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Published on: February 1, 2022
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling
Caleb A Lareau1,2,3, Leif S Ludwig4,5, Christoph Muus6,7
1Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. clareau@broadinstitute.org.
This study introduces a new method combining mitochondrial DNA (mtDNA) mutation analysis with single-cell ATAC sequencing (scATAC-seq). This allows researchers to track cell lineages, study cell states, and understand clonal evolution in complex tissues.
Area of Science:
- Genomics
- Cell Biology
- Epigenetics
Background:
- Mitochondrial DNA (mtDNA) mutations are key to understanding cell clonal relationships.
- Profiling mtDNA alongside cell state requires high-throughput methods for complex human tissues.
- Existing methods lack the capacity to integrate mtDNA profiling with large-scale chromatin accessibility data.
Purpose of the Study:
- To develop a high-throughput, droplet-based assay combining mtDNA mutation profiling with single-cell ATAC sequencing (scATAC-seq).
- To enable simultaneous inference of mtDNA heteroplasmy, clonal relationships, cell state, and chromatin accessibility at the single-cell level.
- To investigate cellular population dynamics and clonal evolution in various biological contexts.
Main Methods:
- Developed a droplet-based scATAC-seq assay incorporating mtDNA mutation calling.
- Applied the method to profile thousands of single cells from human tissues and in vitro models.
- Integrated mtDNA heteroplasmy data with accessible chromatin profiles for comprehensive single-cell analysis.
Main Results:
- Achieved high-confidence mtDNA mutation calling in thousands of single cells.
- Revealed single-cell variation in heteroplasmy of a pathogenic mtDNA variant, linked to chromatin variability and clonal evolution.
- Successfully traced cell lineages in cancers, connecting epigenomic variability to subclonal evolution.
- Inferred cellular dynamics during hematopoietic cell differentiation in vitro and in vivo.
Conclusions:
- The developed method provides a powerful tool for studying cellular population dynamics and clonal properties.
- It enables the simultaneous investigation of mtDNA heteroplasmy, epigenomic variation, and cell state.
- This approach facilitates deeper understanding of clonal evolution and cellular heterogeneity in complex biological systems.
