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Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis

ABSTRACT: Colorectal cancer (CRC) is the most common gastrointestinal malignancy in the U.S.A. and approximately 50% of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Despite our understanding of circular RNAs (circRNAs) in primary cancer, their role throughout mCRC remains poorly characterized. Further, despite the availability of bulk RNA-Seq data for monitoring circRNA expression little is known about their cell-type specific expression profiles to fully understand their functions between tumor cells and the microenvironment. To evaluate circRNAs in mCRC progression, total RNA-Seq was performed on 30 matched normal, primary, and distant metastatic samples from 14 mCRC patients. Additionally, the transcriptome of five CRC cell lines were sequenced to construct a circRNA catalog in CRC. Differential expression (DE) analysis identified circRNAs dysregulated between normal, primary, and metastatic tissues. Differential backsplicing (DS) analysis was used to highlight circRNAs with an altered tendency in backsplicing as compared to their linear counterparts. Cell-type deconvolution was performed using published CRC single-cell RNA-Seq datasets as signature matrices. The cell-type specific expression of circRNAs was then estimated through a non-negative least squares statistical model.

ORGANISM(S): Homo sapiens

PROVIDER: GSE221240 | GEO | 2023/05/04

REPOSITORIES: GEO

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