Integrated analysis of long noncoding <scp>RNA</scp> associated‐competing endogenous <scp>RNA</scp> as prognostic biomarkers in clear cell renal carcinoma

Yin, Hang; Wang, Xiaoyuan; Zhang, Xue; Wang, Yan; Zeng, Yongquan; Xiong, Yudi; Li, Tianqi; Lin, Rongjie; Zhou, Qian; Ling, Huan; Zhou, Fuxiang; Zhou, Youwen

doi:10.1111/cas.13778

Cited by 35 publications

(31 citation statements)

References 39 publications

(72 reference statements)

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“…The SCCT cases data of clinical and RNA expression were collected from TCGA database. The exclusion criteria were including: (i) histological diagnosis was not SCCT; (ii) no complete data (including gender, age, survival status, stage, and survival time) for analysis [28]. 118 SCCT patients were enrolled in the study.…”

Section: Patients and Samplesmentioning

confidence: 99%

Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue

et al. 2019

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Background: Numerous studies have highlighted that long non-coding RNAs (lncRNAs) can bind to microRNA (miRNA) sites as competing endogenous RNAs (ceRNAs), thereby affecting and regulating the expression of mRNAs and target genes. These lncRNA-associated ceRNAs have been theorized to play a significant role in cancer initiation and progression. However, the roles and functions of the lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of the tongue (SCCT) are still unclear. Methods: The miRNA, mRNA and lncRNA expression profiles from 138 patients with SCCT were downloaded from The Cancer Genome Atlas database. We identified the differential expression of miRNAs, mRNAs, and lncRNAs using the limma package of R software. We used the clusterProfiler package for GO and KEGG pathway annotations. The survival package was used to estimate survival analysis according to the Kaplan-Meier curve. Finally, the GDCRNATools package was used to construct the lncRNA-miRNA-mRNA ceRNA network.

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Section: Patients and Samplesmentioning

confidence: 99%

Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue

et al. 2019

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“…It has been known that lncRNAs can act as ceRNAs to bind with target miRNAs. 7,8 Therefore, we speculated that LINC00473 might regulate radiosensitivity of ESCC cells via this mechanism. By searching LncBase (http://carolina.imis.athena-innovation.…”

Section: Mir-374a-5p Was Targeted By Linc00473 and Downregulated Inmentioning

confidence: 99%

LINC00473/miR‐374a‐5p regulates esophageal squamous cell carcinoma via targeting SPIN1 to weaken the effect of radiotherapy

Chen¹,

Zhang²,

Wang³

et al. 2019

J of Cellular Biochemistry

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Esophageal squamous cell carcinoma (ESCC) is the most prevalent type in esophageal cancers. Despite accumulating achievements in treatments of ESCC, patients still suffer from recurrence because of the treatment failures, one of the reasons for which is radioresistance. Therefore, it is a necessity to explore the molecular mechanism underlying ESCC radioresistance. Long intergenic noncoding RNA 473 (LINC00473) has been reported to be aberrantly expressed in several human malignancies. However, its biological function in radiosensitivity of ESCC remains to be fully understood. This study explored the role of LINC00473 in radiosensitivity of ESCC cells and whether LINC00473 acted as a competing endogenous RNA to realize its modulation on radioresistance. We found that LINC00473 was markedly upregulated in ESCC tissues and cell lines, and its expression was remarkably related to cellular response to irradiation. In addition, knockdown of LINC00473 could sensitize ESCC cells to radiation in vitro. As for the underlying mechanism, we uncovered that there was a mutual inhibition between LINC00473 and miR‐374a‐5p. Spindlin1 (SPIN1) was verified as a downstream target of miR‐374a‐5p, and LINC00473 upregulated SPIN1 expression through negatively modulating miR‐374a‐5p expression. Furthermore, we revealed that SPIN1 could aggravate the radioresistance of ESCC cells. Finally, overexpression of SPIN1 reversed the LINC00473 silencing‐enhanced radiosensitivity in ESCC cells. To sum up, we demonstrated that LINC00473 facilitated radioresistance by regulating the miR‐374a‐5p/SPIN1 axis in ESCC.

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“…Numerical evidence pronounce that lncRNAs can associate with miRNA to weaken the effects of miRNA on in mediating mRNA expression 20 . Some recent studies have suggested that aberrant lncRNA expression is associated with ccRCC, and many potential biomarkers have been uncovered in ccRCC [21][22][23] . However, these results rely on a temporary TCGA database that lacks external www.nature.com/scientificreports/ validation sets, hence, it poses difficulty in assessing the accuracy of the model.…”

Section: Discussionmentioning

confidence: 99%

Identification of 12 immune-related lncRNAs and molecular subtypes for the clear cell renal cell carcinoma based on RNA sequencing data

Zhong

Chen

Zhong

et al. 2020

Sci Rep

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Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cell carcinoma (RCC). Despite the existing extensive research, the molecular and pathogenic mechanisms of ccRCC are elusive. We aimed to identify the immune-related lncRNA signature and molecular subtypes associated with ccRCC. By integrating 4 microarray datasets from Gene Expression Omnibus database, we identified 49 immune-related genes. The corresponding immune-related lncRNAs were further identified in the TCGA dataset. 12-lncRNAs prognostic and independent signature was identified through survival analysis and survival difference between risk groups was further identified based on the risk score. Besides, we identified 3 molecular subtypes and survival analysis result showed that cluster 2 has a better survival outcome. Further, ssGSEA enrichment analysis for the immune-associated gene sets revealed that cluster 1 corresponded to a high immune infiltration level. While cluster 2 and cluster 3 corresponded to low and medium immune infiltration level, respectively. In addition, we validated the 12-lncRNA prognostic signature and molecular subtypes in an external validation dataset from the ICGC database. In summary, we identified a 12-lncRNA prognostic signature which may provide new insights into the molecular mechanisms of ccRCC and the molecular subtypes provided a theoretical basis for personalized treatment by clinicians. Renal cell carcinoma (RCC) accounts for over 90% of all kidney cancer cases among human adults 1. Clear cell renal cell carcinoma (ccRCC) is the most common RCC histological subtype which responsible for 70-80% of RCC cases 2. Recent studies estimate that 102,000 patients succumb to ccRCC and 202,000 new cases are diagnosed annually throughout the globe 3. Besides, ccRCC has no clear symptoms in its early stages therefore can only be diagnosed in advanced stages 4. Despite interventions through chemotherapy and radiotherapy, ccRCC is prone to distant metastasis. These metastases occur in lung, bone, liver, distant lymph nodes, and renal vein 5. A few effective biomarkers, particularly in both early and advanced stages of ccRCC, have been identified. The recent version of the human genome annotation transcribes approximately 16,000 long non-coding RNAs (lncRNAs) responsible for 26.7% of the total genes (https ://www.genco degen es.org/human /) 6. lncRNAs are non-coding RNAs composed of about 200 nucleotides in length. They include the antisense lncRNAs, intronic transcripts, large intergenic noncoding RNAs (lincRNAs), promoter-associated lncRNAs, and UTR associated lncRNAs 7. Previous studies have revealed that lncRNA plays an important role in regulating gene expression, epigenetics, cell differentiation, and ontogeny 8,9. Additionally, studies have shown that massive aberrantly expressed

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Integrated analysis of long noncoding RNA associated‐competing endogenous RNA as prognostic biomarkers in clear cell renal carcinoma

Cited by 35 publications

References 39 publications

Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue

Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue

LINC00473/miR‐374a‐5p regulates esophageal squamous cell carcinoma via targeting SPIN1 to weaken the effect of radiotherapy

Identification of 12 immune-related lncRNAs and molecular subtypes for the clear cell renal cell carcinoma based on RNA sequencing data

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