Table of Contents
Main questions #
Materials and methods #
Tumor and germline DNA from 825 patients
- Agilent mRNA expresion microarrays (n=547)
- Illumina Infinium DNA methylation chips (n=802, 1222 miRBase)
- Unsupervised clustering analysis
- Affymetrix Genome-Wide Human SNP Array 6.0 (n=773)
- microRNA sequencing (n=697)
- Exome sequencing (n=507)
- Reverse Phase Protein Array (n=403)
- Unsupervised hierarchical clustering analysis
- PARADIGM analysis for patient-specific pathway activites
- MEMo analysis to identify multually exclusive alterations targetting frequently altered genes likely to belong to the same pathway
And 17 months Survival analysis
Refer TCGA Data summary
Main finding of the paper #
Significantly mutated genes in breast cancer #
Association between mutations and mRNA-expression subtypes #
TP53 mutations in Basal-like tumors were mostly nonsense and frame-shift, while missense mutations predominated in Luminal A and B tumors
Germline BRCA1 mutation is associated with basal-like breast cancers.
Gene expression analyses (mRNA and microRNA) #
There was little correlation with mutation status and microRNA subtype.
DNA methylation #
5 distinct DNA methylation groups.
A DAVID functional annotation analysis identified ‘Extracellular region part’ and ‘Wnt signaling pathway’ to be associated with this 490 gene-set; the Group 3 hyper-methylated samples showed fewer PIK3CA and MAP3K1 mutations, and lower expression of Wnt-pathway genes.
DNA copy number #
NMF clustering of GISTIC segments identified five copy number clusters/groups that correlated with mRNA-subtypes, ER, PR and HER2 clinical status, and TP53 mutation status
Reverse Phase Protein Arrays (RPPA) #
It identifies 7 subtypes
Multi-platform subtype discovery #
Luminal/ER-positive summary analysis #
Across all breast cancers, MEMo identified a set of modules that highlight the differential activation events within the Receptor tyrosine kinase (RTK)/PI3K pathway; mutations of PIK3CA were very common in Luminal/ER-positive cancers while PTEN loss was more common in Basal-like tumors.
HER2-based classifications and summary analysis #
Many therapeutic advances have been made for clinically HER2-positive disease. This study has identified additional somatic mutations that represent potential therapeutic targets within this group, including
- a high frequency of PIK3CA mutations (39%)
- a lower frequency of PTEN and PIK3R1 mutations (Supplemental Table 6)
- genomic losses of PTEN and INPP4B.
Other possible druggable mutations included variants within HER-family members including two somatic mutations in HER2, two within HER1/EGFR, and five within HER3.
Pertuzumab, in combination with Trastuzumab, targets the HER2-HER3 heterodimer48, however, these data suggest that targeting HER1 with HER2 could also be beneficial. Lastly, the HER2E-mRNA-subtype typically showed high aneuploidy, the highest somatic mutation rate (Table 1), and DNA amplification of other potential therapeutic targets including FGFRs, HER1/EGFR, CDK4 and Cyclin D1.