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Bhayana S, Schytz PA, Olesen ETB, Soh K, Das V. Review: Single Cell Advances in investigating and understanding Chronic Kidney Disease and Diabetic Kidney Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00273-6. [PMID: 39097167 DOI: 10.1016/j.ajpath.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 08/05/2024]
Abstract
Chronic Kidney Disease (CKD) and its subset Diabetic Kidney Disease (DKD) are progressive conditions that affect more than 850 million people worldwide. Diabetes, hypertension, and glomerulonephritis are the most common causes of CKD, which is associated with significant patient morbidity and an increased risk of cardiovascular events, such as heart failure, ultimately leading to premature death. Despite newly approved drugs, increasing evidence shows that patients respond to treatment differently given the complexity of disease heterogeneity and complicated pathophysiology. This review paper presents an integrative approach to understanding and addressing CKD through the lens of precision medicine and therapeutics. Leveraging advancements in single cell omics technologies and artificial intelligence (AI), we can explore the intricate cellular mechanisms underlying CKD and DKD pathogenesis. By dissecting the cellular heterogeneity and identifying rare cell populations using single cell approaches it will be possible to uncover novel therapeutic targets and biomarkers for personalized treatment strategies. Finally, we discuss the potential of AI-driven analyses in predicting disease progression and treatment response, thereby paving the way for tailored interventions.
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Affiliation(s)
- Sagar Bhayana
- Kidney Biology, Global Drug Development, Novo Nordisk A/S, Denmark
| | - Philip Andreas Schytz
- Cardiovascular, Kidney and Alzheimer Disease, Medical and Science, Development, Novo Nordisk A/S, Denmark
| | - Emma Tina Bisgaard Olesen
- Cardiovascular, Kidney and Alzheimer Disease, Medical and Science, Development, Novo Nordisk A/S, Denmark
| | - Keng Soh
- Integrated Omics, AI and Analytics, Development, Novo Nordisk A/S, Denmark
| | - Vivek Das
- Integrated Omics, AI and Analytics, Development, Novo Nordisk A/S, Denmark.
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Huang Q, Gu Y, Wu J, Zhan Y, Deng Z, Chen S, Peng M, Yang R, Chen J, Xie J. DACH1 Attenuates Airway Inflammation in Chronic Obstructive Pulmonary Disease by Activating NRF2 Signaling. Am J Respir Cell Mol Biol 2024; 71:121-132. [PMID: 38587806 DOI: 10.1165/rcmb.2023-0337oc] [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: 09/19/2023] [Accepted: 04/05/2024] [Indexed: 04/09/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease of the airways characterized by impaired lung function induced by cigarette smoke (CS). Reduced DACH1 (dachshund homolog 1) expression has a detrimental role in numerous disorders, but its role in COPD remains understudied. This study aimed to elucidate the role and underlying mechanism of DACH1 in airway inflammation in COPD by measuring DACH1 expression in lung tissues of patients with COPD. Airway epithelium-specific DACH1-knockdown mice and adenoassociated virus-transfected DACH1-overexpressing mice were used to investigate the role of DACH1 and the potential for therapeutic targeting in experimental COPD caused by CS. Furthermore, we discovered a potential mechanism of DACH1 in inflammation induced by CS extract stimulation in vitro. Compared with nonsmokers and smokers without COPD, patients with COPD had reduced DACH1 expression, especially in the airway epithelium. Airway epithelium-specific DACH1 knockdown aggravated airway inflammation and lung function decline caused by CS in mice, whereas DACH1 overexpression protected mice from airway inflammation and lung function decline. DACH1 knockdown and overexpression promoted and inhibited IL-6 and IL-8 secretion, respectively, in 16HBE human bronchial epidermal cells after CS extract stimulation. NRF2 (nuclear factor erythroid 2-related factor 2) was discovered to be a novel downstream target of DACH1, which binds directly to its promoter. By activating NRF2 signaling, DACH1 induction reduced inflammation. DACH1 levels are lower in smokers and nonsmoking patients with COPD than in nonsmokers. DACH1 has protective effects against inflammation induced by CS by activating the NRF2 signaling pathway. Targeting DACH1 is a potentially viable therapeutic approach for COPD treatment.
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Affiliation(s)
- Qian Huang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Yiya Gu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Jixing Wu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Yuan Zhan
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Zhesong Deng
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Shanshan Chen
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Maocuo Peng
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Ruonan Yang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Jinkun Chen
- Department of Science, Western University, London, Ontario, Canada
| | - Jungang Xie
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
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Si S, Liu H, Xu L, Zhan S. Identification of novel therapeutic targets for chronic kidney disease and kidney function by integrating multi-omics proteome with transcriptome. Genome Med 2024; 16:84. [PMID: 38898508 PMCID: PMC11186236 DOI: 10.1186/s13073-024-01356-x] [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: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a progressive disease for which there is no effective cure. We aimed to identify potential drug targets for CKD and kidney function by integrating plasma proteome and transcriptome. METHODS We designed a comprehensive analysis pipeline involving two-sample Mendelian randomization (MR) (for proteins), summary-based MR (SMR) (for mRNA), and colocalization (for coding genes) to identify potential multi-omics biomarkers for CKD and combined the protein-protein interaction, Gene Ontology (GO), and single-cell annotation to explore the potential biological roles. The outcomes included CKD, extensive kidney function phenotypes, and different CKD clinical types (IgA nephropathy, chronic glomerulonephritis, chronic tubulointerstitial nephritis, membranous nephropathy, nephrotic syndrome, and diabetic nephropathy). RESULTS Leveraging pQTLs of 3032 proteins from 3 large-scale GWASs and corresponding blood- and tissue-specific eQTLs, we identified 32 proteins associated with CKD, which were validated across diverse CKD datasets, kidney function indicators, and clinical types. Notably, 12 proteins with prior MR support, including fibroblast growth factor 5 (FGF5), isopentenyl-diphosphate delta-isomerase 2 (IDI2), inhibin beta C chain (INHBC), butyrophilin subfamily 3 member A2 (BTN3A2), BTN3A3, uromodulin (UMOD), complement component 4A (C4a), C4b, centrosomal protein of 170 kDa (CEP170), serologically defined colon cancer antigen 8 (SDCCAG8), MHC class I polypeptide-related sequence B (MICB), and liver-expressed antimicrobial peptide 2 (LEAP2), were confirmed. To our knowledge, 20 novel causal proteins have not been previously reported. Five novel proteins, namely, GCKR (OR 1.17, 95% CI 1.10-1.24), IGFBP-5 (OR 0.43, 95% CI 0.29-0.62), sRAGE (OR 1.14, 95% CI 1.07-1.22), GNPTG (OR 0.90, 95% CI 0.86-0.95), and YOD1 (OR 1.39, 95% CI 1.18-1.64,) passed the MR, SMR, and colocalization analysis. The other 15 proteins were also candidate targets (GATM, AIF1L, DQA2, PFKFB2, NFATC1, activin AC, Apo A-IV, MFAP4, DJC10, C2CD2L, TCEA2, HLA-E, PLD3, AIF1, and GMPR1). These proteins interact with each other, and their coding genes were mainly enrichment in immunity-related pathways or presented specificity across tissues, kidney-related tissue cells, and kidney single cells. CONCLUSIONS Our integrated analysis of plasma proteome and transcriptome data identifies 32 potential therapeutic targets for CKD, kidney function, and specific CKD clinical types, offering potential targets for the development of novel immunotherapies, combination therapies, or targeted interventions.
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Affiliation(s)
- Shucheng Si
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Hongyan Liu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Lu Xu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Siyan Zhan
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China.
- Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
- Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
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Lin J, Li B, Xu Q, Liu YS, Kang YL, Wang X, Wang Y, Lei Y, Bai YL, Li XM, Zhou J. DACH1 attenuated PA-induced renal tubular injury through TLR4/MyD88/NF-κB and TGF-β/Smad signalling pathway. J Endocrinol Invest 2024; 47:1531-1544. [PMID: 38147289 DOI: 10.1007/s40618-023-02253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Palmitic acid (PA), the major saturated fatty acid in the blood, often induces the initiation and progression of diabetic kidney disease (DKD). However, the underlying mechanism remains unclear. DACH1 is an important regulator of kidney functions. Herein, we investigated the roles of DACH1 in PA-induced kidney injury. METHODS Clinical data from the NHANES database were subjected to analyse the association between serum PA (sPA), blood glucose and kidney function. Molecular docking of PA was performed with DACH1. Immunohistochemistry, cell viability, annexin V/7-AAD double staining, TUNEL assay, immunofluorescent staining, autophagic flux analysis, qRT-PCR and western blot were performed. RESULTS Clinical data confirmed that sPA was increased significantly in the pathoglycemia individuals compared with controls and correlated negatively with renal function. Our findings suggested that PA could dock with DACH1. DACH1 enhances cell viability by inhibiting apoptosis and attenuating autophagy blockage induced by PA. Furthermore, the results demonstrated that DACH1 ameliorated inflammation and fibrosis through TLR4/MyD88/NF-κB and TGF-β/Smad signalling pathway in PA-treated renal tubular epithelial cell line (HK-2). CONCLUSIONS This study proved that sPA presents a risk factor for kidney injuries and DACH1 might serve as a protective target against renal function deterioration in diabetic patients.
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Affiliation(s)
- J Lin
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No.127 Changle West Road, Xi'an, 710032, China
| | - B Li
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No.127 Changle West Road, Xi'an, 710032, China
| | - Q Xu
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No.127 Changle West Road, Xi'an, 710032, China
| | - Y S Liu
- Department of Pharmacology, Key Laboratory of Gastrointestinal Pharmacology of Chinese Materia Medical of the State Administration of Traditional Chinese Medicine, School of Pharmacy, Air Force Medical University, Xi'an, 710032, China
| | - Y L Kang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi'an, 710032, China
| | - X Wang
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No.127 Changle West Road, Xi'an, 710032, China
| | - Y Wang
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No.127 Changle West Road, Xi'an, 710032, China
| | - Y Lei
- The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, 712099, China
| | - Y L Bai
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi'an, 710032, China.
| | - X M Li
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No.127 Changle West Road, Xi'an, 710032, China.
| | - J Zhou
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, No.127 Changle West Road, Xi'an, 710032, China.
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Tanaka K, Hayasaka H, Matsusaka T. Dach1 is essential for maintaining normal mature podocytes. PLoS One 2024; 19:e0303910. [PMID: 38805434 PMCID: PMC11132487 DOI: 10.1371/journal.pone.0303910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
Dach1 is highly expressed in normal podocytes, but this expression rapidly disappears after podocyte injury. To investigate the role of Dach1 in podocytes in vivo, we analyzed global, podocyte-specific, and inducible Dach1 knockout mice. Global Dach1 knockout (Dach1-/-) mice were assessed immediately after birth because they die within a day. The kidneys of Dach1-/- mice were slightly smaller than those of control mice but maintained a normal structure and normal podocyte phenotypes, including ultrastructure. To study the role of Dach1 in mature podocytes, we generated Dach1 knockout mice by mating Dach1fl/fl mice with Nphs1-Cre or ROSA-CreERT2 mice. Due to inefficient Cre recombination, only a small number of podocytes lacked Dach1 staining in these mice. However, all eleven Nphs1-Cre/Dach1fl/fl mice displayed abnormal albuminuria, and seven (63%) of them developed focal segmental glomerulosclerosis. Among 13 ROSA-CreERT2/Dach1fl/fl mice, eight (61%) exhibited abnormal albuminuria after treatment with tamoxifen, and five (38%) developed early sclerotic lesions. These results indicate that while Dach1 does not determine the fate of differentiation into podocytes, it is indispensable for maintaining the normal integrity of mature podocytes.
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Affiliation(s)
- Keiko Tanaka
- Departments of Physiology, Tokai University School of Medicine, Kanagawa, Japan
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Haruko Hayasaka
- Department of Science, Faculty of Science & Engineering, Graduate School of Science and Engineering, Kindai University, Osaka, Japan
| | - Taiji Matsusaka
- Departments of Physiology, Tokai University School of Medicine, Kanagawa, Japan
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Huang Y, Geng J, Wang M, Liu W, Hu H, Shi W, Li M, Huo G, Huang G, Xu A. A simple protocol to establish a conditionally immortalized mouse podocyte cell line. Sci Rep 2024; 14:11591. [PMID: 38773220 PMCID: PMC11109129 DOI: 10.1038/s41598-024-62547-5] [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: 01/23/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
Podocytes are specialized terminally differentiated cells in the glomerulus that are the primary target cells in many glomerular diseases. However, the current podocyte cell lines suffer from prolonged in vitro differentiation and limited survival time, which impede research progress. Therefore, it is necessary to establish a cell line that exhibits superior performance and characteristics. We propose a simple protocol to obtain an immortalized mouse podocyte cell (MPC) line from suckling mouse kidneys. Primary podocytes were cultured in vitro and infected with the SV40 tsA58 gene to obtain immortalized MPCs. The podocytes were characterized using Western blotting and quantitative real-time PCR. Podocyte injury was examined using the Cell Counting Kit-8 assay and flow cytometry. First, we successfully isolated an MPC line and identified 39 °C as the optimal differentiation temperature. Compared to undifferentiated MPCs, the expression of WT1 and synaptopodin was upregulated in differentiated MPCs. Second, the MPCs ceased proliferating at a nonpermissive temperature after day 4, and podocyte-specific proteins were expressed normally after at least 15 passages. Finally, podocyte injury models were induced to simulate podocyte injury in vitro. In summary, we provide a simple and popularized protocol to establish a conditionally immortalized MPC, which is a powerful tool for the study of podocytes.
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Affiliation(s)
- Yujiao Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jie Geng
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Mengdan Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Wenbin Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Haikun Hu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Wei Shi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Mei Li
- Dongfang Hospital of Beijing University of Chinese Medicine, Beijing, 100078, China
| | - Guiyang Huo
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Guangrui Huang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China.
| | - Anlong Xu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China.
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Collier L, Seah C, Hicks EM, Holtzheimer PE, Krystal JH, Girgenti MJ, Huckins LM, Johnston KJA. The impact of chronic pain on brain gene expression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.20.24307630. [PMID: 38826319 PMCID: PMC11142271 DOI: 10.1101/2024.05.20.24307630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Chronic pain affects one fifth of American adults, contributing significant public health burden. Chronic pain mechanisms can be further understood through investigating brain gene expression. Methods We tested differentially expressed genes (DEGs) in chronic pain, migraine, lifetime fentanyl and oxymorphone use, and with chronic pain genetic risk in four brain regions (dACC, DLPFC, MeA, BLA) and imputed cell type expression data from 304 postmortem donors. We compared findings across traits and with independent transcriptomics resources, and performed gene-set enrichment. Results We identified two chronic pain DEGs: B4GALT and VEGFB in bulk dACC. We found over 2000 (primarily BLA microglia) chronic pain cell type DEGs. Findings were enriched for mouse microglia pain genes, and for hypoxia and immune response. Cross-trait DEG overlap was minimal. Conclusions Chronic pain-associated gene expression is heterogeneous across cell type, largely distinct from that in pain-related traits, and shows BLA microglia are a key cell type.
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Affiliation(s)
- Lily Collier
- Department of Biological Sciences, Columbia University, New York City, NY
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
| | - Carina Seah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Emily M Hicks
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Paul E Holtzheimer
- National Center for PTSD, U.S. Department of Veterans Affairs
- Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - John H Krystal
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
- Clinical Neuroscience Division, National Center for PTSD, VA Connecticut Healthcare System, West Haven, CT
| | - Matthew J Girgenti
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
- Clinical Neuroscience Division, National Center for PTSD, VA Connecticut Healthcare System, West Haven, CT
| | - Laura M Huckins
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
| | - Keira J A Johnston
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
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Wang C, Pan Z, Sun L, Li Q. Integrative transcriptomic and proteomic profile revealed inhibition of oxidative phosphorylation and peroxisomes during renal interstitial fibrosis. J Proteomics 2024; 298:105144. [PMID: 38431085 DOI: 10.1016/j.jprot.2024.105144] [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: 10/05/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Effective therapies of chronic kidney disease (CKD) are lacking due to the unclear molecular pathogenesis. Previous single omics-studies have described potential molecular regulation mechanism of CKD only at the level of transcription or translation. Therefore, this study generated an integrated transcriptomic and proteomic profile to provide deep insights into the continuous transcription-translation process during CKD. The comprehensive datasets identified 14,948 transcripts and 6423 proteins, 233 up-regulated and 364 down-regulated common differentially expressed genes of transcriptome and proteome were selected to further combined bioinformatics analysis. The obtained results revealed reactive oxygen species (ROS) metabolism and antioxidant system due to imbalance of mitochondria and peroxisomes were significantly repressed in CKD. Overall, this study presents a valuable multi-omics analysis that sheds light on the molecular mechanisms underlying CKD. SIGNIFICANCE: Chronic kidney disease (CKD) is a progressive and irreversible condition that results in abnormal kidney function and structure, and is ranked 18th among the leading causes of death globally, leading to a significant societal burden. Hence, there is an urgent need for research to detect new, sensitive, and specific biomarkers. Omics-based studies offer great potential to identify underlying disease mechanisms, aid in clinical diagnosis, and develop novel treatment strategies for CKD. Previous studies have mainly focused on the regulation of gene expression or protein synthesis in CKD, thereby compelling us to conduct a meticulous analysis of transcriptomic and proteomic data from the UUO mouse model. Here, we have performed a unified analysis of CKD model by integrating transcriptomes and protein suites for the first time. Our study contributes to a deeper understanding of the pathogenesis of CKD and provides a basis for subsequent disease management and drug development.
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Affiliation(s)
- Cheng Wang
- Department of Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, PR China
| | - Zhuo Pan
- Department of General Surgery, First People's Hospital of Huzhou, Huzhou, Zhejiang 313000, PR China
| | - Linxiao Sun
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Medical University First Affiliated Hospital, Wenzhou, Zhejiang 325000, PR China
| | - Qiangqiang Li
- Department of General Surgery, the People's Hospital of Yuhuan, Taizhou 317600, Zhejiang, PR China.
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Wen J, Zhang J, Zhang H, Zhang N, Lei R, Deng Y, Cheng Q, Li H, Luo P. Large-scale genome-wide association studies reveal the genetic causal etiology between air pollutants and autoimmune diseases. J Transl Med 2024; 22:392. [PMID: 38685026 PMCID: PMC11057084 DOI: 10.1186/s12967-024-04928-y] [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: 08/14/2023] [Accepted: 01/23/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Epidemiological evidence links a close correlation between long-term exposure to air pollutants and autoimmune diseases, while the causality remained unknown. METHODS Two-sample Mendelian randomization (TSMR) was used to investigate the role of PM10, PM2.5, NO2, and NOX (N = 423,796-456,380) in 15 autoimmune diseases (N = 14,890-314,995) using data from large European GWASs including UKB, FINNGEN, IMSGC, and IPSCSG. Multivariable Mendelian randomization (MVMR) was conducted to investigate the direct effect of each air pollutant and the mediating role of common factors, including body mass index (BMI), alcohol consumption, smoking status, and household income. Transcriptome-wide association studies (TWAS), two-step MR, and colocalization analyses were performed to explore underlying mechanisms between air pollution and autoimmune diseases. RESULTS In TSMR, after correction of multiple testing, hypothyroidism was causally associated with higher exposure to NO2 [odds ratio (OR): 1.37, p = 9.08 × 10-4] and NOX [OR: 1.34, p = 2.86 × 10-3], ulcerative colitis (UC) was causally associated with higher exposure to NOX [OR: 2.24, p = 1.23 × 10-2] and PM2.5 [OR: 2.60, p = 5.96 × 10-3], rheumatoid arthritis was causally associated with higher exposure to NOX [OR: 1.72, p = 1.50 × 10-2], systemic lupus erythematosus was causally associated with higher exposure to NOX [OR: 4.92, p = 6.89 × 10-3], celiac disease was causally associated with lower exposure to NOX [OR: 0.14, p = 6.74 × 10-4] and PM2.5 [OR: 0.17, p = 3.18 × 10-3]. The risky effects of PM2.5 on UC remained significant in MVMR analyses after adjusting for other air pollutants. MVMR revealed several common mediators between air pollutants and autoimmune diseases. Transcriptional analysis identified specific gene transcripts and pathways interconnecting air pollutants and autoimmune diseases. Two-step MR revealed that POR, HSPA1B, and BRD2 might mediate from air pollutants to autoimmune diseases. POR pQTL (rs59882870, PPH4=1.00) strongly colocalized with autoimmune diseases. CONCLUSION This research underscores the necessity of rigorous air pollutant surveillance within public health studies to curb the prevalence of autoimmune diseases.
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Affiliation(s)
- Jie Wen
- The Animal Laboratory Center, Hunan Cancer Hospital, and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jingwei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ruoyan Lei
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yujia Deng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- First Clinical Department, Changsha Medical University, Changsha, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - He Li
- The Animal Laboratory Center, Hunan Cancer Hospital, and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Johnston KJA, Cote AC, Hicks E, Johnson J, Huckins LM. Genetically Regulated Gene Expression in the Brain Associated With Chronic Pain: Relationships With Clinical Traits and Potential for Drug Repurposing. Biol Psychiatry 2024; 95:745-761. [PMID: 37678542 PMCID: PMC10924073 DOI: 10.1016/j.biopsych.2023.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 07/20/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Chronic pain is a common, poorly understood condition. Genetic studies including genome-wide association studies have identified many relevant variants, which have yet to be translated into full understanding of chronic pain. Transcriptome-wide association studies using transcriptomic imputation methods such as S-PrediXcan can help bridge this genotype-phenotype gap. METHODS We carried out transcriptomic imputation using S-PrediXcan to identify genetically regulated gene expression associated with multisite chronic pain in 13 brain tissues and whole blood. Then, we imputed genetically regulated gene expression for over 31,000 Mount Sinai BioMe participants and performed a phenome-wide association study to investigate clinical relationships in chronic pain-associated gene expression changes. RESULTS We identified 95 experiment-wide significant gene-tissue associations (p < 7.97 × 10-7), including 36 unique genes and an additional 134 gene-tissue associations reaching within-tissue significance, including 53 additional unique genes. Of the 89 unique genes in total, 59 were novel for multisite chronic pain and 18 are established drug targets. Chronic pain genetically regulated gene expression for 10 unique genes was significantly associated with cardiac dysrhythmia, metabolic syndrome, disc disorders/dorsopathies, joint/ligament sprain, anemias, and neurologic disorder phecodes. Phenome-wide association study analyses adjusting for mean pain score showed that associations were not driven by mean pain score. CONCLUSIONS We carried out the largest transcriptomic imputation study of any chronic pain trait to date. Results highlight potential causal genes in chronic pain development and tissue and direction of effect. Several gene results were also drug targets. Phenome-wide association study results showed significant associations for phecodes including cardiac dysrhythmia and metabolic syndrome, thereby indicating potential shared mechanisms.
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Affiliation(s)
- Keira J A Johnston
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| | - Alanna C Cote
- Pamela Sklar Division of Psychiatric Genetics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emily Hicks
- Pamela Sklar Division of Psychiatric Genetics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jessica Johnson
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Laura M Huckins
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
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11
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Xu X, Khunsriraksakul C, Eales JM, Rubin S, Scannali D, Saluja S, Talavera D, Markus H, Wang L, Drzal M, Maan A, Lay AC, Prestes PR, Regan J, Diwadkar AR, Denniff M, Rempega G, Ryszawy J, Król R, Dormer JP, Szulinska M, Walczak M, Antczak A, Matías-García PR, Waldenberger M, Woolf AS, Keavney B, Zukowska-Szczechowska E, Wystrychowski W, Zywiec J, Bogdanski P, Danser AHJ, Samani NJ, Guzik TJ, Morris AP, Liu DJ, Charchar FJ, Tomaszewski M. Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets. Nat Commun 2024; 15:2359. [PMID: 38504097 PMCID: PMC10950894 DOI: 10.1038/s41467-024-46132-y] [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: 07/26/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
Genetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identified 889 kidney genes associated with BP of which 399 were prioritised as contributors to BP regulation. Imputation of kidney proteome and microRNAome uncovered 97 renal proteins and 11 miRNAs associated with BP. Integration with plasma proteomics and metabolomics illuminated circulating levels of myo-inositol, 4-guanidinobutanoate and angiotensinogen as downstream effectors of several kidney BP genes (SLC5A11, AGMAT, AGT, respectively). We showed that genetically determined reduction in renal expression may mimic the effects of rare loss-of-function variants on kidney mRNA/protein and lead to an increase in BP (e.g., ENPEP). We demonstrated a strong correlation (r = 0.81) in expression of protein-coding genes between cells harvested from urine and the kidney highlighting a diagnostic potential of urinary cell transcriptomics. We uncovered adenylyl cyclase activators as a repurposing opportunity for hypertension and illustrated examples of BP-elevating effects of anticancer drugs (e.g. tubulin polymerisation inhibitors). Collectively, our studies provide new biological insights into genetic regulation of BP with potential to drive clinical translation in hypertension.
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Affiliation(s)
- Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | | | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sebastien Rubin
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - David Scannali
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Havell Markus
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Lida Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Maciej Drzal
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Akhlaq Maan
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Abigail C Lay
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Priscilla R Prestes
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Australia
| | - Jeniece Regan
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Avantika R Diwadkar
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Grzegorz Rempega
- Department of Urology, Medical University of Silesia, Katowice, Poland
| | - Jakub Ryszawy
- Department of Urology, Medical University of Silesia, Katowice, Poland
| | - Robert Król
- Department of General, Vascular and Transplant Surgery, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - John P Dormer
- Department of Cellular Pathology, University Hospitals of Leicester, Leicester, UK
| | - Monika Szulinska
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Marta Walczak
- Department of Internal Diseases, Metabolic Disorders and Arterial Hypertension, Poznan University of Medical Sciences, Poznan, Poland
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Pamela R Matías-García
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Center Munich, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Royal Manchester Children's Hospital and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester Royal Infirmary, Manchester, UK
| | | | - Wojciech Wystrychowski
- Department of General, Vascular and Transplant Surgery, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Joanna Zywiec
- Department of Internal Medicine, Diabetology and Nephrology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Bogdanski
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - A H Jan Danser
- Department of Internal Medicine, Division of Pharmacology and Vascular Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Tomasz J Guzik
- Department of Internal Medicine, Jagiellonian University Medical College, Kraków, Poland
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Fadi J Charchar
- Health Innovation and Transformation Centre, Federation University Australia, Ballarat, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- Department of Physiology, University of Melbourne, Melbourne, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester Royal Infirmary, Manchester, UK.
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12
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El-Achkar TM, Eadon MT, Kretzler M, Himmelfarb J. Precision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine Project. Am J Kidney Dis 2024; 83:402-410. [PMID: 37839688 PMCID: PMC10922684 DOI: 10.1053/j.ajkd.2023.08.015] [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: 03/17/2023] [Revised: 08/20/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023]
Abstract
Chronic kidney disease (CKD) and acute kidney injury (AKI) are heterogeneous syndromes defined clinically by serial measures of kidney function. Each condition possesses strong histopathologic associations, including glomerular obsolescence or acute tubular necrosis, respectively. Despite such characterization, there remains wide variation in patient outcomes and treatment responses. Precision medicine efforts, as exemplified by the Kidney Precision Medicine Project (KPMP), have begun to establish evolving, spatially anchored, cellular and molecular atlases of the cell types, states, and niches of the kidney in health and disease. The KPMP atlas provides molecular context for CKD and AKI disease drivers and will help define subtypes of disease that are not readily apparent from canonical functional or histopathologic characterization but instead are appreciable through advanced clinical phenotyping, pathomic, transcriptomic, proteomic, epigenomic, and metabolomic interrogation of kidney biopsy samples. This perspective outlines the structure of the KPMP, its approach to the integration of these diverse datasets, and its major outputs relevant to future patient care.
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Affiliation(s)
- Tarek M El-Achkar
- Division of Nephrology, School of Medicine, Indiana University, and Richard L. Roudebush Veteran Affairs Medical Center, Indianapolis, Indiana
| | - Michael T Eadon
- Division of Nephrology, School of Medicine, Indiana University, and Richard L. Roudebush Veteran Affairs Medical Center, Indianapolis, Indiana
| | - Matthias Kretzler
- Department of Computational Medicine & Bioinformatics, and Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jonathan Himmelfarb
- Kidney Research Institute and Division of Nephrology, University of Washington, Seattle, Washington.
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13
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Guo M, Zhuang Y, Wu Y, Zhang C, Cheng X, Xu D, Zhang Z. The cell fate regulator DACH1 modulates ferroptosis through affecting P53/SLC25A37 signaling in fibrotic disease. Hepatol Commun 2024; 8:e0396. [PMID: 38437058 PMCID: PMC10914241 DOI: 10.1097/hc9.0000000000000396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/11/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Dachshund homolog 1 (DACH1) is widely acknowledged for its involvement in regulating diverse cell fates, but its precise regulatory mechanism in ferroptosis remains elusive. In this study, we investigated whether DACH1 modulates ferroptosis through affecting P53/solute carrier family 25 member 37 (SLC25A37) signaling in hepatic fibrogenesis. METHODS CRISPR-Cas9 system was used to knockout DACH1 in HSC to determine the effect of DACH1 on ferroptosis. Immunoprecipitation, pulldown, and mouse model of hepatic fibrogenesis were used to analyze the potential molecular mechanism of ferroptosis regulation by DACH1. RESULTS We found that ferroptosis inducers increased the protein expression of DACH1 by suppressing the ubiquitin-proteasome signaling. DACH1 knockout can resist ferroptosis, whereas DACH1 knockin can enhance it. Interestingly, the upregulation of DACH1 resulted in the mitochondrial translocation of p53 by inducing phosphorylation at serine 392. The mutation of serine 392 can prevent the combination of DACH1 and p53, the mitochondrial translocation of p53, and DACH1-mediated ferroptosis. Moreover, SLC25A37 was identified as a candidate target for mitochondrial p53. The binding of p53 to SLC25A37 can enhance the iron uptake capacity of SLC25A37, which may cause an overload of iron in the mitochondria and hyperactive mitochondrial electron transport chain. Knockdown of SLC25A37 can impair p53-mediated mitochondrial iron overload and ferroptosis. Furthermore, treatment with erastin can induce HSC ferroptosis and relieve fibrotic lesion damage in the mouse model of hepatic fibrogenesis. HSC-specific knockdown of DACH1, p53, and SLC25A37 can abolish the induction of HSC ferroptosis and reversal of hepatic fibrogenesis by erastin treatment. CONCLUSIONS Our findings suggest that the DACH1/P53/SLC25A37 signaling pathway is a promising target for fibrotic disorders and reveals new regulatory mechanisms of ferroptosis.
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Affiliation(s)
- Mei Guo
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yanshuang Zhuang
- Taizhou Hospital of Traditional Chinese Medicine, Taizhou, China
| | - Yang Wu
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chun Zhang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Xudong Cheng
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Dong Xu
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zili Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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14
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Hu X, Chen S, Ye S, Chen W, Zhou Y. New insights into the role of immunity and inflammation in diabetic kidney disease in the omics era. Front Immunol 2024; 15:1342837. [PMID: 38487541 PMCID: PMC10937589 DOI: 10.3389/fimmu.2024.1342837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 03/17/2024] Open
Abstract
Diabetic kidney disease (DKD) is becoming the leading cause of chronic kidney disease, especially in the industrialized world. Despite mounting evidence has demonstrated that immunity and inflammation are highly involved in the pathogenesis and progression of DKD, the underlying mechanisms remain incompletely understood. Substantial molecules, signaling pathways, and cell types participate in DKD inflammation, by integrating into a complex regulatory network. Most of the studies have focused on individual components, without presenting their importance in the global or system-based processes, which largely hinders clinical translation. Besides, conventional technologies failed to monitor the different behaviors of resident renal cells and immune cells, making it difficult to understand their contributions to inflammation in DKD. Recently, the advancement of omics technologies including genomics, epigenomics, transcriptomics, proteomics, and metabolomics has revolutionized biomedical research, which allows an unbiased global analysis of changes in DNA, RNA, proteins, and metabolites in disease settings, even at single-cell and spatial resolutions. They help us to identify critical regulators of inflammation processes and provide an overview of cell heterogeneity in DKD. This review aims to summarize the application of multiple omics in the field of DKD and emphasize the latest evidence on the interplay of inflammation and DKD revealed by these technologies, which will provide new insights into the role of inflammation in the pathogenesis of DKD and lead to the development of novel therapeutic approaches and diagnostic biomarkers.
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Affiliation(s)
- Xinrong Hu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Sixiu Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Siyang Ye
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Yi Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
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15
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Yamashita N, Kramann R. Mechanisms of kidney fibrosis and routes towards therapy. Trends Endocrinol Metab 2024; 35:31-48. [PMID: 37775469 DOI: 10.1016/j.tem.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023]
Abstract
Kidney fibrosis is the final common pathway of virtually all chronic kidney diseases (CKDs) and is therefore considered to be a promising therapeutic target for these conditions. However, despite great progress in recent years, no targeted antifibrotic therapies for the kidney have been approved, likely because the complex mechanisms that initiate and drive fibrosis are not yet completely understood. Recent single-cell genomic approaches have allowed novel insights into kidney fibrosis mechanisms in mouse and human, particularly the heterogeneity and differentiation processes of myofibroblasts, the role of injured epithelial cells and immune cells, and their crosstalk mechanisms. In this review we summarize the key mechanisms that drive kidney fibrosis, including recent advances in understanding the mechanisms, as well as potential routes for developing novel targeted antifibrotic therapeutics.
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Affiliation(s)
- Noriyuki Yamashita
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rafael Kramann
- Department of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany; Department of Internal Medicine, Nephrology, and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands.
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16
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Schlosser P, Zhang J, Liu H, Surapaneni AL, Rhee EP, Arking DE, Yu B, Boerwinkle E, Welling PA, Chatterjee N, Susztak K, Coresh J, Grams ME. Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage. Genome Biol 2023; 24:150. [PMID: 37365616 DOI: 10.1186/s13059-023-02993-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The pathophysiological causes of kidney disease are not fully understood. Here we show that the integration of genome-wide genetic, transcriptomic, and proteomic association studies can nominate causal determinants of kidney function and damage. RESULTS Through transcriptome-wide association studies (TWAS) in kidney cortex, kidney tubule, liver, and whole blood and proteome-wide association studies (PWAS) in plasma, we assess for effects of 12,893 genes and 1342 proteins on kidney filtration (glomerular filtration rate (GFR) estimated by creatinine; GFR estimated by cystatin C; and blood urea nitrogen) and kidney damage (albuminuria). We find 1561 associations distributed among 260 genomic regions that are supported as putatively causal. We then prioritize 153 of these genomic regions using additional colocalization analyses. Our genome-wide findings are supported by existing knowledge (animal models for MANBA, DACH1, SH3YL1, INHBB), exceed the underlying GWAS signals (28 region-trait combinations without significant GWAS hit), identify independent gene/protein-trait associations within the same genomic region (INHBC, SPRYD4), nominate tissues underlying the associations (tubule expression of NRBP1), and distinguish markers of kidney filtration from those with a role in creatinine and cystatin C metabolism. Furthermore, we follow up on members of the TGF-beta superfamily of proteins and find a prognostic value of INHBC for kidney disease progression even after adjustment for measured glomerular filtration rate (GFR). CONCLUSION In summary, this study combines multimodal, genome-wide association studies to generate a catalog of putatively causal target genes and proteins relevant to kidney function and damage which can guide follow-up studies in physiology, basic science, and clinical medicine.
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Affiliation(s)
- Pascal Schlosser
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Jingning Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongbo Liu
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditya L Surapaneni
- Welch Center for Prevention Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bing Yu
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Paul A Welling
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Katalin Susztak
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Morgan E Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, NY, USA
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17
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Li L, Tian Z, Chen J, Tan Z, Zhang Y, Zhao H, Wu X, Yao X, Wen W, Chen W, Guo L. Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis. Genome Biol 2023; 24:141. [PMID: 37337206 DOI: 10.1186/s13059-023-02984-z] [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: 12/10/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits. RESULTS Using a widely targeted metabolomics analysis in a natural population of 388 B. napus inbred lines, we quantify 2172 metabolites in mature seeds by liquid chromatography mass spectrometry, in which 131 marker metabolites are identified to be correlated with seed oil content. These metabolites are then selected for further metabolite genome-wide association study and metabolite transcriptome-wide association study. Combined with weighted correlation network analysis, we construct a triple relationship network, which includes 21,000 edges and 4384 nodes among metabolites, metabolite quantitative trait loci, genes, and co-expression modules. We validate the function of BnaA03.TT4, BnaC02.TT4, and BnaC05.UK, three candidate genes predicted by multi-omics analysis, which show significant impacts on seed oil content through regulating flavonoid metabolism in B. napus. CONCLUSIONS This study demonstrates the advantage of utilizing marker metabolites integrated with multi-omics analysis to dissect the genetic basis of agronomic traits in crops.
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Affiliation(s)
- Long Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaowei Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Pregizer S, Vreven T, Mathur M, Robinson LN. Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development. Front Mol Biosci 2023; 10:1176856. [PMID: 37091871 PMCID: PMC10113659 DOI: 10.3389/fmolb.2023.1176856] [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: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
Single cell sequencing technologies have rapidly advanced in the last decade and are increasingly applied to gain unprecedented insights by deconstructing complex biology to its fundamental unit, the individual cell. First developed for measurement of gene expression, single cell sequencing approaches have evolved to allow simultaneous profiling of multiple additional features, including chromatin accessibility within the nucleus and protein expression at the cell surface. These multi-omic approaches can now further be applied to cells in situ, capturing the spatial context within which their biology occurs. To extract insights from these complex datasets, new computational tools have facilitated the integration of information across different data types and the use of machine learning approaches. Here, we summarize current experimental and computational methods for generation and integration of single cell multi-omic datasets. We focus on opportunities for multi-omic single cell sequencing to augment therapeutic development for kidney disease, including applications for biomarkers, disease stratification and target identification.
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19
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Huang R, Fu P, Ma L. Kidney fibrosis: from mechanisms to therapeutic medicines. Signal Transduct Target Ther 2023; 8:129. [PMID: 36932062 PMCID: PMC10023808 DOI: 10.1038/s41392-023-01379-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023] Open
Abstract
Chronic kidney disease (CKD) is estimated to affect 10-14% of global population. Kidney fibrosis, characterized by excessive extracellular matrix deposition leading to scarring, is a hallmark manifestation in different progressive CKD; However, at present no antifibrotic therapies against CKD exist. Kidney fibrosis is identified by tubule atrophy, interstitial chronic inflammation and fibrogenesis, glomerulosclerosis, and vascular rarefaction. Fibrotic niche, where organ fibrosis initiates, is a complex interplay between injured parenchyma (like tubular cells) and multiple non-parenchymal cell lineages (immune and mesenchymal cells) located spatially within scarring areas. Although the mechanisms of kidney fibrosis are complicated due to the kinds of cells involved, with the help of single-cell technology, many key questions have been explored, such as what kind of renal tubules are profibrotic, where myofibroblasts originate, which immune cells are involved, and how cells communicate with each other. In addition, genetics and epigenetics are deeper mechanisms that regulate kidney fibrosis. And the reversible nature of epigenetic changes including DNA methylation, RNA interference, and chromatin remodeling, gives an opportunity to stop or reverse kidney fibrosis by therapeutic strategies. More marketed (e.g., RAS blockage, SGLT2 inhibitors) have been developed to delay CKD progression in recent years. Furthermore, a better understanding of renal fibrosis is also favored to discover biomarkers of fibrotic injury. In the review, we update recent advances in the mechanism of renal fibrosis and summarize novel biomarkers and antifibrotic treatment for CKD.
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Affiliation(s)
- Rongshuang Huang
- Kidney Research Institute, Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Fu
- Kidney Research Institute, Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Liang Ma
- Kidney Research Institute, Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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20
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Doke T, Mukherjee S, Mukhi D, Dhillon P, Abedini A, Davis JG, Chellappa K, Chen B, Baur JA, Susztak K. NAD + precursor supplementation prevents mtRNA/RIG-I-dependent inflammation during kidney injury. Nat Metab 2023; 5:414-430. [PMID: 36914909 PMCID: PMC10230446 DOI: 10.1038/s42255-023-00761-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 02/09/2023] [Indexed: 03/16/2023]
Abstract
Our understanding of how global changes in cellular metabolism contribute to human kidney disease remains incompletely understood. Here we show that nicotinamide adenine dinucleotide (NAD+) deficiency drives mitochondrial dysfunction causing inflammation and kidney disease development. Using unbiased global metabolomics in healthy and diseased human kidneys, we identify NAD+ deficiency as a disease signature. Furthermore using models of cisplatin- or ischaemia-reperfusion induced kidney injury in male mice we observed NAD+ depletion Supplemental nicotinamide riboside or nicotinamide mononucleotide restores NAD+ levels and improved kidney function. We find that cisplatin exposure causes cytosolic leakage of mitochondrial RNA (mtRNA) and activation of the cytosolic pattern recognition receptor retinoic acid-inducible gene I (RIG-I), both of which can be ameliorated by restoring NAD+. Male mice with RIG-I knock-out (KO) are protected from cisplatin-induced kidney disease. In summary, we demonstrate that the cytosolic release of mtRNA and RIG-I activation is an NAD+-sensitive mechanism contributing to kidney disease.
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Affiliation(s)
- Tomohito Doke
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarmistha Mukherjee
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dhanunjay Mukhi
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Poonam Dhillon
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Amin Abedini
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - James G Davis
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karthikeyani Chellappa
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beishan Chen
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A Baur
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.
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21
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Tsao CW, Aday AW, Almarzooq ZI, Anderson CAM, Arora P, Avery CL, Baker-Smith CM, Beaton AZ, Boehme AK, Buxton AE, Commodore-Mensah Y, Elkind MSV, Evenson KR, Eze-Nliam C, Fugar S, Generoso G, Heard DG, Hiremath S, Ho JE, Kalani R, Kazi DS, Ko D, Levine DA, Liu J, Ma J, Magnani JW, Michos ED, Mussolino ME, Navaneethan SD, Parikh NI, Poudel R, Rezk-Hanna M, Roth GA, Shah NS, St-Onge MP, Thacker EL, Virani SS, Voeks JH, Wang NY, Wong ND, Wong SS, Yaffe K, Martin SS. Heart Disease and Stroke Statistics-2023 Update: A Report From the American Heart Association. Circulation 2023; 147:e93-e621. [PMID: 36695182 DOI: 10.1161/cir.0000000000001123] [Citation(s) in RCA: 1209] [Impact Index Per Article: 1209.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The American Heart Association, in conjunction with the National Institutes of Health, annually reports the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, diet, and weight) and health factors (cholesterol, blood pressure, and glucose control) that contribute to cardiovascular health. The Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, congenital heart disease, rhythm disorders, subclinical atherosclerosis, coronary heart disease, heart failure, valvular disease, venous disease, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs). METHODS The American Heart Association, through its Epidemiology and Prevention Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States to provide the most current information available in the annual Statistical Update with review of published literature through the year before writing. The 2023 Statistical Update is the product of a full year's worth of effort in 2022 by dedicated volunteer clinicians and scientists, committed government professionals, and American Heart Association staff members. The American Heart Association strives to further understand and help heal health problems inflicted by structural racism, a public health crisis that can significantly damage physical and mental health and perpetuate disparities in access to health care, education, income, housing, and several other factors vital to healthy lives. This year's edition includes additional COVID-19 (coronavirus disease 2019) publications, as well as data on the monitoring and benefits of cardiovascular health in the population, with an enhanced focus on health equity across several key domains. RESULTS Each of the chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics. CONCLUSIONS The Statistical Update represents a critical resource for the lay public, policymakers, media professionals, clinicians, health care administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.
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22
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Zhu S, Li W, Zhang H, Yan Y, Mei Q, Wu K. Retinal determination gene networks: from biological functions to therapeutic strategies. Biomark Res 2023; 11:18. [PMID: 36750914 PMCID: PMC9906957 DOI: 10.1186/s40364-023-00459-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
The retinal determinant gene network (RDGN), originally discovered as a critical determinator in Drosophila eye specification, has become an important regulatory network in tumorigenesis and progression, as well as organogenesis. This network is not only associated with malignant biological behaviors of tumors, such as proliferation, and invasion, but also regulates the development of multiple mammalian organs. Three members of this conservative network have been extensively investigated, including DACH, SIX, and EYA. Dysregulated RDGN signaling is associated with the initiation and progression of tumors. In recent years, it has been found that the members of this network can be used as prognostic markers for cancer patients. Moreover, they are considered to be potential therapeutic targets for cancer. Here, we summarize the research progress of RDGN members from biological functions to signaling transduction, especially emphasizing their effects on tumors. Additionally, we discuss the roles of RDGN members in the development of organs and tissue as well as their correlations with the pathogenesis of chronic kidney disease and coronary heart disease. By summarizing the roles of RDGN members in human diseases, we hope to promote future investigations into RDGN and provide potential therapeutic strategies for patients.
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Affiliation(s)
- Shuangli Zhu
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Wanling Li
- grid.412793.a0000 0004 1799 5032Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,grid.470966.aCancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032 China
| | - Hao Zhang
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Yuheng Yan
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Qi Mei
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China.
| | - Kongming Wu
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China. .,Cancer Center, Tongji hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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23
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Lu Y, Tang K, Wang S, Tian Z, Fan Y, Li B, Wang M, Zhao J, Xie J. Dach1 deficiency drives alveolar epithelium apoptosis in pulmonary fibrosis via modulating C-Jun/Bim activity. Transl Res 2023; 257:54-65. [PMID: 36754276 DOI: 10.1016/j.trsl.2023.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/10/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023]
Abstract
Dysregulation of type II alveolar epithelial cells (AECII) plays a vital role in the initiation and development of pulmonary fibrosis (PF). Dachshund homolog 1 (Dach1), frequently expressed in epithelial cells with stem cell potential, controls cell proliferation, apoptosis, and cell cycle in tissue development and disease process. In this study, we demonstrated that the lungs collected from PF patients and mice of Bleomycin (BLM)-treated were characterized by low expression of Dachshund homolog 1 (Dach1), especially in AECII. Dach1 deficiency in the alveolar epithelium exacerbated PF in BLM-treated mice, as evidenced by reduced pulmonary function and increased expression of fibrosis markers. Rather, treatment with lung-specific overexpression of Dach1 alleviated histopathological damage, lung compliance, and fibrosis in BLM-treated mice. Moreover, overexpression of Dach1 could inhibit epithelial apoptosis in vitro. Conversely, primary AECII with Dach1 depletion were more susceptible to apoptosis in vivo. Mechanically, Dach1 combined with C-Jun protooncogene selectively bound to the promoter of B-cell lymphoma 2 interacting mediators of cell death (Bim), by which it repressed Bim expression and alleviated epithelial apoptosis. Taken together, our data support that Dach1 in AECII contributes to the progression of PF and may be a viable target for the prevention and treatment of PF.
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Affiliation(s)
- Yanjiao Lu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kum Tang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shanshan Wang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhen Tian
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yan Fan
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Boyu Li
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meijia Wang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianping Zhao
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Jungang Xie
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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24
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Rayego-Mateos S, Rodrigues-Diez RR, Fernandez-Fernandez B, Mora-Fernández C, Marchant V, Donate-Correa J, Navarro-González JF, Ortiz A, Ruiz-Ortega M. Targeting inflammation to treat diabetic kidney disease: the road to 2030. Kidney Int 2023; 103:282-296. [PMID: 36470394 DOI: 10.1016/j.kint.2022.10.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 12/07/2022]
Abstract
Diabetic kidney disease (DKD) is one of the fastest growing causes of chronic kidney disease and associated morbidity and mortality. Preclinical research has demonstrated the involvement of inflammation in its pathogenesis and in the progression of kidney damage, supporting clinical trials designed to explore anti-inflammatory strategies. However, the recent success of sodium-glucose cotransporter-2 inhibitors and the nonsteroidal mineralocorticoid receptor antagonist finerenone has changed both guidelines and standard of care, rendering obsolete older studies directly targeting inflammatory mediators and the clinical development was discontinued for most anti-inflammatory drugs undergoing clinical trials for DKD in 2016. Given the contribution of inflammation to the pathogenesis of DKD, we review the impact on kidney inflammation of the current standard of care, therapies undergoing clinical trials, or repositioned drugs for DKD. Moreover, we review recent advances in the molecular regulation of inflammation in DKD and discuss potential novel therapeutic strategies with clinical relevance. Finally, we provide a road map for future research aimed at integrating the growing knowledge on inflammation and DKD into clinical practice to foster improvement of patient outcomes.
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Affiliation(s)
- Sandra Rayego-Mateos
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma, Madrid, Spain; Ricord2040, Instituto de Salud Carlos II, Spain
| | - Raul R Rodrigues-Diez
- Ricord2040, Instituto de Salud Carlos II, Spain; Translational Immunology, Instituto de Investigación Sanitaria del Principado de Asturias ISPA, Oviedo, Asturias, Spain
| | - Beatriz Fernandez-Fernandez
- Ricord2040, Instituto de Salud Carlos II, Spain; Division of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz-Universidad Autónoma, Madrid, Spain
| | - Carmen Mora-Fernández
- Ricord2040, Instituto de Salud Carlos II, Spain; Research Unit, University Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Vanessa Marchant
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma, Madrid, Spain; Ricord2040, Instituto de Salud Carlos II, Spain
| | - Javier Donate-Correa
- Ricord2040, Instituto de Salud Carlos II, Spain; Research Unit, University Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Juan F Navarro-González
- Ricord2040, Instituto de Salud Carlos II, Spain; Research Unit, University Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; Nephrology Service, University Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Alberto Ortiz
- Ricord2040, Instituto de Salud Carlos II, Spain; Division of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz-Universidad Autónoma, Madrid, Spain
| | - Marta Ruiz-Ortega
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma, Madrid, Spain; Ricord2040, Instituto de Salud Carlos II, Spain.
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25
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Lyle SM, Ahmed S, Elliott JE, Stener-Victorin E, Nachtigal MW, Drögemöller BI. Transcriptome-wide association analyses identify an association between ARL14EP and polycystic ovary syndrome. J Hum Genet 2023; 68:347-353. [PMID: 36720993 DOI: 10.1038/s10038-023-01120-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 02/02/2023]
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrine disorder, which is accompanied by a variety of comorbidities including metabolic, reproductive, and psychiatric disorders. Genome-wide association studies have identified several genetic variants that are associated with PCOS. However, these variants often occur outside of coding regions and require further investigation to understand their contribution to PCOS. A transcriptome-wide association study (TWAS) was performed to uncover heritable gene expression profiles that are associated with PCOS in two independent cohorts. Causal gene prioritization was subsequently performed and expression of genes prioritized through these analyses was examined in 49 PCOS patients and 30 controls. TWAS analyses revealed that increased expression of ARL14EP was significantly associated with PCOS risk in the discovery (P = 1.6 × 10-6) and replication cohorts (P = 2.0 × 10-13). Gene prioritization pipelines provided further evidence that ARL14EP is the most likely causal gene at this locus. ARL14EP gene expression was shown to be significantly different between PCOS cases and controls, after adjusting for body mass index, age and testosterone levels (P = 1.2 × 10-13). This study has provided evidence for the role of ARL14EP in PCOS. Given that ARL14EP has been reported to play an important role in chromatin remodeling, variants affecting the expression of ARL14EP may also affect the expression of other genes that contribute to PCOS pathogenesis.
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Affiliation(s)
- Sarah M Lyle
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Samah Ahmed
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jason E Elliott
- Department of Obstetrics, Gynecology and Reproductive Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | | | - Mark W Nachtigal
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Obstetrics, Gynecology and Reproductive Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada. .,Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada. .,CancerCare Manitoba Research Institute, Winnipeg, MB, Canada.
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26
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Zhou XJ, Zhong XH, Duan LX. Integration of artificial intelligence and multi-omics in kidney diseases. FUNDAMENTAL RESEARCH 2023; 3:126-148. [PMID: 38933564 PMCID: PMC11197676 DOI: 10.1016/j.fmre.2022.01.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 10/18/2022] Open
Abstract
Kidney disease is a leading cause of death worldwide. Currently, the diagnosis of kidney diseases and the grading of their severity are mainly based on clinical features, which do not reveal the underlying molecular pathways. More recent surge of ∼omics studies has greatly catalyzed disease research. The advent of artificial intelligence (AI) has opened the avenue for the efficient integration and interpretation of big datasets for discovering clinically actionable knowledge. This review discusses how AI and multi-omics can be applied and integrated, to offer opportunities to develop novel diagnostic and therapeutic means in kidney diseases. The combination of new technology and novel analysis pipelines can lead to breakthroughs in expanding our understanding of disease pathogenesis, shedding new light on biomarkers and disease classification, as well as providing possibilities of precise treatment.
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Affiliation(s)
- Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Beijing 100034, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing 100034, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing 100034, China
| | - Xu-Hui Zhong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Li-Xin Duan
- The Big Data Research Center, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
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27
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Xia J, Hou Y, Cai A, Xu Y, Yang W, Huang M, Mou S. An integrated co-expression network analysis reveals novel genetic biomarkers for immune cell infiltration in chronic kidney disease. Front Immunol 2023; 14:1129524. [PMID: 36875100 PMCID: PMC9981626 DOI: 10.3389/fimmu.2023.1129524] [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: 12/22/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Background Chronic kidney disease (CKD) is characterized by persistent damage to kidney function or structure. Progression to end-stage leads to adverse effects on multiple systems. However, owing to its complex etiology and long-term cause, the molecular basis of CKD is not completely known. Methods To dissect the potential important molecules during the progression, based on CKD databases from Gene Expression Omnibus, we used weighted gene co-expression network analysis (WGCNA) to identify the key genes in kidney tissues and peripheral blood mononuclear cells (PBMC). Correlation analysis of these genes with clinical relevance was evaluated based on Nephroseq. Combined with a validation cohort and receiver operating characteristic curve (ROC), we found the candidate biomarkers. The immune cell infiltration of these biomarkers was evaluated. The expression of these biomarkers was further detected in folic acid-induced nephropathy (FAN) murine model and immunohistochemical staining. Results In total, eight genes (CDCP1, CORO1C, DACH1, GSTA4, MAFB, TCF21, TGFBR3, and TGIF1) in kidney tissue and six genes (DDX17, KLF11, MAN1C1, POLR2K, ST14, and TRIM66) in PBMC were screened from co-expression network. Correlation analysis of these genes with serum creatinine levels and estimated glomerular filtration rate from Nephroseq showed a well clinical relevance. Validation cohort and ROC identified TCF21, DACH1 in kidney tissue and DDX17 in PBMC as biomarkers for the progression of CKD. Immune cell infiltration analysis revealed that DACH1 and TCF21 were correlated with eosinophil, activated CD8 T cell, activated CD4 T cell, while the DDX17 was correlated with neutrophil, type-2 T helper cell, type-1 T helper cell, mast cell, etc. FAN murine model and immunohistochemical staining confirmed that these three molecules can be used as genetic biomarkers to distinguish CKD patients from healthy people. Moreover, the increase of TCF21 in kidney tubules might play important role in the CKD progression. Discussion We identified three promising genetic biomarkers which could play important roles in the progression of CKD.
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Affiliation(s)
- Jia Xia
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yutong Hou
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Anxiang Cai
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingjie Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Masha Huang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Mou
- Department of Nephrology, Molecular Cell Lab for Kidney Disease, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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28
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Liu Z, Li H, Dang Q, Weng S, Duo M, Lv J, Han X. Integrative insights and clinical applications of single-cell sequencing in cancer immunotherapy. Cell Mol Life Sci 2022; 79:577. [DOI: 10.1007/s00018-022-04608-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/03/2022]
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29
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Doke T, Susztak K. The multifaceted role of kidney tubule mitochondrial dysfunction in kidney disease development. Trends Cell Biol 2022; 32:841-853. [PMID: 35473814 PMCID: PMC9464682 DOI: 10.1016/j.tcb.2022.03.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022]
Abstract
More than 800 million people suffer from kidney disease. Genetic studies and follow-up animal models and cell biological experiments indicate the key role of proximal tubule metabolism. Kidneys have one of the highest mitochondrial densities. Mitochondrial biogenesis, mitochondrial fusion and fission, and mitochondrial recycling, such as mitophagy are critical for proper mitochondrial function. Mitochondrial dysfunction can lead to an energetic crisis, orchestrate different types of cell death (apoptosis, necroptosis, pyroptosis, and ferroptosis), and influence cellular calcium levels and redox status. Collectively, mitochondrial defects in renal tubules contribute to epithelial atrophy, inflammation, or cell death, orchestrating kidney disease development.
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Affiliation(s)
- Tomohito Doke
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
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30
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Wilson PC, Muto Y, Wu H, Karihaloo A, Waikar SS, Humphreys BD. Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression. Nat Commun 2022; 13:5253. [PMID: 36068241 PMCID: PMC9448792 DOI: 10.1038/s41467-022-32972-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
The proximal tubule is a key regulator of kidney function and glucose metabolism. Diabetic kidney disease leads to proximal tubule injury and changes in chromatin accessibility that modify the activity of transcription factors involved in glucose metabolism and inflammation. Here we use single nucleus RNA and ATAC sequencing to show that diabetic kidney disease leads to reduced accessibility of glucocorticoid receptor binding sites and an injury-associated expression signature in the proximal tubule. We hypothesize that chromatin accessibility is regulated by genetic background and closely-intertwined with metabolic memory, which pre-programs the proximal tubule to respond differently to external stimuli. Glucocorticoid excess has long been known to increase risk for type 2 diabetes, which raises the possibility that glucocorticoid receptor inhibition may mitigate the adverse metabolic effects of diabetic kidney disease.
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Affiliation(s)
- Parker C Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Anil Karihaloo
- Novo Nordisk Research Center Seattle Inc, Seattle, WA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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31
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Tomaszewski M, Morris AP, Howson JMM, Franceschini N, Eales JM, Xu X, Dikalov S, Guzik TJ, Humphreys BD, Harrap S, Charchar FJ. Kidney omics in hypertension: from statistical associations to biological mechanisms and clinical applications. Kidney Int 2022; 102:492-505. [PMID: 35690124 PMCID: PMC9886011 DOI: 10.1016/j.kint.2022.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/10/2022] [Accepted: 04/22/2022] [Indexed: 02/06/2023]
Abstract
Hypertension is a major cardiovascular disease risk factor and contributor to premature death globally. Family-based investigations confirmed a significant heritable component of blood pressure (BP), whereas genome-wide association studies revealed >1000 common and rare genetic variants associated with BP and/or hypertension. The kidney is not only an organ of key relevance to BP regulation and the development of hypertension, but it also acts as the tissue mediator of genetic predisposition to hypertension. The identity of kidney genes, pathways, and related mechanisms underlying the genetic associations with BP has started to emerge through integration of genomics with kidney transcriptomics, epigenomics, and other omics as well as through applications of causal inference, such as Mendelian randomization. Single-cell methods further enabled mapping of BP-associated kidney genes to cell types, and in conjunction with other omics, started to illuminate the biological mechanisms underpinning associations of BP-associated genetic variants and kidney genes. Polygenic risk scores derived from genome-wide association studies and refined on kidney omics hold the promise of enhanced diagnostic prediction, whereas kidney omics-informed drug discovery is likely to contribute new therapeutic opportunities for hypertension and hypertension-mediated kidney damage.
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Affiliation(s)
- Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK; Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, UK
| | - Joanna M M Howson
- Department of Genetics, Novo Nordisk Research Centre Oxford, Novo Nordisk Ltd, Oxford, UK
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sergey Dikalov
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK; Department of Internal and Agricultural Medicine, Jagiellonian University College of Medicine, Kraków, Poland
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Stephen Harrap
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Fadi J Charchar
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia; Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
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32
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Zhuo WQ, Wen Y, Luo HJ, Luo ZL, Wang L. Mechanisms of ferroptosis in chronic kidney disease. Front Mol Biosci 2022; 9:975582. [PMID: 36090053 PMCID: PMC9448928 DOI: 10.3389/fmolb.2022.975582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Ferroptosis is a newly identified form of regulated cell death characterized by iron accumulation and lipid peroxidation. Ferroptosis plays an essential role in the pathology of numerous diseases and has emerged as a key area of focus in studies of chronic kidney disease (CKD). CKD is a major public health problem with high incidence and mortality that is characterized by a gradual loss of kidney function over time. The severity and complexity of CKD combined with the limited knowledge of its underlying molecular mechanism(s) have led to increased interest in this disease area. Here, we summarize recent advances in our understanding of the regulatory mechanism(s) of ferroptosis and highlight recent studies describing its role in the pathogenesis and progression of CKD. We further discuss the potential therapeutic benefits of targeting ferroptosis for the treatment of CKD and the major hurdles to overcome for the translation of in vitro studies into the clinic.
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Affiliation(s)
- Wen-Qing Zhuo
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Yi Wen
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command (Chengdu Military General Hospital), Chengdu, Sichuan, China
| | - Hui-Jun Luo
- Department of Biochemistry and Molecular Biology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Zhu-Lin Luo
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command (Chengdu Military General Hospital), Chengdu, Sichuan, China
- *Correspondence: Zhu-Lin Luo, ; Li Wang,
| | - Li Wang
- Department of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Zhu-Lin Luo, ; Li Wang,
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33
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Mohammadi-Shemirani P, Chong M, Perrot N, Pigeyre M, Steinberg GR, Paré G, Krepinsky JC, Lanktree MB. ACLY and CKD: A Mendelian Randomization Analysis. Kidney Int Rep 2022; 7:1673-1681. [PMID: 35812273 PMCID: PMC9263230 DOI: 10.1016/j.ekir.2022.04.013] [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: 03/08/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Introduction Adenosine triphosphate-citrate lyase (ACLY) inhibition is a therapeutic strategy under investigation for atherosclerotic cardiovascular disease, nonalcoholic steatohepatitis, and metabolic syndrome. Mouse models suggest that ACLY inhibition could reduce inflammation and kidney fibrosis. Genetic analysis of ACLY in chronic kidney disease (CKD) has not been performed. Methods We constructed a genetic instrument by selecting variants associated with ACLY expression in the expression quantitative trait loci genetics consortium (eQTLGen) from blood samples from 31,684 participants. In a 2-sample Mendelian randomization analysis, we evaluated the effect of genetically predicted ACLY expression on the risk of CKD, estimated glomerular filtration rate (eGFR), and albumin-to-creatinine ratio (ACR) using the CKD Genetics (CKDGen) consortium, UK Biobank, and the Finnish Genetics (FinnGen) consortium totaling 66,396 CKD cases and 958,517 controls. Results ACLY is constitutively expressed in all cell types including in whole blood. The genetic instrument included 13 variants and explained 1.5% of the variation in whole blood ACLY gene expression. A 34% reduction in ACLY expression score was associated with a 0.04 mmol/l reduced low-density lipoprotein (LDL) cholesterol (P = 3.4 × 10-4) and a 9% reduced risk of CKD (stages 3, 4, 5, dialysis, or eGFR < 60 ml/min per 1.73 m2) (odds ratio [OR] = 0.91, 95% CI: 0.85-0.98, P = 0.008), but no association was observed with either eGFR or ACR. Conclusion Mendelian randomization analyses revealed that genetically reduced ACLY expression was associated with reduced risk of CKD but had no effect on either eGFR or ACR. Further evaluation of ACLY in kidney disease is warranted.
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Affiliation(s)
- Pedrum Mohammadi-Shemirani
- Department of Biomarkers and Genetics, Population Health Research Institute, Hamilton, Ontario, Canada.,Experimental Program, Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Medical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Michael Chong
- Department of Biomarkers and Genetics, Population Health Research Institute, Hamilton, Ontario, Canada.,Experimental Program, Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Medical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Nicolas Perrot
- Department of Biomarkers and Genetics, Population Health Research Institute, Hamilton, Ontario, Canada
| | - Marie Pigeyre
- Department of Biomarkers and Genetics, Population Health Research Institute, Hamilton, Ontario, Canada.,Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Gregory R Steinberg
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Centre for Metabolism, Obesity, and Diabetes Research, McMaster University, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Guillaume Paré
- Department of Biomarkers and Genetics, Population Health Research Institute, Hamilton, Ontario, Canada.,Experimental Program, Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, Ontario, Canada
| | - Joan C Krepinsky
- Centre for Metabolism, Obesity, and Diabetes Research, McMaster University, Hamilton, Ontario, Canada.,Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Division of Nephrology, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Matthew B Lanktree
- Department of Biomarkers and Genetics, Population Health Research Institute, Hamilton, Ontario, Canada.,Department of Health Research Methods, Evidence & Impact, McMaster University, Hamilton, Ontario, Canada.,Division of Nephrology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Division of Nephrology, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
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34
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Hill C, Avila-Palencia I, Maxwell AP, Hunter RF, McKnight AJ. Harnessing the Full Potential of Multi-Omic Analyses to Advance the Study and Treatment of Chronic Kidney Disease. FRONTIERS IN NEPHROLOGY 2022; 2:923068. [PMID: 37674991 PMCID: PMC10479694 DOI: 10.3389/fneph.2022.923068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/30/2022] [Indexed: 09/08/2023]
Abstract
Chronic kidney disease (CKD) was the 12th leading cause of death globally in 2017 with the prevalence of CKD estimated at ~9%. Early detection and intervention for CKD may improve patient outcomes, but standard testing approaches even in developed countries do not facilitate identification of patients at high risk of developing CKD, nor those progressing to end-stage kidney disease (ESKD). Recent advances in CKD research are moving towards a more personalised approach for CKD. Heritability for CKD ranges from 30% to 75%, yet identified genetic risk factors account for only a small proportion of the inherited contribution to CKD. More in depth analysis of genomic sequencing data in large cohorts is revealing new genetic risk factors for common diagnoses of CKD and providing novel diagnoses for rare forms of CKD. Multi-omic approaches are now being harnessed to improve our understanding of CKD and explain some of the so-called 'missing heritability'. The most common omic analyses employed for CKD are genomics, epigenomics, transcriptomics, metabolomics, proteomics and phenomics. While each of these omics have been reviewed individually, considering integrated multi-omic analysis offers considerable scope to improve our understanding and treatment of CKD. This narrative review summarises current understanding of multi-omic research alongside recent experimental and analytical approaches, discusses current challenges and future perspectives, and offers new insights for CKD.
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Affiliation(s)
| | | | | | | | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
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35
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Osaki Y, Manolopoulou M, Ivanova AV, Vartanian N, Mignemi MP, Kern J, Chen J, Yang H, Fogo AB, Zhang M, Robinson-Cohen C, Gewin LS. Blocking cell cycle progression through CDK4/6 protects against chronic kidney disease. JCI Insight 2022; 7:e158754. [PMID: 35730565 PMCID: PMC9309053 DOI: 10.1172/jci.insight.158754] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/04/2022] [Indexed: 11/17/2022] Open
Abstract
Acute and chronic kidney injuries induce increased cell cycle progression in renal tubules. While increased cell cycle progression promotes repair after acute injury, the role of ongoing tubular cell cycle progression in chronic kidney disease is unknown. Two weeks after initiation of chronic kidney disease, we blocked cell cycle progression at G1/S phase by using an FDA-approved, selective inhibitor of CDK4/6. Blocking CDK4/6 improved renal function and reduced tubular injury and fibrosis in 2 murine models of chronic kidney disease. However, selective deletion of cyclin D1, which complexes with CDK4/6 to promote cell cycle progression, paradoxically increased tubular injury. Expression quantitative trait loci (eQTLs) for CCND1 (cyclin D1) and the CDK4/6 inhibitor CDKN2B were associated with eGFR in genome-wide association studies. Consistent with the preclinical studies, reduced expression of CDKN2B correlated with lower eGFR values, and higher levels of CCND1 correlated with higher eGFR values. CDK4/6 inhibition promoted tubular cell survival, in part, through a STAT3/IL-1β pathway and was dependent upon on its effects on the cell cycle. Our data challenge the paradigm that tubular cell cycle progression is beneficial in the context of chronic kidney injury. Unlike the reparative role of cell cycle progression following acute kidney injury, these data suggest that blocking cell cycle progression by inhibiting CDK4/6, but not cyclin D1, protects against chronic kidney injury.
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Affiliation(s)
- Yosuke Osaki
- Division of Nephrology and Hypertension, Department of Medicine, Washington University St. Louis, St. Louis, Missouri, USA
- Division of Nephrology and Hypertension, Department of Medicine, and
| | | | - Alla V. Ivanova
- Division of Nephrology and Hypertension, Department of Medicine, and
| | | | | | - Justin Kern
- Division of Nephrology and Hypertension, Department of Medicine, Washington University St. Louis, St. Louis, Missouri, USA
| | - Jianchun Chen
- Division of Nephrology and Hypertension, Department of Medicine, and
| | - Haichun Yang
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee, USA
| | - Agnes B. Fogo
- Division of Nephrology and Hypertension, Department of Medicine, and
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee, USA
| | - Mingzhi Zhang
- Division of Nephrology and Hypertension, Department of Medicine, and
| | | | - Leslie S. Gewin
- Division of Nephrology and Hypertension, Department of Medicine, Washington University St. Louis, St. Louis, Missouri, USA
- Division of Nephrology and Hypertension, Department of Medicine, and
- Department of Medicine, Veterans Affairs Hospital, St. Louis VA, St. Louis, Missouri, USA
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36
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Doke T, Abedini A, Aldridge DL, Yang YW, Park J, Hernandez CM, Balzer MS, Shrestra R, Coppock G, Rico JMI, Han SY, Kim J, Xin S, Piliponsky AM, Angelozzi M, Lefebvre V, Siracusa MC, Hunter CA, Susztak K. Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Nat Immunol 2022; 23:947-959. [PMID: 35552540 DOI: 10.1038/s41590-022-01200-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/01/2022] [Indexed: 02/06/2023]
Abstract
Inflammation is an important component of fibrosis but immune processes that orchestrate kidney fibrosis are not well understood. Here we apply single-cell sequencing to a mouse model of kidney fibrosis. We identify a subset of kidney tubule cells with a profibrotic-inflammatory phenotype characterized by the expression of cytokines and chemokines associated with immune cell recruitment. Receptor-ligand interaction analysis and experimental validation indicate that CXCL1 secreted by profibrotic tubules recruits CXCR2+ basophils. In mice, these basophils are an important source of interleukin-6 and recruitment of the TH17 subset of helper T cells. Genetic deletion or antibody-based depletion of basophils results in reduced renal fibrosis. Human kidney single-cell, bulk gene expression and immunostaining validate a function for basophils in patients with kidney fibrosis. Collectively, these studies identify basophils as contributors to the development of renal fibrosis and suggest that targeting these cells might be a useful clinical strategy to manage chronic kidney disease.
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Affiliation(s)
- Tomohito Doke
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Amin Abedini
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel L Aldridge
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Ya-Wen Yang
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Jihwan Park
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Christina M Hernandez
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Michael S Balzer
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Rojesh Shrestra
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Gaia Coppock
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Juan M Inclan Rico
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Seung Yub Han
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sheng Xin
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Adrian M Piliponsky
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Marco Angelozzi
- Division of Orthopaedic Surgery, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Veronique Lefebvre
- Division of Orthopaedic Surgery, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark C Siracusa
- Center for Immunity and Inflammation, Department of Medicine, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, NJ, USA
| | - Christopher A Hunter
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA.
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37
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Multi-omics studies reveal genes critical for AKI and ferroptosis. Kidney Int 2022; 101:665-667. [DOI: 10.1016/j.kint.2021.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/28/2021] [Indexed: 11/21/2022]
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38
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Abstract
The field of single-cell genomics and spatial technologies is rapidly evolving and has already provided unprecedented insights into complex tissues. Major advances have been made in dissecting the cellular composition and spatiotemporal interactions that mediate developmental processes in the fetal kidney. Single-cell technologies have also provided detailed insights into the heterogeneity of cell types within the healthy adult and shed light on the complex cellular mechanisms that contribute to kidney disease. The in-depth characterization of specific cell types associated with acute kidney injury and glomerular diseases has potential for the development of prognostic biomarkers and new therapeutics. Analyses of pathway activity in clear-cell renal cell carcinoma can predict the sensitivity of tumour cells to specific inhibitors. The identification of the cell of origin of renal cell carcinoma and of new cell types within the tumour microenvironment also has implications for the development of targeted therapeutics. Similarly, single-cell sequencing has provided new insights into the mechanisms underlying kidney fibrosis, specifically our understanding of myofibroblast origins and the contribution of cell crosstalk within the fibrotic niche to disease progression. These and future studies will enable the creation of a map to aid our understanding of the cellular processes and interactions in the developing, healthy and diseased kidney.
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39
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Eadon MT, Dagher PC, El-Achkar TM. Cellular and molecular interrogation of kidney biopsy specimens. Curr Opin Nephrol Hypertens 2022; 31:160-167. [PMID: 34982521 PMCID: PMC8799512 DOI: 10.1097/mnh.0000000000000770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Traditional histopathology of the kidney biopsy specimen has been an essential and successful tool for the diagnosis and staging of kidney diseases. However, it is likely that the full potential of the kidney biopsy has not been tapped so far. Indeed, there is now a concerted worldwide effort to interrogate kidney biopsy samples at the cellular and molecular levels with unprecedented rigor and depth. This review examines these novel approaches to study kidney biopsy specimens and highlights their potential to refine our understanding of the pathophysiology of kidney disease and lead to precision-based diagnosis and therapy. RECENT FINDINGS Several consortia are now active at studying kidney biopsy samples from various patient cohorts with state-of-the art cellular and molecular techniques. These include advanced imaging approaches as well as deep molecular interrogation with tools such as epigenetics, transcriptomics, proteomics and metabolomics. The emphasis throughout is on rigor, reproducibility and quality control. SUMMARY Although these techniques to study kidney biopsies are complementary, each on its own can yield novel ways to define and classify kidney disease. Therefore, great efforts are needed in order to generate an integrated output that can propel the diagnosis and treatment of kidney disease into the realm of precision medicine.
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Affiliation(s)
- Michael T Eadon
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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40
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Hirohama D, Susztak K. From mapping kidney function to mechanism and prediction. Nat Rev Nephrol 2022; 18:76-77. [PMID: 34819631 DOI: 10.1038/s41581-021-00512-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daigoro Hirohama
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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41
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Liu X, Xu H, Zang Y, Liu W, Sun X. Radix Rehmannia Glutinosa inhibits the development of renal fibrosis by regulating miR-122-5p/PKM axis. Am J Transl Res 2022; 14:103-119. [PMID: 35173832 PMCID: PMC8829622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE It is acknowledged that Radix Rehmanniae Praeparata (RR) can regulate hormone metabolism, reduce blood glucose, resist aging, help to sedate patients and promote diuresis. The study aims to investigate the mechanism of how RR influences the development of renal fibrosis by regulating the miR-122-5p/PKM axis. METHODS Unilateral ureteral obstruction (UUO) was applied to induce renal fibrosis in mice in vivo, and human tubular epithelial HK2 cells treated by transforming growth factor-β (TGF-β1) were used to induce renal fibrosis in vitro. Interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α) in mouse serum were detected by Enzyme-linked immunosorbent assay (ELISA); fibronectin (FN) and type I collagen (Col-I) in renal tissue were detected by Western blotting; serum creatinine (Cr) and blood urea nitrogen (BUN) were analyzed by kits. Hematoxylin-eosin (HE) staining and Masson staining were utilized to assess the degree of pathological damage and fibrosis. Cell viability and apoptosis in the in vitro model were detected by MTT and Flow cytometry. Dual-luciferase reporter assay was performed to determine intermolecular targeting relationships. RESULTS RR could inhibit IL-6 and TNF-α levels, decrease the levels of FN and Col-I and improve the renal function indexes (serum Cr and BUN) in UUO mice (all P<0.05). In addition, RR was able to promote the up-regulation of miR-122-5p expression in UUO mice in vivo (P<0.05). MiR-122-5p expression was down-regulated and PKM expression was up-regulated in HK2 cells treated with TGF-β1 (all P<0.05). RR inhibited renal fibrosis progression by regulating the miR-122-5p/PKM axis. Inhibition of miR-122-5p or overexpression of PKM could promote apoptosis of TGF-β1-treated HK2 cells, inhibit their viability, aggravate fibrosis, and attenuate the protective effect of RR on the cells. The protective effect of RR promoted by overexpression of miR-122-5p was partially counteracted by PKM. CONCLUSION RR can inhibit renal fibrosis progression by regulating the miR-122-5p/PKM axis.
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Affiliation(s)
- Xinhua Liu
- Department of Nephrology, Hiser Medical Center of QingdaoQingdao 266000, Shandong Province, China
| | - Honglan Xu
- Department of Nephrology, Qingdao Municipal HospitalQingdao 266011, Shandong Province, China
| | - Yunhua Zang
- Department of Neurology, Hiser Medical Center of QingdaoQingdao 266000, Shandong Province, China
| | - Weiguo Liu
- Department of Orthopedics and Traumatology, Hiser Medical Center of QingdaoQingdao 266000, Shandong Province, China
| | - Xiangbo Sun
- Department of Nephrology, Hiser Medical Center of QingdaoQingdao 266000, Shandong Province, China
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42
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Little MH, Humphreys BD. Regrow or Repair: An Update on Potential Regenerative Therapies for the Kidney. J Am Soc Nephrol 2022; 33:15-32. [PMID: 34789545 PMCID: PMC8763179 DOI: 10.1681/asn.2021081073] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fifteen years ago, this journal published a review outlining future options for regenerating the kidney. At that time, stem cell populations were being identified in multiple tissues, the concept of stem cell recruitment to a site of injury was of great interest, and the possibility of postnatal renal stem cells was growing in momentum. Since that time, we have seen the advent of human induced pluripotent stem cells, substantial advances in our capacity to both sequence and edit the genome, global and spatial transcriptional analysis down to the single-cell level, and a pandemic that has challenged our delivery of health care to all. This article will look back over this period of time to see how our view of kidney development, disease, repair, and regeneration has changed and envision a future for kidney regeneration and repair over the next 15 years.
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Affiliation(s)
- Melissa H. Little
- Murdoch Children’s Research Institute, Parkville, Melbourne, Victoria, Australia,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Melbourne, Victoria, Australia,Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, Missouri
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Ghasemi S, Becker T, Grabe HJ, Teumer A. Discovery of novel eGFR-associated multiple independent signals using a quasi-adaptive method. Front Genet 2022; 13:997302. [PMID: 36386835 PMCID: PMC9660290 DOI: 10.3389/fgene.2022.997302] [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: 07/18/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
A decreased estimated glomerular filtration rate (eGFR) leading to chronic kidney disease is a significant public health problem. Kidney function is a heritable trait, and recent application of genome-wide association studies (GWAS) successfully identified multiple eGFR-associated genetic loci. To increase statistical power for detecting independent associations in GWAS loci, we improved our recently developed quasi-adaptive method estimating SNP-specific alpha levels for the conditional analysis, and applied it to the GWAS meta-analysis results of eGFR among 783,978 European-ancestry individuals. Among known eGFR loci, we revealed 19 new independent association signals that were subsequently replicated in the United Kingdom Biobank (n = 408,608). These associations have remained undetected by conditional analysis using the established conservative genome-wide significance level of 5 × 10-8. Functional characterization of known index SNPs and novel independent signals using colocalization of conditional eGFR association results and gene expression in cis across 51 human tissues identified two potentially causal genes across kidney tissues: TSPAN33 and TFDP2, and three candidate genes across other tissues: SLC22A2, LRP2, and CDKN1C. These colocalizations were not identified in the original GWAS. By applying our improved quasi-adaptive method, we successfully identified additional genetic variants associated with eGFR. Considering these signals in colocalization analyses can increase the precision of revealing potentially functional genes of GWAS loci.
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Affiliation(s)
- Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.,Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Tim Becker
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.,German Center for Neurodegenerative Diseases DZNE, Site Rostock/Greifswald, Greifswald, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
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Shintani A, Fukai S, Nobusawa R, Taniguchi K, Hatatani T, Nagai H, Sakai T, Yoshimura T, Miyasaka M, Hayasaka H. Dach1 transcription factor regulates the expression of peripheral node addressin and lymphocyte trafficking in lymph nodes. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:175-185. [PMID: 36045707 PMCID: PMC9421177 DOI: 10.1016/j.crimmu.2022.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/01/2022] Open
Abstract
Lymphocytes regulate the immune response by circulating between the vascular and lymphatic systems. High endothelial venules, HEVs, special blood vessels expressing selective adhesion molecules, such as PNAd and MAdCAM-1, mediate naïve lymphocyte migration from the vasculature into the lymph nodes and Peyer's patches. We have identified that DACH1 is abundantly expressed in developing HEV-type endothelial cells. DACH1 showed a restricted expression pattern in lymph node blood vessels during the late fetal and early neonatal periods, corresponding to HEV development. The proportion of MAdCAM-1+ and CD34+ endothelial cells is reduced in the lymph nodes of neonatal conventional and vascular-specific Dach1-deficient mice. Dach1-deficient lymph nodes in adult mice demonstrated a lower proportion of PNAd+ cells and lower recruitment of intravenously administered lymphocytes from GFP transgenic mice. These findings suggest that DACH1 promotes the expression of HEV-selective adhesion molecules and mediates lymphocyte trafficking across HEVs into lymph nodes. The high endothelial venules, HEVs, develop in a tissue-specific manner and permit lymphocyte trafficking. The transcription factor DACH1 exhibit a restricted expression pattern in the blood vessels of developing lymph nodes. The blood vessel-specific Dach1-deficient lymph nodes exhibit a reduced proportion of HEVs and lymphocyte recruitment.
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45
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Claussnitzer M, Susztak K. Gaining insight into metabolic diseases from human genetic discoveries. Trends Genet 2021; 37:1081-1094. [PMID: 34315631 PMCID: PMC8578350 DOI: 10.1016/j.tig.2021.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022]
Abstract
Human large-scale genetic association studies have identified sequence variations at thousands of genetic risk loci that are more common in patients with diverse metabolic disease compared with healthy controls. While these genetic associations have been replicated in multiple large cohorts and sometimes can explain up to 50% of heritability, the molecular and cellular mechanisms affected by common genetic variation associated with metabolic disease remains mostly unknown. A variety of new genome-wide data types, in conjunction with novel biostatistical and computational analytical methodologies and foundational experimental technologies, are paving the way for a principled approach to systematic variant-to-function (V2F) studies for metabolic diseases, turning associated regions into causal variants, cell types and states of action, effector genes, and cellular and physiological mechanisms. Identification of new target genes and cellular programs for metabolic risk loci will improve mechanistic understanding of disease biology and identification of novel therapeutic strategies.
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Affiliation(s)
- Melina Claussnitzer
- Beth Israel Deaconess Medical Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Katalin Susztak
- Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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46
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Doke T, Huang S, Qiu C, Sheng X, Seasock M, Liu H, Ma Z, Palmer M, Susztak K. Genome-wide association studies identify the role of caspase-9 in kidney disease. SCIENCE ADVANCES 2021; 7:eabi8051. [PMID: 34739325 PMCID: PMC8570608 DOI: 10.1126/sciadv.abi8051] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic risk regions for kidney dysfunction [estimated glomerular filtration rate (eGFR)]; however, the causal genes, cell types, and pathways are poorly understood. Integration of GWAS and human kidney expression of quantitative trait analysis using Bayesian colocations, transcriptome-wide association studies, and summary-based Mendelian randomization studies prioritized caspase-9 (CASP9) as a kidney disease risk gene. Human kidney single-cell epigenetic and immunostaining studies indicated kidney tubule cells as a disease-causing cell type. Mice with genetic deletion or pharmacological inhibition of CASP9 showed lower apoptosis while having improved mitophagy, resulting in dampened activation of cytosolic nucleotide sensing pathways (cGAS-STING), reduction of inflammation, and protection from acute kidney disease or renal fibrosis. In summary, here, we prioritized CASP9 as an eGFR GWAS target gene and demonstrated the causal role of CASP9 in kidney disease development via improving mitophagy and lowering inflammation and apoptosis.
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Affiliation(s)
- Tomohito Doke
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shizheng Huang
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chengxiang Qiu
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xin Sheng
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Seasock
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongbo Liu
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ziyuan Ma
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Palmer
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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A key gene in Drosophila eye development provides protection for tubules and glomeruli upon injury. Kidney Int 2021; 101:9-12. [PMID: 34655648 DOI: 10.1016/j.kint.2021.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/24/2021] [Indexed: 11/21/2022]
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49
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Guan Y, Liang X, Ma Z, Hu H, Liu H, Miao Z, Linkermann A, Hellwege JN, Voight BF, Susztak K. A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis. Nat Commun 2021; 12:5078. [PMID: 34426578 PMCID: PMC8382756 DOI: 10.1038/s41467-021-25377-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified loci for kidney disease, but the causal variants, genes, and pathways remain unknown. Here we identify two kidney disease genes Dipeptidase 1 (DPEP1) and Charged Multivesicular Body Protein 1 A (CHMP1A) via the triangulation of kidney function GWAS, human kidney expression, and methylation quantitative trait loci. Using single-cell chromatin accessibility and genome editing, we fine map the region that controls the expression of both genes. Mouse genetic models demonstrate the causal roles of both genes in kidney disease. Cellular studies indicate that both Dpep1 and Chmp1a are important regulators of a single pathway, ferroptosis and lead to kidney disease development via altering cellular iron trafficking.
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Affiliation(s)
- Yuting Guan
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiujie Liang
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ziyuan Ma
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hailong Hu
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhen Miao
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Jacklyn N Hellwege
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, 37232, USA
| | - Benjamin F Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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50
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Merscher S, Faul C. DACH1 as a multifaceted and potentially druggable susceptibility factor for kidney disease. J Clin Invest 2021; 131:149043. [PMID: 33998596 PMCID: PMC8121511 DOI: 10.1172/jci149043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Kidney diseases affect more than 15% of adults in the US, yet drug development in the kidney field, when compared with that for other common diseases, has been lagging behind. Modifiers that increase the susceptibility to injury and contribute to the pathogenesis and progression of kidney disease include genetic and environmental factors and epigenetic mechanisms. In this issue of the JCI, Cao et al. and Doke et al. independently report the identification of a susceptibility factor called Dachshund homolog 1 (DACH1). Both groups identify an association of reduced DACH1 expression with kidney disease, using different screening approaches, studying different types of human kidney diseases, and using different experimental models, making the fact that both stumbled over the same protein very compelling. Combined, these studies highlight DACH1 as a key safeguard in the kidney, granting various cell types proper function by modulating several molecular pathways.
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Affiliation(s)
- Sandra Merscher
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Christian Faul
- Division of Nephrology, Department of Medicine, The University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
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