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Vu GT, Awad V, Norberto MF, Bowman TV, Trompouki E. Nucleic acid-induced inflammation on hematopoietic stem cells. Exp Hematol 2024; 131:104148. [PMID: 38151171 PMCID: PMC11061806 DOI: 10.1016/j.exphem.2023.104148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Hematopoiesis, the process of generating blood cells, starts during development with the primitive, pro-definitive, and definitive hematopoietic waves. The first two waves will generate erythrocytes and myeloid cells, although the definitive wave will give rise to hematopoietic stem cells (HSCs) that are multipotent and can produce most of the blood cells in an adult. Although HSCs are highly proliferative during development, during adulthood they remain quiescent in the bone marrow. Inflammatory signaling in the form of interferons, interleukins, tumor necrosis factors, and others is well-established to influence both developmental and adult hematopoiesis. Here we discuss the role of specific inflammatory pathways that are induced by sensing nucleic acids. We discuss the role of RNA-sensing members of the Toll-like, Rig-I-like, nucleotide-binding oligomerization domain (NOD)-like, and AIM2-like protein kinase receptors and the DNA-sensing receptors, DEAD-Box helicase 41 (DDX41) and cGAS. The main downstream pathways of these receptors are discussed, as well as their influence on developmental and adult hematopoiesis, including hematopoietic pathologies.
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Affiliation(s)
- Giang To Vu
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France
| | - Valerie Awad
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Maria Feliz Norberto
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology and Gottesman Institute of Stem Cell Biology and Regenerative Medicine Bronx, Albert Einstein College of Medicine, NY; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY.
| | - Eirini Trompouki
- IRCAN Institute for Research on Cancer and Aging, INSERM Unité 1081, CNRS UMR 7284, Université Côte d'Azur, Nice, France.
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2
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Mastrogiovanni M, Martínez-Navarro FJ, Bowman TV, Cayuela ML. Inflammation in Development and Aging: Insights from the Zebrafish Model. Int J Mol Sci 2024; 25:2145. [PMID: 38396822 PMCID: PMC10889087 DOI: 10.3390/ijms25042145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Zebrafish are an emergent animal model to study human diseases due to their significant genetic similarity to humans, swift development, and genetic manipulability. Their utility extends to the exploration of the involvement of inflammation in host defense, immune responses, and tissue regeneration. Additionally, the zebrafish model system facilitates prompt screening of chemical compounds that affect inflammation. This study explored the diverse roles of inflammatory pathways in zebrafish development and aging. Serving as a crucial model, zebrafish provides insights into the intricate interplay of inflammation in both developmental and aging contexts. The evidence presented suggests that the same inflammatory signaling pathways often play instructive or beneficial roles during embryogenesis and are associated with malignancies in adults.
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Affiliation(s)
- Marta Mastrogiovanni
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Francisco Juan Martínez-Navarro
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria-Arrixaca, 30120 Murcia, Spain
| | - Teresa V. Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - María L. Cayuela
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120 Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria-Arrixaca, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 30100 Murcia, Spain
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3
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Cusan M, Shen H, Zhang B, Liao A, Yang L, Jin M, Fernandez M, Iyer P, Wu Y, Hart K, Gutierrez C, Nik S, Pruett-Miller SM, Stark J, Obeng EA, Bowman TV, Wu CJ, Lin RJ, Wang L. SF3B1 mutation and ATM deletion codrive leukemogenesis via centromeric R-loop dysregulation. J Clin Invest 2023; 133:e163325. [PMID: 37463047 PMCID: PMC10471171 DOI: 10.1172/jci163325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
RNA splicing factor SF3B1 is recurrently mutated in various cancers, particularly in hematologic malignancies. We previously reported that coexpression of Sf3b1 mutation and Atm deletion in B cells, but not either lesion alone, leads to the onset of chronic lymphocytic leukemia (CLL) with CLL cells harboring chromosome amplification. However, the exact role of Sf3b1 mutation and Atm deletion in chromosomal instability (CIN) remains unclear. Here, we demonstrated that SF3B1 mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segregation, altered spindle architecture, and aneuploidy, which could be alleviated by removal of cen-R-loop and exaggerated by deletion of ATM. Aberrant splicing of key genes involved in R-loop processing underlay augmentation of cen-R-loop, as overexpression of the normal isoform, but not the altered form, mitigated mitotic stress in SF3B1-mutant cells. Our study identifies a critical role of splice variants in linking RNA splicing dysregulation and CIN and highlights cen-R-loop augmentation as a key mechanism for leukemogenesis.
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Affiliation(s)
- Martina Cusan
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Haifeng Shen
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Bo Zhang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Department of Hematology, Union Hospital Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aijun Liao
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Department of Hematology, Affiliated Shengjing Hospital of China Medical University, Shenyang, China
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Meiling Jin
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Mike Fernandez
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Prajish Iyer
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Yiming Wu
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Kevyn Hart
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sara Nik
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jeremy Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Esther A. Obeng
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Teresa V. Bowman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ren-Jang Lin
- Center for RNA Biology and Therapeutics, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
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De La Rosa-Reyes V, Jacobson S, Bowman TV, Fraint E. High Throughput Drug Screening in Zebrafish for Identifying Novel Compounds That Influence Engraftment Efficiency. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00443-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Fraint E, Lv P, Liu F, Bowman TV, Tamplin OJ. Hematopoietic Stem and Progenitor Cell Identification and Transplantation in Zebrafish. Methods Mol Biol 2023; 2567:233-249. [PMID: 36255705 DOI: 10.1007/978-1-0716-2679-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The zebrafish as a model organism is well known for its versatile genetics, rapid development, and straightforward live imaging. It is an excellent model to study hematopoiesis because of its highly conserved ontogeny and gene regulatory networks. Recently developed highly specific transgenic reporter lines have allowed direct imaging and tracking of hematopoietic stem and progenitor cells (HSPCs) in live zebrafish. These reporter lines can also be used for fluorescence-activated cell sorting (FACS) of HSPCs. Similar to mammalian models, HSPCs can be transplanted to reconstitute the entire hematopoietic system of zebrafish recipients. However, the zebrafish provides unique advantages to study HSPC biology, such as transplants into embryos and high-throughput chemical screening. This chapter will outline the methods needed to identify, isolate, and transplant HSPCs in zebrafish.
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Affiliation(s)
- Ellen Fraint
- Department of Pediatrics (Pediatric Hematology/Oncology and Cellular Therapy) and Department of Developmental and Molecular Biology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Peng Lv
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Teresa V Bowman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Department of Developmental and Molecular Biology, and Department of Medicine (Oncology), Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Owen J Tamplin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA.
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Potts KS, Cameron RC, Metidji A, Ghazale N, Wallace L, Leal-Cervantes AI, Palumbo R, Barajas JM, Gupta V, Aluri S, Pradhan K, Myers JA, McKinstry M, Bai X, Choudhary GS, Shastri A, Verma A, Obeng EA, Bowman TV. Splicing factor deficits render hematopoietic stem and progenitor cells sensitive to STAT3 inhibition. Cell Rep 2022; 41:111825. [PMID: 36516770 PMCID: PMC9994853 DOI: 10.1016/j.celrep.2022.111825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 10/01/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) sustain lifelong hematopoiesis. Mutations of pre-mRNA splicing machinery, especially splicing factor 3b, subunit 1 (SF3B1), are early lesions found in malignancies arising from HSPC dysfunction. However, why splicing factor deficits contribute to HSPC defects remains incompletely understood. Using zebrafish, we show that HSPC formation in sf3b1 homozygous mutants is dependent on STAT3 activation. Clinically, mutations in SF3B1 are heterozygous; thus, we explored if targeting STAT3 could be a vulnerability in these cells. We show that SF3B1 heterozygosity confers heightened sensitivity to STAT3 inhibition in zebrafish, mouse, and human HSPCs. Cells carrying mutations in other splicing factors or treated with splicing modulators are also more sensitive to STAT3 inhibition. Mechanistically, we illustrate that STAT3 inhibition exacerbates aberrant splicing in SF3B1 mutant cells. Our findings reveal a conserved vulnerability of splicing factor mutant HSPCs that could allow for their selective targeting in hematologic malignancies.
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Affiliation(s)
- Kathryn S Potts
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rosannah C Cameron
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amina Metidji
- Department of Oncology, St. Jude's Children Research Hospital, Memphis, TN 38105, USA
| | - Noura Ghazale
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - LaShanale Wallace
- Department of Oncology, St. Jude's Children Research Hospital, Memphis, TN 38105, USA
| | - Ana I Leal-Cervantes
- Department of Oncology, St. Jude's Children Research Hospital, Memphis, TN 38105, USA
| | - Reid Palumbo
- Department of Oncology, St. Jude's Children Research Hospital, Memphis, TN 38105, USA
| | - Juan Martin Barajas
- Department of Oncology, St. Jude's Children Research Hospital, Memphis, TN 38105, USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Srinivas Aluri
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Kith Pradhan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Jacquelyn A Myers
- Department of Oncology, St. Jude's Children Research Hospital, Memphis, TN 38105, USA
| | - Mia McKinstry
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiaoying Bai
- Department of Obstetrics and Gynecology, University of Texas, Dallas, TX, USA
| | - Gaurav S Choudhary
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Aditi Shastri
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA; Montefiore Einstein Cancer Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Amit Verma
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA; Montefiore Einstein Cancer Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA
| | - Esther A Obeng
- Department of Oncology, St. Jude's Children Research Hospital, Memphis, TN 38105, USA.
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Oncology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA; Montefiore Einstein Cancer Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY 10461, USA.
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7
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Weinreb JT, Bowman TV. Clinical and mechanistic insights into the roles of DDX41 in haematological malignancies. FEBS Lett 2022; 596:2736-2745. [PMID: 36036093 PMCID: PMC9669125 DOI: 10.1002/1873-3468.14487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022]
Abstract
DEAD-box Helicase 41 (DDX41) is a member of the DExD/H-box helicase family that has a variety of cellular functions. Of note, germline and somatic mutations in the DDX41 gene are prevalently found in myeloid malignancies. Here, we present a comprehensive and analytic review covering relevant clinical, translational and basic science findings on DDX41. We first describe the initial characterisation of DDX41 mutations in patients affected by myelodysplastic syndromes, their associated clinical characteristics, and current treatment modalities. We then cover the known cellular functions of DDX41, spanning from its discovery in Drosophila as a neuroregulator through its more recently described roles in inflammatory signalling, R-loop metabolism and snoRNA processing. We end with a summary of the identified basic functions of DDX41 that when perturbed may contribute to the underlying pathology of haematologic neoplasms.
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Affiliation(s)
- Joshua T. Weinreb
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA
- Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Teresa V. Bowman
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA
- Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
- Albert Einstein College of Medicine and the Montefiore Medical Center, Department of Oncology, Bronx, NY, USA
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8
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Choudhary GS, Pellagatti A, Agianian B, Smith MA, Bhagat TD, Gordon-Mitchell S, Sahu S, Pandey S, Shah N, Aluri S, Aggarwal R, Aminov S, Schwartz L, Steeples V, Booher RN, Ramachandra M, Samson M, Carbajal M, Pradhan K, Bowman TV, Pillai MM, Will B, Wickrema A, Shastri A, Bradley RK, Martell RE, Steidl UG, Gavathiotis E, Boultwood J, Starczynowski DT, Verma A. Activation of targetable inflammatory immune signaling is seen in myelodysplastic syndromes with SF3B1 mutations. eLife 2022; 11:e78136. [PMID: 36040792 PMCID: PMC9427103 DOI: 10.7554/elife.78136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background Mutations in the SF3B1 splicing factor are commonly seen in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), yet the specific oncogenic pathways activated by mis-splicing have not been fully elucidated. Inflammatory immune pathways have been shown to play roles in the pathogenesis of MDS, though the exact mechanisms of their activation in splicing mutant cases are not well understood. Methods RNA-seq data from SF3B1 mutant samples was analyzed and functional roles of interleukin-1 receptor-associated kinase 4 (IRAK4) isoforms were determined. Efficacy of IRAK4 inhibition was evaluated in preclinical models of MDS/AML. Results RNA-seq splicing analysis of SF3B1 mutant MDS samples revealed retention of full-length exon 6 of IRAK4, a critical downstream mediator that links the Myddosome to inflammatory NF-kB activation. Exon 6 retention leads to a longer isoform, encoding a protein (IRAK4-long) that contains the entire death domain and kinase domain, leading to maximal activation of NF-kB. Cells with wild-type SF3B1 contain smaller IRAK4 isoforms that are targeted for proteasomal degradation. Expression of IRAK4-long in SF3B1 mutant cells induces TRAF6 activation leading to K63-linked ubiquitination of CDK2, associated with a block in hematopoietic differentiation. Inhibition of IRAK4 with CA-4948, leads to reduction in NF-kB activation, inflammatory cytokine production, enhanced myeloid differentiation in vitro and reduced leukemic growth in xenograft models. Conclusions SF3B1 mutation leads to expression of a therapeutically targetable, longer, oncogenic IRAK4 isoform in AML/MDS models. Funding This work was supported by Cincinnati Children's Hospital Research Foundation, Leukemia Lymphoma Society, and National Institute of Health (R35HL135787, RO1HL111103, RO1DK102759, RO1HL114582), Gabrielle's Angel Foundation for Cancer Research, and Edward P. Evans Foundation grants to DTS. AV is supported by Edward P. Evans Foundation, National Institute of Health (R01HL150832, R01HL139487, R01CA275007), Leukemia and Lymphoma Society, Curis and a gift from the Jane and Myles P. Dempsey family. AP and JB are supported by Blood Cancer UK (grants 13042 and 19004). GC is supported by a training grant from NYSTEM. We acknowledge support of this research from The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. MS is supported by a National Institute of Health Research Training and Career Development Grant (F31HL132420).
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Affiliation(s)
- Gaurav S Choudhary
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Andrea Pellagatti
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Bogos Agianian
- Department of Biochemistry, Albert Einstein College of MedicineThe BronxUnited States
| | - Molly A Smith
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Tushar D Bhagat
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Shanisha Gordon-Mitchell
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Srabani Sahu
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Sanjay Pandey
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Nishi Shah
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Srinivas Aluri
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Ritesh Aggarwal
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Sarah Aminov
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Leya Schwartz
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Violetta Steeples
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
| | | | | | | | - Milagros Carbajal
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Kith Pradhan
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Teresa V Bowman
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | | | - Britta Will
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | | | - Aditi Shastri
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | | | | | - Ulrich G Steidl
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
| | - Evripidis Gavathiotis
- Department of Biochemistry, Albert Einstein College of MedicineThe BronxUnited States
| | - Jacqueline Boultwood
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Daniel T Starczynowski
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Amit Verma
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical CenterThe BronxUnited States
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9
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Ito K, Bowman TV. Paul S. Frenette (1965-2021). FASEB Bioadv 2022; 4:5-8. [PMID: 35024568 PMCID: PMC8728104 DOI: 10.1096/fba.2021-00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/11/2022] Open
Affiliation(s)
- Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine ResearchAlbert Einstein College of MedicineBronxNew YorkUSA
- Departments of Cell Biology and MedicineMontefiore Medical CenterAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Teresa V. Bowman
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine ResearchAlbert Einstein College of MedicineBronxNew YorkUSA
- Department of Developmental and Molecular BiologyAlbert Einstein College of MedicineBronxNew YorkUSA
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10
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Bowman TV, Jamieson C, Steidl U, Stanley ER, Gritsman K, Wagner D, Manwani D, Trumpp A, Suda T, Ito K, Dawlaty M, Lucas D, Pinho S. Paul S. Frenette (1965-2021). Cell Stem Cell 2021; 28:1686-1689. [PMID: 34624230 DOI: 10.1016/j.stem.2021.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Teresa V Bowman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Catriona Jamieson
- Department of Medicine, Division of Hematology-Oncology, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Ulrich Steidl
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Departments of Cell Biology and of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - E Richard Stanley
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kira Gritsman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Departments of Cell Biology and of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Denisa Wagner
- Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepa Manwani
- Department of Pediatrics, Division of Hematology-Oncology, Children's Hospital at Montefiore, Bronx, NY, USA
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Keisuke Ito
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Departments of Cell Biology and of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Meelad Dawlaty
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daniel Lucas
- Department of Pediatrics, Division of Experimental Hematology & Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sandra Pinho
- Department of Pharmacology and Regenerative Medicine, University of Illinois, Chicago, Chicago, IL, USA
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11
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Bowman TV, Jamieson C, Steidl U, Stanley ER, Gritsman K, Wagner D, Manwani D, Trumpp A, Suda T, Ito K, Dawlaty M, Lucas D, Pinho S. Paul S. Frenette (1965–2021). Dev Cell 2021. [DOI: 10.1016/j.devcel.2021.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Bowman TV, Jamieson C, Steidl U, Stanley ER, Gritsman K, Wagner D, Manwani D, Trumpp A, Suda T, Ito K, Dawlaty M, Lucas D, Pinho S. Paul S. Frenette (1965-2021). Cell 2021; 184:5073-5076. [PMID: 34597597 DOI: 10.1016/j.cell.2021.08.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Teresa V Bowman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Catriona Jamieson
- Department of Medicine, Division of Hematology-Oncology, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Ulrich Steidl
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Departments of Cell Biology and of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - E Richard Stanley
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kira Gritsman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Departments of Cell Biology and of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Denisa Wagner
- Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepa Manwani
- Department of Pediatrics, Division of Hematology-Oncology, Children's Hospital at Montefiore, Bronx, NY, USA
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Keisuke Ito
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Departments of Cell Biology and of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Meelad Dawlaty
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daniel Lucas
- Department of Pediatrics, Division of Experimental Hematology & Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sandra Pinho
- Department of Pharmacology and Regenerative Medicine, University of Illinois, Chicago, Chicago, IL, USA
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13
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Ulloa BA, Habbsa SS, Potts KS, Lewis A, McKinstry M, Payne SG, Flores JC, Nizhnik A, Feliz Norberto M, Mosimann C, Bowman TV. Definitive hematopoietic stem cells minimally contribute to embryonic hematopoiesis. Cell Rep 2021; 36:109703. [PMID: 34525360 PMCID: PMC8928453 DOI: 10.1016/j.celrep.2021.109703] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 01/23/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are rare cells that arise in the embryo
and sustain adult hematopoiesis. Although the functional potential of nascent
HSCs is detectable by transplantation, their native contribution during
development is unknown, in part due to the overlapping genesis and marker gene
expression with other embryonic blood progenitors. Using single-cell
transcriptomics, we define gene signatures that distinguish nascent HSCs from
embryonic blood progenitors. Applying a lineage-tracing approach to selectively
track HSC output in situ, we find significantly delayed
lymphomyeloid contribution. An inducible HSC injury model demonstrates a
negligible impact on larval lymphomyelopoiesis following HSC depletion. HSCs are
not merely dormant at this developmental stage, as they showed robust
regeneration after injury. Combined, our findings illuminate that nascent HSCs
self-renew but display differentiation latency, while HSC-independent embryonic
progenitors sustain developmental hematopoiesis. Understanding these differences
could improve de novo generation and expansion of functional
HSCs. Ulloa et al. demonstrate that nascent HSCs robustly regenerate but
display differentiation latency, while HSC-independent embryonic progenitors
sustain developmental hematopoiesis. Their findings have implications for
dissecting the programs underlying the genesis of bona fide HSCs.
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Affiliation(s)
- Bianca A Ulloa
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Samima S Habbsa
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Kathryn S Potts
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Alana Lewis
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Mia McKinstry
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Sara G Payne
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Julio C Flores
- Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Anastasia Nizhnik
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Maria Feliz Norberto
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine and Children's Hospital Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Teresa V Bowman
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA; Albert Einstein College of Medicine and Montefiore Medical Center, Department of Medicine (Oncology), Bronx, NY, USA.
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14
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Lévesque JP, Purton LE, Hidalgo A, Zon LI, Katayama Y, Scadden DT, Bowman TV, Stanley ER, Lucas D, Pinho S. In memory of Paul Sylvain Frenette, a pioneering explorer of the hematopoietic stem cell niche who left far too early. Exp Hematol 2021; 101-102:S0301-472X(21)00282-4. [PMID: 34403758 DOI: 10.1016/j.exphem.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/08/2021] [Indexed: 11/21/2022]
Affiliation(s)
- Jean-Pierre Lévesque
- Mater Research Institute, University of Queensland, Woollongabba, Queensland, Australia
| | - Louise E Purton
- St. Vincent's Research Institute, Fitzroy, Victoria, Australia
| | - Andrés Hidalgo
- National Center for Cardiovascular Research, Madrid, Spain
| | - Leonard I Zon
- Boston Children's Hospital, Boston, MA; Harvard Medical School, Cambridge, MA
| | | | - David T Scadden
- Harvard Medical School, Cambridge, MA; Massachusetts General Hospital, Boston, MA
| | | | | | - Daniel Lucas
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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15
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Weinreb JT, Gupta V, Sharvit E, Weil R, Bowman TV. Ddx41 inhibition of DNA damage signaling permits erythroid progenitor expansion in zebrafish. Haematologica 2021; 107:644-654. [PMID: 33763998 PMCID: PMC8883538 DOI: 10.3324/haematol.2020.257246] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 11/22/2022] Open
Abstract
DEAD-box Helicase 41 (DDX41) is a recently identified factor mutated in hematologic malignancies whose function in hematopoiesis is unknown. Using an in vivo model of Ddx41 deficiency, we unveiled a critical role for this helicase in regulating erythropoiesis. We demonstrated that loss of ddx41 leads to anemia caused by diminished proliferation and defective differentiation of erythroid progenitors. Mis-expression and alternative splicing of cell cycle genes is rampant in ddx41 mutant erythroid progenitors. We delineated that the DNA damage response is activated in mutant cells resulting in an Ataxiatelangiectasia mutated (ATM) and Ataxia-telangiectasia and Rad3-related (ATR)-triggered cell cycle arrest. Inhibition of these kinases partially suppressed ddx41 mutant anemia. These findings establish a critical function for Ddx41 in promoting healthy erythropoiesis via protection from genomic stress and delineate a mechanistic framework to explore a role for ATM and ATR signaling in DDX41-mutant hematopoietic pathologies.
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Affiliation(s)
- Joshua T Weinreb
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY
| | - Varun Gupta
- Albert Einstein College of Medicine, Department of Cell Biology, Bronx, NY
| | - Elianna Sharvit
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY
| | - Rachel Weil
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY
| | - Teresa V Bowman
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA; Albert Einstein College of Medicine and Montefiore Medical Center, Department of Medicine (Oncology), Bronx, NY.
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16
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Weinreb JT, Ghazale N, Pradhan K, Gupta V, Potts KS, Tricomi B, Daniels NJ, Padgett RA, De Oliveira S, Verma A, Bowman TV. Excessive R-loops trigger an inflammatory cascade leading to increased HSPC production. Dev Cell 2021; 56:627-640.e5. [PMID: 33651979 DOI: 10.1016/j.devcel.2021.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/01/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) arise during embryonic development and are essential for sustaining the blood and immune systems throughout life. Tight regulation of HSPC numbers is critical for hematopoietic homeostasis. Here, we identified DEAD-box helicase 41 (Ddx41) as a gatekeeper of HSPC production. Using zebrafish ddx41 mutants, we unveiled a critical role for this helicase in regulating HSPC production at the endothelial-to-hematopoietic transition. We determined that Ddx41 suppresses the accumulation of R-loops, nucleic acid structures consisting of RNA:DNA hybrids and ssDNAs whose equilibrium is essential for cellular fitness. Excess R-loop levels in ddx41 mutants triggered the cGAS-STING inflammatory pathway leading to increased numbers of hemogenic endothelium and HSPCs. Elevated R-loop accumulation and inflammatory signaling were observed in human cells with decreased DDX41, suggesting possible conservation of mechanism. These findings delineate that precise regulation of R-loop levels during development is critical for limiting cGAS-STING activity and HSPC numbers.
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Affiliation(s)
- Joshua T Weinreb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Noura Ghazale
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kith Pradhan
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kathryn S Potts
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brad Tricomi
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Noah J Daniels
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Richard A Padgett
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sofia De Oliveira
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Hepatology) and Marion Bessin Liver Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Amit Verma
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Oncology), Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Oncology), Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA.
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17
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Choudhuri A, Trompouki E, Abraham BJ, Colli LM, Kock KH, Mallard W, Yang ML, Vinjamur DS, Ghamari A, Sporrij A, Hoi K, Hummel B, Boatman S, Chan V, Tseng S, Nandakumar SK, Yang S, Lichtig A, Superdock M, Grimes SN, Bowman TV, Zhou Y, Takahashi S, Joehanes R, Cantor AB, Bauer DE, Ganesh SK, Rinn J, Albert PS, Bulyk ML, Chanock SJ, Young RA, Zon LI. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nat Genet 2020; 52:1333-1345. [PMID: 33230299 DOI: 10.1038/s41588-020-00738-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies identify genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell-type-specific enhancers, but the molecular mechanisms governing phenotypic variation are less well understood. Here, we show that many enhancer variants associated with red blood cell (RBC) traits map to enhancers that are co-bound by lineage-specific master transcription factors (MTFs) and signaling transcription factors (STFs) responsive to extracellular signals. The majority of enhancer variants reside on STF and not MTF motifs, perturbing DNA binding by various STFs (BMP/TGF-β-directed SMADs or WNT-induced TCFs) and affecting target gene expression. Analyses of engineered human blood cells and expression quantitative trait loci verify that disrupted STF binding leads to altered gene expression. Our results propose that the majority of the RBC-trait-associated variants that reside on transcription-factor-binding sequences fall in STF target sequences, suggesting that the phenotypic variation of RBC traits could stem from altered responsiveness to extracellular stimuli.
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Affiliation(s)
- Avik Choudhuri
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Eirini Trompouki
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leandro M Colli
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA.,Department of Medical Imaging, Hematology, and Medical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - William Mallard
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Min-Lee Yang
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Divya S Vinjamur
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alireza Ghamari
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Audrey Sporrij
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Karen Hoi
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Barbara Hummel
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Sonja Boatman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Victoria Chan
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sierra Tseng
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Asher Lichtig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Michael Superdock
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Seraj N Grimes
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Teresa V Bowman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yi Zhou
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | | | - Roby Joehanes
- Hebrew Senior Life, Harvard Medical School, Boston, MA, USA.,Framingham Heart Study, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan B Cantor
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Rinn
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Paul S Albert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonard I Zon
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
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18
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Lefkopoulos S, Polyzou A, Derecka M, Bergo V, Clapes T, Cauchy P, Jerez-Longres C, Onishi-Seebacher M, Yin N, Martagon-Calderón NA, Potts KS, Klaeylé L, Liu F, Bowman TV, Jenuwein T, Mione MC, Trompouki E. Repetitive Elements Trigger RIG-I-like Receptor Signaling that Regulates the Emergence of Hematopoietic Stem and Progenitor Cells. Immunity 2020; 53:934-951.e9. [DOI: 10.1016/j.immuni.2020.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
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19
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Fraint E, Ulloa BA, Feliz Norberto M, Potts KS, Bowman TV. Advances in preclinical hematopoietic stem cell models and possible implications for improving therapeutic transplantation. Stem Cells Transl Med 2020; 10:337-345. [PMID: 33058566 PMCID: PMC7900582 DOI: 10.1002/sctm.20-0294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/04/2020] [Accepted: 09/20/2020] [Indexed: 12/11/2022] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) is a treatment for many malignant, congenital, and acquired hematologic diseases. Some outstanding challenges in the HSCT field include the paucity of immunologically‐matched donors, our inability to effectively expand hematopoeitic stem cells (HSCs) ex vivo, and the high infection risk during engraftment. Scientists are striving to develop protocols to generate, expand, and maintain HSCs ex vivo, however these are not yet ready for clinical application. Given these problems, advancing our understanding of HSC specification, regulation, and differentiation in preclinical models is essential to improve the therapeutic utility of HSCT. In this review, we link biomedical researchers and transplantation clinicians by discussing the potential therapeutic implications of recent fundamental HSC research in model organisms. We consider deficiencies in current HSCT practice, such as problems achieving adequate cell dose for successful and rapid engraftment, immense inflammatory cascade activation after myeloablation, and graft‐vs‐host disease. Furthermore, we discuss recent advances in the field of HSC biology and transplantation made in preclinical models of zebrafish, mouse, and nonhuman primates that could inform emerging practice for clinical application.
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Affiliation(s)
- Ellen Fraint
- Department of Pediatrics, Children's Hospital at Montefiore, Bronx, New York, USA
| | - Bianca A Ulloa
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - María Feliz Norberto
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kathryn S Potts
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Medicine (Oncology), Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
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20
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Abstract
Mutations in spliceosomal components are prevalent in myelodysplastic syndromes, but less so in acute myeloid leukemia (AML). However, aberrant splicing is prolific in AML, suggesting deregulated splicing could contribute broadly to tumorigenesis. Elevated stress responses correlate with splicing dysfunction across myeloid malignancies, representing potentially novel therapeutic targets.See related article by Anande et al., p. 3597.
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Affiliation(s)
- Teresa V Bowman
- Departments of Developmental & Molecular Biology and Medicine (Oncology), Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York.
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21
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Feliz MA, Fraint E, Bowman TV. Zebrafish as a Model System for the Interrogation of Hematopoietic Stem Cell Engraftment. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ellen Fraint
- Children’s Hospital at Montefiore Division of Pediatric Hematology/Oncology & Bone Marrow Transplant
| | - Teresa V Bowman
- Albert Einstein College of Medicine
- Department of Medicine (Oncology) Albert Einstein College of Medicine
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22
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Li P, Lahvic JL, Binder V, Pugach EK, Riley EB, Tamplin OJ, Panigrahy D, Bowman TV, Barrett FG, Heffner GC, McKinney-Freeman S, Schlaeger TM, Daley GQ, Zeldin DC, Zon LI. Author Correction: Epoxyeicosatrienoic acids enhance embryonic haematopoiesis and adult marrow engraftment. Nature 2019; 573:E1. [PMID: 31435017 DOI: 10.1038/s41586-019-1489-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Pulin Li
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.,Chemical Biology Program, Harvard University, Cambridge, MA, 02138, USA
| | - Jamie L Lahvic
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Vera Binder
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Emily K Pugach
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth B Riley
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Owen J Tamplin
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Dipak Panigrahy
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Teresa V Bowman
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Francesca G Barrett
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Garrett C Heffner
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Thorsten M Schlaeger
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - George Q Daley
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Darryl C Zeldin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA. .,Chemical Biology Program, Harvard University, Cambridge, MA, 02138, USA.
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23
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De La Garza A, Cameron RC, Gupta V, Fraint E, Nik S, Bowman TV. The splicing factor Sf3b1 regulates erythroid maturation and proliferation via TGFβ signaling in zebrafish. Blood Adv 2019; 3:2093-2104. [PMID: 31300417 PMCID: PMC6650725 DOI: 10.1182/bloodadvances.2018027714] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The spliceosomal component Splicing Factor 3B, subunit 1 (SF3B1) is one of the most prevalently mutated factors in the bone marrow failure disorder myelodysplastic syndrome. There is a strong clinical correlation between SF3B1 mutations and erythroid defects, such as refractory anemia with ringed sideroblasts, but the role of SF3B1 in normal erythroid development is largely unknown. Loss-of-function zebrafish mutants for sf3b1 develop a macrocytic anemia. Here, we explore the underlying mechanism for anemia associated with sf3b1 deficiency in vivo. We found that sf3b1 mutant erythroid progenitors display a G0/G1 cell-cycle arrest with mutant erythrocytes showing signs of immaturity. RNA-sequencing analysis of sf3b1 mutant erythroid progenitors revealed normal expression of red blood cell regulators such as gata1, globin genes, and heme biosynthetic factors, but upregulation of genes in the transforming growth factor β (TGFβ) pathway. As TGFβ signaling is a known inducer of quiescence, the data suggest that activation of the pathway could trigger sf3b1 deficiency-induced anemia via cell-cycle arrest. Indeed, we found that inhibition of TGFβ signaling released the G0/G1 block in erythroid progenitors. Surprisingly, removal of this checkpoint enhanced rather than suppressed the anemia, indicating that the TGFβ-mediated cell-cycle arrest is protective for sf3b1-mutant erythrocytes. Together, these data suggest that macrocytic anemia arising from Sf3b1 deficiency is likely due to pleiotropic and distinct effects on cell-cycle progression and maturation.
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Affiliation(s)
- Adriana De La Garza
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
| | - Rosannah C Cameron
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
| | | | - Ellen Fraint
- Department of Pediatrics, Montefiore Hospital, Bronx, NY; and
| | - Sara Nik
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology
- Gottesman Institute of Stem Cell Biology and Regenerative Medicine
- Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY
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24
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Nik S, Bowman TV. Splicing and neurodegeneration: Insights and mechanisms. Wiley Interdiscip Rev RNA 2019; 10:e1532. [PMID: 30895702 DOI: 10.1002/wrna.1532] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
Splicing is the global cellular process whereby intervening sequences (introns) in precursor messenger RNA (pre-mRNA) are removed and expressed regions (exons) are ligated together, resulting in a mature mRNA transcript that is exported and translated in the cytoplasm. The tightly regulated splicing cycle is also flexible allowing for the inclusion or exclusion of some sequences depending on the specific cellular context. Alternative splicing allows for the generation of many transcripts from a single gene, thereby expanding the proteome. Although all cells require the function of the spliceosome, neurons are highly sensitive to splicing perturbations with numerous neurological diseases linked to splicing defects. The sensitivity of neurons to splicing alterations is largely due to the complex neuronal cell types and functions in the nervous system that require specific splice isoforms to maintain cellular homeostasis. In the past several years, the relationship between RNA splicing and the nervous system has been the source of significant investigation. Here, we review the current knowledge on RNA splicing in neurobiology and discuss its potential role and impact in neurodegenerative diseases. We will examine the impact of alternative splicing and the role of splicing regulatory proteins on neurodegeneration, highlighting novel animal models including mouse and zebrafish. We will also examine emerging technologies and therapeutic interventions that aim to "drug" the spliceosome. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Sara Nik
- Department of Developmental and Molecular Biology and Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Department of Medicine (Oncology), and Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York
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25
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Rajshekar S, Yao J, Arnold PK, Payne SG, Zhang Y, Bowman TV, Schmitz RJ, Edwards JR, Goll M. Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. eLife 2018; 7:39658. [PMID: 30484769 PMCID: PMC6261255 DOI: 10.7554/elife.39658] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/04/2018] [Indexed: 12/13/2022] Open
Abstract
Pericentromeric satellite repeats are enriched in 5-methylcytosine (5mC). Loss of 5mC at these sequences is common in cancer and is a hallmark of Immunodeficiency, Centromere and Facial abnormalities (ICF) syndrome. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. To address this deficiency, we generated a viable animal model of pericentromeric hypomethylation through mutation of the ICF-gene ZBTB24. Deletion of zebrafish zbtb24 caused a progressive loss of 5mC at pericentromeres and ICF-like phenotypes. Hypomethylation of these repeats triggered derepression of pericentromeric transcripts and activation of an interferon-based innate immune response. Injection of pericentromeric RNA is sufficient to elicit this response in wild-type embryos, and mutation of the MDA5-MAVS dsRNA-sensing machinery blocks the response in mutants. These findings identify activation of the innate immune system as an early consequence of pericentromeric hypomethylation, implicating derepression of pericentromeric transcripts as a trigger of autoimmunity. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter). Cells package DNA into structures called chromosomes. When cells divide, each chromosome duplicates, and a structure called a centromere initially holds the copies together. The sequences of DNA on either side of the centromeres are often highly repetitive. In backboned animals, this DNA normally also has extra chemical modifications called methyl groups attached to it. The role that these methyl groups play in this region is not known, although in other DNA regions they often stop the DNA being ‘transcribed’ into molecules of RNA. The cells of people who have a rare human genetic disorder called ICF syndrome, lack the methyl groups near the centromere. The methyl groups may also be lost in old and cancerous cells. Researchers often use ‘model’ animals to investigate the effects of DNA modifications. But, until now, there were no animal models that lose methyl groups from the DNA around centromeres in the same way as seen in ICF syndrome. Rajshekar et al. have developed a new zebrafish model for ICF syndrome that loses the methyl groups around its centromeres over time. Studying the cells of these zebrafish showed that when the methyl groups are missing, the cell starts to transcribe the DNA sequences around the centromeres. The resulting RNA molecules appear to be mistaken by the cell for viral RNA. They activate immune sensors that normally detect RNA viruses, which triggers an immune response. The new zebrafish model can now be used in further studies to help researchers to understand the key features of ICF syndrome. Future work could also investigate whether the loss of methyl groups around the centromeres plays a role in other diseases where the immune system attacks healthy tissues.
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Affiliation(s)
- Srivarsha Rajshekar
- Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Jun Yao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Paige K Arnold
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sara G Payne
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, United States
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, United States
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, United States
| | - John R Edwards
- Department of Medicine, Center for Pharmacogenomics, Washington University in St. Louis School of Medicine, Missouri, United States
| | - Mary Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Genetics, University of Georgia, Georgia, United States
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26
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Sorrells S, Nik S, Casey MJ, Cameron RC, Truong H, Toruno C, Gulfo M, Lowe A, Jette C, Stewart RA, Bowman TV. Spliceosomal components protect embryonic neurons from R-loop-mediated DNA damage and apoptosis. Dis Model Mech 2018; 11:dmm.031583. [PMID: 29419415 PMCID: PMC5894942 DOI: 10.1242/dmm.031583] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/18/2018] [Indexed: 02/02/2023] Open
Abstract
RNA splicing factors are essential for the viability of all eukaryotic cells; however, in metazoans some cell types are exquisitely sensitive to disruption of splicing factors. Neuronal cells represent one such cell type, and defects in RNA splicing factors can lead to neurodegenerative diseases. The basis for this tissue selectivity is not well understood owing to difficulties in analyzing the consequences of splicing factor defects in whole-animal systems. Here, we use zebrafish mutants to show that loss of spliceosomal components, including splicing factor 3b, subunit 1 (sf3b1), causes increased DNA double-strand breaks and apoptosis in embryonic neurons. Moreover, these mutants show a concomitant accumulation of R-loops, which are non-canonical nucleic acid structures that promote genomic instability. Dampening R-loop formation by conditional induction of ribonuclease H1 in sf3b1 mutants reduced neuronal DNA damage and apoptosis. These findings show that splicing factor dysfunction leads to R-loop accumulation and DNA damage that sensitizes embryonic neurons to apoptosis. Our results suggest that diseases associated with splicing factor mutations could be susceptible to treatments that modulate R-loop levels. Summary: Loss of RNA splicing factors causes R-loop accumulation and DNA damage in embryonic neurons, sensitizing them to radiation-induced cell death. These findings suggest that diseased cells with mutations in splicing factors are vulnerable to radiotherapy.
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Affiliation(s)
- Shelly Sorrells
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Sara Nik
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mattie J Casey
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Rosannah C Cameron
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Harold Truong
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Cristhian Toruno
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Michelle Gulfo
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Albert Lowe
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cicely Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Rodney A Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Teresa V Bowman
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA .,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Abstract
Human myeloid malignancies represent a substantial disease burden to individuals, with significant morbidity and death. The genetic underpinnings of disease formation and progression remain incompletely understood. Large-scale human population studies have identified a high frequency of potential driver mutations in spliceosomal and epigenetic regulators that contribute to malignancies, such as myelodysplastic syndromes (MDS) and leukemias. The high conservation of cell types and genes between humans and model organisms permits the investigation of the underlying mechanisms of leukemic development and potential therapeutic testing in genetically pliable pre-clinical systems. Due to the many technical advantages, such as large-scale screening, lineage-tracing studies, tumor transplantation, and high-throughput drug screening approaches, zebrafish is emerging as a model system for myeloid malignancies. In this review, we discuss recent advances in MDS and leukemia using the zebrafish model.
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Affiliation(s)
- Kathryn S Potts
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, United States
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28
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Habbsa S, McKinstry M, Bowman TV. “Sea”-ing Is Believing: In Vivo Imaging of Hematopoietic Stem Cells and Cancer Using Zebrafish. Curr Stem Cell Rep 2017. [DOI: 10.1007/s40778-017-0088-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Abstract
Hematopoietic stem cells (HSCs) posses the ability to maintain the blood system of an organism from birth to adulthood. The behavior of HSCs is modulated by its microenvironment. During development, HSCs acquire the instructions to self-renew and differentiate into all blood cell fates by passing through several developmental microenvironments. In this chapter, we discuss the signals and cell types that inform HSC decisions throughout ontogeny with a focus on HSC specification, mobilization, migration, and engraftment.
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Affiliation(s)
- Sara Nik
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joshua T Weinreb
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Teresa V Bowman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Departments of Molecular Biology and Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, USA.
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30
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Trompouki E, Flores-Figueroa E, Lucas D, Bowman TV. From the bedside to the bench: new discoveries on blood cell fate and function. Exp Hematol 2016; 47:24-30. [PMID: 27931853 DOI: 10.1016/j.exphem.2016.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 11/17/2022]
Abstract
Controversy and context: two words that exemplified this year's International Society for Experimental Hematology meeting. Leaders in the field of hematology from around the world gathered in San Diego in August of 2016 to discuss cutting-edge research on diverse topics such as hemoglobin switching, hematopoietic stem cell emergence, leukemogenesis, and aging. Major questions discussed included the "when, where, and how" of hematopoietic emergence, bone marrow residence, and disease origination. This meeting summary covers some of the conference highlights.
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Affiliation(s)
- Eirini Trompouki
- Max Planck Institute of Immunobiology and Epigenetics, Department of Cellular and Molecular Immunology, Freiburg, Germany
| | - Eugenia Flores-Figueroa
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social), Mexico City, Mexico
| | - Daniel Lucas
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Teresa V Bowman
- Departments of Developmental and Molecular Biology and Medicine (Oncology), Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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31
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De La Garza A, Sinha A, Bowman TV. Concise Review: Hematopoietic Stem Cell Origins: Lessons from Embryogenesis for Improving Regenerative Medicine. Stem Cells Transl Med 2016; 6:60-67. [PMID: 28170201 PMCID: PMC5442726 DOI: 10.5966/sctm.2016-0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/16/2016] [Indexed: 12/04/2022] Open
Abstract
Hematopoietic stem cells (HSCs) have extensive regenerative capacity to replace all blood cell types, an ability that is harnessed in the clinic for bone marrow transplantation. Finding appropriate donors remains a major limitation to more extensive usage of HSC‐based therapies. Derivation of patient‐specific HSCs from pluripotent stem cells offers great promise to remedy this problem if scientists could crack the code on how to make robust, transplantable HSCs in a dish. Studies delving into the native origins of HSC production during embryonic development should supply the necessary playbook. This review presents recent discoveries from animal models, with a focus on zebrafish, and discusses the implications of these new advances in the context of prior knowledge. The focus is on the latest research exploring the role of epigenetic regulation, signaling pathways, and niche components needed for proper HSC formation. These studies provide new directions that should be explored for de novo generation and expansion of HSCs for regenerative therapies. Stem Cells Translational Medicine2017;6:60–67
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Affiliation(s)
- Adriana De La Garza
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Arpan Sinha
- Division of Pediatric Hematology/Oncology, Children's Hospital at Montefiore, Bronx, New York, USA
| | - Teresa V. Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, New York, USA
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32
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De La Garza A, Cameron RC, Nik S, Payne SG, Bowman TV. Spliceosomal component Sf3b1 is essential for hematopoietic differentiation in zebrafish. Exp Hematol 2016; 44:826-837.e4. [PMID: 27260753 DOI: 10.1016/j.exphem.2016.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/29/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
SF3B1 (Splicing factor 3b, subunit 1) is one of the most commonly mutated factors in myelodysplastic syndrome (MDS). Although the genetic correlation between SF3B1 mutations and MDS etiology are quite strong, no in vivo model currently exists to explore how SF3B1 loss alters blood cell development. Using zebrafish mutants, we show here that proper function of Sf3b1 is required for all hematopoietic lineages. As in MDS patients, zebrafish sf3b1 mutants develop a macrocytic-anemia-like phenotype due to a block in maturation at a late progenitor stage. The mutant embryos also develop neutropenia, because their primitive myeloid cells fail to mature and turn on differentiation markers such as l-plastin and myeloperoxidase. In contrast, production of definitive hematopoietic stem and progenitor cells (HSPCs) from hemogenic endothelial cells within the dorsal aorta is greatly diminished, whereas arterial endothelial cells are correctly fated. Notch signaling, imperative for the endothelial-to-hematopoietic transition, is also normal, indicating that HSPC induction is blocked in sf3b1 mutants downstream or independent of Notch signaling. The data demonstrate that Sf3b1 function is necessary during key differentiation fate decisions in multiple blood cell types. Zebrafish sf3b1 mutants offer a novel animal model with which to explore the role of splicing in hematopoietic development and provide an excellent in vivo system with which to delve into the question of why and how Sf3b1 dysfunction is detrimental to hematopoietic differentiation, which could improve MDS diagnosis and treatment.
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Affiliation(s)
- Adriana De La Garza
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rosannah C Cameron
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sara Nik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sara G Payne
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, USA.
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33
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Huang J, Liu X, Li D, Shao Z, Cao H, Zhang Y, Trompouki E, Bowman TV, Zon LI, Yuan GC, Orkin SH, Xu J. Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Dev Cell 2016; 36:9-23. [PMID: 26766440 DOI: 10.1016/j.devcel.2015.12.014] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/15/2015] [Accepted: 12/10/2015] [Indexed: 11/19/2022]
Abstract
Enhancers are the primary determinants of cell identity, but the regulatory components controlling enhancer turnover during lineage commitment remain largely unknown. Here we compare the enhancer landscape, transcriptional factor occupancy, and transcriptomic changes in human fetal and adult hematopoietic stem/progenitor cells and committed erythroid progenitors. We find that enhancers are modulated pervasively and direct lineage- and stage-specific transcription. GATA2-to-GATA1 switch is prevalent at dynamic enhancers and drives erythroid enhancer commissioning. Examination of lineage-specific enhancers identifies transcription factors and their combinatorial patterns in enhancer turnover. Importantly, by CRISPR/Cas9-mediated genomic editing, we uncover functional hierarchy of constituent enhancers within the SLC25A37 super-enhancer. Despite indistinguishable chromatin features, we reveal through genomic editing the functional diversity of several GATA switch enhancers in which enhancers with opposing functions cooperate to coordinate transcription. Thus, genome-wide enhancer profiling coupled with in situ enhancer editing provide critical insights into the functional complexity of enhancers during development.
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Affiliation(s)
- Jialiang Huang
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dan Li
- Harvard College, Cambridge, MA 02138, USA
| | - Zhen Shao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Cao
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Eirini Trompouki
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Teresa V Bowman
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Leonard I Zon
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Flores-Figueroa E, Essers M, Bowman TV. Hematopoiesis "awakens": Evolving technologies, the force behind them. Exp Hematol 2015; 44:101-5. [PMID: 26546749 DOI: 10.1016/j.exphem.2015.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 11/24/2022]
Abstract
Amid the beauty of the Kyoto countryside, leaders in the field of hematology met at the 44th annual International Society for Experimental Hematology (ISEH) meeting in late September 2015. Led by ISEH President Paul Frenette and President-Elect David Traver, the meeting covered many aspects of hematopoiesis with a focus on technology. At the meeting, it became clear that the future of hematology is being shaped by innovations in single-cell "omics" and imaging approaches that will provide answers to age-old questions on cellular identity. In this meeting review, we highlight the advances presented in understanding the hematopoietic stem cell (HSC) niche, heterogeneity, stress response, epigenetics, and how these processes change from birth to old age.
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Affiliation(s)
- Eugenia Flores-Figueroa
- Oncology Research Unit, Oncology Hospital, National Medical Center, IMSS, Mexico City, Mexico
| | - Marieke Essers
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM GmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Hematopoietic Stem Cells and Stress Group, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Teresa V Bowman
- Departments of Developmental and Molecular Biology and Medicine (Oncology), Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY.
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35
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Li P, Lahvic JL, Binder V, Pugach EK, Riley EB, Tamplin OJ, Panigrahy D, Bowman TV, Barrett FG, Heffner GC, McKinney-Freeman S, Schlaeger TM, Daley GQ, Zeldin DC, Zon LI. Epoxyeicosatrienoic acids enhance embryonic haematopoiesis and adult marrow engraftment. Nature 2015. [PMID: 26201599 PMCID: PMC4754787 DOI: 10.1038/nature14569] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Haematopoietic stem and progenitor cell (HSPC) transplant is a widely used treatment for life-threatening conditions including leukemia; however, the molecular mechanisms regulating HSPC engraftment of the recipient niche remain incompletely understood. Here, we developed a competitive HSPC transplant method in adult zebrafish, using in vivo imaging as a non-invasive readout. We used this system to conduct a chemical screen and identified epoxyeicosatrienoic acids (EET) as a family of lipids1,2 that enhance HSPC engraftment. EETs’ pro-haematopoietic effects were conserved in the developing zebrafish embryo, where 11,12-EET promoted HSPC specification by activating a unique AP-1/runx1 transcription program autonomous to the haemogenic endothelium. This effect required the activation of the PI3K pathway, specifically PI3Kγ. In adult HSPCs, 11,12-EET induced transcriptional programs, including AP-1 activation, which modulate multiple cellular processes, such as migration, to promote engraftment. Finally, we demonstrated that the EET effects on enhancing HSPC homing and engraftment are conserved in mammals. Our study established a novel method to explore the molecular mechanisms of HSPC engraftment, and discovered a previously unrecognized, evolutionarily conserved pathway regulating multiple haematopoietic generation and regeneration processes. EETs may have clinical application in marrow or cord blood transplantation.
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Affiliation(s)
- Pulin Li
- 1] Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA [2] Chemical Biology Program, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jamie L Lahvic
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Vera Binder
- 1] Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA [2] Department of Hematology and Oncology, Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, 80337 Munich, Germany
| | - Emily K Pugach
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Elizabeth B Riley
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Owen J Tamplin
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Dipak Panigrahy
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Teresa V Bowman
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Francesca G Barrett
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Garrett C Heffner
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Shannon McKinney-Freeman
- Department of Haematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Thorsten M Schlaeger
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - George Q Daley
- Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA
| | - Darryl C Zeldin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Leonard I Zon
- 1] Stem Cell Program and Division of Haematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachuestts 02115, USA [2] Chemical Biology Program, Harvard University, Cambridge, Massachusetts 02138, USA
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Bowman TV, Trompouki E, Zon LI. Linking hematopoietic regeneration to developmental signaling pathways: a story of BMP and Wnt. Cell Cycle 2012; 11:424-5. [PMID: 22262185 DOI: 10.4161/cc.11.3.19161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Abstract
In recent years in vivo chemical screening in zebrafish has emerged as a rapid and efficient method to identify lead compounds that modulate specific biological processes. By performing primary screening in vivo, the bioactivity, toxicity, and off-target side effects are determined from the onset of drug development. A recent study demonstrates that in vivo screening can be used successfully to perform structure-activity relationship (SAR) studies. This work validates the zebrafish as an effective model for not only drug discovery but also drug optimization.
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Affiliation(s)
- Teresa V. Bowman
- Stem Cell Program and Division of Hematology and Oncology, Children’s Hospital Boston and Howard Hughes Medical Institute, 300 Longwood Avenue, Boston, Massachusetts 02115
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology and Oncology, Children’s Hospital Boston and Howard Hughes Medical Institute, 300 Longwood Avenue, Boston, Massachusetts 02115
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Lengerke C, Schmitt S, Bowman TV, Jang IH, Maouche-Chretien L, McKinney-Freeman S, Davidson AJ, Hammerschmidt M, Rentzsch F, Green JBA, Zon LI, Daley GQ. BMP and Wnt specify hematopoietic fate by activation of the Cdx-Hox pathway. Cell Stem Cell 2009; 2:72-82. [PMID: 18371423 DOI: 10.1016/j.stem.2007.10.022] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 10/11/2007] [Accepted: 10/31/2007] [Indexed: 01/10/2023]
Abstract
The formation of blood in the embryo is dependent on bone morphogenetic protein (BMP), but how BMP signaling intersects with other regulators of hematopoietic development is unclear. Using embryonic stem (ES) cells, we show that BMP4 first induces ventral-posterior (V-P) mesoderm and subsequently directs mesodermal cells toward blood fate by activating Wnt3a and upregulating Cdx and Hox genes. When BMP signaling is blocked during this latter phase, enforced expression of either Cdx1 or Cdx4 rescues hematopoietic development, thereby placing BMP4 signaling upstream of the Cdx-Hox pathway. Wnt signaling cooperates in BMP-induced hemogenesis, and the Wnt effector LEF1 mediates BMP4 activation of Cdx genes. Our data suggest that BMP signaling plays two distinct and sequential roles during blood formation, initially as an inducer of mesoderm, and later to specify blood via activation of Wnt signaling and the Cdx-Hox pathway.
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Affiliation(s)
- Claudia Lengerke
- Division of Pediatric Hematology/Oncology, Children's Hospital Boston and Dana Farber Cancer Institute, Boston, MA 02115, USA
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Abstract
Gene expression profiling using microarrays is a powerful method for studying the biology of hematopoietic stem cells (HSCs). Here, we present methods for activating HSCs with the chemotherapeutic drug 5-Fluorouracil, isolating HSCs from whole bone marrow, and performing microarray analysis. We also discuss quality control criteria for identifying good arrays and bioinformatics strategies for analyzing them. Using these methods, we have characterized the gene expression signatures of HSC quiescence and proliferation and have constructed a molecular model of HSC activation and self-renewal.
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Affiliation(s)
- Teresa V Bowman
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
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40
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North TE, Goessling W, Walkley CR, Lengerke C, Kopani KR, Lord AM, Weber GJ, Bowman TV, Jang IH, Grosser T, Fitzgerald GA, Daley GQ, Orkin SH, Zon LI. Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature 2007; 447:1007-11. [PMID: 17581586 PMCID: PMC2775137 DOI: 10.1038/nature05883] [Citation(s) in RCA: 866] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 04/30/2007] [Indexed: 11/08/2022]
Abstract
Haematopoietic stem cell (HSC) homeostasis is tightly controlled by growth factors, signalling molecules and transcription factors. Definitive HSCs derived during embryogenesis in the aorta-gonad-mesonephros region subsequently colonize fetal and adult haematopoietic organs. To identify new modulators of HSC formation and homeostasis, a panel of biologically active compounds was screened for effects on stem cell induction in the zebrafish aorta-gonad-mesonephros region. Here, we show that chemicals that enhance prostaglandin (PG) E2 synthesis increased HSC numbers, and those that block prostaglandin synthesis decreased stem cell numbers. The cyclooxygenases responsible for PGE2 synthesis were required for HSC formation. A stable derivative of PGE2 improved kidney marrow recovery following irradiation injury in the adult zebrafish. In murine embryonic stem cell differentiation assays, PGE2 caused amplification of multipotent progenitors. Furthermore, ex vivo exposure to stabilized PGE2 enhanced spleen colony forming units at day 12 post transplant and increased the frequency of long-term repopulating HSCs present in murine bone marrow after limiting dilution competitive transplantation. The conserved role for PGE2 in the regulation of vertebrate HSC homeostasis indicates that modulation of the prostaglandin pathway may facilitate expansion of HSC number for therapeutic purposes.
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Affiliation(s)
- Trista E North
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Bowman TV, McCooey AJ, Merchant AA, Ramos CA, Fonseca P, Poindexter A, Bradfute SB, Oliveira DM, Green R, Zheng Y, Jackson KA, Chambers SM, McKinney-Freeman SL, Norwood KG, Darlington G, Gunaratne PH, Steffen D, Goodell MA. Differential mRNA processing in hematopoietic stem cells. Stem Cells 2005; 24:662-70. [PMID: 16373690 DOI: 10.1634/stemcells.2005-0552] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Hematopoietic stem cells (HSCs) maintain tissue homeostasis by rapidly responding to environmental changes. Although this function is well understood, the molecular mechanisms governing this characteristic are largely unknown. We used a sequenced-based strategy to explore the role of both transcriptional and post-transcriptional regulation in HSC biology. We characterized the gene expression differences between HSCs, both quiescent and proliferating, and their differentiated progeny. This analysis revealed a large fraction of sequence tags aligned to intronic sequences, which we showed were derived from unspliced transcripts. A comparison of the biological properties of the observed spliced versus unspliced transcripts in HSCs showed that the unspliced transcripts were enriched in genes involved in DNA binding and RNA processing. In addition, levels of unspliced message decreased in a transcript-specific fashion after HSC activation in vivo. This change in unspliced transcript level coordinated with increases in gene expression of splicing machinery components. Combined, these results suggest that post-transcriptional regulation is important in HSC activation in vivo.
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Affiliation(s)
- Teresa V Bowman
- Cell and Gene Therapy Center, Baylor College of Medicine, N1030, One Baylor Plaza, Houston, Texas 77030, USA
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