Consortium, I. | Search bioRxiv

bioRxiv2020

Highly multiplexed molecular and cellular mapping of breast cancer tissue in three dimensions using mass tomography.

A holistic understanding of tissue and organ structures and their functions requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) makes possible the detection of up to 40 antigens and specific nucleic acids simultaneously using metal-tagged antibodies or nucleic acid probes, respectively, but has so far been restricted to two-dimensional imaging. To enable use of IMC for 3D tissue analyses, we developed mass tomography, which combines quasi deformation-free serial sectioning with novel computational methods. We utilized mass tomography to analyze a breast cancer sample. The resulting 3D representation reveals spatial and cellular heterogeneity, preferential cell-to-cell interactions, detailed tissue-architecture motifs, and the unique microenvironment of a micro-invasion, where micro-metastases clonality is examined, showing that cells arising from the same invasive area, displaying very distinct phenotypes, are all able to produce initial invasive lesions. Mass tomography will provide invaluable insights into the tissue microenvironment, cellular neighborhoods, and tissue organization.

cell biology↗

bioRxiv2020

Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer

Tumour fitness landscapes underpin selection in cancer, impacting etiology, evolution and response to treatment. Progress in defining fitness landscapes has been impeded by a lack of timeseries perturbation experiments over realistic intervals at single cell resolution. We studied the nature of clonal dynamics induced by genetic and pharmacologic perturbation with a quantitative fitness model developed to ascribe quantitative selective coefficients to individual cancer clones, enable prediction of clone-specific growth potential, and forecast competitive clonal dynamics over time. We applied the model to serial single cell genome (>60,000 cells) and transcriptome (>58,000 cells) experiments ranging from 10 months to 2.5 years in duration. We found that genetic perturbation of TP53 in epithelial cell lines induces multiple forms of copy number alteration that confer increased fitness to clonal populations with measurable consequences on gene expression. In patient derived xenografts, predicted selective coefficients accurately forecasted clonal competition dynamics, that were validated with timeseries sampling of experimentally engineered mixtures of low and high fitness clones. In cisplatin-treated patient derived xenografts, the fitness landscape was inverted in a time-dependent manner, whereby a drug resistant clone emerged from a phylogenetic lineage of low fitness clones, and high fitness clones were eradicated. Moreover, clonal selection mediated reversible drug response early in the selection process, whereas late dynamics in genomically fixed clones were associated with transcriptional plasticity on a fixed clonal genotype. Together, our findings outline causal mechanisms with implication for interpreting how mutations and multi-faceted drug resistance mechanisms shape the etiology and cellular fitness of human cancers.

cancer biology↗