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Wang W, Jia H, Hua X, Song J. New insights gained from cellular landscape changes in myocarditis and inflammatory cardiomyopathy. Heart Fail Rev 2024; 29:883-907. [PMID: 38896377 DOI: 10.1007/s10741-024-10406-w] [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] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
Advances in the etiological classification of myocarditis and inflammatory cardiomyopathy (ICM) have reached a consensus. However, the mechanism of myocarditis/ICM remains unclear, which affects the development of treatment and the improvement of outcome. Cellular transcription and metabolic reprogramming, and the interactions between cardiomyocytes and non-cardiomyocytes, such as the immune cells, contribute to the process of myocarditis/ICM. Recent efforts have been made by multi-omics techniques, particularly in single-cell RNA sequencing, to gain a better understanding of the cellular landscape alteration occurring in disease during the progression. This article aims to provide a comprehensive overview of the latest studies in myocarditis/ICM, particularly as revealed by single-cell sequencing.
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Affiliation(s)
- Weiteng Wang
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China
| | - Hao Jia
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China
| | - Xiumeng Hua
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China
| | - Jiangping Song
- Beijing Key Laboratory of Preclinical Research and Evaluation for Cardiovascular Implant Materials, Animal Experimental Centre, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 167 Beilishi Road, Xicheng District, Beijing, 100037, China.
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen, 518057, China.
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 10037, China.
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2
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Chen Y, Wang X, Na X, Zhang Y, Cai L, Song J, Yang C. DMF-DM-seq: Digital-Microfluidics Enabled Dual-Modality Sequencing of Single-Cell mRNA and microRNA with High Integration, Sensitivity, and Automation. Anal Chem 2024; 96:12916-12926. [PMID: 39038243 DOI: 10.1021/acs.analchem.4c03378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Multimodal measurement of single cells provides deep insights into the intricate relationships between individual molecular layers and the regulatory mechanisms underlying intercellular variations. Here, we reported DMF-DM-seq, a highly integrated, sensitive, and automated platform for single-cell mRNA and microRNA (miRNA) co-sequencing based on digital microfluidics. This platform first integrates the processes of single-cell isolation, lysis, component separation, and simultaneous sequencing library preparation of mRNA and miRNA within a single DMF device. Compared with the current half-cell measuring strategy, DMF-DM-seq enables complete separation of single-cell mRNA and miRNA via a magnetic field application, resulting in a higher miRNA detection ability. DMF-DM-seq revealed differential expression patterns of single cells of noncancerous breast cells and noninvasive and aggressive breast cancer cells at both mRNA and miRNA levels. The results demonstrated the anticorrelated relationship between miRNA and their mRNA targets. Further, we unravel the tumor growth and metastasis-associated biological processes enriched by miRNA-targeted genes, along with important miRNA-interaction networks involved in significant signaling pathways. We also deconstruct the miRNA regulatory mechanisms underlying different signaling pathways across different breast cell types. In summary, DMF-DM-seq offers a powerful tool for a comprehensive study of the expression heterogeneity of single-cell mRNA and miRNA, which will be widely applied in basic and clinical research.
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Affiliation(s)
- Yingwen Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xuanqun Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Na
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yingkun Zhang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Linfeng Cai
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jia Song
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chaoyong Yang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, No. 55, Zhenhai Road, Siming District, Xiamen 361003, China
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3
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Xia Y, Liu Y, Li T, He S, Chang H, Wang Y, Zhang Y, Ge W. Assessing parameter efficient methods for pre-trained language model in annotating scRNA-seq data. Methods 2024; 228:12-21. [PMID: 38759908 DOI: 10.1016/j.ymeth.2024.05.007] [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: 04/12/2024] [Revised: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024] Open
Abstract
Annotating cell types of single-cell RNA sequencing (scRNA-seq) data is crucial for studying cellular heterogeneity in the tumor microenvironment. Recently, large-scale pre-trained language models (PLMs) have achieved significant progress in cell-type annotation of scRNA-seq data. This approach effectively addresses previous methods' shortcomings in performance and generalization. However, fine-tuning PLMs for different downstream tasks demands considerable computational resources, rendering it impractical. Hence, a new research branch introduces parameter-efficient fine-tuning (PEFT). This involves optimizing a few parameters while leaving the majority unchanged, leading to substantial reductions in computational expenses. Here, we utilize scBERT, a large-scale pre-trained model, to explore the capabilities of three PEFT methods in scRNA-seq cell type annotation. Extensive benchmark studies across several datasets demonstrate the superior applicability of PEFT methods. Furthermore, downstream analysis using models obtained through PEFT showcases their utility in novel cell type discovery and model interpretability for potential marker genes. Our findings underscore the considerable potential of PEFT in PLM-based cell type annotation, presenting novel perspectives for the analysis of scRNA-seq data.
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Affiliation(s)
- Yucheng Xia
- Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu, 610209, China
| | - Yuhang Liu
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Tianhao Li
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Sihan He
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Hong Chang
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Yaqing Wang
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Yongqing Zhang
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China
| | - Wenyi Ge
- School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China.
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Perez-Gutierrez L, Li P, Ferrara N. Endothelial cell diversity: the many facets of the crystal. FEBS J 2024; 291:3287-3302. [PMID: 36266750 DOI: 10.1111/febs.16660] [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: 07/17/2022] [Revised: 10/03/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Endothelial cells (ECs) form the inner lining of blood vessels and play crucial roles in angiogenesis. While it has been known for a long time that there are considerable differences among ECs from lymphatic and blood vessels, as well as among arteries, veins and capillaries, the full repertoire of endothelial diversity is only beginning to be elucidated. It has become apparent that the role of ECs is not just limited to their exchange functions. Indeed, a multitude of organ-specific functions, including release of growth factors, regulation of immune functions, have been linked to ECs. Recent years have seen a surge into the identification of spatiotemporal molecular and functional heterogeneity of ECs, supported by technologies such as single-cell RNA sequencing (scRNA-seq), lineage tracing and intersectional genetics. Together, these techniques have spurred the generation of epigenomic, transcriptomic and proteomic signatures of ECs. It is now clear that ECs across organs and in different vascular beds, but even within the same vessel, have unique molecular identities and employ specialized molecular mechanisms to fulfil highly specialized needs. Here, we focus on the molecular heterogeneity of the endothelium in different organs and pathological conditions.
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Affiliation(s)
- Lorena Perez-Gutierrez
- Department of Pathology, Moores Cancer Center, University of California, San Diego, CA, USA
| | - Pin Li
- Department of Pathology, Moores Cancer Center, University of California, San Diego, CA, USA
| | - Napoleone Ferrara
- Department of Pathology, Moores Cancer Center, University of California, San Diego, CA, USA
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Liu J, Xia B, Jiang X, Cao L, Xi Z, Liang L, Zhang S, Zhang H, Li W. Single-cell landscape reveals the immune heterogeneity of bone marrow involvement in peripheral T-cell lymphoma. Cancer Sci 2024; 115:2540-2552. [PMID: 38845192 PMCID: PMC11309951 DOI: 10.1111/cas.16227] [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: 12/01/2023] [Revised: 03/03/2024] [Accepted: 05/02/2024] [Indexed: 08/10/2024] Open
Abstract
The prognosis of patients with peripheral T-cell lymphoma (PTCL) depends on bone marrow involvement (BMI). The bone marrow (BM) tumor microenvironment in PTCL remains unclear. We performed single-cell RNA sequencing (scRNA-seq) on 11 fresh BM samples from patients with BMI to reveal the associations of immune landscape and genetic variations with the prognosis of PTCL patients. Compared with PTCL not otherwise specified (NOS), angioimmunoblastic T-cell lymphoma (AITL) had a higher number of T cells, lower number of lymphocytes, and greater inflammation. Immune heterogeneity in AITL is associated with prognosis. In particular, specific T-cell receptor (TCR) T cells are enriched in patients with good response to anti-CD30 therapy. We observed RhoA mutation-associated neoantigens. Chidamide-treated patients had a higher number of CD4+ regulatory cells and a better treatment response compared with other patients. In the nonresponder group, T-cell enrichment progressed to secondary B-cell enrichment and subsequently diffuse large B-cell lymphoma. Moreover, AITL patients with lymphoma-associated hemophagocytic syndrome had more T follicular helper (Tfh) cells with copy number variations in CHR5. To our knowledge, this study is the first to reveal the single-cell landscape of BM microenvironment heterogeneity in PTCL patients with BMI. scRNA-seq can be used to investigate the immune heterogeneity and genetic variations in AITL associated with prognosis.
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Affiliation(s)
- Jun Liu
- Medical Research institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
- Department of Precision Medicine, Shenzhen HospitalSouthern Medical UniversityShenzhenChina
| | - Baijing Xia
- Medical Research institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
- Guangdong Cardiovascular Institute, Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Xinmiao Jiang
- Department of Lymphoma, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Lixue Cao
- Medical Research institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Zhihui Xi
- Medical Research institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Liting Liang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Shaojun Zhang
- Medical Research institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Hui Zhang
- Medical Research institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Wenyu Li
- Medical Research institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
- Department of Lymphoma, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
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Zhu Y, Zhang Y, He S, Yi S, Feng H, Xia X, Fang X, Gong X, Zhao P. Integrating single-nucleus RNA sequencing and spatial transcriptomics to elucidate a specialized subpopulation of astrocytes, microglia and vascular cells in brains of mouse model of lipopolysaccharide-induced sepsis-associated encephalopathy. J Neuroinflammation 2024; 21:169. [PMID: 38961424 PMCID: PMC11223438 DOI: 10.1186/s12974-024-03161-0] [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: 02/22/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Understanding the mechanism behind sepsis-associated encephalopathy (SAE) remains a formidable task. This study endeavors to shed light on the complex cellular and molecular alterations that occur in the brains of a mouse model with SAE, ultimately unraveling the underlying mechanisms of this condition. METHODS We established a murine model using intraperitoneal injection of lipopolysaccharide (LPS) in wild type and Anxa1-/- mice and collected brain tissues for analysis at 0-hour, 12-hour, 24-hour, and 72-hour post-injection. Utilizing advanced techniques such as single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq, we conducted a comprehensive characterization of the cellular responses and molecular patterns within the brain. RESULTS Our study uncovered notable temporal differences in the response to LPS challenge between Anxa1-/- (annexin A1 knockout) and wild type mice, specifically at the 12-hour and 24-hour time points following injection. We observed a significant increase in the proportion of Astro-2 and Micro-2 cells in these mice. These cells exhibited a colocalization pattern with the vascular subtype Vas-1, forming a distinct region known as V1A2M2, where Astro-2 and Micro-2 cells surrounded Vas-1. Moreover, through further analysis, we discovered significant upregulation of ligands and receptors such as Timp1-Cd63, Timp1-Itgb1, Timp1-Lrp1, as well as Ccl2-Ackr1 and Cxcl2-Ackr1 within this region. In addition, we observed a notable increase in the expression of Cd14-Itgb1, Cd14-Tlr2, and Cd14-C3ar1 in regions enriched with Micro-2 cells. Additionally, Cxcl10-Sdc4 showed broad upregulation in brain regions containing both Micro-2 and Astro-2 cells. Notably, upon LPS challenge, there was an observed increase in Anxa1 expression in the mouse brain. Furthermore, our study revealed a noteworthy increase in mortality rates following Anxa1 knockdown. However, we did not observe substantial differences in the types, numbers, or distribution of other brain cells between Anxa1-/- and wildtype mice over time. Nevertheless, when comparing the 24-hour post LPS injection time point, we observed a significant decrease in the proportion and distribution of Micro-2 and Astro-2 cells in the vicinity of blood vessels in Anxa1-/- mice. Additionally, we noted reduced expression levels of several ligand-receptor pairs including Cd14-Tlr2, Cd14-C3ar1, Cd14-Itgb1, Cxcl10-Sdc4, Ccl2-Ackr1, and Cxcl2-Ackr1. CONCLUSIONS By combining snRNA-seq and Stereo-seq techniques, our study successfully identified a distinctive cellular colocalization, referred to as a special pathological niche, comprising Astro-2, Micro-2, and Vas-1 cells. Furthermore, we observed an upregulation of ligand-receptor pairs within this niche. These findings suggest a potential association between this cellular arrangement and the underlying mechanisms contributing to SAE or the increased mortality observed in Anxa1 knockdown mice.
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Grants
- 2021A1515012429 Natural Science Foundation of Guangdong Province, China
- 211102114530659 Shaoguan Municipal Science and Technology Program, China
- 20221807 Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer Program, China
- KEYANSHEN (2023) 01 Research Fund for Joint Laboratory for Digital and Precise Detection of Clinical Pathogens, Yuebei People's Hospital Affiliated to Shantou University Medical College, China
- RS202001 Research Project for Outstanding Scholar of Yuebei People's Hospital, Shantou University Medical College, China
- Research Fund for Joint Laboratory for Digital and Precise Detection of Clinical Pathogens, Yuebei People’s Hospital Affiliated to Shantou University Medical College, China
- Research Project for Outstanding Scholar of Yuebei People’s Hospital, Shantou University Medical College, China
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Affiliation(s)
- Yanyan Zhu
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China
| | - Yin Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Sheng He
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China
| | - Sanjun Yi
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China
| | - Hao Feng
- Jiaxing University Master Degree Cultivation Base, Zhejiang Chinese Medical University, Jiaxing, 314001, China
| | - Xianzhu Xia
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China
| | | | - Xiaoqian Gong
- Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China.
| | - Pingsen Zhao
- Department of Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, No 133, Huimin Road South, Wujiang District, Shaoguan, 512025, China.
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China.
- Research Center for Interdisciplinary & High-quality Innovative Development in Laboratory Medicine, Shaoguan, 512025, China.
- Shaoguan Municipal Quality Control Center for Laboratory Medicine, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512025, China.
- Shaoguan Municipal Quality Control Center for Surveillance of Bacterial Resistance, Shaoguan, 512025, China.
- Shaoguan Engineering Research Center for Research and Development of Molecular and Cellular Technology in Rapid Diagnosis of Infectious Diseases and Cancer, Shaoguan, 512025, China.
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Abu Nahia K, Sulej A, Migdał M, Ochocka N, Ho R, Kamińska B, Zagorski M, Winata CL. scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. iScience 2024; 27:110083. [PMID: 38872974 PMCID: PMC11170199 DOI: 10.1016/j.isci.2024.110083] [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: 10/06/2023] [Revised: 01/26/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.
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Affiliation(s)
- Karim Abu Nahia
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdał
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Natalia Ochocka
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Richard Ho
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
- The Njord Centre, Department of Physics, University of Oslo, Oslo, Norway
| | - Bożena Kamińska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcin Zagorski
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
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8
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Palmer JA, Rosenthal N, Teichmann SA, Litvinukova M. Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics. Circ Res 2024; 134:1681-1702. [PMID: 38843288 PMCID: PMC11149945 DOI: 10.1161/circresaha.124.323672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Throughout our lifetime, each beat of the heart requires the coordinated action of multiple cardiac cell types. Understanding cardiac cell biology, its intricate microenvironments, and the mechanisms that govern their function in health and disease are crucial to designing novel therapeutical and behavioral interventions. Recent advances in single-cell and spatial omics technologies have significantly propelled this understanding, offering novel insights into the cellular diversity and function and the complex interactions of cardiac tissue. This review provides a comprehensive overview of the cellular landscape of the heart, bridging the gap between suspension-based and emerging in situ approaches, focusing on the experimental and computational challenges, comparative analyses of mouse and human cardiac systems, and the rising contextualization of cardiac cells within their niches. As we explore the heart at this unprecedented resolution, integrating insights from both mouse and human studies will pave the way for novel diagnostic tools and therapeutic interventions, ultimately improving outcomes for patients with cardiovascular diseases.
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Affiliation(s)
- Jack A. Palmer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
| | - Nadia Rosenthal
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME (N.R.)
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.R.)
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
- Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory (S.A.T.), University of Cambridge, United Kingdom
| | - Monika Litvinukova
- University Hospital Würzburg, Germany (M.L.)
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany (M.L.)
- Helmholtz Pioneer Campus, Helmholtz Munich, Germany (M.L.)
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9
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Lee H, Kim SY, Kwon NJ, Jo SJ, Kwon O, Kim JI. Single-Cell and Spatial Transcriptome Analysis of Dermal Fibroblast Development in Perinatal Mouse Skin: Dynamic Lineage Differentiation and Key Driver Genes. J Invest Dermatol 2024; 144:1238-1250.e11. [PMID: 38072389 DOI: 10.1016/j.jid.2023.11.008] [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: 02/20/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/21/2024]
Abstract
Several single-cell RNA studies of developing mouse skin have elucidated the molecular and cellular processes involved in skin development. However, they have primarily focused on either the fetal or early postnatal period, leaving a gap in our understanding of skin development. In this study, we conducted a comprehensive time-series analysis by combining single-cell RNA-sequencing datasets collected at different stages of development (embryonic days 13.5, 14.5, and 16.5 and postnatal days 0, 2, and 4) and validated our findings through multipanel in situ spatial transcriptomics. Our analysis indicated that embryonic fibroblasts exhibit heterogeneity from a very early stage and that the rapid determination of each lineage occurs within days after birth. The expression of putative key driver genes, including Hey1, Ebf1, Runx3, and Sox11 for the dermal papilla trajectory; Lrrc15 for the dermal sheath trajectory; Zfp536 and Nrn1 for the papillary fibroblast trajectory; and Lrrn4cl and Mfap5 for the fascia fibroblast trajectory, was detected in the corresponding, spatially identified cell types. Finally, cell-to-cell interaction analysis indicated that the dermal papilla lineage is the primary source of the noncanonical Wnt pathway during skin development. Together, our study provides a transcriptomic reference for future research in the field of skin development and regeneration.
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Affiliation(s)
- Hanjae Lee
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea
| | - So Young Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | | | - Seong Jin Jo
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Laboratory of Cutaneous Aging and Hair Research, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea; Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Ohsang Kwon
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Laboratory of Cutaneous Aging and Hair Research, Clinical Research Institute, Seoul National University Hospital, Seoul, Korea; Institute of Human-Environment Interface Biology, Seoul National University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea; Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University, Seoul, Korea
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10
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Lin P, Gan YB, He J, Lin SE, Xu JK, Chang L, Zhao LM, Zhu J, Zhang L, Huang S, Hu O, Wang YB, Jin HJ, Li YY, Yan PL, Chen L, Jiang JX, Liu P. Advancing skeletal health and disease research with single-cell RNA sequencing. Mil Med Res 2024; 11:33. [PMID: 38816888 PMCID: PMC11138034 DOI: 10.1186/s40779-024-00538-3] [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: 12/27/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Orthopedic conditions have emerged as global health concerns, impacting approximately 1.7 billion individuals worldwide. However, the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders. The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity. Nevertheless, investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges. In this comprehensive review, we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines. By utilizing these methodologies, crucial insights into the developmental dynamics, maintenance of homeostasis, and pathological processes involved in spine, joint, bone, muscle, and tendon disorders have been uncovered. Specifically focusing on the joint diseases of degenerative disc disease, osteoarthritis, and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension. These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.
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Grants
- 2022YFA1103202 National Key Research and Development Program of China
- 82272507 National Natural Science Foundation of China
- 32270887 National Natural Science Foundation of China
- 32200654 National Natural Science Foundation of China
- CSTB2023NSCQ-ZDJO008 Natural Science Foundation of Chongqing
- BX20220397 Postdoctoral Innovative Talent Support Program
- SFLKF202201 Independent Research Project of State Key Laboratory of Trauma and Chemical Poisoning
- 2021-XZYG-B10 General Hospital of Western Theater Command Research Project
- 14113723 University Grants Committee, Research Grants Council of Hong Kong, China
- N_CUHK472/22 University Grants Committee, Research Grants Council of Hong Kong, China
- C7030-18G University Grants Committee, Research Grants Council of Hong Kong, China
- T13-402/17-N University Grants Committee, Research Grants Council of Hong Kong, China
- AoE/M-402/20 University Grants Committee, Research Grants Council of Hong Kong, China
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Affiliation(s)
- Peng Lin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yi-Bo Gan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian He
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
- Pancreatic Injury and Repair Key Laboratory of Sichuan Province, the General Hospital of Western Theater Command, Chengdu, 610031, China
| | - Si-En Lin
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Jian-Kun Xu
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Liang Chang
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Li-Ming Zhao
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Sacramento, CA, 94305, USA
| | - Jun Zhu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liang Zhang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Sha Huang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ou Hu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ying-Bo Wang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Huai-Jian Jin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yang-Yang Li
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Pu-Lin Yan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Lin Chen
- Center of Bone Metabolism and Repair, State Key Laboratory of Trauma and Chemical Poisoning, Trauma Center, Research Institute of Surgery, Laboratory for the Prevention and Rehabilitation of Military Training Related Injuries, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian-Xin Jiang
- Wound Trauma Medical Center, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Peng Liu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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11
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Huang S, Shi W, Li S, Fan Q, Yang C, Cao J, Wu L. Advanced sequencing-based high-throughput and long-read single-cell transcriptome analysis. LAB ON A CHIP 2024; 24:2601-2621. [PMID: 38669201 DOI: 10.1039/d4lc00105b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Cells are the fundamental building blocks of living systems, exhibiting significant heterogeneity. The transcriptome connects the cellular genotype and phenotype, and profiling single-cell transcriptomes is critical for uncovering distinct cell types, states, and the interplay between cells in development, health, and disease. Nevertheless, single-cell transcriptome analysis faces daunting challenges due to the low abundance and diverse nature of RNAs in individual cells, as well as their heterogeneous expression. The advent and continuous advancements of next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies have solved these problems and facilitated the high-throughput, sensitive, full-length, and rapid profiling of single-cell RNAs. In this review, we provide a broad introduction to current methodologies for single-cell transcriptome sequencing. First, state-of-the-art advancements in high-throughput and full-length single-cell RNA sequencing (scRNA-seq) platforms using NGS are reviewed. Next, TGS-based long-read scRNA-seq methods are summarized. Finally, a brief conclusion and perspectives for comprehensive single-cell transcriptome analysis are discussed.
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Affiliation(s)
- Shanqing Huang
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weixiong Shi
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shiyu Li
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Qian Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jiao Cao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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12
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An C, Li Z, Chen Y, Huang S, Yang F, Hu Y, Xu T, Zhang C, Ge S. The cGAS-STING pathway in cardiovascular diseases: from basic research to clinical perspectives. Cell Biosci 2024; 14:58. [PMID: 38720328 PMCID: PMC11080250 DOI: 10.1186/s13578-024-01242-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
The cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase-stimulator of interferon genes (cGAS-STING) signaling pathway, an important component of the innate immune system, is involved in the development of several diseases. Ectopic DNA-induced inflammatory responses are involved in several pathological processes. Repeated damage to tissues and metabolic organelles releases a large number of damage-associated molecular patterns (mitochondrial DNA, nuclear DNA, and exogenous DNA). The DNA fragments released into the cytoplasm are sensed by the sensor cGAS to initiate immune responses through the bridging protein STING. Many recent studies have revealed a regulatory role of the cGAS-STING signaling pathway in cardiovascular diseases (CVDs) such as myocardial infarction, heart failure, atherosclerosis, and aortic dissection/aneurysm. Furthermore, increasing evidence suggests that inhibiting the cGAS-STING signaling pathway can significantly inhibit myocardial hypertrophy and inflammatory cell infiltration. Therefore, this review is intended to identify risk factors for activating the cGAS-STING pathway to reduce risks and to simultaneously further elucidate the biological function of this pathway in the cardiovascular field, as well as its potential as a therapeutic target.
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Affiliation(s)
- Cheng An
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230032, Anhui, China
| | - Zhen Li
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yao Chen
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230032, Anhui, China
| | - Shaojun Huang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230032, Anhui, China
| | - Fan Yang
- Department of Ophthalmology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Chengxin Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230032, Anhui, China.
| | - Shenglin Ge
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Hefei, 230032, Anhui, China.
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13
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Shu C, Street K, Breton CV, Bastain TM, Wilson ML. A review of single-cell transcriptomics and epigenomics studies in maternal and child health. Epigenomics 2024; 16:775-793. [PMID: 38709139 DOI: 10.1080/17501911.2024.2343276] [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: 12/18/2023] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
Single-cell sequencing technologies enhance our understanding of cellular dynamics throughout pregnancy. We outlined the workflow of single-cell sequencing techniques and reviewed single-cell studies in maternal and child health. We conducted a literature review of single cell studies on maternal and child health using PubMed. We summarized the findings from 16 single-cell atlases of the human and mammalian placenta across gestational stages and 31 single-cell studies on maternal exposures and complications including infection, obesity, diet, gestational diabetes, pre-eclampsia, environmental exposure and preterm birth. Single-cell studies provides insights on novel cell types in placenta and cell type-specific marks associated with maternal exposures and complications.
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Affiliation(s)
- Chang Shu
- Center for Genetic Epidemiology, Division of Epidemiology & Genetics, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Kelly Street
- Division of Biostatistics, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Carrie V Breton
- Division of Environmental Health, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Theresa M Bastain
- Division of Environmental Health, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Melissa L Wilson
- Division of Disease Prevention, Policy, & Global Health, Department of Population & Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles,CA USA
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14
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Zhong J, Chen H, Liu Q, Zhou S, Liu Z, Xiao Y. GLP-1 receptor agonists and myocardial metabolism in atrial fibrillation. J Pharm Anal 2024; 14:100917. [PMID: 38799233 PMCID: PMC11127228 DOI: 10.1016/j.jpha.2023.12.007] [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: 07/02/2023] [Revised: 10/15/2023] [Accepted: 12/07/2023] [Indexed: 05/29/2024] Open
Abstract
Atrial fibrillation (AF) is the most common cardiac arrhythmia. Many medical conditions, including hypertension, diabetes, obesity, sleep apnea, and heart failure (HF), increase the risk for AF. Cardiomyocytes have unique metabolic characteristics to maintain adenosine triphosphate production. Significant changes occur in myocardial metabolism in AF. Glucagon-like peptide-1 receptor agonists (GLP-1RAs) have been used to control blood glucose fluctuations and weight in the treatment of type 2 diabetes mellitus (T2DM) and obesity. GLP-1RAs have also been shown to reduce oxidative stress, inflammation, autonomic nervous system modulation, and mitochondrial function. This article reviews the changes in metabolic characteristics in cardiomyocytes in AF. Although the clinical trial outcomes are unsatisfactory, the findings demonstrate that GLP-1 RAs can improve myocardial metabolism in the presence of various risk factors, lowering the incidence of AF.
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Affiliation(s)
- Jiani Zhong
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Xiangya School of Medicine, Central South University, Changsha, 410008, China
| | - Hang Chen
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Xiangya School of Medicine, Central South University, Changsha, 410008, China
| | - Qiming Liu
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Shenghua Zhou
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zhenguo Liu
- Center for Precision Medicine and Division of Cardiovascular Medicine, Department of Medicine, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Yichao Xiao
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha, 410011, China
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15
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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res 2024; 34:484-497. [PMID: 38580401 PMCID: PMC11067882 DOI: 10.1101/gr.277926.123] [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: 03/27/2023] [Accepted: 02/21/2024] [Indexed: 04/07/2024]
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
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Affiliation(s)
- Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joonhyuk Choi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alia Segura
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alper Genceroglu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nereida Ramirez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yeejin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
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16
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Lin S, Lin R, Zhu P, Sun X, Qiu C, Zhang B, He Y, Xu Q, Zhang H. Neutrophil extracellular traps promoting fibroblast activation and aggravating limb ischemia through Wnt5a pathway. Am J Cancer Res 2024; 14:1866-1879. [PMID: 38726275 PMCID: PMC11076237 DOI: 10.62347/sqoc7984] [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: 03/03/2024] [Accepted: 03/31/2024] [Indexed: 05/12/2024] Open
Abstract
Although the formation of NETs contributes to cancer cell invasion and distant metastasis, its role in the pathological progression of limb ischemia remains unknown. This study investigated the functional significance of NETs in cell-cell crosstalk during limb ischemia. The changes of cell subsets in lower limb ischemia samples were detected by single-cell RNA sequencing. The expression of neutrophil extracellular traps (NETs) related markers in lower limb ischemia samples was detected by immunohistochemistry and Western blotting. The signaling pathway of NETs activation in fibroblasts was verified by immunofluorescence, PCR and Western blotting. Through single-cell RNA sequencing (scRNA-seq), we identified 9 distinct cell clusters, with significantly upregulated activation levels in fibroblasts and neutrophils and phenotypic transformation of smooth muscle cells (SMCs) into a proliferative state in ischemic tissue. At the same time, the interaction between fibroblasts and smooth muscle cells was significantly enhanced in ischemic tissue. NETs levels rise and fibroblast activation is induced in ischemic conditions. Mechanistically, activated fibroblasts promote smooth muscle cell proliferation through the Wnt5a pathway. In ischemic mice, inhibition of Wnt5a mitigated vascular remodeling and subsequent ischemia. These findings highlighting the role of cell-cell crosstalk in ischemia and vascular remodeling. We found that the NETs-initiated fibroblast-SMC interaction is a critical regulator of limb ischemia via Wnt5a pathway, a potential therapeutic target for the treatment.
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Affiliation(s)
- Shigang Lin
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Ruoran Lin
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Pengwei Zhu
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Xiaotong Sun
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Chenyang Qiu
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Bohuan Zhang
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Yangyan He
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Qingbo Xu
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Hongkun Zhang
- Department of Vascular Surgery, The First Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
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17
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Pepe G, Appierdo R, Ausiello G, Helmer-Citterich M, Gherardini PF. A Meta-Analysis Approach to Gene Regulatory Network Inference Identifies Key Regulators of Cardiovascular Diseases. Int J Mol Sci 2024; 25:4224. [PMID: 38673810 PMCID: PMC11049946 DOI: 10.3390/ijms25084224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Cardiovascular diseases (CVDs) represent a major concern for global health, whose mechanistic understanding is complicated by a complex interplay between genetic predisposition and environmental factors. Specifically, heart failure (HF), encompassing dilated cardiomyopathy (DC), ischemic cardiomyopathy (ICM), and hypertrophic cardiomyopathy (HCM), is a topic of substantial interest in basic and clinical research. Here, we used a Partial Correlation Coefficient-based algorithm (PCC) within the context of a meta-analysis framework to construct a Gene Regulatory Network (GRN) that identifies key regulators whose activity is perturbed in Heart Failure. By integrating data from multiple independent studies, our approach unveiled crucial regulatory associations between transcription factors (TFs) and structural genes, emphasizing their pivotal roles in regulating metabolic pathways, such as fatty acid metabolism, oxidative stress response, epithelial-to-mesenchymal transition, and coagulation. In addition to known associations, our analysis also identified novel regulators, including the identification of TFs FPM315 and OVOL2, which are implicated in dilated cardiomyopathies, and TEAD1 and TEAD2 in both dilated and ischemic cardiomyopathies. Moreover, we uncovered alterations in adipogenesis and oxidative phosphorylation pathways in hypertrophic cardiomyopathy and discovered a role for IL2 STAT5 signaling in heart failure. Our findings underscore the importance of TF activity in the initiation and progression of cardiac disease, highlighting their potential as pharmacological targets.
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Affiliation(s)
- Gerardo Pepe
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (R.A.)
| | - Romina Appierdo
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (R.A.)
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Gabriele Ausiello
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy; (G.P.); (R.A.)
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18
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Tyagi R, Rosa BA, Swain A, Artyomov MN, Jasmer DP, Mitreva M. Intestinal cell diversity and treatment responses in a parasitic nematode at single cell resolution. BMC Genomics 2024; 25:341. [PMID: 38575858 PMCID: PMC10996262 DOI: 10.1186/s12864-024-10203-7] [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: 12/08/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Parasitic nematodes, significant pathogens for humans, animals, and plants, depend on diverse organ systems for intra-host survival. Understanding the cellular diversity and molecular variations underlying these functions holds promise for developing novel therapeutics, with specific emphasis on the neuromuscular system's functional diversity. The nematode intestine, crucial for anthelmintic therapies, exhibits diverse cellular phenotypes, and unraveling this diversity at the single-cell level is essential for advancing knowledge in anthelmintic research across various organ systems. RESULTS Here, using novel single-cell transcriptomics datasets, we delineate cellular diversity within the intestine of adult female Ascaris suum, a parasitic nematode species that infects animals and people. Gene transcripts expressed in individual nuclei of untreated intestinal cells resolved three phenotypic clusters, while lower stringency resolved additional subclusters and more potential diversity. Clusters 1 and 3 phenotypes displayed variable congruence with scRNA phenotypes of C. elegans intestinal cells, whereas the A. suum cluster 2 phenotype was markedly unique. Distinct functional pathway enrichment characterized each A. suum intestinal cell cluster. Cluster 2 was distinctly enriched for Clade III-associated genes, suggesting it evolved within clade III nematodes. Clusters also demonstrated differential transcriptional responsiveness to nematode intestinal toxic treatments, with Cluster 2 displaying the least responses to short-term intra-pseudocoelomic nematode intestinal toxin treatments. CONCLUSIONS This investigation presents advances in knowledge related to biological differences among major cell populations of adult A. suum intestinal cells. For the first time, diverse nematode intestinal cell populations were characterized, and associated biological markers of these cells were identified to support tracking of constituent cells under experimental conditions. These advances will promote better understanding of this and other parasitic nematodes of global importance, and will help to guide future anthelmintic treatments.
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Affiliation(s)
- Rahul Tyagi
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA
| | - Bruce A Rosa
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, 99164, Pullman, WA, USA.
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, 63110, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, 63110, St Louis, MO, USA.
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19
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Li Z, Brittan M, Mills NL. A Multimodal Omics Framework to Empower Target Discovery for Cardiovascular Regeneration. Cardiovasc Drugs Ther 2024; 38:223-236. [PMID: 37421484 PMCID: PMC10959818 DOI: 10.1007/s10557-023-07484-7] [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] [Accepted: 06/19/2023] [Indexed: 07/10/2023]
Abstract
Ischaemic heart disease is a global healthcare challenge with high morbidity and mortality. Early revascularisation in acute myocardial infarction has improved survival; however, limited regenerative capacity and microvascular dysfunction often lead to impaired function and the development of heart failure. New mechanistic insights are required to identify robust targets for the development of novel strategies to promote regeneration. Single-cell RNA sequencing (scRNA-seq) has enabled profiling and analysis of the transcriptomes of individual cells at high resolution. Applications of scRNA-seq have generated single-cell atlases for multiple species, revealed distinct cellular compositions for different regions of the heart, and defined multiple mechanisms involved in myocardial injury-induced regeneration. In this review, we summarise findings from studies of healthy and injured hearts in multiple species and spanning different developmental stages. Based on this transformative technology, we propose a multi-species, multi-omics, meta-analysis framework to drive the discovery of new targets to promote cardiovascular regeneration.
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Affiliation(s)
- Ziwen Li
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
| | - Mairi Brittan
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Nicholas L Mills
- BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
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20
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Ali I, Zhang H, Zaidi SAA, Zhou G. Understanding the intricacies of cellular senescence in atherosclerosis: Mechanisms and therapeutic implications. Ageing Res Rev 2024; 96:102273. [PMID: 38492810 DOI: 10.1016/j.arr.2024.102273] [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: 11/14/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Cardiovascular disease is currently the largest cause of mortality and disability globally, surpassing communicable diseases, and atherosclerosis is the main contributor to this epidemic. Aging is intimately linked to atherosclerosis development and progression, however, the mechanism of aging in atherosclerosis is not well known. To emphasize the significant research on the involvement of senescent cells in atherosclerosis, we begin by outlining compelling evidence that indicates various types of senescent cells and SASP factors linked to atherosclerotic phenotypes. We subsequently provide a comprehensive summary of the existing knowledge, shedding light on the intricate mechanisms through which cellular senescence contributes to the pathogenesis of atherosclerosis. Further, we cover that senescence can be identified by both structural changes and several senescence-associated biomarkers. Finally, we discuss that preventing accelerated cellular senescence represents an important therapeutic potential, as permanent changes may occur in advanced atherosclerosis. Together, the review summarizes the relationship between cellular senescence and atherosclerosis, and inspects the molecular knowledge, and potential clinical significance of senescent cells in developing senescent-based therapy, thus providing crucial insights into their biology and potential therapeutic exploration.
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Affiliation(s)
- Ilyas Ali
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, PR China
| | - Hongliang Zhang
- Shenzhen University General Hospital, Shenzhen University, Shenzhen 518060, PR China
| | - Syed Aqib Ali Zaidi
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China
| | - Guangqian Zhou
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Sciences Center, Shenzhen University, Shenzhen 518060, PR China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, PR China.
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21
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Ji H, Han Y, Danyang Jie, Yue Li, Hailan Yang, Sun H, You C, Xiao A, Liu Y. Decoding the biology and clinical implication of neutrophils in intracranial aneurysm. Ann Clin Transl Neurol 2024; 11:958-972. [PMID: 38317016 PMCID: PMC11021671 DOI: 10.1002/acn3.52014] [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: 08/20/2023] [Revised: 10/08/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Abundant neutrophils have been identified in both ruptured and unruptured intracranial aneurysm (IA) domes, with their function and clinical implication being poorly characterized. MATERIALS AND METHODS We employed single-cell RNA sequencing (scRNA-Seq) datasets of both human and murine model, and external bulk mRNA sequencing datasets to thoroughly explore the features and functional heterogeneous of neutrophils infiltrating the IA dome. RESULTS We found that both unruptured and ruptured IA dome contain a substantial population of neutrophils, characterized by FCGR3B, G0S2, CSF3R, and CXCR2. These cells exhibited heterogeneity in terms of function and differentiation. Despite similar transcriptional activation, neutrophils in IA dome expressed a repertoire of gene programs that mimicked transcriptomic alterations observed from bone marrow to peripheral blood, showing self-similarity. In addition, the recruitment of neutrophils in unruptured IA was primarily mediated by monocytes/macrophages, and once ruptured, both neutrophils, and a specific subset of inflammatory smooth muscle cells (SMCs) were involved in the process. The receiver operator characteristic curve (ROC) analysis indicated that distinct neutrophil subclusters were associated with IA formation and rupture, respectively. By reviewing current studies, we found that neutrophils play a detrimental role to IA wall integrity through secreting specific ligands, ferroptosis driven by ALOX5AP and PTGS2, and the formation of neutrophil extracellular traps (NETs) mediated by PADI4. INTERPRETATION This study delineated the biology and potential clinical implications of neutrophils in IA dome and provided a reliable basis for future researches.
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Affiliation(s)
- Hang Ji
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yujing Han
- Plevic Floor Disorders Centre, West China Tianfu HospitalSichuan UniversityNo. 3966, Tianfu AvenueChengduSichuanChina
| | - Danyang Jie
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yue Li
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Hailan Yang
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Haogeng Sun
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Chao You
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Anqi Xiao
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
| | - Yi Liu
- Department of Neurosurgery, West China HospitalSichuan UniversityNo. 37 Guoxue LaneChengduSichuanChina
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22
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He B, Quan L, Li C, Yan W, Zhang Z, Zhou L, Wei Q, Li Z, Mo J, Zhang Z, Pan X, Huang J, Liu L. Targeting ERBB2 and PIK3R1 as a therapeutic strategy for dilated cardiomyopathy: A single-cell sequencing and mendelian randomization analysis. Heliyon 2024; 10:e25572. [PMID: 38434379 PMCID: PMC10907741 DOI: 10.1016/j.heliyon.2024.e25572] [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: 07/19/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Background Dilated cardiomyopathy (DCM) is widely recognized as a significant contributor to heart failure. Nevertheless, the absence of pharmaceutical interventions capable of reversing disease progression and improving prognosis underscores the imperative for additional research in this area. Methods First, we identified and evaluated three gene sets, namely "SC-DCM", "EP-DCM" and "Drug", using big data and multiple bioinformatics analysis methods. Accordingly, drug-treatable ("Hub") genes in DCM were identified. Following this, four microarray expression profile datasets were employed to authenticate the expression levels and discriminatory efficacy of "Hub" genes. Additionally, mendelian randomization analysis was conducted to ascertain the causal association between the "Hub genes" and heart failure. Finally, the "DGIdb" was applied to identify "Hub" genes-targeted drugs. The "ssGSEA" algorithm assessed the level of immune cell infiltration in DCM. Results Enrichment analysis showed that the "SC-DCM" and "EP-DCM" gene sets were closely associated with DCM. PIK3R1 and ERBB2 were identified as drug-treatable genes in DCM. Additional analysis using MR supported a causal relationship between ERBB2 and heart failure, but not PIK3R1. Moreover, PIK3R1 was positively correlated with immune activation, while ERBB2 was negatively correlated. We found that everolimus was a pharmacological inhibitor for both PIK3R1 and ERBB2. However, no pharmacological agonist was found for ERBB2. Conclusion PIK3R1 and ERBB2 are drug-treatable genes in DCM. ERBB2 has a causal effect on heart failure, and its normal expression may play a role in preventing the progression of DCM to heart failure. In addition, there is a cross-expression of PIK3R1 and ERBB2 genes in both DCM and tumors. The adaptive immune system and PIK3R1 may be involved in DCM disease progression, while ERBB2 exerts a protective effect against DCM.
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Affiliation(s)
- Bin He
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Liping Quan
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Chengban Li
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
| | - Wei Yan
- Graduate School of Youjiang Medical University for Nationalities, Baise, China
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - ZhuoHua Zhang
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - LiuFan Zhou
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qinjiang Wei
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhile Li
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jianjiao Mo
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhen Zhang
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xingshou Pan
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - JianJun Huang
- College of Clinical Medicine, Youjiang Medical University for Nationalities, Baise, China
- Department of Neurology, Affiliated Hospital of Youjiang Medical University for Nationalities, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Li Liu
- Department of Cardiology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- The Key Laboratory for High Incidence Prevention and Treatment in Guangxi Guixi Area, Baise, 533000, Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
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23
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Garg A, Lavine KJ, Greenberg MJ. Assessing Cardiac Contractility From Single Molecules to Whole Hearts. JACC Basic Transl Sci 2024; 9:414-439. [PMID: 38559627 PMCID: PMC10978360 DOI: 10.1016/j.jacbts.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 04/04/2024]
Abstract
Fundamentally, the heart needs to generate sufficient force and power output to dynamically meet the needs of the body. Cardiomyocytes contain specialized structures referred to as sarcomeres that power and regulate contraction. Disruption of sarcomeric function or regulation impairs contractility and leads to cardiomyopathies and heart failure. Basic, translational, and clinical studies have adapted numerous methods to assess cardiac contraction in a variety of pathophysiological contexts. These tools measure aspects of cardiac contraction at different scales ranging from single molecules to whole organisms. Moreover, these studies have revealed new pathogenic mechanisms of heart disease leading to the development of novel therapies targeting contractility. In this review, the authors explore the breadth of tools available for studying cardiac contractile function across scales, discuss their strengths and limitations, highlight new insights into cardiac physiology and pathophysiology, and describe how these insights can be harnessed for therapeutic candidate development and translational.
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Affiliation(s)
- Ankit Garg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kory J. Lavine
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael J. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
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24
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Li G, Zhao H, Cheng Z, Liu J, Li G, Guo Y. Single-cell transcriptomic profiling of heart reveals ANGPTL4 linking fibroblasts and angiogenesis in heart failure with preserved ejection fraction. J Adv Res 2024:S2090-1232(24)00068-7. [PMID: 38346487 DOI: 10.1016/j.jare.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/19/2024] Open
Abstract
INTRODUCTION Despite the high morbidity and mortality, the effective therapies for heart failure with preserved fraction (HFpEF) are limited as the poor understand of its pathophysiological basis. OBJECTIVE This study was aimed to characterize the cellular heterogeneity and potential mechanisms of HFpEF at single-cell resolution. METHODS An HFpEF mouse model was induced by a high-fat diet with N-nitro-L-arginine methyl ester. Cells from the hearts were subjected to single-cell sequencing. The key protein expression was measured with Immunohistochemistry and immunofluorescence staining. RESULTS In HFpEF hearts, myocardial fibroblasts exhibited higher levels of fibrosis. Furthermore, an increased number of fibroblasts differentiated into high-metabolism and high-fibrosis phenotypes. The expression levels of genes encoding certain pro-angiogenic secreted proteins were decreased in the HFpEF group, as confirmed by bulk RNA sequencing. Additionally, the proportion of the endothelial cell (EC) lineages in the HFpEF group was significantly downregulated, with low angiogenesis and high apoptosis phenotypes observed in these EC lineages. Interestingly, the fibroblasts in the HFpEF heart might cross-link with the EC lineages via over-secretion of ANGPTL4, thus displaying an anti-angiogenic function. Immunohistochemistry and immunofluorescence staining then revealed the downregulation of vascular density and upregulation of ANGPTL4 expression in HFpEF hearts. Finally, we predicted ANGPTL4as a potential druggable target using DrugnomeAI. CONCLUSION In conclusion, this study comprehensively characterized the angiogenesis impairment in HFpEF hearts at single-cell resolution and proposed that ANGPTL4 secretion by fibroblasts may be a potential mechanism underlying this angiogenic abnormality.
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Affiliation(s)
- Guoxing Li
- Institute of Life Sciences, Chongqing Medical University, 400016, China
| | - Huilin Zhao
- Institute of Life Sciences, Chongqing Medical University, 400016, China
| | - Zhe Cheng
- Department of Cardiology, Chongqing University Three Gorges Hospital, Chongqing 404199, China
| | - Junjin Liu
- Department of Geriatrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Gang Li
- Institute of Life Sciences, Chongqing Medical University, 400016, China; Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, 400016, China.
| | - Yongzheng Guo
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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25
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Tian X, Yin Z, Li Z, Wang Z, Xing Z, Liu C, Wang L, Wang C, Zhang J, Dong L. Regeneration of Thyroid Glands in the Spleen Restores Homeostasis in Thyroidectomy Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305913. [PMID: 38059822 PMCID: PMC10853707 DOI: 10.1002/advs.202305913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Surgical removal of the thyroid gland (TG) for treating thyroid disorders leaves the patients on lifelong hormone replacement that partially compensates the physiological needs, but regenerating TG is challenging. Here, an approach is reported to regenerate TG within the spleen for fully restoring the thyroid's functions in mice, by transplanting thyroid tissue blocks to the spleen. Within 48 h, the transplanted tissue efficiently revascularizes, forming thyroid follicles similar to the native gland after 4 weeks. Structurally, the ectopically generated thyroid integrates with the surrounding splenic tissue while maintaining its integrity, separate from the lymphatic tissue. Functionally, it fully restores the native functions of the TG in hormone regulation in response to physiological stimuli, outperforming the established method of oral levothyroxine therapy in maintaining systemic homeostasis. The study demonstrates the full restoration of thyroid functions post-thyroidectomy by intrasplenic TG regeneration, providing fresh insights for designing novel therapies for thyroid-related disorders.
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Affiliation(s)
- Xue‐Jiao Tian
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
| | - Zhi‐Jie Yin
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
| | - Zhen‐Jiang Li
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
| | - Zhen‐Zhen Wang
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
| | - Zhen Xing
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
- NJU Xishan Institute of Applied BiotechnologyXishan DistrictWuxiJiangsu214101China
| | - Chun‐Yan Liu
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
| | - Lin‐Tao Wang
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
| | - Chun‐Ming Wang
- State Key Laboratory of Quality Research in Chinese MedicineInstitute of Chinese Medical SciencesUniversity of MacauTaipaMacau SAR999078China
| | - Jun‐Feng Zhang
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
| | - Lei Dong
- State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing UniversityNanjingJiangsu210023China
- NJU Xishan Institute of Applied BiotechnologyXishan DistrictWuxiJiangsu214101China
- National Resource Center for Mutant MiceNanjing210023China
- Chemistry and Biomedicine Innovative CenterNanjing UniversityNanjingJiangsu210023China
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26
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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27
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Chang JT, Liu LB, Wang PG, An J. Single-cell RNA sequencing to understand host-virus interactions. Virol Sin 2024; 39:1-8. [PMID: 38008383 PMCID: PMC10877424 DOI: 10.1016/j.virs.2023.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has allowed for the profiling of host and virus transcripts and host-virus interactions at single-cell resolution. This review summarizes the existing scRNA-seq technologies together with their strengths and weaknesses. The applications of scRNA-seq in various virological studies are discussed in depth, which broaden the understanding of the immune atlas, host-virus interactions, and immune repertoire. scRNA-seq can be widely used for virology in the near future to better understand the pathogenic mechanisms and discover more effective therapeutic strategies.
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Affiliation(s)
- Jia-Tong Chang
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Li-Bo Liu
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Pei-Gang Wang
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
| | - Jing An
- Department of Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
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28
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He F, Fei R, Gao M, Su L, Zhang X, Xu D. Parameter-Efficient Fine-Tuning Enhances Adaptation of Single Cell Large Language Model for Cell Type Identification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577455. [PMID: 38352605 PMCID: PMC10862733 DOI: 10.1101/2024.01.27.577455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Single-cell sequencing transformed biology and medicine, providing an unprecedented high-resolution view at the cellular level. However, the vast variability inherent in single-cell sequencing data impedes its utility for in-depth downstream analysis. Inspired by the foundation models in natural language processing, recent advancements have led to the development of single-cell Large Language Models (scLLMs). These models are designed to discern universal patterns across diverse single-cell datasets, thereby enhancing the signal-to-noise ratio. Despite their potential, multiple studies indicate existing scLLMs do not perform well in zero-short settings, highlighting a pressing need for more effective adaptation techniques. This research proposes several adaptation techniques for scLLMs by preserving the original model parameters while selectively updating newly introduced tensors. This approach aims to overcome the limitations associated with traditional fine-tuning practices, such as catastrophic forgetting and computational inefficiencies. We introduce two Parameter-Efficient Fine-Tuning (PEFT) strategies specifically tailored to refine scLLMs for cell type identification. Our investigations utilizing scGPT demonstrate that PEFT can enhance performance, with the added benefit of up to a 90% reduction in parameter training compared to conventional fine-tuning methodologies. This work paves the way for a new direction in leveraging single-cell models with greater efficiency and efficacy in single-cell biology.
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Affiliation(s)
- Fei He
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Ruixin Fei
- School of Information Science and Technology, Northeast Normal University, Changchun Jilin 130017, China
| | - Mingyue Gao
- School of Information Science and Technology, Northeast Normal University, Changchun Jilin 130017, China
| | - Li Su
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Xinyu Zhang
- School of Information Science and Technology, Northeast Normal University, Changchun Jilin 130017, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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Qiu M, Chen J, Liu M, Nie Z, Ke M, Dong G, Zhao H, Zhou C, Zeng H, He B, Chen J, Zhuang J, Li X, Ou Y. Single-cell RNA sequencing reveals the role of mitochondrial dysfunction in the cardiogenic toxicity of perfluorooctane sulfonate in human embryonic stem cells. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115945. [PMID: 38183750 DOI: 10.1016/j.ecoenv.2024.115945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/17/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
Perfluorooctane sulfonate (PFOS), an endocrine-disrupting chemical pollutant, affects embryonic heart development; however, the mechanisms underlying its toxicity have not been fully elucidated. Here, Single-cell RNA sequencing (scRNA-seq) was used to investigate the overall effects of PFOS on myocardial differentiation from human embryonic stem cells (hESCs). Additionally, apoptosis, mitochondrial membrane potential, and ATP assays were performed. Downregulated cardiogenesis-related genes and inhibited cardiac differentiation were observed after PFOS exposure in vitro. The percentages of cardiomyocyte and cardiac progenitor cell clusters decreased significantly following exposure to PFOS, while the proportion of primitive endoderm cell was increased in PFOS group. Moreover, PFOS inhibited myocardial differentiation and blocked cellular development at the early- and middle-stage. A Gene Ontology analysis and pseudo-time trajectory illustrated that PFOS disturbed multiple processes related to cardiogenesis and oxidative phosphorylation in the mitochondria. Furthermore, PFOS decreased mitochondrial membrane potential and induced apoptosis. These results offer meaningful insights into the cardiogenic toxicity of PFOS exposure during heart formation as well as the adverse effects of PFOS on mitochondria.
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Affiliation(s)
- Min Qiu
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
| | - Jing Chen
- Medical Research Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
| | - Mingqin Liu
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou 510080, PR China
| | - Zhiqiang Nie
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
| | - Miaola Ke
- Department of Blood Transfusion, Sun Yat-Sen University Cancer Center, Guangzhou 510050, PR China
| | - Guanghui Dong
- Department of Occupational and Environmental, Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Haishan Zhao
- Medical Research Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
| | - Chengbin Zhou
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
| | - Haiyan Zeng
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou 510080, PR China
| | - Biaochuan He
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
| | - Jimei Chen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China.
| | - Xiaohong Li
- Medical Research Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China.
| | - Yanqiu Ou
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, PR China.
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30
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Wei N, Lee C, Duan L, Galdos FX, Samad T, Raissadati A, Goodyer WR, Wu SM. Cardiac Development at a Single-Cell Resolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:253-268. [PMID: 38884716 DOI: 10.1007/978-3-031-44087-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mammalian cardiac development is a complex, multistage process. Though traditional lineage tracing studies have characterized the broad trajectories of cardiac progenitors, the advent and rapid optimization of single-cell RNA sequencing methods have yielded an ever-expanding toolkit for characterizing heterogeneous cell populations in the developing heart. Importantly, they have allowed for a robust profiling of the spatiotemporal transcriptomic landscape of the human and mouse heart, revealing the diversity of cardiac cells-myocyte and non-myocyte-over the course of development. These studies have yielded insights into novel cardiac progenitor populations, chamber-specific developmental signatures, the gene regulatory networks governing cardiac development, and, thus, the etiologies of congenital heart diseases. Furthermore, single-cell RNA sequencing has allowed for the exquisite characterization of distinct cardiac populations such as the hard-to-capture cardiac conduction system and the intracardiac immune population. Therefore, single-cell profiling has also resulted in new insights into the regulation of cardiac regeneration and injury repair. Single-cell multiomics approaches combining transcriptomics, genomics, and epigenomics may uncover an even more comprehensive atlas of human cardiac biology. Single-cell analyses of the developing and adult mammalian heart offer an unprecedented look into the fundamental mechanisms of cardiac development and the complex diseases that may arise from it.
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Affiliation(s)
- Nicholas Wei
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | - Carissa Lee
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | - Lauren Duan
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | | | - Tahmina Samad
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | | | | | - Sean M Wu
- Stanford University, Cardiovascular Institute, Stanford, CA, USA.
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31
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Bhattachan P, Jeschke MG. SINGLE-CELL TRANSCRIPTOME ANALYSIS IN HEALTH AND DISEASE. Shock 2024; 61:19-27. [PMID: 37962963 PMCID: PMC10883422 DOI: 10.1097/shk.0000000000002274] [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] [Indexed: 11/16/2023]
Abstract
ABSTRACT The analysis of the single-cell transcriptome has emerged as a powerful tool to gain insights on the basic mechanisms of health and disease. It is widely used to reveal the cellular diversity and complexity of tissues at cellular resolution by RNA sequencing of the whole transcriptome from a single cell. Equally, it is applied to discover an unknown, rare population of cells in the tissue. The prime advantage of single-cell transcriptome analysis is the detection of stochastic nature of gene expression of the cell in tissue. Moreover, the availability of multiple platforms for the single-cell transcriptome has broadened its approaches to using cells of different sizes and shapes, including the capture of short or full-length transcripts, which is helpful in the analysis of challenging biological samples. And with the development of numerous packages in R and Python, new directions in the computational analysis of single-cell transcriptomes can be taken to characterize healthy versus diseased tissues to obtain novel pathological insights. Downstream analysis such as differential gene expression analysis, gene ontology term analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, cell-cell interaction analysis, and trajectory analysis has become standard practice in the workflow of single-cell transcriptome analysis to further examine the biology of different cell types. Here, we provide a broad overview of single-cell transcriptome analysis in health and disease conditions currently applied in various studies.
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32
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Ju J, Ma M, Zhang Y, Ding Z, Chen J. State transition and intercellular communication of synovial fibroblasts in response to chronic and acute shoulder injuries unveiled by single-cell transcriptomic analyses. Connect Tissue Res 2024; 65:73-87. [PMID: 38090785 DOI: 10.1080/03008207.2023.2295322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024]
Abstract
PURPOSE We aimed to investigate the heterogeneity of synovial fibroblasts and their potential to undergo cell state transitions at the resolution of single cells. MATERIALS AND METHODS We employed the single-cell RNA sequencing (scRNA-seq) approach to comprehensively map the cellular landscape of the shoulder synovium in individuals with chronic rotator cuff tears (RCTs) and acute proximal humerus fractures (PHFs). Utilizing unbiased clustering analysis, we successfully identified distinct subpopulations of fibroblasts within the synovial environment. We utilized Monocle 3 to delineate the trajectory of synovial fibroblast state transition. And we used CellPhone DB v2.1.0 to predict cell-cell communication patterns within the synovial microenvironment. RESULTS We identified eight main cell clusters in the shoulder synovium. Unbiased clustering analysis identified four synovial fibroblast subpopulations, with diverse biological functions associated with protein secretion, ECM remodeling, inflammation regulation and cell division. Lining, mesenchymal, pro-inflammatory and proliferative fibroblasts subsets were identified. Combining the results from StemID and characteristic gene features, mesenchymal fibroblasts exhibited characteristics of fibroblast progenitor cells. The trajectory of synovial fibroblast state transition showed a transition from mesenchymal to pro-inflammatory and lining phenotypes. In addition, the cross talk between fibroblast subclusters increased in degenerative shoulder diseases compared to acute trauma. CONCLUSION We successfully generated the scRNA-seq transcriptomic atlas of the shoulder synovium, which provides a comprehensive understanding of the heterogeneity of synovial fibroblasts, their potential to undergo state transitions, and their intercellular communication in the context of chronic degenerative and acute traumatic shoulder diseases.
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Affiliation(s)
- Jiabao Ju
- Department of Trauma & Orthopedics, Peking University People's Hospital, Beijing, China
| | - Mingtai Ma
- Department of Trauma & Orthopedics, Peking University People's Hospital, Beijing, China
| | - Yichong Zhang
- Department of Trauma & Orthopedics, Peking University People's Hospital, Beijing, China
| | - Zhentao Ding
- Department of Trauma & Orthopedics, Peking University People's Hospital, Beijing, China
| | - Jianhai Chen
- Department of Trauma & Orthopedics, Peking University People's Hospital, Beijing, China
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Liang Q, Huang Y, He S, Chen K. Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity. Nat Commun 2023; 14:8416. [PMID: 38110427 PMCID: PMC10728201 DOI: 10.1038/s41467-023-44206-x] [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: 06/26/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
Advances in single-cell technology have enabled molecular dissection of heterogeneous biospecimens at unprecedented scales and resolutions. Cluster-centric approaches are widely applied in analyzing single-cell data, however they have limited power in dissecting and interpreting highly heterogenous, dynamically evolving data. Here, we present GSDensity, a graph-modeling approach that allows users to obtain pathway-centric interpretation and dissection of single-cell and spatial transcriptomics (ST) data without performing clustering. Using pathway gene sets, we show that GSDensity can accurately detect biologically distinct cells and reveal novel cell-pathway associations ignored by existing methods. Moreover, GSDensity, combined with trajectory analysis can identify curated pathways that are active at various stages of mouse brain development. Finally, GSDensity can identify spatially relevant pathways in mouse brains and human tumors including those following high-order organizational patterns in the ST data. Particularly, we create a pan-cancer ST map revealing spatially relevant and recurrently active pathways across six different tumor types.
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Affiliation(s)
- Qingnan Liang
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yuefan Huang
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Shan He
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
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Ryabov V, Gombozhapova A, Litviakov N, Ibragimova M, Tsyganov M, Rogovskaya Y, Kzhyshkowska J. Microarray Analysis for Transcriptomic Profiling of Myocardium in Patients with Fatal Myocardial Infarction. Biomedicines 2023; 11:3294. [PMID: 38137515 PMCID: PMC10740899 DOI: 10.3390/biomedicines11123294] [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: 11/08/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Transcriptomic evidence from human myocardium in myocardial infarction (MI) is still not sufficient. Thus, there is a need for studies on human cardiac samples in relation to the clinical data of patients. The purpose of our pilot study was to investigate the transcriptomic profile of myocardium in the infarct zone, in comparison to the remote myocardium, in patients with fatal MI, via microarray analysis. This study included four patients with fatal MI type 1. We selected histologically verified samples from within the infarct area (n = 4) and remote myocardium (n = 4). The whole transcriptome was evaluated using microarray analysis. Differentially expressed genes (DEGs) clustered in the infarct area and in the remote myocardium allowed their differentiation. We identified a total of 1785 DEGs (8.32%) in the infarct area, including 1692 up-regulated (94.79%) and 93 down-regulated (5.21%) genes. The top 10 up-regulated genes were TRAIL, SUCLA2, NAE1, PDCL3, OSBPL5, FCGR2C, SELE, CEP63, ST3GAL3 and C4orf3. In the infarct area, we found up-regulation of seventeen apoptosis-related genes, eleven necroptosis-related, and six necrosis-related genes. Transcriptome profiling of the myocardium in patients with MI remains a relevant area of research for the formation of new scientific hypotheses and a potential way to increase the translational significance of studies into myocardial infarction.
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Affiliation(s)
- Vyacheslav Ryabov
- Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634012 Tomsk, Russia;
| | - Aleksandra Gombozhapova
- Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634012 Tomsk, Russia;
| | - Nikolai Litviakov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | - Marina Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | - Matvey Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia; (N.L.); (M.I.); (M.T.)
| | | | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, 69117 Heidelberg, Germany;
- Laboratory of Translational and Cellular Biomedicine, National Research Tomsk State University, 634050 Tomsk, Russia
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35
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Gu Y, Hu Y, Zhang H, Wang S, Xu K, Su J. Single-cell RNA sequencing in osteoarthritis. Cell Prolif 2023; 56:e13517. [PMID: 37317049 PMCID: PMC10693192 DOI: 10.1111/cpr.13517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/30/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Osteoarthritis is a progressive and heterogeneous joint disease with complex pathogenesis. The various phenotypes associated with each patient suggest that better subgrouping of tissues associated with genotypes in different phases of osteoarthritis may provide new insights into the onset and progression of the disease. Recently, single-cell RNA sequencing was used to describe osteoarthritis pathogenesis on a high-resolution view surpassing traditional technologies. Herein, this review summarizes the microstructural changes in articular cartilage, meniscus, synovium and subchondral bone that are mainly due to crosstalk amongst chondrocytes, osteoblasts, fibroblasts and endothelial cells during osteoarthritis progression. Next, we focus on the promising targets discovered by single-cell RNA sequencing and its potential applications in target drugs and tissue engineering. Additionally, the limited amount of research on the evaluation of bone-related biomaterials is reviewed. Based on the pre-clinical findings, we elaborate on the potential clinical values of single-cell RNA sequencing for the therapeutic strategies of osteoarthritis. Finally, a perspective on the future development of patient-centred medicine for osteoarthritis therapy combining other single-cell multi-omics technologies is discussed. This review will provide new insights into osteoarthritis pathogenesis on a cellular level and the field of applications of single-cell RNA sequencing in personalized therapeutics for osteoarthritis in the future.
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Affiliation(s)
- Yuyuan Gu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- School of MedicineShanghai UniversityShanghaiChina
| | - Yan Hu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
| | - Hao Zhang
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
| | - Sicheng Wang
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Department of OrthopedicsShanghai Zhongye HospitalShanghaiChina
| | - Ke Xu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Wenzhou Institute of Shanghai UniversityWenzhouChina
| | - Jiacan Su
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
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36
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Wang YM, Sun Y, Wang B, Wu Z, He XY, Zhao Y. Transfer learning for clustering single-cell RNA-seq data crossing-species and batch, case on uterine fibroids. Brief Bioinform 2023; 25:bbad426. [PMID: 37991248 PMCID: PMC10664408 DOI: 10.1093/bib/bbad426] [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: 09/06/2023] [Revised: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Due to the high dimensionality and sparsity of the gene expression matrix in single-cell RNA-sequencing (scRNA-seq) data, coupled with significant noise generated by shallow sequencing, it poses a great challenge for cell clustering methods. While numerous computational methods have been proposed, the majority of existing approaches center on processing the target dataset itself. This approach disregards the wealth of knowledge present within other species and batches of scRNA-seq data. In light of this, our paper proposes a novel method named graph-based deep embedding clustering (GDEC) that leverages transfer learning across species and batches. GDEC integrates graph convolutional networks, effectively overcoming the challenges posed by sparse gene expression matrices. Additionally, the incorporation of DEC in GDEC enables the partitioning of cell clusters within a lower-dimensional space, thereby mitigating the adverse effects of noise on clustering outcomes. GDEC constructs a model based on existing scRNA-seq datasets and then applying transfer learning techniques to fine-tune the model using a limited amount of prior knowledge gleaned from the target dataset. This empowers GDEC to adeptly cluster scRNA-seq data cross different species and batches. Through cross-species and cross-batch clustering experiments, we conducted a comparative analysis between GDEC and conventional packages. Furthermore, we implemented GDEC on the scRNA-seq data of uterine fibroids. Compared results obtained from the Seurat package, GDEC unveiled a novel cell type (epithelial cells) and identified a notable number of new pathways among various cell types, thus underscoring the enhanced analytical capabilities of GDEC. Availability and implementation: https://github.com/YuzhiSun/GDEC/tree/main.
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Affiliation(s)
- Yu Mei Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tong Ji University, Shanghai , China
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Shanghai First Maternity and Infant Hospital, Shanghai,China
| | - Yuzhi Sun
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Beiying Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tong Ji University, Shanghai , China
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Shanghai First Maternity and Infant Hospital, Shanghai,China
| | - Zhiping Wu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tong Ji University, Shanghai , China
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Shanghai First Maternity and Infant Hospital, Shanghai,China
| | - Xiao Ying He
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tong Ji University, Shanghai , China
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Shanghai First Maternity and Infant Hospital, Shanghai,China
| | - Yuansong Zhao
- University of Texas Health Science Center at Houston, 77030-5400, USA
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Liang X, Cao L, Chen H, Wang L, Wang Y, Fu L, Tan X, Chen E, Ding Y, Tang J. A critical assessment of clustering algorithms to improve cell clustering and identification in single-cell transcriptome study. Brief Bioinform 2023; 25:bbad497. [PMID: 38168839 PMCID: PMC10782910 DOI: 10.1093/bib/bbad497] [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: 06/15/2023] [Revised: 10/13/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Cell clustering is typically the initial step in single-cell RNA sequencing (scRNA-seq) analyses. The performance of clustering considerably impacts the validity and reproducibility of cell identification. A variety of clustering algorithms have been developed for scRNA-seq data. These algorithms generate cell label sets that assign each cell to a cluster. However, different algorithms usually yield different label sets, which can introduce variations in cell-type identification based on the generated label sets. Currently, the performance of these algorithms has not been systematically evaluated in single-cell transcriptome studies. Herein, we performed a critical assessment of seven state-of-the-art clustering algorithms including four deep learning-based clustering algorithms and commonly used methods Seurat, Cosine-based Tanimoto similarity-refined graph for community detection using Leiden's algorithm (CosTaL) and Single-cell consensus clustering (SC3). We used diverse evaluation indices based on 10 different scRNA-seq benchmarks to systematically evaluate their clustering performance. Our results show that CosTaL, Seurat, Deep Embedding for Single-cell Clustering (DESC) and SC3 consistently outperformed Single-Cell Clustering Assessment Framework and scDeepCluster based on nine effectiveness scores. Notably, CosTaL and DESC demonstrated superior performance in clustering specific cell types. The performance of the single-cell Variational Inference tools varied across different datasets, suggesting its sensitivity to certain dataset characteristics. Notably, DESC exhibited promising results for cell subtype identification and capturing cellular heterogeneity. In addition, SC3 requires more memory and exhibits slower computation speed compared to other algorithms for the same dataset. In sum, this study provides useful guidance for selecting appropriate clustering methods in scRNA-seq data analysis.
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Affiliation(s)
- Xiao Liang
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lijie Cao
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Hao Chen
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lidan Wang
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yangyun Wang
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lijuan Fu
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
- Department of Pharmacology, Academician Workstation, Changsha Medical University, Changsha 410219, China
| | - Xiaqin Tan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Enxiang Chen
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yubin Ding
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jing Tang
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
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38
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Wang Y, Liu Z, Bian X, Zhao C, Zhang X, Liu X, Wang N. Function and regulation of ubiquitin-like SUMO system in heart. Front Cell Dev Biol 2023; 11:1294717. [PMID: 38033852 PMCID: PMC10687153 DOI: 10.3389/fcell.2023.1294717] [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: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
The small ubiquitin-related modifier (SUMOylation) system is a conserved, reversible, post-translational protein modification pathway covalently attached to the lysine residues of proteins in eukaryotic cells, and SUMOylation is catalyzed by SUMO-specific activating enzyme (E1), binding enzyme (E2) and ligase (E3). Sentrin-specific proteases (SENPs) can cleave the isopeptide bond of a SUMO conjugate and catalyze the deSUMOylation reaction. SUMOylation can regulate the activity of proteins in many important cellular processes, including transcriptional regulation, cell cycle progression, signal transduction, DNA damage repair and protein stability. Biological experiments in vivo and in vitro have confirmed the key role of the SUMO conjugation/deconjugation system in energy metabolism, Ca2+ cycle homeostasis and protein quality control in cardiomyocytes. In this review, we summarized the research progress of the SUMO conjugation/deconjugation system and SUMOylation-mediated cardiac actions based on related studies published in recent years, and highlighted the further research areas to clarify the role of the SUMO system in the heart by using emerging technologies.
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Affiliation(s)
- Ying Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Zhihao Liu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiyun Bian
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development in Preterm Infants, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Chenxu Zhao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xin Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaozhi Liu
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development in Preterm Infants, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Nan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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39
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Hou W, Ji Z, Chen Z, Wherry EJ, Hicks SC, Ji H. A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nat Commun 2023; 14:7286. [PMID: 37949861 PMCID: PMC10638410 DOI: 10.1038/s41467-023-42841-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories of cells within a biological sample, it remains a challenge to compare pseudotemporal patterns with multiple samples (or replicates) across different experimental conditions. Here, we introduce Lamian, a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. Lamian can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions while adjusting for batch effects, and to detect changes in gene expression, cell density, and topology of a pseudotemporal trajectory. Unlike existing methods that ignore sample variability, Lamian draws statistical inference after accounting for cross-sample variability and hence substantially reduces sample-specific false discoveries that are not generalizable to new samples. Using both real scRNA-seq and simulation data, including an analysis of differential immune response programs between COVID-19 patients with different disease severity levels, we demonstrate the advantages of Lamian in decoding cellular gene expression programs in continuous biological processes.
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Affiliation(s)
- Wenpin Hou
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Zhicheng Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie C Hicks
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Hongkai Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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40
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Cleuren A, Molema G. Organotypic heterogeneity in microvascular endothelial cell responses in sepsis-a molecular treasure trove and pharmacological Gordian knot. Front Med (Lausanne) 2023; 10:1252021. [PMID: 38020105 PMCID: PMC10665520 DOI: 10.3389/fmed.2023.1252021] [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: 07/03/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
In the last decades, it has become evident that endothelial cells (ECs) in the microvasculature play an important role in the pathophysiology of sepsis-associated multiple organ dysfunction syndrome (MODS). Studies on how ECs orchestrate leukocyte recruitment, control microvascular integrity and permeability, and regulate the haemostatic balance have provided a wealth of knowledge and potential molecular targets that could be considered for pharmacological intervention in sepsis. Yet, this information has not been translated into effective treatments. As MODS affects specific vascular beds, (organotypic) endothelial heterogeneity may be an important contributing factor to this lack of success. On the other hand, given the involvement of ECs in sepsis, this heterogeneity could also be leveraged for therapeutic gain to target specific sites of the vasculature given its full accessibility to drugs. In this review, we describe current knowledge that defines heterogeneity of organ-specific microvascular ECs at the molecular level and elaborate on studies that have reported EC responses across organ systems in sepsis patients and animal models of sepsis. We discuss hypothesis-driven, single-molecule studies that have formed the basis of our understanding of endothelial cell engagement in sepsis pathophysiology, and include recent studies employing high-throughput technologies. The latter deliver comprehensive data sets to describe molecular signatures for organotypic ECs that could lead to new hypotheses and form the foundation for rational pharmacological intervention and biomarker panel development. Particularly results from single cell RNA sequencing and spatial transcriptomics studies are eagerly awaited as they are expected to unveil the full spatiotemporal signature of EC responses to sepsis. With increasing awareness of the existence of distinct sepsis subphenotypes, and the need to develop new drug regimen and companion diagnostics, a better understanding of the molecular pathways exploited by ECs in sepsis pathophysiology will be a cornerstone to halt the detrimental processes that lead to MODS.
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Affiliation(s)
- Audrey Cleuren
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Grietje Molema
- Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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41
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Pérez-Gutiérrez L, Ferrara N. Biology and therapeutic targeting of vascular endothelial growth factor A. Nat Rev Mol Cell Biol 2023; 24:816-834. [PMID: 37491579 DOI: 10.1038/s41580-023-00631-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2023] [Indexed: 07/27/2023]
Abstract
The formation of new blood vessels, called angiogenesis, is an essential pathophysiological process in which several families of regulators have been implicated. Among these, vascular endothelial growth factor A (VEGFA; also known as VEGF) and its two tyrosine kinase receptors, VEGFR1 and VEGFR2, represent a key signalling pathway mediating physiological angiogenesis and are also major therapeutic targets. VEGFA is a member of the gene family that includes VEGFB, VEGFC, VEGFD and placental growth factor (PLGF). Three decades after its initial isolation and cloning, VEGFA is arguably the most extensively investigated signalling system in angiogenesis. Although many mediators of angiogenesis have been identified, including members of the FGF family, angiopoietins, TGFβ and sphingosine 1-phosphate, all current FDA-approved anti-angiogenic drugs target the VEGF pathway. Anti-VEGF agents are widely used in oncology and, in combination with chemotherapy or immunotherapy, are now the standard of care in multiple malignancies. Anti-VEGF drugs have also revolutionized the treatment of neovascular eye disorders such as age-related macular degeneration and ischaemic retinal disorders. In this Review, we emphasize the molecular, structural and cellular basis of VEGFA action as well as recent findings illustrating unexpected interactions with other pathways and provocative reports on the role of VEGFA in regenerative medicine. We also discuss clinical and translational aspects of VEGFA. Given the crucial role that VEGFA plays in regulating angiogenesis in health and disease, this molecule is largely the focus of this Review.
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Affiliation(s)
- Lorena Pérez-Gutiérrez
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Napoleone Ferrara
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
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42
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Schneider MK, Wang J, Kare A, Adkar SS, Salmi D, Bell CF, Alsaigh T, Wagh D, Coller J, Mayer A, Snyder SJ, Borowsky AD, Long SR, Lansberg MG, Steinberg GK, Heit JJ, Leeper NJ, Ferrara KW. Combined near infrared photoacoustic imaging and ultrasound detects vulnerable atherosclerotic plaque. Biomaterials 2023; 302:122314. [PMID: 37776766 PMCID: PMC10872807 DOI: 10.1016/j.biomaterials.2023.122314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 10/02/2023]
Abstract
Atherosclerosis is an inflammatory process resulting in the deposition of cholesterol and cellular debris, narrowing of the vessel lumen and clot formation. Characterization of the morphology and vulnerability of the lesion is essential for effective clinical management. Here, near-infrared auto-photoacoustic (NIRAPA) imaging is shown to detect plaque components and, when combined with ultrasound imaging, to differentiate stable and vulnerable plaque. In an ex vivo study of photoacoustic imaging of excised plaque from 25 patients, 88.2% sensitivity and 71.4% specificity were achieved using a clinically-relevant protocol. In order to determine the origin of the NIRAPA signal, immunohistochemistry, spatial transcriptomics and spatial proteomics were co-registered with imaging and applied to adjacent plaque sections. The highest NIRAPA signal was spatially correlated with bilirubin and associated blood-based residue and with the cytoplasmic contents of inflammatory macrophages bearing CD74, HLA-DR, CD14 and CD163 markers. In summary, we establish the potential to apply the NIRAPA-ultrasound imaging combination to detect vulnerable carotid plaque and a methodology for fusing molecular imaging with spatial transcriptomic and proteomic methods.
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Affiliation(s)
- Martin Karl Schneider
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - James Wang
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Aris Kare
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Shaunak S Adkar
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Darren Salmi
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Caitlin F Bell
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tom Alsaigh
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dhananjay Wagh
- Sequencing Group Stanford Genomics, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - John Coller
- Sequencing Group Stanford Genomics, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Sarah J Snyder
- Department of Radiology and Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, UC Davis School of Medicine, Davis, CA 95616, USA
| | - Steven R Long
- Department of Pathology, University of California San Francisco, San Francisco, CA 94110, USA
| | - Maarten G Lansberg
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Gary K Steinberg
- Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jeremy J Heit
- Department of Radiology and Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Nicholas J Leeper
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katherine W Ferrara
- Molecular Imaging Program at Stanford and Bio-X Program, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94305, USA.
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43
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Lu Y, Huo H, Liang F, Xue J, Fang L, Miao Y, Shen L, He B. Role of Pericytes in Cardiomyopathy-Associated Myocardial Infarction Revealed by Multiple Single-Cell Sequencing Analysis. Biomedicines 2023; 11:2896. [PMID: 38001896 PMCID: PMC10668982 DOI: 10.3390/biomedicines11112896] [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: 09/25/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Acute myocardial infarction (AMI) is one of the leading causes of cardiovascular death worldwide. AMI with cardiomyopathy is accompanied by a poor long-term prognosis. However, limited studies have focused on the mechanism of cardiomyopathy associated with AMI. Pericytes are important to the microvascular function in the heart, yet little attention has been paid to their function in myocardial infarction until now. In this study, we integrated single-cell data from individuals with cardiomyopathy and myocardial infarction (MI) GWAS data to reveal the potential function of pericytes in cardiomyopathy-associated MI. We found that pericytes were concentrated in the left atrium and left ventricle tissues. DLC1/GUCY1A2/EGFLAM were the top three uniquely expressed genes in pericytes (p < 0.05). The marker genes of pericytes were enriched in renin secretion, vascular smooth muscle contraction, gap junction, purine metabolism, and diabetic cardiomyopathy pathways (p < 0.05). Among these pathways, the renin secretion and purine metabolism pathways were also found in the process of MI. In cardiomyopathy patients, the biosynthesis of collagen, modulating enzymes, and collagen formation were uniquely negatively regulated in pericytes compared to other cell types (p < 0.05). COL4A2/COL4A1/SMAD3 were the hub genes in pericyte function involved in cardiomyopathy and AMI. In conclusion, this study provides new evidence about the importance of pericytes in the pathogenesis of cardiomyopathy-associated MI. DLC1/GUCY1A2/EGFLAM were highly expressed in pericytes. The hub genes COL4A2/COL4A1/SMAD3 may be potential research targets for cardiomyopathy-associated MI.
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Affiliation(s)
| | | | | | | | | | | | - Lan Shen
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.L.); (H.H.); (F.L.); (J.X.); (L.F.); (Y.M.)
| | - Ben He
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.L.); (H.H.); (F.L.); (J.X.); (L.F.); (Y.M.)
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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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45
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Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023; 14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [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: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and individually measuring multiple molecular characteristics of thousands to millions of single cells, SCS technology can characterize multiple cell types and uncover the mechanisms of gene regulatory networks, the dynamics of transcription, and the functional state of proteomic profiling. In this context, we conducted systematic research on SCS techniques, including the fundamental concepts, procedural steps, and applications of scDNA, scRNA, scATAC, scCITE, and scSNARE methods, focusing on the unique clinical advantages of SCS, particularly in cancer therapy. We have explored challenging but critical areas such as circulating tumor cells (CTCs), lineage tracing, tumor heterogeneity, drug resistance, and tumor immunotherapy. Despite challenges in managing and analyzing the large amounts of data that result from SCS, this technique is expected to reveal new horizons in cancer research. This review aims to emphasize the key role of SCS in cancer research and promote the application of single-cell technologies to cancer therapy.
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Affiliation(s)
- Siyuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Weibo Jiang
- Department of Orthopaedic, The Second Hospital of Jilin University, Changchun, China
| | - Yanhui Du
- Department of Orthopaedics, Jilin Province People’s Hospital, Changchun, China
| | - Manshi Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huan Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
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46
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Zhu M, Liang H, Zhang Z, Jiang H, Pu J, Hang X, Zhou Q, Xiang J, He X. Distinct mononuclear diploid cardiac subpopulation with minimal cell-cell communications persists in embryonic and adult mammalian heart. Front Med 2023; 17:939-956. [PMID: 37294383 DOI: 10.1007/s11684-023-0987-9] [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: 07/31/2022] [Accepted: 01/31/2023] [Indexed: 06/10/2023]
Abstract
A small proportion of mononuclear diploid cardiomyocytes (MNDCMs), with regeneration potential, could persist in adult mammalian heart. However, the heterogeneity of MNDCMs and changes during development remains to be illuminated. To this end, 12 645 cardiac cells were generated from embryonic day 17.5 and postnatal days 2 and 8 mice by single-cell RNA sequencing. Three cardiac developmental paths were identified: two switching to cardiomyocytes (CM) maturation with close CM-fibroblast (FB) communications and one maintaining MNDCM status with least CM-FB communications. Proliferative MNDCMs having interactions with macrophages and non-proliferative MNDCMs (non-pMNDCMs) with minimal cell-cell communications were identified in the third path. The non-pMNDCMs possessed distinct properties: the lowest mitochondrial metabolisms, the highest glycolysis, and high expression of Myl4 and Tnni1. Single-nucleus RNA sequencing and immunohistochemical staining further proved that the Myl4+Tnni1+ MNDCMs persisted in embryonic and adult hearts. These MNDCMs were mapped to the heart by integrating the spatial and single-cell transcriptomic data. In conclusion, a novel non-pMNDCM subpopulation with minimal cell-cell communications was unveiled, highlighting the importance of microenvironment contribution to CM fate during maturation. These findings could improve the understanding of MNDCM heterogeneity and cardiac development, thus providing new clues for approaches to effective cardiac regeneration.
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Affiliation(s)
- Miaomiao Zhu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huamin Liang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhe Zhang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
| | - Hao Jiang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jingwen Pu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoyi Hang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qian Zhou
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiacheng Xiang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China.
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China.
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47
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Du J, Gu XR, Yu XX, Cao YJ, Hou J. Essential procedures of single-cell RNA sequencing in multiple myeloma and its translational value. BLOOD SCIENCE 2023; 5:221-236. [PMID: 37941914 PMCID: PMC10629747 DOI: 10.1097/bs9.0000000000000172] [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: 05/17/2023] [Accepted: 09/18/2023] [Indexed: 11/10/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm characterized by clonal proliferation of abnormal plasma cells. In many countries, it ranks as the second most prevalent malignant neoplasm of the hematopoietic system. Although treatment methods for MM have been continuously improved and the survival of patients has been dramatically prolonged, MM remains an incurable disease with a high probability of recurrence. As such, there are still many challenges to be addressed. One promising approach is single-cell RNA sequencing (scRNA-seq), which can elucidate the transcriptome heterogeneity of individual cells and reveal previously unknown cell types or states in complex tissues. In this review, we outlined the experimental workflow of scRNA-seq in MM, listed some commonly used scRNA-seq platforms and analytical tools. In addition, with the advent of scRNA-seq, many studies have made new progress in the key molecular mechanisms during MM clonal evolution, cell interactions and molecular regulation in the microenvironment, and drug resistance mechanisms in target therapy. We summarized the main findings and sequencing platforms for applying scRNA-seq to MM research and proposed broad directions for targeted therapies based on these findings.
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Affiliation(s)
- Jun Du
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao-Ran Gu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Xiao-Xiao Yu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Yang-Jia Cao
- Department of Hematology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shanxi 710000, China
| | - Jian Hou
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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48
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Luo X, Liu Z, Xu R. Adult tissue-specific stem cell interaction: novel technologies and research advances. Front Cell Dev Biol 2023; 11:1220694. [PMID: 37808078 PMCID: PMC10551553 DOI: 10.3389/fcell.2023.1220694] [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: 05/11/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
Adult tissue-specific stem cells play a dominant role in tissue homeostasis and regeneration. Various in vivo markers of adult tissue-specific stem cells have been increasingly reported by lineage tracing in genetic mouse models, indicating that marked cells differentiation is crucial during homeostasis and regeneration. How adult tissue-specific stem cells with indicated markers contact the adjacent lineage with indicated markers is of significance to be studied. Novel methods bring future findings. Recent advances in lineage tracing, synthetic receptor systems, proximity labeling, and transcriptomics have enabled easier and more accurate cell behavior visualization and qualitative and quantitative analysis of cell-cell interactions than ever before. These technological innovations have prompted researchers to re-evaluate previous experimental results, providing increasingly compelling experimental results for understanding the mechanisms of cell-cell interactions. This review aimed to describe the recent methodological advances of dual enzyme lineage tracing system, the synthetic receptor system, proximity labeling, single-cell RNA sequencing and spatial transcriptomics in the study of adult tissue-specific stem cells interactions. An enhanced understanding of the mechanisms of adult tissue-specific stem cells interaction is important for tissue regeneration and maintenance of homeostasis in organisms.
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Affiliation(s)
| | | | - Ruoshi Xu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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49
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Hu X, Wang Z, Zhang H, Cui P, Li Y, Chen X, Kong C, Wang W, Lu S. Single-cell sequencing: New insights for intervertebral disc degeneration. Biomed Pharmacother 2023; 165:115224. [PMID: 37516017 DOI: 10.1016/j.biopha.2023.115224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/18/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023] Open
Abstract
Over the past decade, single-cell RNA sequencing (scRNA-seq) has revolutionized research on biological mechanisms of diseases. Moreover, this technique has been utilized to identify and characterize unique cell types and subpopulations, thereby illuminating cellular heterogeneity. The true value of scRNA-seq lies in its ability to detect transcriptional alterations or perturbed pathways within specific cell types under pathological conditions. In the context of intervertebral disc degeneration (IVDD), the pathophysiological foundation is largely rooted in inflammation. The primary target cells of IVDD are nucleus pulposus cells, annulus fibrosus cells, cartilage endplate cells, and macrophages. The advancements in scRNA-seq technology have triggered remarkable progress in IVDD treatment, leading to breakthroughs in the identification of cell subsets, functional analysis, novel therapeutic targets, and the differentiation and development of various cell types. This review is the first of its kind to introduce the application of scRNA-seq techniques in IVDD, with a focus on the most recent scRNA-seq studies that have defined the populations of various cell types and specific cell-cell interactions in IVDD. Furthermore, we highlight several promising future research directions for scRNA-seq in IVDD.
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Affiliation(s)
- Xinli Hu
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Zheng Wang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Haojie Zhang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Peng Cui
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yongjin Li
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Xiaolong Chen
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Chao Kong
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Wei Wang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Shibao Lu
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No.45 Changchun Street, Xicheng District, Beijing 100053, China; National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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Tan Y, Huang J, Li D, Zou C, Liu D, Qin B. Single-cell RNA sequencing in dissecting microenvironment of age-related macular degeneration: Challenges and perspectives. Ageing Res Rev 2023; 90:102030. [PMID: 37549871 DOI: 10.1016/j.arr.2023.102030] [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: 09/16/2022] [Revised: 04/29/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Age-related macular degeneration (AMD) is the leading cause of blindness in individuals over the age of 50 years, yet its etiology and pathogenesis largely remain uncovered. Single-cell RNA sequencing (scRNA-seq) technologies are recently developed and have a number of advantages over conventional bulk RNA sequencing techniques in uncovering the heterogeneity of complex microenvironments containing numerous cell types and cell communications during various biological processes. In this review, we summarize the latest discovered cellular components and regulatory mechanisms during AMD development revealed by scRNA-seq. In addition, we discuss the main challenges and future directions in exploring the pathophysiology of AMD equipped with single-cell technologies. Our review underscores the importance of multimodal single-cell platforms (such as single-cell spatiotemporal multi-omics and single-cell exosome omics) as new approaches for basic and clinical AMD research in identifying biomarker, characterizing cellular responses to drug treatment and environmental stimulation.
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Affiliation(s)
- Yao Tan
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
| | - Jianguo Huang
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
| | - Deshuang Li
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China
| | - Chang Zou
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China; Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, China; School of Life and Health Sciences, The Chinese University of Kong Hong, Shenzhen 518000, Guangdong, China.
| | - Dongcheng Liu
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China; Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, China.
| | - Bo Qin
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, China; Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, China; Aier School of Ophthalmology, Central South University, Changsha, China.
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