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Wang J, Liang Y, Xu C, Gao J, Tong J, Shi L. The heterogeneity of erythroid cells: insight at the single-cell transcriptome level. Cell Tissue Res 2024:10.1007/s00441-024-03903-9. [PMID: 38953986 DOI: 10.1007/s00441-024-03903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Erythroid cells, the most prevalent cell type in blood, are one of the earliest products and permeate through the entire process of hematopoietic development in the human body, the oxygen-transporting function of which is crucial for maintaining overall health and life support. Previous investigations into erythrocyte differentiation and development have primarily focused on population-level analyses, lacking the single-cell perspective essential for comprehending the intricate pathways of erythroid maturation, differentiation, and the encompassing cellular heterogeneity. The continuous optimization of single-cell transcriptome sequencing technology, or single-cell RNA sequencing (scRNA-seq), provides a powerful tool for life sciences research, which has a particular superiority in the identification of unprecedented cell subgroups, the analyzing of cellular heterogeneity, and the transcriptomic characteristics of individual cells. Over the past decade, remarkable strides have been taken in the realm of single-cell RNA sequencing technology, profoundly enhancing our understanding of erythroid cells. In this review, we systematically summarize the recent developments in single-cell transcriptome sequencing technology and emphasize their substantial impact on the study of erythroid cells, highlighting their contributions, including the exploration of functional heterogeneity within erythroid populations, the identification of novel erythrocyte subgroups, the tracking of different erythroid lineages, and the unveiling of mechanisms governing erythroid fate decisions. These findings not only invigorate erythroid cell research but also offer new perspectives on the management of diseases related to erythroid cells.
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Affiliation(s)
- Jingwei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yipeng Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Changlu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
- CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin, 300020, China.
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2
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Deleuze V, Soler E, Andrieu-Soler C. Protocol for efficient CRISPR-Cas9-mediated fluorescent tag knockin in hard-to-transfect erythroid cell lines. STAR Protoc 2024; 5:103016. [PMID: 38640065 PMCID: PMC11044133 DOI: 10.1016/j.xpro.2024.103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/01/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024] Open
Abstract
Precise insertion of fluorescent tags by CRISPR-Cas9-mediated homologous recombination (HR) in mammalian genes is a powerful tool allowing to study gene function and protein gene products. Here, we present a protocol for efficient HR-mediated targeted insertion of fluorescent markers in the genome of hard-to-transfect erythroid cell lines MEL (mouse erythroleukemic) and MEDEP (mouse ES cell-derived erythroid progenitor line). We describe steps for plasmid construction, electroporation, amplification, and verification of genome editing. We then detail procedures for isolating positive clones and validating knockin clones. For complete details on the use and execution of this protocol, please refer to Deleuze et al.1.
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Affiliation(s)
- Virginie Deleuze
- IGMM University Montpellier, CNRS, Montpellier, France; Laboratory of Excellence GR-Ex, Université' de Paris, Paris, France
| | - Eric Soler
- IGMM University Montpellier, CNRS, Montpellier, France; Laboratory of Excellence GR-Ex, Université' de Paris, Paris, France.
| | - Charlotte Andrieu-Soler
- IGMM University Montpellier, CNRS, Montpellier, France; Laboratory of Excellence GR-Ex, Université' de Paris, Paris, France.
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3
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Vial Y, Nardelli J, Bonnard AA, Rousselot J, Souyri M, Gressens P, Cavé H, Drunat S. Mcph1, mutated in primary microcephaly, is also crucial for erythropoiesis. EMBO Rep 2024; 25:2418-2440. [PMID: 38605277 PMCID: PMC11094029 DOI: 10.1038/s44319-024-00123-8] [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: 08/30/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
Microcephaly is a common feature in inherited bone marrow failure syndromes, prompting investigations into shared pathways between neurogenesis and hematopoiesis. To understand this association, we studied the role of the microcephaly gene Mcph1 in hematological development. Our research revealed that Mcph1-knockout mice exhibited congenital macrocytic anemia due to impaired terminal erythroid differentiation during fetal development. Anemia's cause is a failure to complete cell division, evident from tetraploid erythroid progenitors with DNA content exceeding 4n. Gene expression profiling demonstrated activation of the p53 pathway in Mcph1-deficient erythroid precursors, leading to overexpression of Cdkn1a/p21, a major mediator of p53-dependent cell cycle arrest. Surprisingly, fetal brain analysis revealed hypertrophied binucleated neuroprogenitors overexpressing p21 in Mcph1-knockout mice, indicating a shared pathophysiological mechanism underlying both erythroid and neurological defects. However, inactivating p53 in Mcph1-/- mice failed to reverse anemia and microcephaly, suggesting that p53 activation in Mcph1-deficient cells resulted from their proliferation defect rather than causing it. These findings shed new light on Mcph1's function in fetal hematopoietic development, emphasizing the impact of disrupted cell division on neurogenesis and erythropoiesis - a common limiting pathway.
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Affiliation(s)
- Yoann Vial
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | | | - Adeline A Bonnard
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | - Justine Rousselot
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | - Michèle Souyri
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
| | - Pierre Gressens
- Université Paris Cité, NeuroDiderot, Inserm, F-75019, Paris, France
| | - Hélène Cavé
- Université Paris Cité, Institut de Recherche Saint-Louis, Inserm UMR_S1131, F-75010, Paris, France
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France
| | - Séverine Drunat
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Laboratoire de Génétique Moléculaire, F-75019, Paris, France.
- Université Paris Cité, NeuroDiderot, Inserm, F-75019, Paris, France.
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4
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Deleuze V, Garcia L, Rouaisnel B, Salma M, Kinoo A, Andrieu-Soler C, Soler E. Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions. iScience 2023; 26:107641. [PMID: 37670779 PMCID: PMC10475484 DOI: 10.1016/j.isci.2023.107641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/09/2023] [Accepted: 08/11/2023] [Indexed: 09/07/2023] Open
Abstract
Targeted genome editing holds great promise in biology. However, efficient genome modification, including gene knock-in (KI), remains an unattained goal in multiple cell types and loci due to poor transfection efficiencies and low target genes expression, impeding the positive selection of recombined cells. Here, we describe a genome editing approach to achieve efficient gene targeting using hard to transfect erythroid cell lines. We demonstrate robust fluorescent protein KI efficiency in low expressed transcription factor (TF) genes (e.g., Myb or Zeb1). We further show the ability to target two independent loci in individual cells, exemplified by MYB-GFP and NuMA-Cherry double KI, allowing multicolor labeling of regulatory factors at physiological endogenous levels. Our KI tagging approach allowed us to perform genome-wide TF analysis at increased signal-to-noise ratios, and highlighted previously unidentified MYB target genes and pathways. Overall, we establish a versatile CRISPR-Cas9-based platform, offering attractive opportunities for the dissection of the erythroid differentiation process.
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Affiliation(s)
| | - Leonor Garcia
- IGMM, University Montpellier, CNRS, Montpellier, France
| | | | - Mohammad Salma
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Alexia Kinoo
- IGMM, University Montpellier, CNRS, Montpellier, France
| | - Charlotte Andrieu-Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Eric Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
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5
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Lu L, Wang J, Fang F, Guo A, Jiang S, Tao Y, Zhang Y, Li Y, Zhang K, Zhang Z, Zhuo R, Chu X, Li X, Tian Y, Ma L, Sang X, Chen Y, Yu J, Yang Y, Cao H, Gao J, Lu J, Hu S, Pan J, He H. LMO2 promotes the development of AML through interaction with transcription co-regulator LDB1. Cell Death Dis 2023; 14:518. [PMID: 37573405 PMCID: PMC10423285 DOI: 10.1038/s41419-023-06039-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023]
Abstract
One of the characteristics of leukemia is that it contains multiple rearrangements of signal transduction genes and overexpression of non-mutant genes, such as transcription factors. As an important regulator of hematopoietic stem cell development and erythropoiesis, LMO2 is considered an effective carcinogenic driver in T cell lines and a marker of poor prognosis in patients with AML with normal karyotype. LDB1 is a key factor in the transformation of thymocytes into T-ALL induced by LMO2, and enhances the stability of carcinogenic related proteins in leukemia. However, the function and mechanism of LMO2 and LDB1 in AML remains unclear. Herein, the LMO2 gene was knocked down to observe its effects on proliferation, survival, and colony formation of NB4, Kasumi-1 and K562 cell lines. Using mass spectrometry and IP experiments, our results showed the presence of LMO2/LDB1 protein complex in AML cell lines, which is consistent with previous studies. Furthermore, in vitro and in vivo experiments revealed that LDB1 is essential for the proliferation and survival of AML cell lines. Analysis of RNA-seq and ChIP-Seq results showed that LDB1 could regulate apoptosis-related genes, including LMO2. In LDB1-deficient AML cell lines, the overexpression of LMO2 partially compensates for the proliferation inhibition. In summary, our findings revealed that LDB1 played an important role in AML as an oncogene, and emphasize the potential importance of the LMO2/LDB1 complex in clinical treatment of patients with AML.
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Affiliation(s)
- Lihui Lu
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Jianwei Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Ailian Guo
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Shuting Jiang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Yanfang Tao
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yongping Zhang
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yan Li
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Kunlong Zhang
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Zimu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Ran Zhuo
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xinran Chu
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xiaolu Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yuanyuan Tian
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Li Ma
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xu Sang
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yanling Chen
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Juanjuan Yu
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yang Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Haibo Cao
- Department of Pediatric Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, 225000, China
| | - Jizhao Gao
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Jun Lu
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Shaoyan Hu
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China.
| | - Hailong He
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China.
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6
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Multimerin-1 and cancer: a review. Biosci Rep 2022; 42:230760. [PMID: 35132992 PMCID: PMC8881648 DOI: 10.1042/bsr20211248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Multimerin-1 (MMRN1) is a platelet protein with a role in haemostasis and coagulation. It is also present in endothelial cells (ECs) and the extracellular matrix (ECM), where it may be involved in cell adhesion, but its molecular functions and protein–protein interactions in these cellular locations have not been studied in detail yet. In recent years, MMRN1 has been identified as a differentially expressed gene (DEG) in various cancers and it has been proposed as a possible cancer biomarker. Some evidence suggest that MMRN1 expression is regulated by methylation, protein interactions, and non-coding RNAs (ncRNAs) in different cancers. This raises the questions if a functional role of MMRN1 is being targeted during cancer development, and if MMRN1’s differential expression pattern correlates with cancer progression. As a result, it is timely to review the current state of what is known about MMRN1 to help inform future research into MMRN1’s molecular mechanisms in cancer.
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7
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Ren Y, Zhu J, Han Y, Li P, Wu J, Qu H, Zhang Z, Fang X. Regulatory association of long noncoding RNAs and chromatin accessibility facilitates erythroid differentiation. Blood Adv 2021; 5:5396-5409. [PMID: 34644394 PMCID: PMC9153002 DOI: 10.1182/bloodadvances.2021005167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/13/2021] [Indexed: 01/17/2023] Open
Abstract
Erythroid differentiation is a dynamic process regulated by multiple factors, whereas the interaction between long noncoding RNAs (lncRNAs) and chromatin accessibility and its influence on erythroid differentiation remains unclear. To elucidate this interaction, we used hematopoietic stem cells, multipotent progenitor cells, common myeloid progenitor cells, megakaryocyte-erythroid progenitor cells, and erythroblasts from human cord blood as an erythroid differentiation model to explore the coordinated regulatory functions of lncRNAs and chromatin accessibility by integrating RNA-seq and ATAC-seq data. We revealed that the integrated network of chromatin accessibility and lncRNAs exhibits stage-specific changes throughout the erythroid differentiation process and that the changes at the erythroblast stage of maturation are dramatic. We identified a subset of stage-specific lncRNAs and transcription factors (TFs) that associate with chromatin accessibility during erythroid differentiation, in which lncRNAs are key regulators of terminal erythroid differentiation via an lncRNA-TF-gene network. LncRNA PCED1B-AS1 was revealed to regulate terminal erythroid differentiation by coordinating GATA1 dynamically binding to the chromatin and interacting with the cytoskeleton network during erythroid differentiation. DANCR, another lncRNA that is highly expressed at the megakaryocyte-erythroid progenitor cell stage, was verified to promote erythroid differentiation by compromising megakaryocyte differentiation and coordinating with chromatin accessibility and TFs, such as RUNX1. Overall, our results identify the associated network of lncRNAs and chromatin accessibility in erythropoiesis and provide novel insights into erythroid differentiation and abundant resources for further study.
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Affiliation(s)
| | - Junwei Zhu
- CAS Key Laboratory of Genome Science & Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
| | - Yuanyuan Han
- Guizhou University, Medical College, Guiyang, China, China; and
| | - Pin Li
- CAS Key Laboratory of Genome Science & Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Jing Wu
- CAS Key Laboratory of Genome Science & Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Science & Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
| | | | - Xiangdong Fang
- CAS Key Laboratory of Genome Science & Information, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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8
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Comprehensive proteomic analysis of murine terminal erythroid differentiation. Blood Adv 2021; 4:1464-1477. [PMID: 32282884 DOI: 10.1182/bloodadvances.2020001652] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/04/2020] [Indexed: 12/12/2022] Open
Abstract
Murine-based cellular models have provided and continue to provide many useful insights into the fundamental mechanisms of erythropoiesis, as well as insights into the pathophysiology of inherited and acquired red cell disorders. Although detailed information on many aspects of these cell models is available, comprehensive proteomic data are lacking. This is a critical knowledge gap, as proteins are effectors of most biologic processes. To address this critical unmet need, proteomes of the murine cell lines Friend erythroleukemia (MEL), GATA1 erythroid (G1ER), and embryonic stem cell-derived erythroid progenitor (MEDEP) and proteomes of cultured murine marrow-derived erythroblasts at different stages of terminal erythroid differentiation were analyzed. The proteomes of MEDEP cells and primary murine erythroid cells were most similar, whereas those of MEL and G1ER cells were more distantly related. We demonstrated that the overall cellular content of histones does not decrease during terminal differentiation, despite strong chromatin condensation. Comparison of murine and human proteomes throughout terminal erythroid differentiation revealed that many noted transcriptomic changes were significantly dampened at the proteome level, especially at the end of the terminal differentiation process. Analysis of the early events associated with induction of terminal differentiation in MEDEP cells revealed divergent alterations in associated transcriptomes and proteomes. These proteomic data are powerful and valuable tools for the study of fundamental mechanisms of normal and disordered erythropoiesis and will be of broad interest to a wide range of investigators for making the appropriate choice of various cell lines to study inherited and acquired diseases of the erythrocyte.
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