mechanisms.

Teaching commitment

Alumni

Partenaires Equipe 6

Sidaction

ANRS

ATIP AVENIR

Hôpitaux de Toulouse

CNRS