TMECircDB

TMECircDB catalogs and annotates circular RNAs (circRNAs) in the tumor microenvironment (TME) of metastatic colorectal cancer (mCRC) to enable functional and cell-type-specific analyses.

Key Features:

• Extensive CircRNA Catalog: Contains 47,869 circRNAs identified from total RNA sequencing (RNA-seq) of 30 matched normal, primary, and metastatic samples from 14 mCRC patients and five CRC cell lines.
• Novel and Unannotated CircRNAs: Reports that 51% of circRNAs were previously unannotated in colorectal cancer (CRC) contexts and 14% represent novel candidates absent from existing circRNA databases.
• Differential Expression Analysis: Identifies 362 circRNAs differentially expressed between primary and metastatic tissues, termed circular RNAs associated with metastasis (CRAMs).
• Cell-Type Specificity: Uses a non-negative least squares statistical model to predict 667 circRNAs as exclusively expressed in specific cell types within the TME.

Scientific Applications:

• Functional Characterization: Enables investigation of circRNA roles in CRC metastasis by providing a comprehensive catalog with differential expression annotations.
• Tumor Microenvironment Studies: Supports analysis of cell-type-specific circRNA expression within the TME to dissect interactions among distinct cellular populations in mCRC.
• Biomarker Discovery: Provides CRAMs and novel circRNA candidates as targets for potential biomarker development for detection, prognosis, or therapeutic targeting in mCRC.

Methodology:

Total RNA sequencing (RNA-seq) of 30 matched normal, primary, and metastatic samples from 14 mCRC patients and five CRC cell lines followed by RNA-seq analysis and application of a non-negative least squares statistical model to deconvolute cell-type-specific circRNA expression and identify differentially expressed circRNAs (CRAMs).