We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at >10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the luminal A subtype. We identified two novel protein-expression-defined subgroups, possibly produced by stromal/microenvironmental elements, and integrated analyses identified specific signalling pathways dominant in each molecular subtype including a HER2/phosphorylated HER2/EGFR/phosphorylated EGFR signature within the HER2-enriched expression subtype. Comparison of basal-like breast tumours with high-grade serous ovarian tumours showed many molecular commonalities, indicating a related aetiology and similar therapeutic opportunities. The biological finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biological subtypes of breast cancer.

/pdf/comprehensive-molecular-portraits-of-human-breast-tumours-4t6h37c9ow.pdf

Comprehensive molecular portraits of human breast tumours

Prospective Cohort Study

Cancers develop in complex tissue environments, which they depend on for sustained growth, invasion and metastasis. Unlike tumor cells, stromal cell types within the tumor microenvironment (TME) are genetically stable and thus represent an attractive therapeutic target with reduced risk of resistance and tumor recurrence. However, specifically disrupting the pro-tumorigenic TME is a challenging undertaking, as the TME has diverse capacities to induce both beneficial and adverse consequences for tumorigenesis. Furthermore, many studies have shown that the microenvironment is capable of normalizing tumor cells, suggesting that re-education of stromal cells, rather than targeted ablation per se, may be an effective strategy for treating cancer. Here we discuss the paradoxical roles of the TME during specific stages of cancer progression and metastasis, as well as recent therapeutic attempts to re-educate stromal cells within the TME to have anti-tumorigenic effects.

/pdf/microenvironmental-regulation-of-tumor-progression-and-4528oymlw6.pdf

Microenvironmental regulation of tumor progression and metastasis.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

Strategies for subtypes—dealing with the diversity of breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011

Panel testing for inherited susceptibility to breast, ovarian, and colorectal cancer.

Ductal lavage (DL) permits noninvasive retrieval of epithelial cells from the breast. Clinical development of this technique has been fueled largely by its potential, as yet unproven, to improve detection of breast cancer and definition of individual risk for development of breast cancer. Early studies demonstrate the feasibility of performing this technique, provide data on cellular yield and findings, and demonstrate the ability to measure molecular markers in DL fluid. However, the sensitivity and specificity of DL for the detection of breast cancer remains unknown, as does the significance of atypia, particularly mild atypia, when found in DL fluid. Although DL appears safe and the device is approved by the US Food and Drug Administration, DL is still best utilized in the setting of clinical trials designed to resolve issues of sensitivity, specificity, and localization.

/pdf/the-utility-of-ductal-lavage-in-breast-cancer-detection-and-5fjp5m9wn9.pdf

The utility of ductal lavage in breast cancer detection and risk assessment.

Gemcitabine and Trastuzumab Combinations for Patients with Metastatic Breast Cancer Overexpressing HER2/neu

In this issue, Parmigiani and colleagues tested the ability of 6 models to discriminate BRCA1 and BRCA2 mutation carriers from noncarriers. According to these researchers, no one type of model is b...

Cancer risk models: translating family history into clinical management.

https://jamanetwork.com/journals/jama/articlepdf/2748486/jama_domchek_2019_ed_190059.pdf

Susan M. Domchek

Papers

Panel testing for inherited susceptibility to breast, ovarian, and colorectal cancer.

The utility of ductal lavage in breast cancer detection and risk assessment.

Gemcitabine and Trastuzumab Combinations for Patients with Metastatic Breast Cancer Overexpressing HER2/neu

Cancer risk models: translating family history into clinical management.

Broadening Criteria for BRCA1/2 Evaluation: Placing the USPSTF Recommendation in Context