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Dorans E, Jagadeesh K, Dey K, Price AL. Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307813. [PMID: 38826240 PMCID: PMC11142273 DOI: 10.1101/2024.05.24.24307813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown great promise in linking regulatory elements to genes. However, existing methods differ in their modeling assumptions and approaches to account for biological and technical noise-leading to low concordance in their linking scores-and do not capture the effects of genomic distance. We propose pgBoost, an integrative modeling framework that trains a non-linear combination of existing linking strategies (including genomic distance) on fine-mapped eQTL data to assign a probabilistic score to each candidate SNP-gene link. We applied pgBoost to single-cell multiome data from 85k cells representing 6 major immune/blood cell types. pgBoost attained higher enrichment for fine-mapped eSNP-eGene pairs (e.g. 21x at distance >10kb) than existing methods (1.2-10x; p-value for difference = 5e-13 vs. distance-based method and < 4e-35 for each other method), with larger improvements at larger distances (e.g. 35x vs. 0.89-6.6x at distance >100kb; p-value for difference < 0.002 vs. each other method). pgBoost also outperformed existing methods in enrichment for CRISPR-validated links (e.g. 4.8x vs. 1.6-4.1x at distance >10kb; p-value for difference = 0.25 vs. distance-based method and < 2e-5 for each other method), with larger improvements at larger distances (e.g. 15x vs. 1.6-2.5x at distance >100kb; p-value for difference < 0.009 for each other method). Similar improvements in enrichment were observed for links derived from Activity-By-Contact (ABC) scores and GWAS data. We further determined that restricting pgBoost to features from a focal cell type improved the identification of SNP-gene links relevant to that cell type. We highlight several examples where pgBoost linked fine-mapped GWAS variants to experimentally validated or biologically plausible target genes that were not implicated by other methods. In conclusion, a non-linear combination of linking strategies, including genomic distance, improves power to identify target genes underlying GWAS associations.
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Kasai F, Mizukoshi K, Nakamura Y. Variable characteristics overlooked in human K-562 leukemia cell lines with a common signature. Sci Rep 2024; 14:9619. [PMID: 38671192 PMCID: PMC11053119 DOI: 10.1038/s41598-024-60271-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024] Open
Abstract
K-562 is a well-known in vitro cellular model that represents human leukemia cell lines. Although the K-562 cells have been extensively characterized, there are inconsistencies in the data across publications, showing the presence of multiple K-562 cell lines. This suggests that analyzing a single K-562 cell line is insufficient to provide reliable reference data. In this study, we compared three K-562 cell lines with different IDs (RCB0027, RCB1635, and RCB1897) to investigate the fundamental characteristics of K-562 cells. Amplifications of the BCR-ABL1 fusion gene and at 13q31 were detected in all three cell lines, whereas each genome exhibited distinctive features of sequence variants and loss of heterozygosity. This implies that each K-562 cell line can be characterized by common and unique features through a comparison of multiple K-562 cell lines. Variations in transcriptome profiles and hemoglobin synthesis were also observed among the three cell lines, indicating that they should be considered sublines that have diverged from the common ancestral K-562 despite no changes from the original cell name. This leads to unintentional differences in genotypes and/or phenotypes among cell lines that share the same name. These data show that characterizing a single K-562 cell line does not necessarily provide data that are applicable to other K-562 cells. In this context, it is essential to modify cell names in accordance with changes in characteristics during cell culture. Furthermore, our data could serve as a reference for evaluating other K-562 sublines, facilitating the discovery of new K-562 sublines with distinct characteristics. This approach results in the accumulation of K-562 sublines with diverged characteristics and expands the options available, which may help in selecting the most suitable K-562 subline for each experiment.
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Affiliation(s)
- Fumio Kasai
- RIKEN Cell Bank, Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan.
| | - Kumiko Mizukoshi
- RIKEN Cell Bank, Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Yukio Nakamura
- RIKEN Cell Bank, Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
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3
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Nai A, Cordero-Sanchez C, Tanzi E, Pagani A, Silvestri L, Di Modica SM. Cellular and animal models for the investigation of β-thalassemia. Blood Cells Mol Dis 2024; 104:102761. [PMID: 37271682 DOI: 10.1016/j.bcmd.2023.102761] [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: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/06/2023]
Abstract
β-Thalassemia is a genetic form of anemia due to mutations in the β-globin gene, that leads to ineffective and extramedullary erythropoiesis, abnormal red blood cells and secondary iron-overload. The severity of the disease ranges from mild to lethal anemia based on the residual levels of globins production. Despite being a monogenic disorder, the pathophysiology of β-thalassemia is multifactorial, with different players contributing to the severity of anemia and secondary complications. As a result, the identification of effective therapeutic strategies is complex, and the treatment of patients is still suboptimal. For these reasons, several models have been developed in the last decades to provide experimental tools for the study of the disease, including erythroid cell lines, cultures of primary erythroid cells and transgenic animals. Years of research enabled the optimization of these models and led to decipher the mechanisms responsible for globins deregulation and ineffective erythropoiesis in thalassemia, to unravel the role of iron homeostasis in the disease and to identify and validate novel therapeutic targets and agents. Examples of successful outcomes of these analyses include iron restricting agents, currently tested in the clinics, several gene therapy vectors, one of which was recently approved for the treatment of most severe patients, and a promising gene editing strategy, that has been shown to be effective in a clinical trial. This review provides an overview of the available models, discusses pros and cons, and the key findings obtained from their study.
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Affiliation(s)
- Antonella Nai
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, via Olgettina 60, Milan, Italy; Vita-Salute San Raffaele University, via Olgettina 58, Milan, Italy.
| | - Celia Cordero-Sanchez
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, via Olgettina 60, Milan, Italy
| | - Emanuele Tanzi
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, via Olgettina 60, Milan, Italy
| | - Alessia Pagani
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, via Olgettina 60, Milan, Italy
| | - Laura Silvestri
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, via Olgettina 60, Milan, Italy; Vita-Salute San Raffaele University, via Olgettina 58, Milan, Italy
| | - Simona Maria Di Modica
- Regulation of Iron Metabolism Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, via Olgettina 60, Milan, Italy
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Gao Z, Li Z, Li X, Xiao J, Li C. Regulation of erythroid differentiation in K562 cells by the EPAS1-IRS2 axis under hypoxic conditions. Front Cell Dev Biol 2023; 11:1161541. [PMID: 37325570 PMCID: PMC10267359 DOI: 10.3389/fcell.2023.1161541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
Red blood cells (RBCs) produced in vitro have the potential to alleviate the worldwide demand for blood transfusion. Hematopoietic cell differentiation and proliferation are triggered by numerous cellular physiological processes, including low oxygen concentration (<5%). In addition, hypoxia inducible factor 2α (HIF-2α) and insulin receptor substrate 2 (IRS2) were found to be involved in the progression of erythroid differentiation. However, the function of the HIF-2α-IRS2 axis in the progression of erythropoiesis is not yet fully understood. Therefore, we used an in vitro model of erythropoiesis generated from K562 cells transduced with shEPAS1 at 5% O2 in the presence or absence of the IRS2 inhibitor NT157. We observed that erythroid differentiation was accelerated in K562 cells by hypoxia. Conversely, knockdown of EPAS1 expression reduced IRS2 expression and erythroid differentiation. Intriguingly, inhibition of IRS2 could impair the progression of hypoxia-induced erythropoiesis without affecting EPAS1 expression. These findings indicated that the EPAS1-IRS2 axis may be a crucial pathway that regulates erythropoiesis and that drugs targeting this pathway may become promising agents for promoting erythroid differentiation.
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Affiliation(s)
- Zhan Gao
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
| | - Zhicai Li
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Xiaowei Li
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
| | - Jun Xiao
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
| | - Cuiying Li
- Department of Blood Transfusion, Air Force Medical Center, Beijing, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
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Luanpitpong S, Kang X, Janan M, Thumanu K, Li J, Kheolamai P, Issaragrisil S. Metabolic sensor O-GlcNAcylation regulates erythroid differentiation and globin production via BCL11A. Stem Cell Res Ther 2022; 13:274. [PMID: 35739577 PMCID: PMC9219246 DOI: 10.1186/s13287-022-02954-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/24/2022] [Indexed: 12/25/2022] Open
Abstract
Background Human erythropoiesis is a tightly regulated, multistep process encompassing the differentiation of hematopoietic stem cells (HSCs) toward mature erythrocytes. Cellular metabolism is an important regulator of cell fate determination during the differentiation of HSCs. However, how O-GlcNAcylation, a posttranslational modification of proteins that is an ideal metabolic sensor, contributes to the commitment of HSCs to the erythroid lineage and to the terminal erythroid differentiation has not been addressed. Methods Cellular O-GlcNAcylation was manipulated using small molecule inhibition or CRISPR/Cas9 manipulation of catalyzing enzyme O-GlcNAc transferase (OGT) and removing enzyme O-GlcNAcase (OGA) in two cell models of erythroid differentiation, starting from: (i) human umbilical cord blood-derived CD34+ hematopoietic stem/progenitor cells (HSPCs) to investigate the erythroid lineage specification and differentiation; and (ii) human-derived erythroblastic leukemia K562 cells to investigate the terminal differentiation. The functional and regulatory roles of O-GlcNAcylation in erythroid differentiation, maturation, and globin production were investigated, and downstream signaling was delineated. Results First, we observed that two-step inhibition of OGT and OGA, which were established from the observed dynamics of O-GlcNAc level along the course of differentiation, promotes HSPCs toward erythroid differentiation and enucleation, in agreement with an upregulation of a multitude of erythroid-associated genes. Further studies in the efficient K562 model of erythroid differentiation confirmed that OGA inhibition and subsequent hyper-O-GlcNAcylation enhance terminal erythroid differentiation and affect globin production. Mechanistically, we found that BCL11A is a key mediator of O-GlcNAc-driven erythroid differentiation and β- and α-globin production herein. Additionally, analysis of biochemical contents using synchrotron-based Fourier transform infrared (FTIR) spectroscopy showed unique metabolic fingerprints upon OGA inhibition during erythroid differentiation, supporting that metabolic reprogramming plays a part in this process. Conclusions The evidence presented here demonstrated the novel regulatory role of O-GlcNAc/BCL11A axis in erythroid differentiation, maturation, and globin production that could be important in understanding erythropoiesis and hematologic disorders whose etiology is related to impaired erythroid differentiation and hemoglobinopathies. Our findings may lay the groundwork for future clinical applications toward an ex vivo production of functional human reticulocytes for transfusion from renewable cell sources, i.e., HSPCs and pluripotent stem cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02954-5.
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Affiliation(s)
- Sudjit Luanpitpong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Siriraj Hospital, Bangkoknoi, Bangkok, 10700, Thailand.
| | - Xing Kang
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Siriraj Hospital, Bangkoknoi, Bangkok, 10700, Thailand
| | - Montira Janan
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Siriraj Hospital, Bangkoknoi, Bangkok, 10700, Thailand
| | - Kanjana Thumanu
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, Thailand
| | - Jingting Li
- Institute of Precision Medicine, Department of Burns, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Pakpoom Kheolamai
- Center of Excellence in Stem Cell Research and Innovation, Faculty of Medicine, Thammasat University, Pathum Thani, 12120, Thailand.
| | - Surapol Issaragrisil
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Siriraj Hospital, Bangkoknoi, Bangkok, 10700, Thailand.,Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Fu YH, Ou DL, Yang YR, Su KW, Chen CY, Tien HF, Lai ZS, Shen CKJ, Chien HF, Lin LI. Cabozantinib promotes erythroid differentiation in K562 erythroleukemia cells through global changes in gene expression and JNK activation. Cancer Gene Ther 2021; 29:784-792. [PMID: 34117374 DOI: 10.1038/s41417-021-00358-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 11/09/2022]
Abstract
Cabozantinib is a potent tyrosine kinase inhibitor with multiple targets including MET, VEGFR2, RET, KIT, and FLT3. Cabozantinib is widely used for the treatment of medullary thyroid cancer and renal cell carcinoma. We recently suggested cabozantinib as a potential therapeutic alternative for acute myeloid leukemia (AML) patients with FLT3-internal tandem duplication (FLT3-ITD). Here, we report that cabozantinib can promote differentiation in erythroid leukemia cells. We found that K562 erythroid leukemia cells treated with 1 μM cabozantinib for 72 h underwent erythroid lineage differentiation. Transcriptomic analysis revealed that various pathways associated with heme biosynthesis, hemoglobin production, and GATA1 targets were upregulated, whereas cell survival pathways were downregulated. Further examination revealed that cabozantinib-induced erythroid differentiation is at least in part regulated by JNK activation and phosphorylation. Levels of phosphorylated BCR-ABL, AKT, STAT5, ERK, and p38 also decreased following cabozantinib treatment. Therefore, we indicate that cabozantinib has dual functions. First, it induces K562 cell differentiation toward the erythroid lineage by upregulating heme biosynthesis, globin synthesis, and erythroid-associated reactions. Second, cabozantinib inhibits K562 cell proliferation by inhibiting the phosphorylation of BCR-ABL and the downstream MAPK, PI3K-AKT, and JAK-STAT signaling pathways.
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Affiliation(s)
- Yu-Hsuan Fu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Da-Liang Ou
- Department of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Ru Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Kuan-Wei Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chien-Yuan Chen
- Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fan Tien
- Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Zheng-Sheng Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,The Ph.D. Program for Neural Regenerative Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsiung-Fei Chien
- Division of Plastic Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, Taiwan. .,TMU Center for Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Liang-In Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan. .,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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7
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Liu Q, Luo L, Ren C, Zou M, Yang S, Cai B, Wu L, Wang Y, Fu S, Hua X, Tang N, Huang S, Huang X, Xin W, Chen F, Zhang X. The opposing roles of the mTOR signaling pathway in different phases of human umbilical cord blood-derived CD34 + cell erythropoiesis. Stem Cells 2020; 38:1492-1505. [PMID: 32871057 PMCID: PMC7693065 DOI: 10.1002/stem.3268] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 02/05/2023]
Abstract
As an indispensable, even lifesaving practice, red blood cell (RBC) transfusion is challenging due to several issues, including supply shortage, immune incompatibility, and blood-borne infections since donated blood is the only source of RBCs. Although large-scale in vitro production of functional RBCs from human stem cells is a promising alternative, so far, no such system has been reported to produce clinically transfusable RBCs due to the poor understanding of mechanisms of human erythropoiesis, which is essential for the optimization of in vitro erythrocyte generation system. We previously reported that inhibition of mammalian target of rapamycin (mTOR) signaling significantly decreased the percentage of erythroid progenitor cells in the bone marrow of wild-type mice. In contrast, rapamycin treatment remarkably improved terminal maturation of erythroblasts and anemia in a mouse model of β-thalassemia. In the present study, we investigated the effect of mTOR inhibition with rapamycin from different time points on human umbilical cord blood-derived CD34+ cell erythropoiesis in vitro and the underlying mechanisms. Our data showed that rapamycin treatment significantly suppressed erythroid colony formation in the commitment/proliferation phase of erythropoiesis through inhibition of cell-cycle progression and proliferation. In contrast, during the maturation phase of erythropoiesis, mTOR inhibition dramatically promoted enucleation and mitochondrial clearance by enhancing autophagy. Collectively, our results suggest contrasting roles for mTOR in regulating different phases of human erythropoiesis.
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Affiliation(s)
- Qian Liu
- Laboratory of Molecular CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
- Shantou University Medical CollegeShantouPeople's Republic of China
| | - Linhong Luo
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Chunhong Ren
- Department of International Medical ServiceThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Muping Zou
- Laboratory of Molecular CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Siqin Yang
- Laboratory of Molecular CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Bozhi Cai
- Laboratory of Molecular CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Libiao Wu
- Laboratory of Molecular CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Yunsheng Wang
- Laboratory of Molecular CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Shan Fu
- Shantou University Medical CollegeShantouPeople's Republic of China
| | - Xu Hua
- Shantou University Medical CollegeShantouPeople's Republic of China
| | - Nianping Tang
- Shantou University Medical CollegeShantouPeople's Republic of China
| | - Shiping Huang
- Shantou University Medical CollegeShantouPeople's Republic of China
| | - Xianxi Huang
- Intensive Care Unit, The First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Wen Xin
- Beijing TransGen Biotech Co., Ltd.BeijingPeople's Republic of China
| | - Feiheng Chen
- Department of HematologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
| | - Xin Zhang
- Laboratory of Molecular CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
- Shantou University Medical CollegeShantouPeople's Republic of China
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
- Laboratory of Medical Molecular ImagingThe First Affiliated Hospital of Shantou University Medical CollegeShantouPeople's Republic of China
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8
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Demirci S, Gudmundsdottir B, Li Q, Haro-Mora JJ, Nassehi T, Drysdale C, Yapundich M, Gamer J, Seifuddin F, Tisdale JF, Uchida N. βT87Q-Globin Gene Therapy Reduces Sickle Hemoglobin Production, Allowing for Ex Vivo Anti-sickling Activity in Human Erythroid Cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:912-921. [PMID: 32405513 PMCID: PMC7210457 DOI: 10.1016/j.omtm.2020.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022]
Abstract
Lentiviral addition of βT87Q-globin, a modified β-globin with an anti-sickling mutation, is currently being used in gene therapy trials for sickle cell disease (SCD) and β-thalassemia patients. βT87Q-globin interferes with sickle hemoglobin (HbS) polymerization. Here, we generated the SCD mutation in an immortalized human erythroid cell line (HUDEP-2) to investigate the anti-sickling activity of βT87Q-globin. Sickle HUDEP-2 (sHUDEP-2) cells produced robust HbS after differentiation and sickled under deoxygenated conditions, comparable with SCD CD34+ progeny. Lentiviral transduction provided 9.5–26.8 pg/cell βT87Q-globin (R2 = 0.83) in a vector copy number (VCN)-dependent manner, resulting in a significant reduction of sickling ratios (R2 = 0.92). Interestingly, βT87Q-globin transduction markedly reduced endogenous βS-globin (R2 = 0.84) to an undetectable level (0.4–16.8 pg/cell) in sHUDEP-2 cells, as well as endogenous β-globin in human CD34+ cell-derived erythroid cells. RNA sequencing (RNA-seq) analysis with βT87Q-transduced sHUDEP-2 and human CD34+-derived cells revealed activation of inflammation- and proliferation-related programs, suggesting minimal changes in background gene expression except for βT87Q-globin expression and endogenous β/βS-globin suppression. In summary, using sHUDEP-2 and CD34+-derived cells, we demonstrated that lentiviral addition of βT87Q-globin strongly reduced endogenous β-/βS-globin expression, resulting in an anti-sickling effect. Our findings should be helpful to understand the anti-sickling effects of therapeutic genes in SCD gene therapy.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Bjorg Gudmundsdottir
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Quan Li
- Laboratory of Chemical Physics, NIDDK, NIH, Bethesda, MD, USA
| | - Juan J Haro-Mora
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tina Nassehi
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Claire Drysdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Morgan Yapundich
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jackson Gamer
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Fayaz Seifuddin
- Bioinformatics and Computational Biology Laboratory, NHLBI, NIH, Bethesda, MD, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
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9
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Haro-Mora JJ, Uchida N, Demirci S, Wang Q, Zou J, Tisdale JF. Biallelic correction of sickle cell disease-derived induced pluripotent stem cells (iPSCs) confirmed at the protein level through serum-free iPS-sac/erythroid differentiation. Stem Cells Transl Med 2020; 9:590-602. [PMID: 32034898 PMCID: PMC7180291 DOI: 10.1002/sctm.19-0216] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 01/14/2020] [Indexed: 12/15/2022] Open
Abstract
New technologies of induced pluripotent stem cells (iPSCs) and genome editing have emerged, allowing for the development of autologous transfusion therapies. We previously demonstrated definitive β‐globin production from human embryonic stem cell (hESC)‐derived erythroid cell generation via hemangioblast‐like ES‐sacs. In this study, we demonstrated normal β‐globin protein production from biallelic corrected sickle cell disease (SCD) iPSCs. We optimized our ES/iPS‐sac method for feeder cell‐free hESC maintenance followed by serum‐free ES‐sac generation, which is preferred for electroporation‐based genome editing. Surprisingly, the optimized protocol improved yields of ES‐sacs (25.9‐fold), hematopoietic‐like spherical cells (14.8‐fold), and erythroid cells (5.8‐fold), compared with our standard ES‐sac generation. We performed viral vector‐free gene correction in SCD iPSCs, resulting in one clone with monoallelic and one clone with biallelic correction, and using this serum‐free iPS‐sac culture, corrected iPSC‐generated erythroid cells with normal β‐globin, confirmed at DNA and protein levels. Our serum‐free ES/iPS‐sac protocol with gene correction will be useful to develop regenerative transfusion therapies for SCD.
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Affiliation(s)
- Juan J Haro-Mora
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland
| | - Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland
| | - Qi Wang
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institutes (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland
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Ruiz JP, Chen G, Haro Mora JJ, Keyvanfar K, Liu C, Zou J, Beers J, Bloomer H, Qanash H, Uchida N, Tisdale JF, Boehm M, Larochelle A. Robust generation of erythroid and multilineage hematopoietic progenitors from human iPSCs using a scalable monolayer culture system. Stem Cell Res 2019; 41:101600. [PMID: 31710911 PMCID: PMC6953424 DOI: 10.1016/j.scr.2019.101600] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/10/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022] Open
Abstract
One of the most promising objectives of clinical hematology is to derive engraftable autologous hematopoietic stem cells (HSCs) from human induced pluripotent stem cells (iPSCs). Progress in translating iPSC technologies to the clinic relies on the availability of scalable differentiation methodologies. In this study, human iPSCs were differentiated for 21 days using STEMdiff™, a monolayer-based approach for hematopoietic differentiation of human iPSCs that requires no replating, co-culture or embryoid body formation. Both hematopoietic and non-hematopoietic cells were functionally characterized throughout differentiation. In the hematopoietic fraction, an early transient population of primitive CD235a+ erythroid progenitor cells first emerged, followed by hematopoietic progenitors with multilineage differentiation activity in vitro but no long-term engraftment potential in vivo. In later stages of differentiation, a nearly exclusive production of definitive erythroid progenitors was observed. In the non-hematopoietic fraction, we identified a prevalent population of mesenchymal stromal cells and limited arterial vascular endothelium (VE), suggesting that the cellular constitution of the monolayer may be inadequate to support the generation of HSCs with durable repopulating potential. Quantitative modulation of WNT/β-catenin and activin/nodal/TGFβ signaling pathways with CHIR/SB molecules during differentiation enhanced formation of arterial VE, definitive multilineage and erythroid progenitors, but was insufficient to orchestrate the generation of engrafting HSCs. Overall, STEMdiff™ provides a clinically-relevant and readily adaptable platform for the generation of erythroid and multilineage hematopoietic progenitors from human pluripotent stem cells.
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Affiliation(s)
- Juan Pablo Ruiz
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), 9000 Rockville, Bethesda, MD 20892, United States
| | - Guibin Chen
- Translational Vascular Medicine Branch, NHLBI, NIH, Bethesda, MD 20892, United States
| | - Juan Jesus Haro Mora
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), 9000 Rockville, Bethesda, MD 20892, United States
| | - Keyvan Keyvanfar
- Clinical Flow Core Facility, NHLBI, NIH, Bethesda, MD 20892, United States
| | - Chengyu Liu
- Transgenic Core Facility, NHLBI, NIH, Bethesda, MD 20892, United States
| | - Jizhong Zou
- iPSC Core Facility, NHLBI, NIH, Bethesda, MD 20892, United States
| | - Jeanette Beers
- iPSC Core Facility, NHLBI, NIH, Bethesda, MD 20892, United States
| | - Hanan Bloomer
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), 9000 Rockville, Bethesda, MD 20892, United States
| | - Husam Qanash
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), 9000 Rockville, Bethesda, MD 20892, United States; College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia; Department of Biology, The Catholic University of America, Washington, DC 20064, United States
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), 9000 Rockville, Bethesda, MD 20892, United States
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), 9000 Rockville, Bethesda, MD 20892, United States
| | - Manfred Boehm
- Translational Vascular Medicine Branch, NHLBI, NIH, Bethesda, MD 20892, United States
| | - Andre Larochelle
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), 9000 Rockville, Bethesda, MD 20892, United States.
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