Analyze lineage commitment during human hematopoiesis using somatic mitochondrial mutations

Abstract

Lineage tracing is a crucial method to provide insights into the evolving landscape of progenitor potential during lineage commitment in human hematopoiesis. A deeper understanding of the hematopoietic process can have promising clinical implications for the development of immune therapies where the composition of the immune system needs to be altered. Numerous lineage tracing techniques which introduce genetic modifications have been employed in model systems. Approaches in humans usually require the detection of somatic mutations in nuclear or mitochondrial DNA at single-cell level. Here, we perform retrospective lineage tracing by detecting somatic mitochondrial mutations in single-cell sequencing data, and use them as natural genetic barcode to link genetic regulators of hematopoietic stem and progenitor cells (HSPCs) to cell fate in PBMCs. We employ previously published scATAC-seq data from two replicates of CD34+ HSPCs and two replicates of PBMCs from the same donor with a three months time interval, to identify mitochondrial variants. Lineages biased clones were quantified with a chi-squared test, and differentially expressed genes and enriched pathways were inferred. In contrast with previously published results, we observed clones with a significant bias towards the lymphoid, myeloid, and HSC self-renewal lineage. However, regulatory networks of these clones showed minimal overlap between the replicates, indicating uncertainty in the results. Despite this uncertainty, the observation of lineage biased clones provide an opportunistic perspective for the suitability of mitochondrial mutations for lineage tracing.