Pan-cancer integrated bioinformatic analysis of RNA polymerase subunits reveal RNA Pol I member CD3EAP regulates cell growth by modulating autophagy

ABSTRACT

Transcription is a crucial stage in gene expression. An integrated study of 34 RNA polymerase subunits (RNAPS) in the six most frequent cancer types identified several genetic and epigenetic modification. We discovered nine mutant RNAPS with a mutation frequency of more than 1% in at least one tumor type. POLR2K and POLR2H were found to be amplified and overexpressed, whereas POLR3D was deleted and downregulated. Multiple RNAPS were also observed to be regulated by variations in promoter methylation. 5-Aza-2-deoxycytidine mediated re-expression in cell lines verified methylation-driven inhibition of POLR2F and POLR2L expression in BRCA and NSCLC, respectively. Next, we showed that CD3EAP, a Pol I subunit, was overexpressed in all cancer types and was associated with worst survival in breast, liver, lung, and prostate cancers. The knockdown studies showed that CD3EAP is required for cell proliferation and induces autophagy but not apoptosis. Furthermore, autophagy inhibition rescued the cell proliferation in CD3EAP knockdown cells. CD3EAP expression correlated with S and G2 phase cell cycle regulators, and CD3EAP knockdown inhibited the expression of S and G2 CDK/cyclins. We also identified POLR2D, an RNA pol II subunit, as a commonly overexpressed and prognostic gene in multiple cancers. POLR2D knockdown also decreased cell proliferation. POLR2D is related to the transcription of just a subset of RNA POL II transcribe genes, indicating a distinct role. Taken together, we have shown the genetic and epigenetic regulation of RNAPS genes in most common tumors. We have also demonstrated the cancer-specific function of CD3EAP and POLR2D genes.

KEYWORDS:

• Pan-cancer
• RNA polymerase
• integrated bioinformatic analysis
• autophagy
• cell cycle

Acknowledgements

The authors acknowledge Ms. Seema Khadirnaikar for her help in data analysis. The Cancer Genome Atlas is acknowledged for the data.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author Contribution

Nikita Bhandari: Designed and Performed Experiments, Wrote the manuscript

Disha Acharya: Designed and Performed Experiments

Annesha Chatterjee: Performed Experiments

Lakshana Mandve: Performed Experiments

Pranjal Kumar: Performed Experiments

Shreesh Pratap: Designed and Performed Experiments

Pushkar Malakar: Designed experiments

Sudhanshu K Shukla: Conceptualization, resources, supervision, writing (reviewing and editing),

Data availability statement

All the data used in this study are publicly available.

Additional information

Funding

This work was funded by a research grant from the Indian Council of Medical Research, Govt. of India (NO. 2020-3806/CMB/ADHOC-BMS and 2021-9513/CMB/ADHOC-BMS).