Differences in gene and protein expression and the effects of race/ethnicity on breast cancer subtypes

Mariana Chavez-MacGregor, Shuying Liu, Debora De Melo-Gagliato, Huiqin Chen, Kim Anh Do, Lajos Pusztai, W. Fraser Symmans, Lakshmy Nair, Gabriel N. Hortobagyi, Gordon Mills, Funda Meric-Bernstam, Ana M. Gonzalez-Angulo

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background: Differences in gene or protein expression patterns between breast cancers according to race/ ethnicity and cancer subtype. Methods: Transcriptional profiling was performed using Affymetrix HG-U133A platform in 376 patients and reverse phase protein array analysis (RPPA) was done for 177 proteins in 255 patients from a separate cohort. Unsupervised clustering was conducted, as well as supervised comparison by race and tumor subtype. Standard statistical methods, BRB-Array tools, and Ingenuity Pathways software packages were used to analyze the data. Results: Median age was 50 years in both the cohorts. In theRPPAcohort, 54.5% of the tumors were hormone receptor-positive (HR-positive), 20.7% HER2-positive, and 24.71% triple-negative (TNBC). One hundred and forty-seven (57.6%), 47 (18.43%), and 46 (18.1%) of the patients were White, Hispanic, and Black, respectively. Unsupervised hierarchical clustering of the protein expression data showed no distinct clusters by race (P values were 0.492, 0.489, and 0.494 for the HR-positive, HER2-positive, and TNBC tumors respectively). In the gene expression cohort, 54.2% of the tumors were HR-positive, 16.5% HER2-positive, and 29.3% TNBC. Two hundred and sixteen (57.5%), 111 (29.52%), and 32 (8.52%) patients were White, Hispanic, and Black, respectively. No probe set with a false discovery rate (FDR) of <0.05 showed an association with race by breast cancer subtype; similar results were obtained using pathway and gene set enrichment analysis methods. Conclusions: We did not detect a significant variation in RNA or protein expression comparing different race/ethnicity groups of women with breast cancer. Impact: More research on the complex network of factors that result in outcomes differences among race/ ethnicities is needed.

Original languageEnglish (US)
Pages (from-to)316-323
Number of pages8
JournalCancer Epidemiology Biomarkers and Prevention
Volume23
Issue number2
DOIs
StatePublished - Feb 1 2014
Externally publishedYes

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Breast Neoplasms
Gene Expression
Proteins
Hormones
Neoplasms
Hispanic Americans
Cluster Analysis
Protein Array Analysis
Software
RNA
Research
Genes
hydroquinone

ASJC Scopus subject areas

  • Epidemiology
  • Oncology

Cite this

Chavez-MacGregor, M., Liu, S., De Melo-Gagliato, D., Chen, H., Do, K. A., Pusztai, L., ... Gonzalez-Angulo, A. M. (2014). Differences in gene and protein expression and the effects of race/ethnicity on breast cancer subtypes. Cancer Epidemiology Biomarkers and Prevention, 23(2), 316-323. https://doi.org/10.1158/1055-9965.EPI-13-0929

Differences in gene and protein expression and the effects of race/ethnicity on breast cancer subtypes. / Chavez-MacGregor, Mariana; Liu, Shuying; De Melo-Gagliato, Debora; Chen, Huiqin; Do, Kim Anh; Pusztai, Lajos; Symmans, W. Fraser; Nair, Lakshmy; Hortobagyi, Gabriel N.; Mills, Gordon; Meric-Bernstam, Funda; Gonzalez-Angulo, Ana M.

In: Cancer Epidemiology Biomarkers and Prevention, Vol. 23, No. 2, 01.02.2014, p. 316-323.

Research output: Contribution to journalArticle

Chavez-MacGregor, M, Liu, S, De Melo-Gagliato, D, Chen, H, Do, KA, Pusztai, L, Symmans, WF, Nair, L, Hortobagyi, GN, Mills, G, Meric-Bernstam, F & Gonzalez-Angulo, AM 2014, 'Differences in gene and protein expression and the effects of race/ethnicity on breast cancer subtypes', Cancer Epidemiology Biomarkers and Prevention, vol. 23, no. 2, pp. 316-323. https://doi.org/10.1158/1055-9965.EPI-13-0929
Chavez-MacGregor, Mariana ; Liu, Shuying ; De Melo-Gagliato, Debora ; Chen, Huiqin ; Do, Kim Anh ; Pusztai, Lajos ; Symmans, W. Fraser ; Nair, Lakshmy ; Hortobagyi, Gabriel N. ; Mills, Gordon ; Meric-Bernstam, Funda ; Gonzalez-Angulo, Ana M. / Differences in gene and protein expression and the effects of race/ethnicity on breast cancer subtypes. In: Cancer Epidemiology Biomarkers and Prevention. 2014 ; Vol. 23, No. 2. pp. 316-323.
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abstract = "Background: Differences in gene or protein expression patterns between breast cancers according to race/ ethnicity and cancer subtype. Methods: Transcriptional profiling was performed using Affymetrix HG-U133A platform in 376 patients and reverse phase protein array analysis (RPPA) was done for 177 proteins in 255 patients from a separate cohort. Unsupervised clustering was conducted, as well as supervised comparison by race and tumor subtype. Standard statistical methods, BRB-Array tools, and Ingenuity Pathways software packages were used to analyze the data. Results: Median age was 50 years in both the cohorts. In theRPPAcohort, 54.5{\%} of the tumors were hormone receptor-positive (HR-positive), 20.7{\%} HER2-positive, and 24.71{\%} triple-negative (TNBC). One hundred and forty-seven (57.6{\%}), 47 (18.43{\%}), and 46 (18.1{\%}) of the patients were White, Hispanic, and Black, respectively. Unsupervised hierarchical clustering of the protein expression data showed no distinct clusters by race (P values were 0.492, 0.489, and 0.494 for the HR-positive, HER2-positive, and TNBC tumors respectively). In the gene expression cohort, 54.2{\%} of the tumors were HR-positive, 16.5{\%} HER2-positive, and 29.3{\%} TNBC. Two hundred and sixteen (57.5{\%}), 111 (29.52{\%}), and 32 (8.52{\%}) patients were White, Hispanic, and Black, respectively. No probe set with a false discovery rate (FDR) of <0.05 showed an association with race by breast cancer subtype; similar results were obtained using pathway and gene set enrichment analysis methods. Conclusions: We did not detect a significant variation in RNA or protein expression comparing different race/ethnicity groups of women with breast cancer. Impact: More research on the complex network of factors that result in outcomes differences among race/ ethnicities is needed.",
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AU - Chen, Huiqin

AU - Do, Kim Anh

AU - Pusztai, Lajos

AU - Symmans, W. Fraser

AU - Nair, Lakshmy

AU - Hortobagyi, Gabriel N.

AU - Mills, Gordon

AU - Meric-Bernstam, Funda

AU - Gonzalez-Angulo, Ana M.

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