1
|
Wojtowicz EE, Mistry JJ, Uzun V, Hellmich C, Scoones A, Chin DW, Kettyle LM, Grasso F, Lord AM, Wright DJ, Etherington GJ, Woll PS, Belderbos ME, Bowles KM, Nerlov C, Haerty W, Bystrykh LV, Jacobsen SEW, Rushworth SA, Macaulay IC. Panhematopoietic RNA barcoding enables kinetic measurements of nucleate and anucleate lineages and the activation of myeloid clones following acute platelet depletion. Genome Biol 2023; 24:152. [PMID: 37370129 PMCID: PMC10294477 DOI: 10.1186/s13059-023-02976-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Platelets and erythrocytes constitute over 95% of all hematopoietic stem cell output. However, the clonal dynamics of HSC contribution to these lineages remains largely unexplored. RESULTS We use lentiviral genetic labeling of mouse hematopoietic stem cells to quantify output from all lineages, nucleate, and anucleate, simultaneously linking these with stem and progenitor cell transcriptomic phenotypes using single-cell RNA-sequencing. We observe dynamic shifts of clonal behaviors through time in same-animal peripheral blood and demonstrate that acute platelet depletion shifts the output of multipotent hematopoietic stem cells to the exclusive production of platelets. Additionally, we observe the emergence of new myeloid-biased clones, which support short- and long-term production of blood cells. CONCLUSIONS Our approach enables kinetic studies of multi-lineage output in the peripheral blood and transcriptional heterogeneity of individual hematopoietic stem cells. Our results give a unique insight into hematopoietic stem cell reactivation upon platelet depletion and of clonal dynamics in both steady state and under stress.
Collapse
Affiliation(s)
- Edyta E Wojtowicz
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
| | - Jayna J Mistry
- Earlham Institute, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Vladimir Uzun
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Charlotte Hellmich
- Norwich Medical School, University of East Anglia, Norwich, UK
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Anita Scoones
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Desmond W Chin
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura M Kettyle
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Francesca Grasso
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Allegra M Lord
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Petter S Woll
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Kristian M Bowles
- Norwich Medical School, University of East Anglia, Norwich, UK
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Leonid V Bystrykh
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center of Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Sten Eirik W Jacobsen
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | | | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
| |
Collapse
|
2
|
Shin TH, Zhou Y, Chen S, Cordes S, Grice MZ, Fan X, Lee BC, Aljanahi AA, Hong SG, Vaughan KL, Mattison JA, Kohama SG, Fabre MA, Uchida N, Demirci S, Corat MA, Métais JY, Calvo KR, Buscarlet M, Natanson H, McGraw KL, List AF, Busque L, Tisdale JF, Vassiliou GS, Yu KR, Dunbar CE. A macaque clonal hematopoiesis model demonstrates expansion of TET2-disrupted clones and utility for testing interventions. Blood 2022; 140:1774-1789. [PMID: 35714307 PMCID: PMC9837449 DOI: 10.1182/blood.2021014875] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/26/2022] [Indexed: 01/21/2023] Open
Abstract
Individuals with age-related clonal hematopoiesis (CH) are at greater risk for hematologic malignancies and cardiovascular diseases. However, predictive preclinical animal models to recapitulate the spectrum of human CH are lacking. Through error-corrected sequencing of 56 human CH/myeloid malignancy genes, we identified natural CH driver mutations in aged rhesus macaques matching genes somatically mutated in human CH, with DNMT3A mutations being the most frequent. A CH model in young adult macaques was generated via autologous transplantation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated gene-edited hematopoietic stem and progenitor cells (HSPCs), targeting the top human CH genes with loss-of-function (LOF) mutations. Long-term follow-up revealed reproducible and significant expansion of multiple HSPC clones with heterozygous TET2 LOF mutations, compared with minimal expansion of clones bearing other mutations. Although the blood counts of these CH macaques were normal, their bone marrows were hypercellular and myeloid-predominant. TET2-disrupted myeloid colony-forming units isolated from these animals showed a distinct hyperinflammatory gene expression profile compared with wild type. In addition, mature macrophages purified from the CH macaques showed elevated NLRP3 inflammasome activity and increased interleukin-1β (IL-1β) and IL-6 production. The model was used to test the impact of IL-6 blockage by tocilizumab, documenting a slowing of TET2-mutated expansion, suggesting that interruption of the IL-6 axis may remove the selective advantage of mutant HSPCs. These findings provide a model for examining the pathophysiology of CH and give insights into potential therapeutic interventions.
Collapse
Affiliation(s)
- Tae-Hoon Shin
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Shirley Chen
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Stefan Cordes
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Max Z. Grice
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Byung-Chul Lee
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Aisha A. Aljanahi
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - So Gun Hong
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Kelli L. Vaughan
- Translational Gerontology Branch, National Institute on Aging, NIH Animal Center, Dickerson, MD
| | - Julie A. Mattison
- Translational Gerontology Branch, National Institute on Aging, NIH Animal Center, Dickerson, MD
| | - Steven G. Kohama
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
| | - Margarete A. Fabre
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Marcus A.F. Corat
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Multidisciplinary Center for Biological Research, University of Campinas, Campinas, Brazil
| | - Jean-Yves Métais
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN
| | - Katherine R. Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD
| | - Manuel Buscarlet
- Hôpital Maisonneuve-Rosemont, Universite de Montreal, Montreal, QC, Canada
| | - Hannah Natanson
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Kathy L. McGraw
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | - Lambert Busque
- Hôpital Maisonneuve-Rosemont, Universite de Montreal, Montreal, QC, Canada
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - George S. Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kyung-Rok Yu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| |
Collapse
|
3
|
Walsh K, Raghavachari N, Kerr C, Bick AG, Cummings SR, Druley T, Dunbar CE, Genovese G, Goodell MA, Jaiswal S, Maciejewski J, Natarajan P, Shindyapina AV, Shuldiner AR, Van Den Akker EB, Vijg J. Clonal Hematopoiesis Analyses in Clinical, Epidemiologic, and Genetic Aging Studies to Unravel Underlying Mechanisms of Age-Related Dysfunction in Humans. FRONTIERS IN AGING 2022; 3:841796. [PMID: 35821803 PMCID: PMC9261374 DOI: 10.3389/fragi.2022.841796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022]
Abstract
Aging is characterized by increased mortality, functional decline, and exponential increases in the incidence of diseases such as cancer, stroke, cardiovascular disease, neurological disease, respiratory disease, etc. Though the role of aging in these diseases is widely accepted and considered to be a common denominator, the underlying mechanisms are largely unknown. A significant age-related feature observed in many population cohorts is somatic mosaicism, the detectable accumulation of somatic mutations in multiple cell types and tissues, particularly those with high rates of cell turnover (e.g., skin, liver, and hematopoietic cells). Somatic mosaicism can lead to the development of cellular clones that expand with age in otherwise normal tissues. In the hematopoietic system, this phenomenon has generally been referred to as "clonal hematopoiesis of indeterminate potential" (CHIP) when it applies to a subset of clones in which mutations in driver genes of hematologic malignancies are found. Other mechanisms of clonal hematopoiesis, including large chromosomal alterations, can also give rise to clonal expansion in the absence of conventional CHIP driver gene mutations. Both types of clonal hematopoiesis (CH) have been observed in studies of animal models and humans in association with altered immune responses, increased mortality, and disease risk. Studies in murine models have found that some of these clonal events are involved in abnormal inflammatory and metabolic changes, altered DNA damage repair and epigenetic changes. Studies in long-lived individuals also show the accumulation of somatic mutations, yet at this advanced age, carriership of somatic mutations is no longer associated with an increased risk of mortality. While it remains to be elucidated what factors modify this genotype-phenotype association, i.e., compensatory germline genetics, cellular context of the mutations, protective effects to diseases at exceptional age, it points out that the exceptionally long-lived are key to understand the phenotypic consequences of CHIP mutations. Assessment of the clinical significance of somatic mutations occurring in blood cell types for age-related outcomes in human populations of varied life and health span, environmental exposures, and germline genetic risk factors will be valuable in the development of personalized strategies tailored to specific somatic mutations for healthy aging.
Collapse
Affiliation(s)
- Kenneth Walsh
- University of Virginia, Charlottesville, VA, United States
| | - Nalini Raghavachari
- National Institute on Aging, NIH, Bethesda, MD, United States,*Correspondence: Nalini Raghavachari,
| | - Candace Kerr
- National Institute on Aging, NIH, Bethesda, MD, United States
| | | | - Steven R. Cummings
- University of California, San Francisco, San Francisco, CA, United States
| | - Todd Druley
- Angle Biosciences, St. Louis, MO, United States
| | - Cynthia E. Dunbar
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD, United States
| | | | | | | | | | | | | | | | | | - Jan Vijg
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|