Identification of prognostic genes in kidney renal clear cell carcinoma by RNA-seq data analysis

Gu, Yanqin; Lu, Lihua; Wu, Lei; Chen, Hao; Zhu, Wei; He, Yi

doi:10.3892/mmr.2017.6194

Cited by 44 publications

(38 citation statements)

References 36 publications

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“…CDCA8 is related to the distant metastasis risk of breast cancer [51,52]. With regard to renal cancer, CDCA8 has also certain prognostic value [53]. CDCA8 promotes the malignant progression of cutaneous melanoma [54].…”

Section: Discussionmentioning

confidence: 99%

Analysis of the Expression of Cell Division Cycle-Associated Genes and Its Prognostic Significance in Human Lung Carcinoma: A Review of the Literature Databases

Chen

Pang

et al. 2020

BioMed Research International

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Background. Lung cancer (LC) has become the top cause responsible for cancer-related deaths. Cell division cycle-associated (CDCA) genes exert an important role in the life process. Dysregulation in the process of cell division may lead to malignancy. Methods. Transcriptional data on CDCA gene family and patient survival data were examined for lung cancer (LC) patients from the GEPIA, Oncomine, cBioPortal, and Kaplan–Meier Plotter databases. Results. CDCA1/2/3/4/5/7/8 expression levels were higher in lung adenocarcinoma tissues, and the CDCA1/2/3/4/5/6/7/8 expression levels were increased in squamous cell LC tissues compared with those in noncarcinoma lung tissues. The expression levels of CDCA1/2/3/4/5/8 showed correlation with tumor classification. The Kaplan–Meier Plotter database was employed to carry out survival analysis, indicating that increased CDCA1/2/3/4/5/6/7/8 expression levels were obviously related to poor overall survival (OS) and progression-free survival (PFS) (P<0.05). Only LC patients with increased CDCA3/4/5/8 expression were significantly related to lower post-progression survival (PPS) (P<0.05). The following processes were affected by CDCA genes’ alteration: R-HAS-2500257: resolution of sister chromatid cohesion; GO:0051301: cell division; CORUM: 1118: chromosomal passenger complex (CPC, including CDCA8, INCENP, AURKB, and BIRC5); CORUM: 127: NDC80 kinetochore complex; M129: the PID PLK1 pathway; and GO: 0007080: mitotic metaphase plate congression, all of which were remarkably modulated since the alterations affected CDCA genes. Conclusions. Upregulated CDCA genes’ expression levels in LC tissues probably play a crucial part in LC oncogenesis. The upregulated CDCA genes’ expression levels are used as the potential prognostic markers to improve patient survival and the LC prognostic accuracy. CDCA genes probably exert their functions in tumorigenesis through the PLK1 pathway.

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Section: Discussionmentioning

confidence: 99%

Analysis of the Expression of Cell Division Cycle-Associated Genes and Its Prognostic Significance in Human Lung Carcinoma: A Review of the Literature Databases

Chen

Pang

et al. 2020

BioMed Research International

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“…It was reported that inactivation of CLDN11 could promote cell migration in nasopharyngeal carcinoma (Li et al, 2018). KIF4A were identified as prognostic gene or key gene involved in the metastasis of renal cell carcinoma in recent survey (Gu et al, 2017;Wei et al, 2019). Anticancer Patients with papillary renal cell carcinoma (pRCC) were divided into low-and high-risk subgroups based on the median value of the risk score calculated.…”

Section: Discussionmentioning

confidence: 99%

A Novel Prognostic Index Based on Alternative Splicing in Papillary Renal Cell Carcinoma

Liu

Sun

et al. 2020

Front. Genet.

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Background: Papillary renal cell carcinoma (pRCC) is a heterogeneous multifocal or isolated tumor with an invasive phenotype. Previous studies presented that alternative splicing, as a crucial posttranscriptional regulator in gene expression, is associated with tumorigenesis. However, the association between alternative splicing and pRCC has not been clarified Methods: The RNA sequencing data and clinical information were downloaded from The Cancer Genome Atlas database and mRNA splicing profiles from TCGASpliceSeq. The percent spliced in data of alternative splicing merged with survival information was firstly calculated by univariate Cox regression analysis to screen for survival-associated alternative splicing events, and survival-associated alternative splicing events were then analyzed by Gene Ontology categories using Kyoto Encyclopedia of Genes and Genomes. Meanwhile, the least absolute shrinkage and selection operator Cox analysis and multivariate Cox analysis were performed to calculate the prognostic index for each alternative splicing type. In addition, clinical factors were introduced to assess the performance of prognostic index. Results: A total of 4,084 candidate survival-associated alternative splicing events in 2,558 genes were screened out. Patients were divided into the low-risk group and the high-risk group based on the median prognostic index value. The Kaplan-Meier survival analysis (p < 0.05) and receiver operating characteristics curves (AUC>0.9) indicated that prognostic index was effective and stable for predicting the prognosis of pRCC patients. Furthermore, a regulatory network was constructed incorporating alternative splicing events and survival-associated splicing factors. Conclusion: Our study provides new insights into the mechanism of alternative splicing events in tumorigenesis and their clinical potential for pRCC.

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“…Human cell division cycle associated 8 (CDCA8) was another hub gene among the overlapping DEGs. As a chromosomal passenger complex component [44], CDCA8 upregulation is related to the carcinogenesis of a variety of tumors [45,46]. CDCA8 has been proven to be a tumor promoter that is overexpressed in various kinds of tumors and is essential for cancer cell survival and malignancy [47].…”

Section: Discussionmentioning

confidence: 99%

Identification and validation of aberrant regulation of miR-445-3p /TTK , miR-140-5p/TTK and miR-133b/CDCA8 in small-cell lung cancer via bioinformatics analysis

Tang¹,

Gao²,

Xin³

et al. 2020

Preprint

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Background: Small-cell lung cancer (SCLC) remains the leading form of malignant lung cancer, but little bioinformation on SCLC is available. This study explored the molecular targets of SCLC by evaluating differentially expressed genes (DEGs) and differentially expressed microRNAs (miRNAs) (DEMs).Methods: Five mRNA expression profiles and two miRNAs expression profiles from Gene Expression Omnibus (GEO) were downloaded. R software was utilized to analyze the DEGs and DEMs between SCLC and normal samples. The DEGs were analyzed via functional enrichment analyses and were used to construct protein-protein interaction (PPI) networks. DEM targets were then predicted and intersected with the DEGs. Furthermore, the hub genes of SCLC in the overlapping DEGs were analyzed in Oncomine. Finally, the expression of DEM-hub gene pairs were verified in tissues by RT-qPCR and Western blotting.Results: In total, 236 common DEGs and 104 common DEMs were identified. Functional enrichment analysis showed the DEGs were primarily enriched in ‘cell cycle’, ‘DNA replication’ and ‘oocyte meiosis’. Twenty hub genes and five modules were identified from the PPI network. Furthermore, 6732 targeted genes of the DEMs were predicted. After intersecting with DEGs, 54 genes and 153 miRNA-mRNA pairs were eventually identified aberrant regulation in SCLC. MiR-445-3p/TTK, miR-140-5p/TTK and miR-133b/CDCA8 were identified as DEM-hub gene pairs. Oncomine analysis confirmed the overexpression of TTK and CDCA8 in SCLC. Further validation demonstrated that TTK and CDCA8 levels in SCLC tissue samples were markedly increased relative to normal controls, while miR-445-3p, miR-140-5p, and miR-133b levels were lower in SCLC samples than in controls.Conclusions: Our results revealed key miRNA-mRNA pairs associated with SCLC, providing new insights into potential disease targets.

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Identification of prognostic genes in kidney renal clear cell carcinoma by RNA-seq data analysis

Cited by 44 publications

References 36 publications

Analysis of the Expression of Cell Division Cycle-Associated Genes and Its Prognostic Significance in Human Lung Carcinoma: A Review of the Literature Databases

Analysis of the Expression of Cell Division Cycle-Associated Genes and Its Prognostic Significance in Human Lung Carcinoma: A Review of the Literature Databases

A Novel Prognostic Index Based on Alternative Splicing in Papillary Renal Cell Carcinoma

Identification and validation of aberrant regulation of miR-445-3p /TTK , miR-140-5p/TTK and miR-133b/CDCA8 in small-cell lung cancer via bioinformatics analysis

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