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Missarova A, Dann E, Rosen L, Satija R, Marioni J. Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome Biol 2024; 25:189. [PMID: 39026254 PMCID: PMC11256449 DOI: 10.1186/s13059-024-03334-3] [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: 09/01/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivity of clustering, which is often suboptimal. To overcome this, we present miloDE-a cluster-free framework for DE testing (available as an open-source R package). We illustrate the performance of miloDE on both simulated and real data. Using miloDE, we identify a transient hemogenic endothelia-like state in mouse embryos lacking Tal1 and detect distinct programs during macrophage activation in idiopathic pulmonary fibrosis.
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Affiliation(s)
- Alsu Missarova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leah Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rahul Satija
- Center for Genomics and Systems Biology, NYU, New York, USA.
- New York Genome Center, New York, USA.
| | - John Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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2
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Zhou W, Zhu C, Shen P, Wang JF, Zhu G, Jia Y, Wu Y, Wang S, Sun J, Yang F, Song Y, Han X, Guan X. Hypoxia stimulates CTC-platelet cluster formation to promote breast cancer metastasis. iScience 2024; 27:109547. [PMID: 38660400 PMCID: PMC11039329 DOI: 10.1016/j.isci.2024.109547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Circulating tumor cell clusters/micro-emboli (CTM) possess greater metastatic capacity and survival advantage compared to individual circulating tumor cell (CTC). However, the formation of CTM subtypes and their role in tumor metastasis remain unclear. In this study, we used a microfluidic Cluster-Chip with easy operation and high efficiency to isolate CTM from peripheral blood, which confirmed their correlation with clinicopathological features and identified the critical role of CTC-platelet clusters in breast cancer metastasis. The correlation between platelets and CTM function was further confirmed in a mouse model and RNA sequencing of CTM identified high-expressed genes related to hypoxia stimulation and platelet activation which possibly suggested the correlation of hypoxia and CTC-platelet cluster formation. In conclusion, we successfully developed the Cluster-Chip platform to realize the clinical capture of CTMs and analyze the biological properties of CTC-platelet clusters, which could benefit the design of potential treatment regimens to prevent CTM-mediated metastasis and tumor malignant progression.
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Affiliation(s)
- Weijia Zhou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chengjun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Peiliang Shen
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jacqueline F. Wang
- Department of Medicine, NYU Langone Health, 550 First Avenue, New York, NY 10016, USA
| | - Gaoshuang Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuanyuan Jia
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yueyao Wu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Siliang Wang
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Jia Sun
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Fang Yang
- The Comprehensive cancer Center of Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yanni Song
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China
| | - Xin Han
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine & Holistic Integrative Medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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3
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Al-Amoodi AS, Kai J, Li Y, Malki JS, Alghamdi A, Al-Ghuneim A, Saera-Vila A, Habuchi S, Merzaban JS. α1,3-fucosylation treatment improves cord blood CD34 negative hematopoietic stem cell navigation. iScience 2024; 27:108882. [PMID: 38322982 PMCID: PMC10845921 DOI: 10.1016/j.isci.2024.108882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/24/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
For almost two decades, clinicians have overlooked the diagnostic potential of CD34neg hematopoietic stem cells because of their limited homing capacity relative to CD34posHSCs when injected intravenously. This has contributed to the lack of appeal of using umbilical cord blood in HSC transplantation because its stem cell count is lower than bone marrow. The present study reveals that the homing and engraftment of CD34negHSCs can be improved by adding the Sialyl Lewis X molecule via α1,3-fucosylation. This unlocks the potential for using this more primitive stem cell to treat blood disorders because our findings show CD34negHSCs have the capacity to regenerate cells in the bone marrow of mice for several months. Furthermore, our RNA sequencing analysis revealed that CD34negHSCs have unique adhesion pathways, downregulated in CD34posHSCs, that facilitate interaction with the bone marrow niche. Our findings suggest that CD34neg cells will best thrive when the HSC resides in its microenvironment.
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Affiliation(s)
- Asma S. Al-Amoodi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jing Kai
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yanyan Li
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jana S. Malki
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Abdullah Alghamdi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Arwa Al-Ghuneim
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | - Satoshi Habuchi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jasmeen S. Merzaban
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST Smart-Health Initiative, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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4
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Lan Y, Yuan S, Guo T, Hou S, Zhao F, Yang W, Cao Y, Chu Y, Jiang E, Yuan W, Wang X. R274X-mutated Phf6 increased the self-renewal and skewed T cell differentiation of hematopoietic stem cells. iScience 2023; 26:106817. [PMID: 37288345 PMCID: PMC10241978 DOI: 10.1016/j.isci.2023.106817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/25/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023] Open
Abstract
The PHD finger protein 6 (PHF6) mutations frequently occurred in hematopoietic malignancies. Although the R274X mutation in PHF6 (PHF6R274X) is one of the most common mutations identified in T cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML) patients, the specific role of PHF6R274X in hematopoiesis remains unexplored. Here, we engineered a knock-in mouse line with conditional expression of Phf6R274X-mutated protein in the hematopoietic system (Phf6R274X mouse). The Phf6R274X mice displayed an enlargement of hematopoietic stem cells (HSCs) compartment and increased proportion of T cells in bone marrow. More Phf6R274X T cells were in activated status than control. Moreover, Phf6R274X mutation led to enhanced self-renewal and biased T cells differentiation of HSCs as assessed by competitive transplantation assays. RNA-sequencing analysis confirmed that Phf6R274X mutation altered the expression of key genes involved in HSC self-renewal and T cell activation. Our study demonstrated that Phf6R274X plays a critical role in fine-tuning T cells and HSC homeostasis.
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Affiliation(s)
- Yanjie Lan
- 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
- Department of Neuro-oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100071, China
| | - Shengnan Yuan
- 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
- School of Medical Technology, Xuzhou Medical University, Xuzhou 221004, China
| | - Tengxiao Guo
- 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
| | - Shuaibing Hou
- 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
| | - Fei Zhao
- 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
| | - Wanzhu Yang
- 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
| | - Yigeng Cao
- 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
| | - Yajing Chu
- 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
| | - Erlie Jiang
- 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
| | - Weiping Yuan
- 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
| | - Xiaomin 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
- Department of Neuro-oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100071, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Hu Q, Zhang S, Yang Y, Li J, Kang H, Tang W, Lyon CJ, Wan M. Extracellular Vesicle ITGAM and ITGB2 Mediate Severe Acute Pancreatitis-Related Acute Lung Injury. ACS NANO 2023; 17:7562-7575. [PMID: 37022097 PMCID: PMC10134486 DOI: 10.1021/acsnano.2c12722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Integrins expressed on extracellular vesicles (EVs) secreted by various cancers are reported to mediate the organotropism of these EVs. Our previous experiment found that pancreatic tissue of mice with severe cases of acute pancreatitis (SAP) overexpresses several integrins and that serum EVs of these mice (SAP-EVs) can mediate acute lung injury (ALI). It is unclear if SAP-EV express integrins that can promote their accumulation in the lung to promote ALI. Here, we report that SAP-EV overexpress several integrins and that preincubation of SAP-EV with the integrin antagonist peptide HYD-1 markedly attenuates their pulmonary inflammation and disrupt the pulmonary microvascular endothelial cell (PMVEC) barrier. Further, we report that injecting SAP mice with EVs engineered to overexpress two of these integrins (ITGAM and ITGB2) can attenuate the pulmonary accumulation of pancreas-derived EVs and similarly decrease pulmonary inflammation and disruption of the endothelial cell barrier. Based on these findings, we propose that pancreatic EVs can mediate ALI in SAP patients and that this injury response could be attenuated by administering EVs that overexpress ITGAM and/or ITGB2, which is worthy of further study due to the lack of effective therapies for SAP-induced ALI.
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Affiliation(s)
- Qian Hu
- Department
of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shu Zhang
- Department
of Emergency Medicine, Emergency Medical Laboratory, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yue Yang
- Department
of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Juan Li
- Department
of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hongxin Kang
- Department
of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wenfu Tang
- Department
of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Christopher J. Lyon
- Center
of Cellular and Molecular Diagnosis, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Meihua Wan
- Department
of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
- West
China Hospital (Airport) of Sichuan University, Chengdu 610299, China
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6
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Montserrat-Vazquez S, Ali NJ, Matteini F, Lozano J, Zhaowei T, Mejia-Ramirez E, Marka G, Vollmer A, Soller K, Sacma M, Sakk V, Mularoni L, Mallm JP, Plass M, Zheng Y, Geiger H, Florian MC. Transplanting rejuvenated blood stem cells extends lifespan of aged immunocompromised mice. NPJ Regen Med 2022; 7:78. [PMID: 36581635 PMCID: PMC9800381 DOI: 10.1038/s41536-022-00275-y] [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: 07/05/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
One goal of regenerative medicine is to rejuvenate tissues and extend lifespan by restoring the function of endogenous aged stem cells. However, evidence that somatic stem cells can be targeted in vivo to extend lifespan is still lacking. Here, we demonstrate that after a short systemic treatment with a specific inhibitor of the small RhoGTPase Cdc42 (CASIN), transplanting aged hematopoietic stem cells (HSCs) from treated mice is sufficient to extend the healthspan and lifespan of aged immunocompromised mice without additional treatment. In detail, we show that systemic CASIN treatment improves strength and endurance of aged mice by increasing the myogenic regenerative potential of aged skeletal muscle stem cells. Further, we show that CASIN modifies niche localization and H4K16ac polarity of HSCs in vivo. Single-cell profiling reveals changes in HSC transcriptome, which underlie enhanced lymphoid and regenerative capacity in serial transplantation assays. Overall, we provide proof-of-concept evidence that a short systemic treatment to decrease Cdc42 activity improves the regenerative capacity of different endogenous aged stem cells in vivo, and that rejuvenated HSCs exert a broad systemic effect sufficient to extend murine health- and lifespan.
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Affiliation(s)
- Sara Montserrat-Vazquez
- grid.417656.7Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain ,grid.417656.7Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet de Llobregat, Barcelona, Spain
| | - Noelle J. Ali
- grid.6582.90000 0004 1936 9748Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - Francesca Matteini
- grid.417656.7Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain ,grid.417656.7Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Lozano
- grid.417656.7Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain ,grid.417656.7Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet de Llobregat, Barcelona, Spain
| | - Tu Zhaowei
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Eva Mejia-Ramirez
- grid.417656.7Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain ,grid.417656.7Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet de Llobregat, Barcelona, Spain ,grid.512890.7Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Gina Marka
- grid.6582.90000 0004 1936 9748Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - Angelika Vollmer
- grid.6582.90000 0004 1936 9748Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - Karin Soller
- grid.6582.90000 0004 1936 9748Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - Mehmet Sacma
- grid.6582.90000 0004 1936 9748Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - Vadim Sakk
- grid.6582.90000 0004 1936 9748Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - Loris Mularoni
- grid.417656.7Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet de Llobregat, Barcelona, Spain
| | | | - Mireya Plass
- grid.417656.7Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet de Llobregat, Barcelona, Spain ,grid.512890.7Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain ,grid.417656.7Gene Regulation of Cell Identity Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Yi Zheng
- grid.239573.90000 0000 9025 8099Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Hartmut Geiger
- grid.6582.90000 0004 1936 9748Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - M. Carolina Florian
- grid.417656.7Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain ,grid.417656.7Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet de Llobregat, Barcelona, Spain ,grid.512890.7Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
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DMAG, a novel countermeasure for the treatment of thrombocytopenia. Mol Med 2021; 27:149. [PMID: 34837956 PMCID: PMC8626956 DOI: 10.1186/s10020-021-00404-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022] Open
Abstract
Background Thrombocytopenia is one of the most common hematological disease that can be life-threatening caused by bleeding complications. However, the treatment options for thrombocytopenia remain limited. Methods In this study, giemsa staining, phalloidin staining, immunofluorescence and flow cytometry were used to identify the effects of 3,3ʹ-di-O-methylellagic acid 4ʹ-glucoside (DMAG), a natural ellagic acid derived from Sanguisorba officinalis L. (SOL) on megakaryocyte differentiation in HEL cells. Then, thrombocytopenia mice model was constructed by X-ray irradiation to evaluate the therapeutic action of DMAG on thrombocytopenia. Furthermore, the effects of DMAG on platelet function were evaluated by tail bleeding time, platelet aggregation and platelet adhesion assays. Next, network pharmacology approaches were carried out to identify the targets of DMAG. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to elucidate the underling mechanism of DMAG against thrombocytopenia. Finally, molecular docking simulation, molecular dynamics simulation and western blot analysis were used to explore the relationship between DAMG with its targets. Results DMAG significantly promoted megakaryocyte differentiation of HEL cells. DMAG administration accelerated platelet recovery and megakaryopoiesis, shortened tail bleeding time, strengthened platelet aggregation and adhesion in thrombocytopenia mice. Network pharmacology revealed that ITGA2B, ITGB3, VWF, PLEK, TLR2, BCL2, BCL2L1 and TNF were the core targets of DMAG. GO and KEGG pathway enrichment analyses suggested that the core targets of DMAG were enriched in PI3K–Akt signaling pathway, hematopoietic cell lineage, ECM-receptor interaction and platelet activation. Molecular docking simulation and molecular dynamics simulation further indicated that ITGA2B, ITGB3, PLEK and TLR2 displayed strong binding ability with DMAG. Finally, western blot analysis evidenced that DMAG up-regulated the expression of ITGA2B, ITGB3, VWF, p-Akt and PLEK. Conclusion DMAG plays a critical role in promoting megakaryocytes differentiation and platelets production and might be a promising medicine for the treatment of thrombocytopenia. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s10020-021-00404-1.
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8
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A robust approach for the generation of functional hematopoietic progenitor cell lines to model leukemic transformation. Blood Adv 2021; 5:39-53. [PMID: 33570624 DOI: 10.1182/bloodadvances.2020003022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022] Open
Abstract
Studies of molecular mechanisms of hematopoiesis and leukemogenesis are hampered by the unavailability of progenitor cell lines that accurately mimic the situation in vivo. We now report a robust method to generate and maintain LSK (Lin-, Sca-1+, c-Kit+) cells, which closely resemble MPP1 cells. HPCLSKs reconstitute hematopoiesis in lethally irradiated recipient mice over >8 months. Upon transformation with different oncogenes including BCR/ABL, FLT3-ITD, or MLL-AF9, their leukemic counterparts maintain stem cell properties in vitro and recapitulate leukemia formation in vivo. The method to generate HPCLSKs can be applied to transgenic mice, and we illustrate it for CDK6-deficient animals. Upon BCR/ABLp210 transformation, HPCLSKsCdk6-/- induce disease with a significantly enhanced latency and reduced incidence, showing the importance of CDK6 in leukemia formation. Studies of the CDK6 transcriptome in murine HPCLSK and human BCR/ABL+ cells have verified that certain pathways depend on CDK6 and have uncovered a novel CDK6-dependent signature, suggesting a role for CDK6 in leukemic progenitor cell homing. Loss of CDK6 may thus lead to a defect in homing. The HPCLSK system represents a unique tool for combined in vitro and in vivo studies and enables the production of large quantities of genetically modifiable hematopoietic or leukemic stem/progenitor cells.
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9
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Yin X, Yang S, Zhang M, Yue Y. The role and prospect of JMJD3 in stem cells and cancer. Biomed Pharmacother 2019; 118:109384. [PMID: 31545292 DOI: 10.1016/j.biopha.2019.109384] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/12/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Currently, stem cells are reported to be involved in tumor formation, drug resistance and recurrence. Inhibiting the proliferation of tumor cells, promoting their senescence and apoptosis has been the most important anti-tumor therapy. Epigenetics is involved in the regulation of gene expression and is closely related to cancer and stem cells. It mainly includes DNA methylation, histone modification, and chromatin remodeling. Histone methylation and demethylation play an important role in histone modification. Histone 3 lysine 27 trimethylation (H3K27me3) induces transcriptional inhibition and plays an important role in gene expression. Jumonji domain-containing protein-3 (JMJD3), one of the demethyases of histone H3K27me3, has been reported to be associated with the prognosis of many cancers and stem cells differentiation. Inhibition of JMJD3 can reduce proliferation and promote apoptosis in tumor cells, as well as suppress differentiation in stem cells. GSK-J4 is an inhibitor of demethylase JMJD3 and UTX, which has been shown to possess anti-cancer and inhibition of embryonic stem cells differentiation effects. In this review, we examine how JMJD3 regulates cellular fates of stem cells and cancer cells and references were identified through searches of PubMed, Medline, Web of Science.
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Affiliation(s)
- Xiaojiao Yin
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China
| | - Siyu Yang
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China
| | - Mingyue Zhang
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China
| | - Ying Yue
- Department of Gynecological Oncology, The First Hospital of Jilin University, Changchun 130000, China.
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10
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Liu F, Wang Z, Li W, Zhou L, Du Y, Zhang M, Wei Y. The mechanisms for the radioprotective effect of beta-d-glucan on high linear-energy-transfer carbon ion irradiated mice. Int J Biol Macromol 2019; 131:282-292. [DOI: 10.1016/j.ijbiomac.2019.03.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 12/15/2022]
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11
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Brown G, Tsapogas P, Ceredig R. The changing face of hematopoiesis: a spectrum of options is available to stem cells. Immunol Cell Biol 2018; 96:898-911. [DOI: 10.1111/imcb.12055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/26/2018] [Accepted: 04/02/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Geoffrey Brown
- Institute of Clinical Sciences; Institute of Immunology and Immunotherapy; College of Medical and Dental Sciences; University of Birmingham; Edgbaston Birmingham UK
| | - Panagiotis Tsapogas
- Developmental and Molecular Immunology; Department of Biomedicine; University of Basel; Basel Switzerland
| | - Rhodri Ceredig
- Discipline of Physiology; College of Medicine & Nursing Health Science; National University of Ireland; Galway Ireland
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12
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Shi L, Jiang F, Ouyang F, Zhang J, Wang Z, Shen X. DNA methylation markers in combination with skeletal and dental ages to improve age estimation in children. Forensic Sci Int Genet 2017; 33:1-9. [PMID: 29172065 DOI: 10.1016/j.fsigen.2017.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/15/2017] [Accepted: 11/11/2017] [Indexed: 12/21/2022]
Abstract
Age estimation is critical in forensic science, in competitive sports and games and in other age-related fields, but the current methods are suboptimal. The combination of age-associated DNA methylation markers with skeletal age (SA) and dental age (DA) may improve the accuracy and precision of age estimation, but no study has examined this topic. In the current study, we measured SA (GP, TW3-RUS, and TW3-Carpal methods) and DA (Demirjian and Willems methods) by X-ray examination in 124 Chinese children (78 boys and 46 girls) aged 6-15 years. To identify age-associated CpG sites, we analyzed methylome-wide DNA methylation profiling by using the Illumina HumanMethylation450 BeadChip system in 48 randomly selected children. Five CpG sites were identified as associated with chronologic age (CA), with an absolute value of Pearson's correlation coefficient (r)>0.5 (p<0.01) and a false discovery rate<0.01. The validation of age-associated CpG sites was performed using droplet digital PCR techniques in all 124 children. After validation, four CpG sites for boys and five CpG sites for girls were further adopted to build the age estimation model with SA and DA using multivariate linear stepwise regressions. These CpG sites were located at 4 known genes: DDO, PRPH2, DHX8, and ITGA2B and at one unknown gene with the Illumina ID number of 22398226. The accuracy of age estimation methods was compared according to the mean absolute error (MAE) and root mean square error (RMSE). The best single measure for SA was the TW3-RUS method (MAE=0.69years, RMSE=0.95years) in boys, and the GP method (MAE=0.74years, RMSE=0.94years) in girls. For DA, the Willems method was the best single measure for both boys (MAE=0.63years, RMSE=0.78years) and girls (MAE=0.54years, RMSE=0.68years). The models that incorporated SA and DA with the methylation levels of age-associated CpG sites provided the highest accuracy of age estimation in both boys (MAE=0.47years, R2=0.886) and girls (MAE=0.33years, R2=0.941). Cross validation of the results confirmed the reliability and validity of the models. In conclusion, age-associated DNA methylation markers in combination with SA and DA greatly improve the accuracy of age estimation in Chinese children. This method may be applied in forensic science, in competitive sports and games and in other age-related fields.
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Affiliation(s)
- Lei Shi
- XinHua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, Shanghai, China; Department of Pediatric Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fan Jiang
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, Shanghai, China
| | - Fengxiu Ouyang
- XinHua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, Shanghai, China
| | - Jun Zhang
- XinHua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, Shanghai, China
| | - Zhimin Wang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center and Shanghai Academy of Science & Technology, Shanghai, China
| | - Xiaoming Shen
- XinHua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, Shanghai, China.
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13
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Transcriptional regulation of SPROUTY2 by MYB influences myeloid cell proliferation and stem cell properties by enhancing responsiveness to IL-3. Leukemia 2016; 31:957-966. [PMID: 27748374 PMCID: PMC5302168 DOI: 10.1038/leu.2016.289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/13/2016] [Indexed: 12/25/2022]
Abstract
Myeloproliferative neoplasms (MPN), which overproduce blood cells in the bone marrow, have recently been linked with a genetically determined decrease in expression of the MYB transcription factor. Here, we use a mouse MYB knockdown model with an MPN-like phenotype to show how lower levels of MYB lead to stem cell characteristics in myeloid progenitors. The altered progenitor properties feature elevated cytokine responsiveness, especially to IL-3, which results from increased receptor expression and increased MAPK activity leading to enhanced phosphorylation of a key regulator of protein synthesis, ribosomal protein S6. MYB acts on MAPK signaling by directly regulating transcription of the gene encoding the negative modulator SPRY2. This mechanistic insight points to pathways that might be targeted therapeutically in MPN.
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Park HJ, Li J, Hannah R, Biddie S, Leal-Cervantes AI, Kirschner K, Flores Santa Cruz D, Sexl V, Göttgens B, Green AR. Cytokine-induced megakaryocytic differentiation is regulated by genome-wide loss of a uSTAT transcriptional program. EMBO J 2016; 35:580-94. [PMID: 26702099 PMCID: PMC4801948 DOI: 10.15252/embj.201592383] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/27/2015] [Accepted: 12/01/2015] [Indexed: 11/29/2022] Open
Abstract
Metazoan development is regulated by transcriptional networks, which must respond to extracellular cues including cytokines. The JAK/STAT pathway is a highly conserved regulatory module, activated by many cytokines, in which tyrosine-phosphorylated STATs (pSTATs) function as transcription factors. However, the mechanisms by which STAT activation modulates lineage-affiliated transcriptional programs are unclear. We demonstrate that in the absence of thrombopoietin (TPO), tyrosine-unphosphorylated STAT5 (uSTAT5) is present in the nucleus where it colocalizes with CTCF and represses a megakaryocytic transcriptional program. TPO-mediated phosphorylation of STAT5 triggers its genome-wide relocation to STAT consensus sites with two distinct transcriptional consequences, loss of a uSTAT5 program that restrains megakaryocytic differentiation and activation of a canonical pSTAT5-driven program which includes regulators of apoptosis and proliferation. Transcriptional repression by uSTAT5 reflects restricted access of the megakaryocytic transcription factor ERG to target genes. These results identify a previously unrecognized mechanism of cytokine-mediated differentiation.
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Affiliation(s)
- Hyun Jung Park
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Juan Li
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Rebecca Hannah
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Simon Biddie
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ana I Leal-Cervantes
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Kristina Kirschner
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - David Flores Santa Cruz
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, Veterinary University Vienna, Vienna, Austria
| | - Berthold Göttgens
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK Department of Haematology, University of Cambridge, Cambridge, UK Department of Haematology, Addenbrooke's Hospital, Cambridge, UK
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15
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Furusawa A, Sadashivaiah K, Singh ZN, Civin CI, Banerjee A. Inefficient megakaryopoiesis in mouse hematopoietic stem-progenitor cells lacking T-bet. Exp Hematol 2016; 44:194-206.e17. [PMID: 26607595 PMCID: PMC4789076 DOI: 10.1016/j.exphem.2015.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/15/2015] [Accepted: 11/05/2015] [Indexed: 12/22/2022]
Abstract
Differentiation of hematopoietic stem-progenitor cells (HSPCs) into mature blood lineages results from the translation of extracellular signals into changes in the expression levels of transcription factors controlling cell fate decisions. Multiple transcription factor families are known to be involved in hematopoiesis. Although the T-box transcription factor family is known to be involved in the differentiation of multiple tissues, and expression of T-bet, a T-box family transcription factor, has been observed in HSPCs, T-box family transcription factors do not have a described role in HSPC differentiation. In the current study, we address the functional consequences of T-bet expression in mouse HSPCs. T-bet protein levels differed among HSPC subsets, with highest levels observed in megakaryo-erythroid progenitor cells (MEPs), the common precursor to megakaryocytes and erythrocytes. HSPCs from T-bet-deficient mice exhibited a defect in megakaryocytic differentiation when cultured in the presence of thrombopoietin. In contrast, erythroid differentiation in culture in the presence of erythropoietin was not substantially altered in T-bet-deficient HSPCs. Differences observed with respect to megakaryocyte number and maturity, as assessed by level of expression of CD41 and CD61, and megakaryocyte ploidy, in T-bet-deficient HSPCs were not associated with altered proliferation or survival in culture. Gene expression micro-array analysis of MEPs from T-bet-deficient mice exhibited diminished expression of multiple genes associated with the megakaryocyte lineage. These data advance our understanding of the transcriptional regulation of megakaryopoiesis by supporting a new role for T-bet in the differentiation of MEPs into megakaryocytes.
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Affiliation(s)
- Aki Furusawa
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD; Program in Oncology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD; Center for Stem Cell Research and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Kavitha Sadashivaiah
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD; Program in Oncology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD; Center for Stem Cell Research and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Zeba N Singh
- Program in Oncology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD; Department of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - Curt I Civin
- Program in Oncology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD; Center for Stem Cell Research and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD; Department of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Arnob Banerjee
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD; Program in Oncology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD; Center for Stem Cell Research and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD.
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16
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Regulation of the Flt3 Gene in Haematopoietic Stem and Early Progenitor Cells. PLoS One 2015; 10:e0138257. [PMID: 26382271 PMCID: PMC4575200 DOI: 10.1371/journal.pone.0138257] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/27/2015] [Indexed: 11/19/2022] Open
Abstract
The MYB transcription factor plays critical roles in normal and malignant haematopoiesis. We previously showed that MYB was a direct activator of FLT3 expression within the context of acute myeloid leukaemia. During normal haematopoiesis, increasing levels of FLT3 expression determine a strict hierarchy within the haematopoietic stem and early progenitor compartment, which associates with lymphoid and myeloid commitment potential. We use the conditional deletion of the Myb gene to investigate the influence of MYB in Flt3 transcriptional regulation within the haematopoietic stem cell (HSC) hierarchy. In accordance with previous report, in vivo deletion of Myb resulted in rapid biased differentiation of HSC with concomitant loss of proliferation capacity. We find that loss of MYB activity also coincided with decreased FLT3 expression. At the chromatin level, the Flt3 promoter is primed in immature HSC, but occupancy of further intronic elements determines expression. Binding to these locations, MYB and C/EBPα need functional cooperation to activate transcription of the locus. This cooperation is cell context dependent and indicates that MYB and C/EBPα activities are inter-dependent in controlling Flt3 expression to influence lineage commitment of multipotential progenitors.
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17
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Song B, Fan Y, He W, Zhu D, Niu X, Wang D, Ou Z, Luo M, Sun X. Improved hematopoietic differentiation efficiency of gene-corrected beta-thalassemia induced pluripotent stem cells by CRISPR/Cas9 system. Stem Cells Dev 2015; 24:1053-65. [PMID: 25517294 DOI: 10.1089/scd.2014.0347] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The generation of beta-thalassemia (β-Thal) patient-specific induced pluripotent stem cells (iPSCs), subsequent homologous recombination-based gene correction of disease-causing mutations/deletions in the β-globin gene (HBB), and their derived hematopoietic stem cell (HSC) transplantation offers an ideal therapeutic solution for treating this disease. However, the hematopoietic differentiation efficiency of gene-corrected β-Thal iPSCs has not been well evaluated in the previous studies. In this study, we used the latest gene-editing tool, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), to correct β-Thal iPSCs; gene-corrected cells exhibit normal karyotypes and full pluripotency as human embryonic stem cells (hESCs) showed no off-targeting effects. Then, we evaluated the differentiation efficiency of the gene-corrected β-Thal iPSCs. We found that during hematopoietic differentiation, gene-corrected β-Thal iPSCs showed an increased embryoid body ratio and various hematopoietic progenitor cell percentages. More importantly, the gene-corrected β-Thal iPSC lines restored HBB expression and reduced reactive oxygen species production compared with the uncorrected group. Our study suggested that hematopoietic differentiation efficiency of β-Thal iPSCs was greatly improved once corrected by the CRISPR/Cas9 system, and the information gained from our study would greatly promote the clinical application of β-Thal iPSC-derived HSCs in transplantation.
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Affiliation(s)
- Bing Song
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University , Guangzhou City, People's Republic of China
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18
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Cabezas-Wallscheid N, Klimmeck D, Hansson J, Lipka DB, Reyes A, Wang Q, Weichenhan D, Lier A, von Paleske L, Renders S, Wünsche P, Zeisberger P, Brocks D, Gu L, Herrmann C, Haas S, Essers MAG, Brors B, Eils R, Huber W, Milsom MD, Plass C, Krijgsveld J, Trumpp A. Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis. Cell Stem Cell 2014; 15:507-522. [PMID: 25158935 DOI: 10.1016/j.stem.2014.07.005] [Citation(s) in RCA: 369] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 06/25/2014] [Accepted: 07/18/2014] [Indexed: 02/07/2023]
Abstract
In this study, we present integrated quantitative proteome, transcriptome, and methylome analyses of hematopoietic stem cells (HSCs) and four multipotent progenitor (MPP) populations. From the characterization of more than 6,000 proteins, 27,000 transcripts, and 15,000 differentially methylated regions (DMRs), we identified coordinated changes associated with early differentiation steps. DMRs show continuous gain or loss of methylation during differentiation, and the overall change in DNA methylation correlates inversely with gene expression at key loci. Our data reveal the differential expression landscape of 493 transcription factors and 682 lncRNAs and highlight specific expression clusters operating in HSCs. We also found an unexpectedly dynamic pattern of transcript isoform regulation, suggesting a critical regulatory role during HSC differentiation, and a cell cycle/DNA repair signature associated with multipotency in MPP2 cells. This study provides a comprehensive genome-wide resource for the functional exploration of molecular, cellular, and epigenetic regulation at the top of the hematopoietic hierarchy.
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Affiliation(s)
- Nina Cabezas-Wallscheid
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Daniel Klimmeck
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jenny Hansson
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Daniel B Lipka
- Division of Epigenomics and Cancer Risk Factors, DKFZ, 69120 Heidelberg, Germany
| | - Alejandro Reyes
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Qi Wang
- Division of Theoretical Bioinformatics, Department of Bioinformatics and Functional Genomics, DKFZ, 69120 Heidelberg, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, DKFZ, 69120 Heidelberg, Germany
| | - Amelie Lier
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Junior Research Group Experimental Hematology, Division of Stem Cells and Cancer, DKFZ, 69120 Heidelberg, Germany
| | - Lisa von Paleske
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Simon Renders
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Peer Wünsche
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Petra Zeisberger
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - David Brocks
- Division of Epigenomics and Cancer Risk Factors, DKFZ, 69120 Heidelberg, Germany
| | - Lei Gu
- Division of Epigenomics and Cancer Risk Factors, DKFZ, 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, Department of Bioinformatics and Functional Genomics, DKFZ, 69120 Heidelberg, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Carl Herrmann
- Division of Theoretical Bioinformatics, Department of Bioinformatics and Functional Genomics, DKFZ, 69120 Heidelberg, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Junior Research Group Stress-induced Activation of Hematopoietic Stem Cells, Division of Stem Cells and Cancer, DKFZ, 69120 Heidelberg, Germany
| | - Marieke A G Essers
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Junior Research Group Stress-induced Activation of Hematopoietic Stem Cells, Division of Stem Cells and Cancer, DKFZ, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, Department of Bioinformatics and Functional Genomics, DKFZ, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, Department of Bioinformatics and Functional Genomics, DKFZ, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Michael D Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Junior Research Group Experimental Hematology, Division of Stem Cells and Cancer, DKFZ, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, DKFZ, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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19
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Johansson C, Tumber A, Che K, Cain P, Nowak R, Gileadi C, Oppermann U. The roles of Jumonji-type oxygenases in human disease. Epigenomics 2014; 6:89-120. [PMID: 24579949 PMCID: PMC4233403 DOI: 10.2217/epi.13.79] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The iron- and 2-oxoglutarate-dependent oxygenases constitute a phylogenetically conserved class of enzymes that catalyze hydroxylation reactions in humans by acting on various types of substrates, including metabolic intermediates, amino acid residues in different proteins and various types of nucleic acids. The discovery of jumonji (Jmj), the founding member of a class of Jmj-type chromatin modifying enzymes and transcriptional regulators, has culminated in the discovery of several branches of histone lysine demethylases, with essential functions in regulating the epigenetic landscape of the chromatin environment. This work has now been considerably expanded into other aspects of epigenetic biology and includes the discovery of enzymatic steps required for methyl-cytosine demethylation as well as modification of RNA and ribosomal proteins. This overview aims to summarize the current knowledge on the human Jmj-type enzymes and their involvement in human pathological processes, including development, cancer, inflammation and metabolic diseases.
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Affiliation(s)
- Catrine Johansson
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - KaHing Che
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Peter Cain
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Radoslaw Nowak
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
| | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
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