Triple Negative Breast Neoplasms study with RNA-Seq, Targeted-Capture + 1 more data on dbGaP (4 participants)

phs001742 — Clonal Mapping of Multi-Organ Metastasis and Chemoresistance in Triple    Negative Breast cancer

<p>Clonal dynamics during metastasis were studied in two patient-derived xenograft (PDX) models established from treatment-naive primary breast tumors from TNBC patients diagnosed with concurrent metastatic disease. Genomic sequencing and barcode-mediated clonal tracking revealed robust alterations in clonal architecture between primary tumors and metastases. Polyclonal seeding and maintenance of low-abundance subclones was observed in each metastatic lesion examined. Lung, liver, and brain metastases were enriched for an identical population of subclones. Clones dominating multi-organ metastases shared a genomic lineage. Thus, properties of rare mammary tumor subclones enabled the seeding and colonization of metastases in multiple secondary organ sites.</p> <p>In this study, patient-derived xenograft (PDX) models of treatment-naive TNBC and serial biopsies from TNBC patients undergoing NACT were used to elucidate mechanisms of chemoresistance in the neoadjuvant setting. Barcode-mediated clonal tracking and genomic sequencing of PDX tumors revealed that residual tumors remaining after chemotherapy maintained the subclonal architecture of untreated tumors yet their transcriptomes, proteomes, and histologic features were distinct from those of untreated tumors. Once treatment was halted, residual tumors gave rise to chemotherapy-sensitive tumors with similar transcriptomes, proteomes, and histological features to those of untreated tumors. Taken together, these results demonstrated that tumors can adopt a reversible drug-tolerant state that does not involve clonal selection as a chemotherapy resistance mechanism. Serial biopsies obtained from patients with TNBC undergoing NACT revealed similar histologic changes as well as maintenance of stable subclonal architecture, demonstrating that PDXs capture molecular features characteristic of human TNBC chemoresistance. </p>