DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

Matthias Farlik,Florian Halbritter,Fabian Müller,Fizzah A Choudry,Peter Ebert,Johanna Klughammer,Samantha Farrow,Antonella Santoro,Valerio Ciaurro,Anthony Mathur,Rakesh Uppal,Hendrik G Stunnenberg,Willem H Ouwehand,Elisa Laurenti,Thomas Lengauer,Mattia Frontini,Christoph Bock

doi:10.1016/j.stem.2016.10.019

Abstract

SummaryHematopoietic stem cells give rise to all blood cells in a differentiation process that involves widespread epigenome remodeling. Here we present genome-wide reference maps of the associated DNA methylation dynamics. We used a meta-epigenomic approach that combines DNA methylation profiles across many small pools of cells and performed single-cell methylome sequencing to assess cell-to-cell heterogeneity. The resulting dataset identified characteristic differences between HSCs derived from fetal liver, cord blood, bone marrow, and peripheral blood. We also observed lineage-specific DNA methylation between myeloid and lymphoid progenitors, characterized immature multi-lymphoid progenitors, and detected progressive DNA methylation differences in maturing megakaryocytes. We linked these patterns to gene expression, histone modifications, and chromatin accessibility, and we used machine learning to derive a model of human hematopoietic differentiation directly from DNA methylation data. Our results contribute to a better understanding of human hematopoietic stem cell differentiation and provide a framework for studying blood-linked diseases.

Highlights

All blood cells originate from hematopoietic stem cells (HSCs), which represent the apex of a differentiation cascade of progenitor cell types that gives rise to billions of new cells every day
We sequenced an average of 26 single-cell methylomes for seven cell types (HSC, multipotent progenitors (MPPs), common lymphoid progenitor [CLP], common myeloid progenitor [CMP], immature multi-lymphoid progenitor [MLP0], granulocyte macrophage progenitor [GMP], and megakaryocytes) to assess cell-to-cell heterogeneity. Based on this dataset, which constitutes a community resource of the BLUEPRINT project (Adams et al, 2012) and the International Human Epigenome Consortium (IHEC; http:// ihec-epigenomes.org), we compared DNA methylation between HSCs derived from different sources, and we studied changes in DNA methylation associated with commitment to the myeloid and lymphoid lineages
DNA methylation libraries were generated by whole genome bisulfite sequencing (WGBS) using the mWGBS protocol (Farlik et al, 2015) and sequenced at low coverage to minimize the number of PCR duplicates

Summary

Introduction

All blood cells originate from hematopoietic stem cells (HSCs), which represent the apex of a differentiation cascade of progenitor cell types that gives rise to billions of new cells every day. HSC differentiation is believed to progress through stepwise restriction of lineage potential, a concept that is summarized by the classical tree model of murine hematopoiesis (Spangrude, 1991; Till and McCulloch, 1980). DNA methylation is well suited for studying cellular differentiation because its patterns are cell-type-specific and retain an epigenetic memory of a cell’s developmental history. Cell-of-origin-specific DNA methylation patterns are detectable among induced pluripotent stem cells (Kim et al, 2011; Polo et al, 2010), and such patterns of epigenetic tissue memory predict primary tumor location in metastatic cancers (Fernandez et al, 2012; Moran et al, 2016)

Results

Discussion

Conclusion