Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment

Genome Biol. 2015 Apr 3;16(1):66. doi: 10.1186/s13059-015-0636-y.

Abstract

Background: To understand the heterogeneous behaviors of individual cancer cells, it is essential to investigate gene expression levels as well as their divergence between different individual cells. Recent advances in next-generation sequencing-related technologies have enabled us to conduct a single-cell RNA-Seq analysis of a series of lung adenocarcinoma cell lines.

Results: We analyze a total of 336 single-cell RNA-Seq libraries from seven cell lines. The results are highly robust regarding both average expression levels and the relative gene expression differences between individual cells. Gene expression diversity is characteristic depending on genes and pathways. Analyses of individual cells treated with the multi-tyrosine kinase inhibitor vandetanib reveal that, while the ribosomal genes and many other so-called house-keeping genes reduce their relative expression diversity during the drug treatment, the genes that are directly targeted by vandetanib, the EGFR and RET genes, remain constant. Rigid transcriptional control of these genes may not allow plastic changes of their expression with the drug treatment or during the cellular acquisition of drug resistance. Additionally, we find that the gene expression patterns of cancer-related genes are sometimes more diverse than expected based on the founder cells. Furthermore, we find that this diversity is occasionally latent in a normal state and initially becomes apparent after the drug treatment.

Conclusions: Characteristic patterns in gene expression divergence, which would not be revealed by transcriptome analysis of bulk cells, may also play important roles when cells acquire drug resistance, perhaps by providing a cellular reservoir for gene expression programs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenocarcinoma / genetics*
  • Adenocarcinoma / metabolism
  • Adenocarcinoma of Lung
  • Cell Line, Tumor
  • Cytoskeletal Proteins / genetics
  • Cytoskeletal Proteins / metabolism
  • Drug Delivery Systems / methods
  • ErbB Receptors / genetics
  • ErbB Receptors / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Genes, Essential
  • Humans
  • Lung Neoplasms / genetics*
  • Lung Neoplasms / metabolism
  • Molecular Targeted Therapy / methods*
  • Piperidines / pharmacology
  • Protein Kinase Inhibitors / pharmacology
  • Proto-Oncogene Proteins c-ret / genetics
  • Proto-Oncogene Proteins c-ret / metabolism
  • Quinazolines / pharmacology
  • RNA / genetics
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • Transcriptome

Substances

  • CCDC6 protein, human
  • Cytoskeletal Proteins
  • Piperidines
  • Protein Kinase Inhibitors
  • Quinazolines
  • RNA
  • EGFR protein, human
  • ErbB Receptors
  • Proto-Oncogene Proteins c-ret
  • RET protein, human
  • N-(4-bromo-2-fluorophenyl)-6-methoxy-7-((1-methylpiperidin-4-yl)methoxy)quinazolin-4-amine