Evidence map›Paper›PMID 28423633›Full record

ArticleOncotarget2017

Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer.

Xue Gong, Zurab Siprashvili, Okyaz Eminaga, Zhewei Shen, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Paul A Khavari, Jonathan R Pollack and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Xue GongDepartment of Urology, School of Medicine, Stanford University, Stanford, California, USA.
Zurab SiprashviliProgram in Epithelial Biology, School of Medicine, Stanford University, Stanford, California, USA.
Okyaz EminagaDepartment of Urology, School of Medicine, Stanford University, Stanford, California, USA.
Zhewei ShenDepartment of Pathology, School of Medicine, Stanford University, Stanford, California, USA.
Yusuke SatoDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Haruki KumeDepartment of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Yukio HommaDepartment of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Seishi OgawaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Paul A KhavariProgram in Epithelial Biology, School of Medicine, Stanford University, Stanford, California, USA.
Jonathan R PollackDepartment of Pathology, School of Medicine, Stanford University, Stanford, California, USA.
James D BrooksDepartment of Urology, School of Medicine, Stanford University, Stanford, California, USA.

Funding

New Tools for Prostate Cancer Detection and PrognosticationU01CA152737 · NCI · STANFORD UNIVERSITY · PI BROOKS, JAMES D., GAMBHIR, SANJIV S · 2010 to 2015
$2.8M
NCI NIH HHS U01 CA152737
6 · The paper itself

Abstract

Clear cell renal cell carcinomas (ccRCC) show a broad range of clinical behavior, and prognostic biomarkers are needed to stratify patients for appropriate management. We sought to determine whether long intergenic non-coding RNAs (lincRNAs) might predict patient survival. Candidate prognostic lincRNAs were identified by mining The Cancer Genome Atlas (TCGA) transcriptome (RNA-seq) data on 466 ccRCC cases (randomized into discovery and validation sets) annotated for ~21,000 lncRNAs. A previously uncharacterized lincRNA, SLINKY (Survival-predictive LINcRNA in KidneY cancer), was the top-ranked prognostic lincRNA, and validated in an independent University of Tokyo cohort (P=0.004). In multivariable analysis, SLINKY expression predicted overall survival independent of tumor stage and grade [TCGA HR=3.5 (CI, 2.2-5.7), P < 0.001; Tokyo HR=8.4 (CI, 1.8-40.2), P = 0.007], and by decision tree, ROC and decision curve analysis, added independent prognostic value. In ccRCC cell lines, SLINKY knockdown reduced cancer cell proliferation (with cell-cycle G1 arrest) and induced transcriptome changes enriched for cell proliferation and survival processes. Notably, the genes affected by SLINKY knockdown in cell lines were themselves prognostic and correlated with SLINKY expression in the ccRCC patient samples. From a screen for binding partners, we identified direct binding of SLINKY to Heterogeneous Nuclear Ribonucleoprotein K (HNRNPK), whose knockdown recapitulated SLINKY knockdown phenotypes. Thus, SLINKY is a robust prognostic biomarker in ccRCC, where it functions possibly together with HNRNPK in cancer cell proliferation.

Indexed as

AdultAgedArea Under CurveBiomarkers, TumorCarcinoma, Renal CellCell ProliferationDisease-Free SurvivalFemaleFlow CytometryGene Expression Regulation, NeoplasticHeterogeneous-Nuclear Ribonucleoprotein KHumansImmunoprecipitationKaplan-Meier EstimateKidney NeoplasmsMaleBiomarkers, TumorHeterogeneous-Nuclear Ribonucleoprotein KHNRNPK protein, humanlong non-coding RNA SLINKY, humanRNA, Long Noncodingbiomarkerkidney cancerlincRNAprognosticationrenal cell carcinoma

Identifiers

PMID28423633
PMCPMC5386637

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.