title: Integrative exploration of genomic profiles for triple negative breast cancer identifies potential drug targets.
abstract: BACKGROUND
  Triple negative breast cancer (TNBC) is high-risk due to its rapid drug resistance and recurrence, metastasis, and lack of targeted therapy. So far, no molecularly targeted therapeutic agents have been clinically approved for TNBC. It is imperative that we discover new targets for TNBC therapy.
  
  
  OBJECTIVE
  A large volume of cancer genomics data are emerging and advancing breast cancer research. We may integrate different types of TNBC genomic data to discover molecular targets for TNBC therapy.
  
  
  METHODS
  We used publicly available TNBC tumor tissue genomic data in the Cancer Genome Atlas database in this study.
  
  
  METHODS
  We integratively explored genomic profiles (gene expression, copy number, methylation, microRNA [miRNA], and gene mutation) in TNBC and identified hyperactivated genes that have higher expression, more copy numbers, lower methylation level, or are targets of miRNAs with lower expression in TNBC than in normal samples. We ranked the hyperactivated genes into different levels based on all the genomic evidence and performed functional analyses of the sets of genes identified. More importantly, we proposed potential molecular targets for TNBC therapy based on the hyperactivated genes.
  
  
  RESULTS
  Some of the genes we identified such as FGFR2, MAPK13, TP53, SRC family, MUC family, and BCL2 family have been suggested to be potential targets for TNBC treatment. Others such as CSF1R, EPHB3, TRIB1, and LAD1 could be promising new targets for TNBC treatment. By utilizing this integrative analysis of genomic profiles for TNBC, we hypothesized that some of the targeted treatment strategies for TNBC currently in development are more likely to be promising, such as poly (ADP-ribose) polymerase inhibitors, while the others are more likely to be discouraging, such as angiogenesis inhibitors.
  
  
  CONCLUSIONS
  The findings in this study need to be experimentally validated in the future.
  
  
  CONCLUSIONS
  This is a systematic study that combined 5 different types of genomic data to molecularly characterize TNBC and identify potential targets for TNBC therapy. The integrative analysis of genomic profiles for TNBC could assist in identifying potential new therapeutic targets and predicting the effectiveness of a targeted treatment strategy for TNBC therapy.
authors.affiliation: School of Basic Medicine and Clinic Pharmacy, China Pharmaceutical University, Nanjing, China Department of Genetics, Cell Biology and Anatomy Bioinformatics and Systems Biology Core Department of Biochemistry and Molecular Biology Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA.
authors.forename: Xiaosheng
authors.initials: X
authors.lastname: Wang
authors.forename: Chittibabu
authors.initials: C
authors.lastname: Guda
mesh_terms: D056915:DNA Copy Number Variations / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D058990:Molecular Targeted Therapy; D015533:Transcriptional Activation / Q000235:genetics; D064726:Triple Negative Breast Neoplasms / Q000235:genetics* / Q000628:therapy; D019061:src-Family Kinases / Q000235:genetics
chemical_list: D035683:MicroRNAs; D019061:src-Family Kinases