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. 2022 May 10;20(1):148.
doi: 10.1186/s12957-022-02618-x.

Construction of an individualized clinical prognostic index based on ubiquitination-associated lncRNA in clear cell renal cell carcinoma patients

Kun Liu #  1 , Xuzhong Liu #  1 , Qing Sun  1 , Zhiwang Tang  1 , Gongcheng Wang  1 , Zongyuan Xu  2
Affiliations

Construction of an individualized clinical prognostic index based on ubiquitination-associated lncRNA in clear cell renal cell carcinoma patients

Kun Liu et al. World J Surg Oncol. .

Abstract

Background: ccRCC is considered as the main subtype of RCC, which accounted for sixth deadliest cancer worldwide. Recently, ubiquitination has been reported to be closely involved in the progression of tumore. The purpose of this study was to identify the ubiquitination-associated genes and co-expressed lncRNAs on the prognosis of clear cell renal cell carcinoma (ccRCC) patients.

Methods and patients: We downloaded 530 cases and the corresponding transcriptome profiling from The Cancer Genome Atlas (TCGA) database. We distinguished mRNA and lncRNA expression data from the transcriptome profiling and then extracted the expression of mRNAs that regulate protein ubiquitination. We obtained lncRNAs associated with protein ubiquitination regulation from the lncRNA data by gene co-expression analysis. Cox regression analysis of survival time, survival status, and lncRNA expression level was carried out, and a prognostic index (PI) was constructed.

Results: The PI was established based on 8 prognostic lncRNAs that regulate protein ubiquitination and distinguish the high-risk group patients from all patients. Multivariate analysis indicated that this PI was an individualized clinical prognostic factor for patients with ccRCC. Regarding clinical characteristics, a ubiquitination-associated clinical-prognostic index (UCPI), containing 8 ubiquitination-related lncRNAs and age, was established and tested with AUC of 0.80.

Conclusion: We established a UCPI containing 8 lncRNAs related to protein ubiquitination. This UCPI may become an appropriate model to predict the prognosis in ccRCC patients and guide clinicians to adjust the follow-up regimen.

Keywords: Bioinformatic analysis; Clear cell renal cell carcinoma; Clinical-prognostic index; Long noncoding RNA; Ubiquitination.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Gene set enrichment analysis of lncRNA signature by GO (A) and KEGG (B)
Fig. 2
Fig. 2
Survival analysis of 8 ubiquitination-related lncRNAs on the ccRCC patients, including AC131009.3 (A), AL365203.2 (B), AC102953.2 (C), LINC01963 (D), LY6E-DT (E), AC006159.2 (F), AP000695.1 (H), and AC092718.4 (G)
Fig. 3
Fig. 3
Analysis of risk signatures on the prediction of survival stautus. A risk score distribution, B ccRCC pateints’ survivial status, C gene expression in high-risk and low-risk groups, D Kaplan-Meier curves of risk signature, and E ROC curves in ccRCC patients
Fig. 4
Fig. 4
Prognositic efficacy of 8-lncRNA-based model on the prognosis of ccRCC. Prognostic value of clinicopathological characteristics and 8-lncRNA RiskScore by univariate (A) and multivariate (B) Cox regression analysis. Principal component analysis (PCA) based on total mRNA (C), ubiquitination-related mRNAs (D), ubiquitination-related lncRNAs (E), and 8 ubiquitination-related risk signatures (F). Analysis of ubiquitination-associated clinical-prognostic index (UCPI) on the prediction of survival stautus. G Kaplan-Meier curves of UCPI and H ROC curves in ccRCC patients
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