Biology subjects

Fink, M.

Publications and source records attributed to Fink, M..

7 recordsLinked to original sources

bioRxiv2026

The metabolic reprogramming of T cells controls airway remodeling in severe asthma

Mixed granulocytic asthma (MGA) is a severe Th2-low endotype, characterized by high Th17/neutrophilic burden and exacerbated airway remodeling. Both features confer resistance to inhaled corticosteroids, and typical asthma treatments. Thus, MGA is an enormous public health burden. Gaps in knowledge include how Th17 cells induce pathological tissue remodeling, and how Th17 differentiation occurs in response to allergens. We generated a Th2-low murine model of asthma that recapitulates major features of human MGA namely, heightened airway reactivity to methacholine, Th17/neutrophilic inflammation, airway remodeling, and resistance to corticosteroid treatment. Two specific biomarkers enriched in human MGA, the TNF superfamily member 14 (aka LIGHT), and the mitochondrial oxidative phosphorylation (OXPHOS) pathway, are upregulated in this model. We show OXPHOS promotes the metabolic reprograming of Th17 cells, to produce LIGHT that controls airway remodeling. Mechanistically, OXPHOS regulates ROR{gamma}t expression and the subsequent transcriptional network to program survival and differentiation of Th17 cells, whereas LIGHT drives airway remodeling by activating the MMP9-dependent TGF{beta} pathway. Additionally, OXPHOS+Th17 cells promote the expression of osteopontin necessary for fibroblast activation. LIGHT antagonistic blockade reduces airway remodeling, whereas OXPHOS chemical inhibition reduces Th17 cells and neutrophilia. Importantly, the dual blockade of LIGHT and OXPHOS reverses all features of MGA and reciprocally increase the numbers of Treg cells. Thus, the dual blockade of LIGHT and OXPHOS constitutes a promising target for clinical interventions in human MGA, possibly extending to other Th17-driven fibrotic diseases.

immunology↗

bioRxiv2025

Lgr5+ Stem Cells Maintain Apex Position in Cell Hierarchy of the Intestinal Epithelium During Homeostasis and Injury

The cellular origin of intestinal epithelial homeostasis and regeneration has been a subject of continued debate, with recent models challenging the primacy of WNT-dependent Lgr5 crypt base columnar (CBC) cells as the central intestinal stem cell population. Here, we revisit this question through quantitative integration of single-cell transcriptomic, chromatin accessibility, spatial, and lineage-tracing analyses across the proximal-to-distal axis of the small intestinal epithelium. Our data show that under homeostatic conditions, Lgr5 cells exclusively sustain epithelial self-renewal in nearly all crypt-villus units along the entire length of the small intestine, a process for which R-spondin is indispensable. Following irradiation or chemotoxic injury, surviving Lgr5 cells and their progeny reprogram into transient fetal-like cell states that initiate epithelial repair. Crucially, successful regeneration depends on the reactivation of canonical WNT/{beta}-catenin signaling, as evidenced by increased TCF motif accessibility and upregulation of WNT target genes in newly forming Lgr5+ stem cells. Accordingly, pharmacological inhibition of WNT signaling blocks the reconstitution of Lgr5 cells and crypt regeneration, leading to epithelial collapse. These findings reconcile prior controversies by demonstrating the central role of Lgr5 CBC cells in epithelial self-renewal and regeneration following injury.

cell biology↗

bioRxiv2024

Chromatin Remodelling in Damaged Intestinal Crypts Orchestrates Redundant TGFβ and Hippo Signalling to Drive Regeneration

Cell state dynamics underlying regeneration are under-characterized. Intestinal damage prompts reprogramming into revival stem cells (revSCs) that reconstitute Lgr5+ intestinal stem cells (ISCs). Single nuclei multiomics of chromatin accessibility and transcriptomes during regeneration from irradition showed revSCs display epigenetic profiles shared with ISCs and differentiated lineages. Furthermore, while revSC genes are accessible throughout homeostatic epithelia, damage-induced global alterations in crypt and revSC chromatin converge on TGF{beta}, as well as Hippo pathways. We show TGF{beta} directly induces functional revSCs and demonstrate individual revSCs form organoids with reconstituted Lgr5+ ISCs. Despite this, loss of TGF{beta} signalling yielded mild regenerative defects. In contrast, interference in both Hippo and TGF{beta} abolished revSCs, precluded generation of new ISCs and led to rapid intestinal collapse. Thus, the epithelium is poised to engage the revSC regenerative program that relies on crypt-localized, transient morphogen cues that function in a compensatory manner to support intestinal regeneration.

molecular biology↗

bioRxiv2024

Giardia Increases Macrophage Production of the Anti-Inflammatory Cytokine Interleukin-10 in Response to Lipopolysaccharide via Macrophage Galactose Binding Lectin (MGL1)

Giardia duodenalis is an intestinal protozoan parasite, common in low- and middle-income countries. Infection is frequently subclinical, even when it is associated with other pathologies like growth stunting in children. Recent longitudinal cohort studies have found Giardia more frequently in patients with milder symptoms and have even suggested that Giardia reduces rotavirus symptom severity. One potential mechanism for limiting disease severity due to other enteropathogens is the promotion of anti-inflammatory responses that limit pathology. Our lab previously showed that Giardia reduced production of IL-12 by dendritic cells stimulated with TLR agonists. In this study, we show that Giardia increases the production of the anti-inflammatory cytokine IL-10 by mouse peritoneal macrophages in response to bacterial LPS. This potentiation is specific to IL-10, as no changes were seen in the production of the pro-inflammatory cytokine TNF-{square}. Moreover, peritoneal macrophages from mice lacking macrophage galactose-binding lectin (MGL1), a pathogen recognition receptor that has been previously shown to bind N-acetylgalactosamine, failed to increase IL-10 production after stimulation with Giardia and LPS. Giardias immunoregulation of the IL-10 response may help us understand the parasites role in reducing diarrheal severity.

immunology↗

bioRxiv2023

p53 promotes revival stem cells in the regenerating intestine after severe radiation injury

Ionizing radiation induces cell death in the gastrointestinal (GI) epithelium by activating p53. However, p53 also prevents animal lethality caused by radiation-induced GI injury. Through single-cell RNA-sequencing of the irradiated mouse intestine, we find that p53 target genes are specifically enriched in stem cells of the regenerating epithelium, including revival stem cells that promote animal survival after GI damage. Accordingly, in mice with p53 deleted specifically in the GI epithelium, ionizing radiation fails to induce revival stem cells. Using intestinal organoids, we show that transient p53 expression is required for the induction of revival stem cells that is controlled by an Mdm2-mediated negative feedback loop. These results suggest that p53 suppresses severe radiation-indued GI injury by promoting intestinal epithelial cell reprogramming. One-Sentence SummaryAfter severe radiation injury to the intestine, transient p53 activity induces revival stem cells to promote regeneration.

cell biology↗

bioRxiv2022

CD95/Fas ligand mRNA is toxic to cells through more than one mechanism

CD95/Fas ligand induces apoptosis through binding of the protein to the CD95 receptor. However, CD95L mRNA also induces toxicity in the absence of CD95. Dying cells exhibit features of DISE (Death Induced by Survival Gene Elimination), a form of cell death mediated by RNA interference (RNAi). DISE relies on targeting mediated by six nucleotides of complementarity between positions 2-7, the 6mer seed sequence of a RISC-bound (R-sRNA), and the 3UTR of an mRNA, a feature that allows to predict the effect of 6mer seed sequences on cell viability. We now report that CD95L mRNA processing generates an sRNA nearly identical to shL3, a commercial CD95L-targeting shRNA that led to the discovery of DISE. Neither of the miRNA biogenesis proteins Drosha or Dicer are required for CD95L mRNA processing. Interestingly, CD95L toxicity depends on the core component of the RISC, Ago 2, in some cell lines, but not in others. In the HCT116 colon cancer cell line, Ago 1-4 appear to function redundantly in RNAi. In fact, Ago 1/2/3 knockout cells retained sensitivity to CD95L mRNA toxicity. Toxicity was only blocked by mutation of all in-frame start codons in the CD95L ORF. Expression of a toxic CD95L mRNA caused an enrichment for R-sRNAs with toxic 6mer seed sequences, while expression of the nontoxic CD95L mutant enriched for loading of R-sRNAs with nontoxic 6mer seeds. However, CD95L was not the only source of these R-sRNAs. We found that CD95L mRNA may induce DISE directly and indirectly, and that alternate mechanisms may underlie CD95L mRNA processing and toxicity.

cell biology↗

bioRxiv2019

Functional ultrasound imaging of deep visual cortex in awake non-human primates

Deep regions of the brain are not easily accessible to investigation at the mesoscale level in awake animals or humans. We have recently developed functional Ultrasound (fUS) imaging fUS imaging technique to uncover deep hemodynamic functional responses. Applying fUS imaging on two awake non-human primates performing a passive fixation task, we reconstructed their retinotopic maps down to the deep calcarine and lunate sulci on visual areas (V1, V2 and V3). These maps were acquired in a single hour session with very few stimuli presentation. The spatial resolution of the technology is illustrated by mapping of Ocular Dominance (OD) columns within superficial and deep layers of the primary visual cortex. These acquisitions showed that OD selectivity is mostly present in layer IV but with evidence also in layers II/III and V. The fUS imaging technology therefore provides a new mesoscale approach to map brain activities at high spatiotemporal resolution in awake subjects within the whole depth of the cortex.

neuroscience↗