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Genotyping of Transcriptomes (GoT) profiles cancer cell transcriptomes by integrating genotyping with single-cell RNA sequencing. This method reveals how CALR mutations impact blood cell development in myeloproliferative neoplasms.

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Area of Science:

  • Genomics
  • Hematology
  • Molecular Biology

Background:

  • Distinguishing malignant cells from normal cells is difficult without specific surface markers.
  • Somatic mutations in myeloproliferative neoplasms (MPNs) disrupt normal blood cell development (hematopoiesis).

Purpose of the Study:

  • To develop a method integrating genotyping with single-cell RNA sequencing to define transcriptomic identities of malignant cells.
  • To investigate the impact of CALR mutations on human hematopoiesis at single-cell resolution.

Main Methods:

  • Developed Genotyping of Transcriptomes (GoT), a novel method combining genotyping with droplet-based single-cell RNA sequencing.
  • Applied GoT to profile 38,290 CD34+ cells from patients with CALR-mutated MPNs.
  • Extended GoT to genotype multiple targets and loci distant from transcript ends.

Main Results:

  • Identified an increasing fitness advantage with myeloid differentiation in cells with mutated CALR.
  • Revealed the unfolded protein response as a predominant outcome of CALR mutations, dependent on cell identity.
  • Observed upregulation of the NF-κB pathway specifically in uncommitted stem cells.

Conclusions:

  • The transcriptional consequences of somatic mutations in MPNs are cell identity-dependent.
  • GoT provides a powerful tool for dissecting cellular heterogeneity and the impact of mutations in complex biological systems.