Abstract 2910: Multi-sites rapid-autopsy data reveals aggressive metastatic colonization and metastasis phenotypes

Metastatic breast cancer is a deadly disease with low 5-year survival rate (22%). Because it is extremely difficult to track metastatic spread in a living patient, the patterns of new organ colonization are currently poorly understood. In this study, we have collected tumor biopsies at initial diagnosis and at mastectomy necessitated by the patient’s relapse, and autopsies from twenty-six metastatic tumors across seven organs and two skin tissues as normal controls via a rapid autopsy procedure within hours after the patient’s death. All samples were subjected to 60X Illumina whole genome sequencing and bulk RNA sequencing. We used copy number variation (CNV) and short variant (SNP, INDEL) data to reconstruct the phylogenetic relationships among the tumor samples, and established how the tumor evolved at the subclone level across different metastatic sites, using our SubcloneSeeker algorithm. We selected tumor samples with the lowest normal tissue contamination for transcriptomic analysis. Differentially expressed gene and pathways were identified from RNA-seq data. Our analysis revealed that the cancer first escaped to the lung, an event that occurred before the time of initial diagnosis. This was followed by four distinct ‘waves’ (G1, G2, G3 and G4) of massive metastatic expansion, beginning with the abdominal organs (involving samples in G1), then the lymph nodes (G2 and G4), brain and bones (G3). We see clear evidence for metastatic “recolonization” where further evolved subclones invaded already established, earlier metastatic sites. Subclone analysis also revealed a bifurcating pattern of evolution in the primary tumor, in which two lineages gave rise to the G1 and G2-G4 metastases respectively. Consistent with the genomic findings, unsupervised clustering based on the gene expression data showed that samples in G1, and samples in G2-G4 formed distinct clusters. Comparing gene expression profiles between G1 (n=4) and G3 (n=9) samples showed that samples in G1 exhibited enrichment in Integrin activation pathways and samples in G3 presented a signature for chromosome 17 amplification. These distinct metastatic phenotypes indicate different survival mechanisms for G1 and G3 metastatic tumors. The high number of sampled sites in this study, 30 in all, allowed us to reconstruct the evolution of the disease in this patient with unprecedented resolution, identify novel patterns of metastatic colonization, and identify distinct metastatic phenotypes. This study suggests the need for more comprehensive collection and evaluation of metastatic sites to ensure that therapies chosen to target specific genomic aberrations are able to combat the tumor at all metastatic sites. Citation Format: Xiaomeng Huang, Yi Qiao, Samuel W. Brady, Adam Cohen, Andrea H. Bild, Gabor T. Marth. Multi-sites rapid-autopsy data reveals aggressive metastatic colonization and metastasis phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2910.