Somatic mutations and cell identity linked by Genotyping of Transcriptomes

Nature. 2019 Jul;571(7765):355-360. doi: 10.1038/s41586-019-1367-0. Epub 2019 Jul 3.


Defining the transcriptomic identity of malignant cells is challenging in the absence of surface markers that distinguish cancer clones from one another, or from admixed non-neoplastic cells. To address this challenge, here we developed Genotyping of Transcriptomes (GoT), a method to integrate genotyping with high-throughput droplet-based single-cell RNA sequencing. We apply GoT to profile 38,290 CD34+ cells from patients with CALR-mutated myeloproliferative neoplasms to study how somatic mutations corrupt the complex process of human haematopoiesis. High-resolution mapping of malignant versus normal haematopoietic progenitors revealed an increasing fitness advantage with myeloid differentiation of cells with mutated CALR. We identified the unfolded protein response as a predominant outcome of CALR mutations, with a considerable dependency on cell identity, as well as upregulation of the NF-κB pathway specifically in uncommitted stem cells. We further extended the GoT toolkit to genotype multiple targets and loci that are distant from transcript ends. Together, these findings reveal that the transcriptional output of somatic mutations in myeloproliferative neoplasms is dependent on the native cell identity.

MeSH terms

  • Animals
  • Antigens, CD34 / metabolism
  • Calreticulin / genetics
  • Cell Line
  • Cell Proliferation
  • Clone Cells / classification
  • Clone Cells / metabolism
  • Clone Cells / pathology
  • Endoribonucleases / metabolism
  • Genotype*
  • Hematopoiesis / genetics
  • Hematopoietic Stem Cells / classification
  • Hematopoietic Stem Cells / metabolism
  • Hematopoietic Stem Cells / pathology
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Mice
  • Models, Molecular
  • Mutation*
  • Myeloproliferative Disorders / classification
  • Myeloproliferative Disorders / genetics*
  • Myeloproliferative Disorders / pathology*
  • NF-kappa B / metabolism
  • Neoplasms / classification
  • Neoplasms / genetics*
  • Neoplasms / pathology*
  • Neoplastic Stem Cells / cytology
  • Neoplastic Stem Cells / metabolism
  • Neoplastic Stem Cells / pathology
  • Primary Myelofibrosis / genetics
  • Primary Myelofibrosis / pathology
  • Protein Serine-Threonine Kinases / metabolism
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis / methods
  • Transcriptome / genetics*
  • Unfolded Protein Response / genetics


  • Antigens, CD34
  • CALR protein, human
  • Calreticulin
  • NF-kappa B
  • ERN1 protein, human
  • Protein Serine-Threonine Kinases
  • Endoribonucleases