Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component

Abstract

Purpose: Although most human cancers display a single histology, there are unusual cases where two or more distinct tissue types present within a primary tumor. One such example is metaplastic breast carcinoma, a rare but aggressive cancer with a heterogeneous histology, including squamous, chondroid, and spindle cells. Metaplastic carcinomas often contain an admixed conventional ductal invasive or in situ mammary carcinoma component, and are typically triple-negative for estrogen receptor, progesterone receptor, and HER-2 amplification/overexpression. An unanswered question is the origin of metaplastic breast cancers. While they may arise independently from their ductal components, their close juxtaposition favors a model that postulates a shared origin, either as two derivatives from the same primary cancer or one histology as an outgrowth of the other. Understanding the mechanism of development of these tumors may inform clinical decisions.Experimental Design: We performed exome sequencing for paired metaplastic and adjacent conventional invasive ductal carcinomas in 8 patients and created a pipeline to identify somatic variants and predict their functional impact, without having normal tissue. We then determined the genetic relationships between the histologically distinct compartments.Results: In each case, the tumor components have nearly identical landscapes of somatic mutation, implying that the differing histologies do not derive from genetic clonal divergence.Conclusions: A shared origin for tumors with differing histologies suggests that epigenetic or noncoding changes may mediate the metaplastic phenotype and that alternative therapeutic approaches, including epigenetic therapies, may be required for metaplastic breast cancers. Clin Cancer Res; 23(16); 4875-84. ©2017 AACR.

Figure 1. Models of intratumoral heterogeneity

Mechanism A: The metaplastic and conventional ductal carcinoma components may arise from independent primary tumors. This trajectory would result in shared germline variants but few, if any, shared somatic variants in any impact category. Mechanism B: The metaplastic and conventional ductal carcinoma components arise from different subclones in the same primary tumor. This would result in shared high impact alleles (potential driver mutations), but minimal overlap in low impact alleles. Mechanism C: The metaplastic and conventional ductal carcinoma components appear as different phenotypes but share a genotype, as they are derived from a single clone. In this model, the ductal and metaplastic cells share both the high impact and low impact alleles, as well as copy number variation structure and subclone architecture.

Figure 2. Clinical and pathologic characteristics

(a) Clinicopathologic characteristics of eight patients with metaplastic breast carcinoma containing both metaplastic and conventional invasive ductal components. (b-c) Paired samples from one patient's tumor (Patient F) contain regions of high grade invasive ductal carcinoma (b) with an adjacent metaplastic component showing chondroid differentiation (c). (d-e) Paired samples from a second patient's tumor (Patient A) contain regions of high grade invasive ductal carcinoma (d) with an adjacent metaplastic component showing spindled and pleomorphic differentiation (e).

Figure 3. Copy number variation (CNV) for metaplastic (MC) and invasive ductal carcinoma (IDC) are similar

A.CNV plots for patients B and C. Copy number in IDC component is on the outer ring, MC is on the inner ring. B. Pearson correlation coefficients for copy number profiles of all 16 samples sequenced.

Figure 4. Variants shared by paired metaplastic (MC) and invasive ductal carcinoma (IDC), represented by one stacked bar per patient

Variants are separated by dbSNP and non-dbSNPs of high, moderate, and low impact. The proportion of variants shared by the specimens is high in the dbSNP category, as expected, and relatively constant across the three stratifications of variant effect.

Figure 5. Allele frequencies are similar for variants in metaplastic (MC) and invasive ductal carcinoma (IDC) samples

Shown are representative plots from patient B, with canonical mutations highlighted. X and Y axis represent allelic frequencies for MC and IDC components, respectively.

Figure 6. Subclone analysis reveals nearly identical structure in the metaplastic (MC) and conventional invasive ductal carcinoma (IDC) components

Shown are representative examples from Patient B. (a) Variants shared by the MC and IDC components are assigned to subclones (designated by different colors and shapes) and suggest nearly identical population architecture. (b) Variant allele frequency plots show the same striking shared allele frequencies when restricted to copy number neutral (diploid) regions of the genomes. In this case, skewing of the allele frequencies around 0.5 may reflect either differential normal contamination or an evolutionary process. X and Y axis represent allelic frequencies for MC and IDC components, respectively.