Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be distinguished by their distinct patterns of gene expression. A total of 115 malignant breast tumors were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into one basal-like, one ERBB2-overexpressing, two luminal-like, and one normal breast tissue-like subgroup. The genes used for classification were selected based on their similar expression levels between pairs of consecutive samples taken from the same tumor separated by 15 weeks of neoadjuvant treatment. Similar cluster analyses of two published, independent data sets representing different patient cohorts from different laboratories, uncovered some of the same breast cancer subtypes. In the one data set that included information on time to development of distant metastasis, subtypes were associated with significant differences in this clinical feature. By including a group of tumors from BRCA1 carriers in the analysis, we found that this genotype predisposes to the basal tumor subtype. Our results strongly support the idea that many of these breast tumor subtypes represent biologically distinct disease entities.

https://www.pnas.org/content/pnas/100/14/8418.full.pdf

Repeated observation of breast tumor subtypes in independent gene expression data sets

Purpose: To compare the clinical features, natural history, and outcomes for women with “triple-negative” breast cancer with women with other types of breast cancer. Experimental Design: We studied a cohort of 1,601 patients with breast cancer, diagnosed between January 1987 and December 1997 at Women9s College Hospital in Toronto. Triple-negative breast cancers were defined as those that were estrogen receptor negative, progesterone receptor negative, and HER2neu negative. The prognostic significance of triple-negative breast cancer was explored. Results: The median follow-up time of the 1,601 women was 8.1 years. One hundred and eighty of 1,601 patients (11.2%) had triple-negative breast cancer. Compared with other women with breast cancer, those with triple-negative breast cancer had an increased likelihood of distant recurrence (hazard ratio, 2.6; 95% confidence interval, 2.0-3.5; P P Conclusions: Triple-negative breast cancers have a more aggressive clinical course than other forms of breast cancer, but the adverse effect is transient.

https://clincancerres.aacrjournals.org/content/clincanres/13/15/4429.full.pdf

Triple-Negative Breast Cancer: Clinical Features and Patterns of Recurrence

ContextGene expression analysis has identified several breast cancer subtypes, including basal-like, human epidermal growth factor receptor-2 positive/estrogen receptor negative (HER2+/ER–), luminal A, and luminal B.ObjectivesTo determine population-based distributions and clinical associations for breast cancer subtypes.Design, Setting, and ParticipantsImmunohistochemical surrogates for each subtype were applied to 496 incident cases of invasive breast cancer from the Carolina Breast Cancer Study (ascertained between May 1993 and December 1996), a population-based, case-control study that oversampled premenopausal and African American women. Subtype definitions were as follows: luminal A (ER+ and/or progesterone receptor positive [PR+], HER2−), luminal B (ER+ and/or PR+, HER2+), basal-like (ER−, PR−, HER2−, cytokeratin 5/6 positive, and/or HER1+), HER2+/ER− (ER−, PR−, and HER2+), and unclassified (negative for all 5 markers).Main Outcome MeasuresWe examined the prevalence of breast cancer subtypes within racial and menopausal subsets and determined their associations with tumor size, axillary nodal status, mitotic index, nuclear pleomorphism, combined grade, p53 mutation status, and breast cancer–specific survival.ResultsThe basal-like breast cancer subtype was more prevalent among premenopausal African American women (39%) compared with postmenopausal African American women (14%) and non–African American women (16%) of any age (P<.001), whereas the luminal A subtype was less prevalent (36% vs 59% and 54%, respectively). The HER2+/ER− subtype did not vary with race or menopausal status (6%-9%). Compared with luminal A, basal-like tumors had more TP53 mutations (44% vs 15%, P<.001), higher mitotic index (odds ratio [OR], 11.0; 95% confidence interval [CI], 5.6-21.7), more marked nuclear pleomorphism (OR, 9.7; 95% CI, 5.3-18.0), and higher combined grade (OR, 8.3; 95% CI, 4.4-15.6). Breast cancer–specific survival differed by subtype (P<.001), with shortest survival among HER2+/ER− and basal-like subtypes.ConclusionsBasal-like breast tumors occurred at a higher prevalence among premenopausal African American patients compared with postmenopausal African American and non–African American patients in this population-based study. A higher prevalence of basal-like breast tumors and a lower prevalence of luminal A tumors could contribute to the poor prognosis of young African American women with breast cancer.

https://jamanetwork.com/journals/jama/articlepdf/202952/joc60046.pdf

Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study.

https://www.ibioinformatics.org/Oncomine.pdf

ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform

Purpose: Expression profiling studies classified breast carcinomas into estrogen receptor (ER)+/luminal, normal breast-like, HER2 overexpressing, and basal-like groups, with the latter two associated with poor outcomes. Currently, there exist clinical assays that identify ER+/luminal and HER2-overexpressing tumors, and we sought to develop a clinical assay for breast basal-like tumors. Experimental Design: To identify an immunohistochemical profile for breast basal-like tumors, we collected a series of known basal-like tumors and tested them for protein patterns that are characteristic of this subtype. Next, we examined the significance of these protein patterns using tissue microarrays and evaluated the prognostic significance of these findings. Results: Using a panel of 21 basal-like tumors, which was determined using gene expression profiles, we saw that this subtype was typically immunohistochemically negative for estrogen receptor and HER2 but positive for basal cytokeratins, HER1, and/or c-KIT. Using breast carcinoma tissue microarrays representing 930 patients with 17.4-year mean follow-up, basal cytokeratin expression was associated with low disease-specific survival. HER1 expression was observed in 54% of cases positive for basal cytokeratins ( versus 11% of negative cases) and was associated with poor survival independent of nodal status and size. c-KIT expression was more common in basal-like tumors than in other breast cancers but did not influence prognosis. Conclusions: A panel of four antibodies (ER, HER1, HER2, and cytokeratin 5/6) can accurately identify basal-like tumors using standard available clinical tools and shows high specificity. These studies show that many basal-like tumors express HER1, which suggests candidate drugs for evaluation in these patients.

https://clincancerres.aacrjournals.org/content/clincanres/10/16/5367.full.pdf

Immunohistochemical and Clinical Characterization of the Basal-Like Subtype of Invasive Breast Carcinoma

While several prognostic factors have been identified in breast carcinoma, the clinical outcome remains hard to predict for individual patients. Better predictive markers are needed to help guide difficult treatment decisions. In a previous study of 78 breast carcinoma specimens, we noted an association between poor clinical outcome and the expression of cytokeratin 17 and/or cytokeratin 5 mRNAs. Here we describe the results of immunohistochemistry studies using monoclonal antibodies against these markers to analyze more than 600 paraffin-embedded breast tumors in tissue microarrays. We found that expression of cytokeratin 17 and/or cytokeratin 5/6 in tumor cells was associated with a poor clinical outcome. Moreover, multivariate analysis showed that in node-negative breast carcinoma, expression of these cytokeratins was a prognostic factor independent of tumor size and tumor grade.

Expression of Cytokeratins 17 and 5 Identifies a Group of Breast Carcinomas with Poor Clinical Outcome

The invention provides a variety of reagents for use in the diagnosis and management of breast cancer. The invention utilizes cDNA microarray technology to identify genes whose expression profile across a large group of tumor samples correlates with that of cytokeratin 5 and cytokeratin 17, markers for basal cells of the normal mammary lactation gland. The invention demonstrates that tumors that express cytokeratin 5/6 and/or 17 have a poor prognosis relative to tumors overall. The invention provides basal marker genes and their expression products and uses of these genes for diagnosis of breast cancer and for identification of therapies for breast cancer. In particular, the invention provides basal marker genes including cadherin3, matrix metalloproteinase 14, and cadherin EGF LAG seven-pass G-type receptor 2. The invention provides antibodies to the polypeptides expressed by these genes and methods of use thereof.

Basal cell markers in breast cancer and uses thereof

The invention provides a protein (BSTP-TRANS) and polynucleotides which identify and encode BSTP-TRANS. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. In addition, the invention provides methods for treating or preventing disorders of cell proliferation, particularly breast cancer, by administering a pharmaceutical composition comprising a polypeptide, polynucleotide, or antibody of the invention. The invention also provides methods of classifying diseases, particularly breast cancer, by detecting expression of BSTP-TRANS or of a polynucleotide encoding BSTP-TRANS, and methods of providing diagnostic, prognostic, and/or predictive information for a patient based on the detection and/or measurement of BSTP-TRANS or of a gene that encodes BSTP-TRANS or of a mutation in the BST-TRANS gene.

Bstp-trans protein and related reagents and methods of use thereof

Methods of classifying, diagnosing, stratifying and treating cancer patients and their tumors

https://ascopubs.org/doi/pdfdirect/10.1200/PO.17.00032

Clinical Activity of Pembrolizumab in a Patient With Metastatic Triple-Negative Breast Cancer Without Tumor Programmed Death-Ligand 1 Expression: A Case Report and Correlative Biomarker Analysis

Rob Seitz

Papers

Expression of Cytokeratins 17 and 5 Identifies a Group of Breast Carcinomas with Poor Clinical Outcome

Basal cell markers in breast cancer and uses thereof

Bstp-trans protein and related reagents and methods of use thereof

Methods of classifying, diagnosing, stratifying and treating cancer patients and their tumors

Clinical Activity of Pembrolizumab in a Patient With Metastatic Triple-Negative Breast Cancer Without Tumor Programmed Death-Ligand 1 Expression: A Case Report and Correlative Biomarker Analysis