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Jiang L, Qu S, Yu Z, Wang J, Liu X. MOASL: Predicting drug mechanism of actions through similarity learning with transcriptomic signature. Comput Biol Med 2024; 169:107853. [PMID: 38104518 DOI: 10.1016/j.compbiomed.2023.107853] [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: 07/19/2023] [Revised: 11/02/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Understanding the mechanisms of actions (MOAs) of compounds is crucial in drug discovery. A common step in drug MOAs annotation is to query the dysregulated gene signatures induced by drugs in a reference library of pre-defined signatures. However, traditional similarity-based computational strategies face challenges when dealing with high-dimensional and noisy transcriptional signature data. To address this issue, we introduce MOASL (MOAs prediction via Similarity Learning), a novel approach that contrastive to learn similarity embeddings among signatures with shared MOAs automatically. We evaluated the accuracy of signature matching on various transcriptional activity score (TAS) datasets and individual cell lines by using MOASL. The results show MOASL achieved higher performance over several statistical and machine learning methods. Furthermore, we provided the rationale of our model by visualizing the signature annotation procedure. Using MOASL, the MOAs label of query signature could be conveniently defined by calculating the similarity between the query embedding and the reference embeddings. Finally, we applied MOASL to repurpose thousands of compounds as glucocorticoid receptor (GR) agonists, accurately identifying 8 out of the top 10 compounds. MOASL is conveniently accessible on GitHub at https://github.com/jianglikun/MOASL, empowering researchers and practitioners in the field of drug discovery to predict the MOAs of drug.
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Affiliation(s)
- Likun Jiang
- Department of Computer Science, Xiamen University, Xiamen 361005, PR China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, PR China
| | - Susu Qu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PR China; Chinese Institute for Brain Research, Beijing 102206, PR China
| | - Zhengqiu Yu
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, PR China; School of Medicine, Xiamen University, Xiamen 361005, PR China
| | - Jianmin Wang
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, South Korea
| | - Xiangrong Liu
- Department of Computer Science, Xiamen University, Xiamen 361005, PR China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, PR China.
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2
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Martinez-Navajas G, Ceron-Hernandez J, Simon I, Lupiañez P, Diaz-McLynn S, Perales S, Modlich U, Guerrero JA, Martin F, Sevivas T, Lozano ML, Rivera J, Ramos-Mejia V, Tersteeg C, Real PJ. Lentiviral gene therapy reverts GPIX expression and phenotype in Bernard-Soulier syndrome type C. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:75-92. [PMID: 37416759 PMCID: PMC10320622 DOI: 10.1016/j.omtn.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023]
Abstract
Bernard-Soulier syndrome (BSS) is a rare congenital disease characterized by macrothrombocytopenia and frequent bleeding. It is caused by pathogenic variants in three genes (GP1BA, GP1BB, or GP9) that encode for the GPIbα, GPIbβ, and GPIX subunits of the GPIb-V-IX complex, the main platelet surface receptor for von Willebrand factor, being essential for platelet adhesion and aggregation. According to the affected gene, we distinguish BSS type A1 (GP1BA), type B (GP1BB), or type C (GP9). Pathogenic variants in these genes cause absent, incomplete, or dysfunctional GPIb-V-IX receptor and, consequently, a hemorrhagic phenotype. Using gene-editing tools, we generated knockout (KO) human cellular models that helped us to better understand GPIb-V-IX complex assembly. Furthermore, we developed novel lentiviral vectors capable of correcting GPIX expression, localization, and functionality in human GP9-KO megakaryoblastic cell lines. Generated GP9-KO induced pluripotent stem cells produced platelets that recapitulated the BSS phenotype: absence of GPIX on the membrane surface and large size. Importantly, gene therapy tools reverted both characteristics. Finally, hematopoietic stem cells from two unrelated BSS type C patients were transduced with the gene therapy vectors and differentiated to produce GPIX-expressing megakaryocytes and platelets with a reduced size. These results demonstrate the potential of lentiviral-based gene therapy to rescue BSS type C.
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Affiliation(s)
- Gonzalo Martinez-Navajas
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Jorge Ceron-Hernandez
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Iris Simon
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Pablo Lupiañez
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Sofia Diaz-McLynn
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
| | - Sonia Perales
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
| | - Ute Modlich
- Department of Gene and Cell Therapy, Institute of Regenerative Medicine, University of Zürich, Wagistrasse 12, 8952 Schlieren-Zürich, Switzerland
| | - Jose A. Guerrero
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Francisco Martin
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, Avenida Ilustracion S/n, 18016 Granada, Spain
| | - Teresa Sevivas
- Serviço de Sangue, Medicina Transfusional e Imunohemoterapia Do Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria L. Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, U765 Murcia, Spain
| | - Jose Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, U765 Murcia, Spain
- Grupo Español de Alteraciones Plaquetarias Congénitas (GEAPC), Madrid, Spain
| | - Veronica Ramos-Mejia
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
| | - Claudia Tersteeg
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - Pedro J. Real
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
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De Novo Generation of Human Hematopoietic Stem Cells from Pluripotent Stem Cells for Cellular Therapy. Cells 2023; 12:cells12020321. [PMID: 36672255 PMCID: PMC9857267 DOI: 10.3390/cells12020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The ability to manufacture human hematopoietic stem cells (HSCs) in the laboratory holds enormous promise for cellular therapy of human blood diseases. Several differentiation protocols have been developed to facilitate the emergence of HSCs from human pluripotent stem cells (PSCs). Most approaches employ a stepwise addition of cytokines and morphogens to recapitulate the natural developmental process. However, these protocols globally lack clinical relevance and uniformly induce PSCs to produce hematopoietic progenitors with embryonic features and limited engraftment and differentiation capabilities. This review examines how key intrinsic cues and extrinsic environmental inputs have been integrated within human PSC differentiation protocols to enhance the emergence of definitive hematopoiesis and how advances in genomics set the stage for imminent breakthroughs in this field.
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Functional Evaluation of KEL as an Oncogenic Gene in the Progression of Acute Erythroleukemia. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5885342. [PMID: 35140839 PMCID: PMC8819426 DOI: 10.1155/2022/5885342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022]
Abstract
Acute erythroleukemia (AEL) is an infrequent subtype of acute myeloid leukemia (AML) with worse prognosis. Though the last decade has seen major advances in the novel features and genomic landscape in AEL, there is still a lack of specific therapeutic targets and effective treatment approaches for this disease. Here, we found a novel oncogene KEL that specifically and aberrantly expressed in patients with AEL. In this study, we demonstrated that KEL promoted cell proliferation and the downregulation of KEL reversed drug resistance in AEL cells to JQ1. Our findings suggested that KEL contributed to gain of H3K27 acetylation and promoted erythroid differentiation induced by GATA1. Additionally, GATA1 and TAL1 as cotranscription factors (TFs) modulated the expression of KEL. Maintaining cell viability and differentiation, KEL also played parts in the immune evasion of tumor cells. Our work expands the current knowledge regarding molecular mechanisms involved in cancer onset and progression, offering promising therapeutic target to broaden the treatment options.
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Mehrpouri M, Pourbagheri-Sigaroodi A, Bashash D. The contributory roles of histone deacetylases (HDACs) in hematopoiesis regulation and possibilities for pharmacologic interventions in hematologic malignancies. Int Immunopharmacol 2021; 100:108114. [PMID: 34492531 DOI: 10.1016/j.intimp.2021.108114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 12/17/2022]
Abstract
Although the definitive role of epigenetic modulations in a wide range of hematologic malignancies, spanning from leukemia to lymphoma and multiple myeloma, has been evidenced, few articles reviewed the task. Given the high accessibility of histone deacetylase (HDACs) to necessary transcription factors involved in hematopoiesis, this review aims to outline physiologic impacts of these enzymes in normal hematopoiesis, and also to outline the original data obtained from international research laboratories on their regulatory role in the differentiation and maturation of different hematopoietic lineages. Questions on how aberrant expression of HDACs contributes to the formation of hematologic malignancies are also responded, because these classes of enzymes have a respectable share in the development, progression, and recurrence of leukemia, lymphoma, and multiple myeloma. The last section provides a special focus on the therapeutic perspectiveof HDACs inhibitors, either as single agents or in a combined-modal strategy, in these neoplasms. In conclusion, optimizing the dose and the design of more patient-tailored inhibitors, while maintaining low toxicity against normal cells, will help improve clinical outcomes of HDAC inhibitors in hematologic malignancies.
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Affiliation(s)
- Mahdieh Mehrpouri
- Department of Laboratory Sciences, School of Allied Medical Sciences, Alborz University of Medical Sciences, Karaj, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Wang H, He J, Xu C, Chen X, Yang H, Shi S, Liu C, Zeng Y, Wu D, Bai Z, Wang M, Wen Y, Su P, Xia M, Huang B, Ma C, Bian L, Lan Y, Cheng T, Shi L, Liu B, Zhou J. Decoding Human Megakaryocyte Development. Cell Stem Cell 2020; 28:535-549.e8. [PMID: 33340451 DOI: 10.1016/j.stem.2020.11.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 09/25/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022]
Abstract
Despite our growing understanding of embryonic immune development, rare early megakaryocytes (MKs) remain relatively understudied. Here we used single-cell RNA sequencing of human MKs from embryonic yolk sac (YS) and fetal liver (FL) to characterize the transcriptome, cellular heterogeneity, and developmental trajectories of early megakaryopoiesis. In the YS and FL, we found heterogeneous MK subpopulations with distinct developmental routes and patterns of gene expression that could reflect early functional specialization. Intriguingly, we identified a subpopulation of CD42b+CD14+ MKs in vivo that exhibit high expression of genes associated with immune responses and can also be derived from human embryonic stem cells (hESCs) in vitro. Furthermore, we identified THBS1 as an early marker for MK-biased embryonic endothelial cells. Overall, we provide important insights and invaluable resources for dissection of the molecular and cellular programs underlying early human megakaryopoiesis.
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Affiliation(s)
- Hongtao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Changlu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Xiaoyuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Hua Yang
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin 300052, China
| | - Shujuan Shi
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin 300052, China
| | - Cuicui Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Yang Zeng
- Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Dan Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Mengge Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Yuqi Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Pei Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Meijuan Xia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Baiming Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Chunyu Ma
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Lihong Bian
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China.
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China.
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China.
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Keenan AB, Wojciechowicz ML, Wang Z, Jagodnik KM, Jenkins SL, Lachmann A, Ma'ayan A. Connectivity Mapping: Methods and Applications. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021211] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Connectivity mapping resources consist of signatures representing changes in cellular state following systematic small-molecule, disease, gene, or other form of perturbations. Such resources enable the characterization of signatures from novel perturbations based on similarity; provide a global view of the space of many themed perturbations; and allow the ability to predict cellular, tissue, and organismal phenotypes for perturbagens. A signature search engine enables hypothesis generation by finding connections between query signatures and the database of signatures. This framework has been used to identify connections between small molecules and their targets, to discover cell-specific responses to perturbations and ways to reverse disease expression states with small molecules, and to predict small-molecule mimickers for existing drugs. This review provides a historical perspective and the current state of connectivity mapping resources with a focus on both methodology and community implementations.
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Affiliation(s)
- Alexandra B. Keenan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan L. Wojciechowicz
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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8
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Bueno C, Calero-Nieto FJ, Wang X, Valdés-Mas R, Gutiérrez-Agüera F, Roca-Ho H, Ayllon V, Real PJ, Arambilet D, Espinosa L, Torres-Ruiz R, Agraz-Doblas A, Varela I, de Boer J, Bigas A, Gottgens B, Marschalek R, Menendez P. Enhanced hemato-endothelial specification during human embryonic differentiation through developmental cooperation between AF4-MLL and MLL-AF4 fusions. Haematologica 2019; 104:1189-1201. [PMID: 30679325 PMCID: PMC6545840 DOI: 10.3324/haematol.2018.202044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/21/2019] [Indexed: 12/18/2022] Open
Abstract
The t(4;11)(q21;q23) translocation is associated with high-risk infant pro-B-cell acute lymphoblastic leukemia and arises prenatally during embryonic/fetal hematopoiesis. The developmental/pathogenic contribution of the t(4;11)-resulting MLL-AF4 (MA4) and AF4-MLL (A4M) fusions remains unclear; MA4 is always expressed in patients with t(4;11)+ B-cell acute lymphoblastic leukemia, but the reciprocal fusion A4M is expressed in only half of the patients. Because prenatal leukemogenesis manifests as impaired early hematopoietic differentiation, we took advantage of well-established human embryonic stem cell-based hematopoietic differentiation models to study whether the A4M fusion cooperates with MA4 during early human hematopoietic development. Co-expression of A4M and MA4 strongly promoted the emergence of hemato-endothelial precursors, both endothelial- and hemogenic-primed. Double fusion-expressing hemato-endothelial precursors specified into significantly higher numbers of both hematopoietic and endothelial-committed cells, irrespective of the differentiation protocol used and without hijacking survival/proliferation. Functional analysis of differentially expressed genes and differentially enriched H3K79me3 genomic regions by RNA-sequencing and H3K79me3 chromatin immunoprecipitation-sequencing, respectively, confirmed a hematopoietic/endothelial cell differentiation signature in double fusion-expressing hemato-endothelial precursors. Importantly, chromatin immunoprecipitation-sequencing analysis revealed a significant enrichment of H3K79 methylated regions specifically associated with HOX-A cluster genes in double fusion-expressing differentiating hematopoietic cells. Overall, these results establish a functional and molecular cooperation between MA4 and A4M fusions during human hematopoietic development.
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Affiliation(s)
- Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Fernando J Calero-Nieto
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Xiaonan Wang
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | | | - Francisco Gutiérrez-Agüera
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Heleia Roca-Ho
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Veronica Ayllon
- GENyO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government and University of Granada, Department of Biochemistry and Molecular Biology, Granada, Spain
| | - Pedro J Real
- GENyO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government and University of Granada, Department of Biochemistry and Molecular Biology, Granada, Spain
| | - David Arambilet
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
| | - Lluis Espinosa
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Raul Torres-Ruiz
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Jasper de Boer
- Cancer Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Anna Bigas
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Bertie Gottgens
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt, Germany
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Alsayegh K, Cortés-Medina LV, Ramos-Mandujano G, Badraiq H, Li M. Hematopoietic Differentiation of Human Pluripotent Stem Cells: HOX and GATA Transcription Factors as Master Regulators. Curr Genomics 2019; 20:438-452. [PMID: 32194342 PMCID: PMC7062042 DOI: 10.2174/1389202920666191017163837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
Numerous human disorders of the blood system would directly or indirectly benefit from therapeutic approaches that reconstitute the hematopoietic system. Hematopoietic stem cells (HSCs), either from matched donors or ex vivo manipulated autologous tissues, are the most used cellular source of cell therapy for a wide range of disorders. Due to the scarcity of matched donors and the difficulty of ex vivo expansion of HSCs, there is a growing interest in harnessing the potential of pluripotent stem cells (PSCs) as a de novo source of HSCs. PSCs make an ideal source of cells for regenerative medicine in general and for treating blood disorders in particular because they could expand indefinitely in culture and differentiate to any cell type in the body. However, advancement in deriving functional HSCs from PSCs has been slow. This is partly due to an incomplete understanding of the molecular mechanisms underlying normal hematopoiesis. In this review, we discuss the latest efforts to generate human PSC (hPSC)-derived HSCs capable of long-term engraftment. We review the regulation of the key transcription factors (TFs) in hematopoiesis and hematopoietic differentiation, the Homeobox (HOX) and GATA genes, and the interplay between them and microRNAs. We also propose that precise control of these master regulators during the course of hematopoietic differentiation is key to achieving functional hPSC-derived HSCs.
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Affiliation(s)
- Khaled Alsayegh
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lorena V Cortés-Medina
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Gerardo Ramos-Mandujano
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Heba Badraiq
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Mo Li
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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10
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11
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Dhenge A, Kuhikar R, Kale V, Limaye L. Regulation of differentiation of MEG01 to megakaryocytes and platelet-like particles by Valproic acid through Notch3 mediated actin polymerization. Platelets 2018; 30:780-795. [PMID: 30332548 DOI: 10.1080/09537104.2018.1528344] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Valproic acid (VPA) is one of the HDAC inhibitors used for the treatment of neurological disorders and hematological malignancies. Its role in self-renewal and proliferation of hematopoietic stem cells (HSCs) is well studied, but little is known about its involvement in regulating megakaryopoiesis and thrombopoiesis. In this study, we evaluated the role of VPA in megakaryopoiesis by using MEG-01, a megakaryoblast cell line. Our results show that VPA treatment differentiates MEG-01 cells to megakaryocytes (MK) and platelet-like particles. It was confirmed by augmented expression of MK and PLT-specific markers, higher ploidy, and PLT functionality. We assessed the molecular events underlying megakaryopoiesis. In the present study, we found an upregulation of Notch3 and its downstream target PDGFR-β upon VPA treatment. The direct role of Notch3 in megakaryopoiesis has not yet been studied. PDGFR-β is known to control actin organization during vascular smooth muscle cell differentiation. The actin cytoskeleton plays important role during proplatelet and PLT formation. We found an upregulation of Rac/Cdc42 GTPase and its downstream effectors that are the key players during actin polymerization events. We speculate that VPA induces PLT formation through Notch-3 signaling that in turn modulates actin polymerization that is one of the crucial steps necessary for thrombopoiesis. These studies were also confirmed with knockdown of Notch3 in MEG01 by using ShRNA approach as well as with apheresis-derived CD34+ cells. Altogether, these findings provide an evidence for a novel role of Notch3 in regulating platelet formation.
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Affiliation(s)
- Ankita Dhenge
- a National Centre for Cell Science, NCCS Complex , Savitribai Phule Pune University Campus , Pune , India
| | - Rutuja Kuhikar
- a National Centre for Cell Science, NCCS Complex , Savitribai Phule Pune University Campus , Pune , India
| | - Vaijayanti Kale
- a National Centre for Cell Science, NCCS Complex , Savitribai Phule Pune University Campus , Pune , India
| | - Lalita Limaye
- a National Centre for Cell Science, NCCS Complex , Savitribai Phule Pune University Campus , Pune , India
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12
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Kumar PS, Chandrasekhar C, Srikanth L, Sarma PVGK. In vitro large scale production of megakaryocytes to functional platelets from human hematopoietic stem cells. Biochem Biophys Res Commun 2018; 505:168-175. [PMID: 30243726 DOI: 10.1016/j.bbrc.2018.09.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022]
Abstract
Megakaryocytopoiesis results in the formation of platelets, which are essential for hemostasis. Decreased production or increased destruction of platelets can cause thrombocytopenia, in which platelet transfusion is the mode of treatment. The present study is aimed in generation of megakaryocytes (MKs) and platelet from human hematopoietic stem cells (HSCs). The purity of HSCs was assessed through Flow cytometry and immunocytochemistry (ICC) studies. These pure HSCs were induced with thrombopoietin (TPO), similarly with Andrographis paniculata extract (APE) for 21 days to generate MKs. The APE is mainly composed of andrographolide which stimulates TPO from the liver, and this binds to CD110 present on the surface of HSCs and triggers the proliferation of HSCs and initiate higher MKs population subsequently, a large number of platelets. The results of the present study showed increased proliferation of HSCs grown in the presence of APE and revealed a high population of CD41a and CD42b positive MKs as enumerated by Flow cytometry compared with TPO induced MKs. These results also concurred with qRT-PCR and western blot analysis. The scanning electron microscopy (SEM) revealed the morphology of differentiated MKs and platelets were similar to human blood platelets. The differentiated MKs in APE exhibited polyploidy up to 32 N while TPO induced MKs showed polyploidy of 8 N, these results corroborated with colony forming unit assay. On thrombin stimulation, high expression of P-selectin (CD62p) and fibrinogen binding were detected in APE induced platelets. Autologous transplantation of platelets generated from APE may be a useful option in thrombocytopenia condition.
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Affiliation(s)
- Pasupuleti Santhosh Kumar
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, 517507, Andhra Pradesh, India
| | - Chodimella Chandrasekhar
- Department of Hematology, Sri Venkateswara Institute of Medical Sciences, Tirupati, 517507, Andhra Pradesh, India
| | - Lokanathan Srikanth
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, 517507, Andhra Pradesh, India
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13
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Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform 2018; 19:506-523. [PMID: 28069634 PMCID: PMC5952941 DOI: 10.1093/bib/bbw112] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
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Affiliation(s)
- Aliyu Musa
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Laleh Soltan Ghoraie
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, Northern Ireland, UK
| | - Galina Glazko
- University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York, USA
| | - Olli Yli-Harja
- Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, Hall in Tyrol, Austria
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Frank Emmert-Streib
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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14
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Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform 2018. [PMID: 28069634 DOI: 10.1093/bib] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
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Affiliation(s)
- Aliyu Musa
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Laleh Soltan Ghoraie
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry BT47 6SB, Northern Ireland, UK
| | - Galina Glazko
- University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York 14642, USA
| | - Olli Yli-Harja
- Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, 6060 Hall in Tyrol, Austria
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Frank Emmert-Streib
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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15
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Vagapova ER, Spirin PV, Lebedev TD, Prassolov VS. The Role of TAL1 in Hematopoiesis and Leukemogenesis. Acta Naturae 2018; 10:15-23. [PMID: 29713515 PMCID: PMC5916730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
TAL1 (SCL/TAL1, T-cell acute leukemia protein 1) is a transcription factor that is involved in the process of hematopoiesis and leukemogenesis. It participates in blood cell formation, forms mesoderm in early embryogenesis, and regulates hematopoiesis in adult organisms. TAL1 is essential in maintaining the multipotency of hematopoietic stem cells (HSC) and keeping them in quiescence (stage G0). TAL1 forms complexes with various transcription factors, regulating hematopoiesis (E2A/HEB, GATA1-3, LMO1-2, Ldb1, ETO2, RUNX1, ERG, FLI1). In these complexes, TAL1 regulates normal myeloid differentiation, controls the proliferation of erythroid progenitors, and determines the choice of the direction of HSC differentiation. The transcription factors TAL1, E2A, GATA1 (or GATA2), LMO2, and Ldb1 are the major components of the SCL complex. In addition to normal hematopoiesis, this complex may also be involved in the process of blood cell malignant transformation. Upregulation of C-KIT expression is one of the main roles played by the SCL complex. Today, TAL1 and its partners are considered promising therapeutic targets in the treatment of T-cell acute lymphoblastic leukemia.
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Affiliation(s)
- E. R. Vagapova
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - P. V. Spirin
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - T. D. Lebedev
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - V. S. Prassolov
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
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16
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Navarro-Montero O, Ayllon V, Lamolda M, López-Onieva L, Montes R, Bueno C, Ng E, Guerrero-Carreno X, Romero T, Romero-Moya D, Stanley E, Elefanty A, Ramos-Mejia V, Menendez P, Real PJ. RUNX1c Regulates Hematopoietic Differentiation of Human Pluripotent Stem Cells Possibly in Cooperation with Proinflammatory Signaling. Stem Cells 2017; 35:2253-2266. [PMID: 28869683 DOI: 10.1002/stem.2700] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 07/19/2017] [Accepted: 08/02/2017] [Indexed: 02/07/2023]
Abstract
Runt-related transcription factor 1 (Runx1) is a master hematopoietic transcription factor essential for hematopoietic stem cell (HSC) emergence. Runx1-deficient mice die during early embryogenesis due to the inability to establish definitive hematopoiesis. Here, we have used human pluripotent stem cells (hPSCs) as model to study the role of RUNX1 in human embryonic hematopoiesis. Although the three RUNX1 isoforms a, b, and c were induced in CD45+ hematopoietic cells, RUNX1c was the only isoform induced in hematoendothelial progenitors (HEPs)/hemogenic endothelium. Constitutive expression of RUNX1c in human embryonic stem cells enhanced the appearance of HEPs, including hemogenic (CD43+) HEPs and promoted subsequent differentiation into blood cells. Conversely, specific deletion of RUNX1c dramatically reduced the generation of hematopoietic cells from HEPs, indicating that RUNX1c is a master regulator of human hematopoietic development. Gene expression profiling of HEPs revealed a RUNX1c-induced proinflammatory molecular signature, supporting previous studies demonstrating proinflammatory signaling as a regulator of HSC emergence. Collectively, RUNX1c orchestrates hematopoietic specification of hPSCs, possibly in cooperation with proinflammatory signaling. Stem Cells 2017;35:2253-2266.
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Affiliation(s)
- Oscar Navarro-Montero
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Veronica Ayllon
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Mar Lamolda
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Granada, Spain
| | - Lourdes López-Onieva
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Rosa Montes
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute and Biomedicine Department, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Elizabeth Ng
- Blood Cell Development and Disease Laboratory, Murdoch Childrens Research Institute. The Royal Children's Hospital, Parkville, Australia
| | - Xiomara Guerrero-Carreno
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Tamara Romero
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Damià Romero-Moya
- Josep Carreras Leukemia Research Institute and Biomedicine Department, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Ed Stanley
- Stem Cell Technology Laboratory, Murdoch Childrens Research Institute. The Royal Children's Hospital, Parkville, Australia
| | - Andrew Elefanty
- Blood Cell Development and Disease Laboratory, Murdoch Childrens Research Institute. The Royal Children's Hospital, Parkville, Australia
| | - Verónica Ramos-Mejia
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Biomedicine Department, School of Medicine, University of Barcelona, Barcelona, Spain.,Instituciò Catalana de Reserca i EstudisAvançats (ICREA), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, Barcelona, Spain
| | - Pedro J Real
- Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, GENYO: Centre for Genomics and Oncological Research Pfizer-University of Granada-Junta de Andalucía, PTS Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Granada, Spain
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17
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Generating autologous hematopoietic cells from human-induced pluripotent stem cells through ectopic expression of transcription factors. Curr Opin Hematol 2017; 24:283-288. [DOI: 10.1097/moh.0000000000000343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Aryl hydrocarbon receptor inhibition promotes hematolymphoid development from human pluripotent stem cells. Blood 2017; 129:3428-3439. [PMID: 28533309 DOI: 10.1182/blood-2016-07-730440] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 05/04/2017] [Indexed: 12/11/2022] Open
Abstract
deletion, we further demonstrate a marked enhancement of hematopoietic differentiation relative to wild-type hESCs. We also evaluated whether AHR antagonism could promote innate lymphoid cell differentiation from hESCs. SR-1 increased conventional natural killer (cNK) cell differentiation, whereas TCDD treatment blocked cNK development and supported group 3 innate lymphoid cell (ILC3) differentiation. Collectively, these results demonstrate that AHR regulates early human hematolymphoid cell development and may be targeted to enhance production of specific cell populations derived from human pluripotent stem cells.
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19
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Giorgetti A, Castaño J, Bueno C, Díaz de la Guardia R, Delgado M, Bigas A, Espinosa L, Menendez P. Proinflammatory signals are insufficient to drive definitive hematopoietic specification of human HSCs in vitro. Exp Hematol 2017; 45:85-93.e2. [DOI: 10.1016/j.exphem.2016.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 10/24/2022]
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20
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Ackermann M, Liebhaber S, Klusmann JH, Lachmann N. Lost in translation: pluripotent stem cell-derived hematopoiesis. EMBO Mol Med 2016; 7:1388-402. [PMID: 26174486 PMCID: PMC4644373 DOI: 10.15252/emmm.201505301] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pluripotent stem cells (PSCs) such as embryonic stem cells or induced pluripotent stem cells represent a promising cell type to gain novel insights into human biology. Understanding the differentiation process of PSCs in vitro may allow for the identification of cell extrinsic/intrinsic factors, driving the specification process toward all cell types of the three germ layers, which may be similar to the human in vivo scenario. This would not only lay the ground for an improved understanding of human embryonic development but would also contribute toward the generation of novel cell types used in cell replacement therapies. In this line, especially the developmental process of mesodermal cells toward the hematopoietic lineage is of great interest. Therefore, this review highlights recent progress in the field of hematopoietic specification of pluripotent stem cell sources. In addition, we would like to shed light on emerging factors controlling primitive and definitive hematopoietic development and to highlight recent approaches to improve the differentiation potential of PSC sources toward hematopoietic stem/progenitor cells. While the generation of fully defined hematopoietic stem cells from PSCs remains challenging in vitro, we here underline the instructive role of cell extrinsic factors such as cytokines for the generation of PSC-derived mature hematopoietic cells. Thus, we have comprehensively examined the role of cytokines for the derivation of mature hematopoietic cell types such as macrophages, granulocytes, megakaryocytes, erythrocytes, dendritic cells, and cells of the B- and T-cell lineage.
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Affiliation(s)
- Mania Ackermann
- RG Reprogramming and Gene Therapy, REBIRTH Cluster of Excellence Hannover Medical School, Hannover, Germany Institute of Experimental Hematology Hannover Medical School, Hannover, Germany
| | - Steffi Liebhaber
- RG Reprogramming and Gene Therapy, REBIRTH Cluster of Excellence Hannover Medical School, Hannover, Germany Institute of Experimental Hematology Hannover Medical School, Hannover, Germany
| | | | - Nico Lachmann
- RG Reprogramming and Gene Therapy, REBIRTH Cluster of Excellence Hannover Medical School, Hannover, Germany Institute of Experimental Hematology Hannover Medical School, Hannover, Germany JRG Translational Hematology of Congenital Diseases, REBIRTH Cluster of Excellence Hannover Medical School, Hannover, Germany
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21
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Moreau T, Evans AL, Vasquez L, Tijssen MR, Yan Y, Trotter MW, Howard D, Colzani M, Arumugam M, Wu WH, Dalby A, Lampela R, Bouet G, Hobbs CM, Pask DC, Payne H, Ponomaryov T, Brill A, Soranzo N, Ouwehand WH, Pedersen RA, Ghevaert C. Large-scale production of megakaryocytes from human pluripotent stem cells by chemically defined forward programming. Nat Commun 2016; 7:11208. [PMID: 27052461 PMCID: PMC4829662 DOI: 10.1038/ncomms11208] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 03/02/2016] [Indexed: 02/02/2023] Open
Abstract
The production of megakaryocytes (MKs)--the precursors of blood platelets--from human pluripotent stem cells (hPSCs) offers exciting clinical opportunities for transfusion medicine. Here we describe an original approach for the large-scale generation of MKs in chemically defined conditions using a forward programming strategy relying on the concurrent exogenous expression of three transcription factors: GATA1, FLI1 and TAL1. The forward programmed MKs proliferate and differentiate in culture for several months with MK purity over 90% reaching up to 2 × 10(5) mature MKs per input hPSC. Functional platelets are generated throughout the culture allowing the prospective collection of several transfusion units from as few as 1 million starting hPSCs. The high cell purity and yield achieved by MK forward programming, combined with efficient cryopreservation and good manufacturing practice (GMP)-compatible culture, make this approach eminently suitable to both in vitro production of platelets for transfusion and basic research in MK and platelet biology.
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Affiliation(s)
- Thomas Moreau
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,The Anne McLaren Laboratory, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute and Department of Surgery, University of Cambridge, West Forvie Site, Robinson Way, Cambridge CB2 0SZ, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Amanda L. Evans
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Louella Vasquez
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1RQ, UK
| | - Marloes R. Tijssen
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK
| | - Ying Yan
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1RQ, UK
| | - Matthew W. Trotter
- The Anne McLaren Laboratory, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute and Department of Surgery, University of Cambridge, West Forvie Site, Robinson Way, Cambridge CB2 0SZ, UK
| | - Daniel Howard
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Maria Colzani
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Meera Arumugam
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Wing Han Wu
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Amanda Dalby
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Riina Lampela
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Guenaelle Bouet
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Catherine M. Hobbs
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Dean C. Pask
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Holly Payne
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tatyana Ponomaryov
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alexander Brill
- Institute of Cardiovascular Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1RQ, UK
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK
| | - Roger A. Pedersen
- The Anne McLaren Laboratory, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute and Department of Surgery, University of Cambridge, West Forvie Site, Robinson Way, Cambridge CB2 0SZ, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK,
| | - Cedric Ghevaert
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Tennis Court Road, Cambridge CB2 1QR, UK,
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