Top

Published in:

Open Access 01-12-2022 | Kidney Cancer | Research

Exploration of the role of Cuproptosis genes and their related long non-coding RNA in clear cell renal cell carcinoma: a comprehensive bioinformatics study

Authors: Dian Xia, Qi Liu, Wen Jiao, Longfei Peng, Qi Wang, ZhouTing Tuo, Liangkuan Bi

Published in: BMC Cancer | Issue 1/2022

Abstract

Clear cell renal cell carcinoma is a common malignant tumor of the urinary system. The mechanism of its occurrence and development is unknown, and there is currently few effective comprehensive predictive markers for prognosis and treatment response. With the discovery of a new cell death process – cuproptosis drew the attention of researchers. We constructed a model for the prediction of clinical prognosis and immunotherapy response through integrative analysis of gene expression datasets from KIRC samples in The Cancer Genome Atlas (TCGA) database. During the course of the study, we found that cuproptosis genes are significantly differentially expressed between clear cell renal cell carcinoma samples and normal samples. Based on this, we put forward the prognostic model for cuproptosis gene related-long non-coding RNA. And through various statistic and external independent cohorts, we proved that the model is accurate and stable, worthy of clinical application and further exploration and validation.

Available only for authorised users

Ljungberg B, Albiges L, Abu-Ghanem Y, et al. European Association of Urology Guidelines on Renal Cell Carcinoma: The 2019 Update. Eur Urol. 2019;75(5):799–810. https://doi.org/10.1016/j.eururo.2019.02.011

Finelli A, Ismaila N, Bro B, et al. Management of small renal masses: American Society of Clinical Oncology Clinical Practice Guideline. J Clin Oncol. 2017;35:668–80. https://doi.org/10.1200/JCO.2016.69.9645.CrossRefPubMed

Motzer RJ, Rini BI, Mcdermott DF, et al. Nivolumab for Metastatic Renal Cell Carcinoma: Results of a Randomized Phase II Trial. J Clin Oncol. 2014;33(13):1430–7. https://doi.org/10.1200/JCO.2014.59.0703.CrossRefPubMedPubMedCentral

Motzer RJ, Escudier B, Mcdermott DF, et al. Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma. N Engl J Med. 2015;373(19):917–27. https://doi.org/10.1056/NEJMoa1510665.CrossRef

Slack FJ, Chinnaiyan AM. The role of non-coding rnas in oncology. Cell. 2019;179(5):1033–55. https://doi.org/10.1016/j.cell.2019.10.017.CrossRefPubMedPubMedCentral

Gandhi M, Caudron-Herger M, Diederichs S. Rna motifs and combinatorial prediction of interactions, stability and localization of noncoding rnas. Nat Struct Mol Biol. 2018. https://doi.org/10.1038/s41594-018-0155-0.CrossRefPubMed

Derrien T, Johnson R, Bussotti G, Tanzer A, Guigó R. The gencode v7 catalog of human long noncoding rnas: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22(9):1775–89. https://doi.org/10.1101/gr.132159.111.CrossRefPubMedPubMedCentral

Carninci P, Kasukawa T, Katayama S, Gough J, Hayashizaki Y. The transcriptional landscape of the mammalian genome. Science. 2005;309(5740):1559–63. https://doi.org/10.1126/science.1112014.CrossRefPubMed

Wang K, Jin W, Song Y, Fei X. LncRNA rp11–436h11.5, functioning as a competitive endogenous rna, upregulates bcl-w expression by sponging mir-335–5p and promotes proliferation and invasion in renal cell carcinoma. Molecular Cancer. 2017;16(1):166. https://doi.org/10.1186/s12943-017-0735-3.CrossRefPubMedPubMedCentral

10.

D’Aniello C, Pisconti S, Facchini S, Imbimbo C, Cavaliere C. Long noncoding rna gihcg is a potential diagnostic and prognostic biomarker and therapeutic target for renal cell carcinoma. Eur Rev Med Pharmacol Sci. 2018;22:1169.

11.

Tsvetkov P, Coy S, Petrova B, Dreishpoon M, Verma A, Abdusamad M, et al. Copper induces cell death by targeting lipoylated TCA cycle proteins. Science. 2022;375(6586):1254–61. https://doi.org/10.1126/science.abf0529.CrossRefPubMedPubMedCentral

12.

Martínez-Reyes I, Cardona LR, Kong H, Vasan K, McElroy GS, Werner M, et al. Mitochondrial ubiquinol oxidation is necessary for tumour growth. Nature. 2020;585(7824):288–92. https://doi.org/10.1038/s41586-020-2475-6.CrossRefPubMedPubMedCentral

13.

Hui S, Ghergurovich JM, Morscher RJ, Jang C, Teng X, Lu W, et al. Glucose feeds the TCA cycle via circulating lactate. Nature. 2017;551(7678):115–8. https://doi.org/10.1038/nature24057.CrossRefPubMedPubMedCentral

14.

Byrne C, Divekar SD, Storchan GB, Parodi DA, Martin MB. Metals and breast cancer. J Mammary Gland Biol Neoplasia. 2013;18(1):63–73. https://doi.org/10.1007/s10911-013-9273-9.CrossRefPubMedPubMedCentral

15.

Boschi A, Martini P, Janevik-Ivanovska E, Duatti A. The emerging role of copper-64 radiopharmaceuticals as cancer theranostics. Drug Discov Today. 2018;23(8):1489–501. https://doi.org/10.1016/j.drudis.2018.04.002.CrossRefPubMed

16.

Xu F, Zhan X, Zheng X, Xu H, Li Y, Huang X, et al. A signature of immune-related gene pairs predicts oncologic outcomes and response to immunotherapy in lung adenocarcinoma. Genomics. 2020;112(6):4675–83. https://doi.org/10.1016/j.ygeno.2020.08.014.CrossRefPubMed

17.

Li X, Li Y, Yu X, Jin F. Identification and validation of stemness-related lncRNA prognostic signature for breast cancer. J Transl Med. 2021;18(1):331. https://doi.org/10.1186/s12967-020-02497-4.CrossRef

18.

Xu F F, Huang X, Li Y, Chen Y, Lin L. mA-related lncRNAs are potential biomarkers for predicting prognoses and immune responses in patients with LUAD. Mol Ther Nucleic Acids. 2021;24:780–91. https://doi.org/10.1016/j.omtn.2021.04.003.CrossRefPubMedPubMedCentral

19.

He Y, Jiang Z, Chen C, Wang X. Classification of triple-negative breast cancers based on Immunogenomic profiling. J Exp Clin Cancer Res. 2018;37(1):327. https://doi.org/10.1186/s13046-018-1002-1.CrossRefPubMedPubMedCentral

20.

Zeng D, Ye Z, Wu J, Zhou R, Fan X, Wang G, et al. Macrophage correlates with immunophenotype and predicts anti-PD-L1 response of urothelial cancer. Theranostics. 2020;10(15):7002–14. https://doi.org/10.7150/thno.46176.CrossRefPubMedPubMedCentral

21.

Hwang S, Kwon AY, Jeong JY, Kim S, Kang H, Park J, et al. Immune gene signatures for predicting durable clinical benefit of anti-PD-1 immunotherapy in patients with non-small cell lung cancer. Sci Rep. 2020;10(1):643. https://doi.org/10.1038/s41598-019-57218-9.CrossRefPubMedPubMedCentral

22.

Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science (New York, NY). 2016;352(6282):189–96. https://doi.org/10.1126/science.aad0501.CrossRef

23.

Cheng P, Guan Y, Li H, Chen W, Gang Z. Urologic cancer in china. Jpn J Clin Oncol. 2016;46(6):497. https://doi.org/10.1093/jjco/hyw034.CrossRef

24.

Bianchi M, Gandaglia G, Trinh QD, et al. A population-based competing-risks analysis of survival after nephrectomy for renal cell carcinoma. Urol Oncol. 2014;32(46): e1. https://doi.org/10.1016/j.urolonc.2013.06.010.CrossRef

25.

Funakoshi T, Lee CH, Hsieh JJ. A systematic review of predictive and prognostic biomarkers for vegf-targeted therapy in renal cell carcinoma. Cancer Treat Rev. 2014;40(4):533–47. https://doi.org/10.1016/j.ctrv.2013.11.008.CrossRefPubMed

26.

Ge EJ, Bush AI, Casini A, Cobine PA, Cross JR, DeNicola GM, et al. Connecting copper and cancer: from transition metal signalling to metalloplasia. Nat Rev Cancer. 2022;22(2):102–13. https://doi.org/10.1038/s41568-021-00417-2.CrossRefPubMed

27.

Solmonson A, DeBerardinis RJ. Lipoic acid metabolism and mitochondrial redox regulation. J Biol Chem. 2018;293(20):7522–30. https://doi.org/10.1074/jbc.TM117.000259.CrossRefPubMed

28.

Mayr JA, Feichtinger RG, Tort F, Ribes A, Sperl W. Lipoic acid biosynthesis defects. J Inherit Metab Dis. 2014;37(4):553–63. https://doi.org/10.1007/s10545-014-9705-8.CrossRefPubMed

29.

Boroughs LK, Deberardinis RJ. Metabolic pathways promoting cancer cell survival and growth. Nat Cell Biol. 2015;17(4):351. https://doi.org/10.1038/ncb3124.CrossRefPubMedPubMedCentral

30.

Hurley HJ, Dewald H, Rothkopf ZS, Singh S, Jenkins F, Deb P, et al. Frontline Science: AMPK regulates metabolic reprogramming necessary for interferon production in human plasmacytoid dendritic cells. J Leukoc Biol. 2021;109(2):299–308. https://doi.org/10.1002/JLB.3HI0220-130.CrossRefPubMed

31.

Liu H, Chen P, Jiang C, et al. Screening for the Key lncRNA Targets Related With Metastasis of Renal Clear Cell Carcinoma. Medicine. 2016;95(2): e2507. https://doi.org/10.1097/MD.0000000000002507.CrossRefPubMedPubMedCentral

32.

He H, Xu M, Kuang Y, et al. Biomarker and competing endogenous RNA potential of tumor-specific long noncoding RNA in chromophobe renal cell carcinoma. Oncotargets Ther. 2016;9:6399–406. https://doi.org/10.2147/OTT.S116392.CrossRef

33.

Xiao H, Tang K, Liu P, et al. LncRNA MALAT1 functions as a competing endogenous RNA to regulate ZEB2 expression by sponging miR-200s in clear cell kidney carcinoma. Oncotarget. 2015;6(35):38005–15.CrossRefPubMedPubMedCentral

34.

Chen S, Ma P, et al. Biological function and mechanism of MALAT-1 in renal cell carcinoma proliferation and apoptosis: role of the MALAT-1–Livin protein interaction. J Physiol Sci. 2016. https://doi.org/10.1007/s12576-016-0486-8.CrossRefPubMed

35.

Xue Z, Zhang Z, Liu H, Li W, Guo X, Zhang Z, et al. Lincrna-cox2 regulates NLRP3 inflammasome and autophagy mediated neuroinflammation. Cell Death Differ. 2018. https://doi.org/10.1038/s41418-018-0105-8.CrossRefPubMedPubMedCentral

36.

Kumar A, Nallabelli N, Sharma U, Kumari N, Singh SK, Kakkar N, et al. In vitro evidence of NLRP3 inflammasome regulation by histone demethylase LSD2 in renal cancer: a pilot study. Mol Biol Rep. 2020;47(9):7273–6. https://doi.org/10.1007/s11033-020-05692-0.CrossRefPubMed

37.

Wang G, Ye Q, Ning S, Yang Z, Han J. LncRNA MEG3 promotes endoplasmic reticulum stress and suppresses proliferation and invasion of colorectal carcinoma cells through the MEG3/miR-103a-3p/PDHB ceRNA pathway. Neoplasma. 2021;68(2):362–74. https://doi.org/10.4149/neo_2020_200813N858

38.

Batista PJ, Chang HY. Long noncoding rnas: cellular address codes in development and disease. Cell. 2013;152(6):1298–307. https://doi.org/10.1016/j.cell.2013.02.012.CrossRefPubMedPubMedCentral

Title: Exploration of the role of Cuproptosis genes and their related long non-coding RNA in clear cell renal cell carcinoma: a comprehensive bioinformatics study
Authors: Dian Xia
Qi Liu
Wen Jiao
Longfei Peng
Qi Wang
ZhouTing Tuo
Liangkuan Bi
Publication date: 01-12-2022
Publisher: BioMed Central
Keywords: Kidney Cancer
Kidney Cancer
Kidney Cancer
Published in: BMC Cancer / Issue 1/2022
Electronic ISSN: 1471-2407
DOI: https://doi.org/10.1186/s12885-022-10278-z

Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras

Prof. Fabrice Barlesi

Developed by: Springer Medicine

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 1/2022

Suppressive effect of α-mangostin for cancer stem cells in colorectal cancer via the Notch pathway

Early postoperative decrease of skeletal muscle mass predicts recurrence and poor survival after surgical resection for perihilar cholangiocarcinoma

Identification and validation of methylated PENK gene for early detection of bladder cancer using urine DNA

Serum-based measurements of stromal activation through ADAM12 associate with poor prognosis in colorectal cancer

Factors associated with response to compression-based physical therapy for secondary lower limb lymphedema after gynecologic cancer treatment: a multicenter retrospective study

LMOD1, an oncogene associated with Lauren classification, regulates the metastasis of gastric cancer cells through the FAK-AKT/mTOR pathway

Keynote webinar | Spotlight on antibody–drug conjugates in cancer