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Zhang L, Leonard N, Passaro R, Luan MS, Van Tuyen P, Han LTN, Cam NH, Vogelnest L, Lynch M, Fine AE, Nga NTT, Van Long N, Rawson BM, Behie A, Van Nguyen T, Le MD, Nadler T, Walter L, Marques-Bonet T, Hofreiter M, Li M, Liu Z, Roos C. Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur. Nat Commun 2024; 15:8531. [PMID: 39358348 PMCID: PMC11447269 DOI: 10.1038/s41467-024-52811-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.
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Affiliation(s)
- Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- International Max Planck Research School for Genome Science (IMPRS-GS), University of Göttingen, Göttingen, Germany.
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Neahga Leonard
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Rick Passaro
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Mai Sy Luan
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Pham Van Tuyen
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Le Thi Ngoc Han
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Nguyen Huy Cam
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Larry Vogelnest
- Taronga Conservation Society Australia, Mosman, NSW, Australia
| | - Michael Lynch
- Melbourne Zoo, Zoos Victoria, Parkville, VIC, Australia
| | - Amanda E Fine
- Wildlife Conservation Society (WCS), Health Program, New York, NY, USA
| | | | - Nguyen Van Long
- Wildlife Conservation Society (WCS), Vietnam Country Program, Hanoi, Vietnam
| | - Benjamin M Rawson
- World Wildlife Fund for Nature (WWF) International, Gland, Switzerland
| | - Alison Behie
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
| | - Truong Van Nguyen
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Minh D Le
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Tilo Nadler
- Three Monkeys Wildlife Conservancy, Nho Quan District, Ninh Binh Province, Ninh Binh, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany.
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China.
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
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Zohar K, Linial M. Knockdown of DJ-1 Resulted in a Coordinated Activation of the Innate Immune Antiviral Response in HEK293 Cell Line. Int J Mol Sci 2024; 25:7550. [PMID: 39062793 PMCID: PMC11277157 DOI: 10.3390/ijms25147550] [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: 06/19/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
PARK7, also known as DJ-1, plays a critical role in protecting cells by functioning as a sensitive oxidation sensor and modulator of antioxidants. DJ-1 acts to maintain mitochondrial function and regulate transcription in response to different stressors. In this study, we showed that cell lines vary based on their antioxidation potential under basal conditions. The transcriptome of HEK293 cells was tested following knockdown (KD) of DJ-1 using siRNAs, which reduced the DJ-1 transcripts to only 12% of the original level. We compared the expression levels of 14k protein-coding transcripts and 4.2k non-coding RNAs relative to cells treated with non-specific siRNAs. Among the coding genes, approximately 200 upregulated differentially expressed genes (DEGs) signified a coordinated antiviral innate immune response. Most genes were associated with the regulation of type 1 interferons (IFN) and the induction of inflammatory cytokines. About a quarter of these genes were also induced in cells treated with non-specific siRNAs that were used as a negative control. Beyond the antiviral-like response, 114 genes were specific to the KD of DJ-1 with enrichment in RNA metabolism and mitochondrial functions. A smaller set of downregulated genes (58 genes) was associated with dysregulation in membrane structure, cell viability, and mitophagy. We propose that the KD DJ-1 perturbation diminishes the protective potency against oxidative stress. Thus, it renders the cells labile and responsive to the dsRNA signal by activating a large number of genes, many of which drive apoptosis, cell death, and inflammatory signatures. The KD of DJ-1 highlights its potency in regulating genes associated with antiviral responses, RNA metabolism, and mitochondrial functions, apparently through alteration in STAT activity and downstream signaling. Given that DJ-1 also acts as an oncogene in metastatic cancers, targeting DJ-1 could be a promising therapeutic strategy where manipulation of the DJ-1 level may reduce cancer cell viability and enhance the efficacy of cancer treatments.
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Affiliation(s)
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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Sun K, Wang YL, Hou CC, Shang D, Du LJ, Bai L, Zhang XY, Hao CM, Duan SZ. Collecting duct NCOR1 controls blood pressure by regulating mineralocorticoid receptor. J Adv Res 2024:S2090-1232(24)00053-5. [PMID: 38341030 DOI: 10.1016/j.jare.2024.02.003] [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: 08/07/2023] [Revised: 11/29/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024] Open
Abstract
INTRODUCTION Nuclear receptor corepressor 1(NCOR1) is reported to play crucial roles in cardiovascular diseases, but its function in the kidney has remained obscure. OBJECTIVE We aim to elucidate the role of collecting duct NCOR1 in blood pressure (BP) regulation. METHODS AND RESULTS Collecting duct NCOR1 knockout (KO) mice manifested increased BP and aggravated vascular and renal injury in an angiotensin II (Ang II)-induced hypertensive model. KO mice also showed significantly higher BP than littermate control (LC) mice in deoxycorticosterone acetate (DOCA)-salt model. Further study showed that collecting duct NCOR1 deficiency aggravated volume and sodium retention after saline challenge. Among the sodium transporter in the collecting duct, the expression of the three epithelial sodium channel (ENaC) subunits was markedly increased in the renal medulla of KO mice. Consistently, BP in Ang II-infused KO mice decreased significantly to the similar level as those in LC mice after amiloride treatment. ChIP analysis revealed that NCOR1 deficiency increased the enrichment of mineralocorticoid receptor (MR) on the promoters of the three ENaC genes in primary inner medulla collecting duct (IMCD) cells. Co-IP results showed interaction between NCOR1 and MR, and luciferase reporter results demonstrated that NCOR1 inhibited the transcriptional activity of MR. Knockdown of MR eliminated the increased ENaC expression in primary IMCD cells isolated from KO mice. Finally, BP was significantly decreased in Ang II-infused KO mice after treatment of MR antagonist spironolactone and the difference between LC and KO mice was abolished. CONCLUSIONS NCOR1 interacts with MR to control ENaC activity in the collecting duct and to regulate sodium reabsorption and ultimately BP. Targeting NCOR1 might be a promising tactic to interrupt the volume and sodium retention of the collecting duct in hypertension.
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Affiliation(s)
- Ke Sun
- Department of Nephrology, Zhejiang University Medical College Affiliated Sir Run Run Shaw Hospital, Hangzhou, Zhejiang Province 310016, China; Division of Nephrology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yong-Li Wang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chen-Chen Hou
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Da Shang
- Division of Nephrology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lin-Juan Du
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Lan Bai
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Xing-Yu Zhang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chuan-Ming Hao
- Division of Nephrology, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Sheng-Zhong Duan
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine; State Key Laboratory of Transvascular Implantation Devices, Hangzhou, Zhejiang 310000, China.
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Xiao X, Li R, Cui B, Lv C, Zhang Y, Zheng J, Hui R, Wang Y. Liver ACSM3 deficiency mediates metabolic syndrome via a lauric acid-HNF4α-p38 MAPK axis. EMBO J 2024; 43:507-532. [PMID: 38191811 PMCID: PMC10897460 DOI: 10.1038/s44318-023-00020-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
Metabolic syndrome combines major risk factors for cardiovascular disease, making deeper insight into its pathogenesis important. We here explore the mechanistic basis of metabolic syndrome by recruiting an essential patient cohort and performing extensive gene expression profiling. The mitochondrial fatty acid metabolism enzyme acyl-CoA synthetase medium-chain family member 3 (ACSM3) was identified to be significantly lower expressed in the peripheral blood of metabolic syndrome patients. In line, hepatic ACSM3 expression was decreased in mice with metabolic syndrome. Furthermore, Acsm3 knockout mice showed glucose and lipid metabolic abnormalities, and hepatic accumulation of the ACSM3 fatty acid substrate lauric acid. Acsm3 depletion markedly decreased mitochondrial function and stimulated signaling via the p38 MAPK pathway cascade. Consistently, Acsm3 knockout mouse exhibited abnormal mitochondrial morphology, decreased ATP contents, and enhanced ROS levels in their livers. Mechanistically, Acsm3 deficiency, and lauric acid accumulation activated nuclear receptor Hnf4α-p38 MAPK signaling. In line, the p38 inhibitor Adezmapimod effectively rescued the Acsm3 depletion phenotype. Together, these findings show that disease-associated loss of ACSM3 facilitates mitochondrial dysfunction via a lauric acid-HNF4a-p38 MAPK axis, suggesting a novel therapeutic vulnerability in systemic metabolic dysfunction.
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Affiliation(s)
- Xiao Xiao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruofei Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bing Cui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Lv
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Zheng
- Rizhao Port Hospital, Shandong, China
| | - Rutai Hui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Yu L, Xu M, Yan Y, Huang S, Yuan M, Cui B, Lv C, Zhang Y, Wang H, Jin X, Hui R, Wang Y. ZFYVE28 mediates insulin resistance by promoting phosphorylated insulin receptor degradation via increasing late endosomes production. Nat Commun 2023; 14:6833. [PMID: 37884540 PMCID: PMC10603069 DOI: 10.1038/s41467-023-42657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
Insulin resistance is associated with many pathological conditions, and an in-depth understanding of the mechanisms involved is necessary to improve insulin sensitivity. Here, we show that ZFYVE28 expression is decreased in insulin-sensitive obese individuals but increased in insulin-resistant individuals. Insulin signaling inhibits ZFYVE28 expression by inhibiting NOTCH1 via the RAS/ERK pathway, whereas ZFYVE28 expression is elevated due to impaired insulin signaling in insulin resistance. While Zfyve28 overexpression impairs insulin sensitivity and causes lipid accumulation, Zfyve28 knockout in mice can significantly improve insulin sensitivity and other indicators associated with insulin resistance. Mechanistically, ZFYVE28 colocalizes with early endosomes via the FYVE domain, which inhibits the generation of recycling endosomes but promotes the conversion of early to late endosomes, ultimately promoting phosphorylated insulin receptor degradation. This effect disappears with deletion of the FYVE domain. Overall, in this study, we reveal that ZFYVE28 is involved in insulin resistance by promoting phosphorylated insulin receptor degradation, and ZFYVE28 may be a potential therapeutic target to improve insulin sensitivity.
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Affiliation(s)
- Liang Yu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengchen Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yupeng Yan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuchen Huang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengmeng Yuan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bing Cui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Lv
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongrui Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolei Jin
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Rutai Hui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Jiang K, Kang L, Jiang A, Zhao Q. Development and Validation of a Diagnostic Model Based on Hypoxia-Related Genes in Myocardial Infarction. Int J Gen Med 2023; 16:2111-2123. [PMID: 37275329 PMCID: PMC10238209 DOI: 10.2147/ijgm.s407759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Purpose Myocardial infarction (MI) is a common cardiovascular disease, and its underlying pathological mechanism remains unclear. We aimed to develop a diagnostic model to distinguish different subtypes of MI. Patients and Methods The gene expression profiles of MI from the GEO database and hypoxia-related genes (HRGs) from MSigDB were downloaded. Then, the different MI subtypes based on HRGs were identified with unsupervised clustering. The difference of expression patterns and hypoxic-immune status among different subtypes of MI were investigated. The diagnostic model to distinguish the different subtypes of MI was developed and validated. Results Based on HRGs, MI samples were divided into two subtypes, cluster A and cluster B. A total of 211 genes showed significant changes in expression between the two subtypes. Cluster A was characterized by high hypoxia status and low immunity status. Based on weighted gene co-expression network analysis, ROC analysis and LASSO regression algorithm, 5 genes were identified as potential diagnostic markers. Finally, a diagnostic model based on these 5 genes was established, which can distinguish the two subtypes well. Conclusion The five hub genes, including ANKRD36, HLTF, KIF3A, OXCT1 and VPS13A, may be associated with the different subtypes of MI.
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Affiliation(s)
- Ke Jiang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, Shandong, People’s Republic of China
| | - Ling Kang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, Shandong, People’s Republic of China
| | - Andong Jiang
- Medical Imaging Department, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, Shandong, People’s Republic of China
| | - Qiang Zhao
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, Shandong, People’s Republic of China
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Pan S, Li Z, Wang Y, Liang L, Liu F, Qiao Y, Liu D, Liu Z. A Comprehensive Weighted Gene Co-expression Network Analysis Uncovers Potential Targets in Diabetic Kidney Disease. J Transl Int Med 2022; 10:359-368. [PMID: 36860636 PMCID: PMC9969566 DOI: 10.2478/jtim-2022-0053] [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] [Indexed: 01/15/2023] Open
Abstract
Background and Objectives Diabetic kidney disease (DKD) is one of the most common microvascular complications of diabetes. It has always been difficult to explore novel biomarkers and therapeutic targets of DKD. We aimed to identify new biomarkers and further explore their functions in DKD. Methods The weighted gene co-expression network analysis (WGCNA) method was used to analyze the expression profile data of DKD, obtain key modules related to the clinical traits of DKD, and perform gene enrichment analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the mRNA expression of the hub genes in DKD. Spearman's correlation coefficients were used to determine the relationship between gene expression and clinical indicators. Results Fifteen gene modules were obtained via WGCNA analysis, among which the green module had the most significant correlation with DKD. Gene enrichment analysis revealed that the genes in this module were mainly involved in sugar and lipid metabolism, regulation of small guanosine triphosphatase (GTPase) mediated signal transduction, G protein-coupled receptor signaling pathway, peroxisome proliferator-activated receptor (PPAR) molecular signaling pathway, Rho protein signal transduction, and oxidoreductase activity. The qRT-PCR results showed that the relative expression of nuclear pore complex-interacting protein family member A2 (NPIPA2) and ankyrin repeat domain 36 (ANKRD36) was notably increased in DKD compared to the control. NPIPA2 was positively correlated with the urine albumin/creatinine ratio (ACR) and serum creatinine (Scr) but negatively correlated with albumin (ALB) and hemoglobin (Hb) levels. ANKRD36 was positively correlated with the triglyceride (TG) level and white blood cell (WBC) count. Conclusion NPIPA2 expression is closely related to the disease condition of DKD, whereas ANKRD36 may be involved in the progression of DKD through lipid metabolism and inflammation, providing an experimental basis to further explore the pathogenesis of DKD.
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Affiliation(s)
- Shaokang Pan
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
| | - Zhengyong Li
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
| | - Yixue Wang
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
| | - Lulu Liang
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
| | - Fengxun Liu
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
| | - Yingjin Qiao
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
| | - Dongwei Liu
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
| | - Zhangsuo Liu
- Department of TCM-Integrated Department of Nephrology, the First Affiliated Hospital of Zhengzhou University; Research Institute of Nephrology, Zhengzhou University; Research Center for Kidney Disease, Henan Province; Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province; Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou 450052, Henan Province, China
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Xiao X, Li R, Wu C, Yan Y, Yuan M, Cui B, Zhang Y, Zhang C, Zhang X, Zhang W, Hui R, Wang Y. A genome-wide association study identifies a novel association between SDC3 and apparent treatment-resistant hypertension. BMC Med 2022; 20:463. [PMID: 36447229 PMCID: PMC9710180 DOI: 10.1186/s12916-022-02665-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Compared with patients who require fewer antihypertensive agents, those with apparent treatment-resistant hypertension (aTRH) are at increased risk for cardiovascular and all-cause mortality, independent of blood pressure control. However, the etiopathogenesis of aTRH is still poorly elucidated. METHODS We performed a genome-wide association study (GWAS) in first cohort including 586 aTRHs and 871 healthy controls. Next, expression quantitative trait locus (eQTL) analysis was used to identify genes that are regulated by single nucleotide polymorphisms (SNPs) derived from the GWAS. Then, we verified the genes obtained from the eQTL analysis in the validation cohort including 65 aTRHs, 96 hypertensives, and 100 healthy controls through gene expression profiling analysis and real-time quantitative polymerase chain reaction (RT-qPCR) assay. RESULTS The GWAS in first cohort revealed four suggestive loci (1p35, 4q13.2-21.1, 5q22-23.2, and 15q11.1-q12) represented by 23 SNPs. The 23 significant SNPs were in or near LAPTM5, SDC3, UGT2A1, FTMT, and NIPA1. eQTL analysis uncovered 14 SNPs in 1p35 locus all had same regulation directions for SDC3 and LAPTM5. The disease susceptible alleles of SNPs in 1p35 locus were associated with lower gene expression for SDC3 and higher gene expression for LAPTM5. The disease susceptible alleles of SNPs in 4q13.2-21.1 were associated with higher gene expression for UGT2B4. GTEx database did not show any statistically significant eQTLs between the SNPs in 5q22-23.2 and 15q11.1-q12 loci and their influenced genes. Then, gene expression profiling analysis in the validation cohort confirmed lower expression of SDC3 in aTRH but no significant differences on LAPTM5 and UGT2B4, when compared with controls and hypertensives, respectively. RT-qPCR assay further verified the lower expression of SDC3 in aTRH. CONCLUSIONS Our study identified a novel association of SDC3 with aTRH, which contributes to the elucidation of its etiopathogenesis and provides a promising therapeutic target.
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Affiliation(s)
- Xiao Xiao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Rui Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Cunjin Wu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Yupeng Yan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Mengmeng Yuan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Bing Cui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Yu Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Channa Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Xiaoxia Zhang
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi, China
| | - Weili Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Rutai Hui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China
| | - Yibo Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishi Rd, Beijing, China.
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A comprehensive weighted gene co-expression network analysis uncovers potential targets in diabetic kidney disease. J Transl Int Med 2022. [DOI: 10.2478/jtim-2022-0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background and Objectives
Diabetic kidney disease (DKD) is one of the most common microvascular complications of diabetes. It has always been difficult to explore novel biomarkers and therapeutic targets of DKD. We aimed to identify new biomarkers and further explore their functions in DKD.
Methods
The weighted gene co-expression network analysis (WGCNA) method was used to analyze the expression profile data of DKD, obtain key modules related to the clinical traits of DKD, and perform gene enrichment analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the mRNA expression of the hub genes in DKD. Spearman’s correlation coefficients were used to determine the relationship between gene expression and clinical indicators.
Results
Fifteen gene modules were obtained via WGCNA analysis, among which the green module had the most significant correlation with DKD. Gene enrichment analysis revealed that the genes in this module were mainly involved in sugar and lipid metabolism, regulation of small guanosine triphosphatase (GTPase) mediated signal transduction, G protein-coupled receptor signaling pathway, peroxisome proliferator-activated receptor (PPAR) molecular signaling pathway, Rho protein signal transduction, and oxidoreductase activity. The qRT-PCR results showed that the relative expression of nuclear pore complex-interacting protein family member A2 (NPIPA2) and ankyrin repeat domain 36 (ANKRD36) was notably increased in DKD compared to the control. NPIPA2 was positively correlated with the urine albumin/creatinine ratio (ACR) and serum creatinine (Scr) but negatively correlated with albumin (ALB) and hemoglobin (Hb) levels. ANKRD36 was positively correlated with the triglyceride (TG) level and white blood cell (WBC) count.
Conclusion
NPIPA2 expression is closely related to the disease condition of DKD, whereas ANKRD36 may be involved in the progression of DKD through lipid metabolism and inflammation, providing an experimental basis to further explore the pathogenesis of DKD.
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Ehret E, Hummler E. Lessons learned about epithelial sodium channels from transgenic mouse models. Curr Opin Nephrol Hypertens 2022; 31:493-501. [PMID: 35894285 PMCID: PMC10022670 DOI: 10.1097/mnh.0000000000000821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review provides an up-to-date understanding about the regulation of epithelial sodium channel (ENaC) expression and function. In particular, we will focus on its implication in renal Na+ and K+ handling and control of blood pressure using transgenic animal models. RECENT FINDINGS In kidney, the highly amiloride-sensitive ENaC maintains whole body Na+ homeostasis by modulating Na+ transport via epithelia. This classical role is mostly confirmed using genetically engineered animal models. Recently identified key signaling pathways that regulate ENaC expression and function unveiled some nonclassical and unexpected channel regulatory processes. If aberrant, these dysregulated mechanisms may also result in the development of salt-dependent hypertension.The purpose of this review is to highlight the most recent findings in renal ENaC regulation and function, in considering data obtained from animal models. SUMMARY Increased ENaC-mediated Na+ transport is a prerequisite for salt-dependent forms of hypertension. To treat salt-sensitive hypertension it is crucial to fully understand the function and regulation of ENaC.
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Affiliation(s)
- Elodie Ehret
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne
| | - Edith Hummler
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne
- National Center of Competence in Research, Kidney.CH, Zurich, Switzerland
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