Analysis of gene expression patterns in triple negative breast cancer: MERTK and WHSC1L1.

Triple Negative ◽

Molecular Subtype ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Primary Tumors

Triple negative breast cancer (TNBC) shares overlap with the basal molecular subtype of breast cancer and is more frequently diagnosed in African-American (black) women for reasons not understood (1,2). To understand genes whose expression may be of pertinence to the development or progression of triple negative breast cancer, we mined published microarray data (3,4) comparing global gene expression profiles of TNBC histology groups, identifying genes whose expression changed the least between among TNBCs, suggesting that these genes may be important for TNBC biology. We identified the MER proto-oncogene tyrosine kinase MERTK and the Wolf-Hirschhorn syndrome candidate 1-like 1 WHSC1L1 among the genes whose expression differed the least when comparing TNBC cases and subtypes. In another dataset, MERTK and WHSCL1 were found to be differentially expressed in TNBC when comparing primary tumors of the breast to normal breast tissue. Kaplan-Meier survival analysis revealed that expression levels of MERTK and WHSCL1 correlated with survival outcomes in human breast cancer, and that this correlation differed based on race of the patient. MERTK and WHSCL1 may be of relevance in understanding the etiology or progression of triple negative breast cancer.

Analysis of gene expression patterns in triple negative breast cancer II: TNBC molecular subtype.

10.31219/osf.io/hu5wg ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Black Women ◽

Human Breast Cancer ◽

Triple Negative ◽

Molecular Subtype ◽

Expression Profiles ◽

Expression Patterns ◽

Human Breast

Triple negative breast cancer (TNBC) shares overlap with the basal molecular subtype of breast cancer and is more frequently diagnosed in African-American (black) women for reasons not understood (1,2). To understand genes whose expression may be of pertinence to the development or progression of triple negative breast cancer, we mined published microarray data (3) comparing global gene expression profiles of TNBC molecular subtypes, identifying genes whose expression changed the least between among TNBCs, suggesting that these genes may be important for TNBC biology. We identified PVT1, PHC3, WNT8B, MLLT6, MSH3, IHH, and WNT2B among the genes whose expression differed the least when comparing TNBC cases and subtypes. Kaplan-Meier survival analysis revealed that expression levels of each of these genes correlated with survival outcomes in human breast cancer; in some cases, this correlation differed based on race of the patient, and in other cases, this correlation was found in the basal subtype of human breast cancer, which shares significant overlap with triple negative breast cancer at the level of gene expression (2). PVT1, PHC3, WNT8B, MLLT6, MSH3, IHH, and WNT2B may be of relevance in understanding the etiology or progression of triple negative breast cancer.

PAX5 expression associates with survival in triple negative breast cancer.

10.31219/osf.io/rh6xb ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cancer Patients ◽

Microarray Data ◽

Triple Negative ◽

Molecular Subtype ◽

Breast Cancer Patients ◽

Primary Tumors ◽

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival following treatment: dead or alive. We observed significant transcriptome-wide differential expression of paired box 5, encoded by PAX5 when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, PAX5 expression was significantly correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. PAX5 may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

LAX1 expression associates with survival in triple negative breast cancer.

10.31219/osf.io/7mhje ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cancer Patients ◽

Microarray Data ◽

Triple Negative ◽

Molecular Subtype ◽

Breast Cancer Patients ◽

Primary Tumors ◽

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival at time of analysis: dead or alive. We observed significant transcriptome-wide differential expression of lymphocyte transmembrane adaptor 1, encoded by LAX1 when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, LAX1 expression was significantly correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. LAX1 may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

SELL expression associates with survival in triple negative breast cancer.

10.31219/osf.io/mjvc9 ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cancer Patients ◽

Microarray Data ◽

Triple Negative ◽

Molecular Subtype ◽

Breast Cancer Patients ◽

Primary Tumors ◽

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival at time of analysis: dead or alive. We observed significant transcriptome-wide differential expression of selectin L, encoded by SELL, when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, SELL expression was significantly correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. SELL may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

RASGRP1 expression associates with survival in triple negative breast cancer.

10.31219/osf.io/m2x3j ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cancer Patients ◽

Microarray Data ◽

Triple Negative ◽

Molecular Subtype ◽

Breast Cancer Patients ◽

Primary Tumors ◽

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival following treatment: dead or alive. We observed significant transcriptome-wide differential expression of RAS guanyl releasing protein 1 (calcium and DAG-regulated), encoded by RASGRP1 when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, RASGRP1 expression was correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. RASGRP1 may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

TUBA1C expression associates with survival in triple negative breast cancer.

10.31219/osf.io/qytd6 ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cancer Patients ◽

Microarray Data ◽

Triple Negative ◽

Molecular Subtype ◽

Breast Cancer Patients ◽

Primary Tumors ◽

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival following treatment: dead or alive. We observed significant transcriptome-wide differential expression of tubulin, alpha 1c, encoded by TUBA1C when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, TUBA1C expression was correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. TUBA1C may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

GSR expression associates with survival in triple negative breast cancer.

10.31219/osf.io/unkvz ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cancer Patients ◽

Microarray Data ◽

Triple Negative ◽

Molecular Subtype ◽

Breast Cancer Patients ◽

Primary Tumors ◽

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer patients based on survival following treatment: dead or alive. We observed significant transcriptome-wide differential expression of glutathione reductase, encoded by GSR when comparing the primary tumors of triple negative breast cancer patients dead or alive. Importantly, GSR expression was correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. GSR may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.

Abstract 4698: Gene expression profiles of triple negative breast cancer epithelial and stromal cells are predictive of treatment response.

10.1158/1538-7445.am2013-4698 ◽

2013 ◽

Author(s):

Bojana Jovanovic ◽

Steven X. Chen ◽

Brian D. Lehmann ◽

Kimberly N. Johnson ◽

Violeta Sanchez ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Treatment Response ◽

Stromal Cells ◽

Triple Negative ◽

Expression Profiles ◽

Gene Expression Profiles

TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer

Cancer Informatics ◽

10.4137/cin.s9983 ◽

2012 ◽

Vol 11 ◽

pp. CIN.S9983 ◽

Cited By ~ 108

Author(s):

Xi Chen ◽

Jiang Li ◽

William H. Gray ◽

Brian D. Lehmann ◽

Joshua A. Bauer ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Triple Negative ◽

Expression Profiles ◽

Expression Patterns ◽

Genomic Research ◽

Data Matrix ◽

Cancer Data ◽

Subtyping Tool

Motivation Triple-negative breast cancer (TNBC) is a heterogeneous breast cancer group, and identification of molecular subtypes is essential for understanding the biological characteristics and clinical behaviors of TNBC as well as for developing personalized treatments. Based on 3,247 gene expression profiles from 21 breast cancer data sets, we discovered six TNBC subtypes from 587 TNBC samples with unique gene expression patterns and ontologies. Cell line models representing each of the TNBC subtypes also displayed different sensitivities to targeted therapeutic agents. Classification of TNBC into subtypes will advance further genomic research and clinical applications. Result We developed a web-based subtyping tool TNBCtype for candidate TNBC samples using our gene expression meta data and classification methods. Given a gene expression data matrix, this tool will display for each candidate sample the predicted subtype, the corresponding correlation coefficient, and the permutation P-value. We offer a user-friendly web interface to predict the subtypes for new TNBC samples that may facilitate diagnostics, biomarker selection, drug discovery, and the more tailored treatment of breast cancer.

PARP15 expression associates with survival in triple negative breast cancer.

10.31219/osf.io/dgjwx ◽

2021 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Overall Survival ◽

Microarray Data ◽

Triple Negative ◽

Molecular Subtype ◽

Breast Cancer Patients ◽

Primary Tumors ◽

We mined published microarray data (1) to understand the most significant gene expression differences in the tumors of triple negative breast cancer (TNBC) patients based on survival at time of analysis: dead or alive. The poly (ADP-ribose) polymerase family, member 15, PARP15, emerged as among the most differentially expressed genes, transcriptome-wide, when comparing the primary tumors of triple negative breast cancer patients dead or alive. PARP15 mRNA was present at significantly higher quantities in the tumors of TNBC patients alive. Importantly, PARP15 expression was significantly correlated with overall survival in basal subtype breast cancer, a molecular subtype sharing significant overlap with triple negative breast cancer. PARP15 may be of relevance as a biomarker or as a molecule of interest in understanding the etiology or progression of triple negative breast cancer.