2. Academic Validation
  3. Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids

Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids

  • Adv Sci (Weinh). 2026 Jan 21:e18084. doi: 10.1002/advs.202518084.
Yan Xue 1,  Junhao Su 1 2,  Yiming Chao 1 3,  Lu Liu 1 3,  Xinyi Lin 1,  Yang Xiang 1,  Mun Kay Ho 1,  Zezhuo Su 4,  Junyi Chen 2,  Zhuojuan Luo 5,  Chengqi Lin 6,  Ruibang Luo 7,  Theo Aurich 1 3 8,  Jianfeng Wu 9,  Kelvin Sin Chi Cheung 4,  Yuanhua Huang 1 3 10,  Joshua W K Ho 1 2 11,  Ryohichi Sugimura 1 3
Affiliations

Affiliations

  • 1 School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
  • 2 Laboratory of Data Discovery For Health Limited (D24H), Hong Kong Science Park, Hong Kong, Hong Kong.
  • 3 Inno HK Centre For Translational Stem Cell Biology, Hong Kong, China.
  • 4 Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
  • 5 Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, China.
  • 6 Jiangsu Province Hi-Tech Key Laboratory For Biomedical Research, Southeast University, Nanjing, China.
  • 7 Department of Computer Science, School of Computing and Data Science, The University of Hong Kong, Hong Kong SAR, China.
  • 8 Heidelberg University Hospital, Germany.
  • 9 Department of Diagnostic Radiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
  • 10 Department of Statistics and Actuarial Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China.
  • 11 School of Biomedical Engineering, The University of Hong Kong, Hong Kong SAR, China.
PMID: 41560697 DOI: 10.1002/advs.202518084
Abstract

Lineage tracing at single-cell resolution is vital for mapping cell fate decisions, yet synthetic barcoding faces limitations in precision, diversity, and toxicity-especially in human pluripotent stem cells (hPSCs). Here, we repurpose naturally occurring somatic mutations in mitochondrial transcripts from single-cell RNA Sequencing as endogenous genetic barcodes. By enriching mitochondrial reads and applying a robust computational pipeline, we identified clonally informative variants to trace hematopoietic lineage emergence from hPSCs during early embryogenesis. Integrating mitochondrial barcoding with synthetic lineage tracing, we modeled embryonic tissue development and reconstructed the transcriptional logic and regulatory networks driving fate specification using a dynamical systems model. Extending this approach to spatial transcriptomics, we mapped the clonal architecture of human embryonic organoids, revealing spatial zonation orchestrated by NOTCH-mediated crosstalk between stromal cells and hematopoietic progenitors. This multimodal strategy links clonal dynamics with niche-driven fate decisions, offering a scalable, non-invasive method to dissect tissue organization in development and disease. Together, our work establishes a scalable, non-invasive multimodal framework that leverages endogenous mitochondrial DNA variants to reconstruct high-resolution spatiotemporal clonal dynamics and decode niche-driven fate decisions in a human stem cell-derived model. This approach provides a powerful strategy for dissecting tissue self-organization in development and disease.

Keywords

cell fate decisions; hematopoietic organoids; mitochondrial DNA variant; single‐cell lineage tracing; spatial transcriptomics.

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