Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

• Published in: Genome Biology Vol. 16; no. 1; p. 127
• Main Authors: Kim, Kyu-Tae, Lee, Hye Won, Lee, Hae-Ock, Kim, Sang Cheol, Seo, Yun Jee, Chung, Woosung, Eum, Hye Hyeon, Nam, Do-Hyun, Kim, Junhyong, Joo, Kyeung Min, Park, Woong-Yang
• Format: Journal Article
• Language: English
• Published: England BioMed Central 19.06.2015
• Subjects: Adenocarcinoma; Adenocarcinoma - drug therapy; Adenocarcinoma - genetics; Adenocarcinoma - metabolism; Adenocarcinoma of Lung; Animals; Antineoplastic Agents - therapeutic use; Bioinformatics; Cancer therapies; Drug resistance; Drug Resistance, Neoplasm - genetics; Gene expression; Gene Expression Profiling; Genetic Heterogeneity; Genomes; Humans; Kinases; Lung cancer; Lung Neoplasms - drug therapy; Lung Neoplasms - genetics; Lung Neoplasms - metabolism; Lungs; Male; Mice; Middle Aged; Mutation; Patients; Phenotype; Population genetics; Prognosis; RNA, Messenger - chemistry; Sequence Analysis, RNA; Single-Cell Analysis; Tumor cells; Tumor Cells, Cultured; Tumors; Xenograft Model Antitumor Assays; Xenografts
• ISSN: 1465-6906; 1474-7596; 1474-760X; 1465-6906; 1465-6914
• DOI: 10.1186/s13059-015-0692-3

Intra-tumoral genetic and functional heterogeneity correlates with cancer clinical prognoses. However, the mechanisms by which intra-tumoral heterogeneity impacts therapeutic outcome remain poorly understood. RNA sequencing (RNA-seq) of single tumor cells can provide comprehensive information about gene expression and single-nucleotide variations in individual tumor cells, which may allow for the translation of heterogeneous tumor cell functional responses into customized anti-cancer treatments. We isolated 34 patient-derived xenograft (PDX) tumor cells from a lung adenocarcinoma patient tumor xenograft. Individual tumor cells were subjected to single cell RNA-seq for gene expression profiling and expressed mutation profiling. Fifty tumor-specific single-nucleotide variations, including KRAS(G12D), were observed to be heterogeneous in individual PDX cells. Semi-supervised clustering, based on KRAS(G12D) mutant expression and a risk score representing expression of 69 lung adenocarcinoma-prognostic genes, classified PDX cells into four groups. PDX cells that survived in vitro anti-cancer drug treatment displayed transcriptome signatures consistent with the group characterized by KRAS(G12D) and low risk score. Single-cell RNA-seq on viable PDX cells identified a candidate tumor cell subgroup associated with anti-cancer drug resistance. Thus, single-cell RNA-seq is a powerful approach for identifying unique tumor cell-specific gene expression profiles which could facilitate the development of optimized clinical anti-cancer strategies.