Somatic mutations and cell identity linked by Genotyping of Transcriptomes.

TitleSomatic mutations and cell identity linked by Genotyping of Transcriptomes.
Publication TypeJournal Article
Year of Publication2019
AuthorsNam AS, Kim K-T, Chaligne R, Izzo F, Ang C, Taylor J, Myers RM, Abu-Zeinah G, Brand R, Omans ND, Alonso A, Sheridan C, Mariani M, Dai X, Harrington E, Pastore A, Cubillos-Ruiz JR, Tam W, Hoffman R, Rabadan R, Scandura JM, Abdel-Wahab O, Smibert P, Landau DA
Date Published2019 07
KeywordsAnimals, Antigens, CD34, Calreticulin, Cell Line, Cell Proliferation, Clone Cells, Endoribonucleases, Genotype, Hematopoiesis, Hematopoietic Stem Cells, High-Throughput Nucleotide Sequencing, Humans, Mice, Models, Molecular, Mutation, Myeloproliferative Disorders, Neoplasms, Neoplastic Stem Cells, NF-kappa B, Primary Myelofibrosis, Protein-Serine-Threonine Kinases, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptome, Unfolded Protein Response

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.

Alternate JournalNature
PubMed ID31270458
PubMed Central IDPMC6782071
Grant ListP01 CA108671 / CA / NCI NIH HHS / United States
U54 CA193313 / CA / NCI NIH HHS / United States
R01 HL145283 / HL / NHLBI NIH HHS / United States
R01 CA229902 / CA / NCI NIH HHS / United States
DP2 CA239065 / CA / NCI NIH HHS / United States