Evidence map›Paper›PMID 31595577›Full record

ArticleJournal of cellular biochemistry2020

Microarray and RNA in situ hybridization assay for recurrence risk markers of breast carcinoma and ductal carcinoma in situ: Evidence supporting the use of diverse pathways panels.

Mark Francis Evans, Pamela Mary Vacek, Brian Lee Sprague, Gary Stephen Stein, Janet Lee Stein, Donald Lee Weaver

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

Article in Journal of cellular biochemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed, 1 pooled it
1.0field-weighted citation impact, top 29% 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

8 citing papers in PubMed, 1 synthesis or guideline pooled it, 14 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Review
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

6 authors at 1 institution in 1 country.

Mark Francis EvansDepartment of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont.ORCID 0000-0003-3708-890X
Pamela Mary VacekUniversity of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont.
Brian Lee SpragueUniversity of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont.
Gary Stephen SteinUniversity of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont.
Janet Lee SteinUniversity of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, Vermont.
Donald Lee WeaverDepartment of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont.
University of Vermont · US

Funding

Vermont Screening Process Documentation UnitU54CA163303 · NCI · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI SPRAGUE, BRIAN L · 2011 to 2017
$6.4M
Vermont Breast Cancer Molecular Characterization LaboratoryU01CA196383 · NCI · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI SPRAGUE, BRIAN L, STEIN, JANET L · 2015 to 2020
$5.4M
NCI NIH HHS U01 CA196383NCI NIH HHS U54 CA163303
6 · The paper itself

Abstract

Breast tumor stratification by recurrence-risk is critical for deciding patient treatment. Here an approach combining cancer pathways microarray data complemented by RNA in situ hybridization (ISH) was investigated as a means for recurrence marker discovery and visualization in pathology specimens. LncRNA and mRNA expressions in breast carcinomas with low (n = 8) vs intermediate/high (n = 10) recurrence-scores as estimated by 21-gene assay and pathology review were compared by microarray assay. Tissue microarrays were prepared from breast carcinomas (n = 20) and ductal carcinoma in situ (DCIS) specimens (n = 84 patients) with known outcomes. Thirteen RNA ISH assays were performed: lncRNAs (BBC3-1, FER3, RAD21-AS1, ZEB1-2) and mRNAs (GLO1, GLTSCR2, TGFB1, TLR2) (implicated by the microarray data); MKI67; a pooled panel of recurrence-associated proliferation markers (BIRC5, Cyclin B1, MKI67, MYBL2, STK15); a pooled panel of non-proliferation recurrence-associated markers (CEACAM5, HTF9C, NDRG1, TP53, SLC7A5); and lncRNAs H19 and HOTAIR. Seven lncRNAs and 10 mRNAs showed significantly (P < .05) altered upregulation or downregulation by microarray assay: carcinoma RNA ISH staining did not mirror these patterns. HOTAIR staining was associated with a higher breast cancer recurrence score (P = .0152); qualitatively, H19 was massively expressed in a metaplastic triple negative breast carcinoma. Among the DCIS cohort, significant associations with multiple outcome variables were noted for TGFB1 and the non-proliferation panel (P-value range: .0001 to .047); proliferation panel staining showed an association with increasing DCIS grade (P = .0269) but not with outcomes. The findings support recurrence-risk estimation by the use of multi-marker panels that are representative of diverse cellular pathways rather than over-reliance on proliferation targets. H19, HOTAIR, and TGFB1 RNA ISH show potential for selective diagnostics.

Indexed as

Gene Expression Regulation, NeoplasticAdultAgedAged, 80 and overBiomarkers, TumorBreast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, Intraductal, NoninfiltratingFemaleFollow-Up StudiesHumansIn Situ HybridizationMicroarray AnalysisMiddle AgedNeoplasm Recurrence, LocalPrognosisBiomarkers, Tumorbreast cancerDCISin situ hybridizationlncRNAmicroarray analysismRNArecurrence

Identifiers

PMID31595577
PMCPMC6923596
OpenAlexW2979906138

What OpenQuestion holds

Textmetadata
LicenceTDM
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.