Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets

Bethan Psaila; Guanlin Wang; Alba Rodriguez-Meira; Rong Li; Elisabeth F Heuston; Lauren Murphy; Daniel Yee; Ian S Hitchcock; Nikolaos Sousos; Jennifer O'Sullivan; Stacie Anderson; Yotis A Senis; Olga K Weinberg; Monica L Calicchio; NIH Intramural Sequencing Center; Deena Iskander; Daniel Royston; Dragana Milojkovic; Irene Roberts; David M Bodine; Supat Thongjuea; Adam J Mead

doi:10.1016/j.molcel.2020.04.008

Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets

Mol Cell. 2020 May 7;78(3):477-492.e8. doi: 10.1016/j.molcel.2020.04.008.

Authors

Bethan Psaila¹, Guanlin Wang², Alba Rodriguez-Meira², Rong Li³, Elisabeth F Heuston⁴, Lauren Murphy³, Daniel Yee⁵, Ian S Hitchcock⁵, Nikolaos Sousos³, Jennifer O'Sullivan³, Stacie Anderson⁶, Yotis A Senis⁷, Olga K Weinberg⁸, Monica L Calicchio⁸; NIH Intramural Sequencing Center⁹; Deena Iskander¹⁰, Daniel Royston¹¹, Dragana Milojkovic¹⁰, Irene Roberts¹², David M Bodine⁴, Supat Thongjuea¹³, Adam J Mead¹⁴

Affiliations

¹ Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford OX3 9DS, UK; MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; NIHR Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; Hematopoiesis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4442, USA. Electronic address: bethan.psaila@ndcls.ox.ac.uk.
² Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford OX3 9DS, UK; MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; NIHR Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; MRC WIMM Centre for Computational Biology, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK.
³ Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford OX3 9DS, UK; MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; NIHR Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK.
⁴ Hematopoiesis Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4442, USA.
⁵ York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK.
⁶ NHGRI Flow Cytometry Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4442, USA.
⁷ Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche-S 1255, Etablissement Français du Sang Grand Est, Strasbourg 67065, France.
⁸ Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA.
⁹ National Institutes of Health, Bethesda MD 20892-442, USA.
¹⁰ Centre for Haematology, Hammersmith Hospital, Imperial College of Medicine, London W12 OHS, UK.
¹¹ Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
¹² MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; NIHR Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK.
¹³ NIHR Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; MRC WIMM Centre for Computational Biology, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK. Electronic address: supat.thongjuea@imm.ox.ac.uk.
¹⁴ Haematopoietic Stem Cell Biology Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford OX3 9DS, UK; MRC Molecular Haematology Unit, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK; NIHR Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK. Electronic address: adam.mead@imm.ox.ac.uk.

Abstract

Myelofibrosis is a severe myeloproliferative neoplasm characterized by increased numbers of abnormal bone marrow megakaryocytes that induce fibrosis, destroying the hematopoietic microenvironment. To determine the cellular and molecular basis for aberrant megakaryopoiesis in myelofibrosis, we performed single-cell transcriptome profiling of 135,929 CD34⁺ lineage^- hematopoietic stem and progenitor cells (HSPCs), single-cell proteomics, genomics, and functional assays. We identified a bias toward megakaryocyte differentiation apparent from early multipotent stem cells in myelofibrosis and associated aberrant molecular signatures. A sub-fraction of myelofibrosis megakaryocyte progenitors (MkPs) are transcriptionally similar to healthy-donor MkPs, but the majority are disease specific, with distinct populations expressing fibrosis- and proliferation-associated genes. Mutant-clone HSPCs have increased expression of megakaryocyte-associated genes compared to wild-type HSPCs, and we provide early validation of G6B as a potential immunotherapy target. Our study paves the way for selective targeting of the myelofibrosis clone and illustrates the power of single-cell multi-omics to discover tumor-specific therapeutic targets and mediators of tissue fibrosis.

Keywords: G6B; TARGET-seq; bone marrow; fibrosis; immunotherapy; megakaryopoiesis; myeloproliferative neoplasm; platelets; single-cell multi-omics.

Publication types

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

MeSH terms

Aged
Aged, 80 and over
Cell Differentiation
Female
Gene Expression Regulation
Hematopoiesis / genetics
Hematopoiesis / physiology*
Hematopoietic Stem Cells / pathology
High-Throughput Nucleotide Sequencing
Humans
Male
Megakaryocytes / pathology*
Megakaryocytes / physiology
Middle Aged
Mutation
Primary Myelofibrosis / blood*
Receptors, Immunologic / genetics
Single-Cell Analysis / methods

Substances

MPIG6B protein, human
Receptors, Immunologic

Abstract

Publication types

MeSH terms

Substances

Grants and funding