Transcriptome sequencing (RNA-Seq) reveals non-coding pseudogene CDC27P9 role in cervical cancer

Non-Coding regions contains genomic remnants called as Pseudogenes. For a long time, pseudogenes have been regarded as non-functional. This study investigates the previously unstudied Pseudogene CDC27P9 role in cervical cancer. Whole RNA-transcriptome profiling was performed from blood samples of n = 10 cervical cancer patients and n = 10 age matched healthy controls. CDC27P9 expression was validated in patient samples using RT-PCR. The putative CDC27P9-encoded protein structure was predicted using ChimeraX 1.9, refined predicted protein using (GROMACS 2022.2) and evaluated by Ramachandran plot. Post docking using (HADDOCK2.4) with parent gene CDC27 and other interacting genes, a 100ns MD Simulation (GROMACS 2022.2) was done. Functional studies done by siRNA-mediated silencing of CDC27P9 in HeLa cells to study Anaphase Promoting Complex/Cyclosome Pathway using RT-PCR. Cell Cycle, Mitochondrial Membrane Potential Loss and Apoptosis, using Flow Cytometry. Cell death and Chromatin Condensation was visualised using Laser Scanning Confocal Microscopy and validated in multimode microplate reader. Transcriptome sequencing revealed CDC27P9 upregulated with log₂FC = 10.68. RT-PCR validated overexpression of CDC27P9 in cervical cancer patients. Putative CDC27P9-encoded protein had an 93.11% of the residues point to protein structure reliability. Molecular docking and MD simulation showed strongest interactions with CDC27 and CDC20. Silencing of CDC27P9, downregulated CDC27 and Anaphase Promoting Complex/Cyclosome genes UBE2L3, PTTG1, ESPL1. In parallel downregulation of anti-apoptotic gene BCL2 while upregulation of pro-apoptotic BAX was observed. Silencing of CDC27P9 induced cell cycle arrest at S-phase, induces apoptosis and mitochondrial membrane potential loss. Observation of Condensed chromatin structure post silencing was an indicative of apoptotic signalling. Further cell death, growth inhibition and morphology changes was observed. Interestingly, silencing of CDC27P9 in cervical cancer HeLa cells caused downregulation of HPV 18. This study is the first to identify pseudogene CDC27P9 as functional with active transcripts and putative protein‑coding potential. Our findings suggest that CDC27P9 may contribute to cervical cancer progression by modulating APC/C‑mediated cell‑cycle pathways, prevent apoptosis thereby sustains cell survival in cancer cells and could be involved in HPV18-associated cellular pathways.