Abstract P1-05-04: Intra-tumor genetic heterogeneity and histologic heterogeneity within metaplastic breast cancers: Genotypic-phenotypic correlations
Authors: Geyer FC , Burke KA , Papanastatiou AD , Macedo GS , Brogi E , Norton L , Wen YH , Weigelt B , Reis-Filho JS 
Published: March 2017

Abstract
Introduction: Metaplastic breast carcinoma (MBC) is characterized by the presence of neoplastic cells displaying squamous and/or mesenchymal differentiation. Morphologic intra-tumor heterogeneity is frequent in MBCs and reported to be reflected at the transcriptomic level: whilst squamous and chondroid MBCs are preferentially of basal-like subtype, spindle cell MBCs are of claudin-low subtype. Likewise, histologically distinct components within MBCs have been shown to display distinct focal copy number alterations. Here we sought to investigate whether histologically distinct components within MBCs would be underpinned by different mutational profiles and mutational signatures.
Methods: Ten MBCs with two histologically distinct components (spindle, chondroid, osseous, squamous and/ or ductal) were retrieved from the Department of Pathology of the authors' institution. The distinct components of each case and, in two cases, two regions of the same component were separately microdissected. DNA extracted from tumor samples (n=22) and matched normal tissues was subjected to whole-exome sequencing. Somatic genetic alterations were identified using state-of-the-art bioinformatics algorithms. Somatic mutations were classified as clonal (i.e., present virtually in all tumor cells) or subclonal using ABSOLUTE and FACETS. Mutational signatures were defined using non-negative matrix factorization.
Results: Medians of 146 (56-290) somatic mutations and 108 non-synonymous somatic mutations (39-222) per tumor component were identified. The histologically distinct components of each case harbored identical clonal TP53 mutations. Additional recurrent mutations in cancer genes included those affecting PI3K pathway genes (PIK3CA, 2 cases; PIK3R1, 2 cases). Shared mutations between components of each case ranged from 34% to 99% of all mutations, with a median of 84%, of which 24% (12%-53%) were truncal (i.e., shared by and clonal in both components). Private mutations (i.e., found in only one component) ranged from 1% to 66%, with a median of 16%, of which 72% (0-100%) were non-synonymous and 1% (0-52%) were clonal. In two cases, the comparison of two histologically similar regions revealed less heterogeneity, with 94% (87%-100%) of shared mutations, whereas in these samples the median of private mutations was 6% (0-13%), of which 70% (0-100%) were non-synonymous and none were clonal. Private non-synonymous mutations affecting cancer genes included those in PIK3R1, MED12 and NOTCH1. The mutational signatures (e.g. aging or BRCA) were concordant between distinct components of each case; however, differences in the mutational signatures were observed between truncal somatic mutations and mutations restricted to individual components.
Conclusions: MBCs display substantial genetic intra-tumor heterogeneity, which is more overt between histologically distinct components than between regions of similar histology. Our data suggest a genotypic-phenotypic correlation and corroborate the notion that distinct components within MBCs, although clonally related, may be driven by distinct somatic genetic alterations.
Citation Format: Geyer FC, Burke KA, Papanastatiou AD, Macedo GS, Brogi E, Norton L, Wen YH, Weigelt B, Reis-Filho JS. Intra-tumor genetic heterogeneity and histologic heterogeneity within metaplastic breast cancers: Genotypic-phenotypic correlations [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-04.