Biology subjects

Humblet-Baron, S.

Publications and source records attributed to Humblet-Baron, S..

7 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↗

bioRxiv2025

AutoSpectral improves spectral flow cytometry accuracy through optimised spectral unmixing and autofluorescence-matching at the cellular level

The advent of spectral flow cytometry has seen a rapid rise in the complexity of flow cytometry experiments, allowing the construction of assays with at least 50 fluorescent parameters. To correctly determine the contributions of each fluorophores signal to the high parameter data an accurate unmixing matrix needs to be generated. Even with single-stained controls, however, these matrixes include errors such as spillover spread, which compounds with each additional parameter, functionally limiting panel design. An additional source of errors is heterogeneity of cellular autofluorescence, which can affect both the unmixing matrix and misalign signals when the matrix is applied to individual cells in complex cell mixtures. Here we developed AutoSpectral, a statistical approach to automate the production of minimal-residual error unmixing matrixes and pair multiple distinct multifluorescent spectra to individual cells within a mixed sample, via an R-based software tool. AutoSpectral improves unmixing accuracy, improving incorrectly assigned cell positions by up to 9000-fold, reduces spread, particularly in samples with variable autofluorescence, and allows multi-lineage analysis of mixed populations, providing superior data for spectral flow cytometry experiments.

immunology↗

bioRxiv2024

Adults patients with autoinflammation of unknown origin partially phenocopy the immune presentation of Still's disease

Autoinflammation of unknown origin remains amongst the most enigmatic of systemic autoinflammatory disorders (SAIDs), immunological disorders characterized by inappropriate activation of the innate immune response. Recent clinical research has identified multiple distinct disorders, although overlap in clinical characteristics and genetic drivers impede rapid and precise diagnosis, and the immunological underpinning of disease is poorly understood. Here we aimed to understand the immunological process behind patients with autoinflammation of unknown origin. In a multi-center European trial, we collected samples from 36 patients with recent disease activity, and used deep immunophenotyping and plasma proteomics to compare to 58 healthy controls and an additional demographically-similar 92 SAID patients. Key immunological changes were upregulation of CD38 and HLA across T cell subsets and upregulation of acute phase plasma proteins in autoinflammation of unknown origin patients. These previously poorly characterised patients partially phenocopied the Stills disease presentation. Together this study identifies potential biomarkers and disease-mediators in autoinflammation of unknown origin.

immunology↗

bioRxiv2021

Simultaneous inhibition of human CD4 and 4-1BB biogenesis suppresses cytotoxic T lymphocyte proliferation

The small molecule cyclotriazadisulfonamide (CADA) down-modulates the human CD4 receptor, an important factor in T cell activation. Here, we addressed the immunosuppressive potential of CADA using in vitro activation models. CADA inhibited lymphocyte proliferation in a mixed lymphocyte reaction, and when human PBMCs were stimulated with CD3/CD28 beads or phytohemagglutinin. The immunosuppressive effect of CADA involved both CD4+ and CD8+ T cells but was, surprisingly, most prominent in the CD8+ T cell subpopulation where it inhibited cell-mediated lympholysis. We discovered a direct down-modulatory effect of CADA on 4-1BB (CD137) expression, a survival factor for activated CD8+ T cells. More specifically, CADA blocked 4-1BB protein biosynthesis by inhibition of its co-translational translocation across the ER membrane in a signal peptide-dependent way. This study demonstrates that CADA, as potent down-modulator of human CD4 and 4-1BB, has promising in vitro immunomodulatory characteristics for future in vivo exploration as immunosuppressive drug.

immunology↗

bioRxiv2020

AutoSpill: a method for calculating spillover coefficients in high-parameter flow cytometry

Compensating in classical flow cytometry or unmixing in spectral systems is an unavoidable challenge in the data analysis of fluorescence-based flow cytometry. In both cases, spillover coefficients are estimated for each fluorophore using single-color controls. This approach has remained essentially unchanged since its inception, and is increasingly limited in its ability to deal with high-parameter flow cytometry. Here, we present AutoSpill, a novel approach for calculating spillover coefficients or spectral signatures of fluorophores. The approach combines automated gating of cells, calculation of an initial spillover matrix based on robust linear regression, and iterative refinement to reduce error. Moreover, autofluorescence can be compensated out, by processing it as an endogenous dye in an unstained control. AutoSpill uses single-color controls and is compatible with common flow cytometry software, but it differs in two key aspects from current methods: (1) it is much less demanding in the preparation of controls, as it does not require the presence of well-defined positive and negative populations, and (2) it does not require manual tuning of the spillover matrix, as the algorithm iteratively computes the tuning, producing an optimal compensation matrix. Another algorithm, AutoSpread, complements this approach, providing a robust estimate of the Spillover Spreading Matrix (SSM), while avoiding the need for well-defined positive and negative populations. Together, AutoSpill and AutoSpread provide a superior solution to the problem of fluorophore spillover, allowing simpler and more robust workflows in high-parameter flow cytometry.

immunology↗

bioRxiv2018

Machine learning identifies the immunological signature of Juvenile Idiopathic Arthritis

Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease, with a strongly debated pathophysiological origin. Both adaptive and innate immune processes have been proposed as primary drivers, which may account for the observed clinical heterogeneity, but few high-depth studies have been performed. Here we profiled the adaptive immune system of 85 JIA patients and 43 age-matched controls, identifying immunological changes unique to JIA and others common across a broad spectrum of childhood inflammatory diseases. The JIA immune signature was shared between clinically distinct subsets, but was accentuated in the systemic JIA patients and those patients with active disease. Despite the extensive overlap in the immunological spectrum exhibited by healthy children and JIA patients, machine learning analysis of the dataset proved capable of diagnosis of JIA patients with ~90% accuracy. These results pave the way for large-scale longitudinal studies of JIA, where machine learning could be used to predict immune signatures that correspond to treatment response group.

immunology↗

bioRxiv2018

Mice deficient in nucleoporin Nup210 develop peripheral T cell alterations

The nucleopore is an essential structure of the eukaryotic cell, regulating passage between the nucleus and cytoplasm. While individual functions of core nucleopore proteins have been identified, the role of other components, such as Nup210, are poorly defined. Here, through the use of an unbiased ENU mutagenesis screen for mutations effecting the peripheral T cell compartment, we identified a Nup210 mutation in a mouse strain with altered CD4 / CD8 T cell ratios. Through the generation of Nup210 knockout mice we identified Nup210 as having a T cell-intrinsic function in the peripheral homeostasis of T cells. Remarkably, despite the deep evolutionary conservation of this key nucleopore complex member, no other major phenotypes developed, with viable and healthy knockout mice. These results identify Nup210 as an important nucleopore complex component for peripheral T cells, and raise further questions of why this nucleopore component shows deep evolutionary conservation despite seemingly redundant functions in most cell types.

immunology↗