Prediction of clinical outcome and survival in soft-tissue sarcoma using a ten-lncRNA signature

Kidney renal papillary cell carcinoma (KIRP) accounts for 10%–15% of renal cell carcinoma (RCC), patients with KIRP tend to have a poor prognosis, and there was a lack of effective prognostic indicators for this type of cancer. Currently, owing to the availability of The Cancer Genome Atlas (TCGA), long non-coding RNAs (LncRNAs) have been discovered to indicate a prognostic value in some tumors. In that regard, we analyzed lncRNA-sequencing data of KIRP in TCGA, and among 780 differentially-expressed lncRNAs, we selected 37 lncRNAs which were able to assist the prognosis. In addition, by using the multivariate cox regression analysis, the prognosis index (PI) that consisted of 7 lncRNAs (including AFAP1-AS1, GAS6-AS1, RP11-1C8.7, RP11-21L19.1, RP11-503C24.1, RP11-536I6.2, and RP11-63A11.1) could predict the progression and outcomes of KIRP with accuracy. More importantly, the PI was considered an independent indicator for prognostication of KIRP. Moreover, having categorized patients with KIRP into cohorts of high risk and low risk, according to the PI, we found that the key genes and pathways varied in these two groups. Overall, these LncRNAs, especially the PI, may be conceived as biomarkers and helpful for determining the different pathological stages for KIRP patients. However, their biological functions need to be further confirmed.

show abstract

“…The calculation formula is as follows: PI = βDEL1 × exprDEL1 + βDEL2 × exprDEL2+ ··· + βDELn × exprDELn. [ 53 – 55 ].…”

Section: Methodsmentioning

confidence: 99%

Survival prediction of kidney renal papillary cell carcinoma by comprehensive LncRNA characterization

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Multiple stepwise Cox regression analysis was performed for potentially relevant genes in the preliminary screening, and the impact of these molecules on the survival time and the survival outcome was also analyzed. The screened molecules were used to construct the prognostic index (PI) model: (β 1 Exp 1 +β 2 Exp 2 +…+β x Exp x ) [16][17][18][19][20][21]. The larger the PI was, the greater the patient's risk and the worse the prognosis.…”

Section: Prognostic Factors Of Left-and Right-sided Colon Cancers Andmentioning

confidence: 99%

Distinguishable Prognostic Signatures of Left- and Right-Sided Colon Cancer: a Study Based on Sequencing Data

Liang

Zeng

Qin

et al. 2018

Cell Physiol Biochem

Self Cite

View full text Add to dashboard Cite

Key WordsLeft-and right-sided • Colon cancer • Prognosis • TCGA Abstract Background/Aims: Left-and right-sided colon cancers are considered to be two different diseases and have altered outcomes. However, specific molecules to predict the prognosis of left-and right-sided colon cancers are currently lacking. Methods: Expression profiling of colon cancer were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) of left-and right-sided colon cancers were compared by DESeq analysis. The prognostic values of DEGs were assessed by univariate and multivariate Cox regression. Prognostic index models of two side colon cancers were conducted with prognostic values genes, respectively. Interaction of DEGs was then analyzed by the protein-protein interaction (PPI). Different biology function of two sides of colon cancer was assessed by Gene Set Enrichment Analysis (GSEA). Results: A total of 167 DEGs were identified between left-and right-sided colon cancers based on TCGA data. Using univariate COX regression analysis, five genes (PHACTR3, CKMT2, CYP2W1, ERFE, HOXC4) were related to overall survival in left-sided, and eight distinguishable genes (EREG, ERFE, HOXC6, SLC22A31, TFF1, GFI1, ZG16, RASL10B) in right-sided. Further, left-sided prognostic model was established with PHACTR3 and CKMT2 (HR=2.040; 95%CI=1.004-4.145; P=0.049). Distinguishable prognostic signature for right-sided colon cancer was established based on EREG, ERFE, GFI1, and RASL10B (HR=3.530; 95%CI: 1.934-6.444; P<0.001) in multivariate analysis. PPI analysis of 167 DEGs showed that CCL5, GNG4, GNLY, GZMH, DRD2, and FASLG genes were at the core of interaction network. In GSEA function analysis, four pathways, including antigen processing and presentation, natural killer cell mediated cytotoxicity, intestinal immune network for Iga production, and type I diabetes mellitus, were significantly enriched in the DEGs of the right-sided colon cancer. Conclusions: This study constructs a panel of potential prognostic model of left-and right-sided colon cancers, respectively. We also provide molecular biological alterations between left-and rightsided colon cancers.

show abstract

“…3 Meanwhile, the functions of other lncRNAs, such as lncRNA BLACAT1 4 and linc-ITGB1, 5 have also been reported in NSCLC. Moreover, previous studies have demonstrated that LINC00680 was an independent prognostic indicator for poor prognosis of the patients with soft tissue sarcoma, 6 suggesting that LINC00680 exerts a role in tumorigenesis. Nevertheless, the function of LINC00680 in NSCLC was scarcely researched.…”

Section: Introductionmentioning

confidence: 98%

<p>LINC00680 Promotes the Progression of Non-Small Cell Lung Cancer and Functions as a Sponge of miR-410-3p to Enhance HMGB1 Expression</p>

Wang

Li²,

Zheng³

et al. 2020

OTT

View full text Add to dashboard Cite

Purpose: LINC00680 was reported to be involved in various cancers through multiple mechanisms. Therefore, we intended to investigate its role in the progression of non-small cell lung cancer (NSCLC). Materials and Methods: Firstly, quantitative real-time polymerase chain reaction (qRT-PCR) was used to test LINC00680 in NSCLC tissue and cell lines. Subsequently, A549 and H1299 cells were transfected with LINC00680 overexpressing plasmids and their proliferation and colony formation and apoptosis was tested by Transwell assay and flow cytometry. In addition, xenograft tumor experiments in nude mice also affirmed. Meanwhile, we predicted that miR-410-3p, LINC00680 and high-mobility group protein box 1(HMGB1) relationship by Starbase, dual-luciferase reporter and RIP assay. Finally, the carcinogenic effects of LINC00680 were reversed by ethyl pyruvate (EP), a specific inhibitor of HMGB1. Results: LINC00680 was upregulated in NSCLC and was closely related to the malignancy and poor prognosis of NSCLC patients. LINC00680 promoted proliferation and colony formation and inhibited apoptosis of A549 and H1299 cells. In addition, overexpressing LINC00680 accelerated the growth of NSCLC cells in xenograft tumor experiments in nude mice also affirmed. Meanwhile, high-mobility group protein box 1(HMGB1) was astoundingly amplified in NSCLC and was negatively regulated by miR-410-3p. Further, HMGB1 acted as a downstream target of miR-410-3p, upregulating miR-410-3p to attenuate HMGB1, while LINC00680 strengthened the expression of HMGB1 in A549 and H1299 cells. Discussion: Thus, these results indicated that LINC00680 was cancerogenic in NSCLC by upregulating HMGB1 via sponging miR-410-3p.

show abstract

Prediction of clinical outcome and survival in soft-tissue sarcoma using a ten-lncRNA signature

Cited by 22 publications

References 36 publications

Survival prediction of kidney renal papillary cell carcinoma by comprehensive LncRNA characterization

Survival prediction of kidney renal papillary cell carcinoma by comprehensive LncRNA characterization

Distinguishable Prognostic Signatures of Left- and Right-Sided Colon Cancer: a Study Based on Sequencing Data

<p>LINC00680 Promotes the Progression of Non-Small Cell Lung Cancer and Functions as a Sponge of miR-410-3p to Enhance HMGB1 Expression</p>

Contact Info

Product

Resources

About