Journal Article
. 2019 Oct;57(11).
doi: 10.1007/s11517-019-02038-2.

GSIAR: gene-subcategory interaction-based improved deep representation learning for breast cancer subcategorical analysis using gene expression, applicable for precision medicine

Chiranjib Sur 1 
  • PMID: 31591679
  •     46 References


Tumor subclass detection and diagnosis is inevitable requirement for personalized medical treatment and refinement of the effects that the somatic cells show towards other clinical conditions. The genome of these somatic cells exhibits mutations and genetic variations of the breast cancer cells and helps in understanding the characteristic behavior of the cancer cells. But their analysis is limited to clustering and there is requirement to analyze what else can be done with the data for identifying the tumor subcategory and the stages of subclasses. In this work, we have extended the work with similar data (consisting of 105 breast tumor cell lines) to solve other detection and characterization problems through computation and intelligent representation learning. Most of our work comprises of systematic data cleaning, analysis, and building prediction models with deep computational architectures and establish that the transformed data can help in better distinction of the respective categories. Our main contribution is the novel gene-subcategory interaction-based regularization (GSIAR) based data selection and analysis concept, alongside the prediction, proven to enhance the performance of the classification techniques. Graphical Abstract A graphical abstract of our model - Gene-subcategory interaction affinity-based regularization (GSIAR).

Keywords: Data-driven analysis; Dual phase deep learning; Proteome (PAM50) genetic analysis; Regularized representation learning; Subcategory driven analysis.

Molecular alterations in triple-negative breast cancer-the road to new treatment strategies.
Carsten Denkert, Cornelia Liedtke, Andrew Tutt, Gunter von Minckwitz.
Lancet, 2016 Dec 13; 389(10087). PMID: 27939063
Highly Cited. Review.
MicroRNA gene expression deregulation in human breast cancer.
Marilena V Iorio, Manuela Ferracin, +17 authors, Carlo M Croce.
Cancer Res, 2005 Aug 17; 65(16). PMID: 16103053
Highly Cited.
Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer.
Jenny C Chang, Eric C Wooten, +8 authors, Peter O'Connell.
Lancet, 2003 Aug 09; 362(9381). PMID: 12907009
Highly Cited.
Breast cancer classification and prognosis based on gene expression profiles from a population-based study.
Christos Sotiriou, Soek-Ying Neo, +7 authors, Edison T Liu.
Proc Natl Acad Sci U S A, 2003 Aug 15; 100(18). PMID: 12917485    Free PMC article.
Highly Cited.
Angiopoietin pathway gene expression associated with poor breast cancer survival.
Rajesh Ramanathan, Amy L Olex, +3 authors, Kazuaki Takabe.
Breast Cancer Res Treat, 2017 Jan 08; 162(1). PMID: 28062977    Free PMC article.
Genes that mediate breast cancer metastasis to lung.
Andy J Minn, Gaorav P Gupta, +7 authors, Joan Massagué.
Nature, 2005 Jul 29; 436(7050). PMID: 16049480    Free PMC article.
Highly Cited.
Proteogenomics connects somatic mutations to signalling in breast cancer.
Philipp Mertins, D R Mani, +34 authors, NCI CPTAC.
Nature, 2016 Jun 03; 534(7605). PMID: 27251275    Free PMC article.
Highly Cited.
Breast cancer prognostic classification in the molecular era: the role of histological grade.
Emad A Rakha, Jorge S Reis-Filho, +15 authors, Ian O Ellis.
Breast Cancer Res, 2010 Sep 02; 12(4). PMID: 20804570    Free PMC article.
Highly Cited. Review.
Expression of RET is associated with Oestrogen receptor expression but lacks prognostic significance in breast cancer.
Robert Mechera, Savas D Soysal, +10 authors, Simone Muenst.
BMC Cancer, 2019 Jan 10; 19(1). PMID: 30621641    Free PMC article.
HER2-positive breast-cancer cell lines are sensitive to KDM5 inhibition: definition of a gene-expression model for the selection of sensitive cases.
Gabriela Paroni, Marco Bolis, +8 authors, Enrico Garattini.
Oncogene, 2018 Dec 13; 38(15). PMID: 30538297
A breast cancer prediction model incorporating familial and personal risk factors.
Jonathan Tyrer, Stephen W Duffy, Jack Cuzick.
Stat Med, 2004 Apr 02; 23(7). PMID: 15057881
Highly Cited.
Clinical utility of gene-expression signatures in early stage breast cancer.
Maryann Kwa, Andreas Makris, Francisco J Esteva.
Nat Rev Clin Oncol, 2017 Jun 01; 14(10). PMID: 28561071
Highly Cited. Review.
Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer.
Soonmyung Paik, Gong Tang, +11 authors, Norman Wolmark.
J Clin Oncol, 2006 May 25; 24(23). PMID: 16720680
Highly Cited.
Breast Cancer Cell Line Classification and Its Relevance with Breast Tumor Subtyping.
Xiaofeng Dai, Hongye Cheng, Zhonghu Bai, Jia Li.
J Cancer, 2017 Nov 22; 8(16). PMID: 29158785    Free PMC article.
Highly Cited. Review.
A specific gene expression signature for visceral organ metastasis in breast cancer.
C D Savci-Heijink, H Halfwerk, +2 authors, M J van de Vijver.
BMC Cancer, 2019 Apr 10; 19(1). PMID: 30961553    Free PMC article.
Gene expression profiling in breast cancer: classification, prognostication, and prediction.
Jorge S Reis-Filho, Lajos Pusztai.
Lancet, 2011 Nov 22; 378(9805). PMID: 22098854
Highly Cited. Review.
Prediction of BRCA1 status in patients with breast cancer using estrogen receptor and basal phenotype.
Sunil R Lakhani, Jorge S Reis-Filho, +34 authors, Breast Cancer Linkage Consortium.
Clin Cancer Res, 2005 Jul 22; 11(14). PMID: 16033833
Highly Cited.
The Prognostic Role of Androgen Receptor in Patients with Early-Stage Breast Cancer: A Meta-analysis of Clinical and Gene Expression Data.
Ivana Bozovic-Spasojevic, Dimitrios Zardavas, +8 authors, Christos Sotiriou.
Clin Cancer Res, 2017 Feb 06; 23(11). PMID: 28151718
Systematic Review.
A study on several machine-learning methods for classification of malignant and benign clustered microcalcifications.
Liyang Wei, Yongyi Yang, Robert M Nishikawa, Yulei Jiang.
IEEE Trans Med Imaging, 2005 Mar 10; 24(3). PMID: 15754987
Intrinsic Subtypes and Gene Expression Profiles in Primary and Metastatic Breast Cancer.
Juan M Cejalvo, Eduardo Martínez de Dueñas, +24 authors, Aleix Prat.
Cancer Res, 2017 Mar 03; 77(9). PMID: 28249905    Free PMC article.
Highly Cited.
Prediction of risk of distant recurrence using the 21-gene recurrence score in node-negative and node-positive postmenopausal patients with breast cancer treated with anastrozole or tamoxifen: a TransATAC study.
Mitch Dowsett, Jack Cuzick, +11 authors, Steven Shak.
J Clin Oncol, 2010 Mar 10; 28(11). PMID: 20212256
Highly Cited.
Progesterone receptor status significantly improves outcome prediction over estrogen receptor status alone for adjuvant endocrine therapy in two large breast cancer databases.
Valerie-Jeanne Bardou, Grazia Arpino, +2 authors, Gary M Clark.
J Clin Oncol, 2003 May 14; 21(10). PMID: 12743151
Highly Cited.
Axillary dissection of level I and II lymph nodes is important in breast cancer classification. The Danish Breast Cancer Cooperative Group (DBCG).
C K Axelsson, H T Mouridsen, K Zedeler.
Eur J Cancer, 1992 Jan 01; 28A(8-9). PMID: 1515262
Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns.
S Gruvberger, M Ringnér, +6 authors, P S Meltzer.
Cancer Res, 2001 Aug 17; 61(16). PMID: 11507038
Highly Cited.
A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification.
Alexander Statnikov, Lily Wang, Constantin F Aliferis.
BMC Bioinformatics, 2008 Jul 24; 9. PMID: 18647401    Free PMC article.
Highly Cited.
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer.
Yixin Wang, Jan G M Klijn, +11 authors, John A Foekens.
Lancet, 2005 Feb 22; 365(9460). PMID: 15721472
Highly Cited.
Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.
Hector L Franco, Anusha Nagari, +14 authors, W Lee Kraus.
Genome Res, 2017 Dec 24; 28(2). PMID: 29273624    Free PMC article.
Supervised risk predictor of breast cancer based on intrinsic subtypes.
Joel S Parker, Michael Mullins, +17 authors, Philip S Bernard.
J Clin Oncol, 2009 Feb 11; 27(8). PMID: 19204204    Free PMC article.
Highly Cited.
An integrative bioinformatics approach reveals coding and non-coding gene variants associated with gene expression profiles and outcome in breast cancer molecular subtypes.
Balázs Győrffy, Lőrinc Pongor, +6 authors, Libero Santarpia.
Br J Cancer, 2018 Mar 22; 118(8). PMID: 29559730    Free PMC article.
The current state of breast cancer classification.
G Viale.
Ann Oncol, 2012 Sep 26; 23 Suppl 10. PMID: 22987963
Predicting the clinical status of human breast cancer by using gene expression profiles.
M West, C Blanchette, +7 authors, J R Nevins.
Proc Natl Acad Sci U S A, 2001 Sep 20; 98(20). PMID: 11562467    Free PMC article.
Highly Cited.
Identification of the breast cancer susceptibility gene BRCA2.
R Wooster, G Bignell, +7 authors, G Micklem.
Nature, 1995 Dec 21; 378(6559). PMID: 8524414
Highly Cited.
Image analysis and machine learning applied to breast cancer diagnosis and prognosis.
W H Wolberg, W N Street, O L Mangasarian.
Anal Quant Cytol Histol, 1995 Apr 01; 17(2). PMID: 7612134
Microarrays in the 2010s: the contribution of microarray-based gene expression profiling to breast cancer classification, prognostication and prediction.
Pierre-Emmanuel Colombo, Fernanda Milanezi, Britta Weigelt, Jorge S Reis-Filho.
Breast Cancer Res, 2011 Jul 27; 13(3). PMID: 21787441    Free PMC article.
Network-based classification of breast cancer metastasis.
Han-Yu Chuang, Eunjung Lee, +2 authors, Trey Ideker.
Mol Syst Biol, 2007 Oct 18; 3. PMID: 17940530    Free PMC article.
Highly Cited.
Gain Fat-Lose Metastasis: Converting Invasive Breast Cancer Cells into Adipocytes Inhibits Cancer Metastasis.
Dana Ishay-Ronen, Maren Diepenbruck, +8 authors, Gerhard Christofori.
Cancer Cell, 2019 Jan 16; 35(1). PMID: 30645973
Highly Cited.
Online accounts of gene expression profiling in early-stage breast cancer: Interpreting genomic testing for chemotherapy decision making.
Emily Ross, Julia Swallow, Anne Kerr, Sarah Cunningham-Burley.
Health Expect, 2018 Nov 06; 22(1). PMID: 30387238    Free PMC article.
G9a drives hypoxia-mediated gene repression for breast cancer cell survival and tumorigenesis.
Francesco Casciello, Fares Al-Ejeh, +9 authors, Jason S Lee.
Proc Natl Acad Sci U S A, 2017 Jun 21; 114(27). PMID: 28630300    Free PMC article.
Molecular classification and molecular forecasting of breast cancer: ready for clinical application?
James D Brenton, Lisa A Carey, Ahmed Ashour Ahmed, Carlos Caldas.
J Clin Oncol, 2005 Sep 08; 23(29). PMID: 16145060
Highly Cited. Review.
The contribution of gene expression profiling to breast cancer classification, prognostication and prediction: a retrospective of the last decade.
Britta Weigelt, Frederick L Baehner, Jorge S Reis-Filho.
J Pathol, 2009 Nov 21; 220(2). PMID: 19927298
Highly Cited. Review.
Genetic Ancestry-dependent Differences in Breast Cancer-induced Field Defects in the Tumor-adjacent Normal Breast.
Harikrishna Nakshatri, Brijesh Kumar, +5 authors, Anna Maria V Storniolo.
Clin Cancer Res, 2019 Feb 06; 25(9). PMID: 30718355
A gene-expression signature as a predictor of survival in breast cancer.
Marc J van de Vijver, Yudong D He, +18 authors, René Bernards.
N Engl J Med, 2002 Dec 20; 347(25). PMID: 12490681
Highly Cited.
Gene expression predictors of breast cancer outcomes.
Erich Huang, Skye H Cheng, +10 authors, Andrew T Huang.
Lancet, 2003 May 16; 361(9369). PMID: 12747878
Highly Cited.
Refinement of breast cancer classification by molecular characterization of histological special types.
B Weigelt, H M Horlings, +7 authors, J L Peterse.
J Pathol, 2008 Aug 23; 216(2). PMID: 18720457
Highly Cited.
Breast cancer: prediction with artificial neural network based on BI-RADS standardized lexicon.
J A Baker, P J Kornguth, +2 authors, C E Floyd.
Radiology, 1995 Sep 01; 196(3). PMID: 7644649
Ensemble machine learning on gene expression data for cancer classification.
Aik Choon Tan, David Gilbert.
Appl Bioinformatics, 2004 May 08; 2(3 Suppl). PMID: 15130820