Single-cell mitochondrial variant enrichment resolved clonal tracking and spatial architecture in human embryonic hematopoiesis

Abstract

AbstractThe ability to perform lineage tracing at the single-cell level is critical to reconstructing dynamic transitions during cell differentiation. However, prospective tracing approaches inevitably encounter outstanding challenges including barcoding precision, barcode diversity, and detection efficiency, which can skew inferred lineage relationships. Human pluripotent stem cells (hPSC) even face risks of DNA-damage-induced toxicity-related cell death. We explored the use of naturally occurring somatic mutations in mitochondrial transcripts detected in single-cell RNA-seq as genetic lineage barcodes in HPSC. In this study, we used an enrichment of scRNA-seq mitochondrial reads and a robust computational method to identify clonally relevant mitochondrial variants as endogenous genetic barcodes for clonal tracking of early embryonic hematopoiesis from hPSC. We modeled the development of embryonic tissues from hPSCs and delineated the ontogeny of hematopoietic cells by mitochondrial variant lineage tracing. We identified multiple waves of erythropoiesis in time-series scRNA-seq data. We further applied mitochondrial variant lineage tracing to spatial transcriptomics and identified the clonal development of both erythro-myeloid progenitors and their niche cells. Our study highlights the power of mitochondrial variants as an endogenous marker for clonal tracking in modeling human development from stem cells.