Biology subjects

Modave, E.

Publications and source records attributed to Modave, E..

6 recordsLinked to original sources

bioRxiv2026

Cirrhosis-associated immune dysfunction presents with preserved circulating lymphocyte function and altered intestinal intraepithelial lymphocyte profile

Bacterial infections are major drivers of decompensation and mortality in cirrhosis, yet the mechanisms underlying cirrhosis-associated immune dysfunction remain incompletely understood. Although current models frequently invoke adaptive immune exhaustion, intestinal intraepithelial lymphocytes (IELs), a central barrier immune compartment responsible for epithelial surveillance and microbial containment, have remained largely unexplored in cirrhosis. Here, we performed integrated immune profiling of paired duodenal biopsies and peripheral blood from healthy volunteers and patients with compensated or decompensated cirrhosis using spectral flow cytometry, plasma proteomics, immunofluorescence, and single-cell RNA sequencing. The healthy duodenal epithelium was dominated by CD8{beta} IELs, whereas cirrhosis was associated with marked depletion of these cells together with expansion of innate cytotoxic populations. Residual IELs exhibited attenuation of antimicrobial transcriptional programs alongside enrichment of innate-like cytotoxic pathways. Loss of CD8{beta} IELs was associated with coordinated reduction of CCR9 surface expression across circulating and mucosal CD8 T-cell compartments together with persistent systemic elevation of CCL25. In contrast, circulating lymphocytes retained functional competence and lacked enrichment of canonical exhaustion markers despite progressive inflammatory remodeling. Collectively, these findings identify defective intestinal IEL compartmentalization as a central feature of cirrhosis-associated immune dysfunction and implicate dysregulation of the CCL25-CCR9 axis in impaired mucosal immune surveillance. HighlightsO_LICirrhosis-associated immune dysfunction reflects defective mucosal immune compartmentalization rather than global adaptive immune paralysis C_LIO_LICirculating lymphocytes retain effector function and do not exhibit canonical exhaustion phenotypes C_LIO_LICD8{beta} intraepithelial lymphocytes are selectively depleted from the duodenal epithelium in cirrhosis C_LIO_LIPersistent systemic CCL25 elevation is associated with coordinated CCR9 loss across mucosal and circulating CD8 T-cell compartments C_LI

immunology↗

bioRxiv2024

Single cell transcriptomics reveal mast cell heterogeneity in the human gut

Gut mast cells are key players in infection and inflammation, as well as in homeostasis. Mast cells regulate gastrointestinal (GI) function by controlling vascular and epithelial permeability, and interacting with the immune system and the enteric nervous system. Mucosal (MCT) and connective tissue (MCTC) mast cells coexist in the gastrointestinal tract, but are located in distinct microanatomical niches. However, little is known about the transcriptional heterogeneity of human intestinal mast cells. Additionally, whether distinct microanatomical niches instruct mast cell phenotypes in the human gut is currently unknown. We therefore performed 10x single cell RNA sequencing on healthy rectal biopsies and on dissected layers of human sigmoid colon. We identified five transcriptionally distinct mast cell subsets (MC1-5) which exhibited a layer-specific distribution in the healthy human colon and distinct cytokine, chemokine, protease, and transcription factor profiles, and were associated with putative immune and neuro-immune functions. This study provides a framework for the integration of mast cell heterogeneity in the study of gastrointestinal disease mechanisms in humans.

immunology↗

bioRxiv2022

Neuro-immune Crosstalk in the Enteric Nervous System from Early Postnatal Development to Adulthood

Correct development and maturation of the enteric nervous system (ENS) is critical for survival. Early in life, the ENS requires significant refinement in order to adapt to the evolving needs of the tissue, changing from milk to solid food at the time of weaning. Here, we demonstrate that resident macrophages of the muscularis externa, MM{phi}, refine the ENS early in life by pruning synapses and phagocytosing abundant enteric neurons. After weaning, MM{phi} continue to closely interact with the ENS, acquire a microglia-like phenotype and are crucial for the survival of enteric neurons. Of note, this microglia-like phenotype is instructed by TGF{beta} produced by the ENS, introducing a novel reciprocal cell-cell communication responsible for the maintenance of the neuron-associated MM[FE] niche in the gut. These findings elucidate a novel role of intestinal macrophages in ENS refinement early in life, and open new opportunities to treat intestinal neurodegenerative disorders by manipulating the ENS-macrophage niche.

immunology↗

bioRxiv2021

CD8+ T Cell Metabolic Rewiring Defined by Single-Cell RNA-Sequencing Identifies a Critical Role of ASNS Expression Dynamics in T Cell Differentiation

Cytotoxic T cells dynamically rewire their metabolism during the course of an immune response. While T-cell metabolism has been extensively studied at phenotypic endpoints of activation and differentiation, the underlying dynamics remain largely elusive. Here, we leverage on single-cell RNA-sequencing (scRNA-seq) measurements of in vitro activated and differentiated CD8+ T cells cultured in physiological media to resolve these metabolic dynamics. We find that our scRNA-seq analysis identifies most metabolic changes previously defined in in vivo experiments, such as a rewiring from an oxidative to an anabolism-promoting metabolic program during activation to an effector state, which is later reverted upon memory polarization. Importantly, our scRNA-seq data further provide a dynamic description of these changes. In this sense, our data predict a differential time-dependent reliance of CD8+ T cells on the synthesis versus uptake of various non-essential amino acids during T-cell activation, which we corroborate with additional functional in vitro experiments. We further exploit our scRNA-seq data to identify metabolic genes that could potentially dictate the outcome of T-cell differentiation, by ranking them based on their expression dynamics. Among the highest-ranked hits, we find asparagine synthetase (Asns), whose expression sharply peaks for effector CD8+ T cells and further decays towards memory polarization. We then confirm that these in vitro Asns expression dynamics are representative of an in vivo situation in a mouse model of viral infection. Moreover, we find that disrupting these expression dynamics in vitro, by depleting asparagine from the culture media, delays central-memory polarization. Accordingly, we find that preventing the decay of ASNS by stable overexpression at the protein level in vivo leads to a significant increase in effector CD8+ T-cell expansion, and a concomitant decrease in central-memory formation, in a mouse model of viral infection. This shows that ASNS expression dynamics dictate the fate of CD8+ T-cell differentiation. In conclusion, we provide a resource of dynamic expression changes during CD8+ T-cell activation and differentiation that is expected to increase our understanding of the dynamic metabolic requirements of T cells progressing along the immune response cascade.

immunology↗

bioRxiv2020

A multi-layered systems approach for renal cell carcinoma

Renal cell carcinoma (RCC) still lacks prognostic and predictive biomarkers to monitor the disease and the response to therapy. The usual strategy in translational research is to start from human samples, to identify molecular markers and gene networks and then to functionally validate them in vitro and in animal models. We devised herein a completely opposite strategy from "mouse to man" by performing an aggressiveness screen and used functional genomics, imaging, clinical data and computational approaches in order to discover molecular pathways and players in renal cancer development and metastasis. Multiple cell lines for primary tumor growth, survival in the blood circulation and lung metastasis or metastatic spread from the primary tumor were generated and analyzed using a multi-layered approach which includes large-scale transcriptome, genome and methylome analyses. Transcriptome and methylome analyses demonstrated distinct clustering in three different groups. Remarkably, DNA sequencing did not show significant genomic variations in the different groups which indicates absence of clonal selection during the in vivo amplification process. Transcriptome analysis revealed distinct signatures of tumor aggressiveness which were validated in patient cohorts. Methylome analysis of full-length DNA allowed clustering of the same groups and revealed clinically relevant signatures. Furthermore, we identified SAA2 and CFB as soluble prognostic and predictive biomarkers of the therapeutic response. We also uncovered IL34 as another soluble prognostic biomarker and key regulator of renal cell carcinoma (RCC) progression. This was also functionally validated in vivo, and a mathematical model of IL34-dependent primary tumor growth and metastasis development was provided. These results indicate that such multilayered analysis in a RCC animal model leads to meaningful results that are of translational significance. One Sentence SummaryAn aggressiveness screen with multilayer systems analysis to identify signatures and biomarkers for renal cell carcinoma aggressiveness.

cancer biology↗

bioRxiv2019

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, impacting the accuracy of PDX modeling of human cancer. Here we exhaustively analyze copy number alterations (CNAs) in 1451 PDX and matched patient tumor (PT) samples from 509 PDX models. CNA inferences based on DNA sequencing and microarray data displayed substantially higher resolution and dynamic range than gene expression-based inferences, and they also showed strong CNA conservation from PTs through late-passage PDXs. CNA recurrence analysis of 130 colorectal and breast PT/PDX-early/PDX-late trios confirmed high-resolution CNA retention. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multi-region samples within patients. Our study demonstrates the lack of systematic copy number evolution driven by the PDX mouse host.

cancer biology↗