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Öztan G, Bozbuğa N, İşsever H, Oğuz F, Canıaz İ, Yazıksız N, Ertan M, Alpagut İU. Comparative Analysis of Transcriptome Profiles in Patients with Thromboangiitis Obliterans. Genes (Basel) 2023; 15:19. [PMID: 38275601 PMCID: PMC10815726 DOI: 10.3390/genes15010019] [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: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Thromboangiitis obliterans (TAO) causes vascular insufficiency due to chronic inflammation and abrupt thrombosis of the medium and small arteries of the extremities. In our study, we aimed to determine biomarkers for the diagnosis of TAO by evaluating 15 male TAO patients with Shinoya diagnostic criteria and 5 healthy controls who did not have TAO-related symptoms in their family histories. METHODS The Clariom D Affymetrix platform was used to conduct microarray analysis on total RNA extracted from whole blood. A total of 477 genes (FC ≤ 5 or >5) common to the fifteen patient and five control samples were selected using comparative microarray analysis; among them, 79 genes were upregulated and 398 genes were downregulated. RESULTS According to FC ≤ 10 or >10, in the same TAO patient and control group, 13 genes out of 28 were upregulated, whereas 15 genes were downregulated. The 11 key genes identified according to their mean log2FC values were PLP2, RPL27A, CCL4, FMNL1, EGR1, EIF4A1, RPL9, LAMP2, RNF149, EIF4G2, and DGKZ. The genes were ranked according to their relative expression as follows: FMNL1 > RNF149 > RPL27A > EIF4G2 > EIF4A1 > LAMP2 > EGR1 > PLP2 > DGKZ > RPL9 > CCL4. Using protein-protein interaction network analysis, RPL9, RPL27A, and RPL32 were found to be closely related to EIF4G2 and EIF4A1. The Reactome pathway found pathways linked to 28 genes. These pathways included the immune system, cellular responses to stress, cytokine signaling in the immune system, and signaling by ROBO receptors. CONCLUSIONS By figuring out the protein expression levels of the genes that have been found to explain how TAO disease works at the molecular level, it will be possible to figure out how well these chosen transcripts can diagnose and predict the disease.
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Affiliation(s)
- Gözde Öztan
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey;
| | - Nilgün Bozbuğa
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - Halim İşsever
- Department of Public Health, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey;
| | - Fatma Oğuz
- Department of Medical Biology, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey;
| | - İrem Canıaz
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - Nilgün Yazıksız
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - Melike Ertan
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
| | - İbrahim Ufuk Alpagut
- Department of Cardiovascular Surgery, Istanbul Faculty of Medicine, Istanbul University, Topkapi, 34093 Istanbul, Turkey; (N.B.); (İ.C.); (N.Y.); (M.E.); (İ.U.A.)
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Zhang X, Zhao Q, Wang T, Long Q, Sun Y, Jiao L, Gullerova M. DNA damage response, a double-edged sword for vascular aging. Ageing Res Rev 2023; 92:102137. [PMID: 38007046 DOI: 10.1016/j.arr.2023.102137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/03/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Vascular aging is a major risk factor for age-related cardiovascular diseases, which have high rates of morbidity and mortality. It is characterized by changes in the blood vessels, such as macroscopically increased vascular diameter and intima-medial thickness, chronic inflammation, vascular calcification, arterial stiffening, and atherosclerosis. DNA damage and the subsequent various DNA damage response (DDR) pathways are important causative factors of vascular aging. Deficient DDR, which may result in the accumulation of unrepaired damaged DNA or mutations, can lead to vascular aging. On the other hand, over-activation of some DDR proteins, such as poly (ADP ribose) polymerase (PARP) and ataxia telangiectasia mutated (ATM), also can enhance the process of vascular aging, suggesting that DDR can have both positive and negative effects on vascular aging. Despite the evidence reviewed in this paper, the role of DDR in vascular aging and potential therapeutic targets remain poorly understood and require further investigation.
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Affiliation(s)
- Xiao Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qing Zhao
- M.D. Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Tao Wang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China
| | - Qilin Long
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Yixin Sun
- First Hospital, Peking University, Beijing, China
| | - Liqun Jiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; China International Neuroscience Institute (China-INI), Beijing 100053, China; Department of Interventional Neuroradiology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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3
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Kaarbø M, Yang M, Hov JR, Holm K, de Sousa MML, Macpherson ME, Reims HM, Kran AMB, Halvorsen B, Karlsen TH, Aukrust P, Lundin KEA, Fevang B, Bjørås M, Jørgensen SF. Duodenal inflammation in common variable immunodeficiency has altered transcriptional response to viruses. J Allergy Clin Immunol 2023; 151:767-777. [PMID: 36220400 DOI: 10.1016/j.jaci.2022.09.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND A substantial proportion of common variable immunodeficiency (CVID) patients has duodenal inflammation of largely unknown etiology. However, because of its histologic similarities with celiac disease, gluten sensitivity has been proposed as a potential mechanism. OBJECTIVE We aimed to elucidate the role of the duodenal microenvironment in the pathogenesis of duodenal inflammation in CVID by investigating the transcriptional, proteomic, and microbial signatures of duodenal biopsy samples in CVID. METHODS DNA, total RNA, and protein were isolated from snap-frozen pieces of duodenal biopsy samples from CVID (with and without duodenal inflammation), healthy controls, and patients with celiac disease (untreated). RNA sequencing, mass spectrometry-based proteomics, and 16S ribosomal DNA sequencing (bacteria) were then performed. RESULTS CVID separated from controls in regulation of transcriptional response to lipopolysaccharide and cellular immune responses. These differences were independent of mucosal inflammation. Instead, CVID patients with duodenal inflammation displayed alterations in transcription of genes involved in response to viral infections. Four proteins were differently regulated between CVID patients and healthy controls-DBNL, TRMT11, GCHFR, and IGHA2-independent of duodenal inflammation. Despite similar histology, there were major differences in CVID with duodenal inflammation and celiac disease both at the RNA and protein level. No significant difference was observed in the bacterial gut microbial signature between CVID, celiac, and healthy controls. CONCLUSION Our findings suggest the existence of altered functions of the duodenal epithelium, particularly in response to lipopolysaccharide and viruses. The latter finding was related to duodenal inflammation, suggesting that viruses, not gluten sensitivity, could be related to duodenal inflammation in CVID.
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Affiliation(s)
- Mari Kaarbø
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Mingyi Yang
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Johannes R Hov
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Kristian Holm
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway; Proteomics and Modomics Experimental Core Facility (PROMEC) at Norwegian University of Science and Technology, Trondheim, Norway
| | - Magnhild E Macpherson
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Department of Infectious Diseases, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Henrik M Reims
- Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Anne-Marte Bakken Kran
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Bente Halvorsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway; Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Pål Aukrust
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway; K. G. Jebsen Celiac Disease Research Centre, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Børre Fevang
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Silje Fjellgård Jørgensen
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
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Yu L, Zhang Y, Liu C, Wu X, Wang S, Sui W, Zhang Y, Zhang C, Zhang M. Heterogeneity of macrophages in atherosclerosis revealed by single-cell RNA sequencing. FASEB J 2023; 37:e22810. [PMID: 36786718 DOI: 10.1096/fj.202201932rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Technology at the single-cell level has advanced dramatically in characterizing molecular heterogeneity. These technologies have enabled cell subtype diversity to be seen in all tissues, including atherosclerotic plaques. Critical in atherosclerosis pathogenesis and progression are macrophages. Previous studies have only determined macrophage phenotypes within the plaque, mainly by bulk analysis. However, recent progress in single-cell technologies now enables the comprehensive mapping of macrophage subsets and phenotypes present in plaques. In this review, we have updated and discussed the definition and classification of macrophage subsets in mice and humans using single-cell RNA sequencing. We summarized the different classification methods and perspectives: traditional classification with an updated scoring system, inflammatory macrophages, foamy macrophages, and atherosclerotic-resident macrophages. In addition, some special types of macrophages were identified by specific markers, including IFN-inducible and cavity macrophages. Furthermore, we discussed macrophage subset-specific markers and their functions. In the future, these novel insights into the characteristics and phenotypes of these macrophage subsets within atherosclerotic plaques can provide additional therapeutic targets for cardiovascular diseases.
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Affiliation(s)
- Liwen Yu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yujie Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Changhao Liu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiao Wu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shasha Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenhai Sui
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Cheng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Meng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
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5
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Wen J, Ling R, Chen R, Zhang S, Dai Y, Zhang T, Guo F, Wang Q, Wang G, Jiang Y. Diversity of arterial cell and phenotypic heterogeneity induced by high-fat and high-cholesterol diet. Front Cell Dev Biol 2023; 11:971091. [PMID: 36910156 PMCID: PMC9997679 DOI: 10.3389/fcell.2023.971091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Lipid metabolism disorder is the basis of atherosclerotic lesions, in which cholesterol and low-density lipoprotein (LDL) is the main factor involved with the atherosclerotic development. A high-fat and high-cholesterol diet can lead to this disorder in the human body, thus accelerating the process of disease. The development of single-cell RNA sequencing in recent years has opened the possibility to unbiasedly map cellular heterogeneity with high throughput and high resolution; alterations mediated by a high-fat and high-cholesterol diet at the single-cell transcriptomic level can be explored with this mean afterward. We assessed the aortic arch of 16-week old Apoe-/- mice of two control groups (12 weeks of chow diet) and two HFD groups (12 weeks of high fat, high cholesterol diet) to process single-cell suspension and use single-cell RNA sequencing to anatomize the transcripts of 5,416 cells from the control group and 2,739 from the HFD group. Through unsupervised clustering, 14 cell types were divided and defined. Among these cells, the cellular heterogeneity exhibited in endothelial cells and immune cells is the most prominent. Subsequent screening delineated ten endothelial cell subsets with various function based on gene expression profiling. The distribution of endothelial cells and immune cells differs significantly between the control group versus the HFD one. The existence of pathways that inhibit atherosclerosis was found in both dysfunctional endothelial cells and foam cells. Our data provide a comprehensive transcriptional landscape of aortic arch cells and unravel the cellular heterogeneity brought by a high-fat and high-cholesterol diet. All these findings open new perspectives at the transcriptomic level to studying the pathology of atherosclerosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yizhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Di X, Xiang L, Jian Z. YAP-mediated mechanotransduction in urinary bladder remodeling: Based on RNA-seq and CUT&Tag. Front Genet 2023; 14:1106927. [PMID: 36741311 PMCID: PMC9895788 DOI: 10.3389/fgene.2023.1106927] [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: 11/24/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
Yes-associated protein (YAP) is an important transcriptional coactivator binding to transcriptional factors that engage in many downstream gene transcription. Partial bladder outlet obstruction (pBOO) causes a massive burden to patients and finally leads to bladder fibrosis. Several cell types engage in the pBOO pathological process, including urothelial cells, smooth muscle cells, and fibroblasts. To clarify the function of YAP in bladder fibrosis, we performed the RNA-seq and CUT&Tag of the bladder smooth muscle cell to analyze the YAP ablation of human bladder smooth muscle cells (hBdSMCs) and immunoprecipitation of YAP. 141 differentially expressed genes (DEGs) were identified through RNA-seq between YAP-knockdown and nature control. After matching with the results of CUT&Tag, 36 genes were regulated directly by YAP. Then we identified the hub genes in the DEGs, including CDCA5, CENPA, DTL, NCAPH, and NEIL3, that contribute to cell proliferation. Thus, our study provides a regulatory network of YAP in smooth muscle proliferation. The possible effects of YAP on hBdSMC might be a vital target for pBOO-associated bladder fibrosis.
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Affiliation(s)
- Xingpeng Di
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyuan Xiang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, China,Department of Clinical Research Management, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhongyu Jian
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, China,*Correspondence: Zhongyu Jian,
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7
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Biological Functions of the DNA Glycosylase NEIL3 and Its Role in Disease Progression Including Cancer. Cancers (Basel) 2022; 14:cancers14235722. [PMID: 36497204 PMCID: PMC9737245 DOI: 10.3390/cancers14235722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
The accumulation of oxidative DNA base damage can severely disrupt the integrity of the genome and is strongly associated with the development of cancer. DNA glycosylase is the critical enzyme that initiates the base excision repair (BER) pathway, recognizing and excising damaged bases. The Nei endonuclease VIII-like 3 (NEIL3) is an emerging DNA glycosylase essential in maintaining genome stability. With an in-depth study of the structure and function of NEIL3, we found that it has properties related to the process of base damage repair. For example, it not only prefers the base damage of single-stranded DNA (ssDNA), G-quadruplex and DNA interstrand crosslinks (ICLs), but also participates in the maintenance of replication fork stability and telomere integrity. In addition, NEIL3 is strongly associated with the progression of cancers and cardiovascular and neurological diseases, is incredibly significantly overexpressed in cancers, and may become an independent prognostic marker for cancer patients. Interestingly, circNEIL3, a circular RNA of exon-encoded origin by NEIL3, also promotes the development of multiple cancers. In this review, we have summarized the structure and the characteristics of NEIL3 to repair base damage. We have focused on NEIL3 and circNEIL3 in cancer development, progression and prognosis.
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8
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Karlsen TR, Olsen MB, Kong XY, Yang K, Quiles-Jiménez A, Kroustallaki P, Holm S, Lines GT, Aukrust P, Skarpengland T, Bjørås M, Dahl TB, Nilsen H, Gregersen I, Halvorsen B. NEIL3-deficient bone marrow displays decreased hematopoietic capacity and reduced telomere length. Biochem Biophys Rep 2022; 29:101211. [PMID: 35079641 PMCID: PMC8777121 DOI: 10.1016/j.bbrep.2022.101211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/24/2022] Open
Abstract
Deficiency of NEIL3, a DNA repair enzyme, has significant impact on mouse physiology, including vascular biology and gut health, processes related to aging. Leukocyte telomere length (LTL) is suggested as a marker of biological aging, and shortened LTL is associated with increased risk of cardiovascular disease. NEIL3 has been shown to repair DNA damage in telomere regions in vitro. Herein, we explored the role of NEIL3 in telomere maintenance in vivo by studying bone marrow cells from atherosclerosis-prone NEIL3-deficient mice. We found shortened telomeres and decreased activity of the telomerase enzyme in bone marrow cells derived from Apoe -/- Neil3 -/- as compared to Apoe -/- mice. Furthermore, Apoe -/- Neil3 -/- mice had decreased leukocyte levels as compared to Apoe -/- mice, both in bone marrow and in peripheral blood. Finally, RNA sequencing of bone marrow cells from Apoe -/- Neil3 -/- and Apoe -/- mice revealed different expression levels of genes involved in cell cycle regulation, cellular senescence and telomere protection. This study points to NEIL3 as a telomere-protecting protein in murine bone marrow in vivo.
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Affiliation(s)
- Tom Rune Karlsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maria B. Olsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Xiang Y. Kong
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Kuan Yang
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Penelope Kroustallaki
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | | | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tonje Skarpengland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tuva B. Dahl
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Department of Research and Development, Division of Emergencies and Critical Care, Oslo University Hospital HF, Rikshospitalet, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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9
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McQueen LW, Ladak SS, Abbasciano R, George SJ, Suleiman MS, Angelini GD, Murphy GJ, Zakkar M. Next-Generation and Single-Cell Sequencing Approaches to Study Atherosclerosis and Vascular Inflammation Pathophysiology: A Systematic Review. Front Cardiovasc Med 2022; 9:849675. [PMID: 35419441 PMCID: PMC8996078 DOI: 10.3389/fcvm.2022.849675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022] Open
Abstract
Background and Aims Atherosclerosis is a chronic inflammatory disease that remains the leading cause of morbidity and mortality worldwide. Despite decades of research into the development and progression of this disease, current management and treatment approaches remain unsatisfactory and further studies are required to understand the exact pathophysiology. This review aims to provide a comprehensive assessment of currently published data utilizing single-cell and next-generation sequencing techniques to identify key cellular and molecular contributions to atherosclerosis and vascular inflammation. Methods Electronic searches of Cochrane Central Register of Controlled Trials, MEDLINE, and EMBASE databases were undertaken from inception until February 2022. A narrative synthesis of all included studies was performed for all included studies. Quality assessment and risk of bias analysis was evaluated using the ARRIVE and SYRCLE checklist tools. Results Thirty-four studies were eligible for narrative synthesis, with 16 articles utilizing single-cell exclusively, 10 utilizing next-generation sequencing and 8 using a combination of these approaches. Studies investigated numerous targets, ranging from exploratory tissue and plaque analysis, cell phenotype investigation and physiological/hemodynamic contributions to disease progression at both the single-cell and whole genome level. A significant area of focus was placed on smooth muscle cell, macrophage, and stem/progenitor contributions to disease, with little focus placed on contributions of other cell types including lymphocytes and endothelial cells. A significant level of heterogeneity exists in the outcomes from single-cell sequencing of similar samples, leading to inter-sample and inter-study variation. Conclusions Single-cell and next-generation sequencing methodologies offer novel means of elucidating atherosclerosis with significantly higher resolution than previous methodologies. These approaches also show significant potential for translatability into other vascular disease states, by facilitating cell-specific gene expression profiles between disease states. Implementation of these technologies may offer novel approaches to understanding the disease pathophysiology and improving disease prevention, management, and treatment.Systematic Review Registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021229960, identifier: CRD42021229960.
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Affiliation(s)
- Liam W McQueen
- Department of Cardiovascular Sciences, Clinical Science Wing, Glenfield Hospital, University of Leicester, Leicester, United Kingdom
| | - Shameem S Ladak
- Department of Cardiovascular Sciences, Clinical Science Wing, Glenfield Hospital, University of Leicester, Leicester, United Kingdom
| | - Riccardo Abbasciano
- Department of Cardiovascular Sciences, Clinical Science Wing, Glenfield Hospital, University of Leicester, Leicester, United Kingdom
| | - Sarah J George
- Bristol Heart Institute and Translational Biomedical Research Centre, Bristol Medical School, Bristol Royal Infirmary, University of Bristol, Bristol, United Kingdom
| | - M-Saadeh Suleiman
- Bristol Heart Institute and Translational Biomedical Research Centre, Bristol Medical School, Bristol Royal Infirmary, University of Bristol, Bristol, United Kingdom
| | - Gianni D Angelini
- Bristol Heart Institute and Translational Biomedical Research Centre, Bristol Medical School, Bristol Royal Infirmary, University of Bristol, Bristol, United Kingdom
| | - Gavin J Murphy
- Department of Cardiovascular Sciences, Clinical Science Wing, Glenfield Hospital, University of Leicester, Leicester, United Kingdom
| | - Mustafa Zakkar
- Department of Cardiovascular Sciences, Clinical Science Wing, Glenfield Hospital, University of Leicester, Leicester, United Kingdom
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10
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Karlsen TR, Kong XY, Holm S, Quiles-Jiménez A, Dahl TB, Yang K, Sagen EL, Skarpengland T, S Øgaard JD, Holm K, Vestad B, Olsen MB, Aukrust P, Bjørås M, Hov JR, Halvorsen B, Gregersen I. NEIL3-deficiency increases gut permeability and contributes to a pro-atherogenic metabolic phenotype. Sci Rep 2021; 11:19749. [PMID: 34611194 PMCID: PMC8492623 DOI: 10.1038/s41598-021-98820-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
Atherosclerosis and its consequences cause considerable morbidity and mortality world-wide. We have previously shown that expression of the DNA glycosylase NEIL3 is regulated in human atherosclerotic plaques, and that NEIL3-deficiency enhances atherogenesis in Apoe-/- mice. Herein, we identified a time point prior to quantifiable differences in atherosclerosis between Apoe-/-Neil3-/- mice and Apoe-/- mice. Mice at this age were selected to explore the metabolic and pathophysiological processes preceding extensive atherogenesis in NEIL3-deficient mice. Untargeted metabolomic analysis of young Apoe-/-Neil3-/- mice revealed significant metabolic disturbances as compared to mice expressing NEIL3, particularly in metabolites dependent on the gut microbiota. 16S rRNA gene sequencing of fecal bacterial DNA indeed confirmed that the NEIL3-deficient mice had altered gut microbiota, as well as increased circulating levels of the bacterially derived molecule LPS. The mice were challenged with a FITC-conjugated dextran to explore gut permeability, which was significantly increased in the NEIL3-deficient mice. Further, immunohistochemistry showed increased levels of the proliferation marker Ki67 in the colonic epithelium of NEIL3-deficient mice, suggesting increased proliferation of intestinal cells and gut leakage. We suggest that these metabolic alterations serve as drivers of atherosclerosis in NEIL3-deficient mice.
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Affiliation(s)
- Tom Rune Karlsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tuva B Dahl
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Research and Development, Division of Emergencies and Critical Care, Oslo University Hospital HF, Rikshospitalet, Oslo, Norway
| | - Kuan Yang
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ellen L Sagen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tonje Skarpengland
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jonas D S Øgaard
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Kristian Holm
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Maria B Olsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
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11
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Kansakar U, Jankauskas SS, Gambardella J, Santulli G. Targeting the phenotypic switch of vascular smooth muscle cells to tackle atherosclerosis. Atherosclerosis 2021; 324:117-120. [PMID: 33832772 PMCID: PMC8195811 DOI: 10.1016/j.atherosclerosis.2021.03.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 02/08/2023]
Affiliation(s)
- Urna Kansakar
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York City, 10461, NY, United States
| | - Stanislovas S Jankauskas
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York City, 10461, NY, United States; Department of Medicine (Division of Cardiology), Albert Einstein College of Medicine - Montefiore University Hospital, New York City, 10461, NY, United States
| | - Jessica Gambardella
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York City, 10461, NY, United States; Department of Medicine (Division of Cardiology), Albert Einstein College of Medicine - Montefiore University Hospital, New York City, 10461, NY, United States; Department of Advanced Biomedical Sciences, "Federico II" University, Naples, 80131, Italy
| | - Gaetano Santulli
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York City, 10461, NY, United States; Department of Medicine (Division of Cardiology), Albert Einstein College of Medicine - Montefiore University Hospital, New York City, 10461, NY, United States; Department of Advanced Biomedical Sciences, "Federico II" University, Naples, 80131, Italy; International Translational Research and Medical Education (ITME), Naples, 80100, Italy.
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