MBCproject: multi-omic profiling of metastatic breast cancer evolution through patient-partnered research

The Metastatic Breast Cancer project (MBCproject) is a patient-partnered research study that has collected clinical, genomic, and survey data through online enrollment. The cohort includes whole exome sequencing from 379 tumor biopsies (bxs) with matched germline from 301 patients (pts) and RNA-seq from 200 bxs (141 pts). In addition to confirming prior observations, this multi-omics cohort has enabled the discovery of novel MBC characteristics. Tumor evolutionary analysis was performed for 56 pts with multiple bxs from different timepoints and sites (115 bxs). Acquired ESR1 mutations were observed in six pts, all of whom received endocrine therapy between bxs. Mutations in TP53 , GATA3 , and PTEN were almost always truncal. However, mutations in PIK3CA , CDH1 , and KMT2C exhibited complex clonal dynamics with gain/loss events across paired bxs, contrary to the common assumption that such mutations are truncal. For pts with distinct CDH1 mutant status across bxs, the presence of CDH1 mutations at the bx level is associated with lobular histology (ILC), and the lack of CDH1 mutations is associated with ductal histology (IDC). The cohort includes three pts with bilateral breast cancers, which we found to be phylogenetically unrelated. Only one pt harbored a pathogenic germline mutation ( CHEK2 ). In one pt, bilateral bxs had distinct histology yet shared copy number variations (CNVs) such as 1q gain and 6q loss. In another, left and right ILCs had distinct PIK3CA and CDH1 mutations and dissimilar CNV profiles. The shared altered genes and CNVs from independent tumors in the same pt suggest convergent evolution through tumorigenesis. To further explore evolution over disease progression, we compared treatment-naive primary and treatment-exposed metastatic bxs in the full cohort. TBX3 mutations were enriched in metastatic bxs (p=0.024, FDR<0.25), driven by higher prevalence in HR+/HER2- and HER2+ subtypes, and co-occurred with CDH1 (p=0.0016) and ERBB2 oncogenic mutations (p=0.039). All MBCproject TBX3 - ERBB2 mutant bxs were from pts with ILC and had CDH1 mutations. MSK IMPACT confirmed TBX3 - CDH1 (p=4.4e-8) and TBX3 - ERBB2 (p=6.1e-5) co-occurrence and showed TBX3 - ERBB2 mutations also co-occurred in IDC bxs without CDH1 mutations (p=9.2e-4), suggesting that TBX3 - ERBB2 mutations are independent of ILC and CDH1 status. TBX3 -only mutant bxs had a proliferation RNA-seq signature score higher than Luminal A bxs (p=0.032 MBCproject, p=0.0047 TCGA) and more similar to that of IDC than ILC tumors. Overall, this indicates that TBX3 mutations drive distinct tumor behavior independent of histology and CDH1 alterations. The MBCproject demonstrates the power of patient-partnered research and multi-omics evolutionary analysis to uncover novel insights into metastatic breast cancer biology.