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Zeng X, Shi C, Han Y, Hu K, Li X, Wei C, Ding L, Cui J, Huang S, Xu Y, Zhang M, Shan W, Luo Q, Yu J, Zheng Z, Li X, Qian P, Huang H. A metabolic atlas of blood cells in young and aged mice identifies uridine as a metabolite to rejuvenate aged hematopoietic stem cells. NATURE AGING 2024:10.1038/s43587-024-00669-1. [PMID: 39020094 DOI: 10.1038/s43587-024-00669-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/19/2024] [Indexed: 07/19/2024]
Abstract
Aging of hematopoietic stem cells (HSCs) is accompanied by impaired self-renewal ability, myeloid skewing, immunodeficiencies and increased susceptibility to malignancies. Although previous studies highlighted the pivotal roles of individual metabolites in hematopoiesis, comprehensive and high-resolution metabolomic profiles of different hematopoietic cells across ages are still lacking. In this study, we created a metabolome atlas of different blood cells across ages in mice. We reveal here that purine, pyrimidine and retinol metabolism are enriched in young hematopoietic stem and progenitor cells (HSPCs), whereas glutamate and sphingolipid metabolism are concentrated in aged HSPCs. Through metabolic screening, we identified uridine as a potential regulator to rejuvenate aged HSPCs. Mechanistically, uridine treatment upregulates the FoxO signaling pathway and enhances self-renewal while suppressing inflammation in aged HSCs. Finally, we constructed an open-source platform for public easy access and metabolomic analysis in blood cells. Collectively, we provide a resource for metabolic studies in hematopoiesis that can contribute to future anti-aging metabolite screening.
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Affiliation(s)
- Xiangjun Zeng
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Ce Shi
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yingli Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Kejia Hu
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Xiaoqing Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Cong Wei
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Lijuan Ding
- Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jiazhen Cui
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Simao Huang
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yulin Xu
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Meng Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Wei Shan
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Qian Luo
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Jian Yu
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | | | - Xia Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Institute of Hematology, Zhejiang University, Hangzhou, China.
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.
| | - Pengxu Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Institute of Hematology, Zhejiang University, Hangzhou, China.
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - He Huang
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
- Institute of Hematology, Zhejiang University, Hangzhou, China.
- Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.
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2
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Shahbaz S, Rosero EP, Syed H, Hnatiuk M, Bozorgmehr N, Rahmati A, Zia S, Plemel J, Osman M, Elahi S. Bipotential B-neutrophil progenitors are present in human and mouse bone marrow and emerge in the periphery upon stress hematopoiesis. mBio 2024:e0159924. [PMID: 39012145 DOI: 10.1128/mbio.01599-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/30/2024] [Indexed: 07/17/2024] Open
Abstract
Hematopoiesis is a tightly regulated process that gets skewed toward myelopoiesis. This restrains lymphopoiesis, but the role of lymphocytes in this process is not well defined. To unravel the intricacies of neutrophil responses in COVID-19, we performed bulk RNAseq on neutrophils from healthy controls and COVID-19 patients. Principal component analysis revealed distinguishing neutrophil gene expression alterations in COVID-19 patients. ICU and ward patients displayed substantial transcriptional changes, with ICU patients exhibiting a more pronounced response. Intriguingly, neutrophils from COVID-19 patients, notably ICU patients, exhibited an enrichment of immunoglobulin (Ig) and B cell lineage-associated genes, suggesting potential lineage plasticity. We validated our RNAseq findings in a larger cohort. Moreover, by reanalyzing single-cell RNA sequencing (scRNAseq) data on human bone marrow (BM) granulocytes, we identified the cluster of granulocyte-monocyte progenitors (GMP) enriched with Ig and B cell lineage-associated genes. These cells with lineage plasticity may serve as a resource depending on the host's needs during severe systemic infection. This distinct B cell subset may play a pivotal role in promoting myelopoiesis in response to infection. The scRNAseq analysis of BM neutrophils in infected mice further supported our observations in humans. Finally, our studies using an animal model of acute infection implicate IL-7/GM-CSF in influencing neutrophil and B cell dynamics. Elevated GM-CSF and reduced IL-7 receptor expression in COVID-19 patients imply altered hematopoiesis favoring myeloid cells over B cells. Our findings provide novel insights into the relationship between the B-neutrophil lineages during severe infection, hinting at potential implications for disease pathogenesis. IMPORTANCE This study investigates the dynamics of hematopoiesis in COVID-19, focusing on neutrophil responses. Through RNA sequencing of neutrophils from healthy controls and COVID-19 patients, distinct gene expression alterations are identified, particularly in ICU patients. Notably, neutrophils from COVID-19 patients, especially in the ICU, exhibit enrichment of immunoglobulin and B cell lineage-associated genes, suggesting potential lineage plasticity. Validation in a larger patient cohort and single-cell analysis of bone marrow granulocytes support the presence of granulocyte-monocyte progenitors with B cell lineage-associated genes. The findings propose a link between B-neutrophil lineages during severe infection, implicating a potential role for these cells in altered hematopoiesis favoring myeloid cells over B cells. Elevated GM-CSF and reduced IL-7 receptor expression in stress hematopoiesis suggest cytokine involvement in these dynamics, providing novel insights into disease pathogenesis.
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Affiliation(s)
- Shima Shahbaz
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, Canada
| | - Eliana Perez Rosero
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, Canada
| | - Hussain Syed
- Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Canada
| | - Mark Hnatiuk
- Division of Hematology, University of Alberta, Edmonton, Canada
| | - Najmeh Bozorgmehr
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, Canada
| | - Amirhossein Rahmati
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, Canada
| | - Sameera Zia
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Jason Plemel
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
- Division of Neurology, Department of Medicine, University of Alberta, Edmonton, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Canada
| | - Mohammed Osman
- Department of Medicine, Division of Rheumatology, University of Alberta, Edmonton, Canada
| | - Shokrollah Elahi
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, Canada
- Glycomics Institute of Alberta, University of Alberta, Edmonton, Canada
- Women and Children Health Research Institute, University of Alberta, Edmonton, Canada
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3
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Kim Y, Calderon AA, Favaro P, Glass DR, Tsai AG, Ho D, Borges L, Greenleaf WJ, Bendall SC. Terminal deoxynucleotidyl transferase and CD84 identify human multi-potent lymphoid progenitors. Nat Commun 2024; 15:5910. [PMID: 39003273 PMCID: PMC11246490 DOI: 10.1038/s41467-024-49883-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/24/2024] [Indexed: 07/15/2024] Open
Abstract
Lymphoid specification in human hematopoietic progenitors is not fully understood. To better associate lymphoid identity with protein-level cell features, we conduct a highly multiplexed single-cell proteomic screen on human bone marrow progenitors. This screen identifies terminal deoxynucleotidyl transferase (TdT), a specialized DNA polymerase intrinsic to VDJ recombination, broadly expressed within CD34+ progenitors prior to B/T cell emergence. While these TdT+ cells coincide with granulocyte-monocyte progenitor (GMP) immunophenotype, their accessible chromatin regions show enrichment for lymphoid-associated transcription factor (TF) motifs. TdT expression on GMPs is inversely related to the SLAM family member CD84. Prospective isolation of CD84lo GMPs demonstrates robust lymphoid potentials ex vivo, while still retaining significant myeloid differentiation capacity, akin to LMPPs. This multi-omic study identifies human bone marrow lymphoid-primed progenitors, further defining the lympho-myeloid axis in human hematopoiesis.
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Affiliation(s)
- YeEun Kim
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ariel A Calderon
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - David R Glass
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Albert G Tsai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Daniel Ho
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Luciene Borges
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
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4
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Ruoss S, Nasamran CA, Ball ST, Chen JL, Halter KN, Bruno KA, Whisenant TC, Parekh JN, Dorn SN, Esparza MC, Bremner SN, Fisch KM, Engler AJ, Ward SR. Comparative single-cell transcriptional and proteomic atlas of clinical-grade injectable mesenchymal source tissues. SCIENCE ADVANCES 2024; 10:eadn2831. [PMID: 38996032 PMCID: PMC11244553 DOI: 10.1126/sciadv.adn2831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/06/2024] [Indexed: 07/14/2024]
Abstract
Bone marrow aspirate concentrate (BMAC) and adipose-derived stromal vascular fraction (ADSVF) are the most marketed stem cell therapies to treat a variety of conditions in the general population and elite athletes. Both tissues have been used interchangeably clinically even though their detailed composition, heterogeneity, and mechanisms of action have neither been rigorously inventoried nor compared. This lack of information has prevented investigations into ideal dosages and has facilitated anecdata and misinformation. Here, we analyzed single-cell transcriptomes, proteomes, and flow cytometry profiles from paired clinical-grade BMAC and ADSVF. This comparative transcriptional atlas challenges the prevalent notion that there is one therapeutic cell type present in both tissues. We also provide data of surface markers that may enable isolation and investigation of cell (sub)populations. Furthermore, the proteome atlas highlights intertissue and interpatient heterogeneity of injected proteins with potentially regenerative or immunomodulatory capacities. An interactive webtool is available online.
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Affiliation(s)
- Severin Ruoss
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Chanond A. Nasamran
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
| | - Scott T. Ball
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Jeffrey L. Chen
- Department of Anesthesiology, Center for Pain, UC San Diego, La Jolla, CA, USA
| | - Kenneth N. Halter
- Department of Anesthesiology, Center for Pain, UC San Diego, La Jolla, CA, USA
| | - Kelly A. Bruno
- Department of Anesthesiology, Center for Pain, UC San Diego, La Jolla, CA, USA
| | - Thomas C. Whisenant
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
| | - Jesal N. Parekh
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Shanelle N. Dorn
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | - Mary C. Esparza
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
| | | | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, UC San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, UC San Diego, La Jolla, CA, USA
| | - Adam J. Engler
- Chien-Lay Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Samuel R. Ward
- Department of Orthopaedic Surgery, UC San Diego, La Jolla, CA, USA
- Chien-Lay Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Department of Radiology, UC San Diego, La Jolla, CA, USA
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5
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Wang J, Liang Y, Xu C, Gao J, Tong J, Shi L. The heterogeneity of erythroid cells: insight at the single-cell transcriptome level. Cell Tissue Res 2024:10.1007/s00441-024-03903-9. [PMID: 38953986 DOI: 10.1007/s00441-024-03903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Erythroid cells, the most prevalent cell type in blood, are one of the earliest products and permeate through the entire process of hematopoietic development in the human body, the oxygen-transporting function of which is crucial for maintaining overall health and life support. Previous investigations into erythrocyte differentiation and development have primarily focused on population-level analyses, lacking the single-cell perspective essential for comprehending the intricate pathways of erythroid maturation, differentiation, and the encompassing cellular heterogeneity. The continuous optimization of single-cell transcriptome sequencing technology, or single-cell RNA sequencing (scRNA-seq), provides a powerful tool for life sciences research, which has a particular superiority in the identification of unprecedented cell subgroups, the analyzing of cellular heterogeneity, and the transcriptomic characteristics of individual cells. Over the past decade, remarkable strides have been taken in the realm of single-cell RNA sequencing technology, profoundly enhancing our understanding of erythroid cells. In this review, we systematically summarize the recent developments in single-cell transcriptome sequencing technology and emphasize their substantial impact on the study of erythroid cells, highlighting their contributions, including the exploration of functional heterogeneity within erythroid populations, the identification of novel erythrocyte subgroups, the tracking of different erythroid lineages, and the unveiling of mechanisms governing erythroid fate decisions. These findings not only invigorate erythroid cell research but also offer new perspectives on the management of diseases related to erythroid cells.
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Affiliation(s)
- Jingwei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yipeng Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Changlu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin, 300020, China.
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6
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Garg S, Ni W, Chowdhury B, Weisberg EL, Sattler M, Griffin JD. BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation. Cell Death Differ 2024; 31:868-880. [PMID: 38816579 PMCID: PMC11239944 DOI: 10.1038/s41418-024-01306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Bromodomain containing protein 9 (BRD9), a member of the non-canonical BRG1/BRM-associated factor (ncBAF) chromatin remodeling complex, has been implicated as a synthetic lethal target in AML but its function in normal human hematopoiesis is unknown. In hematopoietic stem and progenitor cells (HSPC) genomic or chemical inhibition of BRD9 led to a proliferative disadvantage and loss of stem cells in vitro. Human HSPCs with reduced BRD9 protein levels produced lower numbers of immature mixed multipotent GEMM colonies in semi-solid media. In lineage-promoting culture conditions, cells with reduced BRD9 levels failed to differentiate into the megakaryocytic lineage and showed delayed differentiation into erythroid cells but enhanced terminal myeloid differentiation. HSPCs with BRD9 knock down (KD) had reduced long-term multilineage engraftment in a xenotransplantation assay. An increased number of downregulated genes in RNAseq analysis after BRD9 KD coupled with a gain in chromatin accessibility at the promoters of several repressive transcription factors (TF) suggest that BRD9 functions in the maintenance of active transcription during HSC differentiation. In particular, the hematopoietic master regulator GATA1 was identified as one of the core TFs regulating the gene networks modulated by BRD9 loss in HSPCs. BRD9 inhibition reduced a GATA1-luciferase reporter signal, further suggesting a role for BRD9 in regulating GATA1 activity. BRD9 is therefore an additional example of epigenetic regulation of human hematopoiesis.
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Affiliation(s)
- Swati Garg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Wei Ni
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Basudev Chowdhury
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Ellen L Weisberg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Martin Sattler
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - James D Griffin
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA.
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA.
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7
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Moiani A, Letort G, Lizot S, Chalumeau A, Foray C, Felix T, Le Clerre D, Temburni-Blake S, Hong P, Leduc S, Pinard N, Marechal A, Seclen E, Boyne A, Mayer L, Hong R, Pulicani S, Galetto R, Gouble A, Cavazzana M, Juillerat A, Miccio A, Duclert A, Duchateau P, Valton J. Non-viral DNA delivery and TALEN editing correct the sickle cell mutation in hematopoietic stem cells. Nat Commun 2024; 15:4965. [PMID: 38862518 PMCID: PMC11166989 DOI: 10.1038/s41467-024-49353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
Sickle cell disease is a devastating blood disorder that originates from a single point mutation in the HBB gene coding for hemoglobin. Here, we develop a GMP-compatible TALEN-mediated gene editing process enabling efficient HBB correction via a DNA repair template while minimizing risks associated with HBB inactivation. Comparing viral versus non-viral DNA repair template delivery in hematopoietic stem and progenitor cells in vitro, both strategies achieve comparable HBB correction and result in over 50% expression of normal adult hemoglobin in red blood cells without inducing β-thalassemic phenotype. In an immunodeficient female mouse model, transplanted cells edited with the non-viral strategy exhibit higher engraftment and gene correction levels compared to those edited with the viral strategy. Transcriptomic analysis reveals that non-viral DNA repair template delivery mitigates P53-mediated toxicity and preserves high levels of long-term hematopoietic stem cells. This work paves the way for TALEN-based autologous gene therapy for sickle cell disease.
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Affiliation(s)
| | - Gil Letort
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Sabrina Lizot
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Anne Chalumeau
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Chloe Foray
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Tristan Felix
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | | | | | - Patrick Hong
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Sophie Leduc
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Noemie Pinard
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Alan Marechal
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | | | - Alex Boyne
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Louisa Mayer
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Robert Hong
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | | | - Roman Galetto
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Agnès Gouble
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Marina Cavazzana
- Biotherapy Clinical Investigation Center, Necker Children's Hospital, Assistance Publique Hopitaux de Paris, Paris, France
- Human Lymphohematopoiesis Laboratory, Imagine Institute, INSERM UMR1163, Paris Cité University, Paris, France
- Biotherapy Department, Necker Children's Hospital, Assistance Publique Hopitaux de Paris, Paris, France
| | | | - Annarita Miccio
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | | | | | - Julien Valton
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France.
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8
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Yamada Y, Zheng Z, Jad AK, Yamashita M. Lethal and sublethal effects of programmed cell death pathways on hematopoietic stem cells. Exp Hematol 2024; 134:104214. [PMID: 38582294 DOI: 10.1016/j.exphem.2024.104214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Programmed cell death is an evolutionally conserved cellular process in multicellular organisms that eliminates unnecessary or rogue cells during development, infection, and carcinogenesis. Hematopoietic stem cells (HSCs) are a rare, self-renewing, and multipotent cell population necessary for the establishment and regeneration of the hematopoietic system. Counterintuitively, key components necessary for programmed cell death induction are abundantly expressed in long-lived HSCs, which often survive myeloablative stress by engaging a prosurvival response that counteracts cell death-inducing stimuli. Although HSCs are well known for their apoptosis resistance, recent studies have revealed their unique vulnerability to certain types of programmed necrosis, such as necroptosis and ferroptosis. Moreover, emerging evidence has shown that programmed cell death pathways can be sublethally activated to cause nonlethal consequences such as innate immune response, organelle dysfunction, and mutagenesis. In this review, we summarized recent findings on how divergent cell death programs are molecularly regulated in HSCs. We then discussed potential side effects caused by sublethal activation of programmed cell death pathways on the functionality of surviving HSCs.
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Affiliation(s)
- Yuta Yamada
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Zhiqian Zheng
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Division of Experimental Hematology, Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alaa K Jad
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masayuki Yamashita
- Division of Stem Cell and Molecular Medicine, Centre for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Division of Experimental Hematology, Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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9
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Do BT, Hsu PP, Vermeulen SY, Wang Z, Hirz T, Abbott KL, Aziz N, Replogle JM, Bjelosevic S, Paolino J, Nelson SA, Block S, Darnell AM, Ferreira R, Zhang H, Milosevic J, Schmidt DR, Chidley C, Harris IS, Weissman JS, Pikman Y, Stegmaier K, Cheloufi S, Su XA, Sykes DB, Vander Heiden MG. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress. Dev Cell 2024:S1534-5807(24)00327-7. [PMID: 38823395 DOI: 10.1016/j.devcel.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/14/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.
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Affiliation(s)
- Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peggy P Hsu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02113, USA; Rogel Cancer Center and Division of Hematology and Oncology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sidney Y Vermeulen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhishan Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Najihah Aziz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Bjelosevic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha A Nelson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel Block
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hanyu Zhang
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jelena Milosevic
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Daniel R Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jonathan S Weissman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA; Stem Cell Center, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, Riverside, CA 92521, USA
| | - Xiaofeng A Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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10
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Miyake K, Ito J, Karasuyama H. Novel insights into the ontogeny of basophils. FRONTIERS IN ALLERGY 2024; 5:1402841. [PMID: 38803659 PMCID: PMC11128600 DOI: 10.3389/falgy.2024.1402841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024] Open
Abstract
Basophils are the least common granulocytes, accounting for <1% of peripheral blood leukocytes. In the last 20 years, analytical tools for mouse basophils have been developed, and we now recognize that basophils play critical roles in various immune reactions, including the development of allergic inflammation and protective immunity against parasites. Moreover, the combined use of flow cytometric analyses and knockout mice has uncovered several progenitor cells committed to basophils in mice. Recently, advancements in single-cell RNA sequencing (scRNA-seq) technologies have challenged the classical view of the differentiation of various hematopoietic cell lineages. This is also true for basophil differentiation, and studies using scRNA-seq analysis have provided novel insights into basophil differentiation, including the association of basophil differentiation with that of erythrocyte/megakaryocyte and the discovery of novel basophil progenitor cells in the mouse bone marrow. In this review, we summarize the recent findings of basophil ontogeny in both mice and humans, mainly focusing on studies using scRNA-seq analyses.
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Affiliation(s)
- Kensuke Miyake
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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11
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Filia A, Mitroulis I, Loukogiannaki C, Grigoriou M, Banos A, Sentis G, Giannouli S, Karali V, Athanasiadis E, Kokkinopoulos I, Boumpas DT. Single-cell transcriptomic analysis of hematopoietic progenitor cells from patients with systemic lupus erythematosus reveals interferon-inducible reprogramming in early progenitors. Front Immunol 2024; 15:1383358. [PMID: 38779657 PMCID: PMC11109438 DOI: 10.3389/fimmu.2024.1383358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Immune cells that contribute to the pathogenesis of systemic lupus erythematosus (SLE) derive from adult hematopoietic stem and progenitor cells (HSPCs) within the bone marrow (BM). For this reason, we reasoned that fundamental abnormalities in SLE can be traced to a BM-derived HSPC inflammatory signature. Methods BM samples from four SLE patients, six healthy controls, and two umbilical cord blood (CB) samples were used. CD34+ cells were isolated from BM and CB samples, and single-cell RNA-sequencing was performed. Results A total of 426 cells and 24,473 genes were used in the analysis. Clustering analysis resulted in seven distinct clusters of cell types. Mutually exclusive markers, which were characteristic of each cell type, were identified. We identified three HSPC subpopulations, one of which consisted of proliferating cells (MKI67 expressing cells), one T-like, one B-like, and two myeloid-like progenitor subpopulations. Differential expression analysis revealed i) cell cycle-associated signatures, in healthy BM of HSPC clusters 3 and 4 when compared with CB, and ii) interferon (IFN) signatures in SLE BM of HSPC clusters 3 and 4 and myeloid-like progenitor cluster 5 when compared with healthy controls. The IFN signature in SLE appeared to be deregulated following TF regulatory network analysis and differential alternative splicing analysis between SLE and healthy controls in HSPC subpopulations. Discussion This study revealed both quantitative-as evidenced by decreased numbers of non-proliferating early progenitors-and qualitative differences-characterized by an IFN signature in SLE, which is known to drive loss of function and depletion of HSPCs. Chronic IFN exposure affects early hematopoietic progenitors in SLE, which may account for the immune aberrancies and the cytopenias in SLE.
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Affiliation(s)
- Anastasia Filia
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Ioannis Mitroulis
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Catherine Loukogiannaki
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Maria Grigoriou
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 1st Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aggelos Banos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - George Sentis
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Stavroula Giannouli
- 2nd Department of Internal Medicine, Ippokrateion Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassiliki Karali
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Emmanouil Athanasiadis
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Ioannis Kokkinopoulos
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Dimitrios T. Boumpas
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
- 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
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12
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Gao CF, Vaikuntanathan S, Riesenfeld SJ. Dissection and integration of bursty transcriptional dynamics for complex systems. Proc Natl Acad Sci U S A 2024; 121:e2306901121. [PMID: 38669186 PMCID: PMC11067469 DOI: 10.1073/pnas.2306901121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 03/06/2024] [Indexed: 04/28/2024] Open
Abstract
RNA velocity estimation is a potentially powerful tool to reveal the directionality of transcriptional changes in single-cell RNA-sequencing data, but it lacks accuracy, absent advanced metabolic labeling techniques. We developed an approach, TopicVelo, that disentangles simultaneous, yet distinct, dynamics by using a probabilistic topic model, a highly interpretable form of latent space factorization, to infer cells and genes associated with individual processes, thereby capturing cellular pluripotency or multifaceted functionality. Focusing on process-associated cells and genes enables accurate estimation of process-specific velocities via a master equation for a transcriptional burst model accounting for intrinsic stochasticity. The method obtains a global transition matrix by leveraging cell topic weights to integrate process-specific signals. In challenging systems, this method accurately recovers complex transitions and terminal states, while our use of first-passage time analysis provides insights into transient transitions. These results expand the limits of RNA velocity, empowering future studies of cell fate and functional responses.
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Affiliation(s)
- Cheng Frank Gao
- Department of Chemistry, University of Chicago, Chicago, IL60637
| | - Suriyanarayanan Vaikuntanathan
- Department of Chemistry, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
| | - Samantha J. Riesenfeld
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
- Department of Medicine, University of Chicago, Chicago, IL60637
- Committee on Immunology, Biological Sciences Division, University of Chicago, Chicago, IL60637
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13
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Manso BA, Rodriguez y Baena A, Forsberg EC. From Hematopoietic Stem Cells to Platelets: Unifying Differentiation Pathways Identified by Lineage Tracing Mouse Models. Cells 2024; 13:704. [PMID: 38667319 PMCID: PMC11048769 DOI: 10.3390/cells13080704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Platelets are the terminal progeny of megakaryocytes, primarily produced in the bone marrow, and play critical roles in blood homeostasis, clotting, and wound healing. Traditionally, megakaryocytes and platelets are thought to arise from multipotent hematopoietic stem cells (HSCs) via multiple discrete progenitor populations with successive, lineage-restricting differentiation steps. However, this view has recently been challenged by studies suggesting that (1) some HSC clones are biased and/or restricted to the platelet lineage, (2) not all platelet generation follows the "canonical" megakaryocytic differentiation path of hematopoiesis, and (3) platelet output is the default program of steady-state hematopoiesis. Here, we specifically investigate the evidence that in vivo lineage tracing studies provide for the route(s) of platelet generation and investigate the involvement of various intermediate progenitor cell populations. We further identify the challenges that need to be overcome that are required to determine the presence, role, and kinetics of these possible alternate pathways.
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Affiliation(s)
- Bryce A. Manso
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alessandra Rodriguez y Baena
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Program in Biomedical Sciences and Engineering, Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - E. Camilla Forsberg
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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14
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Zeng X, Wang Y, Dai M, Li W, Huang Q, Qin L, Li Y, Yan Y, Xue X, Yi F, Li W, He L, Liu Q, Qi L. Single-cell transcriptomics dissects the transcriptome alterations of hematopoietic stem cells in myelodysplastic neoplasms. J Transl Med 2024; 22:359. [PMID: 38632656 PMCID: PMC11022353 DOI: 10.1186/s12967-024-05165-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Myelodysplastic neoplasms (MDS) are myeloid neoplasms characterized by disordered differentiation of hematopoietic stem cells and a predisposition to acute myeloid leukemia (AML). The underline pathogenesis remains unclear. METHODS In this study, the trajectory of differentiation and mechanisms of leukemic transformation were explored through bioinformatics analysis of single-cell RNA-Seq data from hematopoietic stem and progenitor cells (HSPCs) in MDS patients. RESULTS Among the HSPC clusters, the proportion of common myeloid progenitor (CMP) was the main cell cluster in the patients with excess blasts (EB)/ secondary AML. Cell cycle analysis indicated the CMP of MDS patients were in an active proliferative state. The genes involved in the cell proliferation, such as MAML3 and PLCB1, were up-regulated in MDS CMP. Further validation analysis indicated that the expression levels of MAML3 and PLCB1 in patients with MDS-EB were significantly higher than those without EB. Patients with high expression of PLCB1 had a higher risk of transformation to AML. PLCB1 inhibitor can suppress proliferation, induce cell cycle arrest, and activate apoptosis of leukemic cells in vitro. CONCLUSION This study revealed the transcriptomic change of HSPCs in MDS patients along the pseudotime and indicated that PLCB1 plays a key role in the transformation of MDS into leukemia.
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Affiliation(s)
- Xiangzong Zeng
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yichen Wang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Min Dai
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wei Li
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qingtian Huang
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Lingsha Qin
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yuquan Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Yanwen Yan
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Xiangjun Xue
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Fang Yi
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Wenhao Li
- Department of Hematology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Langyu He
- Department of Blood Transfusion, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Ling Qi
- Division of Gastroenterology, Institute of Digestive Disease, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China.
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15
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Abedini-Nassab R, Taheri F, Emamgholizadeh A, Naderi-Manesh H. Single-Cell RNA Sequencing in Organ and Cell Transplantation. BIOSENSORS 2024; 14:189. [PMID: 38667182 PMCID: PMC11048310 DOI: 10.3390/bios14040189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Single-cell RNA sequencing is a high-throughput novel method that provides transcriptional profiling of individual cells within biological samples. This method typically uses microfluidics systems to uncover the complex intercellular communication networks and biological pathways buried within highly heterogeneous cell populations in tissues. One important application of this technology sits in the fields of organ and stem cell transplantation, where complications such as graft rejection and other post-transplantation life-threatening issues may occur. In this review, we first focus on research in which single-cell RNA sequencing is used to study the transcriptional profile of transplanted tissues. This technology enables the analysis of the donor and recipient cells and identifies cell types and states associated with transplant complications and pathologies. We also review the use of single-cell RNA sequencing in stem cell implantation. This method enables studying the heterogeneity of normal and pathological stem cells and the heterogeneity in cell populations. With their remarkably rapid pace, the single-cell RNA sequencing methodologies will potentially result in breakthroughs in clinical transplantation in the coming years.
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Affiliation(s)
- Roozbeh Abedini-Nassab
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
| | - Fatemeh Taheri
- Biomedical Engineering Department, University of Neyshabur, Neyshabur P.O. Box 9319774446, Iran
| | - Ali Emamgholizadeh
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
| | - Hossein Naderi-Manesh
- Department of Nanobiotechnology, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran;
- Department of Biophysics, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran
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16
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Bernt KM. Mapping human hematopoiesis. Nat Immunol 2024; 25:590-591. [PMID: 38514889 DOI: 10.1038/s41590-024-01793-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Affiliation(s)
- Kathrin M Bernt
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania and Abramson Cancer Center, Philadelphia, PA, USA.
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17
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Zhang X, Song B, Carlino MJ, Li G, Ferchen K, Chen M, Thompson EN, Kain BN, Schnell D, Thakkar K, Kouril M, Jin K, Hay SB, Sen S, Bernardicius D, Ma S, Bennett SN, Croteau J, Salvatori O, Lye MH, Gillen AE, Jordan CT, Singh H, Krause DS, Salomonis N, Grimes HL. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nat Immunol 2024; 25:703-715. [PMID: 38514887 PMCID: PMC11003869 DOI: 10.1038/s41590-024-01782-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024]
Abstract
Analysis of the human hematopoietic progenitor compartment is being transformed by single-cell multimodal approaches. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) enables coupled surface protein and transcriptome profiling, thereby revealing genomic programs underlying progenitor states. To perform CITE-seq systematically on primary human bone marrow cells, we used titrations with 266 CITE-seq antibodies (antibody-derived tags) and machine learning to optimize a panel of 132 antibodies. Multimodal analysis resolved >80 stem, progenitor, immune, stromal and transitional cells defined by distinctive surface markers and transcriptomes. This dataset enables flow cytometry solutions for in silico-predicted cell states and identifies dozens of cell surface markers consistently detected across donors spanning race and sex. Finally, aligning annotations from this atlas, we nominate normal marrow equivalents for acute myeloid leukemia stem cell populations that differ in clinical response. This atlas serves as an advanced digital resource for hematopoietic progenitor analyses in human health and disease.
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Affiliation(s)
- Xuan Zhang
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati, Cincinnati, OH, USA
| | - Maximillian J Carlino
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kyle Ferchen
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mi Chen
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Evrett N Thompson
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Bailee N Kain
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dan Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stuart B Hay
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sidharth Sen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - David Bernardicius
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Siyuan Ma
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sierra N Bennett
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | | | | | - Austin E Gillen
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Harinder Singh
- Departments of Immunology and Computational and Systems Biology, Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Diane S Krause
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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18
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Tur S, Palii CG, Brand M. Cell fate decision in erythropoiesis: Insights from multiomics studies. Exp Hematol 2024; 131:104167. [PMID: 38262486 PMCID: PMC10939800 DOI: 10.1016/j.exphem.2024.104167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/25/2024]
Abstract
Every second, the body produces 2 million red blood cells through a process called erythropoiesis. Erythropoiesis is hierarchical in that it results from a series of cell fate decisions whereby hematopoietic stem cells progress toward the erythroid lineage. Single-cell transcriptomic and proteomic approaches have revolutionized the way we understand erythropoiesis, revealing it to be a gradual process that underlies a progressive restriction of fate potential driven by quantitative changes in lineage-specifying transcription factors. Despite these major advances, we still know very little about what cell fate decision entails at the molecular level. Novel approaches that simultaneously measure additional properties in single cells, including chromatin accessibility, transcription factor binding, and/or cell surface proteins are being developed at a fast pace, providing the means to exciting new advances in the near future. In this review, we briefly summarize the main findings obtained from single-cell studies of erythropoiesis, highlight outstanding questions, and suggest recent technological advances to address them.
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Affiliation(s)
- Steven Tur
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Carbone Cancer Center, Madison, WI; Cellular and Molecular Biology Graduate Program, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Carmen G Palii
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Carbone Cancer Center, Madison, WI
| | - Marjorie Brand
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Carbone Cancer Center, Madison, WI.
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19
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Calderon A, Mestvirishvili T, Boccalatte F, Ruggles KV, David G. Chromatin accessibility and cell cycle progression are controlled by the HDAC-associated Sin3B protein in murine hematopoietic stem cells. Epigenetics Chromatin 2024; 17:2. [PMID: 38254205 PMCID: PMC10804615 DOI: 10.1186/s13072-024-00526-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Blood homeostasis requires the daily production of millions of terminally differentiated effector cells that all originate from hematopoietic stem cells (HSCs). HSCs are rare and exhibit unique self-renewal and multipotent properties, which depend on their ability to maintain quiescence through ill-defined processes. Defective control of cell cycle progression can eventually lead to bone marrow failure or malignancy. In particular, the molecular mechanisms tying cell cycle re-entry to cell fate commitment in HSCs remain elusive. Previous studies have identified chromatin coordination as a key regulator of differentiation in embryonic stem cells. RESULTS Here, we utilized genetic inactivation of the chromatin-associated Sin3B protein to manipulate cell cycle control and found dysregulated chromatin accessibility and cell cycle progression in HSCs. Single cell transcriptional profiling of hematopoietic stem and progenitor cells (HSPCs) inactivated for Sin3B reveals aberrant progression through the G1 phase of the cell cycle, which correlates with the engagement of specific signaling pathways, including aberrant expression of cell adhesion molecules and the interferon signaling program in LT-HSCs. In addition, we uncover the Sin3B-dependent accessibility of genomic elements controlling HSC differentiation, which points to cell cycle progression possibly dictating the priming of HSCs for differentiation. CONCLUSIONS Our findings provide new insights into controlled cell cycle progression as a potential regulator of HSC lineage commitment through the modulation of chromatin features.
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Affiliation(s)
- Alexander Calderon
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Tamara Mestvirishvili
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Francesco Boccalatte
- Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Kelly V Ruggles
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Gregory David
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
- Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
- Department of Urology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
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20
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Kondoh H. Multiple Cell Lineages Give Rise to a Cell Type. Results Probl Cell Differ 2024; 72:83-104. [PMID: 38509253 DOI: 10.1007/978-3-031-39027-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
It has long been assumed that a specific cell type arises following stepwise specification of cells corresponding to the branching of cell lineages. However, accumulating evidence indicates that multiple and even remote cell lineages can lead to the development of the same cells. Four examples giving different yet new insights will be discussed: skeletal muscle development from precursors with distinct initial histories of transcriptional regulation, lens cell development from remote lineages yet sharing basic transcription factors, blood cell development under intersectional pathways, and neural tissue development from cardiac precursors through the manipulation of just one component of epigenetic regulation. These examples provide flexible and nondogmatic perspectives on developmental cell regulation, fundamentally revising the old model relying on cell lineages.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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21
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Zeng AGX, Iacobucci I, Shah S, Mitchell A, Wong G, Bansal S, Gao Q, Kim H, Kennedy JA, Minden MD, Haferlach T, Mullighan CG, Dick JE. Precise single-cell transcriptomic mapping of normal and leukemic cell states reveals unconventional lineage priming in acute myeloid leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573390. [PMID: 38234771 PMCID: PMC10793439 DOI: 10.1101/2023.12.26.573390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Initial classification of acute leukemia involves the assignment of blasts to cell states within the hematopoietic hierarchy based on morphological and immunophenotypic features. Yet, these traditional classification approaches lack precision, especially at the level of immature blasts. Single-cell RNA-sequencing (scRNA-seq) enables precise determination of cell state using thousands of markers, thus providing an opportunity to re-examine present-day classification schemes of acute leukemia. Here, we developed a detailed reference map of human bone marrow hematopoiesis from 263,519 single-cell transcriptomes spanning 55 cellular states. Cell state annotations were benchmarked against purified cell populations, and in-depth characterization of gene expression programs underlying hematopoietic differentiation was undertaken. Projection of single-cell transcriptomes from 175 samples spanning acute myeloid leukemia (AML), mixed phenotype acute leukemia (MPAL), and acute erythroid leukemia (AEL) revealed 11 subtypes involving distinct stages of hematopoietic differentiation. These included AML subtypes with notable lymphoid or erythroid lineage priming, challenging traditional diagnostic boundaries between AML, MPAL, and AEL. Quantification of lineage priming in bulk patient cohorts revealed specific genetic alterations associated with this unconventional lineage priming. Integration of transcriptional and genetic information at the single-cell level revealed how genetic subclones can induce lineage restriction, differentiation blocks, or expansion of mature myeloid cells. Furthermore, we demonstrate that distinct cellular hierarchies can co-exist within individual patients, providing insight into AML evolution in response to varying selection pressures. Together, precise mapping of hematopoietic cell states can serve as a foundation for refining disease classification in acute leukemia and understanding response or resistance to emerging therapies.
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Affiliation(s)
- Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - Ilaria Iacobucci
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sayyam Shah
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Gordon Wong
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - Suraj Bansal
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
| | - Qingsong Gao
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hyerin Kim
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
| | - James A Kennedy
- Division of Medical Oncology and Hematology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, ON, Canada
| | | | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, Memphis, TN
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network; Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, ON, Canada
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22
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Webb S, Haniffa M. Large-scale single-cell RNA sequencing atlases of human immune cells across lifespan: Possibilities and challenges. Eur J Immunol 2023; 53:e2250222. [PMID: 36826421 DOI: 10.1002/eji.202250222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Single-cell RNA sequencing technologies have successfully been leveraged for immunological insights into human prenatal, pediatric, and adult tissues. These single-cell studies have led to breakthroughs in our understanding of stem, myeloid, and lymphoid cell function. Computational analysis of fetal hematopoietic tissues has uncovered trajectories for T- and B-cell differentiation across multiple organ sites, and how these trajectories might be dysregulated in fetal and pediatric health and disease. As we enter the age of large-scale, multiomic, and integrative single-cell meta-analysis, we assess the advances and challenges of large-scale data generation, analysis, and reanalysis, and data dissemination for a broad range of scientific and clinical communities. We discuss Findable, Accessible, Interoperable, and Reusable data sharing and unified cell ontology languages as strategic areas for progress of the field in the near future. We also reflect on the trend toward deployment of multiomic and spatial genomic platforms within single-cell RNA sequencing projects, and the crucial role these data types will assume in the immediate future toward creation of comprehensive and rich single-cell atlases. We demonstrate using our recent studies of human prenatal and adult hematopoietic tissues the importance of interdisciplinary and collaborative working in science to reveal biological insights in parallel with technological and computational innovations.
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Affiliation(s)
- Simone Webb
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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23
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Guo Y, Zhao T, Chu X, Cheng Z. Development of a diagnostic and risk prediction model for Alzheimer's disease through integration of single-cell and bulk transcriptomic analysis of glutamine metabolism. Front Aging Neurosci 2023; 15:1275793. [PMID: 38020758 PMCID: PMC10667556 DOI: 10.3389/fnagi.2023.1275793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Background In this study, we present a novel system for quantifying glutamine metabolism (GM) to enhance the effectiveness of Alzheimer's disease (AD) diagnosis and risk prediction. Methods Single-cell RNA sequencing (scRNA-seq) analysis was utilized to comprehensively assess the expression patterns of GM. The WGCNA algorithm was applied to investigate the most significant genes related to GM. Subsequently, three machine learning algorithms (Boruta, LASSO, and SVM-RFE) were employed to identify GM-associated characteristic genes and develop a risk model. Patients were divided into high- and low-risk groups based on this model. Moreover, we explored biological properties, distinct signaling pathways, and immunological characteristics of AD patients at different risk levels. Finally, in vitro and in vivo models of AD were constructed to validate the characteristics of the feature genes. Results Both scRNA-seq and bulk transcriptomic analyses revealed increased GM activity in AD patients, specifically in certain cell subsets (pDC, Tem/Effector helper T cells (LTB), and plasma cells). Cells with higher GM scores demonstrated more significant numbers and strengths of interactions with other cell types. The WGCNA algorithm identified 360 genes related to GM, and a risk score was constructed based on nine characteristic genes (ATP13A4, PIK3C2A, CD164, PHF1, CES2, PDGFB, LCOR, TMEM30A, and PLXNA1) identified through multiple machine learning algorithms displayed reliable diagnostic efficacy for AD onset. Nomograms, calibration curves, and decision curve analysis (DCA) based on these characteristic genes provided significant clinical benefits for AD patients. High-risk AD patients exhibited higher levels of immune-related functions and pathways, increased immune cell infiltration, and elevated expressions of immune modulators. RT-qPCR analysis revealed that the majority of the nine characteristic genes were differentially expressed in AD-induced rat neurons. Knocking down PHF1 could protect against neurite loss and alleviate cell injury in AD neurons. In vivo, down-regulation of PHF1 in AD models decreases GM metabolism levels and modulates the immunoinflammatory response in the brain. Conclusion This comprehensive identification of gene expression patterns contributes to a deeper understanding of the underlying pathological mechanisms driving AD pathogenesis. Furthermore, the risk model based on the nine-gene signature offers a promising theoretical foundation for developing individualized treatments for AD patients.
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Affiliation(s)
- Yan Guo
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tingru Zhao
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xi Chu
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenyun Cheng
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, Zhengzhou, Henan, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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24
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Merelli I, Beretta S, Cesana D, Gennari A, Benedicenti F, Spinozzi G, Cesini D, Montini E, D’Agostino D, Calabria A. InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration. Database (Oxford) 2023; 2023:baad069. [PMID: 37935583 PMCID: PMC10630073 DOI: 10.1093/database/baad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/15/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
High-throughput clonal tracking in patients under hematopoietic stem cell gene therapy with integrating vector is instrumental in assessing bio-safety and efficacy. Monitoring the fate of millions of transplanted clones and their progeny across differentiation and proliferation over time leverages the identification of the vector integration sites, used as surrogates of clonal identity. Although γ-tracking retroviral insertion sites (γ-TRIS) is the state-of-the-art algorithm for clonal identification, the computational drawbacks in the tracking algorithm, based on a combinatorial all-versus-all strategy, limit its use in clinical studies with several thousands of samples per patient. We developed the first clonal tracking graph database, InCliniGene (https://github.com/calabrialab/InCliniGene), that imports the output files of γ-TRIS and generates the graph of clones (nodes) connected by arches if two nodes share common genomic features as defined by the γ-TRIS rules. Embedding both clonal data and their connections in the graph, InCliniGene can track all clones longitudinally over samples through data queries that fully explore the graph. This approach resulted in being highly accurate and scalable. We validated InCliniGene using an in vitro dataset, specifically designed to mimic clinical cases, and tested the accuracy and precision. InCliniGene allows extensive use of γ-TRIS in large gene therapy clinical applications and naturally realizes the full data integration of molecular and genomics data, clinical and treatment measurements and genomic annotations. Further extensions of InCliniGene with data federation and with application programming interface will support data mining toward precision, personalized and predictive medicine in gene therapy. Database URL: https://github.com/calabrialab/InCliniGene.
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Affiliation(s)
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniela Cesana
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Alessandro Gennari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniele Cesini
- Centro Nazionale Analisi Fotogrammi (CNAF), Istituto Nazionale di Fisica Nucleare, Viale Carlo Berti Pichat 6/2, Bologna 40127, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniele D’Agostino
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi (DIBRIS), Università degli Studi di Genova, Viale Causa 13, Genoa 16145, Italy
- Institute of Biomedical Technologies, Italian National Research Council, Via Fratelli Cervi 93, Segrate (MI) 20054, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
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25
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Todisco G, Creignou M, Bernard E, Björklund AC, Moura PL, Tesi B, Mortera-Blanco T, Sander B, Jansson M, Walldin G, Barbosa I, Reinsbach SE, Hofman IJ, Nilsson C, Yoshizato T, Dimitriou M, Chang D, Olafsdottir S, Venckute Larsson S, Tobiasson M, Malcovati L, Woll P, Jacobsen SEW, Papaemmanuil E, Hellström-Lindberg E. Integrated Genomic and Transcriptomic Analysis Improves Disease Classification and Risk Stratification of MDS with Ring Sideroblasts. Clin Cancer Res 2023; 29:4256-4267. [PMID: 37498312 PMCID: PMC10570683 DOI: 10.1158/1078-0432.ccr-23-0538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/12/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Ring sideroblasts (RS) define the low-risk myelodysplastic neoplasm (MDS) subgroup with RS but may also reflect erythroid dysplasia in higher risk myeloid neoplasm. The benign behavior of MDS with RS (MDSRS+) is limited to SF3B1-mutated cases without additional high-risk genetic events, but one third of MDSRS+ carry no SF3B1 mutation, suggesting that different molecular mechanisms may underlie RS formation. We integrated genomic and transcriptomic analyses to evaluate whether transcriptome profiles may improve current risk stratification. EXPERIMENTAL DESIGN We studied a prospective cohort of MDSRS+ patients irrespective of World Health Organization (WHO) class with regard to somatic mutations, copy-number alterations, and bone marrow CD34+ cell transcriptomes to assess whether transcriptome profiles add to prognostication and provide input on disease classification. RESULTS SF3B1, SRSF2, or TP53 multihit mutations were found in 89% of MDSRS+ cases, and each mutation category was associated with distinct clinical outcome, gene expression, and alternative splicing profiles. Unsupervised clustering analysis identified three clusters with distinct hemopoietic stem and progenitor (HSPC) composition, which only partially overlapped with mutation groups. IPSS-M and the transcriptome-defined proportion of megakaryocyte/erythroid progenitors (MEP) independently predicted survival in multivariable analysis. CONCLUSIONS These results provide essential input on the molecular basis of SF3B1-unmutated MDSRS+ and propose HSPC quantification as a prognostic marker in myeloid neoplasms with RS.
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Affiliation(s)
- Gabriele Todisco
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy
| | - Maria Creignou
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Phase I Unit, Center for Clinical Cancer Studies, Karolinska University Hospital, Stockholm, Sweden
| | - Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ann-Charlotte Björklund
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pedro Luis Moura
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bianca Tesi
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Teresa Mortera-Blanco
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Sander
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Monika Jansson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Gunilla Walldin
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Indira Barbosa
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Susanne E. Reinsbach
- Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Gothenburg, Sweden
| | - Isabel Juliana Hofman
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christer Nilsson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Tetsuichi Yoshizato
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marios Dimitriou
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David Chang
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Svannildur Olafsdottir
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sigita Venckute Larsson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Tobiasson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Unit of Precision Hematology Oncology, IRCCS S. Matteo Hospital Foundation, Pavia, Italy
| | - Petter Woll
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sten Eirik W. Jacobsen
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
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26
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Tavakol DN, Nash TR, Kim Y, He S, Fleischer S, Graney PL, Brown JA, Liberman M, Tamargo M, Harken A, Ferrando AA, Amundson S, Garty G, Azizi E, Leong KW, Brenner DJ, Vunjak-Novakovic G. Modeling and countering the effects of cosmic radiation using bioengineered human tissues. Biomaterials 2023; 301:122267. [PMID: 37633022 PMCID: PMC10528250 DOI: 10.1016/j.biomaterials.2023.122267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023]
Abstract
Cosmic radiation is the most serious risk that will be encountered during the planned missions to the Moon and Mars. There is a compelling need to understand the effects, safety thresholds, and mechanisms of radiation damage in human tissues, in order to develop measures for radiation protection during extended space travel. As animal models fail to recapitulate the molecular changes in astronauts, engineered human tissues and "organs-on-chips" are valuable tools for studying effects of radiation in vitro. We have developed a bioengineered tissue platform for studying radiation damage in individualized settings. To demonstrate its utility, we determined the effects of radiation using engineered models of two human tissues known to be radiosensitive: engineered cardiac tissues (eCT, a target of chronic radiation damage) and engineered bone marrow (eBM, a target of acute radiation damage). We report the effects of high-dose neutrons, a proxy for simulated galactic cosmic rays, on the expression of key genes implicated in tissue responses to ionizing radiation, phenotypic and functional changes in both tissues, and proof-of-principle application of radioprotective agents. We further determined the extent of inflammatory, oxidative stress, and matrix remodeling gene expression changes, and found that these changes were associated with an early hypertrophic phenotype in eCT and myeloid skewing in eBM. We propose that individualized models of human tissues have potential to provide insights into the effects and mechanisms of radiation during deep-space missions and allow testing of radioprotective measures.
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Affiliation(s)
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Siyu He
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Jessie A Brown
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Manuel Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Andrew Harken
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Sally Amundson
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Guy Garty
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA; Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA.
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27
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Vallelonga V, Gandolfi F, Ficara F, Della Porta MG, Ghisletti S. Emerging Insights into Molecular Mechanisms of Inflammation in Myelodysplastic Syndromes. Biomedicines 2023; 11:2613. [PMID: 37892987 PMCID: PMC10603842 DOI: 10.3390/biomedicines11102613] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Inflammation impacts human hematopoiesis across physiologic and pathologic conditions, as signals derived from the bone marrow microenvironment, such as pro-inflammatory cytokines and chemokines, have been shown to alter hematopoietic stem cell (HSCs) homeostasis. Dysregulated inflammation can skew HSC fate-related decisions, leading to aberrant hematopoiesis and potentially contributing to the pathogenesis of hematological disorders such as myelodysplastic syndromes (MDS). Recently, emerging studies have used single-cell sequencing and muti-omic approaches to investigate HSC cellular heterogeneity and gene expression in normal hematopoiesis as well as in myeloid malignancies. This review summarizes recent reports mechanistically dissecting the role of inflammatory signaling and innate immune response activation due to MDS progression. Furthermore, we highlight the growing importance of using multi-omic techniques, such as single-cell profiling and deconvolution methods, to unravel MDSs' heterogeneity. These approaches have provided valuable insights into the patterns of clonal evolution that drive MDS progression and have elucidated the impact of inflammation on the composition of the bone marrow immune microenvironment in MDS.
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Affiliation(s)
- Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
| | - Francesco Gandolfi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
| | - Francesca Ficara
- Milan Unit, CNR-IRGB, 20090 Milan, Italy
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
| | - Matteo Giovanni Della Porta
- IRCCS Humanitas Research Hospital, 20089 Milan, Italy
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
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28
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Athaya T, Ripan RC, Li X, Hu H. Multimodal deep learning approaches for single-cell multi-omics data integration. Brief Bioinform 2023; 24:bbad313. [PMID: 37651607 PMCID: PMC10516349 DOI: 10.1093/bib/bbad313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023] Open
Abstract
Integrating single-cell multi-omics data is a challenging task that has led to new insights into complex cellular systems. Various computational methods have been proposed to effectively integrate these rapidly accumulating datasets, including deep learning. However, despite the proven success of deep learning in integrating multi-omics data and its better performance over classical computational methods, there has been no systematic study of its application to single-cell multi-omics data integration. To fill this gap, we conducted a literature review to explore the use of multimodal deep learning techniques in single-cell multi-omics data integration, taking into account recent studies from multiple perspectives. Specifically, we first summarized different modalities found in single-cell multi-omics data. We then reviewed current deep learning techniques for processing multimodal data and categorized deep learning-based integration methods for single-cell multi-omics data according to data modality, deep learning architecture, fusion strategy, key tasks and downstream analysis. Finally, we provided insights into using these deep learning models to integrate multi-omics data and better understand single-cell biological mechanisms.
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Affiliation(s)
- Tasbiraha Athaya
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Rony Chowdhury Ripan
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
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29
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Doty RT, Lausted CG, Munday AD, Yang Z, Yan X, Meng C, Tian Q, Abkowitz JL. The transcriptomic landscape of normal and ineffective erythropoiesis at single-cell resolution. Blood Adv 2023; 7:4848-4868. [PMID: 37352261 PMCID: PMC10469080 DOI: 10.1182/bloodadvances.2023010382] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/15/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
The anemias of myelodysplastic syndrome (MDS) and Diamond Blackfan anemia (DBA) are generally macrocytic and always reflect ineffective erythropoiesis yet result from diverse genetic mutations. To delineate shared mechanisms that lead to cell death, we studied the fate of single erythroid marrow cells from individuals with DBA or MDS-5q. We defined an unhealthy (vs healthy) differentiation trajectory using transcriptional pseudotime and cell surface proteins. The pseudotime trajectories diverge immediately after cells upregulate transferrin receptor (CD71), import iron, and initiate heme synthesis, although cell death occurs much later. Cells destined to die express high levels of heme-responsive genes, including ribosomal protein and globin genes, whereas surviving cells downregulate heme synthesis and upregulate DNA damage response, hypoxia, and HIF1 pathways. Surprisingly, 24% ± 12% of cells from control subjects follow the unhealthy trajectory, implying that heme might serve as a rheostat directing cells to live or die. When heme synthesis was inhibited with succinylacetone, more DBA cells followed the healthy trajectory and survived. We also noted high numbers of messages with retained introns that increased as erythroid cells matured, confirmed the rapid cycling of colony forming unit-erythroid, and demonstrated that cell cycle timing is an invariant property of differentiation stage. Including unspliced RNA in pseudotime determinations allowed us to reliably align independent data sets and accurately query stage-specific transcriptomic changes. MDS-5q (unlike DBA) results from somatic mutation, so many normal (unmutated) erythroid cells persist. By independently tracking erythroid differentiation of cells with and without chromosome 5q deletions, we gained insight into why 5q+ cells cannot expand to prevent anemia.
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Affiliation(s)
- Raymond T. Doty
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | | | - Adam D. Munday
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | - Zhantao Yang
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | | | | | - Qiang Tian
- Institute for Systems Biology, Seattle, WA
| | - Janis L. Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
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30
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Chen L, Pronk E, van Dijk C, Bian Y, Feyen J, van Tienhoven T, Yildirim M, Pisterzi P, de Jong MM, Bastidas A, Hoogenboezem RM, Wevers C, Bindels EM, Löwenberg B, Cupedo T, Sanders MA, Raaijmakers MH. A Single-Cell Taxonomy Predicts Inflammatory Niche Remodeling to Drive Tissue Failure and Outcome in Human AML. Blood Cancer Discov 2023; 4:394-417. [PMID: 37470778 PMCID: PMC10472197 DOI: 10.1158/2643-3230.bcd-23-0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/09/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Cancer initiation is orchestrated by an interplay between tumor-initiating cells and their stromal/immune environment. Here, by adapted single-cell RNA sequencing, we decipher the predicted signaling between tissue-resident hematopoietic stem/progenitor cells (HSPC) and their neoplastic counterparts with their native niches in the human bone marrow. LEPR+ stromal cells are identified as central regulators of hematopoiesis through predicted interactions with all cells in the marrow. Inflammatory niche remodeling and the resulting deprivation of critical HSPC regulatory factors are predicted to repress high-output hematopoietic stem cell subsets in NPM1-mutated acute myeloid leukemia (AML), with relative resistance of clonal cells. Stromal gene signatures reflective of niche remodeling are associated with reduced relapse rates and favorable outcomes after chemotherapy across all genetic risk categories. Elucidation of the intercellular signaling defining human AML, thus, predicts that inflammatory remodeling of stem cell niches drives tissue repression and clonal selection but may pose a vulnerability for relapse-initiating cells in the context of chemotherapeutic treatment. SIGNIFICANCE Tumor-promoting inflammation is considered an enabling characteristic of tumorigenesis, but mechanisms remain incompletely understood. By deciphering the predicted signaling between tissue-resident stem cells and their neoplastic counterparts with their environment, we identify inflammatory remodeling of stromal niches as a determinant of normal tissue repression and clinical outcomes in human AML. See related commentary by Lisi-Vega and Méndez-Ferrer, p. 349. This article is featured in Selected Articles from This Issue, p. 337.
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Affiliation(s)
- Lanpeng Chen
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eline Pronk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Claire van Dijk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Yujie Bian
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Jacqueline Feyen
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Tim van Tienhoven
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Meltem Yildirim
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Paola Pisterzi
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Madelon M.E. de Jong
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Alejandro Bastidas
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Chiel Wevers
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eric M. Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Bob Löwenberg
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Tom Cupedo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mathijs A. Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
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31
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Bigot T, Gabinaud E, Hannouche L, Sbarra V, Andersen E, Bastelica D, Falaise C, Bernot D, Ibrahim-Kosta M, Morange PE, Loosveld M, Saultier P, Payet-Bornet D, Alessi MC, Potier D, Poggi M. Single-cell analysis of megakaryopoiesis in peripheral CD34 + cells: insights into ETV6-related thrombocytopenia. J Thromb Haemost 2023; 21:2528-2544. [PMID: 37085035 DOI: 10.1016/j.jtha.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 04/04/2023] [Indexed: 04/23/2023]
Abstract
BACKGROUND Germline mutations in the ETV6 transcription factor gene are responsible for familial thrombocytopenia and leukemia predisposition syndrome. Although previous studies have shown that ETV6 plays an important role in megakaryocyte (MK) maturation and platelet formation, the mechanisms by which ETV6 dysfunction promotes thrombocytopenia remain unclear. OBJECTIVES To decipher the transcriptional mechanisms and gene regulatory network linking ETV6 germline mutations and thrombocytopenia. METHODS Presuming that ETV6 mutations result in selective effects at a particular cell stage, we applied single-cell RNA sequencing to understand gene expression changes during megakaryopoiesis in peripheral CD34+ cells from healthy controls and patients with ETV6-related thrombocytopenia. RESULTS Analysis of gene expression and regulon activity revealed distinct clusters partitioned into 7 major cell stages: hematopoietic stem/progenitor cells, common-myeloid progenitors (CMPs), MK-primed CMPs, granulocyte-monocyte progenitors, MK-erythroid progenitors (MEPs), progenitor MKs/mature MKs, and platelet-like particles. We observed a differentiation trajectory in which MEPs developed directly from hematopoietic stem/progenitor cells and bypassed the CMP stage. ETV6 deficiency led to the development of aberrant cells as early as the MEP stage, which intensified at the progenitor MK/mature MK stage, with a highly deregulated core "ribosome biogenesis" pathway. Indeed, increased translation levels have been documented in patient CD34+-derived MKs with overexpression of ribosomal protein S6 and phosphorylated ribosomal protein S6 in both CD34+-derived MKs and platelets. Treatment of patient MKs with the ribosomal biogenesis inhibitor CX-5461 resulted in an increase in platelet-like particles. CONCLUSION These findings provide novel insight into both megakaryopoiesis and the link among ETV6, translation, and platelet production.
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Affiliation(s)
- Timothée Bigot
- Aix-Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| | - Elisa Gabinaud
- Aix-Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| | | | | | - Elisa Andersen
- Aix-Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| | | | | | - Denis Bernot
- Aix-Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| | | | | | - Marie Loosveld
- Aix-Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | - Paul Saultier
- Aix-Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| | | | - Marie-Christine Alessi
- Aix-Marseille Univ, INSERM, INRAe, C2VN, Marseille, France; AP-HM, CHU Timone, CRPP, Marseille, France
| | | | - Marjorie Poggi
- Aix-Marseille Univ, INSERM, INRAe, C2VN, Marseille, France.
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32
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Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell 2023; 186:3882-3902.e24. [PMID: 37597510 PMCID: PMC10638861 DOI: 10.1016/j.cell.2023.07.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/21/2023]
Abstract
Inflammation can trigger lasting phenotypes in immune and non-immune cells. Whether and how human infections and associated inflammation can form innate immune memory in hematopoietic stem and progenitor cells (HSPC) has remained unclear. We found that circulating HSPC, enriched from peripheral blood, captured the diversity of bone marrow HSPC, enabling investigation of their epigenomic reprogramming following coronavirus disease 2019 (COVID-19). Alterations in innate immune phenotypes and epigenetic programs of HSPC persisted for months to 1 year following severe COVID-19 and were associated with distinct transcription factor (TF) activities, altered regulation of inflammatory programs, and durable increases in myelopoiesis. HSPC epigenomic alterations were conveyed, through differentiation, to progeny innate immune cells. Early activity of IL-6 contributed to these persistent phenotypes in human COVID-19 and a mouse coronavirus infection model. Epigenetic reprogramming of HSPC may underlie altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.
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Affiliation(s)
- Jin-Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Siddhartha Sharma
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Simon A Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Claire K Wingert
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paoline Laurent
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
| | - Sai Ma
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Lucinda Paddock
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Emin Onur Karakaslar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Vinay K Kartha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Jim K Yee
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Minh Y Mays
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chenyang Jiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alexia Martinez de Paz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dughan Ahimovic
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Victor Ramos
- The Rockefeller University, New York, NY 10065, USA
| | | | - Erik Nielsen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Ling Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andrew Earl
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Alisha Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lexi Robbins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | - Karissa L Weidman
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sabrina Racine-Brzostek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - He S Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - David R Price
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Louise Leyre
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - André F Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Junbum Kim
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Northwell Health, Greenvale, NY 11548, USA
| | | | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10065, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert J Kaner
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Virginia Pascual
- Department of Pediatrics, Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jason D Buenrostro
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | - Rachel E Niec
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; The Rockefeller University, New York, NY 10065, USA
| | - Franck J Barrat
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA; HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lindsay Lief
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10065, USA.
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33
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Favaro P, Glass DR, Borges L, Baskar R, Reynolds W, Ho D, Bruce T, Tebaykin D, Scanlon VM, Shestopalov I, Bendall SC. Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555623. [PMID: 37693547 PMCID: PMC10491219 DOI: 10.1101/2023.08.30.555623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine, lower-risk application. To deeply phenotype HSPCs, following a screen of 328 antigens, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary human hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and provide new, detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model were validated with corresponding epigenetic analysis and in vitro clonal differentiation assays. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.
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Affiliation(s)
- Patricia Favaro
- Department of Pathology, Stanford University
- These authors contributed equally
| | - David R. Glass
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Present address: Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Luciene Borges
- Department of Pathology, Stanford University
- Present address: Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
- These authors contributed equally
| | - Reema Baskar
- Department of Pathology, Stanford University
- Present address: Genome Institute of Singapore
| | | | - Daniel Ho
- Department of Pathology, Stanford University
| | | | | | - Vanessa M. Scanlon
- Department of Laboratory Medicine, Yale School of Medicine
- Present address: Center for Regenerative Medicine and Skeletal Biology, University of Connecticut Health
| | | | - Sean C. Bendall
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Lead author
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34
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Wu Z, Gao S, Gao Q, Patel BA, Groarke EM, Feng X, Manley AL, Li H, Ospina Cardona D, Kajigaya S, Alemu L, Quinones Raffo D, Ombrello AK, Ferrada MA, Grayson PC, Calvo KR, Kastner DL, Beck DB, Young NS. Early activation of inflammatory pathways in UBA1-mutated hematopoietic stem and progenitor cells in VEXAS. Cell Rep Med 2023; 4:101160. [PMID: 37586319 PMCID: PMC10439277 DOI: 10.1016/j.xcrm.2023.101160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 04/18/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023]
Abstract
VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is a pleiotropic, severe autoinflammatory disease caused by somatic mutations in the ubiquitin-like modifier activating enzyme 1 (UBA1) gene. To elucidate VEXAS pathophysiology, we performed transcriptome sequencing of single bone marrow mononuclear cells and hematopoietic stem and progenitor cells (HSPCs) from VEXAS patients. HSPCs are biased toward myeloid (granulocytic) differentiation, and against lymphoid differentiation in VEXAS. Activation of multiple inflammatory pathways (interferons and tumor necrosis factor alpha) occurs ontogenically early in primitive hematopoietic cells and particularly in the myeloid lineage in VEXAS, and inflammation is prominent in UBA1-mutated cells. Dysregulation in protein degradation likely leads to higher stress response in VEXAS HSPCs, which positively correlates with inflammation. TCR usage is restricted and there are increased cytotoxicity and IFN-γ signaling in T cells. In VEXAS syndrome, both aberrant inflammation and myeloid predominance appear intrinsic to hematopoietic stem cells mutated in UBA1.
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Affiliation(s)
- Zhijie Wu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Shouguo Gao
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qingyan Gao
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ash Lee Manley
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haoran Li
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniela Ospina Cardona
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lemlem Alemu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amanda K Ombrello
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcela A Ferrada
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter C Grayson
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel L Kastner
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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35
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Kana O, Nault R, Filipovic D, Marri D, Zacharewski T, Bhattacharya S. Generative modeling of single-cell gene expression for dose-dependent chemical perturbations. PATTERNS (NEW YORK, N.Y.) 2023; 4:100817. [PMID: 37602218 PMCID: PMC10436058 DOI: 10.1016/j.patter.2023.100817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/07/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023]
Abstract
Single-cell sequencing reveals the heterogeneity of cellular response to chemical perturbations. However, testing all relevant combinations of cell types, chemicals, and doses is a daunting task. A deep generative learning formalism called variational autoencoders (VAEs) has been effective in predicting single-cell gene expression perturbations for single doses. Here, we introduce single-cell variational inference of dose-response (scVIDR), a VAE-based model that predicts both single-dose and multiple-dose cellular responses better than existing models. We show that scVIDR can predict dose-dependent gene expression across mouse hepatocytes, human blood cells, and cancer cell lines. We biologically interpret the latent space of scVIDR using a regression model and use scVIDR to order individual cells based on their sensitivity to chemical perturbation by assigning each cell a "pseudo-dose" value. We envision that scVIDR can help reduce the need for repeated animal testing across tissues, chemicals, and doses.
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Affiliation(s)
- Omar Kana
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Rance Nault
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology Michigan State University, Michigan State University, East Lansing, MI 48824, USA
| | - David Filipovic
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Daniel Marri
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Tim Zacharewski
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology Michigan State University, Michigan State University, East Lansing, MI 48824, USA
| | - Sudin Bhattacharya
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
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36
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Calvanese V, Mikkola HKA. The genesis of human hematopoietic stem cells. Blood 2023; 142:519-532. [PMID: 37339578 PMCID: PMC10447622 DOI: 10.1182/blood.2022017934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/27/2023] [Accepted: 05/13/2023] [Indexed: 06/22/2023] Open
Abstract
Developmental hematopoiesis consists of multiple, partially overlapping hematopoietic waves that generate the differentiated blood cells required for embryonic development while establishing a pool of undifferentiated hematopoietic stem cells (HSCs) for postnatal life. This multilayered design in which active hematopoiesis migrates through diverse extra and intraembryonic tissues has made it difficult to define a roadmap for generating HSCs vs non-self-renewing progenitors, especially in humans. Recent single-cell studies have helped in identifying the rare human HSCs at stages when functional assays are unsuitable for distinguishing them from progenitors. This approach has made it possible to track the origin of human HSCs to the unique type of arterial endothelium in the aorta-gonad-mesonephros region and document novel benchmarks for HSC migration and maturation in the conceptus. These studies have delivered new insights into the intricate process of HSC generation and provided tools to inform the in vitro efforts to replicate the physiological developmental journey from pluripotent stem cells via distinct mesodermal and endothelial intermediates to HSCs.
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Affiliation(s)
- Vincenzo Calvanese
- Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Hanna K. A. Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA
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Schippel N, Sharma S. Dynamics of human hematopoietic stem and progenitor cell differentiation to the erythroid lineage. Exp Hematol 2023; 123:1-17. [PMID: 37172755 PMCID: PMC10330572 DOI: 10.1016/j.exphem.2023.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Erythropoiesis, the development of erythrocytes from hematopoietic stem cells, occurs through four phases: erythroid progenitor (EP) development, early erythropoiesis, terminal erythroid differentiation (TED), and maturation. According to the classical model that is based on immunophenotypic profiles of cell populations, each of these phases comprises multiple differentiation states that arise in a hierarchical manner. After segregation of lymphoid potential, erythroid priming begins during progenitor development and progresses through progenitor cell types that have multilineage potential. Complete separation of the erythroid lineage is achieved during early erythropoiesis with the formation of unipotent EPs: burst-forming unit-erythroid and colony-forming unit-erythroid. These erythroid-committed progenitors undergo TED and maturation, which involves expulsion of the nucleus and remodeling to form functional biconcave, hemoglobin-filled erythrocytes. In the last decade or so, many studies employing advanced techniques such as single-cell RNA-sequencing (scRNA-seq) as well as the conventional methods, including colony-forming cell assays and immunophenotyping, have revealed heterogeneity within the stem, progenitor, and erythroblast stages, and uncovered alternate paths for segregation of erythroid lineage potential. In this review, we provide an in-depth account of immunophenotypic profiles of all cell types within erythropoiesis, highlight studies that demonstrate heterogeneous erythroid stages, and describe deviations to the classical model of erythropoiesis. Overall, although scRNA-seq approaches have provided new insights, flow cytometry remains relevant and is the primary method for validation of novel immunophenotypes.
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Affiliation(s)
- Natascha Schippel
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ.
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38
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Söderlund S, Boey D, van Midden W, Kjellander M, Ax K, Qian H, Dahlin JS, Ungerstedt J. Proteomic and transcriptomic screening demonstrates increased mast cell-derived CCL23 in systemic mastocytosis. J Allergy Clin Immunol 2023; 152:205-213. [PMID: 36813186 DOI: 10.1016/j.jaci.2023.01.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/16/2022] [Accepted: 01/11/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Systemic mastocytosis (SM) is a heterogeneous group of mast cell-driven diseases diagnosed by bone marrow sampling. However, there are a limited number of available blood disease biomarkers. OBJECTIVE Our aim was to identify mast cell-derived proteins that could potentially serve as blood biomarkers for indolent and advanced forms of SM. METHODS We performed a plasma proteomics screening coupled with single-cell transcriptomic analysis in SM patients and healthy subjects. RESULTS Plasma proteomics screening identified 19 proteins upregulated in indolent disease compared to healthy, and 16 proteins in advanced disease compared to indolent. Among these, 5 proteins, CCL19, CCL23, CXCL13, IL-10, and IL-12Rβ1, were higher in indolent relative to healthy and in advanced disease compared to indolent. Single-cell RNA sequencing demonstrated that CCL23, IL-10, and IL-6 were selectively produced by mast cells. Notably, plasma CCL23 levels correlated positively with known markers of SM disease severity, namely tryptase levels, percentage bone marrow mast cell infiltration, and IL-6. CONCLUSION CCL23 is produced predominantly by mast cells in SM, and CCL23 plasma levels are associated with disease severity, correlating positively with established markers of disease burden, thus suggesting that CCL23 is a specific SM biomarker. In addition, the combination of CCL19, CCL23, CXCL13, IL-10, and IL-12Rβ1 may be useful for defining disease stage.
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Affiliation(s)
- Stina Söderlund
- Section of Hematology, Uppsala University Hospital, Uppsala, Sweden; Center for Hematology and Regenerative Medicine (HERM), NEO, Department for Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Daryl Boey
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Wouter van Midden
- Center for Hematology and Regenerative Medicine (HERM), NEO, Department for Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Matilda Kjellander
- Center for Hematology and Regenerative Medicine (HERM), NEO, Department for Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Kajsa Ax
- Center for Hematology and Regenerative Medicine (HERM), NEO, Department for Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hong Qian
- Center for Hematology and Regenerative Medicine (HERM), NEO, Department for Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Joakim S Dahlin
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Ungerstedt
- Center for Hematology and Regenerative Medicine (HERM), NEO, Department for Medicine, Huddinge, Karolinska Institutet, Stockholm, Sweden; ME Hematology, Karolinska University Hospital, Stockholm, Sweden.
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39
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Araki D, Chen V, Redekar N, Salisbury-Ruf C, Luo Y, Liu P, Li Y, Smith RH, Dagur P, Combs C, Larochelle A. Post-Transplant Administration of G-CSF Impedes Engraftment of Gene Edited Human Hematopoietic Stem Cells by Exacerbating the p53-Mediated DNA Damage Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547089. [PMID: 37425704 PMCID: PMC10327043 DOI: 10.1101/2023.06.29.547089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Granulocyte colony stimulating factor (G-CSF) is commonly used as adjunct treatment to hasten recovery from neutropenia following chemotherapy and autologous transplantation of hematopoietic stem and progenitor cells (HSPCs) for malignant disorders. However, the utility of G-CSF administration after ex vivo gene therapy procedures targeting human HSPCs has not been thoroughly evaluated. Here, we provide evidence that post-transplant administration of G-CSF impedes engraftment of CRISPR-Cas9 gene edited human HSPCs in xenograft models. G-CSF acts by exacerbating the p53-mediated DNA damage response triggered by Cas9- mediated DNA double-stranded breaks. Transient p53 inhibition in culture attenuates the negative impact of G-CSF on gene edited HSPC function. In contrast, post-transplant administration of G-CSF does not impair the repopulating properties of unmanipulated human HSPCs or HSPCs genetically engineered by transduction with lentiviral vectors. The potential for post-transplant G-CSF administration to aggravate HSPC toxicity associated with CRISPR-Cas9 gene editing should be considered in the design of ex vivo autologous HSPC gene editing clinical trials.
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40
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Gao CF, Vaikuntanathan S, Riesenfeld SJ. Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544828. [PMID: 37398022 PMCID: PMC10312759 DOI: 10.1101/2023.06.13.544828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
RNA velocity estimation is a potentially powerful tool to reveal the directionality of transcriptional changes in single-cell RNA-seq data, but it lacks accuracy, absent advanced metabolic labeling techniques. We developed a novel approach, TopicVelo, that disentangles simultaneous, yet distinct, dynamics by using a probabilistic topic model, a highly interpretable form of latent space factorization, to infer cells and genes associated with individual processes, thereby capturing cellular pluripotency or multifaceted functionality. Focusing on process-associated cells and genes enables accurate estimation of process-specific velocities via a master equation for a transcriptional burst model accounting for intrinsic stochasticity. The method obtains a global transition matrix by leveraging cell topic weights to integrate process-specific signals. In challenging systems, this method accurately recovers complex transitions and terminal states, while our novel use of first-passage time analysis provides insights into transient transitions. These results expand the limits of RNA velocity, empowering future studies of cell fate and functional responses.
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Affiliation(s)
| | | | - Samantha J Riesenfeld
- Institute for Biophysical Dynamics, University of Chicago, IL
- Pritzker School of Molecular Engineering, University of Chicago, IL
- Department of Medicine, University of Chicago, IL
- Committee on Immunology, University of Chicago, IL
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41
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Zhao HG, Deininger M. Always stressed but never exhausted: how stem cells in myeloid neoplasms avoid extinction in inflammatory conditions. Blood 2023; 141:2797-2812. [PMID: 36947811 PMCID: PMC10315634 DOI: 10.1182/blood.2022017152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
Chronic or recurrent episodes of acute inflammation cause attrition of normal hematopoietic stem cells (HSCs) that can lead to hematopoietic failure but they drive progression in myeloid malignancies and their precursor clonal hematopoiesis. Mechanistic parallels exist between hematopoiesis in chronic inflammation and the continuously increased proliferation of myeloid malignancies, particularly myeloproliferative neoplasms (MPNs). The ability to enter dormancy, a state of deep quiescence characterized by low oxidative phosphorylation, low glycolysis, reduced protein synthesis, and increased autophagy is central to the preservation of long-term HSCs and likely MPN SCs. The metabolic features of dormancy resemble those of diapause, a state of arrested embryonic development triggered by adverse environmental conditions. To outcompete their normal counterparts in the inflammatory MPN environment, MPN SCs co-opt mechanisms used by HSCs to avoid exhaustion, including signal attenuation by negative regulators, insulation from activating cytokine signals, anti-inflammatory signaling, and epigenetic reprogramming. We propose that new therapeutic strategies may be derived from conceptualizing myeloid malignancies as an ecosystem out of balance, in which residual normal and malignant hematopoietic cells interact in multiple ways, only few of which have been characterized in detail. Disrupting MPN SC insulation to overcome dormancy, interfering with aberrant cytokine circuits that favor MPN cells, and directly boosting residual normal HSCs are potential strategies to tip the balance in favor of normal hematopoiesis. Although eradicating the malignant cell clones remains the goal of therapy, rebalancing the ecosystem may be a more attainable objective in the short term.
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Affiliation(s)
- Helong Gary Zhao
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI
| | - Michael Deininger
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI
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42
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Crawford LB. Hematopoietic stem cells and betaherpesvirus latency. Front Cell Infect Microbiol 2023; 13:1189805. [PMID: 37346032 PMCID: PMC10279960 DOI: 10.3389/fcimb.2023.1189805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 06/23/2023] Open
Abstract
The human betaherpesviruses including human cytomegalovirus (HCMV), human herpesvirus (HHV)-6a and HHV-6b, and HHV-7 infect and establish latency in CD34+ hematopoietic stem and progenitor cells (HPCs). The diverse repertoire of HPCs in humans and the complex interactions between these viruses and host HPCs regulate the viral lifecycle, including latency. Precise manipulation of host and viral factors contribute to preferential maintenance of the viral genome, increased host cell survival, and specific manipulation of the cellular environment including suppression of neighboring cells and immune control. The dynamic control of these processes by the virus regulate inter- and intra-host signals critical to the establishment of chronic infection. Regulation occurs through direct viral protein interactions and cellular signaling, miRNA regulation, and viral mimics of cellular receptors and ligands, all leading to control of cell proliferation, survival, and differentiation. Hematopoietic stem cells have unique biological properties and the tandem control of virus and host make this a unique environment for chronic herpesvirus infection in the bone marrow. This review highlights the elegant complexities of the betaherpesvirus latency and HPC virus-host interactions.
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Affiliation(s)
- Lindsey B Crawford
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, United States
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43
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Kim Y, Greenleaf WJ, Bendall SC. Systems biology approaches to unravel lymphocyte subsets and function. Curr Opin Immunol 2023; 82:102323. [PMID: 37028221 PMCID: PMC10330158 DOI: 10.1016/j.coi.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023]
Abstract
Single-cell technologies have revealed the extensive heterogeneity and complexity of the immune system. Systems biology approaches in immunology have taken advantage of the high-parameter, high-throughput data and analyzed immune cell types in a 'bottom-up' data-driven method. This approach has discovered previously unrecognized cell types and functions. Especially for human immunology, in which experimental manipulations are challenging, systems approach has become a successful means to investigate physiologically relevant contexts. This review focuses on the recent findings in lymphocyte biology, from their development, differentiation into subsets, and heterogeneity in their functions, enabled by these systems approaches. Furthermore, we review examples of the application of findings from systems approach studies and discuss how now to leave the rich dataset in the curse of high dimensionality.
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Affiliation(s)
- YeEun Kim
- Immunology Graduate Program, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
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44
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Crees ZD, Rettig MP, DiPersio JF. Innovations in hematopoietic stem-cell mobilization: a review of the novel CXCR4 inhibitor motixafortide. Ther Adv Hematol 2023; 14:20406207231174304. [PMID: 37250913 PMCID: PMC10214082 DOI: 10.1177/20406207231174304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Hematopoietic stem-cell transplantation (HCT) and stem-cell-based gene therapies rely on the ability to collect sufficient CD34+ hematopoietic stem and progenitor cells (HSPCs), typically via peripheral blood mobilization. Commonly used HSPC mobilization regimens include single-agent granulocyte colony-stimulating factor (G-CSF), plerixafor, chemotherapy, or a combination of these agents. These regimens, however, frequently require multiple days of injections and leukapheresis procedures to collect adequate HSPCs for HCT (minimum = >2 × 106 CD34+ cells/kg; optimal = 5-6 × 106 CD34+ cells/kg). In addition, these regimens frequently yield suboptimal CD34+ HSPC numbers for HSPC-based gene-edited therapies, given the significantly higher HSPC number needed for successful gene-editing and manufacturing. Meanwhile, G-CSF is associated with common adverse events such as bone pain as well as an increased risk of rare but potentially life-threatening splenic rupture. Moreover, G-CSF is unsafe in patients with sickle-cell disease, a key patient population that may benefit from autologous HSPC-based gene-edited therapies, where it has been associated with unacceptable rates of serious vaso-occlusive and thrombotic events. Motixafortide is a novel CXCR4 inhibitor with extended in vivo activity (>48 h) that has been shown in preclinical and clinical trials to rapidly mobilize robust numbers of HSPCs in preparation for HCT, while preferentially mobilizing increased numbers of more primitive HSPCs by immunophenotyping and single-cell RNA expression profiling. In this review, we present a history of stem-cell mobilization and update of recent innovations in novel mobilization strategies with a specific focus on the development of motixafortide, a long-acting CXCR4 inhibitor, as a novel HSPC mobilizing agent.
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Affiliation(s)
- Zachary D. Crees
- Division of Oncology, School of Medicine,
Washington University in St. Louis, 660 S. Euclid Avenue, Campus Box 8007,
St. Louis, MO 63131, USA
| | - Michael P. Rettig
- Division of Oncology, School of Medicine,
Washington University in St. Louis, St. Louis, MO, USA
| | - John F. DiPersio
- Division of Oncology, School of Medicine,
Washington University in St. Louis, St. Louis, MO, USA
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45
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Miyake K, Ito J, Nakabayashi J, Shichino S, Ishiwata K, Karasuyama H. Single cell transcriptomics clarifies the basophil differentiation trajectory and identifies pre-basophils upstream of mature basophils. Nat Commun 2023; 14:2694. [PMID: 37202383 DOI: 10.1038/s41467-023-38356-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/27/2023] [Indexed: 05/20/2023] Open
Abstract
Basophils are the rarest granulocytes and are recognized as critical cells for type 2 immune responses. However, their differentiation pathway remains to be fully elucidated. Here, we assess the ontogenetic trajectory of basophils by single-cell RNA sequence analysis. Combined with flow cytometric and functional analyses, we identify c-Kit-CLEC12Ahi pre-basophils located downstream of pre-basophil and mast cell progenitors (pre-BMPs) and upstream of CLEC12Alo mature basophils. The transcriptomic analysis predicts that the pre-basophil population includes previously-defined basophil progenitor (BaP)-like cells in terms of gene expression profile. Pre-basophils are highly proliferative and respond better to non-IgE stimuli but less to antigen plus IgE stimulation than do mature basophils. Although pre-basophils usually remain in the bone marrow, they emerge in helminth-infected tissues, probably through IL-3-mediated inhibition of their retention in the bone marrow. Thus, the present study identifies pre-basophils that bridge the gap between pre-BMPs and mature basophils during basophil ontogeny.
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Grants
- 20K16277 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22K007115 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H05064 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 19H01025 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H02845 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21gm6210025 Japan Agency for Medical Research and Development (AMED)
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Affiliation(s)
- Kensuke Miyake
- Inflammation, Infection & Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Junya Ito
- Inflammation, Infection & Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Jun Nakabayashi
- College of Liberal Arts and Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Kenji Ishiwata
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Hajime Karasuyama
- Inflammation, Infection & Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Ferrari S, Valeri E, Conti A, Scala S, Aprile A, Di Micco R, Kajaste-Rudnitski A, Montini E, Ferrari G, Aiuti A, Naldini L. Genetic engineering meets hematopoietic stem cell biology for next-generation gene therapy. Cell Stem Cell 2023; 30:549-570. [PMID: 37146580 DOI: 10.1016/j.stem.2023.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
The growing clinical success of hematopoietic stem/progenitor cell (HSPC) gene therapy (GT) relies on the development of viral vectors as portable "Trojan horses" for safe and efficient gene transfer. The recent advent of novel technologies enabling site-specific gene editing is broadening the scope and means of GT, paving the way to more precise genetic engineering and expanding the spectrum of diseases amenable to HSPC-GT. Here, we provide an overview of state-of-the-art and prospective developments of the HSPC-GT field, highlighting how advances in biological characterization and manipulation of HSPCs will enable the design of the next generation of these transforming therapeutics.
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Affiliation(s)
- Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Erika Valeri
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Anastasia Conti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Annamaria Aprile
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Anna Kajaste-Rudnitski
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Giuliana Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy.
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47
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Poto R, Loffredo S, Marone G, Di Salvatore A, de Paulis A, Schroeder JT, Varricchi G. Basophils beyond allergic and parasitic diseases. Front Immunol 2023; 14:1190034. [PMID: 37205111 PMCID: PMC10185837 DOI: 10.3389/fimmu.2023.1190034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Basophils bind IgE via FcεRI-αβγ2, which they uniquely share only with mast cells. In doing so, they can rapidly release mediators that are hallmark of allergic disease. This fundamental similarity, along with some morphological features shared by the two cell types, has long brought into question the biological significance that basophils mediate beyond that of mast cells. Unlike mast cells, which mature and reside in tissues, basophils are released into circulation from the bone marrow (constituting 1% of leukocytes), only to infiltrate tissues under specific inflammatory conditions. Evidence is emerging that basophils mediate non-redundant roles in allergic disease and, unsuspectingly, are implicated in a variety of other pathologies [e.g., myocardial infarction, autoimmunity, chronic obstructive pulmonary disease, fibrosis, cancer, etc.]. Recent findings strengthen the notion that these cells mediate protection from parasitic infections, whereas related studies implicate basophils promoting wound healing. Central to these functions is the substantial evidence that human and mouse basophils are increasingly implicated as important sources of IL-4 and IL-13. Nonetheless, much remains unclear regarding the role of basophils in pathology vs. homeostasis. In this review, we discuss the dichotomous (protective and/or harmful) roles of basophils in a wide spectrum of non-allergic disorders.
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Affiliation(s)
- Remo Poto
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy
| | - Stefania Loffredo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
- Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council (CNR), Naples, Italy
| | - Gianni Marone
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
- Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council (CNR), Naples, Italy
| | - Antonio Di Salvatore
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Amato de Paulis
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
| | - John T. Schroeder
- Division of Allergy and Clinical Immunology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Gilda Varricchi
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- World Allergy Organization (WAO), Center of Excellence (CoE), Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
- Institute of Experimental Endocrinology and Oncology “G. Salvatore”, National Research Council (CNR), Naples, Italy
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48
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Urbanus J, Cosgrove J, Beltman JB, Elhanati Y, Moral RA, Conrad C, van Heijst JW, Tubeuf E, Velds A, Kok L, Merle C, Magnusson JP, Guyonnet L, Frisén J, Fre S, Walczak AM, Mora T, Jacobs H, Schumacher TN, Perié L. DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age. Nat Commun 2023; 14:2184. [PMID: 37069150 PMCID: PMC10110593 DOI: 10.1038/s41467-023-37167-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 03/03/2023] [Indexed: 04/19/2023] Open
Abstract
Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we present an in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis rather than the increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remains constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.
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Affiliation(s)
- Jos Urbanus
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Joost B Beltman
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | | | - Rafael A Moral
- Department of Mathematics and Statistics, Maynooth University, Maynooth, Ireland
| | - Cecile Conrad
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Jeroen W van Heijst
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emilie Tubeuf
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Arno Velds
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lianne Kok
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Candice Merle
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Jens P Magnusson
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Léa Guyonnet
- Cytometry Platform, Institut Curie, 75005, Paris, France
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Silvia Fre
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'École Normale Supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l'École Normale Supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, Paris, France
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
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49
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Wang H, Langlais D, Nijnik A. Histone H2A deubiquitinases in the transcriptional programs of development and hematopoiesis: a consolidated analysis. Int J Biochem Cell Biol 2023; 157:106384. [PMID: 36738766 DOI: 10.1016/j.biocel.2023.106384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Monoubiquitinated lysine 119 of histone H2A (H2AK119ub) is a highly abundant epigenetic mark, associated with gene repression and deposited on chromatin by the polycomb repressor complex 1 (PRC1), which is an essential regulator of diverse transcriptional programs in mammalian development and tissue homeostasis. While multiple deubiquitinases (DUBs) with catalytic activity for H2AK119ub (H2A-DUBs) have been identified, we lack systematic analyses of their roles and cross-talk in transcriptional regulation. Here, we address H2A-DUB functions in epigenetic regulation of mammalian development and tissue maintenance by conducting a meta-analysis of 248 genomics datasets from 32 independent studies, focusing on the mouse model and covering embryonic stem cells (ESCs), hematopoietic, and immune cell lineages. This covers all the publicly available datasets that map genomic H2A-DUB binding and H2AK119ub distributions (ChIP-Seq), and all datasets assessing dysregulation in gene expression in the relevant H2A-DUB knockout models (RNA-Seq). Many accessory datasets for PRC1-2 and DUB-interacting proteins are also analyzed and interpreted, as well as further data assessing chromatin accessibility (ATAC-Seq) and transcriptional activity (RNA-seq). We report co-localization in the binding of H2A-DUBs BAP1, USP16, and to a lesser extent others that is conserved across different cell-types, and also the enrichment of antagonistic PRC1-2 protein complexes at the same genomic locations. Such conserved sites enriched for the H2A-DUBs and PRC1-2 are proximal to transcriptionally active genes that engage in housekeeping cellular functions. Nevertheless, they exhibit H2AK119ub levels significantly above the genomic average that can undergo further increase with H2A-DUB knockout. This indicates a cooperation between H2A-DUBs and PRC1-2 in the modulation of housekeeping transcriptional programs, conserved across many cell types, likely operating through their antagonistic effects on H2AK119ub and the regulation of local H2AK119ub turnover. Our study further highlights existing knowledge gaps and discusses important directions for future work.
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Affiliation(s)
- HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, McGill University, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, McGill University, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill Genome Centre, Montreal, QC, Canada.
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, McGill University, QC, Canada.
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50
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Crees ZD, Rettig MP, Jayasinghe RG, Stockerl-Goldstein K, Larson SM, Arpad I, Milone GA, Martino M, Stiff P, Sborov D, Pereira D, Micallef I, Moreno-Jiménez G, Mikala G, Coronel MLP, Holtick U, Hiemenz J, Qazilbash MH, Hardy N, Latif T, García-Cadenas I, Vainstein-Haras A, Sorani E, Gliko-Kabir I, Goldstein I, Ickowicz D, Shemesh-Darvish L, Kadosh S, Gao F, Schroeder MA, Vij R, DiPersio JF. Motixafortide and G-CSF to mobilize hematopoietic stem cells for autologous transplantation in multiple myeloma: a randomized phase 3 trial. Nat Med 2023; 29:869-879. [PMID: 37069359 PMCID: PMC10115633 DOI: 10.1038/s41591-023-02273-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/22/2023] [Indexed: 04/19/2023]
Abstract
Autologous hematopoietic stem cell transplantation (ASCT) improves survival in multiple myeloma (MM). However, many individuals are unable to collect optimal CD34+ hematopoietic stem and progenitor cell (HSPC) numbers with granulocyte colony-stimulating factor (G-CSF) mobilization. Motixafortide is a novel cyclic-peptide CXCR4 inhibitor with extended in vivo activity. The GENESIS trial was a prospective, phase 3, double-blind, placebo-controlled, multicenter study with the objective of assessing the superiority of motixafortide + G-CSF over placebo + G-CSF to mobilize HSPCs for ASCT in MM. The primary endpoint was the proportion of patients collecting ≥6 × 106 CD34+ cells kg-1 within two apheresis procedures; the secondary endpoint was to achieve this goal in one apheresis. A total of 122 adult patients with MM undergoing ASCT were enrolled at 18 sites across five countries and randomized (2:1) to motixafortide + G-CSF or placebo + G-CSF for HSPC mobilization. Motixafortide + G-CSF enabled 92.5% to successfully meet the primary endpoint versus 26.2% with placebo + G-CSF (odds ratio (OR) 53.3, 95% confidence interval (CI) 14.12-201.33, P < 0.0001). Motixafortide + G-CSF also enabled 88.8% to meet the secondary endpoint versus 9.5% with placebo + G-CSF (OR 118.0, 95% CI 25.36-549.35, P < 0.0001). Motixafortide + G-CSF was safe and well tolerated, with the most common treatment-emergent adverse events observed being transient, grade 1/2 injection site reactions (pain, 50%; erythema, 27.5%; pruritis, 21.3%). In conclusion, motixafortide + G-CSF mobilized significantly greater CD34+ HSPC numbers within two apheresis procedures versus placebo + G-CSF while preferentially mobilizing increased numbers of immunophenotypically and transcriptionally primitive HSPCs. Trial Registration: ClinicalTrials.gov , NCT03246529.
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Affiliation(s)
- Zachary D Crees
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Michael P Rettig
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Reyka G Jayasinghe
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Sarah M Larson
- Division of Hematology-Oncology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Illes Arpad
- Division of Hematology, Department of Internal Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Giulio A Milone
- Unità di Trapianto Emopoietico, Azienda Ospedaliero Universitaria 'Policlinico-San Marco', Catania, Italy
| | - Massimo Martino
- Unit of Stem Cell Transplantation and Cellular Therapies, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | | | - Douglas Sborov
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Denise Pereira
- Sylvester Comprehensive Cancer Center, University of Miami Health System, Miami, FL, USA
| | | | | | - Gabor Mikala
- Center Hospital of Southern Pest, National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | | | - Udo Holtick
- Department I of Internal Medicine, Medical Faculty and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - John Hiemenz
- Division of Hematology-Oncology, University of Florida, Gainesville, FL, USA
| | - Muzaffar H Qazilbash
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nancy Hardy
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tahir Latif
- Division of Hematology-Oncology, University of Cincinnati, Cincinnati, OH, USA
| | - Irene García-Cadenas
- Department of Hematology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | | | | | | | | | | | | | - Feng Gao
- Division of Public Health Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Mark A Schroeder
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Ravi Vij
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John F DiPersio
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
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