High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations

Tony Hui; Qi Cao; Joanna Wegrzyn-Woltosz; Kieran O'Neill; Colin A Hammond; David J H F Knapp; Emma Laks; Michelle Moksa; Samuel Aparicio; Connie J Eaves; Aly Karsan; Martin Hirst

doi:10.1016/j.stemcr.2018.07.003

High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations

Stem Cell Reports. 2018 Aug 14;11(2):578-592. doi: 10.1016/j.stemcr.2018.07.003. Epub 2018 Aug 2.

Authors

Tony Hui¹, Qi Cao², Joanna Wegrzyn-Woltosz³, Kieran O'Neill⁴, Colin A Hammond⁵, David J H F Knapp⁵, Emma Laks⁶, Michelle Moksa², Samuel Aparicio⁷, Connie J Eaves⁸, Aly Karsan⁴, Martin Hirst⁹

Affiliations

¹ Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada.
² Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
³ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada.
⁴ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada.
⁵ Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
⁶ Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada.
⁷ Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada.
⁸ Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
⁹ Department of Microbiology and Immunology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada. Electronic address: mhirst@bcgsc.ca.

Abstract

Increasing evidence of functional and transcriptional heterogeneity in phenotypically similar cells examined individually has prompted interest in obtaining parallel methylome data. We describe the development and application of such a protocol to index-sorted murine and human hematopoietic cells that are highly enriched in their content of functionally defined stem cells. Utilizing an optimized single-cell bisulfite sequencing protocol, we obtained quantitative DNA methylation measurements of up to 5.7 million CpGs in single hematopoietic cells. In parallel, we developed an analytical strategy (PDclust) to define single-cell DNA methylation states through pairwise comparisons of single-CpG methylation measurements. PDclust revealed that a single-cell epigenetic state can be described by a small (<1%) stochastically sampled fraction of CpGs and that these states are reflective of cell identity and state. Using relationships revealed by PDclust, we derive near complete methylomes for epigenetically distinct subpopulations of hematopoietic cells enriched for functional stem cell content.

Keywords: DNA methylation; epigenetics; hematopoietic stem cell; single cell.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Computational Biology / methods
CpG Islands
DNA Methylation*
Epigenesis, Genetic*
Gene Expression Profiling
Genomics / methods
Hematopoietic Stem Cells / cytology*
Hematopoietic Stem Cells / metabolism*
Mice
Single-Cell Analysis

Grants and funding

P1-120589/CIHR/Canada