RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer

Scientific Reports
Jesús Espinal-EnríquezEnrique Hernández-Lemus

Abstract

Breast cancer is a complex heterogeneous disease. Common hallmark features of cancer can be found. Their origin may be traced back to their intricate relationships governing regulatory programs during the development of this disease. To unveil distinctive features of the transcriptional regulation program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy breast samples, at gene expression and network level, was implemented. Inter-chromosomal relationships between genes resulted strikingly scarce in a cancer network, in comparison to its healthy counterpart. We suggest that inter-chromosomal regulation loss may be a novel feature in breast cancer. Additional evidence was obtained by independent validation in microarray and Hi-C data as well as supplementary computational analyses. Functional analysis showed upregulation in processes related to cell cycle and division; while migration, adhesion and cell-to-cell communication, were downregulated. Both the BRCA1 DNA repairing signalling and the Estrogen-mediated G1/S phase entry pathways were found upregulated. In addition, a synergistic underexpression of the γ-protocadherin complex, located at Chr5q31 is also shown. This region has previously ...Continue Reading

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Citations

Dec 6, 2017·Frontiers in Physiology·Sergio Antonio Alcalá-CoronaEnrique Hernández-Lemus
Nov 19, 2017·Molecular Cancer·Ruobing JiaXianqun Fan
Nov 2, 2019·Genes·Enrique Hernández-LemusSoledad Ochoa
Jul 4, 2020·Human Molecular Genetics·Adi Danieli, Argyris Papantonis
Oct 27, 2018·Frontiers in Physiology·Sergio Antonio Alcalá-CoronaEnrique Hernández-Lemus
Dec 19, 2019·Frontiers in Genetics·Diana Tapia-CarrilloEnrique Hernandez-Lemus
Feb 15, 2019·Frontiers in Immunology·Tadeo Enrique Velazquez-CaldelasEnrique Hernandez-Lemus
Aug 28, 2020·Frontiers in Oncology·Diana García-CortésJesús Espinal-Enríquez
Mar 3, 2020·Frontiers in Oncology·Erandi A Serrano-CarbajalEnrique Hernández-Lemus
Nov 27, 2020·Frontiers in Genetics·Jose María Zamora-FuentesJesús Espinal-Enríquez
Feb 2, 2021·Frontiers in Oncology·Enrique Hernández-Lemus, Mireya Martínez-García
Mar 30, 2021·Frontiers in Genetics·Sergio Daniel Andonegui-ElgueraEnrique Hernández-Lemus
Apr 6, 2021·Frontiers in Genetics·Soledad OchoaEnrique Hernández-Lemus
May 8, 2021·Frontiers in Genetics·Diana García-CortésJesús Espinal-Enríquez
Dec 7, 2021·Frontiers in Oncology·Alfredo González-EspinozaJesús Espinal-Enríquez

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Datasets Mentioned

BETA
GSE29431
GSE10810
37
GSE50567

Methods Mentioned

BETA
RNA-Seq
Hi-C
PCA
RNASeq

Software Mentioned

Ingenuity Pathway Analysis
Ingenuity Pathway Analysis ( IPA )
IPA
GeneSet Enrichment Analysis ( GSEA
R
Ensembl
ARSyN R
NOISeq
GeneStart
QIAGEN

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