CircRiC

CircRiC characterizes expression profiles of circular RNAs (circRNAs) across approximately 1000 human cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE), encompassing around 935 cell lines across 22 cancer lineages, to analyze lineage-specific expression, biogenesis, associations with clinically actionable genes, and correlations with drug response.

Key Features:

• Expression Landscape Analysis: Applies four circRNA identification algorithms to polyA-enriched RNA-seq data from CCLE to map circRNA expression across cancer lineages.
• Biogenesis and Functional Insights: Integrates experimental approaches with bioinformatics analyses to identify genes involved in circRNA biogenesis and reveal lineage-specific expression patterns, highlighting a role for TGF-β signaling in promoting circRNA formation.
• Association with Clinically Actionable Genes: Identifies significant associations between clinically actionable genes and circRNA generation and reports an enrichment of RNA-binding protein (RBP) binding sites linked to circRNA-producing genes, including functional effects such as circMYC influencing proliferation.
• Drug Response Correlation: Detects strong correlations between circRNA expression levels and drug response, notably with drugs targeting chromatin histone acetylation.

Scientific Applications:

• Oncogenesis Research: Enables analysis of circRNA roles and lineage-specific expression patterns relevant to cancer biology.
• Biomarker Discovery: Supports identification of circRNAs with potential diagnostic or prognostic value across diverse cancer types.
• Pharmacogenomics and Therapeutic Response: Facilitates investigation of associations between circRNA expression and response to drugs, including agents targeting chromatin histone acetylation.

Methodology:

Applies four circRNA identification algorithms to polyA-enriched CCLE RNA-seq data and performs expression landscape mapping, identification of circRNA biogenesis genes, RBP binding-site enrichment analysis, and correlation analyses between circRNA expression and drug response.