Biology subjects

Rousseau, S.

Publications and source records attributed to Rousseau, S..

9 recordsLinked to original sources

bioRxiv2025

Human RIG-I deficiency confers susceptibility to Kaposi Sarcoma via loss of latency control

Kaposi sarcoma (KS), caused by the DNA-virus Kaposis sarcoma-associated herpesvirus (KSHV), occurs during T cell immunosuppression (HIV, transplant) or sporadically in some immunocompetent and aging individuals (endemic, classic KS respectively). In absence of known T cell immunosuppression KS pathogenesis remains enigmatic. KS therapy with topical or oral retinoid medication, or recombinant alpha interferon, can induce remission and suggests the involvement of two signalling pathways. Retinoic acid-inducible gene-I (RIG-I) encoded by DDX58 is canonically a sensor of RNA-viruses, its function in human immunity against DNA-viruses remains poorly defined. We report a patient with classic KS, carrying a homozygous nonsense (p.Q393*) mutation in DDX58, abolishing RIG-I expression and specifically impairing RIG-I agonist responses. In isogenic cell models, loss of RIG-I compromised responses during both KSHV primary infection and viral reactivation, diminishing induction of type I interferons and interferon-stimulated genes, skewing to a persistent latent viral gene program, and dysregulating cellular pro-oncogenic pathways by transcriptomic and proteomic profiling. This work defines the first innate immunodeficiency underlying classical KS, revealing RIG-Is role in KSHV immunopathogenesis and expanding its function in human antiviral immunity beyond RNA-viruses, while identifying promising therapeutic targets. Significance statementRIG-I deficiency causes classic KS by failing to control KSHV infection and reactivation, expanding its role beyond RNA-viruses.

immunology↗

bioRxiv2024

Disordered regions of human eIF4B orchestrate a dynamic self-association landscape

Eukaryotic translation initiation factor eIF4B is required for efficient cap-dependent translation, it is overexpressed in cancer cells, and may influence stress granule formation. Due to the high degree of intrinsic disorder, eIF4B is rarely observed in cryo-EM structures of translation complexes and only ever by its single structured RNA recognition motif domain, leaving the molecular details of its large intrinsically disordered region (IDR) unknown. By integrating experiments and simulations we demonstrate that eIF4B IDR orchestrates and fine-tunes an intricate transition from monomers to a condensed phase, in which large-size dynamic oligomers form before mesoscopic phase separation. Single-molecule spectroscopy combined with molecular simulations enabled us to characterize the conformational ensembles and underlying intra- and intermolecular dynamics across the oligomerization transition. The observed sensitivity to ionic strength and molecular crowding in the self-association landscape suggests potential regulation of eIF4B nanoscopic and mesoscopic behaviors such as driven by protein modifications, binding partners or changes to the cellular environment.

biophysics↗

bioRxiv2024

B cell-mediated antigen presentation promotes adverse cardiac remodeling in chronic heart failure

The cardio-splenic axis is a promising therapeutic target in ischemic heart failure (HF), but splenic-cardiac interactions after myocardial infarction (MI) are poorly understood. Here, we show that splenic follicular B cells drive ischemic HF via MHC class II-mediated antigen presentation. Transfer of splenic B cells from mice with ischemic HF induced adverse cardiac remodeling and modulated myocardial T-cells in naive recipients. Single-cell RNA sequencing of mouse and human post-MI B cells revealed upregulation of antigen-presentation related pathways. Mass spectrometry of the MHC II peptidome demonstrated enrichment of cardiac-derived peptides in MHC II molecules of splenic B cells from ischemic HF mice. B cell-specific deletion of MHC II suppressed adverse cardiac remodeling after adoptive transfer of post-MI splenic B cells. These results broaden our understanding of B-lymphocyte biology and point towards MHC II-mediated signaling in B-cells as a novel therapeutic target in ischemic HF.

immunology↗

bioRxiv2023

B cells occupy a unique, dynamic, biological niche within the human myocardium

IntroductionGrowing evidence from animal models indicates that the myocardium hosts a population of B cells that play a role in the development of cardiomyopathy. However, there is minimal data on human myocardial B cells in the context of cardiomyopathy. MethodsWe integrated single-cell and single-nuclei datasets from 45 healthy human hearts, 70 hearts with dilated cardiomyopathy (DCM), and 8 hearts with Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC). Interactions between B cells and other cell types were investigated using the CellChat Package. Differential gene expression analysis comparing B cells across conditions was performed using DESeq2. Pathway analysis was performed using Ingenuity, KEGG, and GO pathways analysis. ResultsWe identified 1,100 B cells, including naive B cells and plasma cells. B cells showed an extensive network of interactions within the healthy myocardium that included outgoing signaling to macrophages, T cells, endothelial cells, and pericytes, and incoming signaling from endothelial cells, pericytes, and fibroblasts. This niche relied on ECM-receptor, contact, and paracrine interaction; and changed significantly in the context of cardiomyopathy, displaying disease-specific features. Differential gene expression analysis showed that in the context of DCM both naive and plasma B cells upregulated several pathways related to immune activation, including upregulation of oxidative phosphorylation, upregulation of leukocyte extravasation, and, in naive B cells, antigen presentation. DiscussionThe human myocardium contains naive B cells and plasma cells, integrated into a diverse and dynamic niche that has distinctive features in healthy myocardium, DCM, and ARVC. Naive myocardial-associated B cells likely contribute to the pathogenesis of human DCM.

immunology↗

bioRxiv2023

Intracellular Pseudomonas aeruginosa within the airway epithelium of Cystic Fibrosis lung tissues

RATIONALEPseudomonas aeruginosa (P.a.) is the major bacterial pathogen colonizing the airways of adult cystic fibrosis (CF) patients and causes chronic infections that persist despite antibiotic therapy. Intracellular bacteria may represent an unrecognized reservoir of bacteria that evades the immune system and antibiotic therapy. While the ability of P.a. to invade and survive within epithelial cells has been described in vitro in different epithelial cell models, evidence of this intracellular lifestyle in human lung tissues is currently lacking. OBJECTIVESTo detect and characterize intracellular P.a. in CF airway epithelium from human lung explant tissues. METHODSWe sampled the lung explant tissues from CF and non-CF patients undergoing lung transplantation and analyzed lung tissue sections for the presence of intracellular P.a. by quantitative culture and microscopy, in parallel to histopathology and airway morphometry. MEASUREMENTS AND MAIN RESULTSP.a. was isolated from the lungs of 7 CF patients undergoing lung transplantation. Microscopic assessment revealed the presence of intracellular P.a. within airway epithelial cells in 3 out of the 7 lungs analyzed, at a varying but rare frequency. We observed those events occurring in lung regions with high bacterial burden. CONCLUSIONThis is the first study describing the presence of intracellular P.a. in CF lung tissues. While intracellular P.a. in airway epithelial cells are likely relatively rare events, our findings highlight the plausible occurrence of this intracellular bacterial reservoir in chronic CF infections.

microbiology↗

bioRxiv2023

RAMEN identifies effective indicators for severe COVID and Long COVID patients

The COVID-19 pandemic has significantly altered global socioeconomic structures and individual lives. Understanding the disease mechanisms and facilitating diagnosis requires comprehending the complex interplay among clinical factors like demographics, symptoms, comorbidities, treatments, lab results, complications, and other metrics, and their relation to outcomes such as disease severity and long term outcomes (e.g., post-COVID-19 condition/long COVID). Conventional correlational methods struggle with indirect and directional connections among these factors, while standard graphical methods like Bayesian networks are computationally demanding for extensive clinical variables. In response, we introduced RAMEN, a methodology that integrates Genetic Algorithms with random walks for efficient Bayesian network inference, designed to map the intricate relationships among clinical variables. Applying RAMEN to the Biobanque quebecoise de la COVID-19 (BQC19) dataset, we identified critical markers for long COVID and varying disease severity. The Bayesian Network, corroborated by existing literature and supported through multi-omics analyses, highlights significant clinical variables linked to COVID-19 outcomes. RAMENs ability to accurately map these connections contributes substantially to developing early and effective diagnostics for severe COVID-19 and long COVID.

bioinformatics↗

bioRxiv2022

Inhibition of the TPL2-MKK1/2-ERK1/2 pathway has cytostatic effect on B-Cell Lymphoma

1)Diffuse Large B-Cell Lymphoma (DLBCL) are the most common form of non-Hodgkin lymphoma. Their molecular origin is heterogeneous and therefore treatments aimed at DLBCL must be adapted in function of the underlying molecular mechanisms driving cellular transformation. Constitutive activation of the protein kinases ERK1/2 is a hallmark of many B-cell malignancies. ERK1/2 activation which can occur downstream of the classical MAPK cascade via RAF or, in response to TLR stimulation, via the Tumor Promoting Locus 2 (TPL2) protein kinase. This pathway also relays signals from the MYD88 oncogenic mutant L265P, frequently found in hematologic malignancies. We report here that TPL2 participate to ERK1/2 activation downstream of BCR in a DLBCL cell line (OCI-Ly2). Moreover, we showed that a ERK2[Y316F] mutant increased c-Myc-luciferase reporter expression. We then investigated the impact of ERK1/2 inhibition on the proliferation of OCI-Ly2 cells. We found that blocking ERK1/2 MAPK signaling cascade using either MKK1/2 inhibitors (PD184352 and MEK162) or TPL2 inhibitor (Compound 1) was mainly cytostatic. Finally, we showed that while TPL2-MKK1/2 inhibition leads to cytostatic effect, Compound 1 has cytocidal effect at high concentrations, that is mediated via additional targets. Taken together, this study demonstrates the involvement of TPL2 in oncogenic signaling of DLBCL and supports the idea that combination therapy targeting multiple molecular pathways linked to cellular transformation is a superior avenue for future therapies.

pharmacology and toxicology↗

bioRxiv2021

Impaired SorLA maturation and trafficking as a new mechanism for SORL1 missense variants in Alzheimer disease

The SorLA protein, encoded by the SORL1 gene, is a major player in Alzheimers disease (AD) pathophysiology. Functional and genetic studies demonstrated that SorLA deficiency results in increased production of A{beta} peptides, and thus a higher risk of AD. A large number of SORL1 missense variants have been identified in AD patients, but their functional consequences remain largely undefined. Here, we identified a new pathophysiological mechanism, by which rare SORL1 missense variants identified in AD patients result in altered maturation and trafficking of the SorLA protein. An initial screening, based on the overexpression of 71 SorLA variants in HEK293 cells, revealed that 15 of them (S114R, R332W, G543E, S564G, S577P, R654W, R729W, D806N, Y934C, D1535N, D1545E, P1654L, Y1816C, W1862C, P1914S) induced a maturation and trafficking-deficient phenotype. Three of these variations (R332W, S577P, and R654W) and two maturation-competent variations (S124R and N371T) were further studied in details in CRISPR/Cas9-modified hiPSCs. When expressed at endogenous levels, the R332W, S577P, and R654W SorLA variants also showed a maturation defective profile. We further demonstrated that these variants were largely retained in the endoplasmic reticulum, resulting in a reduction in the delivery of SorLA mature protein to the plasma membrane and to the endosomal system. Importantly, expression of the R332W and R654W variants in hiPSCs was associated with a clear increase of A{beta} secretion, demonstrating a loss-of-function effect of these SorLA variants regarding this ultimate readout, and a direct link with AD pathophysiology. Furthermore, structural analysis of the impact of missense variations on SorLA protein indicated that impaired cellular trafficking of SorLA protein could be due to subtle variations of the protein 3D structure resulting from changes in the interatomic interactions.

cell biology↗

bioRxiv2020

Identification of COVID-19-relevant transcriptional regulatory networks and associated kinases as potential therapeutic targets

Identification of transcriptional regulatory mechanisms and signaling networks involved in the response of host to infection by SARS-CoV-2 is a powerful approach that provides a systems biology view of gene expression programs involved in COVID-19 and may enable identification of novel therapeutic targets and strategies to mitigate the impact of this disease. In this study, we combined a series of recently developed computational tools to identify transcriptional regulatory networks involved in the response of epithelial cells to infection by SARS-CoV-2, and particularly regulatory mechanisms that are specific to this virus. In addition, using network-guided analyses, we identified signaling pathways that are associated with these networks and kinases that may regulate them. The results identified classical antiviral response pathways including Interferon response factors (IRFs), interferons (IFNs), and JAK-STAT signaling as key elements upregulated by SARS-CoV-2 in comparison to mock-treated cells. In addition, comparing SARS-Cov-2 infection of airway epithelial cells to other respiratory viruses identified pathways associated with regulation of inflammation (MAPK14) and immunity (BTK, MBX) that may contribute to exacerbate organ damage linked with complications of COVID-19. The regulatory networks identified herein reflect a combination of experimentally validated hits and novel pathways supporting the computational pipeline to quickly narrow down promising avenue of investigations when facing an emerging and novel disease such as COVID-19.

systems biology↗