Original Research Article
Year: 2019 | Month: December | Volume: 6 | Issue: 12 | Pages: 1-16
The Integrative Analysis of Gene Expression Profile to Identify Gene Signature in Triple Negative Breast Cancer
Mansi Desai1, Prabhudas Patel2, Hemangini Vora3
1Research Associate, Immunohaematology Lab, 2Professor & Head Cancer Biology,
3Associate Professor of Cancer Biology & Head Immunohaematology
The Gujarat Cancer & Research Institute, Asarwa, Ahmedabad - 380008
Corresponding Author: Hemangini Vora
ABSTRACT
TNBC is defined pathologically as lacking expression of the estrogen and progesterone receptors (ER/PR) and amplification of the HER2/neu oncogenes. Due to its aggressive nature and overall poor prognosis, TNBC has gained a huge attention. Because of the absence of specific treatment guidelines for this group of patients, TNBC are managed with standard adjuvant chemotherapy. Hence, it is important to gain insight into the therapeutic targets for TNBC.
The present study used integrative analysis based approach to identify the candidate biomarkers associated with triple negative breast cancer. The microarray data of Affymetrix U133 Plus 2.0 Array and Affymetrix U133A Array platform from Gene expression Omnibus (GEO) and Array express was downloaded and analyzed in a platform/chip-specific manner using GeneSpring to identify gene/ meta-gene signatures.
The common pathways and gene ontology for the gene signatures/meta-gene signatures were predicted using PANTHER and protein-protein interactions were analyzed using STRING. The 12 genes (CHI3L1, COL9A3, EN1, IMPA2, KRT16, KRT81, LOC100129518, MMP1, MSLN, SOD2, TMEM158 and VGLL1) were up regulated, while 5 genes (CSAD, NEAT1, PIP, SCUBE2, SEMA3C) were down regulated in TNBC as compared to non-TNBC as well as reduction mammoplasty tissue. The integrative analysis done in the present study can be useful to find the gene signatures responsible for triple negative pathology of breast cancer.
Key words: Triple negative breast cancer, Meta-analysis, Gene expression analysis, Microarray, meta-gene signature in TNBC
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