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Sun K, Liu X, Lan X. A single-cell atlas of chromatin accessibility in mouse organogenesis. Nat Cell Biol 2024; 26:1200-1211. [PMID: 38977846 DOI: 10.1038/s41556-024-01435-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/29/2024] [Indexed: 07/10/2024]
Abstract
Organogenesis is a highly complex and precisely regulated process. Here we profiled the chromatin accessibility in >350,000 cells derived from 13 mouse embryos at four developmental stages from embryonic day (E) 10.5 to E13.5 by SPATAC-seq in a single experiment. The resulting atlas revealed the status of 830,873 candidate cis-regulatory elements in 43 major cell types. By integrating the chromatin accessibility atlas with the previous transcriptomic dataset, we characterized cis-regulatory sequences and transcription factors associated with cell fate commitment, such as Nr5a2 in the development of gastrointestinal tract, which was preliminarily supported by the in vivo experiment in zebrafish. Finally, we integrated this atlas with the previous single-cell chromatin accessibility dataset from 13 adult mouse tissues to delineate the developmental stage-specific gene regulatory programmes within and across different cell types and identify potential molecular switches throughout lineage development. This comprehensive dataset provides a foundation for exploring transcriptional regulation in organogenesis.
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Affiliation(s)
- Keyong Sun
- School of Medicine, Tsinghua University, Beijing, China
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xin Liu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xun Lan
- School of Medicine, Tsinghua University, Beijing, China.
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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2
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Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat Methods 2023; 20:1355-1367. [PMID: 37443338 PMCID: PMC10482700 DOI: 10.1038/s41592-023-01938-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present a method for the inference of enhancer-driven GRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TFs) and links these enhancers to candidate target genes. To improve both recall and precision of TF identification, we curated and clustered a motif collection with more than 30,000 motifs. We benchmarked SCENIC+ on diverse datasets from different species, including human peripheral blood mononuclear cells, ENCODE cell lines, melanoma cell states and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers and GRNs between human and mouse cell types in the cerebral cortex. Finally, we use SCENIC+ to study the dynamics of gene regulation along differentiation trajectories and the effect of TF perturbations on cell state. SCENIC+ is available at scenicplus.readthedocs.io .
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seppe De Winter
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikolai Hecker
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Jasper Wouters
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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Kamimoto K, Stringa B, Hoffmann CM, Jindal K, Solnica-Krezel L, Morris SA. Dissecting cell identity via network inference and in silico gene perturbation. Nature 2023; 614:742-751. [PMID: 36755098 PMCID: PMC9946838 DOI: 10.1038/s41586-022-05688-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 12/28/2022] [Indexed: 02/10/2023]
Abstract
Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory networks1. Here we use gene-regulatory networks inferred from single-cell multi-omics data to perform in silico transcription factor perturbations, simulating the consequent changes in cell identity using only unperturbed wild-type data. We apply this machine-learning-based approach, CellOracle, to well-established paradigms-mouse and human haematopoiesis, and zebrafish embryogenesis-and we correctly model reported changes in phenotype that occur as a result of transcription factor perturbation. Through systematic in silico transcription factor perturbation in the developing zebrafish, we simulate and experimentally validate a previously unreported phenotype that results from the loss of noto, an established notochord regulator. Furthermore, we identify an axial mesoderm regulator, lhx1a. Together, these results show that CellOracle can be used to analyse the regulation of cell identity by transcription factors, and can provide mechanistic insights into development and differentiation.
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Affiliation(s)
- Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Blerta Stringa
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Christy M Hoffmann
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Kunal Jindal
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine in St Louis, St Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine in St Louis, St Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA.
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4
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Mechanisms of improved erythroid progenitor growth with removal of chronic stress after trauma. Surgery 2022; 172:759-765. [PMID: 35672167 PMCID: PMC9283291 DOI: 10.1016/j.surg.2022.04.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/14/2022] [Accepted: 04/29/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Erythropoietic dysfunction after trauma and critical illness is associated with anemia, persistent inflammation, increased hematopoietic progenitor cell mobilization from the bone marrow, and reduced erythroid progenitor growth. Yet the duration and reversibility of these postinjury bone marrow changes remain unknown. This study sought to determine whether removal of chronic postinjury stress could induce improvements in erythroid progenitor growth. METHODS Sprague-Dawley rats (n = 8-11/group) were assigned to the following: naïve, lung contusion and hemorrhagic shock, lung contusion and hemorrhagic shock plus daily chronic stress for 7 days followed by 7 days of routine handling to allow recovery (lung contusion and hemorrhagic shock + chronic stress 7), or lung contusion and hemorrhagic shock plus chronic stress for 14 days (lung contusion and hemorrhagic shock + chronic stress 14). Circulating CD117+CD71+ erythroid progenitors were detected by flow cytometry. Rodents were killed on day 14, and bone marrow erythroid progenitor growth and erythroid transcription factors were assessed. Differences were assessed by analysis of variance (P < .05). RESULTS Compared to lung contusion and hemorrhagic shock + chronic stress 14, lung contusion and hemorrhagic shock + chronic stress 7 rodents had improved hemoglobin (8% ± 10% increase vs 6% ± 10% decrease) with fewer mobilized erythroid progenitors (898 × vs 1,524 cells), lower granulocyte-colony stimulating factor levels (3.1 ± 1.1 × pg/mL vs 5.9 ± 1.8 pg/mL), and improved erythroid progenitor growth. Cessation of stress had no impact on erythroid transcription factors GATA-1, GATA-2, LMO2, or KLF1. CONCLUSION Improvements in erythroid progenitor growth and reduced hematopoietic progenitor cell mobilization were seen 7 days after cessation of chronic stress and were associated with an improvement in hemoglobin. Early bone marrow erythropoietic functional recovery may result from resolution of hematopoietic progenitor mobilization rather than upregulation of pro-erythroid transcription factors. This study suggests that postinjury anemia is reversible and has the potential to improve with the cessation of stress.
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LSD1 defines erythroleukemia metabolism by controlling the lineage-specific transcription factors GATA1 and C/EBPα. Blood Adv 2021; 5:2305-2318. [PMID: 33929501 DOI: 10.1182/bloodadvances.2020003521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/17/2021] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogenous malignancy characterized by distinct lineage subtypes and various genetic/epigenetic alterations. As with other neoplasms, AML cells have well-known aerobic glycolysis, but metabolic variations depending on cellular lineages also exist. Lysine-specific demethylase-1 (LSD1) has been reported to be crucial for human leukemogenesis, which is currently one of the emerging therapeutic targets. However, metabolic roles of LSD1 and lineage-dependent factors remain to be elucidated in AML cells. Here, we show that LSD1 directs a hematopoietic lineage-specific metabolic program in AML subtypes. Erythroid leukemia (EL) cells particularly showed activated glycolysis and high expression of LSD1 in both AML cell lines and clinical samples. Transcriptome, chromatin immunoprecipitation-sequencing, and metabolomic analyses revealed that LSD1 was essential not only for glycolysis but also for heme synthesis, the most characteristic metabolic pathway of erythroid origin. Notably, LSD1 stabilized the erythroid transcription factor GATA1, which directly enhanced the expression of glycolysis and heme synthesis genes. In contrast, LSD1 epigenetically downregulated the granulo-monocytic transcription factor C/EBPα. Thus, the use of LSD1 knockdown or chemical inhibitor dominated C/EBPα instead of GATA1 in EL cells, resulting in metabolic shifts and growth arrest. Furthermore, GATA1 suppressed the gene encoding C/EBPα that then acted as a repressor of GATA1 target genes. Collectively, we conclude that LSD1 shapes metabolic phenotypes in EL cells by balancing these lineage-specific transcription factors and that LSD1 inhibitors pharmacologically cause lineage-dependent metabolic remodeling.
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Giraud G, Kolovos P, Boltsis I, van Staalduinen J, Guyot B, Weiss-Gayet M, IJcken WV, Morlé F, Grosveld F. Interplay between FLI-1 and the LDB1 complex in murine erythroleukemia cells and during megakaryopoiesis. iScience 2021; 24:102210. [PMID: 33733070 PMCID: PMC7940982 DOI: 10.1016/j.isci.2021.102210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/22/2020] [Accepted: 02/17/2021] [Indexed: 11/29/2022] Open
Abstract
Transcription factors are key players in a broad range of cellular processes such as cell-fate decision. Understanding how they act to control these processes is of critical importance for therapy purposes. FLI-1 controls several hematopoietic lineage differentiation including megakaryopoiesis and erythropoiesis. Its aberrant expression is often observed in cancer and is associated with poor prognosis. We showed that FLI-1 interacts with the LDB1 complex, which also plays critical roles in erythropoiesis and megakaryopoiesis. In this study, we aimed to unravel how FLI-1 and the LDB1 complex act together in murine erythroleukemia cells and in megakaryocyte. Combining omics techniques, we show that FLI-1 enables the recruitment of the LDB1 complex to regulatory sequences of megakaryocytic genes and to enhancers. We show as well for the first time that FLI-1 is able to modulate the 3D chromatin organization by promoting chromatin looping between enhancers and promoters most likely through the LDB1 complex. FLI-1 is important for the recruitment of the LDB1 complex FLI-1 is important for chromatin looping FLI-1 and the LDB1 complex co-regulate megakaryopoiesis
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Affiliation(s)
- Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Jente van Staalduinen
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
| | - Boris Guyot
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Department of Immunity, Virus and Microenvironment, Lyon, France
| | - Michele Weiss-Gayet
- Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217 - Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Wilfred van IJcken
- Biomics Center, Erasmus University Medical Center, 3015CN Rotterdam, the Netherlands
| | - François Morlé
- Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217 - Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands
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Chen L, Wang YY, Li D, Wang C, Wang SY, Shao SH, Zhu ZY, Zhao J, Zhang Y, Ruan Y, Han BM, Xia SJ, Jiang CY, Zhao FJ. LMO2 upregulation due to AR deactivation in cancer-associated fibroblasts induces non-cell-autonomous growth of prostate cancer after androgen deprivation. Cancer Lett 2021; 503:138-150. [PMID: 33503448 DOI: 10.1016/j.canlet.2021.01.017] [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: 10/07/2020] [Revised: 12/16/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
The androgen receptor (AR) is expressed in prostate fibroblasts in addition to normal prostate epithelial cells and prostate cancer (PCa) cells. Moreover, AR activation in fibroblasts dramatically influences prostate cancer (PCa) cell behavior. Androgen deprivation leads to deregulation of AR downstream target genes in both fibroblasts and PCa cells. Here, we identified LIM domain only 2 (LMO2) as an AR target gene in prostate fibroblasts using ChIP-seq and revealed that LMO2 can be repressed directly by AR through binding to androgen response elements (AREs), which results in LMO2 overexpression after AR deactivation due to normal prostate fibroblasts to cancer-associated fibroblasts (CAFs) transformation or androgen deprivation therapy. Next, we investigated the mechanisms of LMO2 overexpression in fibroblasts and the role of this event in non-cell-autonomous promotion of PCa cells growth in the androgen-independent manner through paracrine release of IL-11 and FGF-9. Collectively, our data suggest that AR deactivation deregulates LMO2 expression in prostate fibroblasts, which induces castration resistance in PCa cells non-cell-autonomously through IL-11 and FGF-9.
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Affiliation(s)
- Lei Chen
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Yue-Yang Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Deng Li
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Cheng Wang
- Department of Urology, Jiangsu Jiangyin People's Hospital, Jiangyin, 214400, China
| | - Shi-Yuan Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Si-Hui Shao
- Department of Ultrasound, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Zheng-Yang Zhu
- Clinical Medical College, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Jing Zhao
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Yu Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Yuan Ruan
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Bang-Min Han
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Shu-Jie Xia
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China.
| | - Chen-Yi Jiang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China.
| | - Fu-Jun Zhao
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; Institute of Urology, Shanghai Jiao Tong University, Shanghai, 200080, China.
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Wu S, Cui T, Zhang X, Tian T. A non-linear reverse-engineering method for inferring genetic regulatory networks. PeerJ 2020; 8:e9065. [PMID: 32391205 PMCID: PMC7195839 DOI: 10.7717/peerj.9065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is a highly complex developmental process that produces various types of blood cells. This process is regulated by different genetic networks that control the proliferation, differentiation, and maturation of hematopoietic stem cells (HSCs). Although substantial progress has been made for understanding hematopoiesis, the detailed regulatory mechanisms for the fate determination of HSCs are still unraveled. In this study, we propose a novel approach to infer the detailed regulatory mechanisms. This work is designed to develop a mathematical framework that is able to realize nonlinear gene expression dynamics accurately. In particular, we intended to investigate the effect of possible protein heterodimers and/or synergistic effect in genetic regulation. This approach includes the Extended Forward Search Algorithm to infer network structure (top-down approach) and a non-linear mathematical model to infer dynamical property (bottom-up approach). Based on the published experimental data, we study two regulatory networks of 11 genes for regulating the erythrocyte differentiation pathway and the neutrophil differentiation pathway. The proposed algorithm is first applied to predict the network topologies among 11 genes and 55 non-linear terms which may be for heterodimers and/or synergistic effect. Then, the unknown model parameters are estimated by fitting simulations to the expression data of two different differentiation pathways. In addition, the edge deletion test is conducted to remove possible insignificant regulations from the inferred networks. Furthermore, the robustness property of the mathematical model is employed as an additional criterion to choose better network reconstruction results. Our simulation results successfully realized experimental data for two different differentiation pathways, which suggests that the proposed approach is an effective method to infer the topological structure and dynamic property of genetic regulations.
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Affiliation(s)
- Siyuan Wu
- School of Mathematics, Monash University, Clayton, VIC, Australia
| | - Tiangang Cui
- School of Mathematics, Monash University, Clayton, VIC, Australia
| | - Xinan Zhang
- School of Mathematics and Statistics, Central China Normal University, Wuhan, PR China
| | - Tianhai Tian
- School of Mathematics, Monash University, Clayton, VIC, Australia
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9
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Liu Z, Feng Q, Sun P, Lu Y, Yang M, Zhang X, Jin X, Li Y, Lu SJ, Quan C. Genome-wide DNA methylation drives human embryonic stem cell erythropoiesis by remodeling gene expression dynamics. Epigenomics 2017; 9:1543-1558. [PMID: 29135282 DOI: 10.2217/epi-2017-0039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the role of DNA methylation during erythrocyte production by human embryonic stem cells (hESCs). METHODS We employed an erythroid differentiation model from hESCs, and then tracked the genome-wide DNA methylation maps and gene expression patterns through an Infinium HumanMethylation450K BeadChip and an Ilumina Human HT-12 v4 Expression Beadchip, respectively. RESULTS A negative correlation between DNA methylation and gene expression was substantially enriched during the later differentiation stage and was present in both the promoter and the gene body. Moreover, erythropoietic genes with differentially methylated CpG sites that were primarily enriched in nonisland regions were upregulated, and demethylation of their gene bodies was associated with the presence of enhancers and DNase I hypersensitive sites. Finally, the components of JAK-STAT-NF-κB signaling were DNA hypomethylated and upregulated, which targets the key genes for erythropoiesis. CONCLUSION Erythroid lineage commitment by hESCs requires genome-wide DNA methylation modifications to remodel gene expression dynamics.
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Affiliation(s)
- Zhijing Liu
- Department of Pathology, Qingdao Municipal Hospital, Affiliated with Qingdao University, 1 Jiaozhou Road, Qingdao 266000, Shandong, China
| | - Qiang Feng
- Vcanbio Center for Translational Biotechnology, 21 Strathmore Road, Natick, MA 01760, USA
| | - Pengpeng Sun
- Department of Critical Care Medicine, Qingdao Center Medical Group, Affiliated with Qingdao University, 127 Siliunan Road, Qingdao 266042, Shandong, China
| | - Yan Lu
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Minlan Yang
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Xiaowei Zhang
- Center for Translational Medicine, Central Hospital of Zibo, Affiliated with Shandong University, 54 Gongqingtuan Road, Zibo 255000, Shandong, China
| | - Xiangshu Jin
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Yulin Li
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
| | - Shi-Jiang Lu
- Vcanbio Center for Translational Biotechnology, 21 Strathmore Road, Natick, MA 01760, USA
| | - Chengshi Quan
- Department of Pathology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Avenue, Changchun 130021, China
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10
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Sun KT, Huang YN, Palanisamy K, Chang SS, Wang IK, Wu KH, Chen P, Peng CT, Li CY. Reciprocal regulation of γ-globin expression by exo-miRNAs: Relevance to γ-globin silencing in β-thalassemia major. Sci Rep 2017; 7:202. [PMID: 28303002 PMCID: PMC5427890 DOI: 10.1038/s41598-017-00150-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 02/09/2017] [Indexed: 12/30/2022] Open
Abstract
Induction of fetal hemoglobin (HbF) is a promising strategy in the treatment of β-thalassemia major (β-TM). The present study shows that plasma exosomal miRNAs (exo-miRs) are involved in γ-globin regulation. Exosomes shuttle miRNAs and mediate cell-cell communication. MiRNAs are regulators of biological processes through post-transcriptional targeting. Compared to HD (Healthy Donor), β-TM patients showed increased levels of plasma exosomes and the majority of exosomes had cellular origin from CD34+ cells. Further, HD and β-TM exosomes showed differential miRNA expressions. Among them, deregulated miR-223-3p and miR-138-5p in β-TM exosomes and HD had specific targets for γ-globin regulator and repressor respectively. Functional studies in K562 cells showed that HD exosomes and miR-138-5p regulated γ-globin expression by targeting BCL11A. β-TM exosomes and miR-223-3p down regulated γ-globin expression through LMO2 targeting. Importantly, miR-223-3p targeting through sponge repression resulted in γ-globin activation. Further, hnRNPA1 bound to stem-loop structure of pre-miR-223 and we found that hnRNPA1 knockdown or mutagenesis at miR-223-3p stem-loop sequence resulted in less mature exo-miR-223-3p levels. Altogether, the study shows for the first time on the important clinical evidence that differentially expressed exo-miRNAs reciprocally control γ-globin expressions. Further, the hnRNPA1-exo-miR-223-LMO2 axis may be critical to γ-globin silencing in β-TM.
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Affiliation(s)
- Kuo-Ting Sun
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, 40402, Taiwan
- Department of Pediatric Dentistry, China Medical University Hospital, Taichung, 40402, Taiwan
- School of Dentistry, China Medical University, Taichung, 40402, Taiwan
| | - Yu-Nan Huang
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, 40402, Taiwan
- Department of Life Sciences, National Chung-Hsing University, Taichung, 40402, Taiwan
- Department of Hematology-oncology, Children's Hospital of China Medical University, Taichung, 40402, Taiwan
| | - Kalaiselvi Palanisamy
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, 40402, Taiwan
| | - Shih-Sheng Chang
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, 40402, Taiwan
- Division of Cardiology, Department of Medicine, China Medical University Hospital, Taichung, 40402, Taiwan
| | - I-Kuan Wang
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, 40402, Taiwan
- Division of Nephrology, Department of Medicine, China Medical University Hospital, Taichung, 40402, Taiwan
| | - Kang-Hsi Wu
- Department of Hematology-oncology, Children's Hospital of China Medical University, Taichung, 40402, Taiwan
| | - Ping Chen
- Thalassemia Research Institute, The First Affiliated Hospital, Guangxi Medical University, Guangxi Zhuang Autonomous Region, 530021, China
| | - Ching-Tien Peng
- Department of Hematology-oncology, Children's Hospital of China Medical University, Taichung, 40402, Taiwan.
| | - Chi-Yuan Li
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, 40402, Taiwan.
- Department of Anesthesiology, China Medical University Hospital, Taichung, 40402, Taiwan.
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