Open Access

ARTICLE

Deciphering key genes involved in cisplatin resistance in kidney renal clear cell carcinoma through a combined in silico and in vitro approach

by MUNEEBA MALIK¹, MAMOONA MAQBOOL², TOOBA NISAR³, TAZEEM AKHTER⁴, JAVED AHMED UJAN^5,6, ALANOOD S. ALGARNI⁷, FAKHRIA A. AL JOUFI⁸, SULTAN SHAFI K. ALANAZI⁹, MOHAMMAD HADI ALMOTARED¹⁰, MOUNIR M. SALEM BEKHIT¹¹, MUHAMMAD JAMIL^12,*

1 Services Hospital, Lahore, Pakistan
2 Sabzazar Medical Center, Lahore, Pakistan
3 BHU Pourmiana, Attock, Pakistan
4 Public Health Department, University of Health Sciences, Lahore, Pakistan
5 Department of Zoology, Shah Abdul Latif University, Khairpur, Pakistan
6 Department of Animal Sciences, University of Florida, Gainesville, USA
7 Pharmacology and Toxicology Department College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
8 Department of Pharmacology, College of Pharmacy, Jouf University, Aljouf, Saudi Arabia
9 Regional Laboratory and Blood Bank (Total Laboratory Automation), Riyadh, Saudi Arabia
10 Health Affairs in Najran, New Najran General Hospital, Najran, Saudi Arabia
11 Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
12 PARC Arid Zone Research Center, Dera Ismail Khan, Pakistan

* Corresponding Author: Muhammad Jamil,

(This article belongs to the Special Issue: Cancer Metastasis)

Oncology Research 2023, 31(6), 899-916. https://doi.org/10.32604/or.2023.030760

Received 21 April 2023; Accepted 29 May 2023; Issue published 15 September 2023

Abstract

The low survival rate of Kidney renal clear cell carcinoma (KIRC) patients is largely attributed to cisplatin resistance. Rather than focusing solely on individual proteins, exploring protein-protein interactions could offer greater insight into drug resistance. To this end, a series of in silico and in vitro experiments were conducted to identify hub genes in the intricate network of cisplatin resistance-related genes in KIRC chemotherapy. The genes involved in cisplatin resistance across KIRC were retrieved from the National Center for Biotechnology Information (NCBI) database using search terms as “Kidney renal clear cell carcinoma” and “Cisplatin resistance”. The genes retrieved were analyzed for hub gene identification using the STRING database and Cytoscape tool. Expression and promoter methylation profiling of the hub genes was done using UALCAN, GEPIA, OncoDB, and HPA databases. Mutational, survival, functional enrichment, immune cell infiltration, and drug prediction analyses of the hub genes were performed using the cBioPortal, GEPIA, GSEA, TIMER, and DrugBank databases. Lastly, expression and methylation levels of the hub genes were validated on two cisplatin-resistant RCC cell lines (786-O and A-498) and a normal renal tubular epithelial cell line (HK-2) using two high throughput techniques, including targeted bisulfite sequencing (bisulfite-seq) and RT-qPCR. A total of 124 genes were identified as being associated with cisplatin resistance in KIRC. Out of these genes, MCL1, IGF1R, CCND1, and PTEN were identified as hub genes and were found to have significant (p < 0.05) variations in their mRNA and protein expressions and effects on the overall survival (OS) of the KIRC patients. Moreover, an aberrant promoter methylation pattern was found to be associated with the dysregulation of the hub genes. In addition to this, hub genes were also linked with different cisplatin resistance-causing pathways. Thus, hub genes can be targeted with Alvocidib, Estradiol, Tretinoin, Capsaicin, Dronabinol, Metribolone, Calcitriol, Acetaminophen, Acitretin, Cyclosporine, Azacitidine, Genistein, and Resveratrol drugs. As the pathogenesis of KIRC is complex, targeting hub genes and associated pathways involved in cisplatin resistance could bring a milestone change in the drug discovery and management of drug resistance, which might uplift overall survival among KIRC patients.

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