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Colon, rectum and rectal tumor organoids. Effects of calcitriol (active form of Vitamin D) treatment

ABSTRACT: We have established three-dimensional (3D) organoids from healthy colon and rectum tissue and from tumor tissue of patients with rectal cancer. Global transcriptomic analyses reveal differences in gene expression between these stem cell-derived cultures and distinct response to vitamin D.

ORGANISM(S): Homo sapiens

PROVIDER: GSE143782 | GEO | 2020/09/08

REPOSITORIES: GEO

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Colon, rectum and rectal tumor organoids. Effects of calcitriol (active form of Vitamin D) treatment

Project description:Colon, rectum and rectal tumor organoids. Effects of calcitriol (active form of Vitamin D) treatment

| PRJNA601668 | ENA

Scottish Colorectal Cancer Vitamin D Intervention Study (SCoViDS) [RNA-seq]

Project description:Controversy surrounds whether vitamin D reduces colorectal cancer (CRC) risk, and/or beneficially impacts on CRC survival. We sought to delineate the transcriptomic in vivo response of human colorectal epithelium to vitamin D supplementation, define inter-subject variability and develop a predictive biomarker of response consistent with anti-tumour effects. Methodology Blood and rectal normal mucosa (NM) were sampled (176 subjects) and correlation sought between circulating vitamin D (25-OHD) level and NM gene expression (HT12 microarray) in the observational study. Oral vitamin D (3200IU/day) supplements were administered to 50 participants in an intervention study. Blood and NM (sigmoidoscopic biopsy) were sampled after 12 weeks. Transcriptomic analysis (HT12 and RNAseq) of post-treatment biopsies assessed enrichment for candidate genes and GO processes prioritised in the observational study. We identified transcriptomic changes in rectum that are consistent with anti-tumour responses. We then sought blood biomarkers predicting this response using receiver-operator curves and calculation of C-statistic. An independent expression dataset (BEST-D trial) was then used to validate candidate blood biomarkers of vitamin D response.

2021-06-22 | GSE157982 | GEO

Race-specific patterns of epigenetic aging and age-associated differential methylation in normal rectal biopsies: Implications for the biology of aging and its relationship to rectal cancer

Project description:Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the im-portant role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA), and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epige-nome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n=140 samples)

2022-12-23 | GSE216024 | GEO

Effects of psychological stress on gene expression in the mouse rectum.

2009-02-14 | GSE11910 | GEO

Early dynamic transcriptomic changes as predictors of preoperative radiotherapy efficacy in patients with rectal cancer: a feasibility study.

Project description:With a view to developing novel biomarkers of the efficacy of radiotherapy in patients with rectal cancer, we measured gene expression profiles on biopsies taken before and during preoperative radiotherapy. Repeat biopsy did not increase toxicity. Radiotherapy induced the expression of genes involved in oxidative stress, signal transduction, apoptosis and immune response. Two rectum tumor biospsies for each patient (6 cases) : before RT and one hour after a dose of 7.2 Gy (4th fraction) during RT.

2011-12-12 | E-GEOD-26027 | biostudies-arrayexpress

Differentiating Mouse Colon and Rectum: Transcriptional Differences and Environmental Exposure

2012-08-20 | GSE38753 | GEO

Transcription profiling of mouse rectum after physiological stress

Project description:Using isolation stress model, we showed that goblet cell-dependent mucosal barrier functions in the mouse rectum was more vulnerable to stress than the colon. We also found that isolation stress specifically stimulated IL-18 production only in the rectum. Furthermore, the crucial role of IL-18 in the stress response of the mouse rectum was confirmed using IL-18 knockout mice. Microarray analysis was used to assess the stress response and to identify responsible genes for the vulnerability of the mouse rectum to isolation stress. Experiment Overall Design: Total RNA was prepared from the colon and the rectum of wild-type and IL-18 knockout mice before isolation and 8 days after starting isolation. The one GSM sample of microarray analysis was made by pooling an equal amount of total RNA 5 mice of each group. Agilent whole mouse genome oligonucleotide microarray was used to measure gene expression in these samples according to the manufactureâ??s protocol.

2009-02-26 | E-GEOD-11910 | biostudies-arrayexpress

Human rectal adenoma (8 cases) vs. rectal carcinoma (8 cases)

Project description:Genomic profiling of human rectal adenoma and carcinoma by array-based comparative genomic hybridization Two group experiment, rectal adenoma vs. rectal carcinoma. Biological replicates: 8 adenomas vs. 8 carcinomas

2011-12-20 | E-GEOD-34472 | biostudies-arrayexpress

Differentiating Mouse Colon and Rectum: Transcriptional Differences and Environmental Exposure

Project description:We have demonstrated that the colon and rectum are transcriptionally distinct in mice and that the colon can be differentiated from rectum based on microarray profiles. This transition occurs over the first weeks of life, indicating environmental exposure is an important mediator. Colon and rectum RNA from E18 to 8 week old C57BL/6J mice along with 8 week old gnotobiotic C57BL/6J mice were evaluated with microarray technology. For each array analysis a pool of RNA(2-8) from individual colons or rectums were co-hybridized with a reference pool of 4 RNA samples from mouse small intestine, rectum and colon (SIRC)) to Agilent Mouse Whole Genome 4x44k microarrays and scanned on an Agilent microarray scanner. Files were extracted using Agilent Feature Extraction version 9.5.

2012-08-20 | E-GEOD-38753 | biostudies-arrayexpress

The rectal cancer microRNAome - a comprehensive comparative analysis of microRNA expression in rectal cancer and matched normal mucosa

Project description:Purpose: MicroRNAs play a prominent role in a variety of physiological and pathological biological processes, including cancer. For rectal cancers, only limited data are available on microRNA expression profiles, while the underlying genomic and transcriptomic aberrations have been firmly established. We therefore aimed to comprehensively map the microRNA expression patterns of this disease. Experimental design: Tumor biopsies and corresponding matched mucosa samples were prospectively collected from 72 patients (68 tumors and 70 normal mucosa) with locally advanced rectal cancers. Total RNA was extracted, and tumor and mucosa microRNA expression profiles were subsequently established for all patients. The expression of selected microRNAs was validated using semi-quantitative real-time PCR. Results: Forty-nine microRNAs were significantly differentially expressed (log2-fold difference >0.5 and P<0.001) between rectal cancer and normal rectal mucosa. The predicted targets for the identified microRNAs were enriched for the following KEGG pathways: Wnt, TGF-beta, mTOR, insulin, MAPK, and ErbB signaling. Between rectal tumor and normal tissue, miR-492, miR-542-5p, miR-584, miR-483-5p, miR-144, miR-2110, miR-652*, miR-375, miR-147b, miR-148a, miR-190, miR-26a/b, and miR-338-3p were found to be differentially expressed. Of clinical impact, miR-135b expression correlated significantly with overall survival that could be validated in a larger multicenter patient set (n=94). Conclusion: The comprehensive analysis of the rectal cancer microRNAome uncovered novel microRNAs and pathways associated with rectal cancer. This information contributes to a detailed view of rectal cancer. The identification and validation of miR-135b will help to identify novel molecular targets and pathways for therapeutic exploitation. Paired samples from rectal tumor and matched normal samples. Included are also 2 technical replicates.

2012-10-05 | E-GEOD-38389 | biostudies-arrayexpress

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