Biology subjects

Hillion, S.

Publications and source records attributed to Hillion, S..

4 recordsLinked to original sources

bioRxiv2026

AltraFlowSOM: A Semi-Supervised Framework for Imaging Mass Cytometry Phenotyping

Imaging Mass Cytometry (IMC) enables the simultaneous quantification of 40+ protein markers at single cell resolution in tissue, however biologically faithful phenotyping at scale remains a critical bottleneck. Unsupervised clustering fragments coherent populations or conversely merges biologically incoherent ones into a single cluster, supervised classifiers impose a closed vocabulary, and the presence of rare subsets (encoding clinically relevant biology) in conjunction with abundant subsets may be detrimental to detection performances. We present AltraFlowSOM, a semi-supervised extension of FlowSOM that embeds partial expert annotations directly into self-organizing map training via a two-layer SuperSOM architecture, balancing label-guided topology anchoring with unsupervised discovery. By anchoring the map to biologically labelled reference points, AltraFlowSOM circumvents the canonical dependency between batch correction and clustering. Evaluated under Leave-one-out cross validation on two independent IMC cohorts, Lupus Nephritis (n=22 ROIs) and Sjogren syndrome (n=10 ROIs), AltraFlowSOM outperformed all unsupervised and supervised baseline on Adjusted Rand Index, F1 scores (macro and weighted), weighted purity and in the identification of rare populations. The median Treg cell recovery exceeded that of all comparator methods. AltraFlowSOM resolves the scalability-alignment-discovery trilemma, by establishing a semi-supervised SOM as a generalizable method for high dimensional IMC phenotyping.

bioinformatics↗

bioRxiv2026

FloREN: Decoding Immune Regulatory Networks through Interpretable Graph Transformer Patient Representations.

Single-cell RNA sequencing (scRNA-seq) enables detailed characterization of cellular heterogeneity, yet understanding the full cellular and regulatory environment of complex tissues remains challenging. In the era of large single-cell atlases, this technology has become increasingly accessible, and datasets have grown in scale and statistical power. As a result, sample representation methods have emerged as a promising strategy to summarize patient-level biological variation. However, most existing approaches rely on unsupervised learning frameworks with ambiguous biological interpretability. Here we present a Framework for Learning Over REgulatory-Embedding Networks (FloREN), a supervised and interpretable sample representation method. FloREN models single-cell data as a heterogeneous network integrating cells and genes together with gene regulatory and cell-cell communication relationships. Through condition-aware embeddings and interpretable attention networks, FloREN enables improved sample stratification and biomarker discovery. In addition, the framework supports downstream analyses that found specific immune network mechanisms in immune-mediated inflammatory diseases (IMIDs).

bioinformatics↗

bioRxiv2024

B-Cell Involvement in Immune Checkpoint Inhibitor-Induced Lichen Planus: A Comparative Analysis with Non-Drug-Related Lichen Planus.

BackgroundImmune checkpoint inhibitors (ICI) have significantly improved cancer prognosis but can lead to immune-related adverse events (irAE), including cutaneous manifestations affecting 30% to 60% of ICI-treated patients. However, the physiopathology of cutaneaous irAE remains unclear. ObjectiveThis study investigated the immune infiltration in tissues affected by cutaneous irAE to elucidate their contribution to the pathogenesis of these toxicities. MethodsSkin biopsies from 6 patients with ICI-induced lichenoid eruptions were compared using imaging mass cytometry to samples from 7 controls with non-drug-related lichen planus. ResultsT cells were the predominant cell type within the inflammatory infiltrate in all samples, but we observed a reduced T-cell infiltration and an increased B-cell frequency in ICI-induced lichen planus compared to non-drug related lichen planus. Among B cells, we observed a significant decrease in IgD-CD27-double-negative B cells and an increase in IgD+CD27-naive B cells. Spatial analysis demonstrated that infiltrating B cells were organized in aggregates close to T cells in ICI-induced lichen planus. LimitationsThis is a retrospective single-center study with a relatively small sample size. ConclusionThis study sheds light on the involvement of B cells in the pathogenesis of ICI-induced lichen planus, suggesting distinct immunological mechanisms from non-drug-related lichen planus. CAPSULE SUMMARYO_LILichenoid manifestations are a common but understudied side effect occurring in patients receiving anti-PD-1 antibodies. C_LIO_LIICI-induced lichen planus displays distinct physiopathology from non-drug-related lichen planus, with a decrease of T-cell infiltration concomitantly to the increase of B cells organized in aggregates. C_LI

immunology↗

bioRxiv2021

IL-21 and IFN-α have both opposite and redundant role on human innate precursors and memory B-cell differentiation.

Immunological memory is essential for effective immune protection upon antigen rechallenge. Memory B cells encompass multiple subsets, heterogeneous in terms of phenotypes, origins and precursors, anatomical localization, and functional responses. B-cell responses are conditioned by micro-environmental signals, including cytokines. Here, we analyzed in vitro the effects of two cytokines implicated in B-cell differentiation, interferon-alpha (IFN-) and interleukin (IL)-21, on the early functional response of four different mature B-cell subsets (IgD- CD27- naive, IgD+ CD27+ unswitched, IgD- CD27+ switched and double-negative B cells). The dual response of naive and memory B cells to IL-21 allowed us to uncover a unique IgD+ CD27- CD10- B-cell population (referred to as NARB+) characterized by the expression of marginal zone B-cell markers CD45RB and CD1c. Similar to memory B cells, NARB+ cells were in a pre-activated state, allowing them to rapidly differentiate into plasmablasts upon innate signals while maintaining their susceptibility to IL-21 activation-induced apoptosis as observed for the naive compartment. Both in-depth phenotypic analysis of circulating B cells, and identification of these cells in spleen, tonsil and gut-associated lymphoid tissues, supported that NARB+ are uncommitted precursors of human marginal zone B cells.

immunology↗