Biology subjects

Dufour, C.

Publications and source records attributed to Dufour, C..

6 recordsLinked to original sources

bioRxiv2026

Recipient-driven metabolic and epigenetic remodeling of donor hematopoietic cells after transplantation in Fanconi Anemia.

Background Haematopoietic cell transplantation (HCT) restores donor-derived haematopoiesis in Fanconi anaemia (FA) but leaves recipient stromal and other non-haematopoietic cells genetically uncorrected. We investigated to what extent the persistent FA recipient environment influences the metabolic, redox, inflammatory and epigenetic phenotype of donor-derived haematopoietic cells after HCT. Methods Peripheral blood and, when available, bone marrow samples were analysed from healthy donors, patients with FA before and after HCT, and severe aplastic anaemia (SAA) patients after HCT as transplant controls. Mitochondrial function, cellular energy status, oxidative damage, antioxidant responses and circulating cytokines were assessed. Healthy donor mononuclear cells were exposed to conditioned media from FANCA-deficient mesenchymal stromal cells or FA fibroblasts, with FANCA-corrected fibroblasts as controls. DNA methylation profiling, acute inflammatory stimulation and pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress were also performed. Results Despite stable full donor chimerism, FA recipients retained a pro-inflammatory and pro-oxidative circulating environment after HCT that was not observed in SAA transplant controls. Donor-derived mononuclear cells exposed to this environment acquired a distinct dysfunctional phenotype characterized by impaired mitochondrial oxidative phosphorylation and energy homeostasis, compensatory antioxidant and stress-response activation, and persistent lipid and protein oxidation. These alterations remained detectable after 96 h of ex vivo culture, suggesting relatively stable cellular remodelling, and were accompanied by a DNA methylation profile that, although globally shifted toward the donor state, retained an intermediate FA-associated episignature. Mechanistically, conditioned media from FANCA-deficient stromal cells and FA fibroblasts reproduced mitochondrial and oxidative abnormalities in healthy donor cells, whereas FANCA-corrected fibroblasts did not. Pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress improved energy homeostasis and reduced oxidative damage, supporting a contributory role for chronic inflammation and oxidative stress in the microenvironment-driven phenotype acquired by donor-derived cells. Conclusions HCT corrects FA haematopoiesis without fully normalising the recipient environment. Persistent exposure to the FA milieu promotes metabolic, redox, signalling and epigenetic remodelling of donor-derived haematopoietic cells after transplantation. These findings identify the recipient environment as a determinant of post-HCT cell biology and highlight chronic inflammation and oxidative stress as mechanisms contributing to donor-cell remodelling in FA.

cell biology↗

bioRxiv2025

Transforming Esogastric Cancer Surgery Integrating SpiderMass Mass Spectrometry with Clinical and Microbiome Data for Margin Delineation and Prognosis

Esophageal-gastric cancers (EC) represent a significant global health concern, with esophageal cancer ranking seventh in terms of incidence and mortality worldwide. Gastric cancer is especially concerning, with an estimated one million new cases and 800,000 deaths annually. Late diagnoses often lead to poor outcomes, requiring critical interventions such as radical surgical resection with clear margins, in conjunction with chemotherapy, or radiotherapy to prevent recurrences and enhance survival. Thus, EC represents a significant clinical challenge, especially given the difficulty in achieving precise surgical margins in aggressive subtypes like poorly cohesive carcinoma (PCC). Moreover, pathological intraoperative margin assessment encounters significant issues, especially for PCCs, due to lacks of sensitivity for microscopic infiltration, potentially leading to recurrence and poorer patient outcomes. We address these critical limitations by integrating SpiderMass, an ambient mass spectrometry (MS) technology, with clinical metadata and microbiome profiling couple along with Machine learning. We demonstrate SpiderMass capability in real-time molecular margin delineation and identify distinct lipidomic and microbiome signatures correlating with tissue type and prognosis. Our integrative approach provides a more precise and biologically informative intraoperative diagnostic tool, significantly enhancing surgical decision-makin, to improve patient outcomes and extend survival.

cancer biology↗

bioRxiv2025

miR-29a-3p and TGF-beta Axis in Fanconi Anemia: Mechanisms Driving Metabolic Dysfunction and Genome Stability

Fanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure and cancer susceptibility due to defective DNA double-strand break repair. However, FA cells are also characterized by mitochondrial dysfunction and redox imbalance. To identify a common factor among these alterations, we focused on miR-29a-3p, a microRNA involved in hematopoiesis. Our data show that miR-29a-3p is downregulated in lymphoblasts and fibroblasts mutated for the FANC-A gene, causing the overexpression of its target genes, FOXO3, SGK1, and IGF1, which results in PI3K/AKT pathway hyperactivation, altered mitochondrial metabolism and insufficient antioxidant response. Furthermore, miR-29a-3p downregulation appears associated with hyperactivation of the TGF-{beta} signal. However, restoring miR-29a-3p expression improves mitochondrial metabolism, oxidative stress response, and DNA damage repair by inhibiting the PI3K/AKT pathway and modulating TGF-{beta} signaling by a feedback mechanism. Based on these findings, miR-29a-3p appears as a promising molecular target to address several mechanisms based on FA pathogenesis.

cell biology↗

bioRxiv2022

HIV rapidly targets a diverse pool of CD4+ T cells to establish productive and latent infections

Upon infection, HIV disseminates throughout the human body within 1-2 weeks. However, its early cellular targets remain poorly characterized. We analyzed productively and latently infected cells in blood and lymphoid tissue from individuals in acute infection. The phenotype of productively infected cells rapidly evolved with time and differed between blood and lymph nodes. The TCR repertoire of productively infected cells was heavily biased, with preferential infection of previously expanded/disseminated cells, but composed almost exclusively of unique clonotypes, indicating that they were the product of independent infection events. Latent genetically intact proviruses were already archived early in infection. Hence, productive infection is initially established in a pool of phenotypically and clonotypically distinct T cells in blood and lymph nodes and latently infected cells are generated simultaneously. One-Sentence SummaryHIV initially infects phenotypically and clonotypically distinct T cells and establishes a latent reservoir concomitantly.

microbiology↗

bioRxiv2020

Editing of the TRIM5 gene decreases the permissiveness of human T lymphocytic cells to HIV-1

TRIM5 is a cytoplasmic antiretroviral effector upregulated by type I interferons (IFN-I). We previously showed that two points mutations, R332G/R335G, in the retroviral capsid-binding region confer human TRIM5 the capacity to target and strongly restrict HIV-1 upon over-expression of the mutated protein. Here, we used CRISPR-Cas9-mediated homology-directed repair (HDR) to introduce these two mutations in the endogenous human TRIM5 gene. We found 6 out of 47 isolated cell clones containing at least one HDR-edited allele. One clone (Clone 6) had both alleles containing R332G but only one of the two alleles containing R335G. Upon challenge with an HIV-1 vector, clone 6 was significantly less permissive compared to unmodified cells, whereas the cell clones with monoallelic modifications were only slightly less permissive. Following IFN-{beta} treatment, inhibition of HIV-1 infection in clone 6 was significantly enhanced (~40-fold inhibition). TRIM5 knockdown confirmed that HIV-1 was inhibited by the edited TRIM5 gene products. Quantification of HIV-1 reverse transcription products showed that inhibition occurred through the expected mechanism. In conclusion, we demonstrate the feasibility of potently inhibiting a viral infection through editing of innate effector genes. Our results also emphasize the importance of biallelic modification in order to reach significant levels of inhibition by TRIM5.

microbiology↗

bioRxiv2017

Editing of the Human TRIM5 Gene to Introduce HIV-1 Restrictive Mutations Using CRISPR-Cas9

The type I interferon (IFN-I)-inducible human restriction factor TRIM5 inhibits the infection of human cells by specific nonhuman retroviruses, such as N-MLV and EIAV, but does not generally target HIV-1. However, the introduction of two aminoacid substitutions, R332G and R355G, in the human TRIM5 (huTRIM5) domain responsible for retroviral capsid recognition leads to efficient HIV-1 restriction. Using a DNA transfection-based CRISPR-Cas9 genome editing protocol, we successfully mutated TRIM5 to its HIV-1-restrictive version by homology-directed repair (HDR) in HEK293T cells. Nine clones bearing at least one HDR-edited TRIM5 allele containing both mutations were isolated (5.6% overall efficiency), whereas another one contained only the R332G mutation. Of concern, several of these HDR-edited clones contained on-target undesired mutations, and none had all the alleles corrected. We observed a lack of HIV-1 restriction in the cell clones generated, even when cells were stimulated with IFN-I prior to infection. This, however, was partly explained by the unexpectedly low potential for TRIM5-mediated restriction activity in this cell line. Our study demonstrates the feasibility of editing the TRIM5 gene to in human cells and identifies the main challenges to be addressed in order to use this approach to confer protection from HIV-1.

microbiology↗