Case Report - 16 Year Life History and Genomic Evolution of an ER+ HER2- Breast Cancer

Bing Xu, Anu Amallraja, Padmapriya Swaminathan, Rachel Elsey, Christel Davis, Stephanie Theel, Sarah Viet, Jason Petersen, Amy Krie, Gareth Davies, Casey B Williams, Erik Ehli, Tobias Meissner
Cold Spring Harbor Molecular Case Studies 2020 October 2
Metastatic breast cancer is one of the leading causes of cancer related death in women. Limited studies have been done on the genomic evolution between primary and metastatic breast cancer. We reconstructed the genomic evolution through the sixteen year history of an ER+ HER2- breast cancer patient to investigate molecular mechanisms of disease relapse and treatment resistance after long term exposure to hormonal therapy. Genomic and transcriptome profiling was performed on primary breast tumor (2002), initial recurrence (2012) and liver metastasis (2015) samples. Cell free DNA analysis was performed at eleven timepoints (2015-2017). Mutational analysis revealed a low mutational burden in the primary tumor which doubled at the time of progression, with driver mutations in PI3K-Akt and RAS-RAF signaling pathways. Phylogenetic analysis showed an early branching off between primary tumor and metastasis. Liquid biopsies, while initially negative, started to detect an ESR1 E380Q mutation in 2016 with increasing allele frequency till end of 2017. Transcriptome analysis revealed 721 (193 up, 528 down) genes to be differentially expressed between primary tumor and first relapse. Most significantly down-regulated genes were TFF1 and PGR, indicating resistance to AI therapy. Most up-regulated genes included PTHLH, S100P, and SOX2 promoting tumor growth and metastasis. This phylogenetic reconstruction of the life history of a single patient's cancer as well as monitoring tumor progression through liquid biopsies allowed for uncovering the molecular mechanisms leading to initial relapse, metastatic spread and treatment resistance.

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