Clinical phosphoproteomics reveals aberrant signalling pathways and kinases in treatment-resistant cervical cancer.

person Prashant Kumar Karkinos Healthcare Private Limited, Mumbai, Maharashtra, India info_outline Prashant Kumar, Richa Chauhan, Irene A. George, Janani Sambath, Ekta R. Dhawale, Manisha Singh, Vinita Trivedi, R. Venkataramanan

Authors person Prashant Kumar Karkinos Healthcare Private Limited, Mumbai, Maharashtra, India info_outline Prashant Kumar, Richa Chauhan, Irene A. George, Janani Sambath, Ekta R. Dhawale, Manisha Singh, Vinita Trivedi, R. Venkataramanan Organizations Karkinos Healthcare Private Limited, Mumbai, Maharashtra, India, Mahavir Cancer Sansthan, Patna, India, Manipal Academy of Higher Education (MAHE), Manipal, India, Institute of Bioinformatics, Bangalore, India, Vedantaa Hospital & Research Centre, Palghar, India, Mahavir Cancer Sansthan and Research Centre, Patna, India, Karkinos Healthcare Pvt Ltd., Mumbai, India Abstract Disclosures Research Funding No funding sources reported Background: Cisplatin-based concurrent chemoradiation therapy (CCRT) is the standard for locally advanced cervical cancer. While cisplatin stands out as a highly effective chemotherapeutic option for cervical cancer, resistance to the drug often triggers relapses. Moreover, previous studies have highlighted the detrimental impact of cisplatin's toxicity, which extends beyond treatment efficacy to influence the overall prognosis of patients. Combination treatment with drugs targeting different molecular pathways increases the effectiveness of the treatment by disrupting multiple critical processes that cancer cells rely on for survival. Herein, we analyzed the phosphoproteomic profile of cervical cancer patients resistant to concurrent chemoradiotherapy to identify the crucial kinases responsible for therapeutic resistance. Methods: We used mass spectrometry for phosphoproteomic analysis to study signaling pathways and dysregulated kinases in CCRT resistance. Biopsy samples collected pre-therapy were processed by protein extraction, digestion, and labeling with 10-plex TMT. Peptides were fractionated by basic pH liquid chromatography, enriched using IMAC, and analyzed on an Orbitrap-Fusion-Tribrid mass spectrometer. Data analysis was performed using Proteome Discoverer and various bioinformatics and statistical methods. Results: The phosphoproteomic analysis revealed distinct phosphorylation signatures between the responders and non-responders. In concordance with the phosphoproteomic data the expression of phospho-SMC1A and CSNK2A1 is preserved in non-responder cohort of cervical cancer patients in concordance with the phosphoproteomic data. Further, the pathway analysis showed elevated presence of the DNA repair pathway in the treatment-resistant cohort. Furthermore, dysregulation in the phosphorylation of key DNA repair proteins, such as SMC1A, HMGN1, MGMT, DDB2, and MSH6, suggests their involvement in treatment. The kinase prediction analysis suggested the activation of kinases such as CSNK2A1, PRKDC, PLK1, NEK2 and ATM in non-responders. Subsequently, cell line based functional experiments indicated the potential of CSNK2A1 inhibitor silmitasertib in sensitizing the cells to cisplatin treatment. Conclusions: Phosphoproteomicanalysis of the cervical cancer revealed distinct phosphorylation signature and kinases involved in treatment resistance. Our findings indicated that dysregulated phosphorylation and increased expression of the kinase CSNK2A1 play a pivotal role in the treatment response of cervical cancer patients. Moreover, CSNK2A1 can sensitizes the cells to cisplatin uncovering the potential of combination treatment strategies. Our study uncovers the potential of clinical phosphoproteomics to design tailored treatment strategies in patients resistant to standard treatments.

Pre-clinical