Biology subjects

Scherz-Shouval, R.

Publications and source records attributed to Scherz-Shouval, R..

11 recordsLinked to original sources

bioRxiv2026

TCF21 loss identifies a conserved inflammation-associated fibroblast state across Crohn's disease and ulcerative colitis

Background and Aims: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are associated with stromal remodeling; however, the fibroblast states that contribute to chronic inflammation remain incompletely defined. We aimed to identify conserved pathogenic fibroblast programs across CD and UC and determine whether these states are linked to loss of homeostatic stromal regulators. Methods: We integrated publicly available single-cell RNA sequencing datasets from healthy and inflamed intestinal tissues to define stromal populations across CD, UC, and control samples. Fibroblast subsets were annotated using cluster-specific markers and patient-level abundance analyses. Multiplex immunofluorescence of human gastrointestinal tissue microarrays assessed protein expression. Human colonic fibroblasts were stimulated with IL1B and TNF to model inflammation-associated fibroblast polarization, and restoration of homeostatic factors was evaluated using mRNA-loaded lipid nanoparticles (LNPs). Results: A conserved inflammation-associated fibroblast (IAF) population was expanded in both CD and UC and expressed inflammatory chemokines, matrix-remodeling genes, and activation markers including CXCL1, MMP3, FAP, and PDPN. In contrast, a homeostatic ADAMDEC1/TCF21-enriched fibroblast population was reduced in inflamed tissue. TCF21 expression positively correlated with ADAMDEC1 and negatively correlated with activation markers. Multiplex immunofluorescence confirmed depletion of TCF21-positive non-immune, stromal cells in IBD tissue. In vitro, IL1B and TNF induced an IAF-like phenotype and reduced TCF21. TCF21 mRNA-LNP restoration attenuated inflammatory mediators including IL1B and IL6. Conclusions: TCF21 loss identifies a conserved inflammation-associated fibroblast state across CD and UC. Restoring TCF21 partially suppresses inflammatory fibroblast programs, supporting stromal reprogramming as a therapeutic concept in IBD.

immunology↗

bioRxiv2026

Persistent stromal reprogramming defines incomplete mucosal healing and predicts therapeutic response in ulcerative colitis

Mucosal healing (MH) is the primary therapeutic endpoint in ulcerative colitis (UC), yet frequent relapses suggest it does not reflect complete tissue recovery. To define the basis of this vulnerability, we generated a multimodal atlas of UC integrating single-cell and bulk transcriptomics, Visium HD spatial profiling, and multiplexed imaging across 89 patients. We show that MH represents a distinct biological state marked by persistent stromal remodeling along three axes: emergence of inflammatory fibroblasts, sustained loss of OGN niche-supporting fibroblasts, and expansion of pericytes with matrix-remodeling features and reduced vascular association. Spatial analyses revealed persistent reorganization of mucosal tissue domains despite apparent clinical remission. Across independent cohorts, baseline inflammatory fibroblast and pericyte signatures robustly predicted non-response to anti-TNF therapy. These findings suggest that patients in MH remain in a biologically altered state linked to relapse risk and identify stromal reprogramming as a determinant of disease persistence and therapeutic response in UC.

immunology↗

bioRxiv2026

The U-method: Leveraging expression probability for robust biological marker detection

Reliable identification of cluster-defining markers is fundamental to single-cell transcriptomic analysis, yet current approaches often rely on average expression differences, which can dilute biologically informative signals in sparse and heterogeneous data. Here we introduce the U-method, a fast probability-based framework for identifying uniquely expressed genes (UEGs) by contrasting a genes expression probability within a cluster with its highest expression probability in any other cluster. This highest-probability comparison prioritizes detection consistency over expression magnitude, resulting in markers that consistently identify cell populations across independent datasets analyzed at comparable clustering resolutions. Applied to colorectal, breast, pancreatic, and lung cancer single-cell RNA-sequencing datasets, the U-method identifies canonical lineage markers together with additional genes showing clear cluster specificity. When projected onto Visium HD spatial transcriptomics data using only raw average expression of top UEGs, these signatures reveal coherent and biologically interpretable tissue organization without the need for smoothing, deconvolution, or model-based spatial inference. These results position the U-method as a practical implementation of detection consistency, enabling robust marker discovery and spatial interpretation in single-cell analysis.

bioinformatics↗

bioRxiv2025

A fibroblast-centric network drives cold fibrosis in the tumor microenvironment of lung squamous cell carcinoma

The tumor microenvironment (TME) of chronic inflammation-associated cancers (CIACs) is shaped by cycles of injury and maladaptive repair, yet the principles organizing fibrotic stroma in these tumors remain unclear. Here, we applied the concept of hot versus cold fibrosis, originally credentialed in non-cancerous fibrosis of heart and kidney, to lung squamous cell carcinoma (LUSC), a prototypical CIAC. Single-cell transcriptomics of matched tumor and adjacent-normal tissue from 16 treatment-naive LUSC patients identified a cold fibrotic architecture in the LUSC TME: cancer-associated fibroblasts (CAFs) expanded and adopted myofibroblast and stress-response states, while macrophages were depleted. This macrophage-poor, CAF-rich stroma was maintained by CAF autocrine growth factor loops, including TIMP1, INHBA, TGFB1, and GMFB. In parallel, the immune compartment exhibited a hot tumor phenotype with abundant T and B cells, forming spatially distinct but molecularly engaged networks with CAFs. CAF gene programs typifying cold fibrosis in LUSC were conserved in other CIACs, including esophageal and gastric adenocarcinomas. These results redefine desmoplastic regions of tumors through the lens of a non-cancer fibrosis model, demonstrating that conserved stromal circuits constitute therapeutic vulnerabilities in CIACs.

cancer biology↗

bioRxiv2024

Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism

m6A is the most widespread mRNA modification and is primarily implicated in controlling mRNA stability. Fundamental questions pertaining to m6A are the extent to which it is dynamically modulated within cells and across stimuli, and the forces underlying such modulation. Prior work has focused on investigating active mechanisms governing m6A levels, such as recruitment of m6A writers or erasers leading to either global or site-specific modulation. Here, we propose that changes in m6A levels across subcellular compartments and biological trajectories may result from passive changes in gene-level mRNA metabolism. To predict the intricate interdependencies between m6A levels, mRNA localization, and mRNA decay, we establish a differential model m6ADyn encompassing mRNA transcription, methylation, export, and m6A-dependent and independent degradation. We validate the predictions of m6ADyn in the context of intracellular m6A dynamics, where m6ADyn predicts associations between relative mRNA localization and m6A levels, which we experimentally confirm. We further explore m6ADyn predictions pertaining to changes in m6A levels upon controlled perturbations of mRNA metabolism, which we also experimentally confirm. Finally, we demonstrate the relevance of m6ADyn in the context of cellular heat stress response, where genes subjected to altered mRNA product and export also display predictable changes in m6A levels, consistent with m6ADyn predictions. Our findings establish a framework for dissecting m6A dynamics and suggest the role of passive dynamics in shaping m6A levels in mammalian systems.

systems biology↗

bioRxiv2023

Cancer-associated fibroblasts serve as decoys to suppress NK cell anti-cancer cytotoxicity

Cancer associated fibroblasts (CAFs) are among the most abundant components of the breast tumor microenvironment (TME) and major contributors to immune modulation. CAFs are well-known to regulate the activity of diverse types of immune cells including T cells, macrophages and dendritic cells, however little is known about their interaction with Natural killer (NK) cells, which constitute an important arm of anti-tumor immunity. Here we find, using mouse models of cancer and ex-vivo co-cultures, that CAFs inhibit NK cell cytotoxicity towards cancer cells. We unravel the mechanism by which this suppression occurs, through ligand-receptor engagement between NK cells and CAFs leading to CAF cytolysis, which in turn diminishes the expression of activating receptors on NK cells, promoting cancer escape from NK cell surveillance. Analysis of breast cancer patient samples reveals enrichment of NK cells in CAF-rich regions, and upregulation of NK binding ligands on CAFs which is correlated with poor disease outcome. These results reveal a CAF-mediated immunosuppressive decoy mechanism with implications for treatment of solid tumors.

cancer biology↗

bioRxiv2023

Mapping the tumor stress network reveals dynamic shifts in the stromal oxidative stress response

The tumor microenvironment (TME) is a challenging environment where cells must cope with stressful conditions such as fluctuating pH levels, hypoxia, and free radicals. In response, stress pathways are activated, which can both promote and inhibit tumorigenesis. In this study, we set out to characterize the stress response landscape across four carcinomas: breast, pancreas, ovary, and prostate tumors, focusing on five pathways: Heat shock response, oxidative stress response, unfolded protein response, hypoxia stress response, and DNA damage response. Using a combination of experimental and computational methods, we create an atlas of the stress response landscape across various types of carcinomas. We find that stress responses are heterogeneously activated in the TME, and highly activated near cancer cells. Focusing on the non-immune stroma we find, across tumor types, that NRF2 and the oxidative stress response are distinctly activated in immune-regulatory cancer-associated fibroblasts and in a unique subset of cancer associated pericytes. Our study thus provides an interactome of stress responses in cancer, offering new ways to intersect survival pathways within the tumor, and advance cancer therapy.

cancer biology↗

bioRxiv2023

Loss of EIF4G2 Mediates Aggressiveness in Distinct Human Endometrial Cancer Subpopulations with Poorer Survival Outcome in Patients

The non-canonical translation initiation factor EIF4G2 plays essential roles in embryonic development and differentiation, and contributes to the cellular stress response via translation of selective mRNA cohorts. Currently there is limited and conflicting information regarding the potential involvement of EIF4G2 in cancer development and progression. Endometrial cancer (EC) is the most pervasive gynecological cancer in the developed world, with increasing incidence every year. High grade ECs are largely refractory to conventional treatments, presenting poor survival rates and lacking suitable prognostic markers. Here we assayed a cohort of 280 EC patients across different types, grades, and stages, and found that low EIF4G2 expression highly correlated with poor overall and recurrence free survival in Grade 2 EC patients, monitored over a period of up to 12 years. To establish a causative connection between low EIF4G2 expression and cancer progression, we analyzed in parallel two independent human EC cell lines and demonstrated that stable EIF4G2 knock-down resulted in increased resistance to conventional therapies. Depletion of EIF4G2 also increased the prevalence of molecular markers for aggressive cell subsets, and altered their transcriptional and proteomic landscapes. Prominent among the proteins with decreased abundance were Kinesin-1 motor proteins KIF5B and KLC1, 2, 3. Multiplexed imaging of the tumors from this EC patient cohort showed a correlation between decreased protein expression of either KIF5B or KLC1, and poor survival in patients of certain grades and stages. The findings herein reveal potential novel biomarkers for Grade 2 EC with potential ramifications for patient stratification and therapeutic interventions. SignificanceDecreased EIF4G2 protein results in increased drug resistance of aggressive sub-populations of endometrial cancer cells, is associated with poor patient survival, and may serve as a novel prognosis marker for endometrial cancer.

cancer biology↗

bioRxiv2022

A cell circuit approach to dissect fibroblast-macrophage interactions in the tumor microenvironment

The tumor microenvironment (TME) is composed of various nonmalignant cell types that interact with each other and with cancer cells, impacting all aspects of cancer biology. The TME is complex and heterogeneous, and thus simplifying systems and concepts are needed. Here we provide a tractable experimental system and powerful mathematical circuit concepts to identify the main molecular interactions that govern the composition of the TME. We focus on two major components of the TME - cancer associated fibroblasts (CAFs) and tumor associated macrophages (TAMs), define their interactions and verify our predictions in mouse and human breast cancer. We measure the population dynamics starting from many initial conditions of co-cultures of macrophages and organ-derived fibroblasts from mammary, lung, and fat, and explore the effects of cancer-conditioned medium on the circuits. We define the circuits and their inferred parameters from the data using a mathematical approach, and quantitatively compare the cell circuits in each condition. We find that while the homeostatic steady-states are similar between the organs, the cancer-conditioned medium profoundly changes the circuit. Fibroblasts in all contexts depend on autocrine secretion of growth factors whereas macrophages are more dependent on external cues, including paracrine growth factors secreted from fibroblasts and cancer cells. Transcriptional profiling reveals the molecular underpinnings of the cell circuit interactions and the primacy of the fibroblast autocrine loop. The same fibroblast growth factors are shared by the co-cultures and mouse and human breast cancer. The cell circuit approach thus provides a quantitative account of cell interactions in the cancer microenvironment.

cancer biology↗

bioRxiv2021

BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking CLU+ CAF expression with HSF1 signaling

Cancer-associated fibroblasts (CAFs) give rise to desmoplastic stroma, which supports tumor progression and metastasis, and comprises up to 90% of the tumor mass in pancreatic cancer. Recent work by us and others has shown that CAFs are transcriptionally rewired by adjacent cancer cells to form heterogeneous subtypes. Whether this rewiring is differentially affected by different driver mutations in cancer cells is largely unknown. Here we address this question by dissecting and comparing the stromal landscape of BRCA-mutated and BRCA Wild-type (WT) pancreatic ductal adenocarcinoma (PDAC). We comprehensively analyze PDAC samples from a cohort of 42 patients by laser-capture microdissection, RNA-sequencing and multiplexed immunofluorescence, revealing different CAF subtype compositions in germline BRCA-mutated vs. BRCA-WT tumors. In particular, we detect an increase in a subset of Clusterin (CLU)-positive CAFs in BRCA-mutated tumors. We further unravel a network of stress responses upregulated in BRCA-mutated tumors. Using cancer organoids and cell co-cultures, we show that the transcriptional shift of pancreatic stellate cells into CLU+ CAFs is mediated through activation of heat-shock factor 1 (HSF1), the transcriptional regulator of Clu. Our findings unravel a new dimension of stromal heterogeneity, influenced by germline mutations in cancer cells, with direct translational implications for clinical research. SignificanceBRCA1/2 mutations initiate some of the deadliest cancers, yet the fibroblastic microenvironment of BRCA-mutated cancers remains uncharted. Our work addresses a major unsolved question - to what extent is the tumor microenvironment determined by cancer mutations? We find that BRCA mutations in the cancer cells affect the composition of CAFs in PDAC. These findings have direct implications for diagnosis and for efforts to exploit CAFs for therapy.

cancer biology↗

bioRxiv2020

Cancer-associated fibroblast compositions change with breast cancer progression linking S100A4 and PDPN ratios with clinical outcome

Tumors are supported by cancer-associated fibroblasts (CAFs). CAFs are heterogeneous and carry out distinct cancer-associated functions. Understanding the full repertoire of CAFs and their dynamic changes could improve the precision of cancer treatment. CAFs are usually analyzed at a single time-point using specific markers, and it is therefore unclear whether CAFs display plasticity as tumors evolve. Here, we analyze thousands of CAFs using index and transcriptional single-cell sorting, at several time-points along breast tumor progression in mice, uncovering distinct subpopulations. Strikingly, the transcriptional programs of these subpopulations change over time and in metastases, transitioning from an immune-regulatory program to wound healing and antigen-presentation programs, indicating that CAFs and their functions are dynamic. Two main CAF subpopulations are also found in human breast tumors, where their ratio is associated with disease outcome across subtypes, and is particularly correlated with BRCA mutations in triple-negative breast cancer. These findings indicate that the repertoire of CAFs changes over time in breast cancer progression, with direct clinical implications.

cancer biology↗