Transcriptomics

Dataset Information

0

Multi-omic study of genome-edited human colonoids reveal patterns of microRNA regulation specific to different colorectal cancer mutation profiles


ABSTRACT: Colorectal cancer (CRC) is the third most diagnosed cancer and the second leading cause of cancer-related death worldwide Unique combinations of mutations can affect responsiveness to specific therapeutics. This can be, at least in part, due to mutation-specific alterations in gene regulatory mechanisms. To better understand how unique combinations of mutations affect gene regulation, we generated small RNA-seq, length extension chromatin run-on-seq (leChRO-seq), and RNA-seq data from APC (A-mutant), APC/KRAS (AK-mutant), APC/KRAS/TP53 mutant (AKP-mutant), and iGFP control human colonic organoids. From these analyses, we found that our colonic organoid models demonstrate mutation-specific patterns of miRNA transcription, miRNA expression and transcriptional regulatory element actvitiy. Furthermore, we defined 10 patterns of miRNA expression across organoid models. We highlighted one group of miRNAs that exhibited a unique downregulation of expression in AKP-mutant organoids (including miR-34a-5p and miR-10a-5p). Analysis of miRNA transcription revealed that most changes in miRNA expression are correlated with changes in miRNA transcription. Analysis of leChRO-seq data revealed that transcriptional regulatory elements upregulated in AKP-mutant colonic organoids have an enrichment of predicted binding sites for oncogenic transcription factors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE231436 | GEO | 2023/12/31

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2013-07-02 | GSE39557 | GEO
2013-07-02 | E-GEOD-39557 | biostudies-arrayexpress
2022-11-15 | GSE188212 | GEO
| PRJNA682633 | ENA
2015-05-07 | E-GEOD-65253 | biostudies-arrayexpress
2022-05-13 | E-MTAB-11145 | biostudies-arrayexpress
2023-04-05 | GSE218776 | GEO
2018-08-21 | GSE118055 | GEO
| PRJNA309855 | ENA
2016-03-31 | E-GEOD-76847 | biostudies-arrayexpress