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Genome Med. 2016 Oct 27;8(1):114.

Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer.

Author information

1
School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
2
Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
3
Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA.
4
Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
5
School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. tianxia@hust.edu.cn.
6
Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA. Chao.Cheng@dartmouth.edu.
7
Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA. Chao.Cheng@dartmouth.edu.
8
Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA. Chao.Cheng@dartmouth.edu.

Abstract

Homologous recombination (HR) is the primary pathway for repairing double-strand DNA breaks implicating in the development of cancer. RNAi-based knockdowns of BRCA1 and RAD51 in this pathway have been performed to investigate the resulting transcriptomic profiles. Here we propose a computational framework to utilize these profiles to calculate a score, named RNA-Interference derived Proliferation Score (RIPS), which reflects cell proliferation ability in individual breast tumors. RIPS is predictive of breast cancer classes, prognosis, genome instability, and neoadjuvant chemosensitivity. This framework directly translates the readout of knockdown experiments into potential clinical applications and generates a robust biomarker in breast cancer.

KEYWORDS:

Cancer prognosis; Cell proliferation; Gene knockdown profiles; Genomic instability; Homologous recombination pathway; Neoadjuvant chemotherapy

PMID:
27788678
PMCID:
PMC5084341
DOI:
10.1186/s13073-016-0363-3
[Indexed for MEDLINE]
Free PMC Article

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