Differential interactome proposes subtype-specific biomarkers and potential therapeutics in renal cell carcinomas

Aysegul Caliskan, Gizem Gulfidan, Raghu Sinha, Kazim Yalcin Arga

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Although many studies have been conducted on single gene therapies in cancer patients, the reality is that tumor arises from different coordinating protein groups. Unveiling perturbations in protein interactome related to the tumor formation may contribute to the development of effective diagnosis, treatment strategies, and prognosis. In this study, considering the clinical and tran-scriptome data of three Renal Cell Carcinoma (RCC) subtypes (ccRCC, pRCC, and chRCC) retrieved from The Cancer Genome Atlas (TCGA) and the human protein interactome, the differential pro-tein–protein interactions were identified in each RCC subtype. The approach enabled the identifi-cation of differentially interacting proteins (DIPs) indicating prominent changes in their interaction patterns during tumor formation. Further, diagnostic and prognostic performances were generated by taking into account DIP clusters which are specific to the relevant subtypes. Furthermore, considering the mesenchymal epithelial transition (MET) receptor tyrosine kinase (PDB ID: 3DKF) as a potential drug target specific to pRCC, twenty-one lead compounds were identified through virtual screening of ZINC molecules. In this study, we presented remarkable findings in terms of early diagnosis, prognosis, and effective treatment strategies, that deserve further experimental and clinical efforts.

Original languageEnglish (US)
Article number158
Pages (from-to)1-12
Number of pages12
JournalJournal of Clinical Medicine
Issue number2
StatePublished - Feb 2 2021

All Science Journal Classification (ASJC) codes

  • General Medicine


Dive into the research topics of 'Differential interactome proposes subtype-specific biomarkers and potential therapeutics in renal cell carcinomas'. Together they form a unique fingerprint.

Cite this