Evidence map›Paper›PMID 29723810›Full record

ArticleTranslational oncology2018

Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers.

Anthony J Cesnik, Bing Yang, Andrew Truong, Tyler Etheridge, Michele Spiniello, Maisie I Steinbrink, Michael R Shortreed, Brian L Frey, David F Jarrard, Lloyd M Smith

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Translational oncology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Anthony J CesnikDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: cesnik@wisc.edu.
Bing YangDepartment of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: yangb@urology.wisc.edu.
Andrew TruongDepartment of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: atruong3@wisc.edu.
Tyler EtheridgeDepartment of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: tetheridge@wisc.edu.
Michele SpinielloDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: michele.spiniello@gmail.com.
Maisie I SteinbrinkDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: steinbrink@wisc.edu.
Michael R ShortreedDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: mshort@chem.wisc.edu.
Brian L FreyDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: bfrey@chem.wisc.edu.
David F JarrardDepartment of Urology, University of Wisconsin-Madison, Madison, WI, USA; Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: jarrard@urology.wisc.edu.
Lloyd M SmithDepartment of Chemistry, University of Wisconsin-Madison, Madison, WI, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA. Electronic address: smith@chem.wisc.edu.

Funding

Research Training for Computation and Informatics in Biology and MedicineT15LM007359 · NLM · UNIVERSITY OF WISCONSIN-MADISON · PI Mark W. Craven, Colin Noel Dewey · 2002 to 2026
$22.6M
Sequence-specific Hybridization Capture to Reveal the lncRNA Interactome in Prostate CancerR01CA193481 · NCI · UNIVERSITY OF WISCONSIN-MADISON · PI DAVID F. JARRARD, Lloyd M Smith · 2015 to 2026
$3.4M
NCI NIH HHS R01 CA193481NLM NIH HHS T15 LM007359
6 · The paper itself

Abstract

introductionThe molecular mechanisms underlying aggressive versus indolent disease are not fully understood. Recent research has implicated a class of molecules known as long noncoding RNAs (lncRNAs) in tumorigenesis and progression of cancer. Our objective was to discover lncRNAs that differentiate aggressive and indolent prostate cancers.

methodsWe analyzed paired tumor and normal tissues from six aggressive Gleason score (GS) 8-10 and six indolent GS 6 prostate cancers. Extracted RNA was split for poly(A)+ and ribosomal RNA depletion library preparations, followed byRNA sequencing (RNA-Seq) using an Illumina HiSeq 2000. We developed an RNA-Seq data analysis pipeline to discover and quantify these molecules. Candidate lncRNAs were validated using RT-qPCR on 87 tumor tissue samples: 28 (GS 6), 28 (GS 3+4), 6 (GS 4+3), and 25 (GS 8-10). Statistical correlations between lncRNAs and clinicopathologic variables were tested using ANOVA.

resultsThe 43 differentially expressed (DE) lncRNAs between aggressive and indolent prostate cancers included 12 annotated and 31 novel lncRNAs. The top six DE lncRNAs were selected based on large, consistent fold-changes in the RNA-Seq results. Three of these candidates passed RT-qPCR validation, including AC009014.3 (P < .001 in tumor tissue) and a newly discovered X-linked lncRNA named XPLAID (P = .049 in tumor tissue and P = .048 in normal tissue). XPLAID and AC009014.3 show promise as prognostic biomarkers.

conclusionsWe discovered several dozen lncRNAs that distinguish aggressive and indolent prostate cancers, of which four were validated using RT-qPCR. The investigation into their biology is ongoing.

Identifiers

PMID29723810
PMCPMC6154865

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