Summary We analyzed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, mRNA 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 contributed by stromal/microenvironmental elements, and integrated analyses identified specific signaling pathways dominant in each molecular subtype including a HER2/p-HER2/HER1/p-HER1 signature within the HER2-Enriched expression subtype. Comparison of Basal-like breast tumors with high-grade Serous Ovarian tumors showed many molecular commonalities, suggesting a related etiology and similar therapeutic opportunities. The biologic 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 biologic subtypes of breast cancer.

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies.

SUMMARY We describe the landscape of genomic alterations in cutaneous melanomas through DNA, RNA, and protein-based analysis of 333 primary and/or metastatic melanomas from 331 patients. We establish a framework for genomic classification into one of four subtypes based on the pattern of the most prevalent significantly mutated genes: mutant BRAF, mutant RAS, mutant NF1, and Triple-WT (wild-type). Integrative analysis reveals enrichment of KIT mutations and focal amplifications and complex structural rearrangements as a feature of the Triple-WT subtype. We found no significant outcome correlation with genomic classification, but samples assigned a transcriptomic subclass enriched for immune gene expression associated with lymphocyte infiltrate on pathology review and high LCK protein expression, a T cell marker, were associated with improved patient survival. This clinicopathological and multidimensional analysis suggests that the prognosis of melanoma patients with regional metastases is influenced by tumor stroma immunobiology, offering insights to further personalize therapeutic decision-making.

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Cardiotoxicity is known as a severe clinical problem in oncological practice that reduces the options for cancer therapy. Physical exercise is recognized as a well-established protective measure for many heart and cancer diseases. In our study, we hypothesized that supervised and moderate-intensity exercise training would prevent heart failure and its consequences induced by trastuzumab therapy. The aim of this study was to examine the effect of physical training on ventricular remodeling, serum cardiac markers, and exercise performance in women with human epidermal growth receptor 2 (HER2+) breast cancer (BC) undergoing trastuzumab therapy. This was a prospective, randomized, clinical controlled trial. Forty-six BC women were randomized into either an intervention group (IG) or a control group (CG). An exercise program (IG) was performed after 3–6 months of trastuzumab therapy at 5 d/week (to 80% maximum heart rate (HRmax)) for 9 weeks. We then evaluated their cardiac function using echocardiography, a 6-Minute Walk Test (6MWT), and plasma parameters (C-reactive protein (CRP), myoglobin (MYO), interleukin-6 (IL-6), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and creatine kinase (CK)). After the physical training program, we did not observe any significant changes in the left ventricular (LV) ejection fraction (LVEF) and 6MWT (p > 0.05) in the IG compared to the CG (decrease p < 0.05). The differences in the blood parameters were not significant (p < 0.05). To conclude, moderate-intensity exercise training prevented a decrease in the LVEF and physical capacity during trastuzumab therapy in HER2+ BC. Further research is needed to validate our results.