Farhana Lakadia¹*, Kshitish Acharya² and Kanika Mathuria¹

¹Department of Biotechnology, St. Xavier’s College (Autonomous), Ahmedabad, India
²Founder of Shodhaka Life Sciences Pvt. Ltd., Bengaluru, Karnataka, India

*Corresponding Author: Farhana Lakadia, Department of Biotechnology, St. Xavier’s College (Autonomous), Ahmedabad, India.

Received: December 22, 2023; Published: January 31, 2024

Abstract

Kidney cancer is the seventh most prevalent cancer worldwide, with a better survival rate than some other cancers. However, due to its heterogeneity, it is classified into multiple subtypes, requiring accurate diagnosis to determine the appropriate treatment and prognosis. Gene Expression Profiling can aid in identifying the specific subtype of cancer. The focus of this project is to investigate the metabolism and molecular mechanisms of kidney tumor cells. As cancer progresses to later stages, the success rate of treatment decreases. Therefore, it is crucial to detect biomarkers that can aid in early diagnosis and later after the treatment, in prognosis. These biomarkers can also be targeted through therapies to treat the cancer. Through this project, we aim to identify potential biomarkers by subjecting a list of differentially expressed genes in tumor cells to multiple functional analysis. The bioinformatic tools used for the functional analysis are: DAVID, KEGG, REACTOME, STRING, CYTOSCAPE, JASPAR and miTARBase.

Keywords: Biomarkers; Differentially Expressed Genes; Kidney Cancer

References

1. Hausman DM. “What Is Cancer?”. Perspectives in Biology and Medicine4 (2019): 778-784.
2. Owens B. “Kidney cancer”. Nature7620 (2016): S97.
3. Wu Y., et al. “Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma”. Nature Communications1 (2023): 1-25.
4. Linehan WM., et al. “The Metabolic Basis of Kidney Cancer”. Cancer Discovery8 (2019): 1006-1021.
5. Wu Y., et al. “Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma”. Nature Communications1 (2023): 1681.
6. Lane BR., et al. “Cancer of the kidney”. In: DeVita VT, Lawrence TS, Rosenberg SA, editors. Cancer Principles and Practice of Oncology. Philadelphia, PA: Wolters Kluwer (2015): 865-884.
7. Li F., et al. “Kidney cancer biomarkers and targets for therapeutics: survivin (BIRC5 XIAP, MCL-1, HIF1α, HIF2α, NRF2, MDM2, MDM4, p53, KRAS and AKT in renal cell carcinoma”. Journal of Experimental and Clinical Cancer Research: CR1 (2021): 254.
8. Rini BI. “Vascular endothelial growth factor-targeted therapy in renal cell carcinoma: current status and future directions”. Clinical Cancer Research4 (2007): 1098-1106.
9. Blyth K., et al. “The RUNX genes: gain or loss of function in cancer”. Nature Reviews Cancer 5 (2005): 376-387.
10. Höllein A., et al. “Molecular characterization of AML with RUNX1-RUNX1T1 at diagnosis and relapse reveals net loss of co-mutations. HemaSphere1 (2019): e178.
11. Yuan Y., et al. “AML1-ETO expression is directly involved in the development of acute myeloid leukemia in the presence of additional mutations”. Proceedings of the National Academy of Sciences of the United States of America18 (2001): 10398-10403.
12. Zhang Y W., et al. “A novel transcript encoding an N-terminally truncated AML1/PEBP2 alphaB protein interferes with transactivation and blocks granulocytic differentiation of 32Dcl3 myeloid cells”. Molecular and Cellular Biology7 (1997): 4133-4145.
13. Tanaka T., et al. “An acute myeloid leukemia gene, AML1, regulates hemopoietic myeloid cell differentiation and transcriptional activation antagonistically by two alternative spliced forms”. The EMBO journal,2 (1995): 341-350.
14. Shen Z., et al. “Transcription Factor EBF1 Over-Expression Suppresses Tumor Growth in vivo and in vitro via Modulation of the PNO1/p53 Pathway in Colorectal Cancer”. Frontiers in Oncology 10 (2020): 1035.
15. The Human Protein Atlas (2023).
16. Okamoto J., et al. “EMX2 is epigenetically silenced and suppresses growth in human lung cancer”. Oncogene44 (2010): 5969-5975.
17. Chen F., et al. “IRF1 suppresses Ki-67 promoter activity through interfering with Sp1 activation”. Tumor Biology 33 (2012): 2217-2225.
18. Tolomeo M and Grimaudo S. “The "Janus" Role of C/EBPs Family Members in Cancer Progression”. International Journal of Molecular Sciences12 (2020): 4308.
19. Chen F., et al. “Upregulation of Id3 inhibits cell proliferation and induces apoptosis in A549/DDP human lung cancer cells in vitro”. Molecular Medicine Reports 14 (2016): 313-318.
20. Chen F., et al. “Upregulation of Id3 inhibits cell proliferation and induces apoptosis in A549/DDP human lung cancer cells in vitro”. Molecular Medicine Reports 14 (2016): 313-318.
21. Wang T., et al. “Identification and immunoprofiling of key prognostic genes in the tumor microenvironment of hepatocellular carcinoma”. Bioengineered1 (2021): 1555-1575.
22. Chen Y., et al. “Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments”. Cancer Cell International 20 (2020): 331.
23. Grange C., et al. “Extracellular vesicles and carried miRNAs in the progression of renal cell carcinoma”. International Journal of Molecular Sciences 20 (2019): 1832.
24. Wan B., et al. “Identification of Differentially Methylated Genes Associated with Clear Cell Renal Cell Carcinoma and Their Prognostic Values”. Journal of Environmental and Public Health (2023): 8405945.
25. Shi S N., et al. “Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma”. Aging10 (2020): 9205-9223.
26. Courcier J., et al. “Carbonic Anhydrase IX in Renal Cell Carcinoma, Implications for Disease Management”. International Journal of Molecular Sciences 19 (2020): 7146.
27. Zhong W., et al. “Elevated expression of LIF predicts a poor prognosis and promotes cell migration and invasion of clear cell renal cell carcinoma”. Frontiers in Oncology 12 (2022): 934128.
28. Balkwill F. “TNF-α in promotion and progression of cancer”. Cancer and Metastasis Reviews 25 (2006): 409-416.
29. Rascio F., et al. “The Pathogenic Role of PI3K/AKT Pathway in Cancer Onset and Drug Resistance: An Updated Review”. Cancers16 (2021): 3949.
30. Ren Y., et al. “Essential role of the cGMP/PKG signaling pathway in regulating the proliferation and survival of human renal carcinoma cells”. International Journal of Molecular Medicine5 (2014): 1430-1438.
31. Peng Y and Croce C. “The role of MicroRNAs in human cancer”. Signal Transduction and Targeted Therapy 1 (2016): 15004.

Citation

Citation: Farhana Lakadia., et al. “Gene Expression Profiling of Kidney Cancer"Acta Scientific Biotechnology 5.1 (2024): 15-25.

Copyright

Copyright: © 2024 Farhana Lakadia., et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.