title: Comprehensive profiling of biological processes reveals two major prognostic subtypes in breast cancer.
abstract: Heterogeneity is the major obstacle to breast cancer target therapy. Classification of breast cancer with significant biological process may reduce the influence of heterogeneity of intrinsic tumor. We used survival analysis to filter 95 gene sets and classify 638 breast cancer samples into two subtypes based on those gene sets associated with prognosis. Clinical outcome of two subtypes were evaluated with disease-free survival, distant metastasis-free survival, and overall survival levels in three databases and ER+, PR+ HER2+, and TNBC groups. We established a novel classification with 95 prognostic gene sets. In the training and validation cohorts, the subtype 1 was characterized by significant gene sets associated with regulation of metabolic process and enzyme activity and predicted obviously improved clinical outcome than subtype 2, which was enriched by tumor cell division, mitosis, and cell cycle-related gene sets (P < 0.05). When evaluated prognostic impact of subtypes in ER+, PR+ HER2+, and TNBC groups, we found that patients in subtype 1 showed better prognosis in ER+ and PR+ groups (P < 0.05) but had no difference from prognosis of subtype 2 in HER2+ and TNBC groups. These findings may have implications in understanding of breast cancer and filtering effective therapeutic strategies for targeted therapy.
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Chen
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Gao
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Fengliang
authors.initials: F
authors.lastname: Wang
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Ma
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Min
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Lv
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Ziyi
authors.initials: Z
authors.lastname: Fu
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Lu
authors.affiliation: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing, 210004, China. yinhongtg@163.com.
authors.forename: Hong
authors.initials: H
authors.lastname: Yin
mesh_terms: D001686:Biological Phenomena / Q000235:genetics*; D001943:Breast Neoplasms / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D030541:Databases, Genetic; D018572:Disease-Free Survival; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics / Q000378:metabolism; D011960:Receptors, Estrogen / Q000235:genetics / Q000378:metabolism; D011980:Receptors, Progesterone / Q000235:genetics / Q000378:metabolism; D064726:Triple Negative Breast Neoplasms / Q000235:genetics
chemical_list: D018719:Erb-b2 Receptor Tyrosine Kinases; D011960:Receptors, Estrogen; D011980:Receptors, Progesterone
keywords: Biological process; Breast cancer; Prognosis; Subtypes; Targeted therapy