ABRAXAS1-HELQ is a candidate class-matched reference chimeric RNA and contributes to prostate cell motility through...

RT-qPCR is widely used for RNA expression quantification, and reliable normalization requires appropriate reference genes. Because different RNA classes display distinct expression characteristics, class-matched internal controls are essential for reliable quantification. While class-matched reference genes have been established for microRNAs and circular RNAs, stable reference genes for chimeric RNAs in the prostate remain lacking, limiting the accuracy of expression analyses. Recent evidence indicates that chimeric RNAs also exist under physiological conditions, suggesting that some chimeric RNAs may function as housekeeping-like molecules.

RNA sequencing data from the TCGA and CPGEA prostate cancer cohorts were analyzed to identify candidate class-matched reference chimeric RNAs, followed by experimental evaluation in prostate cell lines and prostate tissue samples. Candidate chimeric RNAs were experimentally validated using touchdown PCR, gel electrophoresis, Sanger sequencing, and RT-qPCR. Subcellular localization and biological functions were further evaluated by nuclear-cytoplasmic fractionation, transcriptome analysis, and functional assays.

Analysis of chimeric RNAs shared between TCGA and CPGEA identified 37 candidate chimeric RNAs without a statistically detectable difference between prostate cancer and matched adjacent tissues. ABRAXAS1-HELQ was detectable in the pooled clinical sample, showed a comparatively consistent expression pattern across nine prostate-derived cell lines, and showed no significant change under selected experimental conditions in three cell lines. siRNA-mediated reduction of ABRAXAS1-HELQ was associated with reduced cell migration, with MCOLN2 identified as a potential downstream mediator.

ABRAXAS1-HELQ represents a candidate class-matched reference chimeric RNA with relatively consistent expression under the tested experimental conditions and serves as a potential reference molecule for chimeric RNA quantification in prostate-related studies.