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5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq]

ABSTRACT: Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human gastric, intestinal and IM organoids.

ORGANISM(S): Homo sapiens

PROVIDER: GSE210991 | GEO | 2024/10/15

REPOSITORIES: GEO

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RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids

Project description:Using RNA sequencing, we profile transcriptome dervied from human normal gastric, intestinal and IM organoids.

2024-10-15 | GSE210993 | GEO

DNA methylation array analysis of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids

Project description:Using DNA methylation array, we profiled epigentic changes of human gastric, intestinal and IM organoids.

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5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq]

Project description:5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq]

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5' droplet-based single cell RNA sequencing of human colorectal cancer and normal organoids

Project description:Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human colorectal cancer organoids carrying either APC mutation or RSPO fusion, and paired normal colon organoids for the later.

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RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids

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The University of Hong Kong Intestinal Metaplasia Organoids Study

Project description:Background: Gastric intestinal metaplasia (IM) is a pre-cancerous stage spanning a morphological spectrum that is poorly represented by human cell line models. Objective: We aim to establish and characterize human IM cell models to better understand IM progression along the cancer spectrum. Design: A large human gastric IM organoid (IMO) cohort (n=28), their clonal derivatives and normal gastric organoids (n=42) for comparison were established. Comprehensive multi-omics profiling and functional characterization were performed. Results: Single-cell transcriptomes revealed IMO cells spanning a spectrum from hybrid gastric/intestinal to advanced intestinal differentiation. Their lineage trajectories connected different cycling and quiescent stem and progenitors, highlighting differences in gastric to IM transition and the potential origin of IM from STMN1 cycling isthmus stem cells. Hybrid IMOs showed impaired differentiation potential, high lineage plasticity beyond gastric or intestinal fates, and reactivation of a fetal gene program. Cell populations in gastric IM and cancer tissues were highly similar to those derived from IMOs and exhibited a fetal signature. Genomically, IMOs showed elevated mutation burden, frequent chromosome 20 gain, and epigenetic de-regulation of many intestinal and gastric genes. Functionally, IMOs were FGF10 independent and showed downregulated FGFR2. Several IMOs exhibited a cell-matrix adhesion independent (CMi) subpopulation that displayed chromosome 20 gain but lacked key cancer driver mutations, potentially representing the earliest neoplastic precursor of IM-induced gastric cancer. Conclusions: Overall, our IM organoid biobank captured the heterogeneous nature of IM, revealing mechanistic insights on IM pathogenesis and progression, offering an ideal platform for studying early gastric neoplastic transformation and chemoprevention.

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DNA methylation array analysis of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids

Project description:DNA methylation array analysis of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids

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RNA sequencing of human gastric cancer drug treatment organoids

Project description:Using RNA sequencing, we profile transcriptome dervied from human gastric cancer organoids after drug treatment.

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Essential role of ALKBH5-mediated RNA demethylation modification in bile acid-induced gastric intestinal metaplasia

Project description:Reflux of bile acids and subsequent caudal-related homeobox 2 (CDX2) activation contribute to gastric intestinal metaplasia (IM), which is a precursor of gastric cancer. However, the underlying mechanism by which bile acids cause this is not entirely clear. Here we demonstrated that alkylation repair homolog protein 5 (ALKBH5), which is a major RNA N6-adenosine demethylase, was required for bile acid-induced gastric IM. Mechanistically, we revealed the N6-methyladenosine (m6A) modification profile in gastric IM for the first time and identified ZNF333 as a bona fide m6A target of ALKBH5. ALKBH5 was shown to demethylate ZNF333 mRNA, leading to enhanced ZNF333 expression by abolishing m6A-YTHDF2-dependent mRNA degradation. In addition, ALKBH5 activated CDX2 and downstream intestinal markers by targeting the ZNF333/CYLD axis and activating NF-κB signaling. Reciprocally, p65, which is the key transcription factor of the canonical NF-κB pathway, enhanced the transcription activity of ALKBH5 in the nucleus, thus forming a positive feed-forward circuit. In addition, ALKBH5 levels were positively correlated with ZNF333 and CDX2 in IM tissues, indicating a significant clinical relevance. Collectively, our findings suggest an m6A modification-associated positive feed-forward loop between ALKBH5 and NF-κB signaling is involved in the generation of the IM phenotype from gastric epithelial cells. Targeting the ALKBH5/ZNF333/CYLD/CDX2 axis might be a useful therapeutic strategy for gastric IM in patients with bile regurgitation.

2021-10-14 | GSE179185 | GEO

Genomic and Epigenomic Profiling of High-Risk Intestinal Metaplasia Reveals Molecular Determinants of Gastric Cancer Progression

Project description:Metaplasia of the gastric epithelia (intestinal metaplasia, IM) is a pre-malignant lesion associated with increased gastric cancer (GC) risk.

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