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Peng Y, Zhu M, Gong Y, Wang C. Identification and functional prediction of lncRNAs associated with intramuscular lipid deposition in Guangling donkeys. Front Vet Sci 2024; 11:1410109. [PMID: 39036793 PMCID: PMC11258529 DOI: 10.3389/fvets.2024.1410109] [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: 03/31/2024] [Accepted: 05/30/2024] [Indexed: 07/23/2024] Open
Abstract
Many studies have shown that long non-coding RNAs (lncRNAs) play key regulatory roles in various biological processes. However, the importance and molecular regulatory mechanisms of lncRNAs in donkey intramuscular fat deposition remain to be further investigated. In this study, we used published transcriptomic data from the longissimus dorsi muscle of Guangling donkeys to identify lncRNAs and obtained 196 novel lncRNAs. Compared with the coding genes, the novel lncRNAs and the known lncRNAs exhibited some typical features, such as shorter transcript length and smaller exons. A total of 272 coding genes and 52 lncRNAs were differentially expressed between the longissimus dorsi muscles of the low-fat and high-fat groups. The differentially expressed genes were found to be involved in various biological processes related to lipid metabolism. The potential target genes of differentially expressed lncRNAs were predicted by cis and trans. Functional analysis of lncRNA targets showed that some lncRNAs may act on potential target genes involved in lipid metabolism processes and regulate lipid deposition in the longissimus dorsi muscle. This study provides valuable information for further investigation of the molecular mechanisms of lipid deposition traits in donkeys, which may improve meat traits and facilitate the selection process of donkeys in future breeding.
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Affiliation(s)
- Yongdong Peng
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | | | | | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
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Zhang J, Lv W, Liu X, Sun Z, Zeng M, Kang J, Zhang Q, Liu F, Ma S, Su J, Cao K, Liu J. Ginsenoside Rh4 prevents endothelial dysfunction as a novel AMPK activator. Br J Pharmacol 2024. [PMID: 38757416 DOI: 10.1111/bph.16403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND AND PURPOSE The AMP-activated protein kinase (AMPK) signalling pathway is a desirable target for various cardiovascular diseases (CVD), while the involvement of AMPK-mediated specific downstream pathways and effective interventions in hyperlipidaemia-induced endothelial dysfunction remain largely unknown. Herein, we aim to identify an effective AMPK activator and to explore its efficacy and mechanism against endothelial dysfunction. EXPERIMENTAL APPROACH Molecular docking technique was adopted to screen for the potent AMPK activator among 11 most common rare ginsenosides. In vivo, poloxamer 407 (P407) was used to induce acute hyperlipidaemia in C57BL/6J mice. In vitro, palmitic acid (PA) was used to induce lipid toxicity in HAEC cells. KEY RESULTS We discovered the strongest binding of ginsenoside Rh4 to AMPKα1 and confirmed the action of Rh4 on AMPK activation. Rh4 effectively attenuated hyperlipidaemia-related endothelial injury and oxidative stress both in vivo and in vitro and restored cell viability, mitochondrial membrane potential and mitochondrial oxygen consumption rate in HAEC cells. Mechanistically, Rh4 bound to AMPKα1 and simultaneously up-regulated AKT/eNOS-mediated NO release, promoted PGC-1α-mediated mitochondrial biogenesis and inhibited P38 MAPK/NFκB-mediated inflammatory responses in both P407-treated mice and PA-treated HAEC cells. The AMPK inhibitor Compound C treatment completely abrogated the regulation of Rh4 on the above pathways and weakened the lowering effect of Rh4 on endothelial impairment markers, suggesting that the beneficial effects of Rh4 are AMPK dependent. CONCLUSION AND IMPLICATIONS Rh4 may serve as a novel AMPK activator to protect against hyperlipidaemia-induced endothelial dysfunction, providing new insights into the prevention and treatment of endothelial injury-associated CVD.
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Affiliation(s)
- Jiawei Zhang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Weiqiang Lv
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xuyun Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhenyu Sun
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Mengqi Zeng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, China
| | - Jiahao Kang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qi Zhang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Fuying Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shaozhou Ma
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jiacan Su
- Department of Orthopaedics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ke Cao
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, China
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Zhao J, Xu L, Wei K, Jiang P, Chang C, Xu L, Shi Y, Zheng Y, Shan Y, Zheng Y, Shen Y, Liu J, Guo S, Wang R, He D. Identification of clinical characteristics biomarkers for rheumatoid arthritis through targeted DNA methylation sequencing. Int Immunopharmacol 2024; 131:111860. [PMID: 38508093 DOI: 10.1016/j.intimp.2024.111860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/24/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
OBJECTIVES Rheumatoid arthritis (RA) is a complex disease with a challenging diagnosis, especially in seronegative patients. The aim of this study is to investigate whether the methylation sites associated with the overall immune response in RA can assist in clinical diagnosis, using targeted methylation sequencing technology on peripheral venous blood samples. METHODS The study enrolled 241 RA patients, 30 osteoarthritis patients (OA), and 30 healthy volunteers control (HC). Fifty significant cytosine guanine (CG) sites between undifferentiated arthritis and RA were selected and analyzed using targeted DNA methylation sequencing. Logistic regression models were used to establish diagnostic models for different clinical features of RA, and six machine learning methods (logit model, random forest, support vector machine, adaboost, naive bayes, and learning vector quantization) were used to construct clinical diagnostic models for different subtypes of RA. Least absolute shrinkage and selection operator regression and detrended correspondence analysis were utilized to screen for important CGs. Spearman correlation was used to calculate the correlation coefficient. RESULTS The study identified 16 important CG sites, including tumor necrosis factort receptor associated factor 5 (TRAF5) (chr1:211500151), mothers against decapentaplegic homolog 3 (SMAD3) (chr15:67357339), tumor endothelial marker 1 (CD248) (chr11:66083766), lysosomal trafficking regulator (LYST) (chr1:235998714), PR domain zinc finger protein 16 (PRDM16) (chr1:3307069), A-kinase anchoring protein 10 (AKAP10) (chr17:19850460), G protein subunit gamma 7 (GNG7) (chr19:2546620), yes1 associated transcriptional regulator (YAP1) (chr11:101980632), PRDM16 (chr1:3163969), histone deacetylase complex subunit sin3a (SIN3A) (chr15:75747445), prenylated rab acceptor protein 2 (ARL6IP5) (chr3:69134502), mitogen-activated protein kinase kinase kinase 4 (MAP3K4) (chr6:161412392), wnt family member 7A (WNT7A) (chr3:13895991), inhibin subunit beta B (INHBB) (chr2:121107018), deoxyribonucleic acid replication helicase/nuclease 2 (DNA2) (chr10:70231628) and chromosome 14 open reading frame 180 (C14orf180) (chr14:105055171). Seven CG sites showed abnormal changes between the three groups (P < 0.05), and 16 CG sites were significantly correlated with common clinical indicators (P < 0.05). Diagnostic models constructed using different CG sites had an area under the receiver operating characteristic curve (AUC) range of 0.64-0.78 for high-level clinical indicators of high clinical value, with specificity ranging from 0.42 to 0.77 and sensitivity ranging from 0.57 to 0.88. The AUC range for low-level clinical indicators of high clinical value was 0.63-0.72, with specificity ranging from 0.48 to 0.74 and sensitivity ranging from 0.72 to 0.88. Diagnostic models constructed using different CG sites showed good overall diagnostic accuracy for the four subtypes of RA, with an accuracy range of 0.61-0.96, a balanced accuracy range of 0.46-0.94, and an AUC range of 0.46-0.94. CONCLUSIONS This study identified potential clinical diagnostic biomarkers for RA and provided novel insights into the diagnosis and subtyping of RA. The use of targeted deoxyribonucleic acid (DNA) methylation sequencing and machine learning methods for establishing diagnostic models for different clinical features and subtypes of RA is innovative and can improve the accuracy and efficiency of RA diagnosis.
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Affiliation(s)
- Jianan Zhao
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Lingxia Xu
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Kai Wei
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ping Jiang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Linshuai Xu
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yiming Shi
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yixin Zheng
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yu Shan
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yuejuan Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Shen
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Jia Liu
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rongsheng Wang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China.
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Tang X, Guo J, Qi F, Rezaei MJ. Role of non-coding RNAs and exosomal non-coding RNAs in vasculitis: A narrative review. Int J Biol Macromol 2024; 261:129658. [PMID: 38266857 DOI: 10.1016/j.ijbiomac.2024.129658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
A category of very uncommon systemic inflammatory blood vessel illnesses known as vasculitides. The pathogenesis and etiology of vasculitis are still poorly known. Despite all of the progress made in understanding the genetics and causes behind vasculitis, there is still more to learn. Epigenetic dysregulation is a significant contributor to immune-mediated illnesses, and epigenetic aberrancies in vasculitis are becoming more widely acknowledged. Less than 2 % of the genome contains protein-encoding DNA. Studies have shown that a variety of RNAs originating from the non-coding genome exist. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) have attracted the most attention in recent years as they are becoming more and more important regulators of different biological processes, such as diseases of the veins. Extracellular vehicles (EVs) such as exosomes, are membrane-bound vesicular structures that break free either during programmed cell death, such as apoptosis, pyroptosis, and necroptosis or during cell activation. Exosomes may be involved in harmful ways in inflammation, procoagulation, autoimmune reactions, endothelial dysfunction/damage, intimal hyperplasia and angiogenesis, all of which may be significant in vasculitis. Herein, we summarized various non-coding RNAs that are involved in vasculitides pathogenesis. Moreover, we highlighted the role of exosomes in vasculitides.
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Affiliation(s)
- Xiuming Tang
- Department of Cardiology, The affiliated hospital to Changchun University of Chinise Medicine, Changchun, Jilin 130021, China.
| | - Jiajuan Guo
- Department of Cardiology, The affiliated hospital to Changchun University of Chinise Medicine, Changchun, Jilin 130021, China
| | - Feng Qi
- Department of Cardiology, The affiliated hospital to Changchun University of Chinise Medicine, Changchun, Jilin 130021, China
| | - Mohammad J Rezaei
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.
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Ouyang S, Zhou ZX, Liu HT, Ren Z, Liu H, Deng NH, Tian KJ, Zhou K, Xie HL, Jiang ZS. LncRNA-mediated Modulation of Endothelial Cells: Novel Progress in the Pathogenesis of Coronary Atherosclerotic Disease. Curr Med Chem 2024; 31:1251-1264. [PMID: 36788688 DOI: 10.2174/0929867330666230213100732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/06/2022] [Accepted: 11/17/2022] [Indexed: 02/16/2023]
Abstract
Coronary atherosclerotic disease (CAD) is a common cardiovascular disease and an important cause of death. Moreover, endothelial cells (ECs) injury is an early pathophysiological feature of CAD, and long noncoding RNAs (lncRNAs) can modulate gene expression. Recent studies have shown that lncRNAs are involved in the pathogenesis of CAD, especially by regulating ECs. In this review, we summarize the novel progress of lncRNA-modulated ECs in the pathogenesis of CAD, including ECs proliferation, migration, adhesion, angiogenesis, inflammation, apoptosis, autophagy, and pyroptosis. Thus, as lncRNAs regulate ECs in CAD, lncRNAs will provide ideal and novel targets for the diagnosis and drug therapy of CAD.
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Affiliation(s)
- Shao Ouyang
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
- Key Laboratory of Heart Failure Prevention & Treatment of Hengyang, Department of Cardiovascular Medicine, Hengyang Medical School, The Second Affiliated Hospital, Clinical Medicine Research Center of Arteriosclerotic Disease of Hunan Province, University of South China, Hunan 421001, China
| | - Zhi-Xiang Zhou
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Hui-Ting Liu
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Zhong Ren
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Huan Liu
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Nian-Hua Deng
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Kai-Jiang Tian
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Kun Zhou
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Hai-Lin Xie
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Zhi-Sheng Jiang
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
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Wu Z, Yin H, Guo Y, Yin H, Li Y. Detection of cell-type-enriched long noncoding RNAs in atherosclerosis using single-cell techniques: A brief review. Life Sci 2023; 333:122138. [PMID: 37805167 DOI: 10.1016/j.lfs.2023.122138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/20/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023]
Abstract
Cardiovascular diseases are the leading causes of mortality and morbidity worldwide. Atherosclerotic plaque underlies the predominant factors and is composed of various cell types, including structure cells, such as endothelial and smooth muscle cells, and immune cells, such as macrophages and T cells. Single-cell RNA sequencing (scRNA-seq) has been extensively applied to decipher these cellular heterogeneities to expand our understanding on the mechanisms of atherosclerosis (AS) and to facilitate identifying cell-type-specific long noncoding RNAs (LncRNAs). LncRNAs have been demonstrated to deeply regulate biological activities at the transcriptional and post-transcriptional levels. A group of well-documented functional lncRNAs in AS have been studied. In our review, we selectively described several lncRNAs involved in the critical process of AS. We highlighted four novel lncRNAs (lncRNA CARMN, LINC00607, PCAT19, LINC01235) detected in scRNA-seq datasets and their functions in AS. We also reviewed open web source and bioinformatic tools, as well as the latest methods to perform an in-depth study of lncRNAs. It is fundamental to annotate functional lncRNAs in the various biological activities of AS, as lncRNAs may represent promising targets in the future for treatment and diagnosis in clinical practice.
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Affiliation(s)
- Zhiyuan Wu
- Department of Vascular Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, PR China
| | - Huarun Yin
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100730 Beijing, PR China
| | - Yongsheng Guo
- Peking University Health Science Center, 100191 Beijing, PR China
| | - Hongchao Yin
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, 100730 Beijing, PR China
| | - Yongjun Li
- Department of Vascular Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730 Beijing, PR China; Peking University Health Science Center, 100191 Beijing, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 100730 Beijing, PR China
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Yang K, Tang J, Li H, Zhang H, Ding J, Li Z, Luo J. LncRNAs in Kawasaki disease and Henoch-Schönlein purpura: mechanisms and clinical applications. Mol Cell Biochem 2023:10.1007/s11010-023-04832-x. [PMID: 37639198 DOI: 10.1007/s11010-023-04832-x] [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: 05/16/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023]
Abstract
Kawasaki disease (KD) and Henoch-Schönlein purpura (HSP) are the two most predominant types of childhood vasculitis. In childhood vasculitis, factors such as lack of sensitive diagnostic indicators and adverse effects of drug therapy may cause multiorgan system involvement and complications and even death. Many studies suggest that long noncoding RNAs (lncRNAs) are involved in the mechanism of vasculitis development in children and can be used to diagnose or predict prognosis by lncRNAs. In existing drug therapies, lncRNAs are also involved in drug-mediated treatment mechanisms and are expected to improve drug toxicity. The aim of this review is to summarize the link between lncRNAs and the pathogenesis of KD and HSP. In addition, we review the potential applications of lncRNAs in multiple dimensions, such as diagnosis, treatment, and prognosis prediction. This review highlights that targeting lncRNAs may be a novel therapeutic strategy to improve and treat KD and HSP.
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Affiliation(s)
- Kangping Yang
- Department of Pediatrics, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Jiayao Tang
- School of Pharmacy, Nanchang University, Nanchang, China
| | - Haoying Li
- Queen Mary School of Nanchang University, Nanchang, China
| | - Hejin Zhang
- The Second Clinical Medical College of Nanchang University, Nanchang, China
| | - Jiatong Ding
- The Second Clinical Medical College of Nanchang University, Nanchang, China
| | - Zelin Li
- The First Clinical Medical College of Nanchang University, Nanchang, China
| | - Jinghua Luo
- Department of Pediatrics, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
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González‐López P, Álvarez‐Villarreal M, Ruiz‐Simón R, López‐Pastor AR, de Ceniga MV, Esparza L, Martín‐Ventura JL, Escribano Ó, Gómez‐Hernández A. Role of miR-15a-5p and miR-199a-3p in the inflammatory pathway regulated by NF-κB in experimental and human atherosclerosis. Clin Transl Med 2023; 13:e1363. [PMID: 37605307 PMCID: PMC10442475 DOI: 10.1002/ctm2.1363] [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: 03/07/2023] [Revised: 07/26/2023] [Accepted: 08/05/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Cardiovascular diseases (CVDs) prevalence has significantly increased in the last decade and atherosclerosis development is the main trigger. MicroRNAs (miRNAs) are non-coding RNAs that negatively regulate gene expression of their target and their levels are frequently altered in CVDs. METHODS By RT-qPCR, we analysed miR-9-5p, miR-15a-5p, miR-16-5p and miR-199a-3p levels in aorta from apolipoprotein knockout (ApoE-/- ) mice, an experimental model of hyperlipidemia-induced atherosclerosis, and in human aortic and carotid atherosclerotic samples. By in silico studies, Western blot analysis and immunofluorescence studies, we detected the targets of the altered miRNAs. RESULTS Our results show that miR-15a-5p and miR-199a-3p are significantly decreased in carotid and aortic samples from patients and mice with atherosclerosis. In addition, we found an increased expression in targets of both miRNAs that participate in the inflammatory pathway of nuclear factor kappa B (NF-κB), such as IKKα, IKKβ and p65. In human vein endothelial cells (HUVECs) and vascular smooth muscle cells (VSMCs), the overexpression of miR-15a-5p or miR-199a-3p decreased IKKα, IKKβ and p65 protein levels as well as NF-κB activation. On the other hand, miR-15a-5p and miR-199a-3p overexpression reduced ox-LDL uptake and the inflammation regulated by NF-κB in VSMCs. Moreover, although miR-15a-5p and miR-199a-3p were significantly increased in exosomes from patients with advanced carotid atherosclerosis, only in the ROC analyses for miR-15a-5p, the area under the curve was 0.8951 with a p value of .0028. CONCLUSIONS Our results suggest that the decrease of miR-199a-3p and miR-15a-5p in vascular samples from human and experimental atherosclerosis could be involved in the NF-κB activation pathway, as well as in ox-LDL uptake by VSMCs, contributing to inflammation and progression atherosclerosis. Finally, miR-15a-5p could be used as a novel diagnostic biomarker for advanced atherosclerosis.
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Affiliation(s)
- Paula González‐López
- Hepatic and Vascular Diseases Laboratory. Biochemistry and Molecular Biology Department, School of PharmacyComplutense University of MadridMadridSpain
| | - Marta Álvarez‐Villarreal
- Hepatic and Vascular Diseases Laboratory. Biochemistry and Molecular Biology Department, School of PharmacyComplutense University of MadridMadridSpain
| | - Rubén Ruiz‐Simón
- Hepatic and Vascular Diseases Laboratory. Biochemistry and Molecular Biology Department, School of PharmacyComplutense University of MadridMadridSpain
| | - Andrea R. López‐Pastor
- Hepatic and Vascular Diseases Laboratory. Biochemistry and Molecular Biology Department, School of PharmacyComplutense University of MadridMadridSpain
| | - Melina Vega de Ceniga
- Department of Angiology and Vascular SurgeryHospital of Galdakao‐UsansoloGaldakaoBizkaiaSpain
- Biocruces Bizkaia Health Research InstituteBarakaldoBizkaiaSpain
| | - Leticia Esparza
- Department of Angiology and Vascular SurgeryHospital of Galdakao‐UsansoloGaldakaoBizkaiaSpain
- Biocruces Bizkaia Health Research InstituteBarakaldoBizkaiaSpain
| | | | - Óscar Escribano
- Hepatic and Vascular Diseases Laboratory. Biochemistry and Molecular Biology Department, School of PharmacyComplutense University of MadridMadridSpain
| | - Almudena Gómez‐Hernández
- Hepatic and Vascular Diseases Laboratory. Biochemistry and Molecular Biology Department, School of PharmacyComplutense University of MadridMadridSpain
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Cheng W, Wang X, Wu Y, Li W, Fu C, Zou L, Zhang J. Huanglian-Houpo extract attenuates DSS-induced UC mice by protecting intestinal mucosal barrier and regulating macrophage polarization. JOURNAL OF ETHNOPHARMACOLOGY 2023; 307:116181. [PMID: 36738944 DOI: 10.1016/j.jep.2023.116181] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Huanglian-Houpo Decoction (HLHP), a classical prescription, has been used to treat gastrointestinal diseases for hundreds of years in TCM. However, the effective constituents and underlying mechanisms of HLHP in the treatment of ulcerative colitis (UC) have not been fully investigated. AIM OF THE STUDY This study aimed to reveal the potential anti-UC mechanisms of 50% ethanol extraction of HL and HP (EHLHP), combining transcriptomes and network pharmacology, as well as the animal experiment verification. METHODS Primarily, we identified the chemical composition of EHLHP via UPLC-QE-MS analysis. A visualization network with components-targets-pathways on UC treatment were constructed using network pharmacology. And then, the transcriptomics sequencing method was applied to screen out the differentially expressed genes (DEGs) of EHLHP in the treatment of UC. The key targets and pathways of EHLHP were selected by the combination of the network pharmacology and transcriptomics results. Ultimately, the potential mechanisms of EHLHP on DSS-induced UC mice were verified. RESULTS A total of 34 components of EHLHP were identified by UPLC-QE-MS analysis. Combined with the analysis of network pharmacology and transcriptomics, there were 262 DEGs between the normal group and the model group, and 151 DEGs between the model group and the EHLHP group. At the same time, there are 79 interaction paths, such as PI3K-Akt signaling pathway, MAPK signaling pathway, etc. These results indicated that the anti-UC mechanisms would be involved in calcium signaling pathway, inflammatory signaling pathway (JAK-STAT, TNF-α, cGMP-PKG) and immune regulation (IL-17, B cell receptor). After 160 mg/kg and 320 mg/kg EHLHP were given to DSS induced UC mice, these typical symptoms could be significantly alleviated, such as the decrease of DAI value and inflammation level. The IHC staining results of ZO-1, Occludin and Claudin-1 suggested that the intestinal barrier of UC mice was enhanced by EHLHP. The expression of macrophages and immune cells in F4/80+, CD11c+, Gr-1+, NK1.1+ by FCM determination indicated that EHLHP could suppress UC by immunosuppression and macrophage polarization M1 to M2. CONCLUSION The potential mechanisms of HLHP extract on DSS-induced UC mice were revealed, by the prediction of integrated analysis of transcriptomes and network pharmacology, and subsequently animal test verification. It would provide a viable strategy to elucidate the mechanisms of TCM classical formula.
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Affiliation(s)
- Weijian Cheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xiao Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yihan Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Li
- School of Preclinical Medicine, Chengdu University, Chengdu, 610106, China
| | - Chaomei Fu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Liang Zou
- School of Food and Biological Engineering Preclinical Medicine, Chengdu University, Chengdu, 610106, China.
| | - Jinming Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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10
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Tao H, Mo Y, Liu W, Wang H. A review on gout: Looking back and looking ahead. Int Immunopharmacol 2023; 117:109977. [PMID: 37012869 DOI: 10.1016/j.intimp.2023.109977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/11/2023] [Accepted: 02/28/2023] [Indexed: 03/17/2023]
Abstract
Gout is a metabolic disease caused by the deposition of monosodium urate (MSU) crystals inside joints, which leads to inflammation and tissue damage. Increased concentration of serum urate is an essential step in the development of gout. Serum urate is regulated by urate transporters in the kidney and intestine, especially GLUT9 (SLC2A9), URAT1 (SLC22A12) and ABCG. Activation of NLRP3 inflammasome bodies and subsequent release of IL-1β by monosodium urate crystals induce the crescendo of acute gouty arthritis, while neutrophil extracellular traps (NETs) are considered to drive the self-resolving of gout within a few days. If untreated, acute gout may eventually develop into chronic tophaceous gout characterized by tophi, chronic gouty synovitis, and structural joint damage, leading the crushing burden of treatment. Although the research on the pathological mechanism of gout has been gradually deepened in recent years, many clinical manifestations of gout are still unable to be fully elucidated. Here, we reviewed the molecular pathological mechanism behind various clinical manifestations of gout, with a view to making contributions to further understanding and treatment.
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11
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Zhou X, Tang Y, Cao T, Ning L, Li Y, Xie X, Hu Y, He B, Peng B, Liu S. Treponema pallidum lipoprotein Tp0768 promotes the migration and adhesion of THP-1 cells to vascular endothelial cells through stress of the endoplasmic reticulum and the NF-κB/HIF-1α pathway. Mol Microbiol 2023; 119:86-100. [PMID: 36480422 DOI: 10.1111/mmi.15010] [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: 02/07/2022] [Revised: 10/23/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022]
Abstract
Endothelial cell injury is a key factor in the spread of infection and pathogenicity of Treponema pallidum. The migration and adhesion reaction mediated by T. pallidum lipoprotein plays an important role. This study aimed to systematically explore the migration and adhesion effect of T. pallidum lipoprotein Tp0768 and its molecular mechanism. Stimulating vascular endothelial cells with Tp0768 increased the expression of ICAM-1, MCP-1, and IL-8. Moreover, it promoted the migration and adhesion of THP-1 cells to vascular endothelial cells. Our results revealed that Tp0768 promoted the THP-1 cells migrating and adhering to vascular endothelial cells by the PERK and IRE-1α pathways of endoplasmic reticulum (ER) stress. We further demonstrated that the inhibition of the NF-κB pathway and the downregulation of hypoxia-inducible factor 1 alpha (HIF-1α) reduced the mRNA levels of ICAM-1, MCP-1, and IL-8 induced by Tp0768. Also, the adhesion rate of THP-1 cells to endothelial cells decreased. After inhibiting ER stress, NF-κB p65 nuclear translocation was weakened, and the mRNA level of HIF-1α was also significantly downregulated. Our results indicated that T. pallidum lipoprotein Tp0768 promoted the migration and adhesion of THP-1 cells to vascular endothelial cells through ER stress and NF-κB/HIF-1α pathway.
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Affiliation(s)
- Xiangping Zhou
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Yun Tang
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Ting Cao
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Lichang Ning
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Yumeng Li
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiaoping Xie
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Yibao Hu
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Bisha He
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Binfeng Peng
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
| | - Shuangquan Liu
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, China
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12
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Song X, Gao F, Li H, Qin W, Chai C, Shi G, Yang H. Long noncoding RNA THRIL promotes foam cell formation and inflammation in macrophages. Cell Biol Int 2023; 47:156-166. [PMID: 36229925 DOI: 10.1002/cbin.11934] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/13/2022] [Indexed: 12/31/2022]
Abstract
Tumor necrosis factor-α (TNF-α) and heterogenous nuclear ribonucleoprotein L (hnRNPL)-related immunoregulatory lincRNA (THRIL) is a long noncoding RNA (lncRNA) involved in various inflammatory diseases. However, its role in atherosclerosis is not known. In this study, we aimed to investigate the function of THRIL in mediating macrophage inflammation and foam cell formation. The expression of THRIL was quantified in THP-1 macrophages after treatment with oxidized low-density lipoprotein (oxLDL). The effect of THRIL overexpression and knockdown on oxLDL-induced inflammatory responses and lipid accumulation was determined. THRIL-associated protein partners were identified by RNA pull-down and RNA immunoprecipitation assays. We show that THRIL is upregulated in macrophages after oxLDL treatment. Knockdown of THRIL blocks oxLDL-induced expression of interleukin-1β (IL-1β), IL-6, and TNF-α and lipid accumulation. Conversely, ectopic expression of THRIL enhances inflammatory gene expression and lipid deposition in oxLDL-treated macrophages. Moreover, THRIL depletion increases cholesterol efflux from macrophages and the expression of ATP-binding cassette transporter (ABC) A1 and ABCG1. FOXO1 is identified as a protein partner of THRIL and promotes macrophage inflammation and lipid accumulation. Furthermore, overexpression of FOXO1 restores lipid accumulation and inflammatory cytokine production in THRIL-depleted macrophages. In conclusion, our data suggest a model where THRIL interacts with FOXO1 to promote macrophage inflammation and foam cell formation. THRIL may represent a therapeutic target for atherosclerosis.
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Affiliation(s)
- Xiaosu Song
- Department of Cardiology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Fen Gao
- Department of Cardiology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Hong Li
- Department of Cardiology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Weiwei Qin
- Department of Cardiology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chanjuan Chai
- Department of Cardiology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Guojuan Shi
- Department of Cardiology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Huiyu Yang
- Department of Cardiology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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13
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He W, Wang Y, Yang R, Ma H, Qin X, Yan M, Rong Y, Xie Y, Li L, Si J, Li X, Ma K. Molecular Mechanism of Naringenin Against High-Glucose-Induced Vascular Smooth Muscle Cells Proliferation and Migration Based on Network Pharmacology and Transcriptomic Analyses. Front Pharmacol 2022; 13:862709. [PMID: 35754483 PMCID: PMC9219407 DOI: 10.3389/fphar.2022.862709] [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: 01/26/2022] [Accepted: 04/20/2022] [Indexed: 12/03/2022] Open
Abstract
Although the protective effects of naringenin (Nar) on vascular smooth muscle cells (VSMCs) have been confirmed, whether it has anti-proliferation and anti-migration effects in high-glucose-induced VSMCs has remained unclear. This study aimed to clarify the potential targets and molecular mechanism of Nar when used to treat high-glucose-induced vasculopathy based on transcriptomics, network pharmacology, molecular docking, and in vivo and in vitro assays. We found that Nar has visible anti-proliferation and anti-migration effects both in vitro (high-glucose-induced VSMC proliferation and migration model) and in vivo (type 1 diabetes mouse model). Based on the results of network pharmacology and molecular docking, vascular endothelial growth factor A (VEGFA), the proto-oncogene tyrosine-protein kinase Src (Src) and the kinase insert domain receptor (KDR) are the core targets of Nar when used to treat diabetic angiopathies, according to the degree value and the docking score of the three core genes. Interestingly, not only the Biological Process (BP), Molecular Function (MF), and KEGG enrichment results from network pharmacology analysis but also transcriptomics showed that phosphatidylinositol-3-kinase (PI3K)/protein kinase B (Akt) is the most likely downstream pathway involved in the protective effects of Nar on VSMCs. Notably, according to the differentially expressed genes (DEGs) in the transcriptomic analysis, we found that cAMP-responsive element binding protein 5 (CREB5) is a downstream protein of the PI3K/Akt pathway that participates in VSMCs proliferation and migration. Furthermore, the results of molecular experiments in vitro were consistent with the bioinformatic analysis. Nar significantly inhibited the protein expression of the core targets (VEGFA, Src and KDR) and downregulated the PI3K/Akt/CREB5 pathway. Our results indicated that Nar exerted anti-proliferation and anti-migration effects on high-glucose-induced VSMCs through decreasing expression of the target protein VEGFA, and then downregulating the PI3K/Akt/CREB5 pathway, suggesting its potential for treating diabetic angiopathies.
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Affiliation(s)
- Wenjun He
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Pathophysiology, Shihezi University School of Medicine, Shihezi, China
| | - Yanming Wang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
| | - Rui Yang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
| | - Huihui Ma
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
| | - Xuqing Qin
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
| | - Meijuan Yan
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Pathophysiology, Shihezi University School of Medicine, Shihezi, China
| | - Yi Rong
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
| | - Yufang Xie
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
| | - Li Li
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China
| | - Junqiang Si
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
| | - Xinzhi Li
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Pathophysiology, Shihezi University School of Medicine, Shihezi, China
| | - Ketao Ma
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education, Shihezi University School of Medicine, Shihezi, China.,NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.,Department of Physiology, Shihezi University School of Medicine, Shihezi, China
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14
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Polarization of Microglia and Its Therapeutic Potential in Sepsis. Int J Mol Sci 2022; 23:ijms23094925. [PMID: 35563317 PMCID: PMC9101892 DOI: 10.3390/ijms23094925] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection, leaving the inflammation process without a proper resolution, leading to tissue damage and possibly sequelae. The central nervous system (CNS) is one of the first regions affected by the peripheral inflammation caused by sepsis, exposing the neurons to an environment of oxidative stress, triggering neuronal dysfunction and apoptosis. Sepsis-associated encephalopathy (SAE) is the most frequent sepsis-associated organ dysfunction, with symptoms such as deliriums, seizures, and coma, linked to increased mortality, morbidity, and cognitive disability. However, the current therapy does not avoid those patients’ symptoms, evidencing the search for a more optimal approach. Herein we focus on microglia as a prominent therapeutic target due to its multiple functions maintaining CNS homeostasis and its polarizing capabilities, stimulating and resolving neuroinflammation depending on the stimuli. Microglia polarization is a target of multiple studies involving nerve cell preservation in diseases caused or aggravated by neuroinflammation, but in sepsis, its therapeutic potential is overlooked. We highlight the peroxisome proliferator-activated receptor gamma (PPARγ) neuroprotective properties, its role in microglia polarization and inflammation resolution, and the interaction with nuclear factor-κB (NF-κB) and mitogen-activated kinases (MAPK), making PPARγ a molecular target for sepsis-related studies to come.
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15
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Wan L, Li W, Meng Y, Hou Y, Chen M, Xu B. Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects. Front Immunol 2022; 13:849451. [PMID: 35514959 PMCID: PMC9063412 DOI: 10.3389/fimmu.2022.849451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of multiple high-throughput sequencing technologies has made it possible to explore the critical roles and mechanisms of functional enhancers and enhancer RNAs (eRNAs). The inflammatory immune response, as a fundamental pathological process in infectious diseases, cancers and immune disorders, coordinates the balance between the internal and external environment of the organism. It has been shown that both active enhancers and intranuclear eRNAs are preferentially expressed over inflammation-related genes in response to inflammatory stimuli, suggesting that enhancer transcription events and their products influence the expression and function of inflammatory genes. Therefore, in this review, we summarize and discuss the relevant inflammatory roles and regulatory mechanisms of eRNAs in inflammatory immune cells, non-inflammatory immune cells, inflammatory immune diseases and tumors, and explore the potential therapeutic effects of enhancer inhibitors affecting eRNA production for diseases with inflammatory immune responses.
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Affiliation(s)
- Lilin Wan
- Medical School, Southeast University, Nanjing, China
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Yuan Meng
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
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16
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MiR-199a-3p Restrains Foaming and Inflammation by Regulating RUNX1 in Macrophages. Mol Biotechnol 2022; 64:1130-1142. [DOI: 10.1007/s12033-022-00484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/20/2022] [Indexed: 10/18/2022]
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17
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Ashrafizadeh M, Zarrabi A, Mostafavi E, Aref AR, Sethi G, Wang L, Tergaonkar V. Non-coding RNA-based regulation of inflammation. Semin Immunol 2022; 59:101606. [PMID: 35691882 DOI: 10.1016/j.smim.2022.101606] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/01/2022] [Accepted: 05/25/2022] [Indexed: 01/15/2023]
Abstract
Inflammation is a multifactorial process and various biological mechanisms and pathways participate in its development. The presence of inflammation is involved in pathogenesis of different diseases such as diabetes mellitus, cardiovascular diseases and even, cancer. Non-coding RNAs (ncRNAs) comprise large part of transcribed genome and their critical function in physiological and pathological conditions has been confirmed. The present review focuses on miRNAs, lncRNAs and circRNAs as ncRNAs and their potential functions in inflammation regulation and resolution. Pro-inflammatory and anti-inflammatory factors are regulated by miRNAs via binding to 3'-UTR or indirectly via affecting other pathways such as SIRT1 and NF-κB. LncRNAs display a similar function and they can also affect miRNAs via sponging in regulating levels of cytokines. CircRNAs mainly affect miRNAs and reduce their expression in regulating cytokine levels. Notably, exosomal ncRNAs have shown capacity in inflammation resolution. In addition to pre-clinical studies, clinical trials have examined role of ncRNAs in inflammation-mediated disease pathogenesis and cytokine regulation. The therapeutic targeting of ncRNAs using drugs and nucleic acids have been analyzed to reduce inflammation in disease therapy. Therefore, ncRNAs can serve as diagnostic, prognostic and therapeutic targets in inflammation-related diseases in pre-clinical and clinical backgrounds.
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Affiliation(s)
- Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, 34396 Istanbul, Turkey.
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Translational Sciences, Xsphera Biosciences Inc. 6, Tide Street, Boston, MA 02210, USA
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.
| | - Lingzhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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18
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Qu F, Li J, Zeng X, She Q, Li Y, Xie W, Cao S, Zhou Y, He Z, Tang J, Mao Z, Wang Y, Fang J, Xu W, Liu Z. Grass carp MAP3K4 participates in the intestinal immune response to bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2022; 120:82-91. [PMID: 34780976 DOI: 10.1016/j.fsi.2021.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/20/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Mitogen-activated protein kinase kinase kinase 4 (MAP3K4) is a multifunctional mediator of the conserved MAPK signaling pathway that plays essential roles in the regulation of immune responses in mammals. However, the function of teleost MAP3K4s in innate immunity, especially in the intestinal immune system, is still poorly understood. In the current study, we identified a fish MAP3K4 homolog (CiMAP3K4) in Ctenopharyngodon idella as well as its immune function in intestine following bacterial infection in vivo and in vitro. The open reading frame (ORF) of CiMAP3K4 encodes putative peptide of 1544 amino acids containing a predicted serine/threonine protein kinase (S_TKc) domain with high identity with other fish MAP3K4s. Phylogenetic analysis revealed the CiMAP3K4 belonged to the fish cluster and showed the closest relationship to Pimephales promelas. Quantitative real-time PCR (qRT-PCR) analysis revealed that CiMAP3K4 transcripts were widely distributed in all tested tissues, especially with high expression in the muscle and intestine of healthy grass carp. In vitro, CiMAP3K4 gene expression was upregulated by bacterial PAMPs (lipolysaccharide (LPS), peptidoglycan (PGN), L-Ala-γ-D-Glu-meso-diaminopimelic acid (Tri-DAP) and muramyl dipeptide (MDP)) and pathogens (Aeromonas hydrophila and Aeromonas veronii) in primary intestinal cells. In vivo, the mRNA expression levels of CiMAP3K4 in the intestine were significantly induced by bacterial MDP challenge in a time-dependent manner; however, this effect could be inhibited by the bioactive dipeptides β-alanyl-l-histidine (carnosine) and alanyl-glutamine (Ala-Gln). Moreover, CiMAP3K4 was located primarily in the cytoplasm, and its overexpression increased the transcriptional activity of AP-1 in HEK293T cells. Collectively, these results suggested that CiMAP3K4 might play an important role in the intestinal immune response to bacterial infections, which paves the way for a better understanding of the intestinal immune system of grass carp.
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Affiliation(s)
- Fufa Qu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Jialing Li
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Xuan Zeng
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Qing She
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Yurong Li
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Wenjie Xie
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Shenping Cao
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Yonghua Zhou
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Zhimin He
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Jianzhou Tang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Zhuangwen Mao
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Yuping Wang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Jiamei Fang
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Wenqian Xu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China
| | - Zhen Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha 410022, China.
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19
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Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:118-141. [PMID: 34791665 PMCID: PMC9808899 DOI: 10.1111/nyas.14713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
The human transcriptome contains many types of noncoding RNAs, which rival the number of protein-coding species. From long noncoding RNAs (lncRNAs) that are over 200 nucleotides long to piwi-interacting RNAs (piRNAs) of only 20 nucleotides, noncoding RNAs play important roles in regulating transcription, epigenetic modifications, translation, and cell signaling. Roles for noncoding RNAs in disease mechanisms are also being uncovered, and several species have been identified as potential drug targets. On May 11-14, 2021, the Keystone eSymposium "Noncoding RNAs: Biology and Applications" brought together researchers working in RNA biology, structure, and technologies to accelerate both the understanding of RNA basic biology and the translation of those findings into clinical applications.
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Affiliation(s)
| | - Edith Heard
- European Molecular Biology Laboratory (EMBL), Heidelberg, Heidelberg, Germany
- Collège de France, Paris, France
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of the Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Sciences, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou, China
| | | | - Sofia A Quinodoz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor and Genetics Program, Stony Brook University, Stony Brook, New York
| | - Sarah D Diermeier
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Allison M Porman
- Biochemistry and Molecular Genetics Department, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Dhiraj Kumar
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xiaohua Shen
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, China
| | - Juan Pablo Unfried
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), Pamplona, Spain
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital; and Department for BioMedical Research University of Bern, Bern, Switzerland
- School of Biology and Environmental Science and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Adelheid Lempradl
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, Michigan
| | - Sean E McGeary
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
- Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Lamia Wahba
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anna Marie Pyle
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Connecticut and Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Róża K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California
- Howard Hughes Medical Institute, Stanford University, Stanford, California
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, California
| | - Joshua T Mendell
- Department of Molecular Biology, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine; and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lin He
- Division of Cellular and Developmental Biology, Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, California
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center and Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University; Bioland Laboratory; Program of Molecular Medicine, Zhongshan School of Medicine, Sun Yat-sen University; and Fountain-Valley Institute for Life Sciences, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences Guangzhou, Guangzhou, China
| | - John L Rinn
- Department of Biochemistry, BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado
| | - Mukesh Kumar Lalwani
- Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, Scotland, United Kingdom
| | - Murat Can Kalem
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, New York
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry and Center for RNA Biology, University of Rochester, Rochester, New York
| | - Xuhang Liu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, New York
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