1
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Thankam FG, La V, Agrawal DK. Single-cell genomics illustrates heterogeneous phenotypes of myocardial fibroblasts under ischemic insults. Biochem Cell Biol 2023; 101:12-51. [PMID: 36458696 DOI: 10.1139/bcb-2022-0229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myocardial regenerative strategies are promising where the choice of ideal cell population is crucial for successful translational applications. Herein, we explored the regenerative/repair responses of infarct zone cardiac fibroblast(s) (CF) by unveiling their phenotype heterogeneity at single-cell resolution. CF were isolated from the infarct zone of Yucatan miniswine that suffered myocardial infarction, cultured under simulated ischemic and reperfusion, and grouped into control, ischemia, and ischemia/reperfusion. The single-cell RNA sequencing analysis revealed 19 unique cell clusters suggesting distinct subpopulations. The status of gene expression (log2 fold change (log2 FC) > 2 and log2 FC < -2) was used to define the characteristics of each cluster unveiling with diverse features, including the pro-survival/cardioprotective (Clusters 1, 3, 5, 9, and 18), vasculoprotective (Clusters 2 and 5), anti-inflammatory (Clusters 4 and 17), proliferative (Clusters 4 and 5), nonproliferative (Clusters 6, 8, 11, 16, 17, and 18), proinflammatory (Cluster 6), profibrotic/pathologic (Clusters 8 and 19), antihypertrophic (Clusters 8 and 10), extracellular matrix restorative (Clusters 9 and 12), angiogenic (Cluster 16), and normal (Clusters 7 and 15) phenotypes. Further understanding of these unique phenotypes of CF will provide significant translational opportunities for myocardial regeneration and cardiac management.
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Affiliation(s)
- Finosh G Thankam
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Vy La
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, Pomona, CA 91766, USA
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2
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Thankam FG, Agrawal DK. Single Cell Genomics Identifies Unique Cardioprotective Phenotype of Stem Cells derived from Epicardial Adipose Tissue under Ischemia. Stem Cell Rev Rep 2021; 18:294-335. [PMID: 34661829 DOI: 10.1007/s12015-021-10273-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 12/21/2022]
Abstract
The conventional management strategies of myocardial infarction (MI) are effective to sustain life; however, myocardial regeneration has not been achieved owing to the inherently poor regenerative capacity of the native myocardium. Stem cell-based therapies are promising; however, lineage specificity and undesired differentiation profile are challenging. Herein, we focused on the epicardial fat (EF) as an ideal source for mesenchymal stem cells (MSCs) owing to the proximity and same microvasculature with cardiac muscle. Unfortunately, the epicardial adipose tissue derived stem cells (EATDS) remain understudied regarding their phenotype heterogeneity and cardiac regeneration potential. As EF closely reflects the cardiac pathology during ischemia, the present study aims to determine the EATDS subpopulations under simulated ischemic and reperfused conditions employing single cell RNA sequencing (scRNAseq). EATDS were isolated from three hyperlipidemic Yucatan microswine and were divided into Control, Ischemia (ISC), and Ischemia/reperfusion (ISC/R). The scRNAseq analysis was performed using 10 genomics platform which revealed 18 unique cell clusters suggesting the existence of heterogeneous phenotypes. The upregulated genes were taken into consideration and subsequent functional assessment revealed the cardioprotective phenotypes with diverse mechanisms including epigenetic regulation (Cluster 1), myocardial homeostasis (Cluster 1), cell integrity and cell cycle (Clusters 2 and 3), prevention of fibroblast differentiation (Cluster 4), differentiation to myocardial lineage (Cluster 6), anti-inflammatory responses (Clusters 5, 8, and 11), prevention of ER-stress (Cluster 9), and increasing the energy metabolism (Cluster 10). These unique phenotypes of heterogeneous EATDS population open significant translational opportunities for myocardial regeneration and cardiac management.
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Affiliation(s)
- Finosh G Thankam
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA.
| | - Devendra K Agrawal
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA, 91766-1854, USA
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3
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Single-Cell Transcriptome Analysis of Human Adipose-Derived Stromal Cells Identifies a Contractile Cell Subpopulation. Stem Cells Int 2021; 2021:5595172. [PMID: 34007285 PMCID: PMC8102097 DOI: 10.1155/2021/5595172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/15/2021] [Accepted: 03/27/2021] [Indexed: 12/02/2022] Open
Abstract
The potential for human adipose-derived stromal cells (hASCs) to be used as a therapeutic product is being assessed in multiple clinical trials. However, much is still to be learned about these cells before they can be used with confidence in the clinical setting. An inherent characteristic of hASCs that is not well understood is their heterogeneity. The aim of this exploratory study was to characterize the heterogeneity of freshly isolated hASCs after two population doublings (P2) using single-cell transcriptome analysis. A minimum of two subpopulations were identified at P2. A major subpopulation was identified as contractile cells which, based on gene expression patterns, are likely to be pericytes and/or vascular smooth muscle cells (vSMCs).
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4
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Derakhshani A, Rostami Z, Safarpour H, Shadbad MA, Nourbakhsh NS, Argentiero A, Taefehshokr S, Tabrizi NJ, Kooshkaki O, Astamal RV, Singh PK, Taefehshokr N, Alizadeh N, Silvestris N, Baradaran B. From Oncogenic Signaling Pathways to Single-Cell Sequencing of Immune Cells: Changing the Landscape of Cancer Immunotherapy. Molecules 2021; 26:2278. [PMID: 33920054 PMCID: PMC8071039 DOI: 10.3390/molecules26082278] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/09/2021] [Accepted: 04/09/2021] [Indexed: 12/19/2022] Open
Abstract
Over the past decade, there have been remarkable advances in understanding the signaling pathways involved in cancer development. It is well-established that cancer is caused by the dysregulation of cellular pathways involved in proliferation, cell cycle, apoptosis, cell metabolism, migration, cell polarity, and differentiation. Besides, growing evidence indicates that extracellular matrix signaling, cell surface proteoglycans, and angiogenesis can contribute to cancer development. Given the genetic instability and vast intra-tumoral heterogeneity revealed by the single-cell sequencing of tumoral cells, the current approaches cannot eliminate the mutating cancer cells. Besides, the polyclonal expansion of tumor-infiltrated lymphocytes in response to tumoral neoantigens cannot elicit anti-tumoral immune responses due to the immunosuppressive tumor microenvironment. Nevertheless, the data from the single-cell sequencing of immune cells can provide valuable insights regarding the expression of inhibitory immune checkpoints/related signaling factors in immune cells, which can be used to select immune checkpoint inhibitors and adjust their dosage. Indeed, the integration of the data obtained from the single-cell sequencing of immune cells with immune checkpoint inhibitors can increase the response rate of immune checkpoint inhibitors, decrease the immune-related adverse events, and facilitate tumoral cell elimination. This study aims to review key pathways involved in tumor development and shed light on single-cell sequencing. It also intends to address the shortcomings of immune checkpoint inhibitors, i.e., their varied response rates among cancer patients and increased risk of autoimmunity development, via applying the data from the single-cell sequencing of immune cells.
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Affiliation(s)
- Afshin Derakhshani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65811, Iran; (A.D.); (M.A.S.); (S.T.); (N.J.T.); (R.V.A.); (N.A.)
- IRCCS Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy;
| | - Zeinab Rostami
- Student Research Committee, Birjand University of Medical Sciences, Birjand 97178-53577, Iran; (Z.R.); (O.K.)
| | - Hossein Safarpour
- Cellular & Molecular Research Center, Birjand University of Medical Sciences, Birjand 97178-53577, Iran;
| | - Mahdi Abdoli Shadbad
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65811, Iran; (A.D.); (M.A.S.); (S.T.); (N.J.T.); (R.V.A.); (N.A.)
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz 51666-14766, Iran
| | | | | | - Sina Taefehshokr
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65811, Iran; (A.D.); (M.A.S.); (S.T.); (N.J.T.); (R.V.A.); (N.A.)
| | - Neda Jalili Tabrizi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65811, Iran; (A.D.); (M.A.S.); (S.T.); (N.J.T.); (R.V.A.); (N.A.)
| | - Omid Kooshkaki
- Student Research Committee, Birjand University of Medical Sciences, Birjand 97178-53577, Iran; (Z.R.); (O.K.)
| | - Reza Vaezi Astamal
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65811, Iran; (A.D.); (M.A.S.); (S.T.); (N.J.T.); (R.V.A.); (N.A.)
| | - Pankaj Kumar Singh
- Principal Research Technologist, Department of Radiation Oncology, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL 32224, USA;
| | - Nima Taefehshokr
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, ON N6A 5C1, Canada;
| | - Nazila Alizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65811, Iran; (A.D.); (M.A.S.); (S.T.); (N.J.T.); (R.V.A.); (N.A.)
| | - Nicola Silvestris
- IRCCS Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy;
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65811, Iran; (A.D.); (M.A.S.); (S.T.); (N.J.T.); (R.V.A.); (N.A.)
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 51666-14766, Iran
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5
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Wu D, Liu X, Zhang J, Li L, Wang X. Significance of single-cell and spatial transcriptomes in cell biology and toxicology. Cell Biol Toxicol 2021; 37:1-5. [PMID: 33398619 DOI: 10.1007/s10565-020-09576-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Duojiao Wu
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Xiaozhuan Liu
- Clinical Center for Single Cell Biomedicine, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiaqiang Zhang
- Clinical Center for Single Cell Biomedicine, People's Hospital of Zhengzhou University, Zhengzhou, China. .,Department of Anesthesiology and Perioperative Medicine, Henan Province People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China.
| | - Li Li
- Clinical Center for Single Cell Biomedicine, People's Hospital of Zhengzhou University, Zhengzhou, China.
| | - Xiangdong Wang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China.
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6
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DNA Methylation in Pulmonary Fibrosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:51-62. [PMID: 32949389 DOI: 10.1007/978-981-15-4494-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DNA methylations, including global methylation pattern and specific gene methylation, are associated with pathogenesis and progress of pulmonary fibrosis. This chapter illustrates alteration of DNA methylation in pulmonary fibrosis as a predictive or prognostic factor. Treatment with the DNA methylation inhibitors will be an emerging anti-fibrosis therapy, although we are still in the pre-clinical stage of using epigenetic markers as potential targets for biomarkers and therapeutic interventions.
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7
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Wang W, Wang X. A refocus on the advances of single-cell biomedicine. Cell Biol Toxicol 2020; 36:395-398. [PMID: 32779088 PMCID: PMC7417105 DOI: 10.1007/s10565-020-09551-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022]
Affiliation(s)
- William Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Shanghai Medical College, Shanghai, China.
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8
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Kamies R, Martinez-Jimenez CP. Advances of single-cell genomics and epigenomics in human disease: where are we now? Mamm Genome 2020; 31:170-180. [PMID: 32270277 PMCID: PMC7368869 DOI: 10.1007/s00335-020-09834-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
Abstract
Cellular heterogeneity is revolutionizing the way to study, monitor and dissect complex diseases. This has been possible with the technological and computational advances associated to single-cell genomics and epigenomics. Deeper understanding of cell-to-cell variation and its impact on tissue function will open new avenues for early disease detection, accurate diagnosis and personalized treatments, all together leading to the next generation of health care. This review focuses on the recent discoveries that single-cell genomics and epigenomics have facilitated in the context of human health. It highlights the potential of single-cell omics to further advance the development of personalized treatments and precision medicine in cancer, diabetes and chronic age-related diseases. The promise of single-cell technologies to generate new insights about the differences in function between individual cells is just emerging, and it is paving the way for identifying biomarkers and novel therapeutic targets to tackle age, complex diseases and understand the effect of life style interventions and environmental factors.
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Affiliation(s)
- Rizqah Kamies
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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9
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Zeng Y, Wang X, Zhang J. Single-cell biomedicine: roles of single-cell nuclear elements. Cell Biol Toxicol 2020; 36:1-3. [PMID: 32008122 DOI: 10.1007/s10565-020-09515-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 01/24/2020] [Indexed: 12/17/2022]
Abstract
Single-cell biomedicine, a new merging discipline of cell biology and medicine to improve the life quality of patients, gains high priority in cell biology and toxicology. Single-cell nuclear elements are specially focused and headlined to understand regulatory mechanisms by which transcriptional factors, DNA elements, and genome organization interact with each other and contribute to the developmental evolution and dynamic formation of genotoxicity. Cell molecular phenomics, clonal genotypes, and structural metamorphoses during the cell cycle at single-cell level provide deep insights to understanding mechanism-based bridges between cell biology and toxicology, between cell sensitive and resistance, and between chronic diseases and cancer.
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Affiliation(s)
- Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Xiangdong Wang
- Centre for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University Shanghai Medical College, Shanghai, China.
| | - Jiaqiang Zhang
- Department of Anesthesiology and Perioperative Medicine, Center for Clinical Single Cell Biomedicine, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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10
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Yan F, Su L, Chen X, Wang X, Gao H, Zeng Y. Molecular regulation and clinical significance of caveolin-1 methylation in chronic lung diseases. Clin Transl Med 2020; 10:151-160. [PMID: 32508059 PMCID: PMC7240871 DOI: 10.1002/ctm2.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/15/2022] Open
Abstract
Chronic lung diseases represent a largely global burden whose pathogenesis remains largely unknown. Research increasingly suggests that epigenetic modifications, especially DNA methylation, play a mechanistic role in chronic lung diseases. DNA methylation can affect gene expression and induce various diseases. Of the caveolae in plasma membrane of cell, caveolin-1 (Cav-1) is a crucial structural constituent involved in many important life activities. With the increasingly advanced progress of genome-wide methylation sequencing technologies, the important impact of Cav-1 DNA methylation has been discovered. The present review overviews the biological characters, functions, and structure of Cav-1; epigenetic modifications of Cav-1 in health and disease; expression and regulation of Cav-1 DNA methylation in the respiratory system and its significance; as well as clinical potential as disease-specific biomarker and targets for early diagnosis and therapy.
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Affiliation(s)
- Furong Yan
- Clinical Center for Molecular Diagnosis and TherapySecond Affiliated Hospital of Fujian Medical UniversityQuanzhouFujianChina
| | - Lili Su
- Clinical Center for Molecular Diagnosis and TherapySecond Affiliated Hospital of Fujian Medical UniversityQuanzhouFujianChina
| | - Xiaoyang Chen
- Department of Pulmonary and Critical Care MedicineRespiratory Medicine Center of Fujian ProvinceSecond Affiliated Hospital of Fujian Medical UniversityQuanzhouFujianChina
| | - Xiangdong Wang
- Clinical Center for Molecular Diagnosis and TherapySecond Affiliated Hospital of Fujian Medical UniversityQuanzhouFujianChina
| | - Hongzhi Gao
- Clinical Center for Molecular Diagnosis and TherapySecond Affiliated Hospital of Fujian Medical UniversityQuanzhouFujianChina
| | - Yiming Zeng
- Department of Pulmonary and Critical Care MedicineRespiratory Medicine Center of Fujian ProvinceSecond Affiliated Hospital of Fujian Medical UniversityQuanzhouFujianChina
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11
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Understanding Diseases from Single-Cell Sequencing and Methylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:1-6. [PMID: 32949386 DOI: 10.1007/978-981-15-4494-1_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Clinical single-cell biomedicine has become a new emerging discipline, which integrates single-cell RNA and DNA sequencing, proteomics, and functions with clinical phenomes, therapeutic responses, and prognosis. It is of great value to discover disease-, phenome-, and therapy-specific diagnostic biomarkers and therapeutic targets on the basis of the principle of clinical single-cell biomedicine. This book reviews the roles of single-cell sequencing and methylation in diseases and explores disease-specific alterations of single-cell sequencing and methylation, especially focusing on potential applications of methodologies on human single-cell sequencing and methylation, on potential correlations between those changes with pulmonary diseases, and on potential roles of signaling pathways that cause heterogeneous cellular responses during treatment. This book also emphasizes the importance of methodologies in clinical practice and application, the potential of perspectives, challenges and solutions, and the significance of single-cell preparation standardization. Alterations of DNA and RNA methylation, demethylation in lung diseases, and a deep knowledge about the regulation and function of target gene methylation for diagnosing and treating diseases at the early stage are also provided. Importantly, this book aims to apply the measurement of single-cell sequencing and methylation for clinical diagnosis and treatment and to understand clinical values of those parameters and to headline and foresee the potential values of the application of single-cell sequencing in non-cancer diseases.
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12
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Yan F, Wang W, Zhang J. CRISPR-Cas12 and Cas13: the lesser known siblings of CRISPR-Cas9. Cell Biol Toxicol 2019; 35:489-492. [PMID: 31468291 DOI: 10.1007/s10565-019-09489-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 08/04/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Fancheng Yan
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - William Wang
- Department of Anaesthesiology, Centre for Clinical Single Cell Biomedicine, Henan provincial People's Hospital, People's hospital of Zhengzhou University, Zhengzhou, China
| | - Jiaqiang Zhang
- Department of Anaesthesiology, Centre for Clinical Single Cell Biomedicine, Henan provincial People's Hospital, People's hospital of Zhengzhou University, Zhengzhou, China.
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13
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Zhu Z, Wang X. Roles of cohesin in chromosome architecture and gene expression. Semin Cell Dev Biol 2019; 90:187-193. [PMID: 30096363 DOI: 10.1016/j.semcdb.2018.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/06/2018] [Indexed: 12/18/2022]
Abstract
Cohesin-mediated chromatin organization plays an important role in formation and stabilization of chromosome architecture and gene regulation. Mechanisms by which cohesin shapes chromosome and regulates gene expression remain unclear. The present article overviews biological characters and functions of cohesin and core subunits and explores roles of regulatory factors (e.g. Pds5, Wapl, and Eco1) in dynamic behaviors of cohesin. Cohesin interacts with CCCTC binding factor (CTCF) and other factors to maintain and stabilize multi-dimensional organizations of topological loops and distances between sites during cell segmentation. We also describe functional roles of cohesin in cell cycle by entrapping sister chromatids to form embrace and handcuff models, loading onto chromatin, establishing cohesion function, and regulating removal of cohesin and associated factors from the chromosome arm through prophase pathway or at onset of anaphase. It is questioned whether those factors associated with cohesin-regulated processes can be identified as biology- or disease-specific biomarkers and druggable targets to dynamically monitor changes during phasing, staging, progressing, and responding of diseases. It is also expected to explore heterogenetic roles of cohesin between single cells and regulatory roles of cohesin in trans-omic profiles and functions. Further understanding of cohesin functions will be beneficial to improve diagnosis and treatment of cohesinopathies.
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Affiliation(s)
- Zhenhua Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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14
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Qian M, Cheng Y, Wang X. The methodology study of three-dimensional (3D) genome research. Semin Cell Dev Biol 2019; 90:12-18. [DOI: 10.1016/j.semcdb.2018.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/12/2022]
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15
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Wang DC, Wang W, Zhang L, Wang X. A tour of 3D genome with a focus on CTCF. Semin Cell Dev Biol 2019; 90:4-11. [PMID: 30031214 DOI: 10.1016/j.semcdb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.
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Affiliation(s)
- Diane C Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - William Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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16
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Hou J, Wang X. The polycomb group proteins functions in epithelial to mesenchymal transition in lung cancer. Semin Cell Dev Biol 2019; 90:138-143. [DOI: 10.1016/j.semcdb.2018.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 07/08/2018] [Indexed: 12/29/2022]
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17
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Fu S, Zhang L, Lv J, Zhu B, Wang W, Wang X. Two main stream methods analysis and visual 3D genome architecture. Semin Cell Dev Biol 2019; 90:43-53. [DOI: 10.1016/j.semcdb.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 01/07/2023]
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18
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Wang DC, Wang X. Off-target genome editing: A new discipline of gene science and a new class of medicine. Cell Biol Toxicol 2019; 35:179-183. [DOI: 10.1007/s10565-019-09475-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 04/18/2019] [Indexed: 12/19/2022]
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Zhang Q, Caudle WM, Pi J, Bhattacharya S, Andersen ME, Kaminski NE, Conolly RB. Embracing Systems Toxicology at Single-Cell Resolution. CURRENT OPINION IN TOXICOLOGY 2019; 16:49-57. [PMID: 31768481 DOI: 10.1016/j.cotox.2019.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
As systems biology expands its multi-omic spectrum to increasing resolutions, distinguishing cells based on single-cell profiles becomes feasible. Unlike traditional bulk assays that average cellular responses and blur the distinct identities of responsive cells, single-cell technologies enable sensitive detection of small cellular changes and precise identification of those cells perturbed by toxicants. Among the suite of omic technologies that continue to expand and become affordable, single-cell RNA sequencing (scRNA-seq) is at the cutting edge and leading the way to transform systems toxicology. Single-cell systems toxicology can provide a wealth of information to elucidate cell-specific alterations and response trajectories, detect points-of-departure, map and develop dynamical models of toxicity pathways.
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Affiliation(s)
- Qiang Zhang
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - W Michael Caudle
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Jingbo Pi
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Sudin Bhattacharya
- Department of Biomedical Engineering, Department of Pharmacology and Toxicology, Center for Research on Ingredient Safety, Institute for Quantitative Health Science and Engineering, and Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| | | | - Norbert E Kaminski
- Departments of Pharmacology and Toxicology and Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Rory B Conolly
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Durham, North Carolina, USA
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20
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Song D, Yang D, Powell CA, Wang X. Cell-cell communication: old mystery and new opportunity. Cell Biol Toxicol 2019; 35:89-93. [PMID: 30815784 DOI: 10.1007/s10565-019-09470-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Dongli Song
- Zhongshan Hospital Institute for Clinical Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dawei Yang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Medical College, Fudan University, Shanghai, China.,Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1232, New York, NY, 10029, USA
| | - Charles A Powell
- Zhongshan Hospital Institute for Clinical Science, Shanghai Medical College, Fudan University, Shanghai, China.,Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1232, New York, NY, 10029, USA
| | - Xiangdong Wang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Medical College, Fudan University, Shanghai, China.
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21
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Definition of clinical gene tests. Cell Biol Toxicol 2019; 35:83-87. [DOI: 10.1007/s10565-019-09464-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/28/2019] [Indexed: 01/20/2023]
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22
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Wang Z, Zhang X. Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:73-87. [PMID: 29943297 DOI: 10.1007/978-981-13-0502-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.
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Affiliation(s)
- Zheng Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China. .,Biomedical Research Center, Zhengzhou University People's Hospital, Zhengzhou, China.
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23
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Is Pooled CRISPR-Screening the Dawn of a New Era for Functional Genomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:171-176. [PMID: 29943304 DOI: 10.1007/978-981-13-0502-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functional genomics aims to develop an in-depth understanding of how specific gene dysfunctions are related to diseases. A common method for investigating the genome and its complex functions is via perturbation of the interactions between the DNA, RNA and their protein respective protein derivatives. Commonly, arrayed and pooled genetic screens are utilized to achieve this and in recent years have been fundamental in achieving the current level of understanding for gene dysfunctions. However, they are limited in specific aspects which scientists have attempted to address. Clustered regularly palindromic repeats (CRISPR)-based methods for genetic screens have in recent years become more prevalent but crucially shared similar properties to previous methods and failing to provide a distinct advantage over previous methods. CROP-seq, Perturb-seq, and CRISPR-seq have combined CRISPR and single-cell RNA-sequencing (scRNA-seq) and is the newest addition to the geneticist's arsenal, providing scientists with methods to edit DNA with improved speed, accuracy, and efficiency which could usher us into a new era of study methods for functional genomics. We briefly overview the CRISPR-Cas9 systems, the evolution of genetic screening in recent years, and evaluate and discuss the significance of CROP-seq, Perturb-seq, and CRISPR-seq.
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24
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Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:149-158. [PMID: 29943302 DOI: 10.1007/978-981-13-0502-3_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.
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25
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Detection and Application of RNA Editing in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:159-170. [PMID: 29943303 DOI: 10.1007/978-981-13-0502-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA editing is the process which happened in the post-transcriptional stage that the genetic information contained in an RNA molecule will be changed. RNA editing has been found to be related with many cancers, so through identifying RNA editing sites, we can find useful information on the process of carcinogenesis. In this review, we will discuss the main types of RNA editing and their role in cancers, as well as the current detection methods of RNA editing and the challenges we should overcome.
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26
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The advances in CRISPR technology and 3D genome. Semin Cell Dev Biol 2018; 90:54-61. [PMID: 30004018 DOI: 10.1016/j.semcdb.2018.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 07/08/2018] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system is a prokaryotic immune system that used to resist foreign genetic factors. It rapidly becomes the hot technology in life sciences and is applies for genome editing to solve the problem of genome-derived diseases. Using CRISPR/Cas technique, the biological DNA sequence can be repaired, cut, replaced, or added. It can effectively change the human stem cells and is expected to achieve results in the treatment. Compared with ZFN and TALEN genome editing techniques, CRISPR is more effective, accurate, and convenient. The application of CRISPR technique in three dimensional (3D) genome structure makes us understand the relationship between linear DNA sequence and 3D chromatin structure. Utilizing CRISPR/Cas9 genome editing to reverse or delete CTCF binding sites, to recognize changes of topological isomerism of the genome and interactions between chromatin loops. The purpose of this review is to introduce the characteristics and classification of the current CRISPR/Cas system, multiple functions, and potential therapeutic uses, as well as to outline the effect of the technique on chromatin loops by changing CTCF sites in 3D genomes. We will also briefly describe the importance of ethical dilemmas to be faced in CRISPR applications and provide a perspective for potential CRISPR considerations.
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27
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Roles of CTCF in conformation and functions of chromosome. Semin Cell Dev Biol 2018; 90:168-173. [PMID: 30031212 DOI: 10.1016/j.semcdb.2018.07.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 02/08/2023]
Abstract
CCCTC-binding factor (CTCF) plays indispensable roles in transcriptional inhibition/activation, insulation, gene imprinting, and regulation of 3Dchromatin structure. CTCF contributes to formation of genome multi-dimensions, regulation of dimensional changes, or control of central signals to transcriptional networks. A large number of factors affect CTCF binding, methylation/demethylation, base mutation, or poly(adp-ribosyl)ation. CTCF is one of the most important elements in the regulation of chromatin folding by combining with CBSs in TADs in a positive-reverse or reverse-positive orders. CTCF acts as a versatile nuclear factor, a transcriptional activator or repressor, an insulator binding factor, or a regulator of genomic imprinting as required for various biological procedures. Although molecular regulatory mechanisms of CTCF in cell differentiation and disease development remains unclear, roles of CTCF in carcinogenesis have been intensively explored. There is little understanding about regulatory roles of CTCF in inflammation-associated transcriptional signaling, cell injury, organ dysfunction, and systemic responses. It is also highly expected that further in-depth studies of CTCF control mechanisms can provide better understanding of disease development and potential disease-specific biomarkers and therapeutic targets.
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28
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Zhang L, Song D, Zhu B, Wang X. The role of nuclear matrix protein HNRNPU in maintaining the architecture of 3D genome. Semin Cell Dev Biol 2018; 90:161-167. [PMID: 29981443 DOI: 10.1016/j.semcdb.2018.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023]
Abstract
The complexity of higher eukaryote genomes is far from being explained by linear information. There is a need to understand roles of genome regulation at the organism level through defining a comprehensive profile of chromosomal organization. Chromosome conformation capture (3C)-based studies reveal that higher-order of chromatin include not only long-range chromatin loops, but also compartments and topologically associating domains as the basis of genome structure and functions. However, the molecular machinery how the genome is spatially organized is still inadequate. Exciting progress has been made with the development of today's technology, we find that heterogeneous nuclear ribonucleoprotein U, initially identified as a structural nuclear protein, plays important role in three-dimensional (3D) genome organization by high-throughput assays. The disruption of this protein not only results in compartment switching on of the genome, it also reduces of TAD boundary strengths at borders between two types of compartments, and regulates chromatin loop by decrease its intensities. In addition, HNRNPU mainly binds to active chromatin. Most of HNRNPU peaks is consistent with CTCF or RAD21.It also plays an irreplaceable role in the processes of mitosis. This review aims to discuss the role of HNRNPU in maintaining the 3D chromatin architecture, as well as the recent development and human diseases involved in this nuclear matrix (NM)-associated protein.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Dongli Song
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China.
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29
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Yan F, Wang X, Zeng Y. 3D genomic regulation of lncRNA and Xist in X chromosome. Semin Cell Dev Biol 2018; 90:174-180. [PMID: 30017906 DOI: 10.1016/j.semcdb.2018.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) act as important regulators in cardiovascular diseases, neural degenerative disease, or cancers, by localizing and spreading across chromatins. lncRNA can regulate the 3D architecture of the enhancer cluster at the target gene locus, relevant to analogous lncRNA-protein coding gene pairs. X inactive specific transcript (Xist) plays a critical role in the process and biological function of lncRNAs. The lncRNA Jpx, Xist activator, is a nonprotein-coding RNA transcribed from a gene within the X-inactivation center and acts as a numerator element to control X-chromosome number and activate Xist transcription by interacting with CCCTC-binding factor. Up-regulated lncRNA Xist initiates X chromosome inactivation process and attracts specific chromatin modifiers. A number of chromatin-modified factors interact with lncRNAs modify 3D genome architecture and mediate Xist function in embryo development. Thus, the regulation of lncRNAs in 3D genome progresses is the key mechanism of Xist, as a therapeutic potential for Xist associated diseases.
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Affiliation(s)
- Furong Yan
- Center for Molecular Diagnosis and Therapy, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiangdong Wang
- Center for Molecular Diagnosis and Therapy, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Fujian Medical University, Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian Province, China.
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30
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Lv J, Bhatia M, Wang X. Roles of Mitochondrial DNA in Energy Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1038:71-83. [PMID: 29178070 DOI: 10.1007/978-981-10-6674-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Mitochondria are independent double-membrane organelles responsible for energy production, specifically by completing oxidative phosphorylation. Mitochondria are essential to regulate energy metabolism, signaling pathways, and cell death. Mitochondrial DNA (mtDNA) can be altered by metabolic disorders, oxidative stress, or inflammation in the progression and development of various diseases. In this chapter, we overview the role of mtDNA in energy metabolism and the diseases that are associated with mtDNA abnormality, with a special focus on the major factors which regulate the mechanism of mtDNA in metabolism.
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Affiliation(s)
- Jiapei Lv
- Zhongshan Hospital Institute of Fudan University, Shanghai Medical School, Shanghai, China
| | - Madhav Bhatia
- Department of Pathology, University of Otago, Wellington, New Zealand
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China.
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31
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The future is now: cutting edge science and understanding toxicology. Cell Biol Toxicol 2018; 34:79-85. [DOI: 10.1007/s10565-018-9421-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/09/2018] [Indexed: 12/13/2022]
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32
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Zeng Y, Chen X, Wang X. Roles of Single Cell Systems Biomedicine in Lung Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:177-185. [PMID: 29943305 DOI: 10.1007/978-981-13-0502-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Single cell sequencing is important to detect the gene heterogeneity between cells, as the part of single-cell systems biology which combines computational science, mathematical modelling and high-throughput technologies with biological function and organization in the cell. We initially arise the question how to integrate the outcomes of single-cell systems biology with clinical phenotype, interpret alterations of single-cell gene sequencing and function in patient response to therapies, and understand the significance of single-cell systems biology in the discovery and development of new molecular diagnostics and therapeutics. The present review furthermore focuses the significance of singe cell systems biology in respiratory diseases and calls the special attention from scientists who are working on single cell systems biology to improve the diagnosis and therapy for patients with lung diseases.
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Affiliation(s)
- Yiming Zeng
- Department of Respiratory Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Xiaoyang Chen
- Department of Respiratory Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiangdong Wang
- Department of Respiratory Pulmonary and Critical Care Medicine, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
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Can the Single Cell Make Biomedicine Different? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:1-6. [PMID: 29943291 DOI: 10.1007/978-981-13-0502-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The single-cell as the basic unit of biological organs and tissues has recently been considered an important window to furthermore understand molecular mechanisms of organ function and biology. The current issue with a special focus on single cell biomedicine is the first effort to collect the evidence of disease-associated single cell research, define the significance of single cell biomedicine in the pathogenesis of diseases, value the correlation of single cell gene sequencing with disease-specific biomarkers, and monitor the dynamics of RNA processes and responses to microenvironmental changes and drug resistances.
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Zhang L, Wang W, Zhu B, Wang X. Regulatory Roles of Mitochondrial Ribosome in Lung Diseases and Single Cell Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:183-200. [PMID: 29178077 DOI: 10.1007/978-981-10-6674-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The mitochondria have the most vital processes in eukaryotic cells to produce ATP composed of polypeptides that are produced via ribosomes, as oxidative phosphorylation. Initially, studies regarding human mitochondrial ribosomes were performed in the model system, bovine mitochondrial ribosome, to investigate how ribosomes are biosynthesized and evolved as well as what their structure and function are. Advances in X-ray crystallography have led to dramatic progresses in structural studies of the ribosome. In recent years, there has been a growing interest in the properties of the mitochondrial ribosome. Although one of its main functions is the production of ATP, it was also linked to multiple diseases. A key area that remains unexplored and requires investigation and exploration is how mitochondrial ribosomal RNA (mt-rRNA) variations can affect the mitochondrial ribosomes in developing disease. This review summarizes the structure, elements, functions, and regulatory roles in associated diseases. With the continuous development of technology, studies on the mechanism of mitochondrial ribosome related diseases are crucial, in order to identify methods of prevention and treatment of these disorders.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China
| | - William Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China.
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Beyond Deubiquitylation: USP30-Mediated Regulation of Mitochondrial Homeostasis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:133-148. [DOI: 10.1007/978-981-10-6674-0_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Zhu Z, Wang X. Significance of Mitochondria DNA Mutations in Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:219-230. [PMID: 29178079 DOI: 10.1007/978-981-10-6674-0_15] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mitochondria are essential double-membraned cytoplasmic organelles to support aerobic respiration and produce cellular energy by oxidative phosphorylation (OXPHOS). Mitochondrial functions are controlled by mitochondrial (mtDNA) and nuclear genomes (nDNA). Mutations of mtDNA result in mitochondrial dysfunction and multisystem diseases through compromising OXPHOS function directly by a point mutation or a large-scale mtDNA rearrangement. One or more of OXPHOS complexes are impaired and dysfunctional to affect tissues with high energy demands. mtDNA is more susceptible to oxidative damage and has more mutations than nDNA. Unlike diploid nDNA, mtDNA is a multi-copy genome transmitted and maternally inherited through oocyte. The multi-copy nature of mtDNA easily causes the heteroplasmy as a unique aspect of mtDNA, making mitochondrial diseases more complex and heterogeneous. mtDNA-associated mitochondrial dysfunction plays the important role in the development of multisystemic primary mitochondrial disease, neurodegeneration, and cancer. The present article overviews the occurrence of mtDNA mutation, interactions with other factors, and molecular mechanisms of mtDNA-associated diseases.
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Affiliation(s)
- Zhenhua Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China.
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Abstract
Telocyte (TC) is a new identified interstitial cell type with a small nuclear and one or several long and thin prolongations with enlargements on them. They were found in many mammals including humans, mouse, rats, dogs, and monkeys and play vital roles in many physiological and pathological conditions. The ultrastructure of mitochondria was observed in TCs, and the alterations were found in TCs from inflammatory ureter tissue. MtDNA is associated with mitochondria normal functions and involved in physiological and pathological processes. However, mitochondria and mtDNA in TCs were not investigated deeply. This review will introduce the origin, distribution, morphology, and functions of TCs and the distribution and functions of TC mitochondria in order to improve a better understanding of the potential functions of mtDNA in TCs.
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Qian M, Spada C, Wang X. Approach, Application, and Bioethics of mtDNA Sequencing in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:23-38. [DOI: 10.1007/978-981-10-6674-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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How Far Can Mitochondrial DNA Drive the Disease? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:1-8. [DOI: 10.1007/978-981-10-6674-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Mitochondrial DNA Methylation and Related Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:117-132. [DOI: 10.1007/978-981-10-6674-0_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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