Evidence map›Paper›PMID 25428913›Full record

ArticleOncotarget2015

A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors.

Farah B Rahmatpanah, Zhenyu Jia, Xin Chen, Jessica E Char, Bozhao Men, Anna-Clara Franke, Frank E Jones, Michael McClelland, Dan Mercola

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

Article in Oncotarget, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.1field-weighted citation impact, top 49% 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

5 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. Article
  5. 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

9 authors at 2 institutions in 1 country.

Farah B RahmatpanahDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Zhenyu JiaDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Xin ChenDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Jessica E CharDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Bozhao MenDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Anna-Clara FrankeDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Frank E JonesDepartment of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana, USA.
Michael McClellandDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
Dan MercolaDepartment of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.
University of California, Irvine · USTulane University · US

Funding

Univ.of Calif., Irvine Cancer Center Support GrantP30CA062203 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Christine Hui · 1994 to 2026
$57.9M
CARCINOGENESIST32CA009054 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI EDINGER, AIMEE L, FRUMAN, DAVID ALEXANDER · 1985 to 2025
$8.6M
Evaluation of Predictive Signatures of Prostate CancerU01CA114810 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI MERCOLA, DAN · 2005 to 2009
$8.2M
The Prostate Cancer Tumor Microenvironment Exhibits Differentially Expressed GeneU01CA152738 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI LEE, CHUNG, MERCOLA, DAN · 2010 to 2015
$3.6M
NCI NIH HHS 5 T32 CA9054-34NCI NIH HHS P30 CA062203NCI NIH HHS P30CA62203NCI NIH HHS T32 CA009054NCI NIH HHS U01 CA114810NCI NIH HHS U01 CA1148102NCI NIH HHS U01 CA152738
6 · The paper itself

Abstract

HER2-positive breast cancer accounts for 25% of all cases and has a poor prognosis. Although progress has been made in understanding signal transduction, little is known of how HER2 achieves gene regulation. We performed whole genome expression analysis on a HER2⁺ and HER2⁻ breast cancer cell lines and compared these results to expression in 812 primary tumors stratified by their HER2 expression level. Chip-on-chip with anti-RNA polymerase II was compared among breast cancer cell lines to identify genes that are potentially activated by HER2. The expression levels of these HER2-dependent POL II binding genes were determined for the 812 HER2+/- breast cancer tissues. Genes differentially expressed between HER2+/- cell lines were generally regulated in the same direction as in breast cancer tissues. We identified genes that had POLII binding in HER2⁺ cell lines, but without significant gene expression. Of 737 such genes "poised" for expression in cell lines, 113 genes were significantly differentially expressed in breast tumors in a HER2-dependent manner. Pathway analysis of these 113 genes revealed that a large group of genes were associated with stem cell and progenitor cell control as indicated by networks centered on NANOG, SOX2, OCT3/4. HER2 directs POL II binding to a large number of genes in breast cancer cells. A "poised" class of genes in HER2⁺ cell lines with POLII binding and low RNA expression but is differentially expressed in primary tumors, strongly suggests a role of the microenvironment and further suggests a role for stem cells proliferation in HER2-regulated breast cancer tissue.

Indexed as

Gene Expression ProfilingGene Expression Regulation, NeoplasticBlotting, WesternBreast NeoplasmsCell Line, TumorErb-b2 Receptor Tyrosine KinasesGene Regulatory NetworksHomeodomain ProteinsHumansMCF-7 CellsNanog Homeobox ProteinNeoplastic Stem CellsOctamer Transcription Factor-3RegulonReverse Transcriptase Polymerase Chain ReactionRNA Polymerase IIErb-b2 Receptor Tyrosine KinasesHomeodomain ProteinsNanog Homeobox ProteinNANOG protein, humanOctamer Transcription Factor-3POU5F1 protein, humanRNA Polymerase IISOX2 protein, humanSOXB1 Transcription Factors

Identifiers

PMID25428913
PMCPMC4359233
OpenAlexW1577685943

What OpenQuestion holds

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LicenceCC BY
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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.