Lung cancer is the leading cause of cancer deaths. Tumor heterogeneity, which hampers development of targeted therapies, was herein deconvoluted via single cell RNA sequencing in aggressive human adenocarcinomas (carrying Kras-mutations) and comparable murine model. We identified a tumor-specific, mutant-KRAS-associated subpopulation which is conserved in both human and murine lung cancer. We previously reported a key role for the oncogene BMI-1 in adenocarcinomas. We therefore investigated the effects of in vivo PTC596 treatment, which affects BMI-1 activity, in our murine model. Post-treatment, MRI analysis showed decreased tumor size, while single cell transcriptomics concomitantly detected near complete ablation of the mutant-KRAS-associated subpopulation, signifying the presence of a pharmacologically targetable, tumor-associated subpopulation. Our findings therefore hold promise for the development of a targeted therapy for KRAS-mutant adenocarcinomas.
Benzimidazoles/pharmacology , Carcinoma, Non-Small-Cell Lung/drug therapy , Epithelial Cells/drug effects , Lung Neoplasms/drug therapy , Mutation , Proto-Oncogene Proteins p21(ras)/genetics , Pyrazines/pharmacology , A549 Cells , Animals , Antineoplastic Agents , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Epithelial Cells/metabolism , Epithelial Cells/pathology , Humans , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Mice, Inbred NOD , Mice, SCID , Mice, Transgenic , Molecular Targeted Therapy , Polycomb Repressive Complex 1/genetics , Polycomb Repressive Complex 1/metabolism , Proto-Oncogene Proteins/genetics , Proto-Oncogene Proteins/metabolism , RNA-Seq , Single-Cell Analysis , Tumor Burden/drug effects , Xenograft Model Antitumor Assays
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.
Algorithms , Cell Nucleus/genetics , Genomics/methods , Neoplasms/genetics , RNA-Seq/methods , Single-Cell Analysis/methods , Adult , Animals , Cell Nucleus/chemistry , Cell Nucleus/metabolism , Child , Computational Biology/methods , Female , Freezing , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic , Humans , Mice , Mice, Knockout , Mice, Nude , Neoplasms/metabolism , Neoplasms/pathology , Sequence Analysis, RNA/methods , Tumor Cells, Cultured , Exome Sequencing/methods
