title: Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer.
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.
authors: School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.|Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
authors: Yue
authors: Y
authors: Wang
authors: Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
authors: Kenneth M K
authors: KM
authors: Mark
authors: Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
authors: Matthew H
authors: MH
authors: Ung
authors: Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA.|Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
authors: Arminja
authors: A
authors: Kettenbach
authors: Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.|Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA.
authors: Todd
authors: T
authors: Miller
authors: School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
authors: Wei
authors: W
authors: Xu
authors: School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
authors: Wenqing
authors: W
authors: Cheng
authors: School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. tianxia@hust.edu.cn.
authors: Tian
authors: T
authors: Xia
authors: Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA. Chao.Cheng@dartmouth.edu.|Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA. Chao.Cheng@dartmouth.edu.|Department of Biomedical Data Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03766, USA. Chao.Cheng@dartmouth.edu.
authors: Chao
authors: C
authors: Cheng
mesh_terms: D019313:BRCA1 Protein / Q000235:genetics; D001943:Breast Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D049109:Cell Proliferation / Q000187:drug effects / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D042822:Genomic Instability; D006801:Humans; D053208:Kaplan-Meier Estimate; D020360:Neoadjuvant Therapy; D017063:Outcome Assessment, Health Care / Q000379:methods / Q000706:statistics & numerical data; D011379:Prognosis; D016016:Proportional Hazards Models; D034622:RNA Interference; D051135:Rad51 Recombinase / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D051135:Rad51 Recombinase
keywords: Cancer prognosis; Cell proliferation; Gene knockdown profiles; Genomic instability; Homologous recombination pathway; Neoadjuvant chemotherapy