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

Abstract

Background 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. Methods We 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. Results We 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. Conclusions Acute 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.

Molecular Crosstalk between T Cells and Tumor Uncovers GBM-Specific T Cell Signatures in Blood: Noninvasive GBM Diagnosis Using Immunosensors

“…Therefore, understanding T cells’ interaction and crosstalk mechanism with tumors is a critical step in using T cells to diagnose GBM. To understand the tumor heterogeneity of glioblastoma and the immunological landscape here, we have used the single-cell RNA sequencing (scRNA-seq) from the cancer single-cell expression map (CancerSCEM) database , ( Figure ). scRNA-seq from tissue biopsy given in GBM-019-05-1D is studied using the uniform manifold approximation and projection (UMAP) analysis, which illustrates the cell composition from the tumor microenvironment displaying clusters of individual cell type populations in the TME.…”

TGFBI secreted by tumor-associated macrophages promotes glioblastoma stem cell-driven tumor growth via integrin αvβ5-Src-Stat3 signaling

“…(A) Venn diagram demonstrating the overlapping of three datasets, GSE37475 (207 genes upregulated in M2-like TAMs) 15 , macrophage cell enhanced genes and genes encoding for secreted proteins from the Human Protein Atlas ( http://www.proteinatlas.org ), comprised three genes: AOAH, TGFBI, TIMP1. (B) t-SNE analysis of 111397 cells of seven glioma patients (GSE148842) 72 . Differential coloring in cell clusters was annotated according to the dominant cell type (left).…”

Functional Precision Oncology: The Next Frontier to Improve Glioblastoma Outcome?

“…Currently, every patient diagnosed with GBM is profiled using a uniformed diagnostic procedure, consisting of MRI scans and “static” measurements of pathological trademark alterations, such as chromosomal rearrangements, mutational patterns and MGMT promotor methylation ( Figure 1 ). Functional testing gives the opportunity to directly evaluate therapy efficacy, either in dissociated GBM samples or tumor tissue slices [ 31 ]. In order to predict tumor cell behavior in such a complex and dynamic system as the GBM/brain, one must first familiarize with the baseline features (mutational status, transcripts, proteins/protein modifications, metabolites) and interactions between these components (gene–RNA, RNA–protein, protein–protein) across various cellular states [ 6 , 32 ].…”

“…Hence, the ideal model for rapid functional assessment of drug sensitivity in GBM would be a system which maximally preservers the native cellular integrity [ 40 ] and interaction of the tumor cells with the microenvironment [ 46 ]. This includes ex-vivo drug treatment of tumor slices [ 31 ] or cellular suspensions of freshly dissociated patients’ biopsies within hours post-surgery. Regarding GBM’s extensive heterogeneity and invasiveness, one must consider sampling from distinct tumor regions in order to gain an “as close as possible” perspective of the therapeutic vulnerabilities of the invading cells that are remaining after tumor debulking.…”