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Genetic Heterogeneity in Therapy-Naïve Synchronous Primary Breast Cancers and Their Metastases
Journal
Clinical cancer research
Volume
23
Number
15
Pages / Article-Number
4402-4415
Mesh terms
Adult; Bone Neoplasms, genetics, pathology, secondary; Breast Neoplasms, genetics, pathology; Class I Phosphatidylinositol 3-Kinases, genetics; Clonal Evolution, genetics; DNA Copy Number Variations, genetics; Epithelial-Mesenchymal Transition, genetics; Exome, genetics; Female; GATA3 Transcription Factor, genetics; Genetic Heterogeneity; Genomics; High-Throughput Nucleotide Sequencing; Humans; Liver Neoplasms, genetics, pathology, secondary; Middle Aged; Mutation; Neoplasm Metastasis, genetics, pathology; Tumor Suppressor Protein p53, genetics
Abstract
Purpose:; Paired primary breast cancers and metachronous metastases after adjuvant treatment are reported to differ in their clonal composition and genetic alterations, but it is unclear whether these differences stem from the selective pressures of the metastatic process, the systemic therapies, or both. We sought to define the repertoire of genetic alterations in breast cancer patients with; de novo; metastatic disease who had not received local or systemic therapy.; Experimental Design:; Up to two anatomically distinct core biopsies of primary breast cancers and synchronous distant metastases from nine patients who presented with metastatic disease were subjected to high-depth whole-exome sequencing. Mutations, copy number alterations and their cancer cell fractions, and mutation signatures were defined using state-of-the-art bioinformatics methods. All mutations identified were validated with orthogonal methods.; Results:; Genomic differences were observed between primary and metastatic deposits, with a median of 60% (range 6%-95%) of shared somatic mutations. Although mutations in known driver genes including; TP53, PIK3CA; , and; GATA3; were preferentially clonal in both sites, primary breast cancers and their synchronous metastases displayed spatial intratumor heterogeneity. Likely pathogenic mutations affecting epithelial-to-mesenchymal transition-related genes, including; SMAD4, TCF7L2; , and; TCF4; (; ITF2; ), were found to be restricted to or enriched in the metastatic lesions. Mutational signatures of trunk mutations differed from those of mutations enriched in the primary tumor or the metastasis in six cases.; Conclusions:; Synchronous primary breast cancers and metastases differ in their repertoire of somatic genetic alterations even in the absence of systemic therapy. Mutational signature shifts might contribute to spatial intratumor genetic heterogeneity.
