1
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Yuan Y, Niu Y, Ye J, Xu Y, He X, Chen S. Identification of diagnostic model in heart failure with myocardial fibrosis and conduction block by integrated gene co-expression network analysis. BMC Med Genomics 2024; 17:52. [PMID: 38355637 PMCID: PMC10868111 DOI: 10.1186/s12920-024-01814-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] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Despite the advancements in heart failure(HF) research, the early diagnosis of HF continues to be a challenging issue in clinical practice. This study aims to investigate the genes related to myocardial fibrosis and conduction block, with the goal of developing a diagnostic model for early treatment of HF in patients. METHOD The gene expression profiles of GSE57345, GSE16499, and GSE9128 were obtained from the Gene Expression Omnibus (GEO) database. After merging the expression profile data and adjusting for batch effects, differentially expressed genes (DEGs) associated with conduction block and myocardial fibrosis were identified. Gene Ontology (GO) resources, Kyoto Encyclopedia of Genes and Genomes (KEGG) resources, and gene set enrichment analysis (GSEA) were utilized for functional enrichment analysis. A protein-protein interaction network (PPI) was constructed using a string database. Potential key genes were selected based on the bioinformatics information mentioned above. SVM and LASSO were employed to identify hub genes and construct the module associated with HF. The mRNA levels of TAC mice and external datasets (GSE141910 and GSE59867) are utilized for validating the diagnostic model. Additionally, the study explores the relationship between the diagnostic model and immune cell infiltration. RESULTS A total of 395 genes exhibiting differential expression were identified. Functional enrichment analysis revealed that these specific genes primarily participate in biological processes and pathways associated with the constituents of the extracellular matrix (ECM), immune system processes, and inflammatory responses. We identified a diagnostic model consisting of 16 hub genes, and its predictive performance was validated using external data sets and a transverse aortic coarctation (TAC) mouse model. In addition, we observed significant differences in mRNA expression of 7 genes in the TAC mouse model. Interestingly, our study also unveiled a correlation between these model genes and immune cell infiltration. CONCLUSIONS We identified sixteen key genes associated with myocardial fibrosis and conduction block, as well as diagnostic models for heart failure. Our findings have significant implications for the intensive management of individuals with potential genetic variants associated with heart failure, especially in the context of advancing cell-targeted therapy for myocardial fibrosis.
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Affiliation(s)
- Yonghua Yuan
- Department of Pediatrics, Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Pediatric Cardiology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Yiwei Niu
- Department of Pediatric Cardiology, Xinhua hospital, School of medicine, Shanghai Jiaotong university, Shanghai, China
| | - Jiajun Ye
- Department of Pediatric Cardiology, Xinhua hospital, School of medicine, Shanghai Jiaotong university, Shanghai, China
| | - Yuejuan Xu
- Department of Pediatric Cardiology, Xinhua hospital, School of medicine, Shanghai Jiaotong university, Shanghai, China
| | - Xuehua He
- Department of Pediatric Cardiology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xinhua hospital, School of medicine, Shanghai Jiaotong university, Shanghai, China.
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2
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Huang R, Chen J, Dong X, Zhang X, Luo W. Transcriptome Data Revealed the circRNA-miRNA-mRNA Regulatory Network during the Proliferation and Differentiation of Myoblasts in Shitou Goose. Animals (Basel) 2024; 14:576. [PMID: 38396545 PMCID: PMC10885906 DOI: 10.3390/ani14040576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
CircRNA, a recently characterized non-coding RNA (ncRNA) variant, functions as a molecular sponge, exerting regulatory control by binding to microRNA (miRNA) and modulating the expression of downstream proteins, either promoting or inhibiting their expression. Among poultry species, geese hold significant importance, prized by consumers for their delectable taste and rich nutritional content. Despite the prominence of geese, research on the growth and development of goose muscle, particularly the regulatory role of circRNAs in goose muscle formation, remains insufficiently explored. In this study, we constructed comprehensive expression profiles of circRNAs and messenger RNAs (mRNAs) within the myoblasts and myotubes of Shitou geese. We identified a total of 96 differentially expressed circRNAs (DEcircRNAs) and 880 differentially expressed mRNAs (DEmRNAs). Notably, the parental genes of DEcircRNAs and DEmRNAs exhibited enrichment in the Wnt signaling pathway, highlighting its potential impact on the proliferation and differentiation of goose myoblasts. Employing RNAhybrid and miRDB, we identified circRNA-miRNA pairs and mRNA-miRNA pairs that may play a role in regulating myogenic differentiation or muscle growth. Subsequently, utilizing Cytoscape, we constructed a circRNA-miRNA-mRNA interaction network aimed at unraveling the intricate regulatory mechanisms involved in goose muscle growth and development, which comprises 93 circRNAs, 351 miRNAs, and 305 mRNAs. Moreover, the identification of 10 hub genes (ACTB, ACTN1, BDNF, PDGFRA, MYL1, EFNA5, MYSM1, THBS1, ITGA8, and ELN) potentially linked to myogenesis, along with the exploration of their circRNA-miRNA-hub gene regulatory axis, was also conducted. These competitive endogenous RNA (ceRNA) regulatory networks elucidate the molecular regulatory mechanisms associated with muscle growth in Shitou geese, providing deeper insights into the reciprocal regulation of circRNA, miRNA, and mRNA in the context of goose muscle formation.
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Affiliation(s)
- Rongqin Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Jiahui Chen
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xu Dong
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Wen Luo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
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3
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He L, Liao J, Liu Z, Wang T, Zhou Y, Wang T, Lei B, Zhou G. Multi-omic analysis of mandibuloacral dysplasia type A patient iPSC-derived MSC senescence reveals miR-311 as a novel biomarker for MSC senescence. Hum Mol Genet 2023; 32:2872-2886. [PMID: 37427980 DOI: 10.1093/hmg/ddad111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/23/2023] [Accepted: 06/02/2023] [Indexed: 07/11/2023] Open
Abstract
Mandibuloacral dysplasia type A (MADA) is a rare genetic progeroid syndrome associated with lamin A/C (LMNA) mutations. Pathogenic mutations of LMNA result in nuclear structural abnormalities, mesenchymal tissue damage and progeria phenotypes. However, it remains elusive how LMNA mutations cause mesenchymal-derived cell senescence and disease development. Here, we established an in vitro senescence model using induced pluripotent stem cell-derived mesenchymal stem cells (iMSCs) from MADA patients with homozygous LMNA p.R527C mutation. When expanded to passage 13 in vitro, R527C iMSCs exhibited marked senescence and attenuation of stemness potential, accompanied by immunophenotypic changes. Transcriptome and proteome analysis revealed that cell cycle, DNA replication, cell adhesion and inflammation might play important roles in senescence. In-depth evaluation of changes in extracellular vesicle (EV) derived iMSCs during senescence revealed that R527C iMSC-EVs could promote surrounding cell senescence by carrying pro-senescence microRNAs (miRNAs), including a novel miRNA called miR-311, which can serve as a new indicator for detecting chronic and acute mesenchymal stem cell (MSC) senescence and play a role in promoting senescence. Overall, this study advanced our understanding of the impact of LMNA mutations on MSC senescence and provided novel insights into MADA therapy as well as the link between chronic inflammation and aging development.
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Affiliation(s)
- Liangge He
- Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopedic Diseases, Department of Medical Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen 518060, 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, China
| | - Jinqi Liao
- Senotherapeutics Ltd, Hangzhou 311100, China
- Lungene Biotech Ltd, Shenzhen 518110, China
| | - Zhen Liu
- Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopedic Diseases, Department of Medical Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen 518060, China
| | - Ting Wang
- Senotherapeutics Ltd, Hangzhou 311100, China
- Lungene Biotech Ltd, Shenzhen 518110, China
| | - Yan Zhou
- Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopedic Diseases, Department of Medical Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen 518060, China
- Lungene Biotech Ltd, Shenzhen 518110, China
| | - Tianfu Wang
- 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, China
| | - Baiying Lei
- 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, China
| | - Guangqian Zhou
- Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-Aging and Regenerative Medicine, Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopedic Diseases, Department of Medical Cell Biology and Genetics, Shenzhen University Medical School, Shenzhen 518060, China
- Senotherapeutics Ltd, Hangzhou 311100, China
- Lungene Biotech Ltd, Shenzhen 518110, China
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4
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Gao X, Sun R, Jiao N, Liang X, Li G, Gao H, Wu X, Yang M, Chen C, Sun X, Chen L, Wu W, Cong Y, Zhu R, Guo T, Liu Z. Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn's disease. Cell Rep Med 2023:101050. [PMID: 37172588 DOI: 10.1016/j.xcrm.2023.101050] [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: 12/06/2022] [Revised: 02/07/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Dysregulated host-microbial interactions play critical roles in initiation and perpetuation of gut inflammation in Crohn's disease (CD). However, the spatial distribution and interaction network across the intestine and its accessory tissues are still elusive. Here, we profile the host proteins and tissue microbes in 540 samples from the intestinal mucosa, submucosa-muscularis-serosa, mesenteric adipose tissues, mesentery, and mesenteric lymph nodes of 30 CD patients and spatially decipher the host-microbial interactions. We observe aberrant antimicrobial immunity and metabolic processes across multi-tissues during CD and determine bacterial transmission along with altered microbial communities and ecological patterns. Moreover, we identify several candidate interaction pairs between host proteins and microbes associated with perpetuation of gut inflammation and bacterial transmigration across multi-tissues in CD. Signature alterations in host proteins (e.g., SAA2 and GOLM1) and microbes (e.g., Alistipes and Streptococcus) are further imprinted in serum and fecal samples as potential diagnostic biomarkers, thus providing a rationale for precision diagnosis.
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Affiliation(s)
- Xiang Gao
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ruicong Sun
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Na Jiao
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao Liang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Gengfeng Li
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Han Gao
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiaohan Wu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Muqing Yang
- Center for Difficult and Complicated Abdominal Surgery, The Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Chunqiu Chen
- Center for Difficult and Complicated Abdominal Surgery, The Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Xiaomin Sun
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Liang Chen
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Wei Wu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yingzi Cong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ruixin Zhu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China.
| | - Zhanju Liu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
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5
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Geng X, Li L, Luo Y, Yang W, Hu J, Zhao Z, Cheng C, Zhang T, Zhang Y, Liu L, Xie Y, Li G, Liu D, Bai R, Bai X, Wang G, Chen H, Wang Y, Chen H, Sun B. Tumor Cell Derived Lnc-FSD2-31:1 Contributes to Cancer-Associated Fibroblasts Activation in Pancreatic Ductal Adenocarcinoma Progression through Extracellular Vesicles Cargo MiR-4736. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203324. [PMID: 36727832 PMCID: PMC10074102 DOI: 10.1002/advs.202203324] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 01/10/2023] [Indexed: 05/11/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) presents with high mortality and short overall survival. Cancer-associated fibroblasts (CAFs) act as refuge for cancer cells in PDAC. Mechanisms of intracelluar communication between CAFs and cancer cells need to be explored. Long noncoding RNAs (lncRNAs) are involved in the modulation of oncogenesis and tumor progression of PDAC; however, specific lncRNAs and their mechanism of action have not been clarified clearly in tumoral microenvironment. This work aims to identify novel lncRNAs involved in cellular interaction between cancer cells and CAFs in PDAC. To this end, differentially expressed lncRNAs between long-term and short-term survival PDAC patients are screened. Lnc-FSD2-31:1 is found to be significantly increased in long-term survival patients. This work then discovers that tumor-derived lnc-FSD2-31:1 restrains CAFs activation via miR-4736 transported by extracellular vesicles (EVs) in vitro and in vivo. Mechanistically, EVs-derived miR-4736 suppresses autophagy and contributes to CAFs activation by targeting ATG7. Furthermore, blocking miR-4736 suppresses tumor growth in genetically engineered KPC (LSL-KrasG12D/+, LSL-Trp53R172H/+, and Pdx-1-Cre) mouse model of PDAC. This study demonstrates that intratumoral lnc-FSD2-31:1 modulates autophagy in CAFs resulting in their activation through EVs-derived miR-4736. Targeting miR-4736 may be a potential biomarker and therapeutic target for PDAC.
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Affiliation(s)
- Xinglong Geng
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Le Li
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yan Luo
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Wenbo Yang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Jisheng Hu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Zhongjie Zhao
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Chundong Cheng
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Tao Zhang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yangyang Zhang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Liwei Liu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yu Xie
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Guanqun Li
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Danxi Liu
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Rui Bai
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Xuewei Bai
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Gang Wang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Hua Chen
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Yongwei Wang
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Hongze Chen
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
| | - Bei Sun
- Department of Pancreatic and Biliary SurgeryThe First Affiliated Hospital of Harbin Medical UniversityKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang150000China
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6
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Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science 2022; 377:eabo1984. [PMID: 35926050 PMCID: PMC9528698 DOI: 10.1126/science.abo1984] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic cardiomyopathy (ACM) convey high risks for the development of heart failure through unknown mechanisms. Using single-nucleus RNA sequencing, we characterized the transcriptome of 880,000 nuclei from 18 control and 61 failing, nonischemic human hearts with pathogenic variants in DCM and ACM genes or idiopathic disease. We performed genotype-stratified analyses of the ventricular cell lineages and transcriptional states. The resultant DCM and ACM ventricular cell atlas demonstrated distinct right and left ventricular responses, highlighting genotype-associated pathways, intercellular interactions, and differential gene expression at single-cell resolution. Together, these data illuminate both shared and distinct cellular and molecular architectures of human heart failure and suggest candidate therapeutic targets.
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Affiliation(s)
- Daniel Reichart
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Department of Medicine I, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Eric L Lindberg
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Henrike Maatz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
| | - Antonio M A Miranda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Anissa Viveiros
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Nikolay Shvetsov
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Emily R Nadelmann
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Lee
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Viktoria Strohmenger
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Walter-Brendel-Centre of Experimental Medicine, Ludwig-Maximilian University of Munich, 81377 Munich, Germany
| | - Daniel M DeLaughter
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrew Woehler
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Christoph Lippert
- Digital Health-Machine Learning group, Hasso Plattner Institute for Digital Engineering, University of Potsdam, 14482 Potsdam, Germany.,Hasso Plattner Institute for Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuri Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Kemar Brown
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiac Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Rasheda A Chowdhury
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | | | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Henrik Fox
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Ahla Ghauri
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Jan Gummert
- Heart and Diabetes Center NRW, Clinic for Thoracic and Cardiovascular Surgery, University Hospital of the Ruhr-University, 32545 Bad Oeynhausen, Germany
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan
| | - Ruoyan Li
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK
| | - Barbara McDonough
- Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Sara Samari
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Farnoush Shahriaran
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline Stanasiuk
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Pantazis I Theotokis
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Fabian J Theis
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany
| | | | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Catherine L Worth
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London SW3 6NR, UK.,MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Young-Ae Lee
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, 32545 Bad Oeynhausen, Germany
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.,British Heart Foundation Centre for Research Excellence and Centre for Regenerative Medicine, Imperial College London, London WC2R 2LS, UK
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.,Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Matthias Heinig
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 85764 Neuherberg, Germany.,Department of Informatics, Technische Universitaet Muenchen (TUM), 85748 Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Munich Heart Association, Partner Site Munich, 10785 Berlin, Germany
| | | | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany.,Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Bethesda, MD 20815, USA
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7
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Doersch KM, Barnett D, Chase A, Johnston D, Gabrielsen JS. The contribution of the immune system to genitourinary fibrosis. Exp Biol Med (Maywood) 2022; 247:765-778. [PMID: 35531654 PMCID: PMC9134766 DOI: 10.1177/15353702221090872] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Fibrotic diseases of the genitourinary tract are devastating and incompletely understood pathologies. These diseases include urethral and ureteral strictures, retroperitoneal fibrosis, and Peyronie's disease. They can contribute to obstructive uropathy and sexual dysfunction. Poor understanding of the pathophysiology of these diseases severely limits our ability to prevent and treat them. Genitourinary fibrotic diseases likely represent related pathologies that share common underlying mechanisms involving wound healing in response to injury. These diseases share the common feature of extracellular matrix abnormalities-such as collagen deposition, transforming growth factor-β accumulation, and dysregulation of collagen maturation-leading to abnormal tissue stiffness. Given the association of many of these diseases with autoimmunity, a systemic pro-inflammatory state likely contributes to their associated fibrogenesis. Herein, we explore the immunologic contribution to fibrogenesis in several fibrotic diseases of the genitourinary system. Better understanding how the immune system contributes to fibrosis in these diseases may improve prevention and therapeutic strategies and elucidate the functions of immunologic contributors to fibrosis in general.
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Affiliation(s)
- Karen M Doersch
- Department of Urology, University of
Rochester Medical Center, Rochester, NY 14642, USA
| | - Daniel Barnett
- Department of Pediatrics, University of
Toledo, Toledo, OH 43614, USA
| | - Abbie Chase
- Department of Urology, University of
Rochester Medical Center, Rochester, NY 14642, USA
| | - Daniel Johnston
- Department of Urology, University of
Rochester Medical Center, Rochester, NY 14642, USA
| | - J Scott Gabrielsen
- Department of Urology, University of
Rochester Medical Center, Rochester, NY 14642, USA
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8
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Li S, Tao W, Huang Z, Yan L, Chen B, Zeng C, Chen F. The Transcriptional Landscapes and Key Genes in Brain Arteriovenous Malformation Progression in a Venous Hypertension Rat Model Revealed by RNA Sequencing. J Inflamm Res 2022; 15:1381-1397. [PMID: 35250290 PMCID: PMC8893156 DOI: 10.2147/jir.s347754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/04/2022] [Indexed: 01/23/2023] Open
Abstract
Background Brain arteriovenous malformations (bAVM) are abnormal vascular lesions characterized by direct connections between arteries and veins without an intervening capillary bed. The primary goal for brain AVM treatment is to prevent rupture and hemorrhage; however, the underlying molecular mechanisms are still unknown. Methods We constructed venous hypertension (VH) rat model with end-to-end anastomosis of the proximal left common carotid artery and the left distal external jugular vein. Thirty-eight adult rats were randomly assigned to four groups: the 0-week (n=5), the 1-week VH group (n=12), the 3-week VH group (n=9), and the 6-week VH group (n=12). We measured the hemodynamics and diameter of the arterialized veins. An RNA sequencing of arterialized veins was conducted, followed by comprehensive bioinformatics analysis to identify key genes and biological pathways involved in VH progression. The candidate genes from RNA-Seq were validated by RT-qPCR and immunostaining in human tissues. Results We observed high-flow and low resistance characteristics in VH models. A total of 317 upregulated and 258 downregulated common genes were consistently differentially expressed during VH progression. Thirteen co-expression modules were obtained by WGCNA analysis, and 4 key modules were identified. Thirteen genes: Adamts8, Adamtsl3, Spon2, Adamtsl2, Chad, Itga7, Comp, Itga8, Bmp6, Fst, Smad6, Smad7, Grem1, and Nog with differential expressions were identified using the density of maximum neighborhood component (DMNC) algorithm in Cytohubba. The expression of five potential genes (Adamts8, Adamtsl3, Spon2, Adamtsl2, Itga8) were increased in RT-qPCR, while in human bAVM tissue, the protein levels of Adamtsl2 and Itga8 were significant elevated and Spon2 and Adamtsl3 were decreased. Conclusion The identified gene networks of Adamtsl3, Spon2, Adamtsl2, and Itga8 provided key genes for further intervention.
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Affiliation(s)
- Shifu Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Wengui Tao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Zheng Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Langchao Yan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Bo Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Chudai Zeng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Fenghua Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
- Correspondence: Fenghua Chen, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People’s Republic of China, Email
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9
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The interaction of S100A16 and GRP78 actives endoplasmic reticulum stress-mediated through the IRE1α/XBP1 pathway in renal tubulointerstitial fibrosis. Cell Death Dis 2021; 12:942. [PMID: 34645789 PMCID: PMC8514525 DOI: 10.1038/s41419-021-04249-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/25/2021] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
Recent studies have indicated that the development of acute and chronic kidney disease including renal fibrosis is associated with endoplasmic reticulum (ER) stress. S100 calcium-binding protein 16 (S100A16) as a novel member of the S100 family is involved in kidney disease; however, few studies have examined fibrotic kidneys for a relationship between S100A16 and ER stress. In our previous study, we identified GRP78 as a protein partner of S100A16 in HK-2 cells. Here, we confirmed a physical interaction between GRP78 and S100A16 in HK-2 cells and a markedly increased expression of GRP78 in the kidneys of unilateral ureteral occlusion mice. S100A16 overexpression in HK-2 cells by infection with Lenti-S100A16 also induced upregulation of ER stress markers, including GRP78, p-IRE1α, and XBP1s. Immunofluorescence staining demonstrated that the interaction between S100A16 and GRP78 predominantly occurred in the ER of control HK-2 cells. By contrast, HK-2 cells overexpressing S100A16 showed colocalization of S100A16 and GRP78 mainly in the cytoplasm. Pretreatment with BAPTA-AM, a calcium chelator, blunted the upregulation of renal fibrosis genes and ER stress markers induced by S100A16 overexpression in HK-2 cells and suppressed the cytoplasmic colocalization of GRP78 and S100A16. Co-immunoprecipitation studies suggested a competitive binding between S100A16 and IRE1α with GRP78 in HK-2 cells. Taken together, our findings demonstrate a significant increase in S100A16 expression in the cytoplasm following renal injury. GRP78 then moves into the cytoplasm and binds with S100A16 to promote the release of IRE1α. The subsequent phosphorylation of IRE1α then leads to XBP1 splicing that activates ER stress.
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10
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Interplay between extracellular matrix components and cellular and molecular mechanisms in kidney fibrosis. Clin Sci (Lond) 2021; 135:1999-2029. [PMID: 34427291 DOI: 10.1042/cs20201016] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 12/13/2022]
Abstract
Chronic kidney disease (CKD) is characterized by pathological accumulation of extracellular matrix (ECM) proteins in renal structures. Tubulointerstitial fibrosis is observed in glomerular diseases as well as in the regeneration failure of acute kidney injury (AKI). Therefore, finding antifibrotic therapies comprises an intensive research field in Nephrology. Nowadays, ECM is not only considered as a cellular scaffold, but also exerts important cellular functions. In this review, we describe the cellular and molecular mechanisms involved in kidney fibrosis, paying particular attention to ECM components, profibrotic factors and cell-matrix interactions. In response to kidney damage, activation of glomerular and/or tubular cells may induce aberrant phenotypes characterized by overproduction of proinflammatory and profibrotic factors, and thus contribute to CKD progression. Among ECM components, matricellular proteins can regulate cell-ECM interactions, as well as cellular phenotype changes. Regarding kidney fibrosis, one of the most studied matricellular proteins is cellular communication network-2 (CCN2), also called connective tissue growth factor (CTGF), currently considered as a fibrotic marker and a potential therapeutic target. Integrins connect the ECM proteins to the actin cytoskeleton and several downstream signaling pathways that enable cells to respond to external stimuli in a coordinated manner and maintain optimal tissue stiffness. In kidney fibrosis, there is an increase in ECM deposition, lower ECM degradation and ECM proteins cross-linking, leading to an alteration in the tissue mechanical properties and their responses to injurious stimuli. A better understanding of these complex cellular and molecular events could help us to improve the antifibrotic therapies for CKD.
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11
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Bo C, Geng X, Zhang J, Sai L, Zhang Y, Yu G, Zhang Z, Liu K, Du Z, Peng C, Jia Q, Shao H. Comparative proteomic analysis of silica-induced pulmonary fibrosis in rats based on tandem mass tag (TMT) quantitation technology. PLoS One 2020; 15:e0241310. [PMID: 33119648 PMCID: PMC7595299 DOI: 10.1371/journal.pone.0241310] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022] Open
Abstract
Silicosis is a systemic disease characterized by chronic persistent inflammation and incurable pulmonary fibrosis with the underlying molecular mechanisms to be fully elucidated. In this study, we employed tandem mass tag (TMT) based on quantitative proteomics technology to detect differentially expressed proteins (DEPs) in lung tissues of silica-exposed rats. A total of 285 DEPs (145 upregulated and 140 downregulated) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the biological pathway and functional classification of the proteins. Results showed that these DEPs were mainly enriched in the phagosome, lysosome function, complement and the coagulation cascade, glutathione metabolism, focal adhesion and ECM-receptor interactions. To validate the proteomics data, we selected and analyzed the expression trends of six proteins including CD14, PSAP, GM2A, COL1A1, ITGA8 and CLDN5 using parallel reaction monitoring (PRM). The consistent result between PRM and TMT indicated the reliability of our proteomic data. These findings will help to reveal the pathogenesis of silicosis and provide potential therapeutic targets. Data are available via ProteomeXchange with identifier PXD020625.
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Affiliation(s)
- Cunxiang Bo
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Xiao Geng
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Juan Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Linlin Sai
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Yu Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Gongchang Yu
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Zhenling Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Kai Liu
- Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, Ji’nan, Shandong, China
| | - Zhongjun Du
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Cheng Peng
- Queensland Alliance for Environmental Health Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Qiang Jia
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
- * E-mail: (QJ); (HS)
| | - Hua Shao
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
- * E-mail: (QJ); (HS)
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12
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Effects of Acute and Chronic Exposure to Residual Level Erythromycin on Human Intestinal Epithelium Cell Permeability and Cytotoxicity. Microorganisms 2019; 7:microorganisms7090325. [PMID: 31489925 PMCID: PMC6780317 DOI: 10.3390/microorganisms7090325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/11/2019] [Accepted: 08/31/2019] [Indexed: 12/16/2022] Open
Abstract
Residual concentrations of erythromycin in food could result in gastrointestinal tract exposure that potentially poses a health-hazard to the consumer, affecting intestinal epithelial permeability, barrier function, microbiota composition, and antimicrobial resistance. We investigated the effects of erythromycin after acute (48 h single treatment with 0.03 μg/mL to 300 μg/mL) or chronic (repeated treatment with 0.3 µg/mL and 300 µg/mL erythromycin for five days) exposures on the permeability of human colonic epithelial cells, a model that mimics a susceptible intestinal surface devoid of commensal microbiota. Transepithelial electrical resistance (TER) measurements indicated that erythromycin above 0.3 µg/mL may compromise the epithelial barrier. Acute exposure increased cytotoxicity, while chronic exposure decreased the cytotoxicity. Quantitative PCR analysis revealed that only ICAM1 (intercellular adhesion molecule 1) was up-regulated during 0.3 μg/mL acute-exposure, while ICAM1, JAM3 (junctional adhesion molecule 3), and ITGA8 (integrin alpha 8), were over-expressed in the 300 μg/mL acute treatment group. However, during chronic exposure, no change in the mRNA expression was observed at 0.3 μg/mL, and only ICAM2 was significantly up-regulated after 300 μg/mL. ICAM1 and ICAM2 are known to be involved in the formation of extracellular matrices. These gene expression changes may be related to the immunoregulatory activity of erythromycin, or a compensatory mechanism of the epithelial cells to overcome the distress caused by erythromycin due to increased permeability.
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13
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Rauchman M, Griggs D. Emerging strategies to disrupt the central TGF-β axis in kidney fibrosis. Transl Res 2019; 209:90-104. [PMID: 31085163 PMCID: PMC6850218 DOI: 10.1016/j.trsl.2019.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
Abstract
Chronic kidney disease (CKD) affects more than 20 million people in the United States and the global burden of this disorder is increasing. Many affected individuals will progress to end stage kidney disease necessitating dialysis or transplantation. CKD is also a major independent contributor to the risk of cardiovascular morbidity and mortality. Tubulointerstitial fibrosis is a final common pathway for most causes of progressive CKD. Currently, there are no clinically available therapies targeting fibrosis that can slow the decline in kidney function. Although it has long been known that TGF-β signaling is a critical mediator of kidney fibrosis, translating this knowledge to the clinic has been challenging. In this review, we highlight some recent insights into the mechanisms of TGF-β signaling that target activation of this cytokine at the site of injury or selectively inhibit pro-fibrotic gene expression. Molecules directed at these targets hold the promise of attaining therapeutic efficacy while limiting toxicity seen with global inhibition of TGF-β. Kidney injury has profound epigenetic effects leading to altered expression of more than a thousand genes. We discuss how drugs targeting epigenetic modifications, some of which are in use for cancer therapy, have the potential to reprogram gene regulatory networks to favor adaptive repair and prevent fibrosis. The lack of reliable biomarkers of kidney fibrosis is a major limitation in designing clinical trials for testing CKD treatments. We conclude by reviewing recent advances in fibrosis biomarker development.
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Affiliation(s)
- Michael Rauchman
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri; VA St. Louis Health Care System, Saint Louis, Missouri.
| | - David Griggs
- Department of Molecular Microbiology and Immunology, Edward A. Doisy Research Center, Saint Louis University, Saint Louis, Missouri.
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14
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Bon H, Hales P, Lumb S, Holdsworth G, Johnson T, Qureshi O, Twomey BM. Spontaneous Extracellular Matrix Accumulation in a Human in vitro Model of Renal Fibrosis Is Mediated by αV Integrins. Nephron Clin Pract 2019; 142:328-350. [PMID: 31048591 DOI: 10.1159/000499506] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/10/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Tubulointerstitial fibrosis is a key feature of chronic kidney diseases leading to renal failure. It is characterised by the infiltration of fibroblasts and aberrant accumulation of extracellular matrix (ECM) proteins, which are associated with progressive loss of renal function. Integrins play a major role in fibrosis, but the mechanisms through which they do this are not fully understood. OBJECTIVE Using a complex cell system, we test the hypothesis that integrins are pro-fibrotic via regulation of functional interactions between tubular epithelial cells and renal fibroblasts. METHOD Contact co-culture of human primary renal proximal tubular epithelial cells and renal fibroblasts promoted the spontaneous accumulation of a mature ECM rich in interstitial collagens, which was considerably in excess of that seen in the individual mono-cultures. Both cell types persisted throughout the culture and were capable of expressing multiple ECM components. RESULTS While ECM accumulation was inhibited by the clinically proven anti-fibrotic, nintedanib, and was partially abrogated by transforming growth factor β neutralisation, its levels did not return to basal, indicating additional pathways were implicated in the pro-ECM response. Application of anti-integrin blocking antibodies and small molecules demonstrated a major role of the αV integrins in the ECM accumulation during fibroblast: epithelial cell interactions. CONCLUSION Integrin-mediated pathways can facilitate the spontaneous accumulation of ECM during fibroblast: epithelial cell interactions, and this direct renal co-culture assay system could provide a translational in vitro assay for investigating novel pathways involved in the pro-ECM response and the screening of renal anti-fibrotic agents.
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15
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Role of integrin alpha8 in murine model of lung fibrosis. PLoS One 2018; 13:e0197937. [PMID: 29813125 PMCID: PMC5973593 DOI: 10.1371/journal.pone.0197937] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/01/2018] [Indexed: 01/13/2023] Open
Abstract
Background Integrin α8 (ITGA8) heterodimerizes with integrin β1 and is highly expressed in stromal cells of the lung. Platelet-derived growth factor receptor beta (PDGFRβ+) cells constitute a major population of contractile myofibroblasts in the lung following bleomycin-induced fibrosis. Integrin α8β1 is upregulated in fibrotic foci in bleomycin-induced lung injury. However, the functional role of ITGA8 in fibrogenesis has not been characterized. In this study, we examined whether genetic deletion of ITGA8 from PDGFRβ+ cells in the lung altered fibrosis. Methods Pdgfrb-Cre/+;Itga8flox/- or Pdgfrb-Cre/+;Itga8flox/flox (Cre+) and control mice (Cre-) were used for in vitro and in vivo studies. Primary cultures of PDGFRβ+ cells were exposed to TGFβ, followed by RNA isolation for qPCR. For in vivo studies, Cre+ and Cre- mice were characterized at baseline and after bleomycin-induced fibrosis. Results PDGFRβ-selected cells from Cre+ animals showed higher levels of Col1a1 expression after treatment with TGFβ. However, Cre- and Cre+ animals showed no significant difference in measures of acute lung injury or fibrosis following bleomycin challenge. Conclusion While ITGA8 deletion in lung PDGFRβ+ stromal cells showed evidence of greater Col1a1 mRNA expression after TGFβ treatment in vitro, no functional difference was detected in vivo.
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16
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Schuppan D, Ashfaq-Khan M, Yang AT, Kim YO. Liver fibrosis: Direct antifibrotic agents and targeted therapies. Matrix Biol 2018; 68-69:435-451. [PMID: 29656147 DOI: 10.1016/j.matbio.2018.04.006] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 12/11/2022]
Abstract
Liver fibrosis and in particular cirrhosis are the major causes of morbidity and mortality of patients with chronic liver disease. Their prevention or reversal have become major endpoints in clinical trials with novel liver specific drugs. Remarkable progress has been made with therapies that efficiently address the cause of the underlying liver disease, as in chronic hepatitis B and C. Highly effective antiviral therapy can prevent progression or even induce reversal in the majority of patients, but such treatment remains elusive for the majority of liver patients with advanced alcoholic or nonalcoholic steatohepatitis, genetic or autoimmune liver diseases. Moreover, drugs that would speed up fibrosis reversal are needed for patients with cirrhosis, since even with effective causal therapy reversal is slow or the disease may further progress. Therefore, highly efficient and specific antifibrotic agents are needed that can address advanced fibrosis, i.e., the detrimental downstream result of all chronic liver diseases. This review discusses targeted antifibrotic therapies that address molecules and mechanisms that are central to fibrogenesis or fibrolysis, including strategies that allow targeting of activated hepatic stellate cells and myofibroblasts and other fibrogenic effector cells. Focus is on collagen synthesis, integrins and cells and mechanisms specific including specific downregulation of TGFbeta signaling, major extracellular matrix (ECM) components, ECM-crosslinking, and ECM-receptors such as integrins and discoidin domain receptors, ECM-crosslinking and methods for targeted delivery of small interfering RNA, antisense oligonucleotides and small molecules to increase potency and reduce side effects. With an increased understanding of the biology of the ECM and liver fibrosis and an improved preclinical validation, the translation of these approaches to the clinic is currently ongoing. Application to patients with liver fibrosis and a personalized treatment is tightly linked to the development of noninvasive biomarkers of fibrosis, fibrogenesis and fibrolysis.
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Affiliation(s)
- Detlef Schuppan
- Institute of Translational Immunology and Research Center for Immunotherapy, University of Mainz Medical Center, Mainz, Germany; Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, USA.
| | - Muhammad Ashfaq-Khan
- Institute of Translational Immunology and Research Center for Immunotherapy, University of Mainz Medical Center, Mainz, Germany
| | - Ai Ting Yang
- Institute of Translational Immunology and Research Center for Immunotherapy, University of Mainz Medical Center, Mainz, Germany
| | - Yong Ook Kim
- Institute of Translational Immunology and Research Center for Immunotherapy, University of Mainz Medical Center, Mainz, Germany
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17
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Choi SE, Jeon N, Choi HY, Shin JI, Jeong HJ, Lim BJ. Lysyl oxidase‑like 2 is expressed in kidney tissue and is associated with the progression of tubulointerstitial fibrosis. Mol Med Rep 2017; 16:2477-2482. [PMID: 28677767 PMCID: PMC5548064 DOI: 10.3892/mmr.2017.6918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/05/2017] [Indexed: 02/02/2023] Open
Abstract
Tubulointerstitial fibrosis is a common end point of chronic kidney diseases, and preventing its progression is key to avoiding renal failure. Transforming growth factor-β (TGF-β) and associated molecules promote tubulointerstitial fibrosis; however, effective therapies targeting these molecules have yet to be developed. Lysyl oxidase-like 2 (LOXL2), which is involved in invasive growth and metastasis of malignant neoplasms, has recently been reported to serve a key role in hepatic and pulmonary fibrosis. However, little is currently known regarding LOXL2 expression in the kidney and its involvement in tubulointerstitial fibrosis. The present study evaluated LOXL2 expression in human and mouse kidney tissues, as well as in cultured renal cells. LOXL2 protein expression was detected in glomerular capillary loops and tubular epithelial cells in human and mouse kidneys. Glomerular LOXL2 was localized to the cytoplasm of podocytes, as determined by double immunofluorescence microscopy using a podocyte marker (synaptopodin). This result was supported by western blot analysis, which demonstrated that LOXL2 protein expression is present in cultured human podocytes and HK-2 human proximal tubular cells. In addition, the mRNA and protein expression levels of LOXL2 were higher in a mouse model of tubulointerstitial fibrosis compared with in control mice. In addition, immunohistochemistry results demonstrated that LOXL2 is present in the fibrous interstitium and infiltrating mononuclear cells in a mouse model of tubulointerstitial fibrosis. The present study demonstrated that LOXL2 is expressed in compartments of renal tissue, where it appears to contribute to the progression of tubulointerstitial fibrosis.
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Affiliation(s)
- Sung-Eun Choi
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Nara Jeon
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hoon Young Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jae Il Shin
- Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyeon Joo Jeong
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Beom Jin Lim
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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18
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Ke B, Zhu N, Luo F, Xu Y, Fang X. Targeted inhibition of endoplasmic reticulum stress: New hope for renal fibrosis (Review). Mol Med Rep 2017. [PMID: 28627612 PMCID: PMC5562070 DOI: 10.3892/mmr.2017.6762] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chronic kidney disease (CKD) has a very high mortality rate and remains a global health challenge. Inhibiting renal fibrosis is one of the most promising therapeutic strategies for CKD. Recent studies have indicated that endoplasmic reticulum stress (ERS) serves an active role in the development of acute and chronic kidney disease, especially with regards to renal fibrosis. In the current review, the authors summarize the latest understanding of the role of ERS during the onset of renal fibrosis. ERS promotes renal fibrosis through multiple signaling pathways, such as transforming growth factor-β, epithelial-mesenchymal transition and oxidative stress. In addition, ERS also causes podocyte damage, leading to increased proteinuria and the development of renal fibrosis in rat models. In conclusion, targeted inhibition of ERS may become a promising therapeutic strategy for renal fibrosis.
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Affiliation(s)
- Ben Ke
- Department of Nephrology, The Third Hospital of Nanchang, Nanchang, Jiangxi 330009, P.R. China
| | - Na Zhu
- Nanchang University School of Medicine, Nanchang, Jiangxi 330006, P.R. China
| | - Fuli Luo
- Department of Nephrology, Chinese Medicine Hospital in Jiangxi Province, Nanchang, Jiangxi 330006, P.R. China
| | - Yang Xu
- Department of Nephrology, Jiangxi Provincial People's Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Xiangdong Fang
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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