1
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Lewis J, Guilcher GMT, Greenway SC. Reviewing the impact of hydroxyurea on DNA methylation and its potential clinical implications in sickle cell disease. Eur J Haematol 2024. [PMID: 38831675 DOI: 10.1111/ejh.14247] [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: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
Hydroxyurea (HU) is the most common drug therapy for sickle cell disease (SCD). The clinical benefits of HU derive from its upregulation of fetal hemoglobin (HbF), which reduces aggregation of the mutated sickle hemoglobin protein (HbS) and reduces SCD symptoms and complications. However, some individuals do not respond to HU, or stop responding over time. Unfortunately, current understanding of the mechanism of action of HU is limited, hindering the ability of clinicians to identify those patients who will respond to HU and to optimize treatment for those receiving HU. Given that epigenetic modifications are essential to erythropoiesis and HbF expression, we hypothesize that some effects of HU may be mediated by epigenetic modifications, specifically DNA methylation. However, few studies have investigated this possibility and the effects of HU on DNA methylation remain relatively understudied. In this review, we discuss the evidence linking HU treatment to DNA methylation changes and associated gene expression changes, with an emphasis on studies that were performed in individuals with SCD. Overall, although HU can affect DNA methylation, research on these changes and their clinical effects remains limited. Further study is likely to contribute to our understanding of hematopoiesis and benefit patients suffering from SCD.
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Affiliation(s)
- Jasmine Lewis
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Gregory M T Guilcher
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Steven C Greenway
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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2
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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024:10.1038/s44320-024-00039-4. [PMID: 38755290 DOI: 10.1038/s44320-024-00039-4] [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: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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3
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Myers G, Sun Y, Wang Y, Benmhammed H, Cui S. Roles of Nuclear Orphan Receptors TR2 and TR4 during Hematopoiesis. Genes (Basel) 2024; 15:563. [PMID: 38790192 PMCID: PMC11121135 DOI: 10.3390/genes15050563] [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: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
TR2 and TR4 (NR2C1 and NR2C2, respectively) are evolutionarily conserved nuclear orphan receptors capable of binding direct repeat sequences in a stage-specific manner. Like other nuclear receptors, TR2 and TR4 possess important roles in transcriptional activation or repression with developmental stage and tissue specificity. TR2 and TR4 bind DNA and possess the ability to complex with available cofactors mediating developmental stage-specific actions in primitive and definitive erythrocytes. In erythropoiesis, TR2 and TR4 are required for erythroid development, maturation, and key erythroid transcription factor regulation. TR2 and TR4 recruit and interact with transcriptional corepressors or coactivators to elicit developmental stage-specific gene regulation during hematopoiesis.
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Affiliation(s)
- Greggory Myers
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (G.M.); (Y.W.)
| | - Yanan Sun
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA 02118, USA; (Y.S.); (H.B.)
| | - Yu Wang
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (G.M.); (Y.W.)
| | - Hajar Benmhammed
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA 02118, USA; (Y.S.); (H.B.)
| | - Shuaiying Cui
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA 02118, USA; (Y.S.); (H.B.)
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4
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Pavani G, Klein JG, Nations CC, Sussman JH, Tan K, An HH, Abdulmalik O, Thom CS, Gearhart PA, Willett CM, Maguire JA, Chou ST, French DL, Gadue P. Modeling primitive and definitive erythropoiesis with induced pluripotent stem cells. Blood Adv 2024; 8:1449-1463. [PMID: 38290102 PMCID: PMC10955655 DOI: 10.1182/bloodadvances.2023011708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024] Open
Abstract
ABSTRACT During development, erythroid cells are produced through at least 2 distinct hematopoietic waves (primitive and definitive), generating erythroblasts with different functional characteristics. Human induced pluripotent stem cells (iPSCs) can be used as a model platform to study the development of red blood cells (RBCs) with many of the differentiation protocols after the primitive wave of hematopoiesis. Recent advances have established that definitive hematopoietic progenitors can be generated from iPSCs, creating a unique situation for comparing primitive and definitive erythrocytes derived from cell sources of identical genetic background. We generated iPSCs from healthy fetal liver (FL) cells and produced isogenic primitive or definitive RBCs which were compared directly to the FL-derived RBCs. Functional assays confirmed differences between the 2 programs, with primitive RBCs showing a reduced proliferation potential, larger cell size, lack of Duffy RBC antigen expression, and higher expression of embryonic globins. Transcriptome profiling by scRNA-seq demonstrated high similarity between FL- and iPSC-derived definitive RBCs along with very different gene expression and regulatory network patterns for primitive RBCs. In addition, iPSC lines harboring a known pathogenic mutation in the erythroid master regulator KLF1 demonstrated phenotypic changes specific to definitive RBCs. Our studies provide new insights into differences between primitive and definitive erythropoiesis and highlight the importance of ontology when using iPSCs to model genetic hematologic diseases. Beyond disease modeling, the similarity between FL- and iPSC-derived definitive RBCs expands potential applications of definitive RBCs for diagnostic and transfusion products.
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Affiliation(s)
- Giulia Pavani
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA
| | - Joshua G. Klein
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Catriana C. Nations
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Cell and Molecular Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jonathan H. Sussman
- Department of Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kai Tan
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hyun Hyung An
- Department of Cell and Molecular Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Osheiza Abdulmalik
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Christopher S. Thom
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Peter A. Gearhart
- Department of Obstetrics and Gynecology, Pennsylvania Hospital, University of Pennsylvania Health System, Philadelphia, PA
| | - Camryn M. Willett
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Stella T. Chou
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Deborah L. French
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA
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5
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Doty RT, Lausted CG, Munday AD, Yang Z, Yan X, Meng C, Tian Q, Abkowitz JL. The transcriptomic landscape of normal and ineffective erythropoiesis at single-cell resolution. Blood Adv 2023; 7:4848-4868. [PMID: 37352261 PMCID: PMC10469080 DOI: 10.1182/bloodadvances.2023010382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/15/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
The anemias of myelodysplastic syndrome (MDS) and Diamond Blackfan anemia (DBA) are generally macrocytic and always reflect ineffective erythropoiesis yet result from diverse genetic mutations. To delineate shared mechanisms that lead to cell death, we studied the fate of single erythroid marrow cells from individuals with DBA or MDS-5q. We defined an unhealthy (vs healthy) differentiation trajectory using transcriptional pseudotime and cell surface proteins. The pseudotime trajectories diverge immediately after cells upregulate transferrin receptor (CD71), import iron, and initiate heme synthesis, although cell death occurs much later. Cells destined to die express high levels of heme-responsive genes, including ribosomal protein and globin genes, whereas surviving cells downregulate heme synthesis and upregulate DNA damage response, hypoxia, and HIF1 pathways. Surprisingly, 24% ± 12% of cells from control subjects follow the unhealthy trajectory, implying that heme might serve as a rheostat directing cells to live or die. When heme synthesis was inhibited with succinylacetone, more DBA cells followed the healthy trajectory and survived. We also noted high numbers of messages with retained introns that increased as erythroid cells matured, confirmed the rapid cycling of colony forming unit-erythroid, and demonstrated that cell cycle timing is an invariant property of differentiation stage. Including unspliced RNA in pseudotime determinations allowed us to reliably align independent data sets and accurately query stage-specific transcriptomic changes. MDS-5q (unlike DBA) results from somatic mutation, so many normal (unmutated) erythroid cells persist. By independently tracking erythroid differentiation of cells with and without chromosome 5q deletions, we gained insight into why 5q+ cells cannot expand to prevent anemia.
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Affiliation(s)
- Raymond T. Doty
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | | | - Adam D. Munday
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | - Zhantao Yang
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | | | | | - Qiang Tian
- Institute for Systems Biology, Seattle, WA
| | - Janis L. Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
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6
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Zhou Y, Song BL. An urgent call on revisions to current genome annotation strategies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1942-1943. [PMID: 37118509 DOI: 10.1007/s11427-023-2350-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023]
Affiliation(s)
- Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Bao-Liang Song
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
- TaiKang Medical School, Wuhan University, Wuhan, 430072, China.
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7
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Yang Y, Wen X, Wu Z, Wang K, Zhu Y. Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1711-1724. [PMID: 37079218 DOI: 10.1007/s11427-022-2341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81% transposable elements (TEs), while only 57% of the 735-Mb G. raimondii genome is occupied by TEs. In this study, we investigated whether there were unknown transcripts associated with TE or TE fragments and, if so, how these new transcripts were evolved and regulated. As sequence depths increased from 4 to 100 G, a total of 10,284 novel intergenic transcripts (intergenic genes) were discovered. On average, approximately 84% of these intergenic transcripts possibly overlapped with the long terminal repeat (LTR) insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low levels. Most of these intergenic transcripts possessed no transcription activation markers, while the majority of the regular genic genes possessed at least one such marker. Genes without transcription activation markers formed their+1 and -1 nucleosomes more closely (only (117±1.4)bp apart), while twice as big spaces (approximately (403.5±46.0) bp apart) were detected for genes with the activation markers. The analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR content. Evolutionary analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7 million years ago (MYA) for all eudicot genomes or 13.7 MYA for the Gossypium family, respectively, while the intergenic transcripts evolved around 1.6 MYA, resultant of the last LTR insertion. The characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.
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Affiliation(s)
- Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Hubei Hongshan Laboratory, Wuhan, 430072, China.
- TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, 430072, China.
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8
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Forester CM, Oses-Prieto JA, Phillips NJ, Miglani S, Pang X, Byeon GW, DeMarco R, Burlingame A, Barna M, Ruggero D. Regulation of eIF4E guides a unique translational program to control erythroid maturation. SCIENCE ADVANCES 2022; 8:eadd3942. [PMID: 36563140 PMCID: PMC9788769 DOI: 10.1126/sciadv.add3942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/22/2022] [Indexed: 05/22/2023]
Abstract
Translation control is essential in balancing hematopoietic precursors and differentiation; however, the mechanisms underlying this program are poorly understood. We found that the activity of the major cap-binding protein eIF4E is unexpectedly regulated in a dynamic manner throughout erythropoiesis that is uncoupled from global protein synthesis rates. Moreover, eIF4E activity directs erythroid maturation, and increased eIF4E expression maintains cells in an early erythroid state associated with a translation program driving the expression of PTPN6 and Igf2bp1. A cytosine-enriched motif in the 5' untranslated region is important for eIF4E-mediated translation specificity. Therefore, selective translation of key target genes necessary for the maintenance of early erythroid states by eIF4E highlights a unique mechanism used by hematopoietic precursors to rapidly elicit erythropoietic maturation upon need.
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Affiliation(s)
- Craig M. Forester
- Department of Pediatrics, University of Colorado, Denver, CO 80045, USA
- Division of Pediatric Hematology/Oncology/Bone Marrow Transplant, Children’s Hospital Colorado, University of Colorado-Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Juan A. Oses-Prieto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nancy J. Phillips
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sohit Miglani
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaming Pang
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94309, USA
| | - Rachel DeMarco
- Department of Pediatrics, University of Colorado, Denver, CO 80045, USA
| | - Al Burlingame
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94309, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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9
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Xu C, He J, Wang H, Zhang Y, Wu J, Zhao L, Li Y, Gao J, Geng G, Wang B, Chen X, Zheng Z, Shen B, Zeng Y, Bai Z, Yang H, Shi S, Dong F, Ma S, Jiang E, Cheng T, Lan Y, Zhou J, Liu B, Shi L. Single-cell transcriptomic analysis identifies an immune-prone population in erythroid precursors during human ontogenesis. Nat Immunol 2022; 23:1109-1120. [PMID: 35761081 DOI: 10.1038/s41590-022-01245-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/17/2022] [Indexed: 01/03/2023]
Abstract
Nonimmune cells can have immunomodulatory roles that contribute to healthy development. However, the molecular and cellular mechanisms underlying the immunomodulatory functions of erythroid cells during human ontogenesis remain elusive. Here, integrated, single-cell transcriptomic studies of erythroid cells from the human yolk sac, fetal liver, preterm umbilical cord blood (UCB), term UCB and adult bone marrow (BM) identified classical and immune subsets of erythroid precursors with divergent differentiation trajectories. Immune-erythroid cells were present from the yolk sac to the adult BM throughout human ontogenesis but failed to be generated in vitro from human embryonic stem cells. Compared with classical-erythroid precursors, these immune-erythroid cells possessed dual erythroid and immune regulatory networks, showed immunomodulatory functions and interacted more frequently with various innate and adaptive immune cells. Our findings provide important insights into the nature of immune-erythroid cells and their roles during development and diseases.
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Affiliation(s)
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Laboratory of Basic Medicine, The General Hospital of Western Theater Command, Chengdu, China
| | - Hongtao 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Yingnan Zhang
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Jing Wu
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Lu Zhao
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Yue Li
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Guangfeng Geng
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Bingrui 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Xiaoyuan Chen
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Zhaofeng Zheng
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Biao Shen
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Yang Zeng
- Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Hua Yang
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Shujuan Shi
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Fang Dong
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Shihui Ma
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Erlie Jiang
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Tao Cheng
- 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, China.,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Jiaxi Zhou
- 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, China. .,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China.
| | - Bing Liu
- 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, China. .,State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China. .,Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China. .,Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 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, China. .,CAMS Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, PUMC, Tianjin, China.
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10
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Yang S, Sun G, Wu P, Chen C, Kuang Y, Liu L, Zheng Z, He Y, Gu Q, Lu T, Zhu C, Wang F, Gou F, Yang Z, Zhao X, Yuan S, Yang L, Lu S, Li Y, Lv X, Dong F, Ma Y, Yu J, Ng LG, Shi L, Liu J, Shi L, Cheng T, Cheng H. WDR82-binding long noncoding RNA lncEry controls mouse erythroid differentiation and maturation. J Exp Med 2022; 219:213079. [PMID: 35315911 PMCID: PMC8943841 DOI: 10.1084/jem.20211688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/18/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic differentiation is controlled by both genetic and epigenetic regulators. Long noncoding RNAs (lncRNAs) have been demonstrated to be important for normal hematopoiesis, but their function in erythropoiesis needs to be further explored. We profiled the transcriptomes of 16 murine hematopoietic cell populations by deep RNA sequencing and identified a novel lncRNA, Gm15915, that was highly expressed in erythroid-related progenitors and erythrocytes. For this reason, we named it lncEry. We also identified a novel lncEry isoform, which was the principal transcript that has not been reported before. lncEry depletion impaired erythropoiesis, indicating the important role of the lncRNA in regulating erythroid differentiation and maturation. Mechanistically, we found that lncEry interacted with WD repeat–containing protein 82 (WDR82) to promote the transcription of Klf1 and globin genes and thus control the early and late stages of erythropoiesis, respectively. These findings identified lncEry as an important player in the transcriptional regulation of erythropoiesis.
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Affiliation(s)
- Shangda Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Peng Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Cong Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yijin Kuang
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Ling Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhaofeng Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Yicheng He
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Quan Gu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Caiying Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Fengjiao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Fanglin Gou
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zining Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiangnan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Shiru Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Liu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Shihong Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Xue Lv
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Lai Guan Ng
- Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Jing Liu
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, China
| | - Lei Shi
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine, Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences, Tianjin, China
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11
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Pan Y, Xu L, Huang H. Expression, functional mechanism and therapy application of long noncoding RNA in β-thalassemia. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2022; 47:252-257. [PMID: 35545416 PMCID: PMC10930521 DOI: 10.11817/j.issn.1672-7347.2022.210411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 06/15/2023]
Abstract
β-thalassemia (β-thal) is one of the most common genetic diseases in the world, its pathogenesis is extremely complex and there is no effective treatment at present. The birth of children with moderate and severe β-thal brings economic pressure to families, social medical and health services. Long noncoding RNA (lncRNA) is a type of noncoding protein transcripts with a length greater than 200 nucleotides, which is involved in a variety of biological processes, such as cell proliferation, differentiation and chromosome variation and plays an important role in the epigenetic and post-transcriptional regulation of genes. It has potential value in the diagnosis, prevention and treatment of β-thal. LncRNA possesses the characteristics such as tissue specificity, cell specificity, developmental stage specificity, space-time specificity and disease specificity, and its complex interaction network has become a challenge to translate research results into clinical practice. Taking lncRNA as an entry point, in-depth understanding of the function of lncRNA in β-thal and explanation of its related regulatory mechanisms will provide theoretical basis for targeting treatment of β-thal, which can improve the diagnosis and treatment of β-thal.
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Affiliation(s)
- Yali Pan
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital/Affiliated Hospital of Fujian Medical University; Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou 350001.
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350004, China.
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital/Affiliated Hospital of Fujian Medical University; Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou 350001
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital/Affiliated Hospital of Fujian Medical University; Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou 350001.
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350004, China.
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12
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Meng Y, Huang Y, Chang X, Liu X, Chen L. Transcriptome analysis method based on differential distribution evaluation. Brief Bioinform 2022; 23:6527752. [PMID: 35151228 DOI: 10.1093/bib/bbab608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying differential genes over conditions provides insights into the mechanisms of biological processes and disease progression. Here we present an approach, the Kullback-Leibler divergence-based differential distribution (klDD), which provides a flexible framework for quantifying changes in higher-order statistical information of genes including mean and variance/covariation. The method can well detect subtle differences in gene expression distributions in contrast to mean or variance shifts of the existing methods. In addition to effectively identifying informational genes in terms of differential distribution, klDD can be directly applied to cancer subtyping, single-cell clustering and disease early-warning detection, which were all validated by various benchmark datasets.
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Affiliation(s)
- Yiwei Meng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanhong Huang
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China.,Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiao Chang
- Institute of Statistics and Applied Mathematics, Anhui University of Finance & Economics, Bengbu 233030, China
| | - Xiaoping Liu
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China.,Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.,Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong 519031, China
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13
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Grzywa TM, Nowis D, Golab J. The role of CD71 + erythroid cells in the regulation of the immune response. Pharmacol Ther 2021; 228:107927. [PMID: 34171326 DOI: 10.1016/j.pharmthera.2021.107927] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/13/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
Complex regulation of the immune response is necessary to support effective defense of an organism against hostile invaders and to maintain tolerance to harmless microorganisms and autoantigens. Recent studies revealed previously unappreciated roles of CD71+ erythroid cells (CECs) in regulation of the immune response. CECs physiologically reside in the bone marrow where erythropoiesis takes place. Under stress conditions, CECs are enriched in some organs outside of the bone marrow as a result of extramedullary erythropoiesis. However, the role of CECs goes well beyond the production of erythrocytes. In neonates, increased numbers of CECs contribute to their vulnerability to infectious diseases. On the other side, neonatal CECs suppress activation of immune cells in response to abrupt colonization with commensal microorganisms after delivery. CECs are also enriched in the peripheral blood of pregnant women as well as in the placenta and are responsible for the regulation of feto-maternal tolerance. In patients with cancer, anemia leads to increased frequency of CECs in the peripheral blood contributing to diminished antiviral and antibacterial immunity, as well as to accelerated cancer progression. Moreover, recent studies revealed the role of CECs in HIV and SARS-CoV-2 infections. CECs use a full arsenal of mechanisms to regulate immune response. These cells suppress proinflammatory responses of myeloid cells and T-cell proliferation by the depletion of ʟ-arginine by arginase. Moreover, CECs produce reactive oxygen species to decrease T-cell proliferation. CECs also secrete cytokines, including transforming growth factor β (TGF-β), which promotes T-cell differentiation into regulatory T-cells. Here, we comprehensively describe the role of CECs in orchestrating immune response and indicate some therapeutic approaches that might be used to regulate their effector functions in the treatment of human conditions.
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Affiliation(s)
- Tomasz M Grzywa
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 Street, 02-097 Warsaw, Poland; Doctoral School, Medical University of Warsaw, Zwirki and Wigury 61 Street, 02-091 Warsaw, Poland; Laboratory of Experimental Medicine, Medical University of Warsaw, Nielubowicza 5 Street, 02-097 Warsaw, Poland.
| | - Dominika Nowis
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 Street, 02-097 Warsaw, Poland; Laboratory of Experimental Medicine, Medical University of Warsaw, Nielubowicza 5 Street, 02-097 Warsaw, Poland.
| | - Jakub Golab
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5 Street, 02-097 Warsaw, Poland; Centre of Preclinical Research, Medical University of Warsaw, Banacha 1b Street, 02-097 Warsaw, Poland.
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14
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ZNF410 represses fetal globin by singular control of CHD4. Nat Genet 2021; 53:719-728. [PMID: 33859416 PMCID: PMC8180380 DOI: 10.1038/s41588-021-00843-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/10/2021] [Indexed: 02/02/2023]
Abstract
Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes encoding γ-globins, but rather its chromatin occupancy is concentrated solely at CHD4, encoding the NuRD nucleosome remodeler, which is itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for the effects of ZNF410 on fetal globin repression. Knockout of ZNF410 or its mouse homolog Zfp410 reduces CHD4 levels by 60%, enough to substantially de-repress HbF while eluding cellular or organismal toxicity. These studies suggest a potential target for HbF induction for β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved TF with singular devotion to regulation of a chromatin subcomplex.
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15
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Ma Y, Liu S, Gao J, Chen C, Zhang X, Yuan H, Chen Z, Yin X, Sun C, Mao Y, Zhou F, Shao Y, Liu Q, Xu J, Cheng L, Yu D, Li P, Yi P, He J, Geng G, Guo Q, Si Y, Zhao H, Li H, Banes GL, Liu H, Nakamura Y, Kurita R, Huang Y, Wang X, Wang F, Fang G, Engel JD, Shi L, Zhang YE, Yu J. Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in β-thalassemia. Dev Cell 2021; 56:478-493.e11. [PMID: 33476555 DOI: 10.1016/j.devcel.2020.12.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023]
Abstract
The human genome harbors 14,000 duplicated or retroposed pseudogenes. Given their functionality as regulatory RNAs and low conservation, we hypothesized that pseudogenes could shape human-specific phenotypes. To test this, we performed co-expression analyses and found that pseudogene exhibited tissue-specific expression, especially in the bone marrow. By incorporating genetic data, we identified a bone-marrow-specific duplicated pseudogene, HBBP1 (η-globin), which has been implicated in β-thalassemia. Extensive functional assays demonstrated that HBBP1 is essential for erythropoiesis by binding the RNA-binding protein (RBP), HNRNPA1, to upregulate TAL1, a key regulator of erythropoiesis. The HBBP1/TAL1 interaction contributes to a milder symptom in β-thalassemia patients. Comparative studies further indicated that the HBBP1/TAL1 interaction is human-specific. Genome-wide analyses showed that duplicated pseudogenes are often bound by RBPs and less commonly bound by microRNAs compared with retropseudogenes. Taken together, we not only demonstrate that pseudogenes can drive human evolution but also provide insights on their functional landscapes.
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Affiliation(s)
- Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China.
| | - Siqi Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhang
- Laboratory of Molecular Cardiology & Medical Molecular Imaging, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Hao Yuan
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongyang Chen
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xiaolin Yin
- 923rd Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Guangxi 530021, China
| | - Chenguang Sun
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yanan Mao
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanqi Zhou
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yi Shao
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Liu
- Shantou University Medical College, Shantou 515041, China
| | - Jiayue Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Li Cheng
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China
| | - Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pingping Li
- 923rd Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Guangxi 530021, China
| | - Ping Yi
- Department of Obstetrics and Gynecology, the Third Affiliated Hospital of Chongqing Medical University (General Hospital), Chongqing 401120, China
| | - Jiahuan He
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Guangfeng Geng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Qing Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yanmin Si
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Hualu Zhao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Haipeng Li
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Graham L Banes
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China; Wisconsin National Primate Research Center, University of Wisconsin Madison, 1220 Capitol Court, Madison, WI 53715, USA
| | - He Liu
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, Beijing 100044, China
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo 105-8521, Japan
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China
| | - Xiaoshuang Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Gang Fang
- NYU Shanghai, 1555 Century Avenue, Shanghai 20012, China; Department of Biology, 1009 Silver Center, New York University, New York, NY 10003, USA; School of Computer Science and Software Engineering, East China Normal University, Shanghai 200062, China
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Science, Chinese Academy of Medical Sciences (CAMS) & School of Basic Medicine, Peking Union Medical College (PUMC), Beijing 100005, China; Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China; State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
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16
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Grzywa TM, Justyniarska M, Nowis D, Golab J. Tumor Immune Evasion Induced by Dysregulation of Erythroid Progenitor Cells Development. Cancers (Basel) 2021; 13:870. [PMID: 33669537 PMCID: PMC7922079 DOI: 10.3390/cancers13040870] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
Cancer cells harness normal cells to facilitate tumor growth and metastasis. Within this complex network of interactions, the establishment and maintenance of immune evasion mechanisms are crucial for cancer progression. The escape from the immune surveillance results from multiple independent mechanisms. Recent studies revealed that besides well-described myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs) or regulatory T-cells (Tregs), erythroid progenitor cells (EPCs) play an important role in the regulation of immune response and tumor progression. EPCs are immature erythroid cells that differentiate into oxygen-transporting red blood cells. They expand in the extramedullary sites, including the spleen, as well as infiltrate tumors. EPCs in cancer produce reactive oxygen species (ROS), transforming growth factor β (TGF-β), interleukin-10 (IL-10) and express programmed death-ligand 1 (PD-L1) and potently suppress T-cells. Thus, EPCs regulate antitumor, antiviral, and antimicrobial immunity, leading to immune suppression. Moreover, EPCs promote tumor growth by the secretion of growth factors, including artemin. The expansion of EPCs in cancer is an effect of the dysregulation of erythropoiesis, leading to the differentiation arrest and enrichment of early-stage EPCs. Therefore, anemia treatment, targeting ineffective erythropoiesis, and the promotion of EPC differentiation are promising strategies to reduce cancer-induced immunosuppression and the tumor-promoting effects of EPCs.
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Affiliation(s)
- Tomasz M. Grzywa
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (T.M.G.); (M.J.)
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
- Laboratory of Experimental Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Magdalena Justyniarska
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (T.M.G.); (M.J.)
| | - Dominika Nowis
- Laboratory of Experimental Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Jakub Golab
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (T.M.G.); (M.J.)
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17
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Romano O, Petiti L, Felix T, Meneghini V, Portafax M, Antoniani C, Amendola M, Bicciato S, Peano C, Miccio A. GATA Factor-Mediated Gene Regulation in Human Erythropoiesis. iScience 2020; 23:101018. [PMID: 32283524 PMCID: PMC7155206 DOI: 10.1016/j.isci.2020.101018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/14/2020] [Accepted: 03/24/2020] [Indexed: 01/31/2023] Open
Abstract
Erythroid commitment and differentiation are regulated by the coordinated action of a host of transcription factors, including GATA2 and GATA1. Here, we explored GATA-mediated transcriptional regulation through the integrative analysis of gene expression, chromatin modifications, and GATA factors' binding in human multipotent hematopoietic stem/progenitor cells, early erythroid progenitors, and late precursors. A progressive loss of H3K27 acetylation and a diminished usage of active enhancers and super-enhancers were observed during erythroid commitment and differentiation. GATA factors mediate transcriptional changes through a stage-specific interplay with regulatory elements: GATA1 binds different sets of regulatory elements in erythroid progenitors and precursors and controls the transcription of distinct genes during commitment and differentiation. Importantly, our results highlight a pivotal role of promoters in determining the transcriptional program activated upon erythroid differentiation. Finally, we demonstrated that GATA1 binding to a stage-specific super-enhancer sustains the expression of the KIT receptor in human erythroid progenitors. GATA2/1 binding to regulatory regions and transcriptional changes during erythropoiesis GATA1 sustains KIT expression in human erythroid progenitors
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Petiti
- Institute of Biomedical Technologies, CNR, Milan, Italy
| | - Tristan Felix
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR, 1163 Paris, France
| | - Vasco Meneghini
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR, 1163 Paris, France
| | - Michel Portafax
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR, 1163 Paris, France
| | - Chiara Antoniani
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR, 1163 Paris, France
| | | | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, CNR, Milan, Italy; Institute of Genetic and Biomedical Research, UOS Milan, National Research Council, Rozzano, Milan, Italy; Genomic Unit, Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy.
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR, 1163 Paris, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France.
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18
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Mild macrocytosis in Williams-Beuren syndrome. Eur J Med Genet 2020; 63:103740. [DOI: 10.1016/j.ejmg.2019.103740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 11/23/2022]
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19
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Gao J, Liu J, Zhang L, Zhang Y, Guo Q, Li Y, Tong J, Wang H, Zhou J, Zhu F, Shi L, Zhao H. Heat shock transcription factor 1 regulates the fetal γ-globin expression in a stress-dependent and independent manner during erythroid differentiation. Exp Cell Res 2019; 387:111780. [PMID: 31874177 DOI: 10.1016/j.yexcr.2019.111780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 01/09/2023]
Abstract
Heat shock transcription factor 1 (HSF1) is a highly versatile transcription factor that, in addition to protecting cells against proteotoxic stress, is also critical during diverse developmental processes. Although the functions of HSF1 have received considerable attention, its potential role in β-globin gene regulation during erythropoiesis has not been fully elucidated. Here, after comparing the transcriptomes of erythrocytes differentiated from cord blood or adult peripheral blood hematopoietic progenitor CD34+ cells in vitro, we constructed the molecular regulatory network associated with β-globin genes and identified novel and putative globin gene regulators by combining the weighted gene coexpression network analysis (WGCNA) and context likelihood of relatedness (CLR) algorithms. Further investigation revealed that one of the identified regulators, HSF1, acts as a key activator of the γ-globin gene in human primary erythroid cells in both erythroid developmental stages. While during stress, HSF1 is required for heat-induced globin gene activation, and HSF1 downregulation markedly decreases globin gene induction in K562 cells. Mechanistically, HSF1 occupies DNase I hypersensitive site 3 of the locus control region upstream of β-globin genes via its canonical binding motif. Hence, HSF1 executes stress-dependent and -independent roles in fetal γ-globin regulation during erythroid differentiation.
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Affiliation(s)
- Jie Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jinhua Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lingling Zhang
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Yingnan Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Qing Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hongtao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Fan Zhu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Hui Zhao
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China.
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20
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Abstract
The transcription of essentially the entire eukaryotic genome produces a huge amount of non-coding RNAs. Among them, long non-coding RNAs (lncRNAs) consist of a significant portion that widely exists across mammal genome, generating from high-throughput transcriptomic studies in the last decade. Although the functions of most lncRNAs remain to be further investigated, many of them have already been shown to play critical roles during normal development and disease conditions. Increasing evidence indicates that lncRNAs involve in versatile biological processes during erythroid proliferation and differentiation, including erythroid cell survival, heme metabolism, globin switching and regulation, erythroid enucleation, etc, via cis- or trans-mediated molecular mechanisms. In this review, we focus on recent advances regarding the functions and mechanisms of lncRNAs in normal erythropoiesis.
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21
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Abstract
Hemoglobinopathies include all genetic diseases of hemoglobin and are grouped into thalassemia syndromes and structural hemoglobin variants. The β-thalassemias constitute a group of severe anemias with monogenic inheritance, caused by β-globin gene mutations. This review is focused on omics studies in hemoglobinopathies and mainly β-thalassemia, and discusses genomic, epigenomic, transcriptomic, proteomic and metabolomic findings. Omics analyses have identified various disease modifiers with an impact on disease severity and efficacy of treatments. These modifiers have contributed to the understanding of globin genes regulation/hemoglobin switching and the development of novel therapies. How omics data and their integration can contribute to efficient patient stratification, therapeutic management, improvements in existing treatments and application of novel personalized therapies is discussed.
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Affiliation(s)
- Eleni Katsantoni
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Soranou tou Ephessiou 4, 115 27, Athens, Greece.
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22
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Lessard S, Beaudoin M, Orkin SH, Bauer DE, Lettre G. 14q32 and let-7 microRNAs regulate transcriptional networks in fetal and adult human erythroblasts. Hum Mol Genet 2019; 27:1411-1420. [PMID: 29432581 DOI: 10.1093/hmg/ddy051] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
In humans, fetal erythropoiesis takes place in the liver whereas adult erythropoiesis occurs in the bone marrow. Fetal and adult erythroid cells are not only produced at different sites, but are also distinguished by their respective transcriptional program. In particular, whereas fetal erythroid cells express γ-globin chains to produce fetal hemoglobin (HbF), adult cells express β-globin chains to generate adult hemoglobin. Understanding the transcriptional regulation of the fetal-to-adult hemoglobin switch is clinically important as re-activation of HbF production in adult erythroid cells would represent a promising therapy for the hemoglobin disorders sickle cell disease and β-thalassemia. We used RNA-sequencing to measure global gene and microRNA (miRNA) expression in human erythroblasts derived ex vivo from fetal liver (n = 12 donors) and bone marrow (n = 12 donors) hematopoietic stem/progenitor cells. We identified 7829 transcripts and 402 miRNA that were differentially expressed (false discovery rate <5%). The miRNA expression patterns were replicated in an independent collection of human erythroblasts using a different technology. By combining gene and miRNA expression data, we developed transcriptional networks which show substantial differences between fetal and adult human erythroblasts. Our analyses highlighted the miRNAs at the imprinted 14q32 locus in fetal erythroblasts and the let-7 miRNA family in adult erythroblasts as key regulators of stage-specific erythroid transcriptional programs. Altogether, our results provide a comprehensive resource to prioritize genes that may modify clinical severity in red blood cell (RBC) disorders, or genes that might be implicated in erythropoiesis by genome-wide association studies of RBC traits.
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Affiliation(s)
- Samuel Lessard
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | | | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
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23
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Integrative view on how erythropoietin signaling controls transcription patterns in erythroid cells. Curr Opin Hematol 2019; 25:189-195. [PMID: 29389768 DOI: 10.1097/moh.0000000000000415] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW Erythropoietin (EPO) is necessary and sufficient to trigger dynamic transcriptional patterns that drive the differentiation of erythroid precursor cells into mature, enucleated red cells. Because the molecular cloning and Food and Drug Administration approval for the therapeutic use of EPO over 30 years ago, a detailed understanding of how EPO works has advanced substantially. Yet, the precise epigenetic and transcriptional mechanisms by which EPO signaling controls erythroid expression patterns remains poorly understood. This review focuses on the current state of erythroid biology in regards to EPO signaling from human genetics and functional genomics perspectives. RECENT FINDINGS The goal of this review is to provide an integrative view of the gene regulatory underpinnings for erythroid expression patterns that are dynamically shaped during erythroid differentiation. Here, we highlight vignettes connecting recent insights into a genome-wide association study linking an EPO mutation to anemia, a study linking EPO-signaling to signal transducer and activator of transcription 5 (STAT5) chromatin occupancy and enhancers, and studies that examine the molecular mechanisms driving topological chromatin organization in erythroid cells. SUMMARY The genetic, epigenetic, and gene regulatory mechanisms underlying how hormone signal transduction influences erythroid gene expression remains only partly understood. A detailed understanding of these molecular pathways and how they intersect with one another will provide the basis for novel strategies to treat anemia and potentially other hematological diseases. As new regulators and signal transducers of EPO-signaling continue to emerge, new clinically relevant targets may be identified that improve the specificity and effectiveness of EPO therapy.
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24
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Liu J, Li Y, Tong J, Gao J, Guo Q, Zhang L, Wang B, Zhao H, Wang H, Jiang E, Kurita R, Nakamura Y, Tanabe O, Engel JD, Bresnick EH, Zhou J, Shi L. Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development. Nat Commun 2018; 9:4386. [PMID: 30349036 PMCID: PMC6197277 DOI: 10.1038/s41467-018-06883-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 10/02/2018] [Indexed: 01/19/2023] Open
Abstract
In addition to serving as a prosthetic group for enzymes and a hemoglobin structural component, heme is a crucial homeostatic regulator of erythroid cell development and function. While lncRNAs modulate diverse physiological and pathological cellular processes, their involvement in heme-dependent mechanisms is largely unexplored. In this study, we elucidated a lncRNA (UCA1)-mediated mechanism that regulates heme metabolism in human erythroid cells. We discovered that UCA1 expression is dynamically regulated during human erythroid maturation, with a maximal expression in proerythroblasts. UCA1 depletion predominantly impairs heme biosynthesis and arrests erythroid differentiation at the proerythroblast stage. Mechanistic analysis revealed that UCA1 physically interacts with the RNA-binding protein PTBP1, and UCA1 functions as an RNA scaffold to recruit PTBP1 to ALAS2 mRNA, which stabilizes ALAS2 mRNA. These results define a lncRNA-mediated posttranscriptional mechanism that provides a new dimension into how the fundamental heme biosynthetic process is regulated as a determinant of erythrocyte development. LncRNAs modulate diverse physiological cellular processes, however, their involvement in heme-dependent processes are not yet clear. Here the authors reveal the role of lncRNA UCA1 in erythroid cell development.
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Affiliation(s)
- Jinhua Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Qing Guo
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lingling Zhang
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Bingrui Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui Zhao
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Hongtao Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ryo Kurita
- Japanese Red Cross Society, Department of Research and Development, Central Blood Institute, Tokyo, 105-8521, Japan
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Cell Engineering Division, Ibaraki, 305-0074, Japan
| | - Osamu Tanabe
- Department of Integrative Genomics Tohoku Medical Megabank, Tohoku University, Sedai, 980-8573, Japan
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emery H Bresnick
- Wisconsin Institutes for Medical Research, Paul Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53562, USA
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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25
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Identification of human glycosyltransferase genes expressed in erythroid cells predicts potential carbohydrate blood group loci. Sci Rep 2018; 8:6040. [PMID: 29662110 PMCID: PMC5902498 DOI: 10.1038/s41598-018-24445-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/08/2018] [Indexed: 01/24/2023] Open
Abstract
Glycans are biologically important structures synthesised by glycosyltransferase (GT) enzymes. Disruptive genetic null variants in GT genes can lead to serious illness but benign phenotypes are also seen, including antigenic differences on the red blood cell (RBC) surface, giving rise to blood groups. To characterise known and potential carbohydrate blood group antigens without a known underlying gene, we searched public databases for human GT loci and investigated their variation in the 1000 Genomes Project (1000 G). We found 244 GT genes, distributed over 44 families. All but four GT genes had missense variants or other variants predicted to alter the amino acid sequence, and 149 GT genes (61%) had variants expected to cause null alleles, often associated with antigen-negative blood group phenotypes. In RNA-Seq data generated from erythroid cells, 155 GT genes were expressed at a transcript level comparable to, or higher than, known carbohydrate blood group loci. Filtering for GT genes predicted to cause a benign phenotype, a set of 30 genes remained, 16 of which had variants in 1000 G expected to result in null alleles. Our results identify potential blood group loci and could serve as a basis for characterisation of the genetic background underlying carbohydrate RBC antigens.
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26
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Morrison TA, Wilcox I, Luo HY, Farrell JJ, Kurita R, Nakamura Y, Murphy GJ, Cui S, Steinberg MH, Chui DHK. A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression. Blood Cells Mol Dis 2018; 69:1-9. [PMID: 29227829 PMCID: PMC5783741 DOI: 10.1016/j.bcmd.2017.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022]
Abstract
The HBS1L-MYB intergenic region (chr6q23) regulates erythroid cell proliferation, maturation, and fetal hemoglobin (HbF) expression. An enhancer element within this locus, highlighted by a 3-bp deletion polymorphism (rs66650371), is known to interact with the promoter of the neighboring gene, MYB, to increase its expression, thereby regulating HbF production. RNA polymerase II binding and a 50-bp transcript from this enhancer region reported in ENCODE datasets suggested the presence of a long noncoding RNA (lncRNA). We characterized a novel 1283bp transcript (HMI-LNCRNA; chr6:135,096,362-135,097,644; hg38) that was transcribed from the enhancer region of MYB. Within erythroid cells, HMI-LNCRNA was almost exclusively present in nucleus, and was much less abundant than the mRNA for MYB. HMI-LNCRNA expression was significantly higher in erythroblasts derived from cultured adult peripheral blood CD34+ cells which expressed more HBB, compared to erythroblasts from cultured cord blood CD34+ cells which expressed much more HBG. Down-regulation of HMI-LNCRNA in HUDEP-2 cells, which expressed mostly HBB, significantly upregulated HBG expression both at the mRNA (200-fold) and protein levels, and promoted erythroid maturation. No change was found in the expression of BCL11A and other key transcription factors known to modulate HBG expression. HMI-LNCRNA plays an important role in regulating HBG expression, and its downregulation can result in a significant increase in HbF. HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia.
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Affiliation(s)
- Tasha A Morrison
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ibifiri Wilcox
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Hong-Yuan Luo
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - John J Farrell
- Department of Medicine, Section of Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - George J Murphy
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Shuaiying Cui
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Martin H Steinberg
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA 02118, USA; Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - David H K Chui
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA 02118, USA; Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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27
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Abstract
PURPOSE OF REVIEW Erythroid progenitors must accurately and efficiently splice thousands of pre-mRNAs as the cells undergo extensive changes in gene expression and cellular remodeling during terminal erythropoiesis. Alternative splicing choices are governed by interactions between RNA binding proteins and cis-regulatory binding motifs in the RNA. This review will focus on recent studies that define the genome-wide scope of splicing in erythroblasts and discuss what is known about its regulation. RECENT FINDINGS RNA-seq analysis of highly purified erythroblast populations has revealed an extensive program of alternative splicing of both exons and introns. During normal erythropoiesis, stage-specific splicing transitions alter the structure and abundance of protein isoforms required for optimized red cell production. Mutation or deficiency of splicing regulators underlies hematopoietic disease in myelopdysplasia syndrome patients via disrupting the splicing program. SUMMARY Erythroid progenitors execute an elaborate alternative splicing program that modulates gene expression posttranscriptionally, ultimately regulating the structure and function of the proteome in a differentiation stage-specific manner during terminal erythropoiesis. This program helps drive differentiation and ensure synthesis of the proper protein isoforms required to produce mechanically stable red cells. Mutation or deficiency of key splicing regulatory proteins disrupts the splicing program to cause disease.
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The orphan nuclear receptor TR4 regulates erythroid cell proliferation and maturation. Blood 2017; 130:2537-2547. [PMID: 29018082 DOI: 10.1182/blood-2017-05-783159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
The orphan nuclear receptors TR4 (NR2C2) and TR2 (NR2C1) are the DNA-binding subunits of the macromolecular complex, direct repeat erythroid-definitive, which has been shown to repress ε- and γ-globin transcription during adult definitive erythropoiesis. Previous studies implied that TR2 and TR4 act largely in a redundant manner during erythroid differentiation; however, during the course of routine genetic studies, we observed multiple variably penetrant phenotypes in the Tr4 mutants, suggesting that indirect effects of the mutation might be masked by multiple modifying genes. To test this hypothesis, Tr4+/- mutant mice were bred into a congenic C57BL/6 background and their phenotypes were reexamined. Surprisingly, we found that homozygous Tr4 null mutant mice expired early during embryogenesis, around embryonic day 7.0, and well before erythropoiesis commences. We further found that Tr4+/- erythroid cells failed to fully differentiate and exhibited diminished proliferative capacity. Analysis of Tr4+/- mutant erythroid cells revealed that reduced TR4 abundance resulted in decreased expression of genes required for heme biosynthesis and erythroid differentiation (Alad and Alas2), but led to significantly increased expression of the proliferation inhibitory factor, cyclin dependent kinase inhibitor (Cdkn1c) These studies support a vital role for TR4 in promoting erythroid maturation and proliferation, and demonstrate that TR4 and TR2 execute distinct, individual functions during embryogenesis and erythroid differentiation.
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29
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Distinct roles for TET family proteins in regulating human erythropoiesis. Blood 2017; 129:2002-2012. [PMID: 28167661 DOI: 10.1182/blood-2016-08-736587] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/29/2017] [Indexed: 12/17/2022] Open
Abstract
The ten-eleven translocation (TET) family of proteins plays important roles in a wide range of biological processes by oxidizing 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine. However, their function in erythropoiesis has remained unclear. We show here that TET2 and TET3 but not TET1 are expressed in human erythroid cells, and we explore the role of these proteins in erythropoiesis. Knockdown experiments revealed that TET2 and TET3 have different functions. Suppression of TET3 expression in human CD34+ cells markedly impaired terminal erythroid differentiation, as reflected by increased apoptosis, the generation of bi/multinucleated polychromatic/orthochromatic erythroblasts, and impaired enucleation, although without effect on erythroid progenitors. In marked contrast, TET2 knockdown led to hyper-proliferation and impaired differentiation of erythroid progenitors. Surprisingly, knockdown of neither TET2 nor TET3 affected global levels of 5mC. Thus, our findings have identified distinct roles for TET2 and TET3 in human erythropoiesis, and provide new insights into their role in regulating human erythroid differentiation at distinct stages of development. Moreover, because knockdown of TET2 recapitulates certain features of erythroid development defects characteristic of myelodysplastic syndromes (MDSs), and the TET2 gene mutation is one of the most common mutations in MDS, our findings may be relevant for improved understanding of dyserythropoiesis of MDS.
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30
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Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biol 2016; 17:222. [PMID: 27782827 PMCID: PMC5080738 DOI: 10.1186/s13059-016-1077-y] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/04/2016] [Indexed: 12/26/2022] Open
Abstract
The ability to quantify cellular heterogeneity is a major advantage of single-cell technologies. However, statistical methods often treat cellular heterogeneity as a nuisance. We present a novel method to characterize differences in expression in the presence of distinct expression states within and among biological conditions. We demonstrate that this framework can detect differential expression patterns under a wide range of settings. Compared to existing approaches, this method has higher power to detect subtle differences in gene expression distributions that are more complex than a mean shift, and can characterize those differences. The freely available R package scDD implements the approach.
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Affiliation(s)
- Keegan D Korthauer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, University of Wisconsin, Madison, 53706, WI, USA
| | - Michael A Newton
- Department of Biostatistics, University of Wisconsin, Madison, 53706, WI, USA.,Department of Statistics, University of Wisconsin, Madison, 53706, WI, USA
| | - Yuan Li
- Department of Statistics, University of Wisconsin, Madison, 53706, WI, USA
| | - James Thomson
- Morgridge Institute for Research, University of Wisconsin, Madison, 53706, WI, USA.,Department of Cell and Regenerative Biology, University of Wisconsin, Madison, 53706, WI, USA.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, 93106, CA, USA
| | - Ron Stewart
- Morgridge Institute for Research, University of Wisconsin, Madison, 53706, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics, University of Wisconsin, Madison, 53706, WI, USA. .,Department of Statistics, University of Wisconsin, Madison, 53706, WI, USA.
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31
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Merryweather-Clarke AT, Tipping AJ, Lamikanra AA, Fa R, Abu-Jamous B, Tsang HP, Carpenter L, Robson KJH, Nandi AK, Roberts DJ. Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors. BMC Genomics 2016; 17:817. [PMID: 27769165 PMCID: PMC5073849 DOI: 10.1186/s12864-016-3134-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 09/27/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Human-induced pluripotent stem cells (hiPSCs) are a potentially invaluable resource for regenerative medicine, including the in vitro manufacture of blood products. HiPSC-derived red blood cells are an attractive therapeutic option in hematology, yet exhibit unexplained proliferation and enucleation defects that presently preclude such applications. We hypothesised that substantial differential regulation of gene expression during erythroid development accounts for these important differences between hiPSC-derived cells and those from adult or cord-blood progenitors. We thus cultured erythroblasts from each source for transcriptomic analysis to investigate differential gene expression underlying these functional defects. RESULTS Our high resolution transcriptional view of definitive erythropoiesis captures the regulation of genes relevant to cell-cycle control and confers statistical power to deploy novel bioinformatics methods. Whilst the dynamics of erythroid program elaboration from adult and cord blood progenitors were very similar, the emerging erythroid transcriptome in hiPSCs revealed radically different program elaboration compared to adult and cord blood cells. We explored the function of differentially expressed genes in hiPSC-specific clusters defined by our novel tunable clustering algorithms (SMART and Bi-CoPaM). HiPSCs show reduced expression of c-KIT and key erythroid transcription factors SOX6, MYB and BCL11A, strong HBZ-induction, and aberrant expression of genes involved in protein degradation, lysosomal clearance and cell-cycle regulation. CONCLUSIONS Together, these data suggest that hiPSC-derived cells may be specified to a primitive erythroid fate, and implies that definitive specification may more accurately reflect adult development. We have therefore identified, for the first time, distinct gene expression dynamics during erythroblast differentiation from hiPSCs which may cause reduced proliferation and enucleation of hiPSC-derived erythroid cells. The data suggest several mechanistic defects which may partially explain the observed aberrant erythroid differentiation from hiPSCs.
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Affiliation(s)
- Alison T Merryweather-Clarke
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Alex J Tipping
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Abigail A Lamikanra
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK. .,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK.
| | - Rui Fa
- Department of Electronic and Computer Engineering, Brunel University London, Middlesex, UB8 3PH, UK
| | - Basel Abu-Jamous
- Department of Electronic and Computer Engineering, Brunel University London, Middlesex, UB8 3PH, UK
| | - Hoi Pat Tsang
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Lee Carpenter
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK.,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK
| | - Kathryn J H Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headington, OX3 9DU, Oxford, UK
| | - Asoke K Nandi
- Department of Electronic and Computer Engineering, Brunel University London, Middlesex, UB8 3PH, UK.,Distinguished Visiting Professor, The Key Laboratory of Embedded Systems and Service Computing, College of Electronic and Information Engineering, Tongji University, Shanghai, People's Republic of China
| | - David J Roberts
- Radcliffe Department of Medicine, University of Oxford, Headington, Oxford, OX3 9DU, UK. .,National Health Service Blood and Transplant, John Radcliffe Hospital, Headington, Oxford, OX3 9BQ, UK.
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32
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Bonizzato A, Gaffo E, te Kronnie G, Bortoluzzi S. CircRNAs in hematopoiesis and hematological malignancies. Blood Cancer J 2016; 6:e483. [PMID: 27740630 PMCID: PMC5098259 DOI: 10.1038/bcj.2016.81] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
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Affiliation(s)
- A Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
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33
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Sánchez-Taltavull D, Ramachandran P, Lau N, Perkins TJ. Bayesian Correlation Analysis for Sequence Count Data. PLoS One 2016; 11:e0163595. [PMID: 27701449 PMCID: PMC5049778 DOI: 10.1371/journal.pone.0163595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/12/2016] [Indexed: 12/21/2022] Open
Abstract
Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities’ measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low—especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities’ signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset.
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Affiliation(s)
- Daniel Sánchez-Taltavull
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Parameswaran Ramachandran
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Nelson Lau
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Theodore J. Perkins
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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34
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Gautier EF, Ducamp S, Leduc M, Salnot V, Guillonneau F, Dussiot M, Hale J, Giarratana MC, Raimbault A, Douay L, Lacombe C, Mohandas N, Verdier F, Zermati Y, Mayeux P. Comprehensive Proteomic Analysis of Human Erythropoiesis. Cell Rep 2016; 16:1470-1484. [PMID: 27452463 PMCID: PMC5274717 DOI: 10.1016/j.celrep.2016.06.085] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/16/2016] [Accepted: 06/22/2016] [Indexed: 01/13/2023] Open
Abstract
Mass spectrometry-based proteomics now enables the absolute quantification of thousands of proteins in individual cell types. We used this technology to analyze the dynamic proteome changes occurring during human erythropoiesis. We quantified the absolute expression of 6,130 proteins during erythroid differentiation from late burst-forming units-erythroid (BFU-Es) to orthochromatic erythroblasts. A modest correlation between mRNA and protein expression was observed. We identified several proteins with unexpected expression patterns in erythroid cells, highlighting a breakpoint in the erythroid differentiation process at the basophilic stage. We also quantified the distribution of proteins between reticulocytes and pyrenocytes after enucleation. These analyses identified proteins that are actively sorted either with the reticulocyte or the pyrenocyte. Our study provides the absolute quantification of protein expression during a complex cellular differentiation process in humans, and it establishes a framework for future studies of disordered erythropoiesis.
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Affiliation(s)
- Emilie-Fleur Gautier
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France
| | - Sarah Ducamp
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France
| | - Marjorie Leduc
- Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France
| | - Virginie Salnot
- Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France
| | - François Guillonneau
- Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France
| | | | - John Hale
- New York Blood Center, New York, NY 10065, USA
| | - Marie-Catherine Giarratana
- Laboratory of Excellence GReX, 75015 Paris, France; UPMC University Paris 06, UMR_S938 CDR Saint-Antoine, INSERM, Prolifération et Différenciation des Cellules Souches, 75012 Paris, France
| | - Anna Raimbault
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France
| | - Luc Douay
- Laboratory of Excellence GReX, 75015 Paris, France; UPMC University Paris 06, UMR_S938 CDR Saint-Antoine, INSERM, Prolifération et Différenciation des Cellules Souches, 75012 Paris, France
| | - Catherine Lacombe
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France
| | | | - Frédérique Verdier
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France
| | - Yael Zermati
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France
| | - Patrick Mayeux
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France.
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35
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Abstract
Mammalian development is under tight control to ensure precise gene expression. Recent studies reveal a new layer of regulation of gene expression mediated by long noncoding RNAs. These transcripts are longer than 200nt that do not have functional protein coding capacity. Interestingly, many of these long noncoding RNAs are expressed with high specificity in different types of cells, tissues, and developmental stages in mammals, suggesting that they may have functional roles in diverse biological processes. Here, we summarize recent findings of long noncoding RNAs in hematopoiesis, which is one of the best-characterized mammalian cell differentiation processes. Then we provide our own perspectives on future studies of long noncoding RNAs in this field.
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Affiliation(s)
- Xu Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
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36
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Abstract
ASXL1 mutations are found in a spectrum of myeloid malignancies with poor prognosis. Recently, we reported that Asxl1+/− mice develop myelodysplastic syndrome (MDS) or MDS and myeloproliferative neoplasms (MPN) overlapping diseases (MDS/MPN). Although defective erythroid maturation and anemia are associated with the prognosis of patients with MDS or MDS/MPN, the role of ASXL1 in erythropoiesis remains unclear. Here, we showed that chronic myelomonocytic leukemia (CMML) patients with ASXL1 mutations exhibited more severe anemia with a significantly increased proportion of bone marrow (BM) early stage erythroblasts and reduced enucleated erythrocytes compared to CMML patients with WT ASXL1. Knockdown of ASXL1 in cord blood CD34+ cells reduced erythropoiesis and impaired erythrocyte enucleation. Consistently, the BM and spleens of VavCre+;Asxl1f/f (Asxl1∆/∆) mice had less numbers of erythroid progenitors than Asxl1f/f controls. Asxl1∆/∆ mice also had an increased percentage of erythroblasts and a reduced erythrocyte enucleation in their BM compared to littermate controls. Furthermore, Asxl1∆/∆ erythroblasts revealed altered expression of genes involved in erythroid development and homeostasis, which was associated with lower levels of H3K27me3 and H3K4me3. Our study unveils a key role for ASXL1 in erythropoiesis and indicates that ASXL1 loss hinders erythroid development/maturation, which could be of prognostic value for MDS/MPN patients.
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37
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E2F and GATA switches turn off WD repeat domain 77 expression in differentiating cells. Biochem J 2016; 473:2331-43. [PMID: 27274086 DOI: 10.1042/bcj20160130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/06/2016] [Indexed: 02/01/2023]
Abstract
WDR77 (WD repeat domain 77) is expressed during earlier lung development when cells are rapidly proliferating, but is absent from adult lung. It is re-activated during lung tumorigenesis and is essential for lung cancer cell proliferation. Signalling pathways/molecules that control WDR77 gene expression are unknown. Promoter mapping, gel shift assay and ChIP revealed that the WDR77 promoter contains bona fide response elements for E2F and GATA transcriptional factors as demonstrated in prostate cancer, lung cancer and erythroid cells, as well as in mouse lung tissues. The WDR77 promoter is transactivated by E2F1, E2F3, GATA1 and GATA6, but suppressed by E2F6, GATA1 and GATA3 in prostate cancer PC3 cells. WDR77 expression is associated with E2F1, E2F3, GATA2 and GATA6 occupancy on the WDR77 gene, whereas, in contrast, E2F6, GATA1 and GATA3 occupancy is associated with the loss of WDR77 expression during erythroid maturation and lung development. More importantly, the loss of WDR77 expression that results from E2F and GATA switches is required for cellular differentiation of erythroid and lung epithelial cells. In contrast, lung cancer cells avoid post-mitotic differentiation by sustaining WDR77 expression. Altogether, the present study provides a novel molecular mechanism by which WDR77 is regulated during erythroid and lung development and lung tumorigenesis.
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38
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Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res 2015; 44:838-51. [PMID: 26531823 PMCID: PMC4737145 DOI: 10.1093/nar/gkv1168] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/21/2015] [Indexed: 01/22/2023] Open
Abstract
Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentally-dynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ∼50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclear-localized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. We conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.
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Affiliation(s)
- Harold Pimentel
- Department of Computer Science, University of California, Berkeley, CA 94720, USA
| | - Marilyn Parra
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sherry L Gee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY 10065, USA
| | - Lior Pachter
- Department of Mathematics, University of California, Berkeley, CA 94720, USA Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - John G Conboy
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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39
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Zhu F, Panwar B, Guan Y. Algorithms for modeling global and context-specific functional relationship networks. Brief Bioinform 2015; 17:686-95. [PMID: 26254431 DOI: 10.1093/bib/bbv065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 02/07/2023] Open
Abstract
Functional genomics has enormous potential to facilitate our understanding of normal and disease-specific physiology. In the past decade, intensive research efforts have been focused on modeling functional relationship networks, which summarize the probability of gene co-functionality relationships. Such modeling can be based on either expression data only or heterogeneous data integration. Numerous methods have been deployed to infer the functional relationship networks, while most of them target the global (non-context-specific) functional relationship networks. However, it is expected that functional relationships consistently reprogram under different tissues or biological processes. Thus, advanced methods have been developed targeting tissue-specific or developmental stage-specific networks. This article brings together the state-of-the-art functional relationship network modeling methods, emphasizes the need for heterogeneous genomic data integration and context-specific network modeling and outlines future directions for functional relationship networks.
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40
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The LSD1 inhibitor RN-1 induces fetal hemoglobin synthesis and reduces disease pathology in sickle cell mice. Blood 2015; 126:386-96. [PMID: 26031919 DOI: 10.1182/blood-2015-02-626259] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/22/2015] [Indexed: 12/30/2022] Open
Abstract
Inhibition of lysine-specific demethylase 1 (LSD1) has been shown to induce fetal hemoglobin (HbF) levels in cultured human erythroid cells in vitro. Here we report the in vivo effects of LSD1 inactivation by a selective and more potent inhibitor, RN-1, in a sickle cell disease (SCD) mouse model. Compared with untreated animals, RN-1 administration leads to induced HbF synthesis and to increased frequencies of HbF-positive cells and mature erythrocytes, as well as fewer reticulocytes and sickle cells, in the peripheral blood of treated SCD mice. In keeping with these observations, histologic analyses of the liver and spleen of treated SCD mice verified that they do not exhibit the necrotic lesions that are usually associated with SCD. These data indicate that RN-1 can effectively induce HbF levels in red blood cells and reduce disease pathology in SCD mice, and may therefore offer new therapeutic possibilities for treating SCD.
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Zhu F, Shi L, Engel JD, Guan Y. Regulatory network inferred using expression data of small sample size: application and validation in erythroid system. Bioinformatics 2015; 31:2537-44. [PMID: 25840044 DOI: 10.1093/bioinformatics/btv186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 03/27/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Modeling regulatory networks using expression data observed in a differentiation process may help identify context-specific interactions. The outcome of the current algorithms highly depends on the quality and quantity of a single time-course dataset, and the performance may be compromised for datasets with a limited number of samples. RESULTS In this work, we report a multi-layer graphical model that is capable of leveraging many publicly available time-course datasets, as well as a cell lineage-specific data with small sample size, to model regulatory networks specific to a differentiation process. First, a collection of network inference methods are used to predict the regulatory relationships in individual public datasets. Then, the inferred directional relationships are weighted and integrated together by evaluating against the cell lineage-specific dataset. To test the accuracy of this algorithm, we collected a time-course RNA-Seq dataset during human erythropoiesis to infer regulatory relationships specific to this differentiation process. The resulting erythroid-specific regulatory network reveals novel regulatory relationships activated in erythropoiesis, which were further validated by genome-wide TR4 binding studies using ChIP-seq. These erythropoiesis-specific regulatory relationships were not identifiable by single dataset-based methods or context-independent integrations. Analysis of the predicted targets reveals that they are all closely associated with hematopoietic lineage differentiation.
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Affiliation(s)
- Fan Zhu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | | | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA, Department of Internal Medicine, and Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
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Lessard S, Beaudoin M, Benkirane K, Lettre G. Comparison of DNA methylation profiles in human fetal and adult red blood cell progenitors. Genome Med 2015; 7:1. [PMID: 25606059 PMCID: PMC4298057 DOI: 10.1186/s13073-014-0122-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/09/2014] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation is an epigenetic modification that plays an important role during mammalian development. Around birth in humans, the main site of red blood cell production moves from the fetal liver to the bone marrow. DNA methylation changes at the β-globin locus and a switch from fetal to adult hemoglobin production characterize this transition. Understanding this globin switch may improve the treatment of patients with sickle cell disease and β-thalassemia, two of the most common Mendelian diseases in the world. The goal of our study was to describe and compare the genome-wide patterns of DNA methylation in fetal and adult human erythroblasts. Methods We used the Illumina HumanMethylation 450 k BeadChip to measure DNA methylation at 402,819 CpGs in ex vivo-differentiated erythroblasts from 12 fetal liver and 12 bone marrow CD34+ donors. Results We identified 5,937 differentially methylated CpGs that overlap with erythroid enhancers and binding sites for erythropoiesis-related transcription factors. Combining this information with genome-wide association study results, we show that erythroid enhancers define particularly promising genomic regions to identify new genetic variants associated with fetal hemoglobin (HbF) levels in humans. Many differentially methylated CpGs are located near genes with unanticipated roles in red blood cell differentiation and proliferation. For some of these new candidate genes, we confirm the correlation between DNA methylation and gene expression levels in red blood cell progenitors. We also provide evidence that DNA methylation and genetic variation at the β-globin locus independently control globin gene expression in adult erythroblasts. Conclusions Our DNA methylome maps confirm the widespread dynamic changes in DNA methylation that occur during human erythropoiesis. These changes tend to happen near erythroid enhancers, further highlighting their importance in erythroid regulation and HbF production. Finally, DNA methylation may act independently of the transcription factor BCL11A to repress fetal hemoglobin production. This provides cues on strategies to more efficiently re-activate HbF production in sickle cell disease and β-thalassemia patients. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0122-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel Lessard
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada ; Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, Québec H3T 1J4 Canada
| | - Mélissa Beaudoin
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada
| | - Karim Benkirane
- Hôpital Maisonneuve-Rosemont, 5415 Boul. de l'Assomption, Montréal, Québec H1T 2M4 Canada
| | - Guillaume Lettre
- Montreal Heart Institute, 5000 Bélanger Street, Montréal, Québec H1T 1C8 Canada ; Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, Québec H3T 1J4 Canada
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Compound loss of function of nuclear receptors Tr2 and Tr4 leads to induction of murine embryonic β-type globin genes. Blood 2015; 125:1477-87. [PMID: 25561507 DOI: 10.1182/blood-2014-10-605022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The orphan nuclear receptors TR2 and TR4 have been shown to play key roles in repressing the embryonic and fetal globin genes in erythroid cells. However, combined germline inactivation of Tr2 and Tr4 leads to periimplantation lethal demise in inbred mice. Hence, we have previously been unable to examine the consequences of their dual loss of function in adult definitive erythroid cells. To circumvent this issue, we generated conditional null mutants in both genes and performed gene inactivation in vitro in adult bone marrow cells. Compound Tr2/Tr4 loss of function led to induced expression of the embryonic εy and βh1 globins (murine counterparts of the human ε- and γ-globin genes). Additionally, TR2/TR4 function is required for terminal erythroid cell maturation. Loss of TR2/TR4 abolished their occupancy on the εy and βh1 gene promoters, and concurrently impaired co-occupancy by interacting corepressors. These data strongly support the hypothesis that the TR2/TR4 core complex is an adult stage-specific, gene-selective repressor of the embryonic globin genes. Detailed mechanistic understanding of the roles of TR2/TR4 and their cofactors in embryonic and fetal globin gene repression may ultimately enhance the discovery of novel therapeutic agents that can effectively inhibit their transcriptional activity and be safely applied to the treatment of β-globinopathies.
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Zhu F, Shi L, Li H, Eksi R, Engel JD, Guan Y. Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. ACTA ACUST UNITED AC 2014; 30:3325-33. [PMID: 25115705 DOI: 10.1093/bioinformatics/btu542] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
MOTIVATION Functional relationship networks, which summarize the probability of co-functionality between any two genes in the genome, could complement the reductionist focus of modern biology for understanding diverse biological processes in an organism. One major limitation of the current networks is that they are static, while one might expect functional relationships to consistently reprogram during the differentiation of a cell lineage. To address this potential limitation, we developed a novel algorithm that leverages both differentiation stage-specific expression data and large-scale heterogeneous functional genomic data to model such dynamic changes. We then applied this algorithm to the time-course RNA-Seq data we collected for ex vivo human erythroid cell differentiation. RESULTS Through computational cross-validation and literature validation, we show that the resulting networks correctly predict the (de)-activated functional connections between genes during erythropoiesis. We identified known critical genes, such as HBD and GATA1, and functional connections during erythropoiesis using these dynamic networks, while the traditional static network was not able to provide such information. Furthermore, by comparing the static and the dynamic networks, we identified novel genes (such as OSBP2 and PDZK1IP1) that are potential drivers of erythroid cell differentiation. This novel method of modeling dynamic networks is applicable to other differentiation processes where time-course genome-scale expression data are available, and should assist in generating greater understanding of the functional dynamics at play across the genome during development. AVAILABILITY AND IMPLEMENTATION The network described in this article is available at http://guanlab.ccmb.med.umich.edu/stageSpecificNetwork.
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Affiliation(s)
- Fan Zhu
- Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA
| | - Lihong Shi
- Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA
| | - Hongdong Li
- Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA
| | - Ridvan Eksi
- Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA
| | - James Douglas Engel
- Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA Department of Computational Medicine and Bioinformatics, Department of Cell and Developmental Biology, Department of Internal Medicine and Department of Computer Science and Engineering, University of Michigan, MI48109, USA
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Fetal globin gene repressors as drug targets for molecular therapies to treat the β-globinopathies. Mol Cell Biol 2014; 34:3560-9. [PMID: 25022757 DOI: 10.1128/mcb.00714-14] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human β-globin locus is comprised of embryonic, fetal, and adult globin genes that are expressed in a developmental stage-specific manner. Mutations in the globin locus give rise to the β-globinopathies, β-thalassemia and sickle cell disease, which begin to manifest symptoms around the time of birth. Although the fetal globin genes are autonomously silenced in adult-stage erythroid cells, mutations lying both within and outside the locus lead to natural variations in the level of fetal globin gene expression, and some of these significantly ameliorate the clinical symptoms of the β-globinopathies. Multiple reports have now identified several transcription factors that are involved in fetal globin gene repression in definitive (adult)-stage erythroid cells (the TR2/TR4 heterodimer, MYB, KLFs, BCL11A, and SOX6). To carry out their repression functions, chromatin-modifying enzymes (such as DNA methyltransferase, histone deacetylases, and lysine-specific histone demethylase 1) are additionally involved as a consequence of forming large macromolecular complexes with the DNA-binding subunits of these cellular machines. This review focuses on the molecular mechanisms underlying fetal globin gene silencing and possible near-future molecularly targeted therapies for treating the β-globinopathies.
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