Genomic Characterization of <i>de novo</i> Metastatic Breast Cancer.

Abstract

In contrast to recurrence after initial diagnosis of stage I-III breast cancer [recurrent metastatic breast cancer (rMBC)], <i>de novo</i> metastatic breast cancer (dnMBC) represents a unique setting to elucidate metastatic drivers in the absence of treatment selection. We present the genomic landscape of dnMBC and association with overall survival (OS). Targeted DNA sequencing (OncoPanel) was prospectively performed on either primary or metastatic tumors from 926 patients (212 dnMBC and 714 rMBC). Single-nucleotide variants, copy-number variations, and tumor mutational burden (TMB) in treatment-naïve dnMBC primary tumors were compared with primary tumors in patients who ultimately developed rMBC, and correlated with OS across all dnMBC. When comparing primary tumors by subtype, <i>MYB</i> amplification was enriched in triple-negative dnMBC versus rMBC (21.1% vs. 0%, <i>P</i> = 0.0005, <i>q</i> = 0.111). Mutations in <i>KMTD2, SETD2</i>, and <i>PIK3CA</i> were more prevalent, and <i>TP53</i> and <i>BRCA1</i> less prevalent, in primary HR⁺/HER2^- tumors of dnMBC versus rMBC, though not significant after multiple comparison adjustment. Alterations associated with shorter OS in dnMBC included TP53 (wild-type: 79.7 months; altered: 44.2 months; <i>P</i> = 0.008, <i>q</i> = 0.107), MYC (79.7 vs. 23.3 months; <i>P</i> = 0.0003, <i>q</i> = 0.011), and cell-cycle (122.7 vs. 54.9 months; <i>P</i> = 0.034, <i>q</i> = 0.245) pathway genes. High TMB correlated with better OS in triple-negative dnMBC (<i>P</i> = 0.041). Genomic differences between treatment-naïve dnMBC and primary tumors of patients who developed rMBC may provide insight into mechanisms underlying metastatic potential and differential therapeutic sensitivity in dnMBC. Alterations associated with poor OS in dnMBC highlight the need for novel approaches to overcome potential intrinsic resistance to current treatments.