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Chen Y, Wang Z, Qu X, Song B, Tang Y, Li B, Cao G, Yi G. An intronic SNP affects skeletal muscle development by regulating the expression of TP63. Front Vet Sci 2024; 11:1396766. [PMID: 38933706 PMCID: PMC11199888 DOI: 10.3389/fvets.2024.1396766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Background Porcine skeletal muscle development is pivotal for improving meat production. TP63, a transcription factor, regulates vital cellular processes, yet its role in skeletal muscle proliferation is unclear. Methods The effects of TP63 on skeletal muscle cell viability and proliferation were investigated using both mouse and porcine skeletal muscle myoblasts. Selective sweep analysis in Western pigs identified TP63 as a potential candidate gene for skeletal muscle development. The correlation between TP63 overexpression and cell proliferation was assessed using quantitative real-time PCR (RT-qPCR) and 5-ethynyl-2'-deoxyuridine (EDU). Results The study revealed a positive correlation between TP63 overexpression and skeletal muscle cell proliferation. Bioinformatics analysis predicted an interaction between MEF2A, another transcription factor, and the mutation site of TP63. Experimental validation through dual-luciferase assays confirmed that a candidate enhancer SNP could influence MEF2A binding, subsequently regulating TP63 expression and promoting skeletal muscle cell proliferation. Conclusion These findings offer experimental evidence for further exploration of skeletal muscle development mechanisms and the advancement of genetic breeding strategies aimed at improving meat production traits.
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Affiliation(s)
- Yufen Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Zhen Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaolu Qu
- Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bangmin Song
- Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yueting Tang
- Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Guoqiang Yi
- Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama, China
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2
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Wang D, Xu L, Liu Y, Wang C, Xu Z, Yang F, Li Z, Bai X, Liao Y, Liu X, Wang Y. Identification of ferroptosis-associated genes and potential pharmacological targets in sepsis-induced myopathy. Heliyon 2024; 10:e29062. [PMID: 38601693 PMCID: PMC11004882 DOI: 10.1016/j.heliyon.2024.e29062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
Background The role of Ferroptosis in the course of sepsis-induced myopathy is yet unclear. The objective of our work is to identify key genes connected with Ferroptosis in sepsis-induced myopathy and investigate possible pharmaceutical targets related to this process. This research aims to provide new insights into the management of sepsis-induced myopathy. Methods We got the GSE13205 dataset from the Gene Expression Omnibus (GEO) and extracted Ferroptosis-associated genes from the FerrDb database. After conducting a functional annotation analysis of these genes, we created a protein-protein interaction network using Cytoscape software to identify important genes. Subsequently, we employed CMap to investigate prospective pharmaceuticals that could target these crucial genes. Results A total of 61 genes that are expressed differently (DEGs) have been found concerning Ferroptosis. These genes are involved in a wide range of biological functions, including reacting to signals from outside the cell and the availability of nutrients, programmed cell death, controlling apoptosis, and responding to peptides, chemical stressors, and hormones. The KEGG pathway study revealed that these pathways are involved in Ferroptosis, autophagy, P53 signaling, PI3K-Akt signaling, mTOR signaling, HIF-1 signaling, endocrine resistance, and different tumorigenic processes. In addition, we created a network that shows the simultaneous expression of important genes and determined the top 10 medications that have the potential to treat sepsis-induced myopathy. Conclusion The bioinformatics research undertaken sheds insight into the probable role of Ferroptosis-associated genes in sepsis-induced myopathy. The identified critical genes show potential as therapeutic targets for treating sepsis-induced myopathy, offering opportunities for the development of tailored medicines.
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Affiliation(s)
- Dongfang Wang
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ligang Xu
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yukun Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chuntao Wang
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhikai Xu
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fan Yang
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhanfei Li
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiangjun Bai
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yiliu Liao
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiangping Liu
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuchang Wang
- Division of Trauma Surgery, Emergency Surgery & Surgical Critical, Tongji Trauma Center, China
- Department of Emergency and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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Saburina IN, Kosheleva NV, Kopylov AT, Lipina TV, Krasina ME, Zurina IM, Gorkun AA, Girina SS, Pulin AA, Kaysheva AL, Morozov SG. Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three-dimensional culture. Proteomics 2021; 22:e2000304. [PMID: 34674377 DOI: 10.1002/pmic.202000304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/24/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022]
Abstract
Myocyte differentiation is featured by adaptation processes, including mitochondria repopulation and cytoskeleton re-organization. The difference between monolayer and spheroid cultured cells at the proteomic level is uncertain. We cultivated alveolar mucosa multipotent mesenchymal stromal cells in spheroids in a myogenic way for the proper conditioning of ECM architecture and cell morphology, which induced spontaneous myogenic differentiation of cells within spheroids. Electron microscopy analysis was used for the morphometry of mitochondria biogenesis, and proteomic was used complementary to unveil events underlying differences between two-dimensional/three-dimensional myoblasts differentiation. The prevalence of elongated mitochondria with an average area of 0.097 μm2 was attributed to monolayer cells 7 days after the passage. The population of small mitochondria with a round shape and area of 0.049 μm2 (p < 0.05) was observed in spheroid cells cultured under three-dimensional conditions. Cells in spheroids were quantitatively enriched in proteins of mitochondria biogenesis (DNM1L, IDH2, SSBP1), respiratory chain (ACO2, ATP5I, COX5A), extracellular proteins (COL12A1, COL6A1, COL6A2), and cytoskeleton (MYL6, MYL12B, MYH10). Most of the Rab-related transducers were inhibited in spheroid culture. The proteomic assay demonstrated delicate mechanisms of mitochondria autophagy and repopulation, cytoskeleton assembling, and biogenesis. Differences in the ultrastructure of mitochondria indicate active biogenesis under three-dimensional conditions.
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Affiliation(s)
- Irina N Saburina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
| | - Nastasia V Kosheleva
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia
| | - Arthur T Kopylov
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia.,Department of Proteomic Research, Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Tatiana V Lipina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Marina E Krasina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Irina M Zurina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Anastasiya A Gorkun
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Svetlana S Girina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
| | - Andrey A Pulin
- Pirogov National Medical Surgical Center, Moscow, Russian Federation
| | - Anna L Kaysheva
- Department of Proteomic Research, Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Sergey G Morozov
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
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Ren P, Deng F, Chen S, Ran J, Li J, Yin L, Wang Y, Yin H, Zhu Q, Liu Y. Whole-genome resequencing reveals loci with allelic transmission ratio distortion in F 1 chicken population. Mol Genet Genomics 2021; 296:331-339. [PMID: 33404883 DOI: 10.1007/s00438-020-01744-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/30/2020] [Indexed: 11/28/2022]
Abstract
Allelic transmission ratio distortion (TRD) is the significant deviation from the expected ratio under Mendelian inheritance theory, which may be resulted from multiple disrupted biological processes, including germline selection, meiotic drive, gametic competition, imprint error, and embryo lethality. However, it is less known that whether or what extent the allelic TRD is present in farm animals. In this study, whole-genome resequencing technology was applied to reveal TRD loci in chicken by constructing a full-sib F1 hybrid population. Through the whole-genome resequencing data of two parents (30 ×) and 38 offspring (5 ×), we detected a total of 2850 TRD SNPs (p-adj < 0.05) located within 400 genes showing TRD, and all of them were unevenly distributed on macrochromosomes and microchromosomes. Our findings suggested that TRD in the chicken chromosome 16 might play an important role in chicken immunity and disease resistance and the MYH1F with significant TRD and allele-specific expression could play a key role in the fast muscle development. In addition, functional enrichment analyses revealed that many genes (e.g., TGFBR2, TGFBR3, NOTCH1, and NCOA1) with TRD were found in the significantly enriched biological process and InterPro terms in relation to embryonic lethality and germline selection. Our results suggested that TRD is considerably prevalent in the chicken genome and has functional implications.
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Affiliation(s)
- Peng Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Feilong Deng
- Special Key Laboratory of Microbial Resources and Drug Development, Zunyi Medical University, Zunyi, 563000, China
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Jinshan Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Jingjing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Lingqian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China. .,Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, 211 Huiming Road, Wenjiang, Sichuan, 611130, China.
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5
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Gökalp F. The inhibition effect of natural food supplement active ingredients on TP63 carcinoma cell. Med Oncol 2020; 37:120. [PMID: 33222005 DOI: 10.1007/s12032-020-01446-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/14/2020] [Indexed: 12/26/2022]
Abstract
In pancreatic cancer, the activities of inhibitory agents were investigated using docking, since the inhibition of TP63, which plays an important role in the spread of cancer with metastasis, in preventing the proliferation and proliferation of this type of cancer. It has been shown that the active ingredients in some plants used as traditional medicines have an inhibitory effect on this cancer type in preventing growth, reproduction and spread. These computational results guide experimental studies, preventing time and item loss; It is an important study in terms of choosing and using the right active substances.
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Affiliation(s)
- Faik Gökalp
- Science Education, Department of Mathematics and Science Education, Education Faculty, Kırıkkale University, 71450, Yahşihan, Kırıkkale, Turkey.
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6
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Khan SA, He J, Deng S, Zhang H, Liu G, Li S, Tang D, Zhang J, Shu Y, Wu H. Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between fast- and slow-growing king ratsnakes (Elaphe carinata). Comp Biochem Physiol B Biochem Mol Biol 2020; 248-249:110482. [DOI: 10.1016/j.cbpb.2020.110482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/18/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
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7
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Wang H, Zhu N, Ye X, Wang L, Wang B, Shan W, Lai X, Tan Y, Fu S, Xiao H, Huang H. PTPN21-CDS long isoform inhibits the response of acute lymphoblastic leukemia cells to NK-mediated lysis via the KIR/HLA-I axis. J Cell Biochem 2020; 121:3298-3312. [PMID: 31898344 DOI: 10.1002/jcb.29601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Protein tyrosine phosphatase non-receptor type 21 (PTPN21) is a member of the non-receptor tyrosine phosphatase family. We have found that PTPN21 is mutated in relapsed Philadelphia chromosome-negative acute lymphoblastic leukemia (ALL) after allogeneic hematopoietic stem cell transplantation. PTPN21 consists of three types of isoforms according to the length of the protein encoded. However, the roles of different isoforms in leukemic cells have not been elucidated. In the study, PTPN21 isoform constitution in five ALL cell lines were identified by transcriptome polymerase chain reaction combined with Sanger sequencing, and the relationship between PTPN21 isoforms and sensitivity to natural killer (NK) cells mediated killing in ALL cell lines were further assessed by knock-out of different isoforms of PTPN21 using CRISPR-Cas9 technique. Subsequently, we explored the functional mechanisms through RNA sequencing and confirmatory testing. The results showed that there was no significant change when all PTPN21 isoforms were knocked out in ALL cells, but the sensitivity of NALM6 cells with PTPN21-CDSlong knock-out (NALM6-PTPN21lk ) to NK-mediated killing was significantly increased. Whole transcriptome sequencing and further validation testing showed that human leukocyte antigen class I (HLA-I) molecules were significantly decreased, accompanied by a significantly downregulated expression of antigen presenting-related chaperones in NALM6-PTPN21lk cells. Our results uncovered a previously unknown mechanism that PTPN21-CDSlong and CDSshort isoforms may play opposite roles in NK-mediated killing in ALL cells, and showed that the endogenous PTPN21-CDSlong isoform inhibited ALL cells to NK cell-mediated lysis by regulating the KIR-HLA-I axis.
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Affiliation(s)
- Huafang Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Ni Zhu
- Department of Hematology, The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xiaohang Ye
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Limengmeng Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Binsheng Wang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Wei Shan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Xiaoyu Lai
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yamin Tan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shan Fu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haowen Xiao
- Department of Hematology, The Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Engineering Laboratory for Stem cell and Immunotherapy, Hangzhou, Zhejiang, China
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