Training & Mentorship

"Mentoring young scientists is central to my research mission, with a focus on fostering intellectual independence, critical thinking, and the ability to navigate complex biological systems across scales—from molecular mechanisms to tissue-level organization."

Training and Mentorship of Young Investigators (2020–present)

👉 View earlier supervision (≤2020)

Postdoctoral Fellows

Dr. Zoi Vahlas: ANRS-funded Postdoctoral Fellow, IPBS-CNRS, Toulouse, France (2021–2023)
- Project: Role of Glycolysis in HIV-1 Transfer Between Macrophages in the Context of TB Co-infection.
- Supervision: Co-supervised with Dr. Christel Vérollet (IPBS-CNRS).
- Synopsis: Dr. Vahlas investigated how tuberculosis-associated microenvironments influence macrophage metabolism and their susceptibility to HIV-1 infection. Using in vitro models that mimic TB-associated conditions, she demonstrated that macrophages exposed to TB-derived factors exhibit increased ATP production, driven primarily by aerobic glycolysis. Transcriptomic analyses confirmed the enrichment of glycolytic pathways in these cells. Functional experiments using metabolic inhibitors and glucose deprivation revealed that glycolysis is required for efficient HIV-1 infection and dissemination between macrophages. Importantly, her work showed that glycolytic metabolism supports the formation of SIGLEC-1–decorated tunneling nanotubes (TNTs), which facilitate the cell-to-cell transfer of HIV-1 between macrophages, thereby promoting viral spread in TB-associated inflammatory environments.
- Significance: This study provided mechanistic insight into how metabolic reprogramming of macrophages during TB may enhance HIV-1 dissemination, highlighting glycolysis as a potential therapeutic target in TB/HIV co-infection.
- Output: Vahlas Z. et al. Life Science Alliance (2026), with Zoi Vahlas as first author and Christel Vérollet and me as senior authors.
- Current position: Team Leader, Evotec, Toulouse, France.

Dr. Elizabeth Bautista Rodríguez: SECIHTI (Mexican funding agency)- and ANRS-funded Postdoctoral Fellow, IPBS-CNRS, Toulouse, France (2025–2028)
- Project: Neuro-immune Regulation of Tuberculosis: Role of Nerve-Associated Macrophages in Granuloma Function and Disease Tolerance.
- upervision: Primary supervisor.
- Synopsis: Dr. Bautista’s project investigates the role of nerve-associated macrophages (NAMs) in the lung microenvironment during Mtb infection, as part of my broader research program on lung immune niches that shape macrophage behavior in TB. Her work aims to characterize the spatial distribution, transcriptional identity, and functional roles of NAMs in relation to granulomas and lung nerves. The project integrates single-cell transcriptomics, spatial multi-omics, conditional mouse genetics, and advanced imaging to dissect how neuronal signals and IFN-I pathways regulate macrophage responses and disease tolerance.
- Significance: This work will generate the first spatial multi-omics atlas of pulmonary NAMs in TB, providing mechanistic insight into neuroimmune circuits that regulate granuloma organization and pathology, and identifying potential host-directed therapeutic targets.
- Current position: Postdoctoral Fellow, IPBS-CNRS, Toulouse, France.

PhD DEGREE CONFERRED

Dr. Sarah Monard: PhD, Doctoral Program, Université de Toulouse, France (2019–2024)
- Thesis title: The Lung Microenvironment in Tuberculosis: from Alveolar Macrophage Characterization to the Discovery of an Atypical Non-immune Cell Population.
- Award: ANRS 4th-year doctoral scholarship.
- Supervision: Co-supervised with Dr. Christel Vérollet (IPBS-CNRS).
- Synopsis: Dr. Monard’s doctoral work explored how the lung microenvironment shapes immune responses during Mtb infection, with a particular focus on cellular components of the granuloma niche. Using immunohistology, tissue clearing, and comparative analyses across multiple species, she identified a previously unrecognized population of β3-tubulin (TUBB3)⁺stromal cells emerging within TB granulomas and inducible bronchus-associated lymphoid tissue (iBALT). These elongated cells were distinct from canonical neuronal structures normally found in peribronchial regions and were frequently located in close proximity to macrophages and T cells within inflammatory infiltrates. Comparative analyses across mouse, guinea pig, non-human primate, and human TB lesions demonstrated that remodeling of TUBB3⁺structures is a conserved feature of TB.
- Significance: This work revealed an unexpected TUBB3⁺stromal component associated with TB granulomas, providing the conceptual foundation for my current research program investigating neuro–immune niches and stromal regulation of immunity in the infected lung.
- Output: Monard S. et al., BioRxiv preprint (2025), with Sarah Monard as first author and Olivier Neyrolles, Christel Vérollet, and me as senior authors.
- Current position: Postdoctoral Fellow, Scott Mueller Laboratory, Doherty Institute for Infection and Immunity, Melbourne, Australia.

Dr. Natacha Faivre: PhD, Doctoral Program, Université de Toulouse, France (2022–2025)
- Thesis title: Macrophages as Therapeutic Targets in HIV-1 Infection and Tuberculosis.
- Supervision: Co-supervised with Dr. Christel Vérollet (IPBS-CNRS, 2023-2024); Mentor (2024-2025)
- Synopsis: Dr. Faivre’s doctoral research focused on the development of human lung models to study host–pathogen interactions and evaluate anti-TB therapies. Building on airway organoid technology, her work integrated airway air–liquid interface (ALI) cultures and alveolar macrophage-like cells to recreate two key lung niches encountered by Mtb: the epithelial airway barrier and the intracellular macrophage compartment. Using these complementary systems, she demonstrated compartment-specific activities of anti-TB drugs: isoniazid, rifampicin, and moxifloxacin were active in both epithelial and macrophage models, whereas pyrazinamide displayed activity primarily in the macrophage compartment. In parallel, host-directed therapies such as ibuprofen and doramapimod reduced inflammatory responses without consistently affecting bacterial burden, illustrating the ability of these models to discriminate antimicrobial versus immunomodulatory effects.
- Significance: This work established an integrated human lung modeling platform for translational evaluation of anti-TB drugs and host-directed therapies, enabling the assessment of therapeutic efficacy across distinct pulmonary niches.
- Output: Bomfim C.C.B., Faivre N. et al., BioRxiv preprint (2025); manuscript under revision at Microbiology Spectrum, with Natacha Faivre and Caio Bomfim as co-first authors and Céline Cougoule and me as senior authors.
- Current position: Seeking a postdoctoral position.

Current PhD Candidates

Maxime Pingret: PhD Candidate, Doctoral Program, Université de Toulouse, France (2024–present).
- Thesis title: Identification of a Distinct TUBB3⁺ Pericyte-like Cell Population in TB Granulomas.
- Supervision: Co-supervised with Dr. Christel Vérollet (IPBS-CNRS).
- Synopsis: Building on the discoveries from Sarah Monard’s doctoral work, Maxime first joined the laboratory as a Master’s student and continued as a PhD candidate to investigate the identity and function of the previously described TUBB3⁺ stromal cells found in TB granulomas. His work has demonstrated that these cells correspond to mural cells of the pulmonary vasculature, including pericytes, revealing their association with the perivascular niche within granulomatous lesions. Using genetically modified mouse models, single-cell RNA sequencing, spatial transcriptomics, and functional assays, his project aims to define the origin, phenotype, and immunological roles of these vascular-associated stromal cells in regulating granuloma organization and macrophage responses.
- Significance: This discovery establishes the conceptual and experimental foundation for an emerging research program in my laboratory focused on the perivascular niche as a regulator of immune responses during TB.

Clara Deyts: PhD Candidate, Doctoral Program, Université de Toulouse, France (2025–present).
- Thesis title: Axonogenesis in Pulmonary TB: Characterization of Innervation, Schwann Cells, and Their Functional Roles.
- Award: EUR UNITEID Doctoral Scholarship (2025–2028).
- Supervision: Co-supervised with Dr. Christel Vérollet (IPBS-CNRS).
- Synopsis: Clara Deyts’ doctoral project investigates neuro-immune interactions in pulmonary tuberculosis, focusing on the mechanisms of peribronchial axonogenesis and Schwann cell reprogramming during infection. Using advanced imaging, spatial multi-omics, and single-cell transcriptomics, her work aims to characterize the spatial distribution and functional roles of pulmonary innervation and Schwann cells in relation to TB granulomas.
- Significance: This project extends our research program on neuro-immune niches in the tuberculous lung to determine how Schwann cell–nerve interactions shape immune responses and disease progression, and whether neurotrophic pathways, such as GDNF signaling, contribute to infection-induced neural remodeling.

Master's DEGREE CONFERRED

EUROPEAN M2R

(1) Hugo Garnier, UPS, Toulouse (2020)

(2) Marine Joly, UPS, Toulouse (2022)

(3) Maxime Pingret, UPS, Toulouse (2024)

(4) Clara Deyts, UPS, Toulouse (2025)

EUROPEAN M1

(1) Hugo Garnier, UPS, Toulouse (2020)

(2) Clara Deyts, UPS, Toulouse (2024)

(3) Laura Decollard, UPS, Toulouse (2025)

Visiting students from foreign institutions

Joaquina Barros, PhD student, IRP Program (Argentina-France):

One-month internship: 2024

Leandro Ferrini, Postdoctoral fellow, IRP Program (Argentina-France):

Two-month internship: 2025

Samantha Cronin, PhD student, Campus France (Australia-France):

Two-month internship: 2025

Elizabeth Bautista, Postdoctoral fellow, Campus France (Mexico-France):

Four-month internship: 2025-2026

Career Mentor (BIG BROTHER)

(1) Stephen Leon-Icaza, doctoral program at UPS, Toulouse, France (2018-2024)

(2) Flor Torres-Juarez, doctoral program at Unidad de Investigación Biomedica de Zacatecas, Mexican Social Security Institute (IMSS), Mexico (2020-2025)

(3) Jose Manuel Sanchez-Lopez, Postdoctoral Fellow at IPBS, Toulouse, France (2025-PRESENT)

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