Evidence map›Paper›PMID 28061773›Full record

ArticleBMC cancer2017

Differential long-term stability of microRNAs and RNU6B snRNA in 12-20 year old archived formalin-fixed paraffin-embedded specimens.

Sarah B Peskoe, John R Barber, Qizhi Zheng, Alan K Meeker, Angelo M De Marzo, Elizabeth A Platz, Shawn E Lupold

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC cancer, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed, 1 pooled it
2.1field-weighted citation impact, top 13% of its field
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

18 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. Article
  4. Canine urothelial carcinoma: a pilot study of microRNA detection in formalin-fixed, paraffin-embedded tissue samples and in normal urine.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2024
    Article
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  8. Reference Genes for qPCR-Based miRNA Expression Profiling in 14 Human Tissues.Medical principles and practice : international journal of the Kuwait University, Health Science Centre · 2022
    Review
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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

7 authors at 3 institutions in 1 country.

Sarah B PeskoeDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
John R BarberDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Qizhi ZhengDepartment of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Alan K MeekerDepartment of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Angelo M De MarzoDepartment of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Elizabeth A PlatzDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Shawn E LupoldThe James Buchanan Brady Urologic Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA. slupold@jhmi.edu.
Johns Hopkins University · USJohns Hopkins Medicine · USSidney Kimmel Comprehensive Cancer Center · US

Funding

TRANSGENIC MODELS FOR PROSTATE CANCER AND AUTOIMMUNITYP50CA058236 · NCI · JOHNS HOPKINS UNIVERSITY · PI ISAACS, JOHN TOD · 1992 to 2020
$43.9M
MicroRNAs in Advanced Prostate Cancer: A miR-21 modelR01CA143299 · NCI · JOHNS HOPKINS UNIVERSITY · PI LUPOLD, SHAWN · 2010 to 2014
$1.6M
NCI NIH HHS P50 CA058236NCI NIH HHS R01 CA143299
6 · The paper itself

Abstract

backgroundThe quantitative analysis of microRNA (miRNA) gene expression in archived formalin-fixed, paraffin embedded (FFPE) tissues has been instrumental to identifying their potential roles in cancer biology, diagnosis, and prognosis. However, it remains unclear whether miRNAs remain stable in FFPE tissues stored for long periods of time.

methodsHere we report Taqman real-time RT-PCR quantification of miR-21, miR-141, miR-221, and RNU6B small nuclear RNA (snRNA) levels from 92 radical prostatectomy specimens stored for 12-20 years in FFPE blocks. The relative stability of each transcript over time was assessed using general linear models. The correlation between transcript quantities, sample age, and RNA integrity number (RIN) were determined utilizing Spearman rank correlation.

resultsAll transcript levels linearly decreased with sample age, demonstrating a clear loss of miRNA stability and RNU6B snRNA stability over time. The most rapid rates of degradation were observed for RNU6B and miR-21, while miR-141 and miR-221 were more stable. RNA quality was not correlated with sample age or with miR-21, miR-221, or RNU6B snRNA levels. Conversely, miR-141 levels increased with RNA quality.

conclusionsMiRNA and snRNA levels gradually decreased over an eight year period in FFPE tissue blocks. Sample age was the most consistent feature associated with miRNA stability. The reference snRNA, RUN6B, was more rapidly degraded when compared to miR-141 and miR-221 miRNAs. Various miRNAs demonstrated differential rates of degradation. Quantitative miRNA studies from long-term archived FFPE tissues may therefore benefit from epidemiologic study design or statistical analysis methods that take into account differential storage-dependent transcript degradation.

Indexed as

FormaldehydeGene Expression Regulation, NeoplasticHumansMaleMicroRNAsParaffin EmbeddingProstatic NeoplasmsReal-Time Polymerase Chain ReactionRNA, Small NuclearTime FactorsTissue FixationFormaldehydeMicroRNAsRNA, Small NuclearFFPEmiRNAProstate cancerRNA stabilityRNU6B

Identifiers

PMID28061773
PMCPMC5219687
OpenAlexW2568041534

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.