Novel temporal and spatial patterns of metastatic colonization from rapid-autopsy tumor biopsies

Huang, X.; Qiao, Y.; Brady, S. W.; Factor, R. E.; Downs-Kelly, E.; Farrell, A.; McQuerry, J. A.; Shrestha, G.; Jenkins, D. F.; Johnson, W. E.; Cohen, A. L.; Bild, A. H.; Marth, G. T.

doi:10.1101/2021.06.03.446803

bioRxiv · 10.1101/2021.06.03.446803

Novel temporal and spatial patterns of metastatic colonization from rapid-autopsy tumor biopsies

Huang, X.·Qiao, Y.·Brady, S. W.·Factor, R. E.·Downs-Kelly, E.·Farrell, A.·McQuerry, J. A.·Shrestha, G.·Jenkins, D. F.·Johnson, W. E.·Cohen, A. L.·Bild, A. H.·Marth, G. T.

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Abstract

BackgroundMetastatic breast cancer is a deadly disease with a low 5-year survival rate. Tracking metastatic spread in living patients is difficult, and thus poorly understood. ResultsVia rapid autopsy, we have collected 30 tumor samples over 3 timepoints and across 8 organs from a triple-negative metastatic breast cancer patient. The large number of sites sampled, together with deep whole genome sequencing and advanced computational analysis, allowed us to comprehensively reconstruct the tumors evolution at subclonal resolution. The most unique, previously not reported aspect of the tumors evolution we observed in this patient was the presence of "subclone incubators", i.e. already metastatic sites where substantial tumor evolution occurred before colonization of additional sites and organs by subclones that evolved at the incubator site. Overall, we identified four discrete waves of metastatic expansions, each of which resulted in a number of new, genetically similar metastasis sites that also enriched for particular organs (e.g. abdominal vs bone and brain). The lung played a critical role in facilitating metastatic spread in this patient: the lung was the first site of metastatic escape from the primary breast lesion; subclones at this site were the source of all four subsequent metastatic waves; and multiple sites in the lung acted as subclone incubators. Finally, functional annotation revealed that many known driver or metastasis-promoting tumor mutations in this patient were shared by some, but not all metastatic sites, highlighting the need for more comprehensive surveys of a patients metastases for effective clinical intervention. ConclusionsOur analysis revealed the presence of substantial tumor evolution at metastatic incubator sites, with potentially important clinical implications. Our study demonstrated that sampling of a large number of metastatic sites affords unprecedented detail for studying metastatic evolution.

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Huang, X., Qiao, Y., Brady, S. W., Factor, R. E., Downs-Kelly, E., Farrell, A., McQuerry, J. A., Shrestha, G., Jenkins, D. F., Johnson, W. E., Cohen, A. L., Bild, A. H., Marth, G. T.. 2021-06-03. Novel temporal and spatial patterns of metastatic colonization from rapid-autopsy tumor biopsies. https://doi.org/10.1101/2021.06.03.446803

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