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Jin C, Yan K, Wang M, Song W, Wang B, Men Y, Niu J, He Y, Zhang Q, Qi J. Dissecting the dynamic cellular transcriptional atlas of adult teleost testis development throughout the annual reproductive cycle. Development 2024; 151:dev202296. [PMID: 38477640 DOI: 10.1242/dev.202296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Teleost testis development during the annual cycle involves dramatic changes in cellular compositions and molecular events. In this study, the testicular cells derived from adult black rockfish at distinct stages - regressed, regenerating and differentiating - were meticulously dissected via single-cell transcriptome sequencing. A continuous developmental trajectory of spermatogenic cells, from spermatogonia to spermatids, was delineated, elucidating the molecular events involved in spermatogenesis. Subsequently, the dynamic regulation of gene expression associated with spermatogonia proliferation and differentiation was observed across spermatogonia subgroups and developmental stages. A bioenergetic transition from glycolysis to mitochondrial respiration of spermatogonia during the annual developmental cycle was demonstrated, and a deeper level of heterogeneity and molecular characteristics was revealed by re-clustering analysis. Additionally, the developmental trajectory of Sertoli cells was delineated, alongside the divergence of Leydig cells and macrophages. Moreover, the interaction network between testicular micro-environment somatic cells and spermatogenic cells was established. Overall, our study provides detailed information on both germ and somatic cells within teleost testes during the annual reproductive cycle, which lays the foundation for spermatogenesis regulation and germplasm preservation of endangered species.
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Affiliation(s)
- Chaofan Jin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China
| | - Kai Yan
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
| | - Mengya Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China
| | - Weihao Song
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
| | - Bo Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China
| | - Yu Men
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
| | - Jingjing Niu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
| | - Yan He
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China
| | - Quanqi Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China
| | - Jie Qi
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266000, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China
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Ali A, Manzoor S, Ali T, Asim M, Muhammad G, Ahmad A, Jamaludin MI, Devaraj S, Munawar N. Innovative aspects and applications of single cell technology for different diseases. Am J Cancer Res 2024; 14:4028-4048. [PMID: 39267684 PMCID: PMC11387862 DOI: 10.62347/vufu1836] [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: 06/21/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Recent developments in single-cell technologies have provided valuable insights from cancer genomics to complex microbial communities. Single-cell technologies including the RNA-seq, next-generation sequencing (NGS), epigenomics, genomics, and transcriptomics can be used to uncover the single cell nature and molecular characterization of individual cells. These technologies also reveal the cellular transition states, evolutionary relationships between genes, the complex structure of single-cell populations, cell-to-cell interaction leading to biological discoveries and more reliable than traditional bulk technologies. These technologies are becoming the first choice for the early detection of inflammatory biomarkers affecting the proliferation and progression of tumor cells in the tumor microenvironment and improving the clinical efficacy of patients undergoing immunotherapy. These technologies also hold a central position in the detection of checkpoint inhibitors and thus determining the signaling pathways evoked by tumor invasion. This review addressed the emerging approaches of single cell-based technologies in cancer immunotherapies and different human diseases at cellular and molecular levels and the emerging role of sequencing technologies leading to drug discovery. Advancements in these technologies paved for discovering novel diagnostic markers for better understanding the pathological and biochemical mechanisms also for controlling the rate of different diseases.
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Affiliation(s)
- Ashiq Ali
- Department of Histology and Embryology, Shantou University Medical College Shantou 515041, Guangdong, China
| | - Saba Manzoor
- Department of Zoology, University of Sialkot Sialkot 51310, Pakistan
| | - Tayyab Ali
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Muhammad Asim
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Ghulam Muhammad
- Jinnah Burn and Reconstructive Surgery Centre, Jinnah Hospital, Allama Iqbal Medical College Lahore 54000, Pakistan
| | - Aftab Ahmad
- Biochemistry/Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad 38040, Pakistan
| | - Mohamad Ikhwan Jamaludin
- BioInspired Device and Tissue Engineering Research Group (BioInspira), Department of Biomedical Engineering and Health Sciences, Faculty of Electrical Engineering, Universiti Teknologi Malaysia Johor Bahru 81310, Johor, Malaysia
| | - Sutha Devaraj
- Graduate School of Medicine, Perdana University Wisma Chase Perdana, Changkat Semantan, Damansara Heights, Kuala Lumpur 50490, Malaysia
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University Al-Ain 15551, United Arab Emirates
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Ma Q, Zhang YH, Guo W, Feng K, Huang T, Cai YD. Machine Learning in Identifying Marker Genes for Congenital Heart Diseases of Different Cardiac Cell Types. Life (Basel) 2024; 14:1032. [PMID: 39202774 PMCID: PMC11355424 DOI: 10.3390/life14081032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
Congenital heart disease (CHD) represents a spectrum of inborn heart defects influenced by genetic and environmental factors. This study advances the field by analyzing gene expression profiles in 21,034 cardiac fibroblasts, 73,296 cardiomyocytes, and 35,673 endothelial cells, utilizing single-cell level analysis and machine learning techniques. Six CHD conditions: dilated cardiomyopathy (DCM), donor hearts (used as healthy controls), hypertrophic cardiomyopathy (HCM), heart failure with hypoplastic left heart syndrome (HF_HLHS), Neonatal Hypoplastic Left Heart Syndrome (Neo_HLHS), and Tetralogy of Fallot (TOF), were investigated for each cardiac cell type. Each cell sample was represented by 29,266 gene features. These features were first analyzed by six feature-ranking algorithms, resulting in several feature lists. Then, these lists were fed into incremental feature selection, containing two classification algorithms, to extract essential gene features and classification rules and build efficient classifiers. The identified essential genes can be potential CHD markers in different cardiac cell types. For instance, the LASSO identified key genes specific to various heart cell types in CHD subtypes. FOXO3 was found to be up-regulated in cardiac fibroblasts for both Dilated and hypertrophic cardiomyopathy. In cardiomyocytes, distinct genes such as TMTC1, ART3, ARHGAP24, SHROOM3, and XIST were linked to dilated cardiomyopathy, Neo-Hypoplastic Left Heart Syndrome, hypertrophic cardiomyopathy, HF-Hypoplastic Left Heart Syndrome, and Tetralogy of Fallot, respectively. Endothelial cell analysis further revealed COL25A1, NFIB, and KLF7 as significant genes for dilated cardiomyopathy, hypertrophic cardiomyopathy, and Tetralogy of Fallot. LightGBM, Catboost, MCFS, RF, and XGBoost further delineated key genes for specific CHD subtypes, demonstrating the efficacy of machine learning in identifying CHD-specific genes. Additionally, this study developed quantitative rules for representing the gene expression patterns related to CHDs. This research underscores the potential of machine learning in unraveling the molecular complexities of CHD and establishes a foundation for future mechanism-based studies.
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Affiliation(s)
- Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China;
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China;
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
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Wei N, Lee C, Duan L, Galdos FX, Samad T, Raissadati A, Goodyer WR, Wu SM. Cardiac Development at a Single-Cell Resolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:253-268. [PMID: 38884716 DOI: 10.1007/978-3-031-44087-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mammalian cardiac development is a complex, multistage process. Though traditional lineage tracing studies have characterized the broad trajectories of cardiac progenitors, the advent and rapid optimization of single-cell RNA sequencing methods have yielded an ever-expanding toolkit for characterizing heterogeneous cell populations in the developing heart. Importantly, they have allowed for a robust profiling of the spatiotemporal transcriptomic landscape of the human and mouse heart, revealing the diversity of cardiac cells-myocyte and non-myocyte-over the course of development. These studies have yielded insights into novel cardiac progenitor populations, chamber-specific developmental signatures, the gene regulatory networks governing cardiac development, and, thus, the etiologies of congenital heart diseases. Furthermore, single-cell RNA sequencing has allowed for the exquisite characterization of distinct cardiac populations such as the hard-to-capture cardiac conduction system and the intracardiac immune population. Therefore, single-cell profiling has also resulted in new insights into the regulation of cardiac regeneration and injury repair. Single-cell multiomics approaches combining transcriptomics, genomics, and epigenomics may uncover an even more comprehensive atlas of human cardiac biology. Single-cell analyses of the developing and adult mammalian heart offer an unprecedented look into the fundamental mechanisms of cardiac development and the complex diseases that may arise from it.
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Affiliation(s)
- Nicholas Wei
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | - Carissa Lee
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | - Lauren Duan
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | | | - Tahmina Samad
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | | | | | - Sean M Wu
- Stanford University, Cardiovascular Institute, Stanford, CA, USA.
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5
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Sun X, Wang G, Luo W, Gu H, Ma W, Wei X, Liu D, Jia S, Cao S, Wang Y, Yuan Z. Small but strong: the emerging role of small nucleolar RNA in cardiovascular diseases. Front Cell Dev Biol 2023; 11:1292925. [PMID: 38033868 PMCID: PMC10682241 DOI: 10.3389/fcell.2023.1292925] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of mortality and disability worldwide. Numerous studies have demonstrated that non-coding RNAs (ncRNAs) play a primary role in CVD development. Therefore, studies on the mechanisms of ncRNAs are essential for further efforts to prevent and treat CVDs. Small nucleolar RNAs (snoRNAs) are a novel species of non-conventional ncRNAs that guide post-transcriptional modifications and the subsequent maturation of small nuclear RNA and ribosomal RNA. Evidently, snoRNAs are extensively expressed in human tissues and may regulate different illnesses. Particularly, as the next-generation sequencing techniques have progressed, snoRNAs have been shown to be differentially expressed in CVDs, suggesting that they may play a role in the occurrence and progression of cardiac illnesses. However, the molecular processes and signaling pathways underlying the function of snoRNAs remain unidentified. Therefore, it is of great value to comprehensively investigate the association between snoRNAs and CVDs. The aim of this review was to collate existing literature on the biogenesis, characteristics, and potential regulatory mechanisms of snoRNAs. In particular, we present a scientific update on these snoRNAs and their relevance to CVDs in an effort to cast new light on the functions of snoRNAs in the clinical diagnosis of CVDs.
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Affiliation(s)
- Xue Sun
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gebang Wang
- Department of Thoracic Surgery, Liaoning Cancer Hospital and Institute, Cancer Hospital of Dalian University of Technology, Shenyang, Liaoning, China
| | - Wenting Luo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wei Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaowei Wei
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shanshan Jia
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Songying Cao
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Wang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Edwards W, Greco TM, Miner GE, Barker NK, Herring L, Cohen S, Cristea IM, Conlon FL. Quantitative proteomic profiling identifies global protein network dynamics in murine embryonic heart development. Dev Cell 2023; 58:1087-1105.e4. [PMID: 37148880 PMCID: PMC10330608 DOI: 10.1016/j.devcel.2023.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 01/27/2023] [Accepted: 04/14/2023] [Indexed: 05/08/2023]
Abstract
Defining the mechanisms that govern heart development is essential for identifying the etiology of congenital heart disease. Here, quantitative proteomics was used to measure temporal changes in the proteome at critical stages of murine embryonic heart development. Global temporal profiles of the over 7,300 proteins uncovered signature cardiac protein interaction networks that linked protein dynamics with molecular pathways. Using this integrated dataset, we identified and demonstrated a functional role for the mevalonate pathway in regulating the cell cycle of embryonic cardiomyocytes. Overall, our proteomic datasets are a resource for studying events that regulate embryonic heart development and contribute to congenital heart disease.
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Affiliation(s)
- Whitney Edwards
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gregory E Miner
- Department of Cell Biology and Physiology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie K Barker
- Department of Pharmacology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura Herring
- Department of Pharmacology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Frank L Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC, 27599 USA.
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Pesce M, Pompilio G, Bartunek J. The LIMA: A Drug-Eluting Graft and Coronary Flow Shock Absorber. Mayo Clin Proc 2023; 98:15-17. [PMID: 36603942 DOI: 10.1016/j.mayocp.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 01/04/2023]
Affiliation(s)
| | - Giulio Pompilio
- Centro Cardiologico Monzino, IRCCS, Milan, Italy; Università di Milano, Milan, Italy
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Jung Y, Kim J, Jang H, Kim G, Kwon YW. Strategy of Patient-Specific Therapeutics in Cardiovascular Disease Through Single-Cell RNA Sequencing. Korean Circ J 2022; 53:1-16. [PMID: 36627736 PMCID: PMC9834554 DOI: 10.4070/kcj.2022.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Recently, single cell RNA sequencing (scRNA-seq) technology has enabled the discovery of novel or rare subtypes of cells and their characteristics. This technique has advanced unprecedented biomedical research by enabling the profiling and analysis of the transcriptomes of single cells at high resolution and throughput. Thus, scRNA-seq has contributed to recent advances in cardiovascular research by the generation of cell atlases of heart and blood vessels and the elucidation of mechanisms involved in cardiovascular development and diseases. This review summarizes the overall workflow of the scRNA-seq technique itself and key findings in the cardiovascular development and diseases based on the previous studies. In particular, we focused on how the single-cell sequencing technology can be utilized in clinical field and precision medicine to treat specific diseases.
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Affiliation(s)
- Yunseo Jung
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes & Cancer, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Juyeong Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Howon Jang
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Gwanhyeon Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Yoo-Wook Kwon
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes & Cancer, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.,Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
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Sreenivasan VKA, Henck J, Spielmann M. Single-cell sequencing: promises and challenges for human genetics. MED GENET-BERLIN 2022; 34:261-273. [PMID: 38836091 PMCID: PMC11006387 DOI: 10.1515/medgen-2022-2156] [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: 06/06/2024]
Abstract
Over the last decade, single-cell sequencing has transformed many fields. It has enabled the unbiased molecular phenotyping of even whole organisms with unprecedented cellular resolution. In the field of human genetics, where the phenotypic consequences of genetic and epigenetic alterations are of central concern, this transformative technology promises to functionally annotate every region in the human genome and all possible variants within them at a massive scale. In this review aimed at the clinicians in human genetics, we describe the current status of the field of single-cell sequencing and its role for human genetics, including how the technology works as well as how it is being applied to characterize and monitor diseases, to develop human cell atlases, and to annotate the genome.
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Affiliation(s)
- Varun K A Sreenivasan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, 23562 Lübeck, 24105 Kiel, Germany
| | - Jana Henck
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, 23562 Lübeck, 24105 Kiel, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, 23562 Lübeck, 24105 Kiel, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
- DZHK e. V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, 23538 Lübeck, Germany
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Zuo JY, Chen HX, Liu ZG, Yang Q, He GW. Identification and functional analysis of variants of MYH6 gene promoter in isolated ventricular septal defects. BMC Med Genomics 2022; 15:213. [PMID: 36209093 PMCID: PMC9548206 DOI: 10.1186/s12920-022-01365-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/21/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Ventricular septal defect is the most common form of congenital heart diseases. MYH6 gene has a critical effect on the growth and development of the heart but the variants in the promoter of MYH6 is unknown. PATIENTS AND METHODS In 604 of the subjects (311 isolated and sporadic ventricular septal defect patients and 293 healthy controls), DNA was extracted from blood samples and MYH6 gene promoter region variants were analyzed by sequencing. Further functional verification was performed by cellular experiments using dual luciferase reporter gene analysis, electrophoretic mobility shift assays, and bioinformatics analysis. RESULTS Nine variants were identified in the MYH6 gene promoter and two of those variants [g.4085G>C(rs1222539675) and g.4716G>A(rs377648095)] were only found in the ventricular septal defect patients. Cellular function experiments showed that these two variants reduced the transcriptional activity of the MYH6 gene promoter (p < 0.001). Further analysis with online JASPAR database suggests that these variants may alter a set of putative transcription factor binding sites that possibly lead to changes in myosin subunit expression and ventricular septal defect formation. CONCLUSIONS Our study for the first time identifies variants in the promoter region of the MYH6 gene in Chinese patients with isolated and sporadic ventricular septal defect. These variants significantly reduced MYH6 gene expression and affected transcription factor binding sites and therefore are pathogenic. The present study provides new insights in the role of the MYH6 gene promoter region to better understand the genetic basis of VSD formation.
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Affiliation(s)
- Ji-Yang Zuo
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
- Clinical School of Cardiovascular Disease, Tianjin Medical University, Tianjin, China
| | - Huan-Xin Chen
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Zhi-Gang Liu
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Qin Yang
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China
| | - Guo-Wei He
- Department of Cardiovascular Surgery, The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, No. 61, the 3rd Ave., Tianjin, 300457, China.
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11
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The need for a standard for informed consent for collection of human fetal material. Stem Cell Reports 2022; 17:1245-1247. [PMID: 35705013 PMCID: PMC9214061 DOI: 10.1016/j.stemcr.2022.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
The ISSCR has developed the Informed Consent Standards for Human Fetal Tissue Donation and Research to promote uniformity and transparency in tissue donation and collection. This standard is designed to assist those working with and overseeing the regulation of such tissue and reassure the wider community and public.
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Swiatlowska P, Iskratsch T. Cardiovascular mechanobiology-a Special Issue to look at the state of the art and the newest insights into the role of mechanical forces in cardiovascular development, physiology and disease. Biophys Rev 2021; 13:575-577. [PMID: 34777612 PMCID: PMC8555016 DOI: 10.1007/s12551-021-00842-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
There has been much progress recently in the area of cardiovascular mechanobiology and this Special Issue aims at taking stock. This editorial gives context of the main motivation for this special issue as well as a brief summary of its content.
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Affiliation(s)
- Pamela Swiatlowska
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
| | - Thomas Iskratsch
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
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13
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Tampakakis E, Kwon C. Heart generation and regeneration. Semin Cell Dev Biol 2021; 118:92-93. [PMID: 34304994 DOI: 10.1016/j.semcdb.2021.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Emmanouil Tampakakis
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Chulan Kwon
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Department of Cell Biology, Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Liu L, Dong X, Tu Y, Miao G, Zhang Z, Zhang L, Wei Z, Yu D, Qiu X. Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics. MICROFLUIDICS AND NANOFLUIDICS 2021; 25:87. [PMID: 34580578 PMCID: PMC8457033 DOI: 10.1007/s10404-021-02485-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/30/2021] [Indexed: 05/14/2023]
Abstract
Single-cell nucleic acid analysis aims at discovering the genetic differences between individual cells which is well known as the cellular heterogeneity. This technology facilitates cancer diagnosis, stem cell research, immune system analysis, and other life science applications. The conventional platforms for single-cell nucleic acid analysis more rely on manual operation or bulky devices. Recently, the emerging microfluidic technology has provided a perfect platform for single-cell nucleic acid analysis with the characteristic of accurate and automatic single-cell manipulation. In this review, we briefly summarized the procedure of single-cell nucleic acid analysis including single-cell isolation, single-cell lysis, nucleic acid amplification, and genetic analysis. And then, three representative microfluidic platforms for single-cell nucleic acid analysis are concluded as valve-, microwell-, and droplet-based platforms. Furthermore, we described the state-of-the-art integrated single-cell nucleic acid analysis systems based on the three platforms. Finally, the future development and challenges of microfluidics-based single-cell nucleic acid analysis are discussed as well.
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Affiliation(s)
- Luyao Liu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Xiaobin Dong
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Yunping Tu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Zhongping Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Zewen Wei
- Department of Biomedical Engineering, School of Life Science, Beijing Institute of Technology, Beijing, 100081 China
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029 China
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
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