Biology subjects

Shivdasani, R.

Publications and source records attributed to Shivdasani, R..

7 recordsLinked to original sources

bioRxiv2026

Epigenetic Gatekeeping of Intestinal Stem Cell Transformation

Widespread cell plasticity recognized in fetal intestinal epithelium is preserved in limited fashion in Wnt-responsive adult stem cells and contributes to tumour initiation, progression, and relapse. It is unclear which epigenetic features maintain stem-cell properties, restrict adult expression of fetal genes, and are attenuated in tumours, allowing non-stem cells to replenish targeted tumour stem cells. Here we show that reversible stemness in normal adult intestinal crypt cells hinges on a dynamic balance between activating H3K27ac and repressive H3K27me3 marks. Cells that leave the Wnt-rich stem-cell niche normally acquire H3K27me3 at thousands of stemness-associated enhancers. Constitutive tumourigenic Wnt activity transforms Apc-/- intestinal stem cells by gradual erosion of H3K27me3 at select enhancers and extends stem-like properties beyond usual anatomic confines; continued depletion of H3K27me3 reactivates enhancers that control growth and expression of a wider swath of fetal genes than appreciated previously. Subsequent focal DNA demethylation at expanded superenhancer domains is associated with tumour growth. Human colorectal cancers also carry evidence of this epigenetic rewiring. Accelerated H3K27me3 loss in mice hastens, and its preservation delays, activation of stemness-related enhancers, superenhancers, and tumour progression. During transformation, H3K27me3 loss at enhancers erases a crucial distinction between stem and non-stem populations, endowing the latter with stemness and providing an explanation for tumour resistance to cancer stem cell targeting. Thus, H3K27me3 at Wnt-responsive enhancers is an intrinsic barrier to intestinal tumourigenesis and aberrant reactivation of hundreds of fetal genes.

cancer biology↗

bioRxiv2024

Epigenetic investigation of multifocal small intestinal neuroendocrine tumours reveals accelerated ageing of tumours and epigenetic alteration of metabolic genes

BackgroundSmall intestinal neuroendocrine tumours (SI-NETs) are the most common malignancy of the small intestine and around 50% of patients present in clinic with multifocal disease. Recent investigations into the genomic architecture of multifocal SI-NETs have found evidence that these synchronous primary tumours evolve independently of each other. They also have extremely low mutational burden and few known driver genes, suggesting that epigenetic dysregulation may be driving tumorigenesis. Very little is known about epigenetic gene regulation, metabolism and ageing in these tumours, and how these traits differ across multiple tumours within individual patients. MethodsIn this study, we performed the first investigation of genome-wide DNA methylation in multifocal SI-NETs, assessing multiple primary tumours within each patient (n=79 primary tumours from 14 patients) alongside matched metastatic tumours (n=12) and normal intestinal epithelial tissue (n=9). We assessed multifocal SI-NET differential methylation using a novel method, comparing primary tumours with matched normal epithelial tissue and an enterochromaffin-enriched cell line to enrich for tumour-specific effects. This method reduced the identification of false positive methylation differences driven by cell composition differences between tumour and normal epithelial tissue. We also assessed tumour ageing using epigenetic clocks and applied metabolic predictors in the dataset to assess methylation variation across key metabolic genes. ResultsWe have identified 12,392 tumour-specific differentially methylated positions (Bonferroni corrected p<0.05) which were enriched for neural pathways. The expression levels of the genes associated with top sites were also found to be significantly altered in SI-NETs. Age acceleration was observed across SI-NETs and a variability in epigenetic age of tumours within each patient, which we believe is reflecting the order in which tumours have developed. This is supported by the correlation of age acceleration with somatic mutational count in the tumours. We have identified SI-NET associated alterations to the methylation patterns in key metabolic genes compared to matched normal tissue, which is more pronounced in metastatic tumours and tumours harbouring chromosome 18 loss of heterozygosity, indicating metabolic differences in these tumour subtypes. ConclusionsWe have identified accelerated ageing and changes to regulation of metabolic genes, alongside an epigenetic signature of multifocal SI-NETs. These findings add to our understanding of multifocal SI-NET biology and their molecular differences which may be instrumental in the development of these elusive tumours.

cancer biology↗

bioRxiv2024

Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation

Enteroendocrine cells (EECs), which secrete serotonin (enterochromaffin cells, EC) or a dominant peptide hormone, serve vital physiologic functions. As with any adult human lineage, the basis for terminal cell diversity remains obscure. We replicated human EEC differentiation in vitro, mapped transcriptional and chromatin dynamics that culminate in discrete cell types, and studied abundant EEC precursors expressing selected transcription factors (TFs) and gene programs. Before expressing the pre-terminal factor NEUROD1, non-replicating precursors oscillated between epigenetically similar but transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor substantially accelerated EEC differentiation and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and hormone-producing cell features. Expressed late in EEC differentiation, the latter TFs mainly bind cis-elements that are accessible in undifferentiated stem cells and tailor the subsequent expression of TF combinations that specify EEC types. Thus, TF oscillations retard EEC maturation to enable accurate EEC diversification.

molecular biology↗

bioRxiv2022

A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin

Plasticity between cell lineages is a fundamental but poorly understood property of regenerative tissues. In the gut tube, small intestine absorbs nutrients whereas colon absorbs electrolytes. In a striking display of inherent plasticity, adult colonic mucosa lacking the chromatin factor SATB2 is converted to small intestine. Using proteomics and CRISPR-Cas9 screen, we identified MTA2 as a crucial component of the molecular machinery that, together with SATB2, restrain colonic plasticity. MTA2 loss in adult mouse colon activated lipid absorptive genes and functional lipid uptake. Mechanistically, MTA2 co-binds with HNF4A, an activating pan-intestine transcription factor (TF), on colonic chromatin. MTA2 loss leads to HNF4A release from colonic and gain on small intestinal chromatin. SATB2 similarly restrains colonic plasticity through a HNF4A-dependent mechanism. Our study provides a generalizable model of lineage plasticity in which broadly-expressed TFs are retained on tissue-specific enhancers to maintain cell identity and prevent activation of alternative lineages; their release unleashes plasticity.

developmental biology↗

bioRxiv2021

Birth and delineation of the intestinal stem cell niche

Wnt and Rspondin (RSPO) signaling drives proliferation, and bone morphogenetic protein inhibitors (BMPi) impede differentiation, of intestinal stem cells (ISCs). Here we identify the adult mouse ISC niche as a complex, multi-layered structure that encompasses distinct mesenchymal and smooth muscle cell populations. Diverse sub-cryptal cells provide redundant supportive factors, with certain BMPi and the most potent Wnt co-factor, RSPO2, restricted to single cell types. Niche functions refine during a critical period of postnatal crypt morphogenesis, in part to oppose dense aggregation of BMP-expressing sub-epithelial myofibroblasts that promote epithelial differentiation. A specialized muscle layer, the muscularis mucosae, first appears during this period and supplements neighboring RSPO and BMPi sources. In vivo ablation of smooth muscle raises BMP activity and potently limits a pre-weaning burst of crypt fission. Thus, distinct and progressively specialized mesenchymal components together create the milieu required to propagate crypts during rapid organ growth and to sustain adult ISCs.

developmental biology↗

bioRxiv2021

Cochlear organoids reveal epigenetic and transcriptional programs of postnatal hair cell differentiation from supporting cells

We explored the transcriptional and epigenetic programs underlying the differentiation of hair cells from postnatal progenitor cells in cochlear organoids. Heterogeneity in the cells including cells with the transcriptional signatures of mature hair cells allowed a full picture of possible cell fates. Construction of trajectories identified Lgr5+ cells as progenitors for hair cells and the genomic data revealed gene regulatory networks leading to hair cells. We validated these networks, demonstrating dynamic changes both in expression and predicted binding sites of these transcription factors during organoid differentiation. We identified known regulators of hair cell development, Atoh1, Pou4f3, and Gfi1, and predicted novel regulatory factors, Tcf4, an E-protein and heterodimerization partner of Atoh1, and Ddit3, a CCAAT/enhancer-binding protein (C/EBP) that represses Hes1 and activates transcription of Wnt signaling-related genes. Deciphering the signals for hair cell regeneration from mammalian cochlear supporting cells reveals candidates for HC regeneration which is limited in the adult.

developmental biology↗

bioRxiv2017

Challenges And Emerging Directions In Single-Cell Analysis

Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data. Here, we discuss the state of the field and recent advances, and look to future opportunities.

genomics↗