Genetic pathways regulating hematopoietic lineage speciation: Factorial latent variable model analysis of single cell transcriptome

Abstract

Genetic pathways regulating hematopoietic lineage commitment at critical stages of development remain incompletely characterized. To better delineate genetic sources of variability regulating cellular speciation during steady-state hematopoiesis, we applied a factorial single-cell latent variable model (f-scLVM) to decompose single-cell transcriptome heterogeneity into interpretable biological factors (refined pathway annotations or gene sets without annotation) dynamically regulating cell fate. Hematopoietic single cell transcriptomic raw sequencing data extracted from 1,920 hematopoietic stem and progenitor cells (HSPCs) derived from 12-week-old female mice were used for data analysis and model development. These single cell RNA sequencing data were subsequently analyzed using the factorial single-cell latent variable model (f-scLVM), with their heterogeneity decomposed into interpretable biological factors. The top biological factors underlying the basal hematopoiesis were subsequently identified for the aggregate, and lineage-restricted (myeloid, megakaryocyte, erythroid) progenitor cells. For a subset of factors, data were independently verified experimentally in a companion research paper [1]. These data facilitate the identification of novel subpopulations and adjust gene sets to discover new marker genes and hidden confounding factors driving basal hematopoiesis.

Keywords

• Single-cell RNA sequencing analysis
• Pathway annotation
• Factor analysis
• Spatial reconstruction