Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq

Wenting Zhao,Marc L Otten,Hanna Mendes Levitin,Michael B Sisti,Peter Canoll,Eleonora Francesca Spinazzi,Pavan Upadhyayula,Matei Alexandru Banu,Tamara Marie,Jeffrey N Bruce,Athanassios Dovas,Tejaswi Sudhakar,Peter A Sims

doi:10.1186/s13073-021-00894-y

Wenting Zhao, Marc L Otten + Show 11 more

Open Access

https://doi.org/10.1186/s13073-021-00894-y

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Abstract

BackgroundPreclinical studies require models that recapitulate the cellular diversity of human tumors and provide insight into the drug sensitivities of specific cellular populations. The ideal platform would enable rapid screening of cell type-specific drug sensitivities directly in patient tumor tissue and reveal strategies to overcome intratumoral heterogeneity.MethodsWe combine multiplexed drug perturbation in acute slice culture from freshly resected tumors with single-cell RNA sequencing (scRNA-seq) to profile transcriptome-wide drug responses in individual patients. We applied this approach to drug perturbations on slices derived from six glioblastoma (GBM) resections to identify conserved drug responses and to one additional GBM resection to identify patient-specific responses.ResultsWe used scRNA-seq to demonstrate that acute slice cultures recapitulate the cellular and molecular features of the originating tumor tissue and the feasibility of drug screening from an individual tumor. Detailed investigation of etoposide, a topoisomerase poison, and the histone deacetylase (HDAC) inhibitor panobinostat in acute slice cultures revealed cell type-specific responses across multiple patients. Etoposide has a conserved impact on proliferating tumor cells, while panobinostat treatment affects both tumor and non-tumor populations, including unexpected effects on the immune microenvironment.ConclusionsAcute slice cultures recapitulate the major cellular and molecular features of GBM at the single-cell level. In combination with scRNA-seq, this approach enables cell type-specific analysis of sensitivity to multiple drugs in individual tumors. We anticipate that this approach will facilitate pre-clinical studies that identify effective therapies for solid tumors.

Highlights

Preclinical studies require models that recapitulate the cellular diversity of human tumors and provide insight into the drug sensitivities of specific cellular populations
Acute slice cultures are an attractive approach to modeling drug response in solid tumors because multiple cultures can be rapidly generated from a single surgical specimen, and they do not require extensive culturing or manipulation, which leads to distortion of the native composition of the tissue, selection, and loss of heterogeneity by diluting populations that do not proliferate rapidly [1,2,3]
With the drug-treated slice cultures where we expect increased cell death, is whether there are elevated levels of ambient mRNA in the scRNA-seq profiles. We examined this by comparing the coverage of cell-identifying barcodes assigned to cells to those assigned to ambient RNA using EmptyDrops as described above and found that drug-treatment did not result in significantly increased background (Additional File 1: Fig. S2)

Summary

Introduction

Preclinical studies require models that recapitulate the cellular diversity of human tumors and provide insight into the drug sensitivities of specific cellular populations. The ideal platform would enable rapid screening of cell type-specific drug sensitivities directly in patient tumor tissue and reveal strategies to overcome intratumoral heterogeneity. While scRNA-seq can determine the cellular composition of complex tumors and even reveal cell type-specific drug sensitivities, these measurements are limited by models of drug response. Acute slice cultures are an attractive approach to modeling drug response in solid tumors because multiple cultures can be rapidly generated from a single surgical specimen, and they do not require extensive culturing or manipulation, which leads to distortion of the native composition of the tissue, selection, and loss of heterogeneity by diluting populations that do not proliferate rapidly [1,2,3]. Screens were completed within 24 h of surgery and analyzed immediately by scRNA-seq using our scalable microwell platform [13, 14] to deconvolve cell type-specific responses to multiple drugs (Fig. 1a)

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