Biology subjects

Valenta, T.

Publications and source records attributed to Valenta, T..

14 recordsLinked to original sources

bioRxiv2026

Acquired epithelial Wnt7b secretion establishes autocrine WNT dependency in BRAF mutant colorectal cancer

Colorectal cancer (CRC) subtypes differ fundamentally in their reliance on WNT signaling, yet the sources and regulation of WNT ligands as well as the subtype-specific requirements for ligand-driven activation remain poorly defined. Here, we generated genetically-engineered organoid models of Apc- and Braf-mutant CRC to systematically dissect ligand dependency across distinct genetic backgrounds and CRC subtypes. Through genetic perturbation and pharmacological inhibition of WNT secretion, we find that BRAF-driven organoids critically depend on autocrine WNT ligand production for survival and proliferation. In contrast, APC-mutant organoids remain viable but undergo discernible transcriptional changes upon ligand withdrawal. We identify Wnt7b as a non-redundant epithelial WNT ligand required to sustain beta-catenin-dependent signaling specifically in BRAF-mutant CRC. Chromatin accessibility and transcriptional profiling reveal that Wnt7b activation occurs early during transformation and coincides with cancer-specific opening of regulatory elements at the Wnt7b locus. Integrative regulatory analyses nominate the transcription factor RFX7 as a candidate upstream regulator of epithelial Wnt7b expression. Consistent with these findings, analysis of human CRC specimens demonstrates WNT7B expression in a subset of BRAF-mutant tumors and reveals an association with poor patient survival. Together, these results redefine ligand dependency in colorectal cancer and uncover autocrine WNT7B signaling as a mechanistically defined vulnerability in aggressive BRAF-mutant disease.

molecular biology↗

bioRxiv2026

APOA1 links a late fetal epithelial program to colonic maturation and injury responses

Developmental programs establish tissue identity and organization, but how their reactivation contributes to adult tissue responses remains poorly understood. Here, we identify a functional contribution of apolipoprotein A-I (APOA1), which marks a late fetal colonic epithelial state that reappears after injury. Spatial and temporal profiling localized Apoa1 transcription predominantly to epithelial cells at the tips of developing proximal colonic folds. Apoa1 loss delayed fold maturation and altered the abundance and composition of developing enteroendocrine populations, linking this apolipoprotein to mucosal architecture and epithelial differentiation. APOA1 protein closely interacted with WNT5A during development and injury, while Apoa1 deficiency increased Wnt5a expression and altered its epithelial protein distribution. Following colonic injury, single-cell and spatial profiling identified genotype-associated transcriptional changes involving stress responses, barrier and immune functions, and metabolism, with a shared component across males and females. These changes accompanied reduced enteroendocrine representation and increased representation of inflammation-associated macrophages. Finally, regional and compartmental expression analyses, together with hindgut explant perturbation, identified HOXB7 transcription factor as a regulator of developmental Apoa1 expression. Together, these findings establish functional relevance for a component of a reactivated late fetal epithelial program, connecting APOA1 to colonic maturation and the epithelial and inflammatory organization of injured tissue.

molecular biology↗

bioRxiv2025

Self-Organizing Assembloids Reveal Enteric Nervous System Dynamics in Gut Homeostasis and Regeneration

The enteric nervous system (ENS) is essential for intestinal health, exhibiting adaptability to environmental and physiological challenges. However, the mechanisms underlying ENS plasticity and resilience remain poorly understood. Organoid technology has revolutionized in vitro modeling by accurately replicating epithelial structures and enabling significant advancements in understanding gastrointestinal biology. However, traditional organoids are limited in their ability to study the ENS, as they lack the multicellular composition and functional architecture necessary to model complex interactions between neurons, glia, mesenchymal, smooth muscle, and epithelial cells. To address these limitations, we developed murine ENS-Rich Assembloids (ERAs) that self-organize to replicate the cellular diversity, including the epithelial structure, and functional architecture of native colonic tissue. These assembloids recreate neuron-glia interactions, reflect regenerative processes, and provide a novel platform for studying ENS dynamics under controlled conditions. Integrating findings from assembloids and an in vivo murine model, we demonstrate that inflammation induces coordinated reorganization of S100b+ glial cells, TUJ1+ neurons, PDGFRA+ mesenchymal cells, and epithelial cells, revealing conserved mechanisms of ENS plasticity. We identify pleiotrophin (PTN) signaling via Protein Tyrosine Phosphatase Receptor Type Z1 (PTPRZ1) as a key pathway facilitating neural elongation and enhancing neuron-glia interactions. Moreover, we show that activated neurons transfer lipids to glial cells, revealing a novel support mechanism during inflammation. These findings position enteric glia as protective hubs for neurons, fostering ENS adaptability and tissue regeneration. By building on the foundational success of organoid technology and addressing its limitations for studying the ENS, ENS-rich assembloids establish a transformative tool for investigating ENS responses in health, disease, and tissue repair.

developmental biology↗

bioRxiv2024

Eosinophils restrict CRC metastasis by inhibiting pro-tumorigenic SPP1+ macrophage differentiation

Eosinophils, traditionally associated with allergic responses, have emerged as critical immune modulators in colorectal cancer (CRC). Here, we reveal that eosinophils actively shape the tumor microenvironment and influence metastatic progression. Using comprehensive transcriptomics analysis of human CRC and a murine orthotopic tumor model, we identify a conserved tumor-specific eosinophil signature and activation profile. Despite their declining presence in advanced CRC, eosinophils suppress metastatic dissemination by counteracting the pro-tumorigenic functions of SPP1+ macrophages - a subset linked to immune exclusion and tumor metastasis. Mechanistically, eosinophils respond to tumor-derived signals and inhibit macrophage differentiation into SPP1+ cells. Eosinophil depletion exacerbates peritoneal tumor spread. These findings highlight the pivotal role of eosinophils in restraining late-stage CRC progression and unveil a novel eosinophil-macrophage axis as potential therapeutic targets.

cancer biology↗

bioRxiv2024

An oncoembryology approach uncovers SoxC-driven regulation of colon development and cancer

Reactivated embryonic programs are associated with cancer progression, yet their role and regulatory mechanisms remain poorly understood. In this study, we introduce oncoembryology, an approach that systematically compares embryonic and cancerous tissues to identify shared molecular programs and assess their functional relevance in disease. Applying this strategy to colorectal cancer, we identified SoxC transcription factors (Sox4, Sox11, Sox12) as critical regulators of both embryonic development and tumorigenesis. SoxC transcription factors regulate diverse downstream targets, including Tead2, Mdk, and Klf4, thereby regulating crucial steps of colon development. Abrogating SoxC function in murine models reduced tumor growth and prevented liver metastasis. Concordantly, a SoxC-driven oncoembryonic gene signature correlated with poor survival in colorectal cancer patients, underscoring the therapeutic potential of targeting SoxC-regulated pathways in cancer treatment.

cancer biology↗

bioRxiv2024

Dissecting heterogeneity of tumor microenvironment in colorectal cancer using high-resolution single-cell atlas

The immune composition of the tumor microenvironment (TME) has a major impact on the therapeutic response and clinical outcome in patients with colorectal cancer (CRC). Here, we comprehensively characterize the TME at the single-cell level by first building a large-scale atlas that integrates 4.27 million single cells from 1,670 patient samples. We then complemented the atlas with single-cell profiles from four CRC cohorts with 266 patients, including cells with low mRNA content, spatial transcriptional profiles from 3.7 million cells, and protein profiles from 0.7 million cells. The analysis of the atlas allows refined tumor classification into four immune phenotypes: immune desert, B cell enriched, T cell enriched, and myeloid cell enriched subtypes. Within the myeloid compartment we uncover distinct subpopulations of neutrophils that acquire new functional properties in blood and in the TME, including anti-tumorigenic capabilities. Further, spatial multimodal single-cell profiling reveals that neutrophils are organized in clusters within distinct functional niches. Finally, using an orthotopic mouse model we show that cancer-derived systemic signals modify neutrophil production in the bone marrow, providing evidence for tumor-induced granulopoiesis. Our study provides a big data resource for the CRC and suggests novel therapeutic strategies targeting neutrophils.

bioinformatics↗

bioRxiv2024

Hepatic iNKT cells facilitate colorectal cancer metastasis by inducing a fibrotic niche in the liver

The liver is an important metastatic organ that contains many innate immune cells, yet little is known about their role in anti-metastatic defense. We investigated how invariant natural killer T (iNKT) cells influence colorectal cancer-derived liver metastasis using different models in immunocompetent mice. We found that hepatic iNKT cells promote metastasis by creating a supportive niche for disseminated cancer cells. Mechanistically, iNKT cells respond to disseminating cancer cells by producing the fibrogenic cytokines IL-4 and IL-13 in a TCR-independent manner. Selective abrogation of IL-4 and IL-13 sensing in hepatic stellate cells prevented their transdifferentiation into extracellular matrix-producing myofibroblasts, which hindered metastatic outgrowth of disseminated cancer cells. This study highlights a novel tumor-promoting axis driven by iNKT cells in the initial stages of metastasis.

immunology↗

bioRxiv2024

The fate of secretory cells during intestinal homeostasis, regeneration, and tumor formation is regulated by Tcf4

The single-layer epithelium of the gastrointestinal tract is a dynamically renewing tissue that ensures nutrient absorption, secretory and barrier functions and is involved in immune responses. The basis for this homeostatic renewal is the Wnt signaling pathway. Blocking this pathway can lead to epithelial damage, while its abnormal activation can result in the development of intestinal tumors. In this study, we investigated the dynamics of intestinal epithelial cells and tumorigenesis using a conditional mouse model. Using single-cell and bulk RNA sequencing and histological analysis, we elucidated the cellular responses following the loss of specific cell types. We focused on the fate of cells in the lower parts of the intestinal crypts and the development of colon adenomas. By partially inactivating the transcription factor Tcf4, a key effector of the Wnt signaling pathway, we analyzed the regeneration of isolated hyperproliferative foci (crypts). Our results suggest that the damaged epithelium is not restored by a specific regeneration program associated with oncofetal gene production, but rather by a standard homeostatic renewal pathway. Moreover, disruption of Tcf4 in secretory progenitors resulted in a significant shift in the cell lineage from Paneth cells to goblet cells, characterized by morphological changes and loss of Paneth cell-specific genes. We also found that hyperactivation of the Wnt signaling pathway in colonic adenomas correlated with the upregulation of genes typical of Paneth cells in the intestine, followed by the emergence of secretory tumor cells producing the Wnt3 ligand. The absence of Tcf4 led to a phenotypic shift of the tumor cells towards goblet cells. Our study presents a new model of epithelial regeneration based on the genetically driven partial elimination of intestinal crypts. We highlight the critical role of Tcf4 in the control of cell lineage decisions in the intestinal epithelium and colon tumors. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=160 HEIGHT=200 SRC="FIGDIR/small/603019v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1d8e5a0org.highwire.dtl.DTLVardef@cb85f7org.highwire.dtl.DTLVardef@1c84ed3org.highwire.dtl.DTLVardef@1af36f3_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

RoCK and ROI: Single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing

Various tools have been developed to reliably identify, trace and analyze single cells in complex tissues. In recent years, these technologies have been combined with transcriptomic profiling approaches to explore molecular mechanisms that drive development, health, and disease. However, current methods still fall short of profiling single cell transcriptomes comprehensively, with one major challenge being high non-detection rates of specific transcripts and transcript regions. Such information is often crucial to understanding the biology of cells or tissues and includes lowly expressed transcripts, sequence variations and exon junctions. Here, we developed a scRNAseq workflow, RoCK and ROI (Robust Capture of Key transcripts and Regions Of Interest), that tackles these limitations. RoCKseq uses targeted capture to enrich for key transcripts, thereby supporting the detection and identification of cell types and complex phenotypes in scRNAseq experiments. ROIseq directs a subset of reads to a specific region of interest via selective priming to ensure detection. Importantly, RoCK and ROI guarantees efficient retrieval of specific sequence information without compromising overall single cell transcriptome information and our workflow is supported by a novel bioinformatics pipeline to analyze the multimodal information. RoCK and ROI represents a significant enhancement over non-targeted single cell sequencing, particularly when cell categorization depends on transcripts that are missed in standard scRNAseq experiments. In addition, it also allows exploration of biological questions that require assessment of specific sequence elements along the targets to be addressed.

genomics↗

bioRxiv2022

Terminal differentiation of enterocytes is governed by distinct members of Tgfβ superfamily

The protective and absorptive functions of the intestinal epithelium rely on differentiated enterocytes in the villi. The differentiation of enterocytes is orchestrated by sub-epithelial mesenchymal cells producing distinct ligands along the villus axis, in particular Bmps and Tgf{beta}. Here we show that individual Bmp ligands and Tgf{beta} drive distinct enterocytic programs specific to villus zonation. Bmp4 is expressed mainly from the center to the upper part of the villus, and it activates preferentially genes connected to lipid uptake and metabolism. In contrast, Bmp2 is produced by villus-tip mesenchymal cells, and it influences the adhesive properties of villus-tip epithelial cells and the expression of immunomodulators. Hence, Bmp2 promotes the terminal enterocytic differentiation at the villus-tip. Additionally, Tgf{beta} induces epithelial gene expression programs similar to that triggered by Bmp2. The inhibition of Bmp receptor type I in vivo and using intestinal organoids lacking Smad4 revealed that Bmp2-driven villus-tip program is activated by a canonical Smad-dependent mechanism. Finally, we established an organoid cultivation system that enriches for villus-tip enterocytes and thereby better mimics the cellular composition of the intestinal epithelium. Altogether our data suggest that not only Bmp gradient, but also the activity of individual Bmp drives specific enterocytic programs.

cell biology↗

bioRxiv2021

Single-cell RNA sequencing unveils intestinal eosinophil development and specialization

Eosinophils are an integral part of the gastrointestinal (GI) immune system that contribute to homeostatic and inflammatory processes. Here, we investigated the existence of functional subsets that carry out specialized tasks in health and disease. We used single-cell transcriptomics and high-dimensional flow cytometry to delineate murine eosinophil subpopulations and their ontogenetic relationship in the steady state and during infection and inflammation. Profiling of eosinophils from bone marrow, blood, spleen and several GI tissues revealed five distinct subsets representing consecutive developmental and maturation stages across organs, each controlled by a specific set of transcription factors. Furthermore, we discovered a highly adapted PD-L1+CD80+ eosinophil subset in the GI tract, characterized by its immune regulatory properties, bactericidal activity upon challenge infection and tissue-protective function during inflammation. Our data provide a framework for the characterization of eosinophil subsets in GI diseases and highlight their crucial contribution to homeostasis, immune regulation and host defense.

immunology↗

bioRxiv2021

Manipulating the murine Lgr5 locus using a rapid, efficient and flexible CRISPR/Cas9 pipeline

The maintenance of adult epithelial tissues, such as the lining of the intestine, depends on their periodical renewal. This is achieved through small populations of adult stem cells. Lgr5 serves as a marker for these cells. Here we report a novel non-variegated Lgr5 mouse model, which was generated via the CRISPR/Cas9 system. We show that this Lgr5-2A-CreERT2-2A-mOrange2 mouse line can be used for lineage tracing, as well as for directing gene expression to Lgr5+ cells. The introduction of the transgene affects neither the expression, nor the function of endogenous Lgr5. Therefore, this new tool will serve to mark and manipulate intestinal stem cells to gain new biological insights.

developmental biology↗

bioRxiv2020

Discrete regulation of b-catenin-mediated transcription governs identity of intestinal epithelial stem cells

The homeostasis of the gut epithelium relies upon continuous renewal and proliferation of crypt-resident intestinal epithelial stem cells (IESCs). Wnt/{beta}-catenin signaling is required for IESC maintenance, however, it remains unclear how this pathway selectively governs the identity and proliferative decisions of IESCs. Here, we demonstrate that C-terminally-recruited transcriptional co-factors of {beta}-catenin act as all-or-nothing regulators of Wnt-target gene expression. Blocking their interactions with {beta}-catenin rapidly induces loss of IESCs and intestinal homeostasis. Conversely, N-terminally recruited co-factors fine-tune {beta}-catenins transcriptional output to ensure proper self-renewal and proliferative behaviour of IESCs. Impairment of N-terminal interactions triggers transient hyperproliferation of IESCs, eventually resulting in exhaustion of the self-renewing stem cell pool. IESC mis-differentiation, accompanied by intrinsic and extrinsic stress signalling results in a process resembling aberrant "villisation" of intestinal crypts. Our data suggest that IESC-specific Wnt/{beta}-catenin output requires discrete regulation of transcription by transcriptional co-factors.

cell biology↗

bioRxiv2018

Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling

Genetic alterations in human BCL9 genes have repeatedly been found in congenital heart disease (CHD) with as-of-yet unclear causality. BCL9 proteins and their Pygopus (Pygo) co-factors can participate in canonical Wnt signaling via binding to {beta}-catenin. Nonetheless, their contributions to vertebrate heart development remain uncharted. Here, combining zebrafish and mouse genetics, we document tissue-specific functions in canonical Wnt signaling for BCL9 and Pygo proteins during heart development. In a CRISPR-Cas9-based genotype-phenotype association screen, we uncovered that zebrafish mutants for bcl9 and pygo genes largely retain {beta}-catenin activity, yet develop cardiac malformations. In mouse, both systemic and lineage-specific loss of the Pygo-BCL9-{beta}-catenin complex caused heart defects with outflow tract malformations, aberrant cardiac septation and valve formation, and compact myocardium hypoplasia. Mechanistically, these phenotypes coincide with transcriptional deregulation during heart patterning, and Pygo2 associates with {beta}-catenin at cis-regulatory regions of cardiac genes. Taken together, our results establish BCL9 and Pygo as tissue-specific {beta}-catenin co-factors during vertebrate heart development. Our results further implicate alterations in BCL9 and BCL9L in human CHDs as possibly causative.

genetics↗