1
|
Hammami NEH, Mérindol N, Plourde MB, Maisonnet T, Lebel S, Berthoux L. SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55. Biochem Cell Biol 2024; 102:73-84. [PMID: 37703582 DOI: 10.1139/bcb-2023-0153] [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] [Indexed: 09/15/2023] Open
Abstract
Human muscle-specific RING fingers (MURFs) are members of the tripartite motif (TRIM) family of proteins characterized by their C-terminal subgroup one signature domain. MURFs play a role in sarcomere formation and microtubule dynamics. It was previously established that some TRIMs undergo post-translational modification by small ubiquitin-like modifier (SUMO). In this study, we explored the putative SUMOylation of MURF proteins as well as their interactions with SUMO. MURF proteins (TRIM54, TRIM55, and TRIM63) were not found to be SUMOylated. However, TRIM55 turnover by proteasomal and lysosomal degradation was higher upon overexpression of SUMO-3 but not of SUMO-1. Furthermore, it is predicted that TRIM55 contains two potential SUMO-interacting motifs (SIMs). We found that SIM1- and SIM2-mutated TRIM55 were more stable than the wild-type (WT) protein partly due to decreased degradation. Consistently, SIM-mutated TRIM55 was less polyubiquitinated than the WT protein, despite similar monoubiquitination levels. Using IF microscopy, we observed that SIM motifs influenced TRIM55 subcellular localization. In conclusion, our results suggest that SUMO-3 or SUMO-3-modified proteins modulate the localization, stability, and RING ubiquitin ligase activity of TRIM55.
Collapse
Affiliation(s)
- Nour-El-Houda Hammami
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Natacha Mérindol
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Mélodie B Plourde
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Tara Maisonnet
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Sophie Lebel
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Lionel Berthoux
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| |
Collapse
|
2
|
Zhang L, Zhou J. Zebrafish: A smart tool for heart disease research. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37824489 DOI: 10.1111/jfb.15585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
The increasing prevalence of heart disease poses a significant threat to human survival and safety. However, the current treatments available for heart disease are quite limited. Therefore, it is of great importance to utilize suitable animal models that can accurately simulate the physiological characteristics of heart disease. This would help improve our understanding of this disease and aid in the development of new treatment methods and drugs. Zebrafish hearts not only exhibit similarities to mammalian hearts, but they also share ~70% of homologous genes with humans. Utilizing zebrafish as an alternative to costly and time-consuming mammalian models offers numerous advantages. Zebrafish models can be easily established and maintained, and compound screening and genetic methods allow for the creation of various economical and easily controlled zebrafish and zebrafish embryonic heart disease models in a short period of time. Consequently, zebrafish have become a powerful tool for exploring the pathological mechanisms of heart disease and identifying new effective genes. In this review, we summarize recent studies on different zebrafish models of heart disease. We also describe the techniques and protocols used to develop zebrafish models of myocardial infarction, heart failure, and congenital heart disease, including surgical procedures, forward and reverse genetics, as well as drug and combination screening. This review aims to promote the utilization of zebrafish models in investigating diverse pathological mechanisms of heart disease, enhancing our knowledge and comprehension of heart disease, and offering novel insights and objectives for exploring the prevention and treatment of heart disease.
Collapse
Affiliation(s)
- Lantian Zhang
- Education Branch, Chongqing Publishing Group, Chongqing, China
| | - Jinrun Zhou
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, China
| |
Collapse
|
3
|
Mhatre I, Abdelhalim H, Degroat W, Ashok S, Liang BT, Ahmed Z. Functional mutation, splice, distribution, and divergence analysis of impactful genes associated with heart failure and other cardiovascular diseases. Sci Rep 2023; 13:16769. [PMID: 37798313 PMCID: PMC10556087 DOI: 10.1038/s41598-023-44127-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
Cardiovascular disease (CVD) is caused by a multitude of complex and largely heritable conditions. Identifying key genes and understanding their susceptibility to CVD in the human genome can assist in early diagnosis and personalized treatment of the relevant patients. Heart failure (HF) is among those CVD phenotypes that has a high rate of mortality. In this study, we investigated genes primarily associated with HF and other CVDs. Achieving the goals of this study, we built a cohort of thirty-five consented patients, and sequenced their serum-based samples. We have generated and processed whole genome sequence (WGS) data, and performed functional mutation, splice, variant distribution, and divergence analysis to understand the relationships between each mutation type and its impact. Our variant and prevalence analysis found FLNA, CST3, LGALS3, and HBA1 linked to many enrichment pathways. Functional mutation analysis uncovered ACE, MME, LGALS3, NR3C2, PIK3C2A, CALD1, TEK, and TRPV1 to be notable and potentially significant genes. We discovered intron, 5' Flank, 3' UTR, and 3' Flank mutations to be the most common among HF and other CVD genes. Missense mutations were less common among HF and other CVD genes but had more of a functional impact. We reported HBA1, FADD, NPPC, ADRB2, ADBR1, MYH6, and PLN to be consequential based on our divergence analysis.
Collapse
Affiliation(s)
- Ishani Mhatre
- Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ, 08901, USA
| | - Habiba Abdelhalim
- Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ, 08901, USA
| | - William Degroat
- Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ, 08901, USA
| | - Shreya Ashok
- Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ, 08901, USA
| | - Bruce T Liang
- Pat and Jim Calhoun Cardiology Center, UConn Health, 263 Farmington Ave, Farmington, CT, USA
- UConn School of Medicine, University of Connecticut, 263 Farmington Ave, Farmington, CT, USA
| | - Zeeshan Ahmed
- Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ, 08901, USA.
- Department of Genetics and Genome Sciences, UConn Health, 400 Farmington Ave, Farmington, CT, USA.
- Department of Medicine/Cardiovascular Disease and Hypertension, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, 125 Paterson St, New Brunswick, NJ, USA.
| |
Collapse
|
4
|
Jiang XY, Guan FF, Ma JX, Dong W, Qi XL, Zhang X, Chen W, Gao S, Gao X, Pan S, Wang JZ, Ma YW, Zhang LF, Lu D. Cardiac-specific Trim44 knockout in rat attenuates isoproterenol-induced cardiac remodeling via inhibition of AKT/mTOR pathway. Dis Model Mech 2023; 16:276033. [PMID: 35855640 PMCID: PMC9441189 DOI: 10.1242/dmm.049444] [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: 01/03/2022] [Accepted: 07/07/2022] [Indexed: 11/20/2022] Open
Abstract
When pathological hypertrophy progresses to heart failure (HF), the prognosis is often very poor. Therefore, it is crucial to find new and effective intervention targets. Here, myocardium-specific Trim44 knockout rats were generated using CRISPR-Cas9 technology. Cardiac phenotypic observations revealed that Trim44 knockout affected cardiac morphology at baseline. Rats with Trim44 deficiency exhibited resistance to cardiac pathological changes in response to stimulation via isoproterenol (ISO) treatment, including improvement of cardiac remodeling and dysfunction by morphological and functional observations, reduced myocardial fibrosis and reduced expression of molecular markers of cardiac stress. Furthermore, signal transduction validation associated with growth and hypertrophy development in vivo and in vitro demonstrated that Trim44 deficiency inhibited the activation of signaling pathways involved in myocardial hypertrophy, especially response to pathological stress. In conclusion, the present study indicates that Trim44 knockout attenuates ISO-induced pathological cardiac remodeling through blocking the AKT/mTOR/GSK3β/P70S6K signaling pathway. This is the first study to demonstrate the function and importance of Trim44 in the heart at baseline and under pathological stress. Trim44 could be a novel therapeutic target for prevention of cardiac hypertrophy and HF. Summary: This is the first study to demonstrate the function of Trim44 in the heart at baseline and under pathological stress. Trim44 could be a novel therapeutic target for prevention of cardiac hypertrophy.
Collapse
Affiliation(s)
- Xiao-Yu Jiang
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Fei-Fei Guan
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Jia-Xin Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Wei Dong
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Xiao-Long Qi
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Xu Zhang
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Wei Chen
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Shan Gao
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Xiang Gao
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Shuo Pan
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Ji-Zheng Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100037, China
| | - Yuan-Wu Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Lian-Feng Zhang
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| | - Dan Lu
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.,Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China.,National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing 100021, China
| |
Collapse
|
5
|
Wang G, Zou R, Liu L, Wang Z, Zou Z, Tan S, Xu W, Fan X. A circular network of purine metabolism as coregulators of dilated cardiomyopathy. J Transl Med 2022; 20:532. [PMID: 36401332 PMCID: PMC9673417 DOI: 10.1186/s12967-022-03739-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The crosstalk of purine biosynthesis and metabolism exists to balance the cell energy production, proliferation, survival and cytoplasmic environment stability, but disorganized mechanics of with respect to developing heart failure (HF) is currently unknown. METHODS We conducted a multi-omics wide analysis, including microarray-based transcriptomes, and full spectrum metabolomics with respect to chronic HF. Based on expression profiling by array, we applied a bioinformatics platform of quantifiable metabolic pathway changes based on gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), Shapley Additive Explanations (SHAP), and Xtreme Gradient Boosting (XGBoost) algorithms to comprehensively analyze the dynamic changes of metabolic pathways and circular network in the HF development. Additionally, left ventricular tissue from patients undergoing myocardial biopsy and transplantation were collected to perform the protein and full spectrum metabolic mass spectrometry. RESULTS Systematic bioinformatics analysis showed the purine metabolism reprogramming was significantly detected in dilated cardiomyopathy. In addition, this result was also demonstrated in metabolomic mass spectrometry. And the differentially expressed metabolites analysis showing the guanine, urea, and xanthine were significantly detected. Hub markers, includes IMPDH1, ENTPD2, AK7, AK2, and CANT1, also significantly identified based on XGBoost, SHAP model and PPI network. CONCLUSION The crosstalk in the reactions involved in purine metabolism may involving in DCM metabolism reprogramming, and as coregulators of development of HF, which may identify as potential therapeutic targets. And the markers of IMPDH1, ENTPD2, AK7, AK2, and CANT1, and metabolites involved in purine metabolism shown an important role.
Collapse
Affiliation(s)
- Ge Wang
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Rongjun Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Libao Liu
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Zongtao Wang
- The First Affiliated Hospital of Guangdong Pharmaceutical University, School of Clinical Medicine of Guangdong Pharmaceutical University, Guangzhou, 510008, Guangdong, China
| | - Zengxiao Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Songtao Tan
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Wenliu Xu
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Xiaoping Fan
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, Guangdong, China.
- The Second Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510405, Guangdong, China.
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
| |
Collapse
|
6
|
Abstract
Heart disease is the leading cause of death worldwide. Despite decades of research, most heart pathologies have limited treatments, and often the only curative approach is heart transplantation. Thus, there is an urgent need to develop new therapeutic approaches for treating cardiac diseases. Animal models that reproduce the human pathophysiology are essential to uncovering the biology of diseases and discovering therapies. Traditionally, mammals have been used as models of cardiac disease, but the cost of generating and maintaining new models is exorbitant, and the studies have very low throughput. In the last decade, the zebrafish has emerged as a tractable model for cardiac diseases, owing to several characteristics that made this animal popular among developmental biologists. Zebrafish fertilization and development are external; embryos can be obtained in high numbers, are cheap and easy to maintain, and can be manipulated to create new genetic models. Moreover, zebrafish exhibit an exceptional ability to regenerate their heart after injury. This review summarizes 25 years of research using the zebrafish to study the heart, from the classical forward screenings to the contemporary methods to model mutations found in patients with cardiac disease. We discuss the advantages and limitations of this model organism and introduce the experimental approaches exploited in zebrafish, including forward and reverse genetics and chemical screenings. Last, we review the models used to induce cardiac injury and essential ideas derived from studying natural regeneration. Studies using zebrafish have the potential to accelerate the discovery of new strategies to treat cardiac diseases.
Collapse
Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital Research Institute, Harvard Medical School, Charlestown, MA
| |
Collapse
|
7
|
Zheng D, Zhang Y, Xia Y, Cheng F. A Novel Gene Signature of Tripartite Motif Family for Predicting the Prognosis in Kidney Renal Clear Cell Carcinoma and Its Association With Immune Cell Infiltration. Front Oncol 2022; 12:840410. [PMID: 35371994 PMCID: PMC8968921 DOI: 10.3389/fonc.2022.840410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/22/2022] [Indexed: 12/26/2022] Open
Abstract
Given the importance of tripartite motif (TRIM) proteins in diverse cellular biological processes and that their dysregulation contributes to cancer progression, we constructed a robust TRIM family signature to stratify patients with kidney renal clear cell carcinoma (KIRC). Transcriptomic profiles and corresponding clinical information of KIRC patients were obtained from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. Prognosis-related TRIM family genes were screened and used to construct a novel TRIM family-based signature for the training cohort. The accuracy and generalizability of the prognostic signature were assessed in testing, entire, and external ICGC cohorts. We analyzed correlations among prognostic signatures, tumor immune microenvironment, and immune cell infiltration. The results of univariate Cox regression and Kaplan-Meier survival analyses revealed 27 TRIMs that were robustly associated with the prognosis of patients with KIRC. We applied Lasso regression and multivariate Cox regression analyses to develop a prognostic signature containing the TRIM1, 13, 35, 26, 55, 2, 47, and 27 genes to predict the survival of patients with KIRC. The accuracy and generalizability of this signature were confirmed in internal and external validation cohorts. We also constructed a predictive nomogram based on the signature and the clinicopathological characteristics of sex, age, and T and M status to aid clinical decision-making. We analyzed immune cell infiltration analysis and found that CD8 T cells, memory resting CD4 T cells, and M2 macrophages were the most enriched components in the KIRC tumor immune microenvironment. A higher level of immune infiltration by plasma cells, follicular helper T cells, and activated NK cells, and a lower level of immune infiltration by memory resting CD4 T cells, M1 and M2 macrophages, and resting dendritic cells were associated with higher risk scores. Overall, our eight-gene TRIM family signature has sufficient accuracy and generalizability for predicting the overall survival of patients with KIRC. Furthermore, this prognostic signature is associated with tumor immune status and distinct immune cell infiltrates in the tumor microenvironment.
Collapse
|
8
|
Narumanchi S, Wang H, Perttunen S, Tikkanen I, Lakkisto P, Paavola J. Zebrafish Heart Failure Models. Front Cell Dev Biol 2021; 9:662583. [PMID: 34095129 PMCID: PMC8173159 DOI: 10.3389/fcell.2021.662583] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
Heart failure causes significant morbidity and mortality worldwide. The understanding of heart failure pathomechanisms and options for treatment remain incomplete. Zebrafish has proven useful for modeling human heart diseases due to similarity of zebrafish and mammalian hearts, fast easily tractable development, and readily available genetic methods. Embryonic cardiac development is rapid and cardiac function is easy to observe and quantify. Reverse genetics, by using morpholinos and CRISPR-Cas9 to modulate gene function, make zebrafish a primary animal model for in vivo studies of candidate genes. Zebrafish are able to effectively regenerate their hearts following injury. However, less attention has been given to using zebrafish models to increase understanding of heart failure and cardiac remodeling, including cardiac hypertrophy and hyperplasia. Here we discuss using zebrafish to study heart failure and cardiac remodeling, and review zebrafish genetic, drug-induced and other heart failure models, discussing the advantages and weaknesses of using zebrafish to model human heart disease. Using zebrafish models will lead to insights on the pathomechanisms of heart failure, with the aim to ultimately provide novel therapies for the prevention and treatment of heart failure.
Collapse
Affiliation(s)
- Suneeta Narumanchi
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
| | - Hong Wang
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
| | - Sanni Perttunen
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
| | - Ilkka Tikkanen
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Päivi Lakkisto
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland.,Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Jere Paavola
- Unit of Cardiovascular Research, Minerva Foundation Institute for Medical Research, Biomedicum Helsinki, Helsinki, Finland
| |
Collapse
|
9
|
McCarthy MW. Harnessing the potential of CRISPR-based platforms to advance the field of hospital medicine. Expert Rev Anti Infect Ther 2020; 18:799-805. [PMID: 32366131 PMCID: PMC7212535 DOI: 10.1080/14787210.2020.1761333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Clustered regularly interspaced short palindromic repeats (CRISPR) are segments of nucleic acid that play a role in prokaryotic defense and form the basis of a genome editing technology that allows permanent alteration of genetic material. This methodology, known as CRISPR-Cas9, is poised to revolutionize molecular biology, but no literature yet exists on how these advances will affect hospitalists. AREAS COVERED These specialists in inpatient medicine care for a wide variety of hospitalized patients, including those with infectious disease, cancer, cardiovascular disease, autoimmune disease, hematologic disease, and a variety of other conditions that may soon be impacted by advances in gene-modifying technology provided by CRISPR-Cas9. A Literature search was performed using PubMed [1 December 2019-17 April 2020]. EXPERT OPINION This paper reviews the remarkable diagnostic and therapeutic potential of the CRISPR-Cas9 platform and concludes with a look at ethical issues and technical hurdles pertaining to the implementation of permanent gene modification in the practice of Hospital Medicine.
Collapse
Affiliation(s)
- Matthew W. McCarthy
- Weill Cornell Medical College, Division of General Internal Medicine, New York-Presbyterian Hospital, New York, NY, USA
| |
Collapse
|