Integrated bioinformatics analysis reveals key candidate genes and pathways in breast cancer

Breast cancer (BC) is the leading malignancy in women worldwide, yet relatively little is known about the genes and signaling pathways involved in BC tumorigenesis and progression. The present study aimed to elucidate potential key candidate genes and pathways in BC. Five gene expression profile data sets (GSE22035, GSE3744, GSE5764, GSE21422 and GSE26910) were downloaded from the Gene Expression Omnibus (GEO) database, which included data from 113 tumorous and 38 adjacent non-tumorous tissue samples. Differentially expressed genes (DEGs) were identified using t-tests in the limma R package. These DEGs were subsequently investigated by pathway enrichment analysis and a protein-protein interaction (PPI) network was constructed. The most significant module from the PPI network was selected for pathway enrichment analysis. In total, 227 DEGs were identified, of which 82 were upregulated and 145 were downregulated. Pathway enrichment analysis results revealed that the upregulated DEGs were mainly enriched in ‘cell division’, the ‘proteinaceous extracellular matrix (ECM)’, ‘ECM structural constituents’ and ‘ECM-receptor interaction’, whereas downregulated genes were mainly enriched in ‘response to drugs’, ‘extracellular space’, ‘transcriptional activator activity’ and the ‘peroxisome proliferator-activated receptor signaling pathway’. The PPI network contained 174 nodes and 1,257 edges. DNA topoisomerase 2-a, baculoviral inhibitor of apoptosis repeat-containing protein 5, cyclin-dependent kinase 1, G2/mitotic-specific cyclin-B1 and kinetochore protein NDC80 homolog were identified as the top 5 hub genes. Furthermore, the genes in the most significant module were predominantly involved in ‘mitotic nuclear division’, ‘mid-body’, ‘protein binding’ and ‘cell cycle’. In conclusion, the DEGs, relative pathways and hub genes identified in the present study may aid in understanding of the molecular mechanisms underlying BC progression and provide potential molecular targets and biomarkers for BC.

[1]  Jessica K. Polka,et al.  Implications for Kinetochore-Microtubule Attachment from the Structure of an Engineered Ndc80 Complex , 2008, Cell.

[2]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[3]  Peter M Schlag,et al.  Identification of early molecular markers for breast cancer , 2011, Molecular Cancer.

[4]  Howard Y. Chang,et al.  Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Gene Ontology Consortium,et al.  The Gene Ontology (GO) project in 2006 , 2005, Nucleic Acids Res..

[6]  S. Cross,et al.  Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21 , 2016, Oncotarget.

[7]  F. Romero,et al.  Both p62/SQSTM1-HDAC6-dependent autophagy and the aggresome pathway mediate CDK1 degradation in human breast cancer , 2017, Scientific Reports.

[8]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[9]  Denis Evoy,et al.  CA 15-3: uses and limitation as a biomarker for breast cancer. , 2010, Clinica chimica acta; international journal of clinical chemistry.

[10]  Gary D. Bader,et al.  An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.

[11]  Stan Pounds,et al.  Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of P-values , 2003, Bioinform..

[12]  Matthias Bache,et al.  Elevated expression level of survivin protein in soft-tissue sarcomas is a strong independent predictor of survival. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.

[13]  Tony Hunter,et al.  Human cyclin A is adenovirus E1A-associated protein p60 and behaves differently from cyclin B , 1990, Nature.

[14]  C. Chelala,et al.  Gene expression profiling of breast cancer in Lebanese women , 2016, Scientific Reports.

[15]  A. Jemal,et al.  Cancer statistics, 2015 , 2015, CA: a cancer journal for clinicians.

[16]  C. Scopa,et al.  Expression of the cell cycle regulatory proteins p34cdc2, p21waf1, and p53 in node negative invasive ductal breast carcinoma , 2003, Molecular pathology : MP.

[17]  F. Pépin,et al.  Stromal gene expression predicts clinical outcome in breast cancer , 2008, Nature Medicine.

[18]  C. Scopa,et al.  Expression of the cell cycle regulatory proteins p34cdc2, p21waf1, and p53 in node negative invasive ductal breast carcinoma , 2003, Molecular Pathology.

[19]  Shridar Ganesan,et al.  X chromosomal abnormalities in basal-like human breast cancer. , 2006, Cancer cell.

[20]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[21]  Weihong Song,et al.  Microarray expression profiling of dysregulated long non-coding RNAs in triple-negative breast cancer , 2015, Cancer biology & therapy.

[22]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[23]  This work is licensed under a Creative Commons Attribution-NonCommercial- NoDerivs 3.0 Licence. To view a copy of the licence please see: http://creativecommons.0rg/licenses/by-nc-nd/3.0/ INEQIMTES IN THE DELIVERY OF SERVICES TO A FEMALE FARM CLIENTELE: SOME~~ , 2010 .

[24]  Jingqin Luo,et al.  Microarray data analysis in neoadjuvant biomarker studies in estrogen receptor-positive breast cancer , 2010, Breast Cancer Research.

[25]  Thomas R Cox,et al.  LOX-mediated collagen crosslinking is responsible for fibrosis-enhanced metastasis. , 2013, Cancer research.

[26]  E. Dı́az-Rodrı́guez,et al.  Hec1 overexpression hyperactivates the mitotic checkpoint and induces tumor formation in vivo , 2008, Proceedings of the National Academy of Sciences.

[27]  Janet M. Gray,et al.  State of the evidence 2017: an update on the connection between breast cancer and the environment , 2017, Environmental Health.

[28]  Pierre Dubus,et al.  Cdk1 is sufficient to drive the mammalian cell cycle , 2007, Nature.

[29]  Brad T. Sherman,et al.  DAVID-WS: a stateful web service to facilitate gene/protein list analysis , 2012, Bioinform..

[30]  Wenqing Li,et al.  CCNB1 is a prognostic biomarker for ER+ breast cancer. , 2014, Medical hypotheses.

[31]  D. Nie,et al.  PPAR gamma, bioactive lipids, and cancer progression. , 2012, Frontiers in bioscience.

[32]  K. Tanaka,et al.  Expression of survivin and its relationship to loss of apoptosis in breast carcinomas. , 2000, Clinical cancer research : an official journal of the American Association for Cancer Research.

[33]  M. Delorenzi,et al.  Identification of Prognostic Molecular Features in the Reactive Stroma of Human Breast and Prostate Cancer , 2011, PloS one.

[34]  K. Horie-Inoue,et al.  Identification of estrogen-responsive genes based on the DNA binding properties of estrogen receptors using high-throughput sequencing technology , 2014, Acta Pharmacologica Sinica.

[35]  E. Boitier,et al.  Advances in understanding the regulation of apoptosis and mitosis by peroxisome-proliferator activated receptors in pre-clinical models: relevance for human health and disease , 2003, Comparative hepatology.

[36]  J. Peters,et al.  The role of peroxisome proliferator-activated receptors in carcinogenesis and chemoprevention , 2012, Nature Reviews Cancer.

[37]  Rosette Lidereau,et al.  Gene Expression Profiling Reveals New Aspects of PIK3CA Mutation in ERalpha-Positive Breast Cancer: Major Implication of the Wnt Signaling Pathway , 2010, PloS one.

[38]  S. Vacher,et al.  Gene Expression Profiling Reveals New Aspects of PIK 3 CA Mutation in ERalpha-Positive Breast Cancer : Major Implication of the Wnt Signaling Pathway , 2010 .

[39]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[40]  E. Nice,et al.  Evidence for a role of tumor-derived laminin-511 in the metastatic progression of breast cancer. , 2007, The American journal of pathology.

[41]  B. Liang,et al.  Identification of key pathways and genes in colorectal cancer using bioinformatics analysis , 2016, Medical Oncology.

[42]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[43]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[44]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[45]  S. Elledge,et al.  The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit. , 1993, Genes & development.

[46]  L. Esserman,et al.  Aggregate Cost of Mammography Screening in the United States: Comparison of Current Practice and Advocated Guidelines , 2014, Annals of Internal Medicine.

[47]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[48]  L. Eissa,et al.  Validity of Osteoprotegerin and Receptor Activator of NF-κB Ligand for the Detection of Bone Metastasis in Breast Cancer , 2017, Oncology research.

[49]  R. Wirtz,et al.  Validity of the proliferation markers Ki67, TOP2A, and RacGAP1 in molecular subgroups of breast cancer , 2012, Breast Cancer Research and Treatment.

[50]  Kevin W Eliceiri,et al.  Postpartum mammary gland involution drives progression of ductal carcinoma in situ through collagen and COX-2 , 2011, Nature Medicine.

[51]  G. Turashvili,et al.  Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis , 2007, BMC Cancer.

[52]  Sevinç Şahin,et al.  Clinicopathological Significance of the Proliferation Markers Ki67, RacGAP1, and Topoisomerase 2 Alpha in Breast Cancer , 2016, International journal of surgical pathology.

[53]  Chunyu Liu,et al.  Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods , 2011, PloS one.

[54]  Aijun A. Wang,et al.  Molecular mechanisms of breast cancer metastasis by gene expression profile analysis , 2017, Molecular medicine reports.

[55]  T. Kinoshita,et al.  Long-term prognostic study of carcinoembryonic antigen (CEA) and carbohydrate antigen 15-3 (CA 15-3) in breast cancer , 2008, International Journal of Clinical Oncology.

[56]  E. Lundberg,et al.  Towards a knowledge-based Human Protein Atlas , 2010, Nature Biotechnology.

[57]  D. Altieri,et al.  A novel anti-apoptosis gene, survivin, expressed in cancer and lymphoma , 1997, Nature Medicine.

[58]  T. Miyazaki,et al.  Two Distinct Controls of Mitotic Cdk1/Cyclin B1 Activity Requisite for Cell Growth Prior to Cell Division , 2007, Cell cycle.

[59]  R. Shirkoohi,et al.  BIRC5 Genomic Copy Number Variation in Early-Onset Breast Cancer , 2016, Iranian biomedical journal.

[60]  C. Nicol,et al.  Loss of PPARγ expression in mammary secretory epithelial cells creates a pro-breast tumorigenic environment , 2013, International journal of cancer.

[61]  C. Rueden,et al.  Bmc Medicine Collagen Density Promotes Mammary Tumor Initiation and Progression , 2022 .

[62]  Reinhard Guthke,et al.  Batch correction of microarray data substantially improves the identification of genes differentially expressed in Rheumatoid Arthritis and Osteoarthritis , 2012, BMC Medical Genomics.

[63]  Chien-Feng Li,et al.  TOP2A overexpression as a poor prognostic factor in patients with nasopharyngeal carcinoma , 2013, Tumor Biology.

[64]  K. Possinger,et al.  PPARgamma ligands and ATRA inhibit the invasion of human breast cancer cells in vitro. , 2003, Breast cancer research and treatment.

[65]  Wanqing Chen,et al.  Breast cancer in China. , 2014, The Lancet. Oncology.

[66]  K. Possinger,et al.  PPARγ Ligands and ATRA Inhibit the Invasion of Human Breast Cancer Cells in vitro , 2003, Breast Cancer Research and Treatment.