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Zhang B, Zhu Y, Zhang Z, Wu F, Ma X, Sheng W, Dai R, Guo Z, Yan W, Hao L, Huang G, Ma D, Hao B, Ma J. SMC3 contributes to heart development by regulating super-enhancer associated genes. Exp Mol Med 2024:10.1038/s12276-024-01293-0. [PMID: 39085358 DOI: 10.1038/s12276-024-01293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/23/2024] [Accepted: 05/21/2024] [Indexed: 08/02/2024] Open
Abstract
Abnormal cardiac development has been observed in individuals with Cornelia de Lange syndrome (CdLS) due to mutations in genes encoding members of the cohesin complex. However, the precise role of cohesin in heart development remains elusive. In this study, we aimed to elucidate the indispensable role of SMC3, a component of the cohesin complex, in cardiac development and its underlying mechanism. Our investigation revealed that CdLS patients with SMC3 mutations have high rates of congenital heart disease (CHD). We utilized heart-specific Smc3-knockout (SMC3-cKO) mice, which exhibit varying degrees of outflow tract (OFT) abnormalities, to further explore this relationship. Additionally, we identified 16 rare SMC3 variants with potential pathogenicity in individuals with isolated CHD. By employing single-nucleus RNA sequencing and chromosome conformation capture high-throughput genome-wide translocation sequencing, we revealed that Smc3 deletion downregulates the expression of key genes, including Ets2, in OFT cardiac muscle cells by specifically decreasing interactions between super-enhancers (SEs) and promoters. Notably, Ets2-SE-null mice also exhibit delayed OFT development in the heart. Our research revealed a novel role for SMC3 in heart development via the regulation of SE-associated genes, suggesting its potential relevance as a CHD-related gene and providing crucial insights into the molecular basis of cardiac development.
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Affiliation(s)
- Bowen Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Yongchang Zhu
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, China
| | - Zhen Zhang
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Feizhen Wu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Xiaojing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Wei Sheng
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Ranran Dai
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Zhenglong Guo
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, China
| | - Weili Yan
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Lili Hao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Guoying Huang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
| | - Bingtao Hao
- Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- Henan Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, 450000, China.
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
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2
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Zhang J, Hu G, Lu Y, Ren H, Huang Y, Wen Y, Ji B, Wang D, Wang H, Liu H, Ma N, Zhang L, Pan G, Qu Y, Wang H, Zhang W, Miao Z, Yao H. CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment. Nat Commun 2024; 15:5524. [PMID: 38951485 PMCID: PMC11217373 DOI: 10.1038/s41467-024-49684-1] [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: 05/12/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explore the regulatory roles of a clinically relevant R567W point mutation, located within the 11th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567W mutation exhibit growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single-cell transcriptome levels. This mutation induces premature stem-like cell exhaustion, accelerates the maturation of GABAergic neurons, and disrupts neurodevelopmental and synaptic pathways. Additionally, it specifically hinders CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrors the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Gongcheng Hu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yuli Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huawei Ren
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Yin Huang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Yulin Wen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Binrui Ji
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Diyang Wang
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Huisheng Liu
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Ning Ma
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Guangjin Pan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yibo Qu
- Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Hua Wang
- Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine (Ministry of Education), Anhui Medical University, Hefei, China
| | - Wei Zhang
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Zhichao Miao
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Department of Basic Research, Guangzhou National Laboratory, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
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3
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Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat Biotechnol 2024; 42:960-974. [PMID: 37640946 DOI: 10.1038/s41587-023-01909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.
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Affiliation(s)
- Emily B Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiara N Berríos
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel R Connolly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Tong Wang
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Flournoy
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Hu P, Rychik J, Zhao J, Bai H, Bauer A, Yu W, Rand EB, Dodds KM, Goldberg DJ, Tan K, Wilkins BJ, Pei L. Single-cell multiomics guided mechanistic understanding of Fontan-associated liver disease. Sci Transl Med 2024; 16:eadk6213. [PMID: 38657025 PMCID: PMC11103255 DOI: 10.1126/scitranslmed.adk6213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The Fontan operation is the current standard of care for single-ventricle congenital heart disease. Individuals with a Fontan circulation (FC) exhibit central venous hypertension and face life-threatening complications of hepatic fibrosis, known as Fontan-associated liver disease (FALD). The fundamental biology and mechanisms of FALD are little understood. Here, we generated a transcriptomic and epigenomic atlas of human FALD at single-cell resolution using multiomic snRNA-ATAC-seq. We found profound cell type-specific transcriptomic and epigenomic changes in FC livers. Central hepatocytes (cHep) exhibited the most substantial changes, featuring profound metabolic reprogramming. These cHep changes preceded substantial activation of hepatic stellate cells and liver fibrosis, suggesting cHep as a potential first "responder" in the pathogenesis of FALD. We also identified a network of ligand-receptor pairs that transmit signals from cHep to hepatic stellate cells, which may promote their activation and liver fibrosis. We further experimentally demonstrated that activins A and B promote fibrotic activation in vitro and identified mechanisms of activin A's transcriptional activation in FALD. Together, our single-cell transcriptomic and epigenomic atlas revealed mechanistic insights into the pathogenesis of FALD and may aid identification of potential therapeutic targets.
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Affiliation(s)
- Po Hu
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Cardiovascular Institute, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
| | - Jack Rychik
- Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
| | - Juanjuan Zhao
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Cardiovascular Institute, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
| | - Huajun Bai
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Cardiovascular Institute, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
| | - Aidan Bauer
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Cardiovascular Institute, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
| | - Wenbao Yu
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
| | - Elizabeth B. Rand
- Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
| | - Kathryn M. Dodds
- Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- School of Nursing, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
| | - David J. Goldberg
- Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
| | - Kai Tan
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Cardiovascular Institute, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA
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5
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Liu C, Hong T, Zhao C, Xue T, Wang S, Ren Z. Single-nucleus transcriptomics and chromatin accessibility analysis of musk gland development in Chinese forest musk deer (Moschus berezovskii). Integr Zool 2024. [PMID: 38644525 DOI: 10.1111/1749-4877.12823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/28/2023] [Accepted: 02/15/2024] [Indexed: 04/23/2024]
Abstract
Musk secreted by male forest musk deer (Moschus berezovskii) musk glands is an invaluable component of medicine and perfume. Musk secretion depends on musk gland maturation; however, the mechanism of its development remains elusive. Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined. Twelve cell types, including two different types of acinar cells (Clusters 0 and 10) were identified. Single-nucleus RNA and single-nucleus ATAC sequencing analyses revealed that seven core target genes associated with musk secretion (Hsd17b2, Acacb, Lss, Vapa, Aldh16a1, Aldh7a1, and Sqle) were regulated by 12 core transcription factors (FOXO1, CUX2, RORA, RUNX1, KLF6, MGA, NFIC, FOXO3, ETV5, NR3C1, HSF4, and MITF) during the development of Cluster 0 acinar cells. Kyoto Encyclopedia of Genes and Genomes enrichment showed significant changes in the pathways associated with musk secretion during acinar cell development. Gene set variation analysis also revealed that certain pathways associated with musk secretion were enriched in 6-year-old acinar cells. A gene co-expression network was constructed during acinar cell development to provide a precise understanding of the connections between transcription factors, genes, and pathways. Finally, intercellular communication analysis showed that intercellular communication is involved in musk gland development. This study provides crucial insights into the changes and key factors underlying musk gland development, which serve as valuable resources for studying musk secretion mechanisms and promoting the protection of this endangered species.
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Affiliation(s)
- Chenmiao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tingting Hong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengcheng Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tao Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhanjun Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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6
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Chamberlin JT, Lee Y, Marth GT, Quinlan AR. Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments. Genome Res 2024; 34:179-188. [PMID: 38355308 PMCID: PMC10984380 DOI: 10.1101/gr.278253.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
A mechanistic understanding of the biological and technical factors that impact transcript measurements is essential to designing and analyzing single-cell and single-nucleus RNA sequencing experiments. Nuclei contain the same pre-mRNA population as cells, but they contain a small subset of the mRNAs. Nonetheless, early studies argued that single-nucleus analysis yielded results comparable to cellular samples if pre-mRNA measurements were included. However, typical workflows do not distinguish between pre-mRNA and mRNA when estimating gene expression, and variation in their relative abundances across cell types has received limited attention. These gaps are especially important given that incorporating pre-mRNA has become commonplace for both assays, despite known gene length bias in pre-mRNA capture. Here, we reanalyze public data sets from mouse and human to describe the mechanisms and contrasting effects of mRNA and pre-mRNA sampling on gene expression and marker gene selection in single-cell and single-nucleus RNA-seq. We show that pre-mRNA levels vary considerably among cell types, which mediates the degree of gene length bias and limits the generalizability of a recently published normalization method intended to correct for this bias. As an alternative, we repurpose an existing post hoc gene length-based correction method from conventional RNA-seq gene set enrichment analysis. Finally, we show that inclusion of pre-mRNA in bioinformatic processing can impart a larger effect than assay choice itself, which is pivotal to the effective reuse of existing data. These analyses advance our understanding of the sources of variation in single-cell and single-nucleus RNA-seq experiments and provide useful guidance for future studies.
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Affiliation(s)
- John T Chamberlin
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA
- Seoul National University, College of Veterinary Medicine, Seoul, 08826, South Korea
| | - Gabor T Marth
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
| | - Aaron R Quinlan
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA;
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
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7
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Chen W, Li C, Chen Y, Bin J, Chen Y. Cardiac cellular diversity and functionality in cardiac repair by single-cell transcriptomics. Front Cardiovasc Med 2023; 10:1237208. [PMID: 37920179 PMCID: PMC10619858 DOI: 10.3389/fcvm.2023.1237208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
Cardiac repair after myocardial infarction (MI) is orchestrated by multiple intrinsic mechanisms in the heart. Identifying cardiac cell heterogeneity and its effect on processes that mediate the ischemic myocardium repair may be key to developing novel therapeutics for preventing heart failure. With the rapid advancement of single-cell transcriptomics, recent studies have uncovered novel cardiac cell populations, dynamics of cell type composition, and molecular signatures of MI-associated cells at the single-cell level. In this review, we summarized the main findings during cardiac repair by applying single-cell transcriptomics, including endogenous myocardial regeneration, myocardial fibrosis, angiogenesis, and the immune microenvironment. Finally, we also discussed the integrative analysis of spatial multi-omics transcriptomics and single-cell transcriptomics. This review provided a basis for future studies to further advance the mechanism and development of therapeutic approaches for cardiac repair.
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Affiliation(s)
- Wei Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Chuling Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Yijin Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Yanmei Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
- Department of Cardiology, Ganzhou People’s Hospital, Ganzhou, China
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8
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Huang X, Fu Y, Lee H, Zhao Y, Yang W, van de Leemput J, Han Z. Single-cell profiling of the developing embryonic heart in Drosophila. Development 2023; 150:dev201936. [PMID: 37526610 PMCID: PMC10482008 DOI: 10.1242/dev.201936] [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: 05/01/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
Drosophila is an important model for studying heart development and disease. Yet, single-cell transcriptomic data of its developing heart have not been performed. Here, we report single-cell profiling of the entire fly heart using ∼3000 Hand-GFP embryos collected at five consecutive developmental stages, ranging from bilateral migrating rows of cardiac progenitors to a fused heart tube. The data revealed six distinct cardiac cell types in the embryonic fly heart: cardioblasts, both Svp+ and Tin+ subtypes; and five types of pericardial cell (PC) that can be distinguished by four key transcription factors (Eve, Odd, Ct and Tin) and include the newly described end of the line PC. Notably, the embryonic fly heart combines transcriptional signatures of the mammalian first and second heart fields. Using unique markers for each heart cell type, we defined their number and location during heart development to build a comprehensive 3D cell map. These data provide a resource to track the expression of any gene in the developing fly heart, which can serve as a reference to study genetic perturbations and cardiac diseases.
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Affiliation(s)
- Xiaohu Huang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yulong Fu
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hangnoh Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yunpo Zhao
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wendy Yang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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9
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Chen C, Ge Y, Lu L. Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1185377. [PMID: 37636094 PMCID: PMC10453814 DOI: 10.3389/fpls.2023.1185377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.
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Affiliation(s)
- Ce Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yining Ge
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lingli Lu
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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10
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Galow AM, Brenmoehl J, Hoeflich A. Synergistic effects of hormones on structural and functional maturation of cardiomyocytes and implications for heart regeneration. Cell Mol Life Sci 2023; 80:240. [PMID: 37541969 PMCID: PMC10403476 DOI: 10.1007/s00018-023-04894-6] [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: 04/04/2023] [Revised: 07/18/2023] [Accepted: 07/22/2023] [Indexed: 08/06/2023]
Abstract
The limited endogenous regenerative capacity of the human heart renders cardiovascular diseases a major health threat, thus motivating intense research on in vitro heart cell generation and cell replacement therapies. However, so far, in vitro-generated cardiomyocytes share a rather fetal phenotype, limiting their utility for drug testing and cell-based heart repair. Various strategies to foster cellular maturation provide some success, but fully matured cardiomyocytes are still to be achieved. Today, several hormones are recognized for their effects on cardiomyocyte proliferation, differentiation, and function. Here, we will discuss how the endocrine system impacts cardiomyocyte maturation. After detailing which features characterize a mature phenotype, we will contemplate hormones most promising to induce such a phenotype, the routes of their action, and experimental evidence for their significance in this process. Due to their pleiotropic effects, hormones might be not only valuable to improve in vitro heart cell generation but also beneficial for in vivo heart regeneration. Accordingly, we will also contemplate how the presented hormones might be exploited for hormone-based regenerative therapies.
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Affiliation(s)
- Anne-Marie Galow
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.
| | - Julia Brenmoehl
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Andreas Hoeflich
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
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11
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Yang H, Song S, Li J, Li Y, Feng J, Sun Q, Qiu X, Chen Z, Bai X, Liu X, Lian H, Liu L, Bai Y, Zhang G, Nie Y. Omentin-1 drives cardiomyocyte cell cycle arrest and metabolic maturation by interacting with BMP7. Cell Mol Life Sci 2023; 80:186. [PMID: 37344704 PMCID: PMC11071824 DOI: 10.1007/s00018-023-04829-1] [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: 08/27/2022] [Revised: 04/05/2023] [Accepted: 06/04/2023] [Indexed: 06/23/2023]
Abstract
Mammalian cardiomyocytes (CMs) undergo maturation during postnatal heart development to meet the increased demands of growth. Here, we found that omentin-1, an adipokine, facilitates CM cell cycle arrest and metabolic maturation. Deletion of omentin-1 causes mouse heart enlargement and dysfunction in adulthood and CM maturation retardation in juveniles, including delayed cell cycle arrest and reduced fatty acid oxidation. Through RNA sequencing, molecular docking analysis, and proximity ligation assays, we found that omentin-1 regulates CM maturation by interacting directly with bone morphogenetic protein 7 (BMP7). Omentin-1 prevents BMP7 from binding to activin type II receptor B (ActRIIB), subsequently decreasing the downstream pathways mothers against DPP homolog 1 (SMAD1)/Yes-associated protein (YAP) and p38 mitogen-activated protein kinase (p38 MAPK). In addition, omentin-1 is required and sufficient for the maturation of human embryonic stem cell-derived CMs. Together, our findings reveal that omentin-1 is a pro-maturation factor for CMs that is essential for postnatal heart development and cardiac function maintenance.
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Affiliation(s)
- Huijun Yang
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
- Department of Cardiovascular Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Shen Song
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Jiacheng Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Yandong Li
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Jie Feng
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Quan Sun
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of Geriatric Medicine, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Street, Xiangya Road, Kaifu District, Changsha, 410008, People's Republic of China
| | - Xueting Qiu
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of Geriatric Medicine, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Street, Xiangya Road, Kaifu District, Changsha, 410008, People's Republic of China
| | - Ziwei Chen
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Xue Bai
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Xinchang Liu
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Hong Lian
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Lihui Liu
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China
| | - Yongping Bai
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Department of Geriatric Medicine, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Street, Xiangya Road, Kaifu District, Changsha, 410008, People's Republic of China.
| | - Guogang Zhang
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Department of Geriatric Medicine, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Street, Xiangya Road, Kaifu District, Changsha, 410008, People's Republic of China.
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Street, Beilishi Road, Xicheng District, Beijing, 100037, People's Republic of China.
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, 518057, China.
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, 450046, China.
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12
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Lin W, Chen X, Wang D, Lu R, Zhang C, Niu Z, Chen J, Ruan X, Wang X. Single-nucleus ribonucleic acid-sequencing and spatial transcriptomics reveal the cardioprotection of Shexiang Baoxin Pill (SBP) in mice with myocardial ischemia-reperfusion injury. Front Pharmacol 2023; 14:1173649. [PMID: 37229263 PMCID: PMC10203427 DOI: 10.3389/fphar.2023.1173649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
Aim: The Shexiang Baoxin Pill (SBP) has been extensively used to treat cardiovascular diseases in China for four decades, and its clinical efficacy has been widely approved. However, the mechanism by which this is achieved remains largely unexplored. Research attempting to understand the underlying mechanism is ongoing, but the findings are controversial. Here, we aimed to explore the possible mechanism of SBP in myocardial ischemia-reperfusion (I/R) injury using heart single-nucleus and spatial ribonucleic acid (RNA) sequencing. Methods: We established a murine myocardial I/R injury model in C57BL/6 mice by ligating and recanalizing the left coronary artery anterior descending branch. Subsequently, single-nucleus RNA-seq and spatial transcriptomics were performed on mice cardiac tissue. We initially assessed the status of cell types and subsets in the model administered with or without SBP. Results: We used single-nucleus RNA sequencing to comprehensively analyze cell types in the cardiac tissue of sham, I/R, and SBP mice. Nine samples from nine individuals were analyzed, and 75,546 cells were obtained. We classified the cells into 28 clusters based on their expression characteristics and annotated them into seven cell types: cardiomyocytes, endothelial cells, fibroblasts, myeloid cells, smooth muscle cells, B cells, and T cells. The SBP group had distinct cellular compositions and features than the I/R group. Furthermore, SBP-induced cardioprotection against I/R was associated with enhanced cardiac contractility, reduced endocardial cell injury, increased endocardial-mediated angiogenesis, and inhibited fibroblast proliferation. In addition, macrophages had active properties. Conclusion: SBP improves the early LVEF of I/R mice and has a cardioprotective effect. Through sequencing analysis, we observed that SBP can increase the gene expression of Nppb and Npr3 in the infarct area of the heart. Npr3 is related to vascular generation mediated by endocardial cells and requires further research. In addition, SBP increases the number of fibroblasts, inhibits the expression of genes related to fibroblast activation and proliferation, and increases the transformation of endothelial cells into fibroblasts. These findings will help to indicate directions for further research.
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Affiliation(s)
- Wenyong Lin
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Cardiovascular Research Institute of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Chen
- Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dongyuan Wang
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Cardiovascular Research Institute of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ruixia Lu
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Cardiovascular Research Institute of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chunling Zhang
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhenchao Niu
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Cardiovascular Research Institute of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jie Chen
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaofen Ruan
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Cardiovascular Research Institute of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaolong Wang
- Branch of National Clinical Research Center for Chinese Medicine Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Cardiovascular Research Institute of Traditional Chinese Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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13
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Miranda AMA, Janbandhu V, Maatz H, Kanemaru K, Cranley J, Teichmann SA, Hübner N, Schneider MD, Harvey RP, Noseda M. Single-cell transcriptomics for the assessment of cardiac disease. Nat Rev Cardiol 2023; 20:289-308. [PMID: 36539452 DOI: 10.1038/s41569-022-00805-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease is the leading cause of death globally. An advanced understanding of cardiovascular disease mechanisms is required to improve therapeutic strategies and patient risk stratification. State-of-the-art, large-scale, single-cell and single-nucleus transcriptomics facilitate the exploration of the cardiac cellular landscape at an unprecedented level, beyond its descriptive features, and can further our understanding of the mechanisms of disease and guide functional studies. In this Review, we provide an overview of the technical challenges in the experimental design of single-cell and single-nucleus transcriptomics studies, as well as a discussion of the type of inferences that can be made from the data derived from these studies. Furthermore, we describe novel findings derived from transcriptomics studies for each major cardiac cell type in both health and disease, and from development to adulthood. This Review also provides a guide to interpreting the exhaustive list of newly identified cardiac cell types and states, and highlights the consensus and discordances in annotation, indicating an urgent need for standardization. We describe advanced applications such as integration of single-cell data with spatial transcriptomics to map genes and cells on tissue and define cellular microenvironments that regulate homeostasis and disease progression. Finally, we discuss current and future translational and clinical implications of novel transcriptomics approaches, and provide an outlook of how these technologies will change the way we diagnose and treat heart disease.
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Affiliation(s)
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Henrike Maatz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Deptartment of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
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14
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Zhao Y, van de Leemput J, Han Z. The opportunities and challenges of using Drosophila to model human cardiac diseases. Front Physiol 2023; 14:1182610. [PMID: 37123266 PMCID: PMC10130661 DOI: 10.3389/fphys.2023.1182610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
The Drosophila heart tube seems simple, yet it has notable anatomic complexity and contains highly specialized structures. In fact, the development of the fly heart tube much resembles that of the earliest stages of mammalian heart development, and the molecular-genetic mechanisms driving these processes are highly conserved between flies and humans. Combined with the fly's unmatched genetic tools and a wide variety of techniques to assay both structure and function in the living fly heart, these attributes have made Drosophila a valuable model system for studying human heart development and disease. This perspective focuses on the functional and physiological similarities between fly and human hearts. Further, it discusses current limitations in using the fly, as well as promising prospects to expand the capabilities of Drosophila as a research model for studying human cardiac diseases.
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Affiliation(s)
- Yunpo Zhao
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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15
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Hasper J, Welle K, Hryhorenko J, Ghaemmaghami S, Buchwalter A. Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes. Mol Syst Biol 2023; 19:e11393. [PMID: 36929723 PMCID: PMC10090950 DOI: 10.15252/msb.202211393] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
The lifespans of proteins range from minutes to years within mammalian tissues. Protein lifespan is relevant to organismal aging, as long-lived proteins accrue damage over time. It is unclear how protein lifetime is shaped by tissue context, where both cell turnover and proteolytic degradation contribute to protein turnover. We develop turnover and replication analysis by 15 N isotope labeling (TRAIL) to quantify protein and cell lifetimes with high precision and demonstrate that cell turnover, sequence-encoded features, and environmental factors modulate protein lifespan across tissues. Cell and protein turnover flux are comparable in proliferative tissues, while protein turnover outpaces cell turnover in slowly proliferative tissues. Physicochemical features such as hydrophobicity, charge, and disorder influence protein turnover in slowly proliferative tissues, but protein turnover is much less sequence-selective in highly proliferative tissues. Protein lifetimes vary nonrandomly across tissues after correcting for cell turnover. Multiprotein complexes such as the ribosome have consistent lifetimes across tissues, while mitochondria, peroxisomes, and lipid droplets have variable lifetimes. TRAIL can be used to explore how environment, aging, and disease affect tissue homeostasis.
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Affiliation(s)
- John Hasper
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kevin Welle
- University of Rochester Mass Spectrometry Resource Laboratory, Rochester, NY, USA
| | - Jennifer Hryhorenko
- University of Rochester Mass Spectrometry Resource Laboratory, Rochester, NY, USA
| | - Sina Ghaemmaghami
- University of Rochester Mass Spectrometry Resource Laboratory, Rochester, NY, USA.,Department of Biology, University of Rochester, Rochester, NY, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
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16
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Li Z, Solomonidis EG, Berkeley B, Tang MNH, Stewart KR, Perez-Vicencio D, McCracken IR, Spiroski AM, Gray GA, Barton AK, Sellers SL, Riley PR, Baker AH, Brittan M. Multi-species meta-analysis identifies transcriptional signatures associated with cardiac endothelial responses in the ischaemic heart. Cardiovasc Res 2023; 119:136-154. [PMID: 36082978 PMCID: PMC10022865 DOI: 10.1093/cvr/cvac151] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/04/2022] [Accepted: 08/10/2022] [Indexed: 11/12/2022] Open
Abstract
AIM Myocardial infarction remains the leading cause of heart failure. The adult human heart lacks the capacity to undergo endogenous regeneration. New blood vessel growth is integral to regenerative medicine necessitating a comprehensive understanding of the pathways that regulate vascular regeneration. We sought to define the transcriptomic dynamics of coronary endothelial cells following ischaemic injuries in the developing and adult mouse and human heart and to identify new mechanistic insights and targets for cardiovascular regeneration. METHODS AND RESULTS We carried out a comprehensive meta-analysis of integrated single-cell RNA-sequencing data of coronary vascular endothelial cells from the developing and adult mouse and human heart spanning healthy and acute and chronic ischaemic cardiac disease. We identified species-conserved gene regulatory pathways aligned to endogenous neovascularization. We annotated injury-associated temporal shifts of the endothelial transcriptome and validated four genes: VEGF-C, KLF4, EGR1, and ZFP36. Moreover, we showed that ZFP36 regulates human coronary endothelial cell proliferation and defined that VEGF-C administration in vivo enhances clonal expansion of the cardiac vasculature post-myocardial infarction. Finally, we constructed a coronary endothelial cell meta-atlas, CrescENDO, to empower future in-depth research to target pathways associated with coronary neovascularization. CONCLUSION We present a high-resolution single-cell meta-atlas of healthy and injured coronary endothelial cells in the mouse and human heart, revealing a suite of novel targets with great potential to promote vascular regeneration, and providing a rich resource for therapeutic development.
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Affiliation(s)
- Ziwen Li
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Emmanouil G Solomonidis
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Bronwyn Berkeley
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Michelle Nga Huen Tang
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Katherine Ross Stewart
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Daniel Perez-Vicencio
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Ian R McCracken
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Ana-Mishel Spiroski
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Gillian A Gray
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Anna K Barton
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Stephanie L Sellers
- Division of Cardiology, Centre for Heart Lung Innovation, Providence Research, University of British Columbia, Vancouver, Canada
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - Andrew H Baker
- Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
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17
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Bak ST, Harvald EB, Ellman DG, Mathiesen SB, Chen T, Fang S, Andersen KS, Fenger CD, Burton M, Thomassen M, Andersen DC. Ploidy-stratified single cardiomyocyte transcriptomics map Zinc Finger E-Box Binding Homeobox 1 to underly cardiomyocyte proliferation before birth. Basic Res Cardiol 2023; 118:8. [PMID: 36862248 PMCID: PMC9981540 DOI: 10.1007/s00395-023-00979-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/31/2022] [Accepted: 01/21/2023] [Indexed: 03/03/2023]
Abstract
Whereas cardiomyocytes (CMs) in the fetal heart divide, postnatal CMs fail to undergo karyokinesis and/or cytokinesis and therefore become polyploid or binucleated, a key process in terminal CM differentiation. This switch from a diploid proliferative CM to a terminally differentiated polyploid CM remains an enigma and seems an obstacle for heart regeneration. Here, we set out to identify the transcriptional landscape of CMs around birth using single cell RNA sequencing (scRNA-seq) to predict transcription factors (TFs) involved in CM proliferation and terminal differentiation. To this end, we established an approach combining fluorescence activated cell sorting (FACS) with scRNA-seq of fixed CMs from developing (E16.5, P1, and P5) mouse hearts, and generated high-resolution single-cell transcriptomic maps of in vivo diploid and tetraploid CMs, increasing the CM resolution. We identified TF-networks regulating the G2/M phases of developing CMs around birth. ZEB1 (Zinc Finger E-Box Binding Homeobox 1), a hereto unknown TF in CM cell cycling, was found to regulate the highest number of cell cycle genes in cycling CMs at E16.5 but was downregulated around birth. CM ZEB1-knockdown reduced proliferation of E16.5 CMs, while ZEB1 overexpression at P0 after birth resulted in CM endoreplication. These data thus provide a ploidy stratified transcriptomic map of developing CMs and bring new insight to CM proliferation and endoreplication identifying ZEB1 as a key player in these processes.
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Affiliation(s)
- Sara Thornby Bak
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Eva Bang Harvald
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Ditte Gry Ellman
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Sabrina Bech Mathiesen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Ting Chen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Shu Fang
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Kristian Skriver Andersen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | | | - Mark Burton
- Clinical Institute, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Clinical Institute, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Ditte Caroline Andersen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark.
- Clinical Institute, University of Southern Denmark, Odense, Denmark.
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18
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Wang T, Zhou LY, Li XM, Liu F, Liang L, Chen XZ, Ju J, Ponnusamy M, Wang K, Liu CY, Yan KW, Wang K. ABRO1 arrests cardiomyocyte proliferation and myocardial repair by suppressing PSPH. Mol Ther 2023; 31:847-865. [PMID: 36639869 PMCID: PMC10014284 DOI: 10.1016/j.ymthe.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
The role of Abraxas 2 (ABRO1 or KIAA0157), a component of the lysine63-linked deubiquitinating system, in the cardiomyocyte proliferation and myocardial regeneration is unknown. Here, we found that ABRO1 regulates cardiomyocyte proliferation and cardiac regeneration in the postnatal heart by targeting METTL3-mediated m6A methylation of Psph mRNA. The deletion of ABRO1 increased cardiomyocyte proliferation in hearts and restored the heart function after myocardial injury. On the contrary, ABRO1 overexpression significantly inhibited the neonatal cardiomyocyte proliferation and cardiac regeneration in mouse hearts. The mechanism by which ABRO1 regulates cardiomyocyte proliferation mainly involved METTL3-mediated Psph mRNA methylation and CDK2 phosphorylation. In the early postnatal period, METTL3-dependent m6A methylation promotes cardiomyocyte proliferation by hypermethylation of Psph mRNA and upregulating PSPH expression. PSPH dephosphorylates cyclin-dependent kinase 2 (CDK2), a positive regulator of cell cycle, at Thr14/Tyr15 and increases its activity. Upregulation of ABRO1 restricts METTL3 activity and halts the cardiomyocyte proliferation in the postnatal hearts. Thus, our study reveals that ABRO1 is an essential contributor in the cell cycle withdrawal and attenuation of proliferative response in the postnatal cardiomyocytes and could act as a potential target to accelerate cardiomyocyte proliferation and cardiac repair in the adult heart.
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Affiliation(s)
- Tao Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China; Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China
| | - Lu-Yu Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xin-Min Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Fang Liu
- Center of Diabetic Systems Medicine, Guangxi Key Laboratory of Excellence, and Department of Anatomy, Guilin Medical University, Guilin 541004, China
| | - Lin Liang
- State Key Laboratory of Cardiovascular Disease, Heart Failure Center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100037, China
| | - Xin-Zhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Jie Ju
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Murugavel Ponnusamy
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
| | - Kao-Wen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China; Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China.
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19
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Bock-Marquette I, Maar K, Maar S, Lippai B, Faskerti G, Gallyas F, Olson EN, Srivastava D. Thymosin beta-4 denotes new directions towards developing prosperous anti-aging regenerative therapies. Int Immunopharmacol 2023; 116:109741. [PMID: 36709593 DOI: 10.1016/j.intimp.2023.109741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
Our dream of defeating the processes of organ damage and aging remains a challenge scientists pursued for hundreds of years. Although the goal is to successfully treat the body as a whole, steps towards regenerating individual organs are even considered significant. Since initial approaches utilizing only progenitor cells appear limited, we propose interconnecting our collective knowledge regarding aging and embryonic development may lead to the discovery of molecules which provide alternatives to effectively reverse cellular damage. In this review, we introduce and summarize our results regarding Thymosin beta-4 (TB4) to support our hypothesis using the heart as model system. Accordingly, we investigated the developmental expression of TB4 in mouse embryos and determined the impact of the molecule in adult animals by systemically injecting the peptide following acute cardiac infarction or with no injury. Our results proved, TB4 is expressed in the developing heart and promotes cardiac cell migration and survival. In adults, the peptide enhances myocyte survival and improves cardiac function after coronary artery ligation. Moreover, intravenous injections of TB4 alter the morphology of the adult epicardium, and the changes resemble the characteristics of the embryo. Reactivation of the embryonic program became equally reflected by the increased number of cardiac vessels and by the alteration of the gene expression profile typical of the embryonic state. Moreover, we discovered TB4 is capable of epicardial progenitor activation, and revealed the effect is independent of hypoxic injury. By observing the above results, we believe, further discoveries and consequential postnatal administration of developmentally relevant candidate molecules such as TB4 may likely result in reversing aging processes and accelerate organ regeneration in the human body.
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Affiliation(s)
- Ildiko Bock-Marquette
- Department of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs H-7624, Hungary; Szentagothai Research Centre, Research Group of Regenerative Science, Sport and Medicine, University of Pecs, Pecs H-7624, Hungary.
| | - Klaudia Maar
- Department of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs H-7624, Hungary; Szentagothai Research Centre, Research Group of Regenerative Science, Sport and Medicine, University of Pecs, Pecs H-7624, Hungary
| | - Szabolcs Maar
- Department of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs H-7624, Hungary; Szentagothai Research Centre, Research Group of Regenerative Science, Sport and Medicine, University of Pecs, Pecs H-7624, Hungary
| | - Balint Lippai
- Department of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs H-7624, Hungary; Szentagothai Research Centre, Research Group of Regenerative Science, Sport and Medicine, University of Pecs, Pecs H-7624, Hungary
| | - Gabor Faskerti
- Department of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs H-7624, Hungary; Szentagothai Research Centre, Research Group of Regenerative Science, Sport and Medicine, University of Pecs, Pecs H-7624, Hungary
| | - Ferenc Gallyas
- Department of Biochemistry and Medical Chemistry, University of Pecs, Medical School, Pecs H-7624, Hungary; Szentagothai Research Centre, Research Group of Regenerative Science, Sport and Medicine, University of Pecs, Pecs H-7624, Hungary
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and Roddenberry Stem Cell Center, Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
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20
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Liu C, Hong T, Yu L, Chen Y, Wang S, Ren Z. Single-nucleus RNA and ATAC sequencing uncovers the molecular and cellular characteristics in the musk gland of Chinese forest musk deer (Moschus berezovskii). FASEB J 2023; 37:e22742. [PMID: 36583723 DOI: 10.1096/fj.202201372r] [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: 08/20/2022] [Revised: 11/21/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022]
Abstract
The Chinese forest musk deer (FMD; Moschus berezovskii) is an endangered artiodactyl mammal. Musk secreted by the musk gland of male has extremely high economic and medicinal value. However, the molecular and cellular characteristics of the musk gland have not been studied. Here, we investigated the diversity and transcriptional composition of musk gland cell types and the effect of cell type-specific chromatin accessibility on gene expression using single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq) association analysis. Based on uniform manifold approximation and projection (UMAP) analysis, we identified 13 cell types from the musk gland, which included two different acinar cells (cluster 0 and cluster 10). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that many pathways related to musk secretion were enriched in acinar cells. Our analysis also revealed acinar cell core transcription factors and core target genes, and further constructed acinar cell-specific regulatory networks. In cluster 0, 11 core target genes (Nedd4l, Adcy9, Akr1c1, Vapb, Me1, Acsl1, Acss3, Srd5a1, Scnn1a, Acadm, and Nceh1) possibly related to musk secretion were regulated by 24 core transcription factors (SP3, NFIC, NR6A1, EHF, RUNX1, TFAP2A, RREB1, GRHL2, NFIB, ELF1, MAX, KLF5, REL, HES1, POU2F3, TFDP1, NR2C1, ATF7, MEIS1, NR4A2, NFIA, PBX1, ZNF652, and NFKB1). In cluster 10, four core target genes (Akr1c1, Pcca, Atp1b1, and Sgk1) possibly related to musk secretion were regulated by 10 core transcription factors (BARX2, EHF, PBX1, RUNX1, NFIB, FOXP1, KLF3, KLF6, ETV6, and NR3C2). Moreover, the credibility of snRNA-seq and snATAC-seq data was verified by fluorescence in situ hybridization and immunohistochemistry. Finally, cell communication analysis demonstrated that the two types of acinar cells mainly have communications in musk secretion-related processes. In conclusion, we provided important insights and invaluable resources for the molecular and cellular characteristics of the musk gland, which will lay a foundation for the study of musk secretion mechanism in the future.
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Affiliation(s)
- Chenmiao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Tingting Hong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lin Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuan Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhanjun Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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21
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Long X, Yuan X, Du J. Single-cell and spatial transcriptomics: Advances in heart development and disease applications. Comput Struct Biotechnol J 2023; 21:2717-2731. [PMID: 37181659 PMCID: PMC10173363 DOI: 10.1016/j.csbj.2023.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Current transcriptomics technologies, including bulk RNA-seq, single-cell RNA sequencing (scRNA-seq), single-nucleus RNA-sequencing (snRNA-seq), and spatial transcriptomics (ST), provide novel insights into the spatial and temporal dynamics of gene expression during cardiac development and disease processes. Cardiac development is a highly sophisticated process involving the regulation of numerous key genes and signaling pathways at specific anatomical sites and developmental stages. Exploring the cell biological mechanisms involved in cardiogenesis also contributes to congenital heart disease research. Meanwhile, the severity of distinct heart diseases, such as coronary heart disease, valvular disease, cardiomyopathy, and heart failure, is associated with cellular transcriptional heterogeneity and phenotypic alteration. Integrating transcriptomic technologies in the clinical diagnosis and treatment of heart diseases will aid in advancing precision medicine. In this review, we summarize applications of scRNA-seq and ST in the cardiac field, including organogenesis and clinical diseases, and provide insights into the promise of single-cell and spatial transcriptomics in translational research and precision medicine.
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Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Correspondence to: Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, 74 Lin Jiang Road Chongqing 4000l0, China.
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Correspondence to: Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, 74 Lin Jiang Road Chongqing 400010, China.
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22
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Gu Y, Zhou Y, Ju S, Liu X, Zhang Z, Guo J, Gao J, Zang J, Sun H, Chen Q, Wang J, Xu J, Xu Y, Chen Y, Guo Y, Dai J, Ma H, Wang C, Jin G, Li C, Xia Y, Shen H, Yang Y, Guo X, Hu Z. Multi-omics profiling visualizes dynamics of cardiac development and functions. Cell Rep 2022; 41:111891. [PMID: 36577384 DOI: 10.1016/j.celrep.2022.111891] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/14/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022] Open
Abstract
Cardiogenesis is a tightly regulated dynamic process through a continuum of differentiation and proliferation events. Key factors and pathways governing this process remain incompletely understood. Here, we investigate mice hearts from embryonic day 10.5 to postnatal week 8 and dissect developmental changes in phosphoproteome-, proteome-, metabolome-, and transcriptome-encompassing cardiogenesis and cardiac maturation. We identify mitogen-activated protein kinases as core kinases involved in transcriptional regulation by mediating the phosphorylation of chromatin remodeling proteins during early cardiogenesis. We construct the reciprocal regulatory network of transcription factors (TFs) and identify a series of TFs controlling early cardiogenesis involved in cycling-dependent proliferation. After birth, we identify cardiac resident macrophages with high arachidonic acid metabolism activities likely involved in the clearance of injured apoptotic cardiomyocytes. Together, our comprehensive multi-omics data offer a panoramic view of cardiac development and maturation that provides a resource for further in-depth functional exploration.
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Affiliation(s)
- Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yan Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Sihan Ju
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Zicheng Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jia Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jimiao Gao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jie Zang
- School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hao Sun
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Qi Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jinghan Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jiani Xu
- School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yiqun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yingjia Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Chaojun Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yang Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China.
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23
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Calcagno DM, Taghdiri N, Ninh VK, Mesfin JM, Toomu A, Sehgal R, Lee J, Liang Y, Duran JM, Adler E, Christman KL, Zhang K, Sheikh F, Fu Z, King KR. Single-cell and spatial transcriptomics of the infarcted heart define the dynamic onset of the border zone in response to mechanical destabilization. NATURE CARDIOVASCULAR RESEARCH 2022; 1:1039-1055. [PMID: 39086770 PMCID: PMC11290420 DOI: 10.1038/s44161-022-00160-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/03/2022] [Indexed: 08/02/2024]
Abstract
The border zone (BZ) of the infarcted heart is a geographically complex and biologically enigmatic interface separating poorly perfused infarct zones (IZs) from remote zones (RZs). The cellular and molecular mechanisms of myocardial BZs are not well understood because microdissection inevitably combines them with uncontrolled amounts of RZs and IZs. Here, we use single-cell/nucleus RNA sequencing, spatial transcriptomics and multiplexed RNA fluorescence in situ hybridization to redefine the BZ based on cardiomyocyte transcriptomes. BZ1 (Nppa + Xirp2 -) forms a hundreds-of-micrometer-thick layer of morphologically intact cells adjacent to RZs that are detectable within an hour of injury. Meanwhile, BZ2 (Nppa + Xirp2 +) forms a near-single-cell-thick layer of morphologically distorted cardiomyocytes at the IZ edge that colocalize with matricellular protein-expressing myofibroblasts and express predominantly mechanotransduction genes. Surprisingly, mechanical injury alone is sufficient to induce BZ genes. We propose a 'loss of neighbor' hypothesis to explain how ischemic cell death mechanically destabilizes the BZ to induce its transcriptional response.
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Affiliation(s)
- D. M. Calcagno
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally: D.M. Calcagno, N. Taghdiri
| | - N. Taghdiri
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- These authors contributed equally: D.M. Calcagno, N. Taghdiri
| | - V. K. Ninh
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J. M. Mesfin
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - A. Toomu
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - R. Sehgal
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - J. Lee
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Y. Liang
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J. M. Duran
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - E. Adler
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - K. L. Christman
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - K. Zhang
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - F. Sheikh
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Z. Fu
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - K. R. King
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Division of Cardiology and Cardiovascular Institute, Department of Medicine, University of California San Diego, La Jolla, CA, USA
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24
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Li Z, Yao F, Yu P, Li D, Zhang M, Mao L, Shen X, Ren Z, Wang L, Zhou B. Postnatal state transition of cardiomyocyte as a primary step in heart maturation. Protein Cell 2022; 13:842-862. [PMID: 35394262 PMCID: PMC9237199 DOI: 10.1007/s13238-022-00908-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/17/2022] [Indexed: 11/26/2022] Open
Abstract
Postnatal heart maturation is the basis of normal cardiac function and provides critical insights into heart repair and regenerative medicine. While static snapshots of the maturing heart have provided much insight into its molecular signatures, few key events during postnatal cardiomyocyte maturation have been uncovered. Here, we report that cardiomyocytes (CMs) experience epigenetic and transcriptional decline of cardiac gene expression immediately after birth, leading to a transition state of CMs at postnatal day 7 (P7) that was essential for CM subtype specification during heart maturation. Large-scale single-cell analysis and genetic lineage tracing confirm the presence of transition state CMs at P7 bridging immature state and mature states. Silencing of key transcription factor JUN in P1-hearts significantly repressed CM transition, resulting in perturbed CM subtype proportions and reduced cardiac function in mature hearts. In addition, transplantation of P7-CMs into infarcted hearts exhibited cardiac repair potential superior to P1-CMs. Collectively, our data uncover CM state transition as a key event in postnatal heart maturation, which not only provides insights into molecular foundations of heart maturation, but also opens an avenue for manipulation of cardiomyocyte fate in disease and regenerative medicine.
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Affiliation(s)
- Zheng Li
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, 518057, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100037, China
| | - Fang Yao
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, 518057, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100037, China
| | - Peng Yu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Dandan Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Mingzhi Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Lin Mao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Xiaomeng Shen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Zongna Ren
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China
| | - Li Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, 518057, China.
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100037, China.
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, People's Republic of China.
| | - Bingying Zhou
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, 518057, China.
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
- Key Laboratory of Pluripotent Stem Cells in Cardiac Repair and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100037, China.
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, People's Republic of China.
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25
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Juan AM, Foong YH, Thorvaldsen JL, Lan Y, Leu NA, Rurik JG, Li L, Krapp C, Rosier CL, Epstein JA, Bartolomei MS. Tissue-specific Grb10/Ddc insulator drives allelic architecture for cardiac development. Mol Cell 2022; 82:3613-3631.e7. [PMID: 36108632 PMCID: PMC9547965 DOI: 10.1016/j.molcel.2022.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
Abstract
Allele-specific expression of imprinted gene clusters is governed by gametic DNA methylation at master regulators called imprinting control regions (ICRs). Non-gametic or secondary differentially methylated regions (DMRs) at promoters and exonic regions reinforce monoallelic expression but do not control an entire cluster. Here, we unveil an unconventional secondary DMR that is indispensable for tissue-specific imprinting of two previously unlinked genes, Grb10 and Ddc. Using polymorphic mice, we mapped an intronic secondary DMR at Grb10 with paternal-specific CTCF binding (CBR2.3) that forms contacts with Ddc. Deletion of paternal CBR2.3 removed a critical insulator, resulting in substantial shifting of chromatin looping and ectopic enhancer-promoter contacts. Destabilized gene architecture precipitated abnormal Grb10-Ddc expression with developmental consequences in the heart and muscle. Thus, we redefine the Grb10-Ddc imprinting domain by uncovering an unconventional intronic secondary DMR that functions as an insulator to instruct the tissue-specific, monoallelic expression of multiple genes-a feature previously ICR exclusive.
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Affiliation(s)
- Aimee M Juan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yee Hoon Foong
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicolae A Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Joel G Rurik
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Li
- Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Krapp
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Casey L Rosier
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Epstein
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, Department of Medicine, Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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26
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Kuwabara JT, Hara A, Heckl JR, Peña B, Bhutada S, DeMaris R, Ivey MJ, DeAngelo LP, Liu X, Park J, Jahansooz JR, Mestroni L, McKinsey TA, Apte SS, Tallquist MD. Regulation of extracellular matrix composition by fibroblasts during perinatal cardiac maturation. J Mol Cell Cardiol 2022; 169:84-95. [PMID: 35569524 PMCID: PMC10149041 DOI: 10.1016/j.yjmcc.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Cardiac fibroblasts are the main non-myocyte population responsible for extracellular matrix (ECM) production. During perinatal development, fibroblast expansion coincides with the transition from hyperplastic to hypertrophic myocardial growth. Therefore, we investigated the consequences of fibroblast loss at the time of cardiomyocyte maturation by depleting fibroblasts in the perinatal mouse. METHODS AND RESULTS We evaluated the microenvironment of the perinatal heart in the absence of fibroblasts and the potential functional impact of fibroblast loss in regulation of cardiomyocyte cell cycle arrest and binucleation. Cre-mediated expression of diphtheria toxin A in PDGFRα expressing cells immediately after birth eliminated 70-80% of the cardiac fibroblasts. At postnatal day 5, hearts lacking fibroblasts appeared similar to controls with normal morphology and comparable numbers of endothelial and smooth muscle cells, despite a pronounced reduction in fibrillar collagen. Immunoblotting and proteomic analysis of control and fibroblast-deficient hearts identified differential abundance of several ECM proteins. In addition, fibroblast loss decreased tissue stiffness and resulted in increased cardiomyocyte mitotic index, DNA synthesis, and cytokinesis. Moreover, decellularized matrix from fibroblast-deficient hearts promoted cardiomyocyte DNA replication. While cardiac architecture was not overtly affected by fibroblast reduction, few pups survived past postnatal day 11, suggesting an overall requirement for PDGFRα expressing fibroblasts. CONCLUSIONS These studies demonstrate the key role of fibroblasts in matrix production and cardiomyocyte cross-talk during mouse perinatal heart maturation and revealed that fibroblast-derived ECM may modulate cardiomyocyte maturation in vivo. Neonatal depletion of fibroblasts demonstrated that although hearts can tolerate reduced ECM composition, fibroblast loss eventually leads to perinatal death as the approach simultaneously reduced fibroblast populations in other organs.
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Affiliation(s)
- Jill T Kuwabara
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America; Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Akitoshi Hara
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Jack R Heckl
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America; Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Brisa Peña
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - Sumit Bhutada
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, United States of America
| | - Regan DeMaris
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Malina J Ivey
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America; Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America; Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH 45267, United States of America
| | - Lydia P DeAngelo
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Xiaoting Liu
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Juwon Park
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Julia R Jahansooz
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America
| | - Luisa Mestroni
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - Timothy A McKinsey
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, United States of America
| | - Michelle D Tallquist
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, United States of America.
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27
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Hu Y, Zhang Y, Liu Y, Gao Y, San T, Li X, Song S, Yan B, Zhao Z. Advances in application of single-cell RNA sequencing in cardiovascular research. Front Cardiovasc Med 2022; 9:905151. [PMID: 35958408 PMCID: PMC9360414 DOI: 10.3389/fcvm.2022.905151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides high-resolution information on transcriptomic changes at the single-cell level, which is of great significance for distinguishing cell subtypes, identifying stem cell differentiation processes, and identifying targets for disease treatment. In recent years, emerging single-cell RNA sequencing technologies have been used to make breakthroughs regarding decoding developmental trajectories, phenotypic transitions, and cellular interactions in the cardiovascular system, providing new insights into cardiovascular disease. This paper reviews the technical processes of single-cell RNA sequencing and the latest progress based on single-cell RNA sequencing in the field of cardiovascular system research, compares single-cell RNA sequencing with other single-cell technologies, and summarizes the extended applications and advantages and disadvantages of single-cell RNA sequencing. Finally, the prospects for applying single-cell RNA sequencing in the field of cardiovascular research are discussed.
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Affiliation(s)
- Yue Hu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Ying Zhang
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Yutong Liu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Yan Gao
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Tiantian San
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Xiaoying Li
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- Department of Emergency, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Sensen Song
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Binglong Yan
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Zhuo Zhao
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- *Correspondence: Zhuo Zhao
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28
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Zheng Y, Gao W, Zhang Q, Cheng X, Liu Y, Qi Z, Li T. Ferroptosis and Autophagy-Related Genes in the Pathogenesis of Ischemic Cardiomyopathy. Front Cardiovasc Med 2022; 9:906753. [PMID: 35845045 PMCID: PMC9279674 DOI: 10.3389/fcvm.2022.906753] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Obesity plays an important role in type 2 diabetes mellitus (T2DM) and myocardial infarction (MI). Ferroptosis and ferritinophagy are related to metabolic pathways, such as fatty acid metabolism and mitochondrial respiration. We aimed to investigate the ferroptosis- and autophagy-related differentially expressed genes (DEGs) that might be potential targets for MI progression. Methods GSE116250 was analyzed to obtain DEGs. A Venn diagram was used to obtain the overlapping ferroptosis- and autophagy-related DEGs. The enrichment pathway analysis was performed and the hub genes were obtained. Pivotal miRNAs, transcription factors, and drugs with the hub genes interactions were also predicted. The MI mice model was constructed, and qPCR analysis and single-cell sequencing were used to validate the hub genes. Results Utilizing the limma package and the Venn diagram, 26 ferroptosis-related and 29 autophagy-related DEGs were obtained. The list of ferroptosis-related DEGs was analyzed, which were involved in the cellular response to a toxic substance, cellular oxidant detoxification, and the IL-17 signaling pathway. The list of autophagy-related DEGs was involved in the regulation of autophagy, the regulation of JAK-STAT signaling pathway, and the regulation of MAPK cascade. In the protein-protein interaction network, the hub DEGs, such as IL-6, PTGS2, JUN, NQO1, NOS3, LEPR, NAMPT, CDKN2A, CDKN1A, and Snai1, were obtained. After validation using qPCR analysis in the MI mice model and single-cell sequencing, the 10 hub genes can be the potential targets for MI deterioration. Conclusion The screened hub genes, IL-6, PTGS2, JUN, NQO1, NOS3, LEPR, NAMPT, CDKN2A, CDKN1A, and Snai1, may be therapeutic targets for patients with MI and may prevent adverse cardiovascular events.
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Affiliation(s)
- Yue Zheng
- School of Medicine, Nankai University, Tianjin, China
- Department of Heart Center, The Third Central Hospital of Tianjin, Tianjin, China
- Nankai University Affiliated Third Center Hospital, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
| | - Wenqing Gao
- School of Medicine, Nankai University, Tianjin, China
- Department of Heart Center, The Third Central Hospital of Tianjin, Tianjin, China
- Nankai University Affiliated Third Center Hospital, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
| | - Qiang Zhang
- School of Medicine, Nankai University, Tianjin, China
- Department of Heart Center, The Third Central Hospital of Tianjin, Tianjin, China
- Nankai University Affiliated Third Center Hospital, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
| | - Xian Cheng
- School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Department of Heart Center, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Yanwu Liu
- School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Department of Heart Center, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Zhenchang Qi
- School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Department of Heart Center, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
| | - Tong Li
- School of Medicine, Nankai University, Tianjin, China
- Department of Heart Center, The Third Central Hospital of Tianjin, Tianjin, China
- Nankai University Affiliated Third Center Hospital, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
- Artificial Cell Engineering Technology Research Center, Tianjin, China
- Department of Heart Center, The Third Central Clinical College of Tianjin Medical University, Tianjin, China
- *Correspondence: Tong Li,
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29
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Wehrens M, de Leeuw AE, Wright-Clark M, Eding JEC, Boogerd CJ, Molenaar B, van der Kraak PH, Kuster DWD, van der Velden J, Michels M, Vink A, van Rooij E. Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy. Cell Rep 2022; 39:110809. [PMID: 35545053 DOI: 10.1016/j.celrep.2022.110809] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic heart disease that is characterized by unexplained segmental hypertrophy that is usually most pronounced in the septum. While sarcomeric gene mutations are often the genetic basis for HCM, the mechanistic origin for the heterogeneous remodeling remains largely unknown. A better understanding of the gene networks driving the cardiomyocyte (CM) hypertrophy is required to improve therapeutic strategies. Patients suffering from HCM often receive a septal myectomy surgery to relieve outflow tract obstruction due to hypertrophy. Using single-cell RNA sequencing (scRNA-seq) on septal myectomy samples from patients with HCM, we identify functional links between genes, transcription factors, and cell size relevant for HCM. The data show the utility of using scRNA-seq on the human hypertrophic heart, highlight CM heterogeneity, and provide a wealth of insights into molecular events involved in HCM that can eventually contribute to the development of enhanced therapies.
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Affiliation(s)
- Martijn Wehrens
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Anne E de Leeuw
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Maya Wright-Clark
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands; Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joep E C Eding
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Cornelis J Boogerd
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Bas Molenaar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands
| | - Petra H van der Kraak
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Diederik W D Kuster
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Michelle Michels
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands
| | - Aryan Vink
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center, Utrecht, the Netherlands; Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands.
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30
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Ren J, Zhang Q, Zhou Y, Hu Y, Lyu X, Fang H, Yang J, Yu R, Shi X, Li Q. A downsampling Method Enables Robust Clustering and Integration of Single-Cell Transcriptome Data. J Biomed Inform 2022; 130:104093. [DOI: 10.1016/j.jbi.2022.104093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/06/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022]
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31
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Capon SJ, Uribe V, Dominado N, Ehrlich O, Smith KA. Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2. Development 2022; 149:275317. [PMID: 35531980 PMCID: PMC9148566 DOI: 10.1242/dev.190421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/28/2022] [Indexed: 12/28/2022]
Abstract
The endocardium plays important roles in the development and function of the vertebrate heart; however, few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here, we describe the Gt(SAGFF27C); Tg(4xUAS:egfp) line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan-endothelium confirms molecular distinction between these populations and time-course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity, we employed npas4l, etv2 and scl loss-of-function models. Endocardial expression is lost in npas4l mutants, significantly reduced in etv2 mutants and only modestly affected upon scl loss-of-function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression, whereas Bmp inhibition decreased expression. Finally, epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast, overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together, these results describe the differentiation of the endocardium, distinct from vasculature, and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Summary: A zebrafish transgenic reporter of the endocardium is identified, permitting transcriptomic analysis and identification of new endocardial markers. Epistasis experiments demonstrate npas4l and etv2 act downstream of Bmp signalling to regulate endocardial differentiation.
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Affiliation(s)
- Samuel J Capon
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Veronica Uribe
- Department of Anatomy & Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Nicole Dominado
- Department of Anatomy & Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Ophelia Ehrlich
- Department of Anatomy & Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kelly A Smith
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Department of Anatomy & Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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Anto Michel N, Ljubojevic-Holzer S, Bugger H, Zirlik A. Cellular Heterogeneity of the Heart. Front Cardiovasc Med 2022; 9:868466. [PMID: 35548426 PMCID: PMC9081371 DOI: 10.3389/fcvm.2022.868466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/23/2022] [Indexed: 11/18/2022] Open
Abstract
Recent advances in technology such as the introduction of high throughput multidimensional tools like single cell sequencing help to characterize the cellular composition of the human heart. The diversity of cell types that has been uncovered by such approaches is by far greater than ever expected before. Accurate identification of the cellular variety and dynamics will not only facilitate a much deeper understanding of cardiac physiology but also provide important insights into mechanisms underlying its pathological transformation. Distinct cellular patterns of cardiac cell clusters may allow differentiation between a healthy heart and a sick heart while potentially predicting future disease at much earlier stages than currently possible. These advances have already extensively improved and will ultimately revolutionize our knowledge of the mechanisms underlying cardiovascular disease as such. In this review, we will provide an overview of the cells present in the human and rodent heart as well as genes that may be used for their identification.
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Deciphering Cardiac Biology and Disease by Single-Cell Transcriptomic Profiling. Biomolecules 2022; 12:biom12040566. [PMID: 35454155 PMCID: PMC9032111 DOI: 10.3390/biom12040566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Abstract
By detecting minute molecular changes in hundreds to millions of single cells, single-cell RNA sequencing allows for the comprehensive characterization of the diversity and dynamics of cells in the heart. Our understanding of the heart has been transformed through the recognition of cellular heterogeneity, the construction of regulatory networks, the building of lineage trajectories, and the mapping of intercellular crosstalk. In this review, we introduce cardiac progenitors and their transcriptional regulation during embryonic development, highlight cellular heterogeneity and cell subtype functions in cardiac health and disease, and discuss insights gained from the study of pluripotent stem-cell-derived cardiomyocytes.
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34
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Chen QM. Nrf2 for protection against oxidant generation and mitochondrial damage in cardiac injury. Free Radic Biol Med 2022; 179:133-143. [PMID: 34921930 DOI: 10.1016/j.freeradbiomed.2021.12.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/16/2021] [Accepted: 12/01/2021] [Indexed: 02/06/2023]
Abstract
Myocardial infarction is the most common form of acute coronary syndrome. Blockage of a coronary artery due to blood clotting leads to ischemia and subsequent cell death in the form of necrosis, apoptosis, necroptosis and ferroptosis. Revascularization by coronary artery bypass graft surgery or non-surgical percutaneous coronary intervention combined with pharmacotherapy is effective in relieving symptoms and decreasing mortality. However, reactive oxygen species (ROS) are generated from damaged mitochondria, NADPH oxidases, xanthine oxidase, and inflammation. Impairment of mitochondria is shown as decreased metabolic activity, increased ROS production, membrane permeability transition, and release of mitochondrial proteins into the cytoplasm. Oxidative stress activates Nrf2 transcription factor, which in turn mediates the expression of mitofusin 2 (Mfn 2) and proteasomal genes. Increased expression of Mfn2 and inhibition of mitochondrial fission due to decreased Drp1 protein by proteasomal degradation contribute to mitochondrial hyperfusion. Damaged mitochondria can be removed by mitophagy via Parkin or p62 mediated ubiquitination. Mitochondrial biogenesis compensates for the loss of mitochondria, but requires mitochondrial DNA replication and initiation of transcription or translation of mitochondrial genes. Experimental evidence supports a role of Nrf2 in mitophagy, via up-regulation of PINK1 or p62 gene expression; and in mitochondrial biogenesis, by influencing the expression of PGC-1α, NResF1, NResF2, TFAM and mitochondrial genes. Oxidative stress causes Nrf2 activation via Keap1 dissociation, de novo protein translation, and nuclear translocation related to inactivation of GSK3β. The mechanism of Keap 1 mediated Nrf2 activation has been hijacked for Nrf2 activation by small molecules derived from natural products, some of which have been shown capable of mitochondrial protection. Multiple lines of evidence support the importance of Nrf2 in protecting mitochondria and preserving or renewing energy metabolism following tissue injury.
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Affiliation(s)
- Qin M Chen
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, 1295 N. Martin Avenue, Tucson, AZ, 85721, United States.
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35
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Single nucleus RNA-sequencing: how it's done, applications and limitations. Emerg Top Life Sci 2021; 5:687-690. [PMID: 34515767 DOI: 10.1042/etls20210074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022]
Abstract
Single nuclei RNA-sequencing (sNuc-Seq) is a methodology which uses isolated nuclei instead of whole cells to profile gene expression. By using droplet microfluidic technologies, users are able to profile thousands of single transcriptomes at high throughput from their chosen tissue. This article aims to introduce sNuc-Seq as a method and its utility in multiple tissue types. Furthermore, we discuss the risks associated with the use of nuclei, which must be considered before committing to a methodology.
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36
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Murphy SA, Chen EZ, Tung L, Boheler KR, Kwon C. Maturing heart muscle cells: Mechanisms and transcriptomic insights. Semin Cell Dev Biol 2021; 119:49-60. [PMID: 33952430 PMCID: PMC8653577 DOI: 10.1016/j.semcdb.2021.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 12/17/2022]
Abstract
Cardiomyocyte (CM) maturation is the transformation of differentiated fetal CMs into adult CMs that involves changes in morphology, cell function and metabolism, and the transcriptome. This process is, however, incomplete and ultimately arrested in pluripotent stem cell-derived CMs (PSC-CMs) in culture, which hinders their broad biomedical application. For this reason, enormous efforts are currently being made with the goal of generating mature PSC-CMs. In this review, we summarize key aspects of maturation observed in native CMs and discuss recent findings on the factors and mechanisms that regulate the process. Particular emphasis is put on transcriptional regulation and single-cell RNA-sequencing analysis that has emerged as a key tool to study time-series gene regulation and to determine the maturation state. We then discuss different biomimetic strategies to enhance PSC-CM maturation and discuss their effects at the single cell transcriptomic and functional levels.
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Affiliation(s)
- Sean A Murphy
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute of Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elaine Zhelan Chen
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leslie Tung
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Kenneth R Boheler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute of Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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37
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Chen Y, Liu Y, Gao X. The Application of Single-Cell Technologies in Cardiovascular Research. Front Cell Dev Biol 2021; 9:751371. [PMID: 34708045 PMCID: PMC8542723 DOI: 10.3389/fcell.2021.751371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/21/2021] [Indexed: 12/21/2022] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of deaths in the world. The intricacies of the cellular composition and tissue microenvironment in heart and vasculature complicate the dissection of molecular mechanisms of CVDs. Over the past decade, the rapid development of single-cell omics technologies generated vast quantities of information at various biological levels, which have shed light on the cellular and molecular dynamics in cardiovascular development, homeostasis and diseases. Here, we summarize the latest single-cell omics techniques, and show how they have facilitated our understanding of cardiovascular biology. We also briefly discuss the clinical value and future outlook of single-cell applications in the field.
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Affiliation(s)
- Yinan Chen
- Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen, China.,State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Liu
- Department of Vascular Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiang Gao
- Department of Vascular Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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38
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Valkov N, Das A, Tucker NR, Li G, Salvador AM, Chaffin MD, Pereira De Oliveira Junior G, Kur I, Gokulnath P, Ziegler O, Yeri A, Lu S, Khamesra A, Xiao C, Rodosthenous R, Srinivasan S, Toxavidis V, Tigges J, Laurent LC, Momma S, Kitchen R, Ellinor P, Ghiran I, Das S. SnRNA sequencing defines signaling by RBC-derived extracellular vesicles in the murine heart. Life Sci Alliance 2021; 4:4/12/e202101048. [PMID: 34663679 PMCID: PMC8548207 DOI: 10.26508/lsa.202101048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/21/2022] Open
Abstract
In a unique model of fluorescent based mapping of EV recipient cells, RBC-EVs were found to signal to cardiac cells and regulate gene expression in a model of ischemic heart failure. Extracellular vesicles (EVs) mediate intercellular signaling by transferring their cargo to recipient cells, but the functional consequences of signaling are not fully appreciated. RBC-derived EVs are abundant in circulation and have been implicated in regulating immune responses. Here, we use a transgenic mouse model for fluorescence-based mapping of RBC-EV recipient cells to assess the role of this intercellular signaling mechanism in heart disease. Using fluorescent-based mapping, we detected an increase in RBC-EV–targeted cardiomyocytes in a murine model of ischemic heart failure. Single cell nuclear RNA sequencing of the heart revealed a complex landscape of cardiac cells targeted by RBC-EVs, with enrichment of genes implicated in cell proliferation and stress signaling pathways compared with non-targeted cells. Correspondingly, cardiomyocytes targeted by RBC-EVs more frequently express cellular markers of DNA synthesis, suggesting the functional significance of EV-mediated signaling. In conclusion, our mouse model for mapping of EV-recipient cells reveals a complex cellular network of RBC-EV–mediated intercellular communication in ischemic heart failure and suggests a functional role for this mode of intercellular signaling.
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Affiliation(s)
- Nedyalka Valkov
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Avash Das
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Nathan R Tucker
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.,Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA.,Masonic Medical Research Institute, Utica, NY, USA
| | - Guoping Li
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ane M Salvador
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | | | - Ivan Kur
- Institute of Neurology (Edinger Institute), University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Priyanka Gokulnath
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Olivia Ziegler
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ashish Yeri
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Shulin Lu
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Aushee Khamesra
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Chunyang Xiao
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Srimeenakshi Srinivasan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - John Tigges
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Stefan Momma
- Institute of Neurology (Edinger Institute), University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Robert Kitchen
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.,Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Ionita Ghiran
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
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39
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Wang M, Gu M, Liu L, Liu Y, Tian L. Single-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations. Vasc Health Risk Manag 2021; 17:641-657. [PMID: 34629873 PMCID: PMC8495612 DOI: 10.2147/vhrm.s288090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases (CVDs) are a group of disorders of the blood vessels and heart, which are considered as the leading causes of death worldwide. The pathology of CVDs could be related to the functional abnormalities of multiple cell types in the heart. Single-cell RNA sequencing (scRNA-seq) technology is a powerful method for characterizing individual cells and elucidating the molecular mechanisms by providing a high resolution of transcriptomic changes at the single-cell level. Specifically, scRNA-seq has provided novel insights into CVDs by identifying rare cardiac cell types, inferring the trajectory tree, estimating RNA velocity, elucidating the cell-cell communication, and comparing healthy and pathological heart samples. In this review, we summarize the different scRNA-seq platforms and published single-cell datasets in the cardiovascular field, and describe the utilities and limitations of this technology. Lastly, we discuss the future perspective of the application of scRNA-seq technology into cardiovascular research.
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Affiliation(s)
- Mingqiang Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mingxia Gu
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yu Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lei Tian
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
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40
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Samad T, Wu SM. Single cell RNA sequencing approaches to cardiac development and congenital heart disease. Semin Cell Dev Biol 2021; 118:129-135. [PMID: 34006454 PMCID: PMC8434959 DOI: 10.1016/j.semcdb.2021.04.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022]
Abstract
The development of single cell RNA sequencing technologies has accelerated the ability of scientists to understand healthy and disease states of the cardiovascular system. Congenital heart defects occur in approximately 40,000 births each year and 1 out of 4 children are born with critical congenital heart disease requiring surgical interventions and a lifetime of monitoring. An understanding of how the normal heart develops and how each cell contributes to normal and pathological anatomy is an important goal in pediatric cardiovascular research. Single cell sequencing has provided the tools to increase the ability to discover rare cell types and novel genes involved in normal cardiac development. Knowledge of gene expression of single cells within cardiac tissue has contributed to the understanding of how each cell type contributes to the anatomic structures of the heart. In this review, we summarize how single cell RNA sequencing has been utilized to understand cardiac developmental processes and congenital heart disease. We discuss the advantages and disadvantages of whole cell versus single nuclei RNA sequencing and describe the approaches to analyze the interactomes, transcriptomes, and differentiation trajectory from single cell data. We summarize the currently available single cell RNA sequencing technologies and technical aspects of performing single cell analysis and how to overcome common obstacles. We also review data from the recently published human and mouse fetal heart atlases and advancements that have occurred within the field due to the application of these single cell tools. Finally we highlight the potential for single cell technologies to uncover novel mechanisms of disease pathogenesis by leveraging findings from genome wide association studies.
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Affiliation(s)
- Tahmina Samad
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA; Clinical and Translational Research Program, Stanford University School of Medicine, Stanford, CA, USA; Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean M Wu
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA; Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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41
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Streef TJ, Smits AM. Epicardial Contribution to the Developing and Injured Heart: Exploring the Cellular Composition of the Epicardium. Front Cardiovasc Med 2021; 8:750243. [PMID: 34631842 PMCID: PMC8494983 DOI: 10.3389/fcvm.2021.750243] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022] Open
Abstract
The epicardium is an essential cell population during cardiac development. It contributes different cell types to the developing heart through epithelial-to-mesenchymal transition (EMT) and it secretes paracrine factors that support cardiac tissue formation. In the adult heart the epicardium is a quiescent layer of cells which can be reactivated upon ischemic injury, initiating an embryonic-like response in the epicardium that contributes to post-injury repair processes. Therefore, the epicardial layer is considered an interesting target population to stimulate endogenous repair mechanisms. To date it is still not clear whether there are distinct cell populations in the epicardium that contribute to specific lineages or aid in cardiac repair, or that the epicardium functions as a whole. To address this putative heterogeneity, novel techniques such as single cell RNA sequencing (scRNA seq) are being applied. In this review, we summarize the role of the epicardium during development and after injury and provide an overview of the most recent insights into the cellular composition and diversity of the epicardium.
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Affiliation(s)
| | - Anke M. Smits
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
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42
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Atmanli A, Chai AC, Cui M, Wang Z, Nishiyama T, Bassel-Duby R, Olson EN. Cardiac Myoediting Attenuates Cardiac Abnormalities in Human and Mouse Models of Duchenne Muscular Dystrophy. Circ Res 2021; 129:602-616. [PMID: 34372664 PMCID: PMC8416801 DOI: 10.1161/circresaha.121.319579] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Ayhan Atmanli
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andreas C. Chai
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Miao Cui
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhaoning Wang
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Takahiko Nishiyama
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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43
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Liu S, Tang L, Zhao X, Nguyen B, Heallen TR, Li M, Wang J, Wang J, Martin JF. Yap Promotes Noncanonical Wnt Signals From Cardiomyocytes for Heart Regeneration. Circ Res 2021; 129:782-797. [PMID: 34424032 DOI: 10.1161/circresaha.121.318966] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Shijie Liu
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston (S.L., T.R.H., J.F.M.)
| | - Li Tang
- Department of Molecular Physiology and Biophysics (L.T., B.N., J.F.M.), Baylor College of Medicine, One Baylor Plaza, Houston, TX.,School of Computer Science and Engineering, Central South University, Changsha, Hunan, China (L.T., Jianxin Wang)
| | - Xiaolei Zhao
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center, Houston (X.Z., J.W.)
| | - Bao Nguyen
- Department of Molecular Physiology and Biophysics (L.T., B.N., J.F.M.), Baylor College of Medicine, One Baylor Plaza, Houston, TX
| | - Todd R Heallen
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston (S.L., T.R.H., J.F.M.)
| | | | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China (L.T., Jianxin Wang)
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center, Houston (X.Z., J.W.)
| | - James F Martin
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston (S.L., T.R.H., J.F.M.).,Department of Molecular Physiology and Biophysics (L.T., B.N., J.F.M.), Baylor College of Medicine, One Baylor Plaza, Houston, TX.,Cardiovascular Research Institute (J.F.M.), Baylor College of Medicine, One Baylor Plaza, Houston, TX
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44
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Zhang M, Qian L, Liu C, Huang GN, Tao G. Editorial: Cardiomyocyte Maturation: Novel Insights for Regenerative Medicine. Front Cell Dev Biol 2021; 9:730622. [PMID: 34409043 PMCID: PMC8365607 DOI: 10.3389/fcell.2021.730622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Min Zhang
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Chun Liu
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States.,Department of Medicine (Division of Cardiology), Stanford University School of Medicine, Stanford, CA, United States
| | - Guo N Huang
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, United States.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Ge Tao
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
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45
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Basile G, Kahraman S, Dirice E, Pan H, Dreyfuss JM, Kulkarni RN. Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets. Genome Med 2021; 13:128. [PMID: 34376240 PMCID: PMC8356387 DOI: 10.1186/s13073-021-00941-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 07/13/2021] [Indexed: 01/09/2023] Open
Abstract
Background Human pancreatic islets are a central focus of research in metabolic studies. Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing (scRNA-seq). We introduce single-nucleus RNA-sequencing (snRNA-seq) as an alternative approach for investigating transplanted human islets. Methods The Nuclei EZ protocol was used to obtain nuclear preparations from fresh and frozen human islet cells. Such preparations were first used to generate snRNA-seq datasets and compared to scRNA-seq output obtained from cells from the same donor. Finally, we employed snRNA-seq to obtain the transcriptomic profile of archived human islets engrafted in immunodeficient animals. Results We observed virtually complete concordance in identifying cell types and gene proportions as well as a strong association of global and islet cell type gene signatures between scRNA-seq and snRNA-seq applied to fresh and frozen cultured or transplanted human islet samples. Conclusions We propose snRNA-seq as a reliable strategy to probe transcriptomic profiles of freshly harvested or frozen sources of transplanted human islet cells especially when scRNA-seq is not ideal. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00941-8.
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Affiliation(s)
- Giorgio Basile
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Sevim Kahraman
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Ercument Dirice
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA.,Current Address: Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY, 10595, USA
| | - Hui Pan
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center and Harvard Medical School, Boston, MA, USA
| | - Jonathan M Dreyfuss
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center and Harvard Medical School, Boston, MA, USA
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA. .,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.
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46
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New perspectives of the cardiac cellular landscape: mapping cellular mediators of cardiac fibrosis using single-cell transcriptomics. Biochem Soc Trans 2021; 48:2483-2493. [PMID: 33259583 DOI: 10.1042/bst20191255] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022]
Abstract
Single-cell transcriptomics enables inference of context-dependent phenotypes of individual cells and determination of cellular diversity of complex tissues. Cardiac fibrosis is a leading factor in the development of heart failure and a major cause of morbidity and mortality worldwide with no effective treatment. Single-cell RNA-sequencing (scRNA-seq) offers a promising new platform to identify new cellular and molecular protagonists that may drive cardiac fibrosis and development of heart failure. This review will summarize the application scRNA-seq for understanding cardiac fibrosis and development of heart failure. We will also discuss some key considerations in interpreting scRNA-seq data and some of its limitations.
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47
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Guan D, Lazar MA. Interconnections between circadian clocks and metabolism. J Clin Invest 2021; 131:e148278. [PMID: 34338232 DOI: 10.1172/jci148278] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Circadian rhythms evolved through adaptation to daily light/dark changes in the environment; they are believed to be regulated by the core circadian clock interlocking feedback loop. Recent studies indicate that each core component executes general and specific functions in metabolism. Here, we review the current understanding of the role of these core circadian clock genes in the regulation of metabolism using various genetically modified animal models. Additionally, emerging evidence shows that exposure to environmental stimuli, such as artificial light, unbalanced diet, mistimed eating, and exercise, remodels the circadian physiological processes and causes metabolic disorders. This Review summarizes the reciprocal regulation between the circadian clock and metabolism, highlights remaining gaps in knowledge about the regulation of circadian rhythms and metabolism, and examines potential applications to human health and disease.
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Affiliation(s)
- Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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48
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Robust integration of multiple single-cell RNA sequencing datasets using a single reference space. Nat Biotechnol 2021; 39:877-884. [PMID: 33767393 PMCID: PMC8456427 DOI: 10.1038/s41587-021-00859-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/16/2021] [Indexed: 01/31/2023]
Abstract
In many biological applications of single-cell RNA sequencing (scRNA-seq), an integrated analysis of data from multiple batches or studies is necessary. Current methods typically achieve integration using shared cell types or covariance correlation between datasets, which can distort biological signals. Here we introduce an algorithm that uses the gene eigenvectors from a reference dataset to establish a global frame for integration. Using simulated and real datasets, we demonstrate that this approach, called Reference Principal Component Integration (RPCI), consistently outperforms other methods by multiple metrics, with clear advantages in preserving genuine cross-sample gene expression differences in matching cell types, such as those present in cells at distinct developmental stages or in perturbated versus control studies. Moreover, RPCI maintains this robust performance when multiple datasets are integrated. Finally, we applied RPCI to scRNA-seq data for mouse gut endoderm development and revealed temporal emergence of genetic programs helping establish the anterior-posterior axis in visceral endoderm.
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49
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Shi SY, Luo X, Yamawaki TM, Li CM, Ason B, Furtado MB. Recent Advances in Single-Cell Profiling and Multispecific Therapeutics: Paving the Way for a New Era of Precision Medicine Targeting Cardiac Fibroblasts. Curr Cardiol Rep 2021; 23:82. [PMID: 34081224 PMCID: PMC8175296 DOI: 10.1007/s11886-021-01517-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 01/22/2023]
Abstract
PURPOSE OF REVIEW Cardiac fibroblast activation contributes to fibrosis, maladaptive remodeling and heart failure progression. This review summarizes the latest findings on cardiac fibroblast activation dynamics derived from single-cell transcriptomic analyses and discusses how this information may aid the development of new multispecific medicines. RECENT FINDINGS Advances in single-cell gene expression technologies have led to the discovery of distinct fibroblast subsets, some of which are more prevalent in diseased tissue and exhibit temporal changes in response to injury. In parallel to the rapid development of single-cell platforms, the advent of multispecific therapeutics is beginning to transform the biopharmaceutical landscape, paving the way for the selective targeting of diseased fibroblast subpopulations. Insights gained from single-cell technologies reveal critical cardiac fibroblast subsets that play a pathogenic role in the progression of heart failure. Combined with the development of multispecific therapeutic agents that have enabled access to previously "undruggable" targets, we are entering a new era of precision medicine.
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Affiliation(s)
- Sally Yu Shi
- Department of Cardiometabolic Disorders, Amgen Discovery Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, CA 94080 USA
| | - Xin Luo
- Genome Analysis Unit, Amgen Discovery Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, CA 94080 USA
| | - Tracy M. Yamawaki
- Genome Analysis Unit, Amgen Discovery Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, CA 94080 USA
| | - Chi-Ming Li
- Genome Analysis Unit, Amgen Discovery Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, CA 94080 USA
| | - Brandon Ason
- Department of Cardiometabolic Disorders, Amgen Discovery Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, CA 94080 USA
| | - Milena B. Furtado
- Department of Cardiometabolic Disorders, Amgen Discovery Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, CA 94080 USA
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Utilizing Developmentally Essential Secreted Peptides Such as Thymosin Beta-4 to Remind the Adult Organs of Their Embryonic State-New Directions in Anti-Aging Regenerative Therapies. Cells 2021; 10:cells10061343. [PMID: 34071596 PMCID: PMC8228050 DOI: 10.3390/cells10061343] [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: 04/09/2021] [Revised: 05/07/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023] Open
Abstract
Our dream of defeating the processes of aging has occupied the curious and has challenged scientists globally for hundreds of years. The history is long, and sadly, the solution is still elusive. Our endeavors to reverse the magnitude of damaging cellular and molecular alterations resulted in only a few, yet significant advancements. Furthermore, as our lifespan increases, physicians are facing more mind-bending questions in their routine practice than ever before. Although the ultimate goal is to successfully treat the body as a whole, steps towards regenerating individual organs are even considered significant. As our initial approach to enhance the endogenous restorative capacity by delivering exogenous progenitor cells appears limited, we propose, utilizing small molecules critical during embryonic development may prove to be a powerful tool to increase regeneration and to reverse the processes associated with aging. In this review, we introduce Thymosin beta-4, a 43aa secreted peptide fulfilling our hopes and capable of numerous regenerative achievements via systemic administration in the heart. Observing the broad capacity of this small, secreted peptide, we believe it is not the only molecule which nature conceals to our benefit. Hence, the discovery and postnatal administration of developmentally relevant agents along with other approaches may result in reversing the aging process.
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