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Mao L, Zhang Q, Wu Q, Zhang Y, Jiang J, Li Z, Chen L, Wang R, Zeng Q, Ren Y, Liu P, Liu M, Luo G. The integration of scRNA-seq with microarray and in-vivo experiments facilitates a comprehensive elucidation of the molecular mechanisms underlying endothelial cell involvement in myocardial infarction. Biochem Biophys Res Commun 2025; 766:151820. [PMID: 40288264 DOI: 10.1016/j.bbrc.2025.151820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2025] [Revised: 04/02/2025] [Accepted: 04/14/2025] [Indexed: 04/29/2025]
Abstract
Myocardial infarction (MI) remains a major global health challenge, with endothelial cell function playing a crucial role in its progression. Advances in single-cell RNA sequencing (scRNA-seq) have enhanced our understanding of MI pathogenesis. This study aims to identify key genes within endothelial cells using scRNA-seq data and validate them through microarray data and in vivo models elucidate their role in the progression of MI. ScRNA-seq and microarray datasets relevant to MI were obtained from the GEO database. The Seurat package was used for data pre-processing and marker gene identification. Endothelial cell subpopulations were characterised using the hdWGCNA package, while intercellular interactions with fibroblasts were assessed using CellChat. Key genes were identified using comprehensive bioinformatics techniques such as scCODE, FindMarkers and protein-protein interaction (PPI) analysis, with validation from microarray data and in vivo experiments (WB, qPCR, immunofluorescence) in the model of MI. The analysis via scRNA-seq revealed 16 distinct cell clusters encompassing 7 unique cell types. Endothelial cells were categorized into 8 subpopulations by hdWGCNA; notably, Endothelial Cells-2 exhibited significant interactions with fibroblasts mediated by PDGF, PROS, and GAS signaling pathways. Integration of hdWGCNA, scCODE and FindMarkers, 10 key genes were identified, which were subsequently refined to DBP, NR1D1, and TEF following PPI analysis. These genes demonstrated marked downregulation the progression of MI, as confirmed by subsequent in vivo experiments. This study highlights the crucial roles of DBP, NR1D1, and TEF in MI development, providing a basis for future research on endothelial cell function in cardiovascular disease.
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Affiliation(s)
- Linshen Mao
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; National Traditional Chinese Medicine Clinical Research Base, Affiliated Traditional Chinese Medicine Hospital, Luzhou, 646000, China
| | - Qingyu Zhang
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; School of Integrated Traditional and Western Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Qin Wu
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; National Traditional Chinese Medicine Clinical Research Base, Affiliated Traditional Chinese Medicine Hospital, Luzhou, 646000, China
| | - Yu Zhang
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; National Traditional Chinese Medicine Clinical Research Base, Affiliated Traditional Chinese Medicine Hospital, Luzhou, 646000, China
| | - Jinhui Jiang
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; School of Integrated Traditional and Western Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Zhengzhou Li
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; School of Integrated Traditional and Western Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Li Chen
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; School of Integrated Traditional and Western Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Raoqiong Wang
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; National Traditional Chinese Medicine Clinical Research Base, Affiliated Traditional Chinese Medicine Hospital, Luzhou, 646000, China
| | - Qihu Zeng
- National Traditional Chinese Medicine Clinical Research Base, Affiliated Traditional Chinese Medicine Hospital, Luzhou, 646000, China
| | - Yanmei Ren
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; School of Integrated Traditional and Western Medicine, Southwest Medical University, Luzhou, 646000, China
| | - Ping Liu
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; School of Integrated Traditional and Western Medicine, Southwest Medical University, Luzhou, 646000, China.
| | - Mengnan Liu
- National Traditional Chinese Medicine Clinical Research Base, Affiliated Traditional Chinese Medicine Hospital, Luzhou, 646000, China.
| | - Gang Luo
- Department of Cardiovascular Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China; National Traditional Chinese Medicine Clinical Research Base, Affiliated Traditional Chinese Medicine Hospital, Luzhou, 646000, China.
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Liu W, Wang X, Yu Y, Lin W, Xu H, Jiang X, Yuan C, Wang Y, Wang X, Song W, He Y. Inflammatory Cell Interactions in the Rotator Cuff Microenvironment: Insights From Single-Cell Sequencing. Int J Genomics 2025; 2025:6175946. [PMID: 40265083 PMCID: PMC12014260 DOI: 10.1155/ijog/6175946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Accepted: 03/18/2025] [Indexed: 04/24/2025] Open
Abstract
Rotator cuff injuries are a common cause of shoulder pain and dysfunction, with chronic inflammation complicating recovery. Recent advances in single-cell RNA sequencing (scRNA-seq) have provided new insights into the immune cell interactions within the rotator cuff microenvironment during injury and healing. This review focuses on the application of scRNA-seq to explore the roles of immune and nonimmune cells, including macrophages, T-cells, fibroblasts, and myofibroblasts, in driving inflammation, tissue repair, and fibrosis. We discuss how immune cell crosstalk and interactions with the extracellular matrix influence the progression of healing or pathology. Single-cell analyses have identified distinct molecular signatures associated with chronic inflammation, which may contribute to persistent tissue damage. Additionally, we highlight the therapeutic potential of targeting inflammation in rotator cuff repair, emphasizing personalized medicine approaches. Overall, the integration of scRNA-seq in studying rotator cuff injuries enhances our understanding of the cellular mechanisms involved and offers new perspectives for developing targeted treatments in regenerative medicine.
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Affiliation(s)
- Wencai Liu
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyu Wang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhao Yu
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiming Lin
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Xu
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiping Jiang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenrui Yuan
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifei Wang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Wang
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Song
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaohua He
- Department of Orthopaedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Liu J, Feng L, Jia Q, Meng J, Zhao Y, Ren L, Yan Z, Wang M, Qin J. A comprehensive bioinformatics analysis identifies mitophagy biomarkers and potential Molecular mechanisms in hypertensive nephropathy. J Biomol Struct Dyn 2025; 43:3204-3223. [PMID: 38334110 DOI: 10.1080/07391102.2024.2311344] [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: 07/31/2023] [Accepted: 12/05/2023] [Indexed: 02/10/2024]
Abstract
Mitophagy, the selective removal of damaged mitochondria, plays a critical role in kidney diseases, but its involvement in hypertensive nephropathy (HTN) is not well understood. To address this gap, we investigated mitophagy-related genes in HTN, identifying potential biomarkers for diagnosis and treatment. Transcriptome datasets from the Gene Expression Omnibus database were analyzed, resulting in the identification of seven mitophagy related differentially expressed genes (MR-DEGs), namely PINK1, ULK1, SQSTM1, ATG5, ATG12, MFN2, and UBA52. Further, we explored the correlation between MR-DEGs, immune cells, and inflammatory factors. The identified genes demonstrated a strong correlation with Mast cells, T-cells, TGFβ3, IL13, and CSF3. Machine learning techniques were employed to screen important genes, construct diagnostic models, and evaluate their accuracy. Consensus clustering divided the HTN patients into two mitophagy subgroups, with Subgroup 2 showing higher levels of immune cell infiltration and inflammatory factors. The functions of their proteins primarily involve complement, coagulation, lipids, and vascular smooth muscle contraction. Single-cell RNA sequencing revealed that mitophagy was most significant in proximal tubule cells (PTC) in HTN patients. Pseudotime analysis of PTC confirmed the expression changes observed in the transcriptome. Intercellular communication analysis suggested that mitophagy might regulate PTC's participation in intercellular crosstalk. Notably, specific transcription factors such as HNF4A, PPARA, and STAT3 showed strong correlations with mitophagy-related genes in PTC, indicating their potential role in modulating PTC function and influencing the onset and progression of HTN. This study offers a comprehensive analysis of mitophagy in HTN, enhancing our understanding of the pathogenesis, diagnosis, and treatment of HTN.
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Affiliation(s)
- Jiayou Liu
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Luda Feng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qi Jia
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia Meng
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yun Zhao
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Ren
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ziming Yan
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Manrui Wang
- The Second Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Jianguo Qin
- Department of Nephropathy, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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Yang Y, Zhu L, Zhao J, Zhang B, Wang X, Cheung WW, Zhao C, Zhou P. Single-Cell Analysis of Endothelial Cell Injury in IgA Nephropathy. Immun Inflamm Dis 2025; 13:e70149. [PMID: 39945225 PMCID: PMC11822453 DOI: 10.1002/iid3.70149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 09/25/2024] [Accepted: 01/21/2025] [Indexed: 02/16/2025] Open
Abstract
BACKGROUND The precise mechanisms responsible for renal injury in IgA nephropathy (IgAN) are not fully understood. Our study employed an extensive scRNA-seq analysis of kidney biopsies obtained from individuals with IgAN, with a specific emphasis on investigating the involvement of renal endothelial cells. METHODS We obtained data from the Gene Expression Omnibus database and conducted bioinformatics analysis, which included enrichment analysis of differentially expressed genes, AUCell analysis, and high-dimensional weighted gene co-expression network analysis (hdWGCNA). The results of these analyses were further validated using human renal glomerular endothelial cells (HRGECs). RESULTS The ScRNA-seq data uncovered notable variations in gene expression between IgAN and control kidney tissues. The enrichment analysis using AUCell demonstrated a high presence of adhesion molecules and components related to the mitogen-activated protein kinase signaling pathway within the renal endothelial cells. Furthermore, through hdWGCNA analysis, it was discovered that interleukin (IL)-6, Rac1, and cadherin exhibited associations with the renal endothelial cells. Stimulation of HRGECs with IL-6/IL-6 receptor resulted in a significant reduction in VE-cad expression while inhibiting Rac1 led to a substantial decrease in Rac1-GTP levels and an increase in VE-cad expression. CONCLUSION This study presents novel findings regarding the contribution of renal endothelial cells to the development of IgAN, as it demonstrates that IL-6 negatively regulates VE-cad expression in HRGECs via Rac1. These results highlight the significant involvement of renal endothelial cells in the pathogenesis of IgAN.
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Affiliation(s)
- Yong‐Chang Yang
- Department of PediatricsShengjing Hospital of China Medical UniversityShenyangChina
| | - Lin Zhu
- Department of Pediatric Nephrology and RheumatologySichuan Provincial Women's and Children's Hospital/The Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengduChina
- Sichuan Clinical Research Center for Pediatric NephrologyChengduChina
| | - Jing‐Ying Zhao
- Department of PediatricsShengjing Hospital of China Medical UniversityShenyangChina
| | - Bo Zhang
- Department of PediatricsShengjing Hospital of China Medical UniversityShenyangChina
| | - Xiao‐Meng Wang
- Department of Pediatric Nephrology and RheumatologySichuan Provincial Women's and Children's Hospital/The Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengduChina
- Sichuan Clinical Research Center for Pediatric NephrologyChengduChina
| | - Wai W. Cheung
- Division of Pediatric Nephrology, Rady Children's HospitalUniversity of CaliforniaSan DiegoCaliforniaUSA
- Yangtze Delta Region Institute of Tsinghua UniversityJiaxingChina
| | - Cheng‐Guang Zhao
- Department of PediatricsShengjing Hospital of China Medical UniversityShenyangChina
- Department of Pediatric Nephrology and RheumatologySichuan Provincial Women's and Children's Hospital/The Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengduChina
| | - Ping Zhou
- Department of Pediatric Nephrology and RheumatologySichuan Provincial Women's and Children's Hospital/The Affiliated Women's and Children's Hospital of Chengdu Medical CollegeChengduChina
- Sichuan Clinical Research Center for Pediatric NephrologyChengduChina
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5
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Wang M, Yao F, Chen N, Wu T, Yan J, Du L, Zeng S, Du C. The advance of single cell transcriptome to study kidney immune cells in diabetic kidney disease. BMC Nephrol 2024; 25:412. [PMID: 39550562 PMCID: PMC11568691 DOI: 10.1186/s12882-024-03853-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: 08/16/2024] [Accepted: 11/05/2024] [Indexed: 11/18/2024] Open
Abstract
Diabetic kidney disease (DKD) is a prevalent microvascular complication of diabetes mellitus and a primary cause of end-stage renal disease (ESRD). Increasing studies suggest that immune cells are involved in regulating renal inflammation, which contributes to the progression of DKD. Compared with conventional methods, single-cell sequencing technology is more developed technique that has advantages in resolving cellular heterogeneity, parallel multi-omics studies, and discovering new cell types. ScRNA-seq helps researchers to analyze specifically gene expressions, signaling pathways, intercellular communication as well as their regulations in various immune cells of kidney biopsy and urine samples. It is still challenging to investigate the function of each cell type in the pathophysiology of kidney due to its complex and heterogeneous structure and function. Here, we discuss the application of single-cell transcriptomics in the field of DKD and highlight several recent studies that explore the important role of immune cells including macrophage, T cells, B cells etc. in DKD through scRNA-seq analyses. Through combing the researches of scRNA-seq on immune cells in DKD, this review provides novel perspectives on the pathogenesis and immune therapeutic strategy for DKD.
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Affiliation(s)
- Mengjia Wang
- Department of Pathology, Key Laboratory of Kidney Diseases of Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China
| | - Fang Yao
- Department of Pathology, Key Laboratory of Kidney Diseases of Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China
- Center of Metabolic Diseases and Cancer Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Ning Chen
- Department of Pathology, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ting Wu
- Department of Pathology, Key Laboratory of Kidney Diseases of Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China
- Center of Metabolic Diseases and Cancer Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Jiaxin Yan
- Department of Pathology, Key Laboratory of Kidney Diseases of Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China
- Center of Metabolic Diseases and Cancer Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Linshan Du
- Department of Pathology, Key Laboratory of Kidney Diseases of Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China
| | - Shijie Zeng
- Department of Pathology, Key Laboratory of Kidney Diseases of Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China
| | - Chunyang Du
- Department of Pathology, Key Laboratory of Kidney Diseases of Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China.
- Center of Metabolic Diseases and Cancer Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China.
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Rroji M, Spasovski G. Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential. Proteomics 2024:e202400151. [PMID: 39523931 DOI: 10.1002/pmic.202400151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024]
Abstract
Omics technologies have significantly advanced the prediction and therapeutic approaches for chronic kidney disease (CKD) by providing comprehensive molecular insights. This is a review of the current state and future prospects of integrating biomarkers into the clinical practice for CKD, aiming to improve patient outcomes by targeted therapeutic interventions. In fact, the integration of genomic, transcriptomic, proteomic, and metabolomic data has enhanced our understanding of CKD pathogenesis and identified novel biomarkers for an early diagnosis and targeted treatment. Advanced computational methods and artificial intelligence (AI) have further refined multi-omics data analysis, leading to more accurate prediction models for disease progression and therapeutic responses. These developments highlight the potential to improve CKD patient care with a precise and individualized treatment plan .
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Affiliation(s)
- Merita Rroji
- Faculty of Medicine, Department of Nephrology, University of Medicine Tirana, Tirana, Albania
| | - Goce Spasovski
- Medical Faculty, Department of Nephrology, University of Skopje, Skopje, North Macedonia
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Wu J, Guo J, Xia S, Chen J, Cao M, Xie L, Yang C, Qiu F, Wang J. A Single-Cell Transcriptome Profiling of Triptolide-Induced Nephrotoxicity in Mice. Adv Biol (Weinh) 2024; 8:e2400120. [PMID: 38864263 DOI: 10.1002/adbi.202400120] [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: 02/29/2024] [Revised: 05/16/2024] [Indexed: 06/13/2024]
Abstract
Triptolide (TP), an active component isolated from the traditional Chinese herb Tripterygium wilfordii Hook F (TWHF), shows great promise for treating inflammation-related diseases. However, its potential nephrotoxic effects remain concerning. The mechanism underlying TP-induced nephrotoxicity is inadequately elucidated, particularly at single-cell resolution. Hence, single-cell RNA sequencing (scRNA-seq) of kidney tissues from control and TP-treated mice is performed to generate a thorough description of the renal cell atlas upon TP treatment. Heterogeneous responses of nephron epithelial cells are observed after TP exposure, attributing differential susceptibility of cell subtypes to excessive reactive oxygen species and increased inflammatory responses. Moreover, TP disrupts vascular function by activating endothelial cell immunity and damaging fibroblasts. Severe immune cell damage and the activation of pro-inflammatory Macro_C1 cells are also observed with TP treatment. Additionally, ligand-receptor crosstalk analysis reveals that the SPP1 (osteopontin) signaling pathway targeting Macro_C1 cells is triggered by TP treatment, which may promote the infiltration of Macro_C1 cells to exacerbate renal toxicity. Overall, this study provides comprehensive information on the transcriptomic profiles and cellular composition of TP-associated nephrotoxicity at single-cell resolution, which can strengthen the understanding of the pathogenesis of TP-induced nephrotoxicity and provide valuable clues for the discovery of new therapeutic targets to ameliorate TP-associated nephrotoxicity.
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Affiliation(s)
- Jiangpeng Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Jinan Guo
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Siyu Xia
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Jiayun Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Min Cao
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Lulin Xie
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Chuanbin Yang
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jigang Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng, 475004, China
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8
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Yoon B, Kim H, Jung SW, Park J. Single-cell lineage tracing approaches to track kidney cell development and maintenance. Kidney Int 2024; 105:1186-1199. [PMID: 38554991 DOI: 10.1016/j.kint.2024.01.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 04/02/2024]
Abstract
The kidney is a complex organ consisting of various cell types. Previous studies have aimed to elucidate the cellular relationships among these cell types in developing and mature kidneys using Cre-loxP-based lineage tracing. However, this methodology falls short of fully capturing the heterogeneous nature of the kidney, making it less than ideal for comprehensively tracing cellular progression during kidney development and maintenance. Recent technological advancements in single-cell genomics have revolutionized lineage tracing methods. Single-cell lineage tracing enables the simultaneous tracing of multiple cell types within complex tissues and their transcriptomic profiles, thereby allowing the reconstruction of their lineage tree with cell state information. Although single-cell lineage tracing has been successfully applied to investigate cellular hierarchies in various organs and tissues, its application in kidney research is currently lacking. This review comprehensively consolidates the single-cell lineage tracing methods, divided into 4 categories (clustered regularly interspaced short palindromic repeat [CRISPR]/CRISPR-associated protein 9 [Cas9]-based, transposon-based, Polylox-based, and native barcoding methods), and outlines their technical advantages and disadvantages. Furthermore, we propose potential future research topics in kidney research that could benefit from single-cell lineage tracing and suggest suitable technical strategies to apply to these topics.
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Affiliation(s)
- Baul Yoon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hayoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Su Woong Jung
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea; Division of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea.
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
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Chen J, Wu J, Bai Y, Yang C, Wang J. Recent advances of single-cell RNA sequencing in toxicology research: Insight into hepatotoxicity and nephrotoxicity. CURRENT OPINION IN TOXICOLOGY 2024; 37:100462. [DOI: 10.1016/j.cotox.2024.100462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
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10
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Luo X, Tang X. Single-cell RNA sequencing in juvenile idiopathic arthritis. Genes Dis 2024; 11:633-644. [PMID: 37692495 PMCID: PMC10491939 DOI: 10.1016/j.gendis.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/01/2023] [Accepted: 04/11/2023] [Indexed: 09/12/2023] Open
Abstract
Juvenile idiopathic arthritis (JIA) is one of the most common chronic inflammatory rheumatic diseases in children, with onset before age 16 and lasting for more than 6 weeks. JIA is a highly heterogeneous condition with various consequences for health and quality of life. For some JIA patients, early detection and intervention remain challenging. As a result, further investigation of the complex and unknown mechanisms underlying JIA is required. Advances in technology now allow us to describe the biological heterogeneity and function of individual cell populations in JIA. Through this review, we hope to provide novel ideas and potential targets for the diagnosis and treatment of JIA by summarizing the current findings of single-cell RNA sequencing studies and understanding how the major cell subsets drive JIA pathogenesis.
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Affiliation(s)
- Xiwen Luo
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Xuemei Tang
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing 400014, China
- Chongqing Key Laboratory of Child Infection and Immunity, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
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11
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Lin M, Zhong Y, Zhou D, Guan B, Hu B, Wang P, Liu F. Proximal tubule cells in blood and urine as potential biomarkers for kidney disease biopsy. PeerJ 2023; 11:e16499. [PMID: 38077419 PMCID: PMC10710128 DOI: 10.7717/peerj.16499] [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: 08/08/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Early diagnosis and treatment are crucial for managing kidney disease, yet there remains a need to further explore pathological mechanisms and develop minimally invasive diagnostic methods. In this study, we employed single-cell RNA sequencing (scRNA-seq) to assess the cellular heterogeneity of kidney diseases. We analyzed gene expression profiles from renal tissue, peripheral blood mononuclear cells (PBMCs), and urine of four patients with nephritis. Our findings identified 12 distinct cell subsets in renal tissues and leukocytes. These subsets encompassed fibroblast cells, mesangial cells, epithelial cells, proximal tubule cells (PTCs), and six immune cell types: CD8+ T cells, macrophages, natural killer cells, dendritic cells, B cells, and neutrophils. Interestingly, PTCs were present in both PBMCs and urine samples but absent in healthy blood samples. Furthermore, several populations of fibroblast cells, mesangial cells, and PTCs exhibited pro-inflammatory or pro-apoptotic behaviors. Our gene expression analysis highlighted the critical role of inflammatory PTCs and fibroblasts in nephritis development and progression. These cells showed high expression of pro-inflammatory genes, which could have chemotactic and activating effect on neutrophils. This was substantiated by the widespread in these cells. Notably, the gene expression profiles of inflammatory PTCs in PBMCs, urine, and kidney tissues had high similarity. This suggests that PTCs in urine and PBMCs hold significant potential as alternative markers to invasive kidney biopsies.
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Affiliation(s)
- Minwa Lin
- Depament of Nephrology, The First People’s Hospital of Foshan, Foshan, China
| | - Yingxue Zhong
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dan Zhou
- Cancer Center, The First People’s Hospital of Foshan, Foshan, China
| | - Baozhang Guan
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Bo Hu
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Panpan Wang
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Fanna Liu
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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12
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Tsai YC, Kuo MC, Huang JC, Chang WA, Wu LY, Huang YC, Chang CY, Lee SC, Hsu YL. Single-cell transcriptomic profiles in the pathophysiology within the microenvironment of early diabetic kidney disease. Cell Death Dis 2023; 14:442. [PMID: 37460555 DOI: 10.1038/s41419-023-05947-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/18/2023] [Accepted: 07/04/2023] [Indexed: 07/20/2023]
Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease, resulting in a huge socio-economic impact. Kidney is a highly complex organ and the pathogenesis underlying kidney organization involves complex cell-to-cell interaction within the heterogeneous kidney milieu. Advanced single-cell RNA sequencing (scRNA-seq) could reveal the complex architecture and interaction with the microenvironment in early DKD. We used scRNA-seq to investigate early changes in the kidney of db/m mice and db/db mice at the 14th week. Uniform Manifold Approximation and Projection were applied to classify cells into different clusters at a proper resolution. Weighted gene co-expression network analysis was used to identify the key molecules specifically expressed in kidney tubules. Information of cell-cell communication within the kidney was obtained using receptor-ligand pairing resources. In vitro model, human subjects, and co-detection by indexing staining were used to identify the pathophysiologic role of the hub genes in DKD. Among four distinct subsets of the proximal tubule (PT), lower percentages of proliferative PT and PT containing AQP4 expression (PTAQP4+) in db/db mice induced impaired cell repair activity and dysfunction of renin-angiotensin system modulation in early DKD. We found that ferroptosis was involved in DKD progression, and ceruloplasmin acted as a central regulator of the induction of ferroptosis in PTAQP4+. In addition, lower percentages of thick ascending limbs and collecting ducts with impaired metabolism function were also critical pathogenic features in the kidney of db/db mice. Secreted phosphoprotein 1 (SPP1) mediated pathogenic cross-talk in the tubular microenvironment, as validated by a correlation between urinary SPP1/Cr level and tubular injury. Finally, mesangial cell-derived semaphorin 3C (SEMA3C) further promoted endothelium-mesenchymal transition in glomerular endothelial cells through NRP1 and NRP2, and urinary SEMA3C/Cr level was positively correlated with glomerular injury. These data identified the hub genes involved in pathophysiologic changes within the microenvironment of early DKD.
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Affiliation(s)
- Yi-Chun Tsai
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of General Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mei-Chuan Kuo
- Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Juan-Chi Huang
- Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-An Chang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ling-Yu Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yung-Chi Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Taiwan, Kaohsiung, Taiwan
| | - Chao-Yuan Chang
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Su-Chu Lee
- Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ya-Ling Hsu
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Taiwan, Kaohsiung, Taiwan.
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13
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Zhu J, Lu J, Weng H. Single-cell RNA sequencing for the study of kidney disease. Mol Med 2023; 29:85. [PMID: 37400792 DOI: 10.1186/s10020-023-00693-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
The kidney is an important organ for maintaining normal metabolism and stabilising the internal environment, in which, the heterogeneity of cell types has hindered the progress in understanding the mechanisms underlying kidney disease. In recent years the application of single-cell RNA sequencing (scRNA-seq) in nephrology has developed rapidly. In this review, we summarized the technical platform related to scRNA-seq and the role of this technology in investigating the onset and development of kidney diseases, starting from several common kidney diseases (mainly including lupus nephritis, renal cell carcinoma, diabetic nephropathy and acute kidney injury), and provide a reference for the application of scRNA-seq in the study of kidney disease diagnosis, treatment and prognosis.
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Affiliation(s)
- Jiayi Zhu
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, 201318, Shanghai, China
| | - Jinrong Lu
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, 201318, Shanghai, China
| | - Huachun Weng
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, 201318, Shanghai, China.
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14
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Li JSY, Raghubar AM, Matigian NA, Ng MSY, Rogers NM, Mallett AJ. The Utility of Spatial Transcriptomics for Solid Organ Transplantation. Transplantation 2023; 107:1463-1471. [PMID: 36584371 DOI: 10.1097/tp.0000000000004466] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Spatial transcriptomics (ST) measures and maps transcripts within intact tissue sections, allowing the visualization of gene activity within the spatial organization of complex biological systems. This review outlines advances in genomic sequencing technologies focusing on in situ sequencing-based ST, including applications in transplant and relevant nontransplant settings. We describe the experimental and analytical pipelines that underpin the current generation of spatial technologies. This context is important for understanding the potential role ST may play in expanding our knowledge, including in organ transplantation, and the important caveats/limitations when interpreting the vast data output generated by such methodological platforms.
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Affiliation(s)
- Jennifer S Y Li
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Arti M Raghubar
- Kidney Health Service, Royal Brisbane and Women's Hospital, QLD, Australia
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Health Support Queensland, QLD, Australia
- Department of Anatomical Pathology, Pathology Queensland, Health Support Queensland, QLD, Australia
- Faculty of Medicine, University of Queensland, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
| | - Nicholas A Matigian
- QCIF Facility for Advanced Bioinformatics, The University of Queensland, QLD, Australia
| | - Monica S Y Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, QLD, Australia
- Conjoint Internal Medicine Laboratory, Pathology Queensland, Health Support Queensland, QLD, Australia
- Faculty of Medicine, University of Queensland, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
- Nephrology Department, Princess Alexandra Hospital, QLD, Australia
| | - Natasha M Rogers
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Department of Renal Medicine, Westmead Hospital, Westmead, NSW, Australia
| | - Andrew J Mallett
- Faculty of Medicine, University of Queensland, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, QLD, Australia
- College of Medicine and Dentistry, James Cook University, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, QLD, Australia
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15
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Zhang X, Chao P, Zhang L, Xu L, Cui X, Wang S, Wusiman M, Jiang H, Lu C. Single-cell RNA and transcriptome sequencing profiles identify immune-associated key genes in the development of diabetic kidney disease. Front Immunol 2023; 14:1030198. [PMID: 37063851 PMCID: PMC10091903 DOI: 10.3389/fimmu.2023.1030198] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/16/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundThere is a growing public concern about diabetic kidney disease (DKD), which poses a severe threat to human health and life. It is important to discover noninvasive and sensitive immune-associated biomarkers that can be used to predict DKD development. ScRNA-seq and transcriptome sequencing were performed here to identify cell types and key genes associated with DKD.MethodsHere, this study conducted the analysis through five microarray datasets of DKD (GSE131882, GSE1009, GSE30528, GSE96804, and GSE104948) from gene expression omnibus (GEO). We performed single-cell RNA sequencing analysis (GSE131882) by using CellMarker and CellPhoneDB on public datasets to identify the specific cell types and cell-cell interaction networks related to DKD. DEGs were identified from four datasets (GSE1009, GSE30528, GSE96804, and GSE104948). The regulatory relationship between DKD-related characters and genes was evaluated by using WGCNA analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) datasets were applied to define the enrichment of each term. Subsequently, immune cell infiltration between DKD and the control group was identified by using the “pheatmap” package, and the connection Matrix between the core genes and immune cell or function was illuminated through the “corrplot” package. Furthermore, RcisTarget and GSEA were conducted on public datasets for the analysis of the regulation relationship of key genes and it revealed the correlation between 3 key genes and top the 20 genetic factors involved in DKD. Finally, the expression of key genes between patients with 35 DKD and 35 healthy controls were examined by ELISA, and the relationship between the development of DKD rate and hub gene plasma levels was assessed in a cohort of 35 DKD patients. In addition, we carried out immunohistochemistry and western blot to verify the expression of three key genes in the kidney tissue samples we obtained.ResultsThere were 8 cell types between DKD and the control group, and the number of connections between macrophages and other cells was higher than that of the other seven cell groups. We identified 356 different expression genes (DEGs) from the RNA-seq, which are enriched in urogenital system development, kidney development, platelet alpha granule, and glycosaminoglycan binding pathways. And WGCNA was conducted to construct 13 gene modules. The highest correlations module is related to the regulation of cell adhesion, positive regulation of locomotion, PI3K-Akt, gamma response, epithelial-mesenchymal transition, and E2F target signaling pathway. Then we overlapped the DEGs, WGCNA, and scRNA-seq, SLIT3, PDE1A and CFH were screened as the closely related genes to DKD. In addition, the findings of immunological infiltration revealed a remarkable positive link between T cells gamma delta, Macrophages M2, resting mast cells, and the three critical genes SLIT3, PDE1A, and CFH. Neutrophils were considerably negatively connected with the three key genes. Comparatively to healthy controls, DKD patients showed high levels of SLIT3, PDE1A, and CFH. Despite this, higher SLIT3, PDE1A, and CFH were associated with an end point rate based on a median follow-up of 2.6 years. And with the gradual deterioration of DKD, the expression of SLIT3, PDE1A, and CFH gradually increased.ConclusionsThe 3 immune-associated genes could be used as diagnostic markers and therapeutic targets of DKD. Additionally, we found new pathogenic mechanisms associated with immune cells in DKD, which might lead to therapeutic targets against these cells.
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Affiliation(s)
- Xueqin Zhang
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Peng Chao
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Lei Zhang
- Department of Endocrine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Lin Xu
- Department of Rheumatology Immunology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Xinyue Cui
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Shanshan Wang
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Miiriban Wusiman
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Hong Jiang
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
- Nephrology Clinical Research Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
- *Correspondence: Chen Lu, ; Hong Jiang,
| | - Chen Lu
- Nephrology Clinical Research Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
- Department of Nephropathy, The First Affiliated Hospital of Xinjiang Medical University, Urumuqi, Xinjiang Uygur Autonomous Region, China
- *Correspondence: Chen Lu, ; Hong Jiang,
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16
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Mao ZH, Gao ZX, Liu Y, Liu DW, Liu ZS, Wu P. Single-cell transcriptomics: A new tool for studying diabetic kidney disease. Front Physiol 2023; 13:1053850. [PMID: 36685214 PMCID: PMC9846140 DOI: 10.3389/fphys.2022.1053850] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023] Open
Abstract
The kidney is a complex organ comprising various functional partitions and special cell types that play important roles in maintaining homeostasis in the body. Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease and is an independent risk factor for cardiovascular diseases. Owing to the complexity and heterogeneity of kidney structure and function, the mechanism of DKD development has not been fully elucidated. Single-cell sequencing, including transcriptomics, epigenetics, metabolomics, and proteomics etc., is a powerful technology that enables the analysis of specific cell types and states, specifically expressed genes or pathways, cell differentiation trajectories, intercellular communication, and regulation or co-expression of genes in various diseases. Compared with other omics, RNA sequencing is a more developed technique with higher utilization of tissues or samples. This article reviewed the application of single-cell transcriptomics in the field of DKD and highlighted the key signaling pathways in specific tissues or cell types involved in the occurrence and development of DKD. The comprehensive understanding of single-cell transcriptomics through single-cell RNA-seq and single-nucleus RNA-seq will provide us new insights into the pathogenesis and treatment strategy of various diseases including DKD.
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Affiliation(s)
- Zi-Hui Mao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhong-Xiuzi Gao
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Yong Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Dong-Wei Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China
| | - Zhang-Suo Liu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China,*Correspondence: Peng Wu, ; Zhang-Suo Liu,
| | - Peng Wu
- Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Institute of Nephrology, Zhengzhou University, Zhengzhou, China,Henan Province Research Center for Kidney Disease, Zhengzhou, China,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China,*Correspondence: Peng Wu, ; Zhang-Suo Liu,
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17
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Yeh H. Applications of Transcriptomics in the Research of Antibody-Mediated Rejection in Kidney Transplantation: Progress and Perspectives. Organogenesis 2022; 18:2131357. [PMID: 36259540 PMCID: PMC9586696 DOI: 10.1080/15476278.2022.2131357] [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] [Indexed: 02/09/2023] Open
Abstract
Antibody-mediated rejection (ABMR) is the major cause of chronic allograft dysfunction and loss in kidney transplantation. The immunological mechanisms of ABMR that have been featured in the latest studies indicate a highly complex interplay between various immune and nonimmune cell types. Clinical diagnostic standards have long been criticized for being arbitrary and the lack of accuracy. Transcriptomic approaches, including microarray and RNA sequencing of allograft biopsies, enable the identification of differential gene expression and the continuous improvement of diagnostics. Given that conventional bulk transcriptomic approaches only reflect the average gene expression but not the status at the single-cell level, thereby ignoring the heterogeneity of the transcriptome across individual cells, single-cell RNA sequencing is rising as a powerful tool to provide a high-resolution transcriptome map of immune cells, which allows the elucidation of the pathogenesis and may facilitate the development of novel strategies for clinical treatment of ABMR.
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Affiliation(s)
- Hsuan Yeh
- Division of Renal-Electrolyte, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,CONTACT Hsuan Yeh S976 Scaife Hall 3550 Terrace Street Pittsburgh, PA 15261
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18
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Lee K, Jang HR. Role of T cells in ischemic acute kidney injury and repair. Korean J Intern Med 2022; 37:534-550. [PMID: 35508946 PMCID: PMC9082442 DOI: 10.3904/kjim.2021.526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/11/2022] [Indexed: 11/27/2022] Open
Abstract
Ischemic acute kidney injury (AKI) is a common medical problem with significant mortality and morbidity, affecting a large number of patients globally. Ischemic AKI is associated with intrarenal inflammation as well as systemic inflammation; thus, the innate and adaptive immune systems are implicated in the pathogenesis of ischemic AKI. Among various intrarenal immune cells, T cells play major roles in the injury process and in the repair mechanism affecting AKI to chronic kidney disease transition. Importantly, T cells also participate in distant organ crosstalk during AKI, which affects the overall outcomes. Therefore, targeting T cell-mediated pathways and T cell-based therapies have therapeutic promise for ischemic AKI. Here, we review the major populations of kidney T cells and their roles in ischemic AKI.
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Affiliation(s)
- Kyungho Lee
- Nephrology Division, Department of Medicine, Samsung Medical Center, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye Ryoun Jang
- Nephrology Division, Department of Medicine, Samsung Medical Center, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
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19
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Ma Z, Hu X, Ding HF, Zhang M, Huo Y, Dong Z. Single-Nucleus Transcriptional Profiling of Chronic Kidney Disease after Cisplatin Nephrotoxicity. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:613-628. [PMID: 35092726 PMCID: PMC8978211 DOI: 10.1016/j.ajpath.2021.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023]
Abstract
Cisplatin induces both acute and chronic nephrotoxicity during chemotherapy in patients with cancer. Presented here is the first study of single-nucleus RNA sequencing (snRNA-seq) of cisplatin-induced nephrotoxicity. Repeated low-dose cisplatin treatment (RLDC) led to decreases in renal function and kidney weight in mice at 9 weeks. The kidneys of these mice showed tubular degeneration and dilation. snRNA-seq identified 16 cell types and 17 cell clusters in these kidneys. Cluster-by-cluster comparison demonstrated cell type-specific changes in gene expression and identified a unique proximal tubule (PT) injury/repair cluster that co-expressed the injury marker kidney injury molecule-1 (Kim1) and the proliferation marker Ki-67. Compared with control, post-RLDC kidneys had 424 differentially expressed genes in PT cells, including tubular transporters and cytochrome P450 enzymes involved in lipid metabolism. snRNA-seq also revealed transcriptional changes in potential PT injury markers (Krt222, Eda2r, Ltbp2, and Masp1) and repair marker (Bex4). RLDC induced inflammation and proinflammatory cytokines (RelB, TNF-α, Il7, Ccl2, and Cxcl2) and the expression of fibrosis markers (fibronectin, collagen I, connective tissue growth factor, vimentin, and α-smooth muscle actin). Together, these results provide new insights into RLDC-induced transcriptional changes at the single-cell level that may contribute to the development of chronic kidney problems in patients with cancer after cisplatin chemotherapy.
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Affiliation(s)
- Zhengwei Ma
- Department of Cellular Biology and Anatomy, Vascular Biology Center, Augusta, Georgia.
| | - Xiaoru Hu
- Department of Cellular Biology and Anatomy, Vascular Biology Center, Augusta, Georgia; Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Han-Fei Ding
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ming Zhang
- Department of Cellular Biology and Anatomy, Vascular Biology Center, Augusta, Georgia
| | - Yuqing Huo
- Department of Cellular Biology and Anatomy, Vascular Biology Center, Augusta, Georgia; Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Vascular Biology Center, Augusta, Georgia; Charlie Norwood VA Medical Center, Augusta, Georgia.
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20
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Khan K, Ahram DF, Liu YP, Westland R, Sampogna RV, Katsanis N, Davis EE, Sanna-Cherchi S. Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations. Kidney Int 2022; 101:473-484. [PMID: 34780871 PMCID: PMC8934530 DOI: 10.1016/j.kint.2021.09.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.
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Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address)
| | - Dina F. Ahram
- Division of Nephrology, Columbia University, New York, USA
| | - Yangfan P. Liu
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, USA.,Department of Pediatric Nephrology, Amsterdam UMC- Emma Children’s Hospital, Amsterdam, NL
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA (current address); Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address).,Department of Pediatrics and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,To whom correspondence should be addressed: ADDRESS CORRESPONDENCE TO: Simone Sanna-Cherchi, MD, Division of Nephrology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA; Phone: 212-851-4925; Fax: 212-851-5461; . Erica E. Davis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7662; Fax: 312-503-7343; , Nicholas Katsanis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7339; Fax: 312-503-7343;
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA.
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21
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Latt KZ, Heymann J, Jessee JH, Rosenberg AZ, Berthier CC, Arazi A, Eddy S, Yoshida T, Zhao Y, Chen V, Nelson GW, Cam M, Kumar P, Mehta M, Kelly MC, Kretzler M, The Nephrotic Syndrome Study Network (NEPTUNE), The Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium, Ray PE, Moxey-Mims M, Gorman GH, Lechner BL, Regunathan-Shenk R, Raj DS, Susztak K, Winkler CA, Kopp JB. Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures. Kidney Int Rep 2022; 7:289-304. [PMID: 35155868 PMCID: PMC8821042 DOI: 10.1016/j.ekir.2021.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Individuals with focal segmental glomerular sclerosis (FSGS) typically undergo kidney biopsy only once, which limits the ability to characterize kidney cell gene expression over time. METHODS We used single-cell RNA sequencing (scRNA-seq) to explore disease-related molecular signatures in urine cells from subjects with FSGS. We collected 17 urine samples from 12 FSGS subjects and captured these as 23 urine cell samples. The inflammatory signatures from renal epithelial and immune cells were evaluated in bulk gene expression data sets of FSGS and minimal change disease (MCD) (The Nephrotic Syndrome Study Network [NEPTUNE] study) and an immune single-cell data set from lupus nephritis (Accelerating Medicines Partnership). RESULTS We identified immune cells, predominantly monocytes, and renal epithelial cells in the urine. Further analysis revealed 2 monocyte subtypes consistent with M1 and M2 monocytes. Shed podocytes in the urine had high expression of marker genes for epithelial-to-mesenchymal transition (EMT). We selected the 16 most highly expressed genes from urine immune cells and 10 most highly expressed EMT genes from urine podocytes as immune signatures and EMT signatures, respectively. Using kidney biopsy transcriptomic data from NEPTUNE, we found that urine cell immune signature and EMT signature genes were more highly expressed in FSGS biopsies compared with MCD biopsies. CONCLUSION The identification of monocyte subsets and podocyte expression signatures in the urine samples of subjects with FSGS suggests that urine cell profiling might serve as a diagnostic and prognostic tool in nephrotic syndrome. Furthermore, this approach may aid in the development of novel biomarkers and identifying personalized therapies targeting particular molecular pathways in immune cells and podocytes.
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Affiliation(s)
- Khun Zaw Latt
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jurgen Heymann
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph H. Jessee
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Celine C. Berthier
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Arnon Arazi
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, USA
| | - Sean Eddy
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Teruhiko Yoshida
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yongmei Zhao
- Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, USA
| | - Vicky Chen
- Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, USA
| | - George W. Nelson
- Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, USA
| | - Margaret Cam
- Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, USA
| | - Parimal Kumar
- Center for Cancer Research Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Monika Mehta
- Center for Cancer Research Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Michael C. Kelly
- Cancer Research Technology Program, Single-Cell Analysis Facility, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
| | - The Nephrotic Syndrome Study Network (NEPTUNE)
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, USA
- Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, USA
- Center for Cancer Research Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
- Cancer Research Technology Program, Single-Cell Analysis Facility, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia, USA
- Division of Nephrology, Children’s National Hospital, Washington, District of Columbia, USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
- Section on Pediatric Nephrology, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
- Department of Pediatrics, Uniformed Services University, Bethesda, Maryland, USA
- Division of Kidney Disease and Hypertension, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
- Department of Medicine, Renal Electrolyte and Hypertension Division, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - The Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, USA
- Advanced Biomedical and Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, USA
- Center for Cancer Research Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
- Cancer Research Technology Program, Single-Cell Analysis Facility, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia, USA
- Division of Nephrology, Children’s National Hospital, Washington, District of Columbia, USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
- Section on Pediatric Nephrology, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
- Department of Pediatrics, Uniformed Services University, Bethesda, Maryland, USA
- Division of Kidney Disease and Hypertension, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
- Department of Medicine, Renal Electrolyte and Hypertension Division, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Patricio E. Ray
- Department of Pediatrics, Child Health Research Center, University of Virginia, Charlottesville, Virginia, USA
| | - Marva Moxey-Mims
- Division of Nephrology, Children’s National Hospital, Washington, District of Columbia, USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Gregory H. Gorman
- Section on Pediatric Nephrology, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
- Department of Pediatrics, Uniformed Services University, Bethesda, Maryland, USA
| | - Brent L. Lechner
- Section on Pediatric Nephrology, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
- Department of Pediatrics, Uniformed Services University, Bethesda, Maryland, USA
| | - Renu Regunathan-Shenk
- Division of Kidney Disease and Hypertension, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
| | - Dominic S. Raj
- Division of Kidney Disease and Hypertension, The George Washington University School of Medicine and Health Sciences, Washington DC, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cheryl A. Winkler
- Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey B. Kopp
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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22
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Altered DNA methylation in kidney disease: useful markers and therapeutic targets. Clin Exp Nephrol 2022; 26:309-315. [PMID: 35024974 PMCID: PMC8930790 DOI: 10.1007/s10157-022-02181-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/04/2022] [Indexed: 01/19/2023]
Abstract
Recent studies have demonstrated the association of altered epigenomes with lifestyle-related diseases. Epigenetic regulation promotes biological plasticity in response to environmental changes, and such plasticity may cause a ‘memory effect’, a sustained effect of transient treatment or an insult in the course of lifestyle-related diseases. We investigated the significance of epigenetic changes in several genes required for renal integrity, including the nephrin gene in podocytes, and the sustained anti-proteinuric effect, focusing on the transcription factor Krüppel-like factor 4 (KLF4). We further reported the role of the DNA repair factor lysine-acetyl transferase 5 (KAT5), which acts coordinately with KLF4, in podocyte injury caused by a hyperglycemic state through the acceleration of DNA damage and epigenetic alteration. In contrast, KAT5 in proximal tubular cells prevents acute kidney injury via glomerular filtration regulation by an epigenetic mechanism as well as promotion of DNA repair, indicating the cell type-specific action and roles of DNA repair factors. This review summarizes epigenetic alterations in kidney diseases, especially DNA methylation, and their utility as markers and potential therapeutic targets. Focusing on transcription factors or DNA damage repair factors associated with epigenetic changes may be meaningful due to their cell-specific expression or action. We believe that a better understanding of epigenetic alterations in the kidney will lead to the development of a novel strategy for chronic kidney disease (CKD) treatment.
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23
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Glassock RJ. Precision medicine for the treatment of glomerulonephritis: A bold goal but not yet a transformative achievement. Clin Kidney J 2021; 15:657-662. [PMID: 35371458 PMCID: PMC8967540 DOI: 10.1093/ckj/sfab270] [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: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
The revolution in our ability to recognize the alterations in fundamental biology brought about by disease has fostered a renewed interest in precision or personalized medicine (“the right treatment, or diagnostic test, for the right patient at the right time”). This nascent field has been led by oncology, immune-hematology and infectious disease, but nephrology is catching up, and quickly. Specific forms of glomerulonephritis thought to represent specific “diseases” have been “downgraded” to “patterns of injury”. New entities have emerged through application of sophisticated molecular technologies; often embraced by the term “multi-omics”. Kidney biopsies are now interpreted by next generation imaging and machine learning. Many opportunities are manifest that will translate these remarkable developments into novel safe and effective treatment regimens for specific pathogenic pathways evoking glomerulonephritis and its progression to kidney failure. A few successes emboldens a positive look to the future. A sustained and highly collaborative engagement with this new paradigm will be required for this field, full of hope and high expectations, to realize its goal of transforming glomerular therapeutics from “one size fits all (or many)” to a true individualized management principle.
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Affiliation(s)
- Richard J Glassock
- Emeritus Professor, Department of Medicine, Geffen School of Medicine. Los Angeles, CA, USA
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24
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Muto Y, Humphreys BD. Recent advances in lineage tracing for the kidney. Kidney Int 2021; 100:1179-1184. [PMID: 34217781 PMCID: PMC8608712 DOI: 10.1016/j.kint.2021.05.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/19/2022]
Abstract
Lineage tracing was originally developed by developmental biologists to identify all progeny of a single cell during morphogenesis. More recently this approach has been applied to other fields, including organ homeostasis and recovery from injury. Modern lineage tracing techniques typically rely on reporter gene expression induced by cell-specific DNA recombination. There have been important scientific advances in the last 10 years that have impacted lineage tracing approaches, including intersectional genetics, optical clearing techniques, and the use of sequencing-based genomic lineage tracing. The latter combines CRISPR-Cas9-based genetic scarring with single-cell RNA-sequencing that, in theory, could allow comprehensive reconstruction of a lineage tree for an entire organism. This review summarizes recent advances in lineage tracing technologies and outlines potential applications for kidney research.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.
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25
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Du C, Ren Y, Li G, Yang Y, Yan Z, Yao F. Single Cell Transcriptome Helps Better Understanding Crosstalk in Diabetic Kidney Disease. Front Med (Lausanne) 2021; 8:657614. [PMID: 34485320 PMCID: PMC8415842 DOI: 10.3389/fmed.2021.657614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 07/26/2021] [Indexed: 12/20/2022] Open
Abstract
Years of research revealed that crosstalk extensively existed among kidney cells, cell factors and metabolites and played an important role in the development of diabetic kidney disease (DKD). In the last few years, single-cell RNA sequencing (scRNA-seq) technology provided new insight into cellular heterogeneity and genetic susceptibility regarding DKD at cell-specific level. The studies based on scRNA-seq enable a much deeper understanding of cell-specific processes such as interaction between cells. In this paper, we aim to review recent progress in single cell transcriptomic analyses of DKD, particularly highlighting on intra- or extra-glomerular cell crosstalk, cellular targets and potential therapeutic strategies for DKD.
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Affiliation(s)
- Chunyang Du
- Key Laboratory of Kidney Diseases of Hebei Province, Department of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Yunzhuo Ren
- Key Laboratory of Kidney Diseases of Hebei Province, Department of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Guixin Li
- Department of Burn, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yan Yang
- Key Laboratory of Kidney Diseases of Hebei Province, Department of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Zhe Yan
- Department of Nephrology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Fang Yao
- Key Laboratory of Kidney Diseases of Hebei Province, Department of Pathology, Hebei Medical University, Shijiazhuang, China
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26
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Deleersnijder D, Callemeyn J, Arijs I, Naesens M, Van Craenenbroeck AH, Lambrechts D, Sprangers B. Current Methodological Challenges of Single-Cell and Single-Nucleus RNA-Sequencing in Glomerular Diseases. J Am Soc Nephrol 2021; 32:1838-1852. [PMID: 34140401 PMCID: PMC8455274 DOI: 10.1681/asn.2021020157] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. This review provides an overview of the technical challenges that should be addressed when designing single-cell transcriptomics experiments that focus on glomerulopathies. The isolation of glomerular cells from core needle biopsy specimens for single-cell transcriptomics remains difficult and depends upon five major factors. First, core needle biopsies generate little tissue material, and several samples are required to identify glomerular cells. Second, both fresh and frozen tissue samples may yield glomerular cells, although every experimental pipeline has different (dis)advantages. Third, enrichment for glomerular cells in human tissue before single-cell analysis is challenging because no effective standardized pipelines are available. Fourth, the current warm cell-dissociation protocols may damage glomerular cells and induce transcriptional artifacts, which can be minimized by using cold dissociation techniques at the cost of less efficient cell dissociation. Finally, snRNA-seq methods may be superior to scRNA-seq in isolating glomerular cells; however, the efficacy of snRNA-seq on core needle biopsy specimens remains to be proven. The field of single-cell omics is rapidly evolving, and the integration of these techniques in multiomics assays will undoubtedly create new insights in the complex pathophysiology of glomerular diseases.
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Affiliation(s)
- Dries Deleersnijder
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Jasper Callemeyn
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Maarten Naesens
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
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27
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Li Q, Lu M, Zhang Z, Zhang R. Single-Cell Sequencing to Identify Six Heat Shock Protein (HSP) Genes-Mediated Progression Subtypes of Clear Cell Renal Cell Carcinoma. Int J Gen Med 2021; 14:3761-3773. [PMID: 34326662 PMCID: PMC8315815 DOI: 10.2147/ijgm.s318271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/06/2021] [Indexed: 02/02/2023] Open
Abstract
Background Heat shock proteins (HSPs) are widely involved in tumor occurrence and development and are prognostic markers for multiple tumors. However, the role of HSPs in clear cell renal cell carcinoma (ccRCC) remains unclear. Methods We used Cytoscape to identify hub genes in the ccRCC single-cell sequencing data set from the Gene Expression Omnibus (GEO) data repository. We identified subtypes, C1 and C2, of The Cancer Genome Atlas (TCGA) patients based on the expression of hub genes using unsupervised consensus clustering. Principal component analysis (PCA) was used to verify the clustering differences, and Kaplan-Meier (K-M) estimate was used to verify the survival differences between C1 and C2 patients. We used TIMER 2.0 and CIBERSORT to evaluate the immune cell infiltration of HSP genes and C1 and C2 patients. The R package "pRRophetic" was used to evaluate the sensitivity in C1 and C2 patients to the four first-line treatment drugs. Results We identified six hub genes (HSP90AA1, HSPH1, HSPA1B, HSPA8, and HSPA1A) encoding HSP, five of which were significantly downregulated in TCGA group, and four had a protective effect on prognosis (p <0.05). Survival analysis showed that C1 patients had a better overall survival (p <0.001). TIMER 2.0 analysis showed that three HSP genes were significantly correlated with the infiltration of CD4+ T cells and CD4+ Th1 cells (|cor|>0.5, p<0.001). CIBERSORT showed significant differences in multiple infiltrating immune cells between C1 and C2 patients. Meanwhile, the expression of PD1 was significantly lower in C1 patients than in C2 patients, and the expression of PDL1 is the another way around. Drug sensitivity analysis showed that C1 patients were more sensitive to sorafenib, pazopanib, and axitinib (p <0.001). Conclusion Our research revealed two molecular subtypes of ccRCC based on 6 HSP genes, and revealed significant differences between the two subtypes in terms of clinical prognosis, immune infiltration, and drug sensitivity.
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Affiliation(s)
- Qinke Li
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Maoqing Lu
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zhechuan Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Ronggui Zhang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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28
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Deleersnijder D, Van Craenenbroeck AH, Sprangers B. Deconvolution of Focal Segmental Glomerulosclerosis Pathophysiology Using Transcriptomics Techniques. GLOMERULAR DISEASES 2021; 1:265-276. [PMID: 36751384 PMCID: PMC9677714 DOI: 10.1159/000518404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022]
Abstract
Background Focal segmental glomerulosclerosis is a histopathological pattern of renal injury and comprises a heterogeneous group of clinical conditions with different pathophysiology, clinical course, prognosis, and treatment. Nevertheless, subtype differentiation in clinical practice often remains challenging, and we currently lack reliable diagnostic, prognostic, and therapeutic biomarkers. The advent of new transcriptomics techniques in kidney research poses great potential in the identification of gene expression biomarkers that can be applied in clinical practice. Summary Transcriptomics techniques have been completely revolutionized in the last 2 decades, with the evolution from low-throughput reverse-transcription polymerase chain reaction and in situ hybridization techniques to microarrays and next-generation sequencing techniques, including RNA-sequencing and single-cell transcriptomics. The integration of human gene expression profiles with functional in vitro and in vivo experiments provides a deeper mechanistic insight into the candidate genes, which enable the development of novel-targeted therapies. The correlation of gene expression profiles with clinical outcomes of large patient cohorts allows for the development of clinically applicable biomarkers that can aid in diagnosis and predict prognosis and therapy response. Finally, the integration of transcriptomics with other "omics" modalities creates a holistic view on disease pathophysiology. Key Messages New transcriptomics techniques allow high-throughput gene expression profiling of patients with focal segmental glomerulosclerosis (FSGS). The integration with clinical outcomes and fundamental mechanistic studies enables the discovery of new clinically useful biomarkers that will finally improve the clinical outcome of patients with FSGS.
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Affiliation(s)
- Dries Deleersnijder
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,*Ben Sprangers,
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29
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Zhao Y, Panzer U, Bonn S, Krebs CF. Single-cell biology to decode the immune cellular composition of kidney inflammation. Cell Tissue Res 2021; 385:435-443. [PMID: 34125286 PMCID: PMC8200789 DOI: 10.1007/s00441-021-03483-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/03/2021] [Indexed: 12/26/2022]
Abstract
Single-cell biology is transforming the ability of researchers to understand cellular signaling and identity across medical and biological disciplines. Especially for immune-mediated diseases, a single-cell look at immune cell subtypes, signaling, and activity might yield fundamental insights into the disease etiology, mechanisms, and potential therapeutic interventions. In this review, we highlight recent advances in the field of single-cell RNA profiling and their application to understand renal function in health and disease. With a focus on the immune system, in particular on T cells, we propose some key directions of understanding renal inflammation using single-cell approaches. We detail the benefits and shortcomings of the various technological approaches outlined and give advice on potential pitfalls and challenges in experimental setup and computational analysis. Finally, we conclude with a brief outlook into a promising future for single-cell technologies to elucidate kidney function.
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Affiliation(s)
- Yu Zhao
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Translational Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Ulf Panzer
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Translational Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian F Krebs
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Translational Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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30
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Chen Z, Zhang T, Mao K, Shao X, Xu Y, Zhu M, Zhou H, Wang Q, Li Z, Xie Y, Yuan X, Ying L, Zhang M, Hu J, Mou S. A single-cell survey of the human glomerulonephritis. J Cell Mol Med 2021; 25:4684-4695. [PMID: 33754492 PMCID: PMC8107090 DOI: 10.1111/jcmm.16407] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/08/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Glomerulonephritis is the one of the major causes of the end-stage kidney disease, whereas the pathological process of glomerulonephritis is still not completely understood. Single-cell RNA sequencing (scRNA-seq) emerges to be a powerful tool to evaluate the full heterogeneity of kidney diseases. To reveal cellular gene expression profiles of glomerulonephritis, we performed scRNA-seq of 2 human kidney transplantation donor samples, 4 human glomerulonephritis samples, 1 human malignant hypertension (MH) sample and 1 human chronic interstitial nephritis (CIN) sample, all tissues were taken from the biopsy. After filtering the cells with < 200 genes and > 10% mitochondria (MT) genes, the resulting 14 932 cells can be divided into 20 cell clusters, consistently with the previous report, in disease samples dramatic immune cells infiltration was found, among which a proximal tubule (PT) subset characterized by wnt-β catenin activation and a natural killer T (NKT) subset high expressing LTB were found. Furthermore, in the cluster of the podocyte, three glomerulonephritis related genes named FXYD5, CD74 and B2M were found. Compared with the mesangial of donor, the gene CLIC1 and RPS26 were up-regulated in mesangial of IgA nephropathy(IgAN), whereas the gene JUNB was up-regulated in podocyte of IgAN in comparison with that of donor. Meanwhile, some membranous nephropathy (MN) high expressed genes such as HLA-DRB5, HLA-DQA2, IFNG, CCL2 and NR4A2, which involve in highest enrichment pathway, display the cellular-specific expression style, whereas monocyte marker of lupus nephritis (LN) named TNFSF13B was also found and interferon alpha/beta signalling pathway was enriched in B and NKT of LN comparing with donor. By scRNA-seq, we first defined the podocyte markers of glomerulonephritis and specific markers in IgA, MN and LN were found at cellular level. Furthermore, the critical role of interferon alpha/beta signalling pathway was enriched in B and NKT of LN was declared.
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Affiliation(s)
- Zhejun Chen
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Zhang
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Kaiqiong Mao
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China
| | - Xinghua Shao
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yao Xu
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Minyan Zhu
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hang Zhou
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Wang
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenyuan Li
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - YuanYuan Xie
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaodong Yuan
- Transplantation Center of Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liang Ying
- Transplantation Center of Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Zhang
- Transplantation Center of Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiajia Hu
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Mou
- Department of Nephrology, Molecular Cell Laboratory for Kidney Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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31
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Rousselle T, Bardhi E, Maluf DG, Mas VR. Epigenetic modifications and the development of kidney graft fibrosis. Curr Opin Organ Transplant 2021; 26:1-9. [PMID: 33315766 PMCID: PMC8059991 DOI: 10.1097/mot.0000000000000839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW To outline recent discoveries in epigenetic regulatory mechanisms that have potential implications in the development of renal fibrosis following kidney transplantation. RECENT FINDINGS The characterization of renal fibrosis following kidney transplantation has shown TGFβ/Smad signaling to play a major role in the progression to chronic allograft dysfunction. The onset of unregulated proinflammatory pathways are only exacerbated by the decline in regulatory mechanisms lost with progressive patient age and comorbidities such as hypertension and diabetes. However, significant developments in the recognition of epigenetic regulatory markers upstream of aberrant TGFβ-signaling has significant clinical potential to provide therapeutic targets for the treatment of renal fibrosis. In addition, discoveries in extracellular vesicles and the characterization of their cargo has laid new framework for the potential to evaluate patient outcomes independent of invasive biopsies. SUMMARY The current review summarizes the main findings in epigenetic machinery specific to the development of renal fibrosis and highlights therapeutic options that have significant potential to translate into clinical practice.
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Affiliation(s)
- Thomas Rousselle
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
| | - Elissa Bardhi
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
| | - Daniel G. Maluf
- Surgical Sciences Division, Department of Surgery, School
of Medicine, University of Maryland
- Program in Transplantation, School of Medicine, University
of Maryland
| | - Valeria R. Mas
- Division of Transplant, Department of Surgery, School of
Medicine, University of Maryland
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32
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Kaur H, Advani A. The study of single cells in diabetic kidney disease. J Nephrol 2021; 34:1925-1939. [PMID: 33476038 DOI: 10.1007/s40620-020-00964-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/29/2020] [Indexed: 12/27/2022]
Abstract
In the past few years there has been a rapid expansion of interest in the study of single cells, especially through the new techniques that involve single-cell RNA sequencing (scRNA-seq). Recently, these techniques have provided new insights into kidney health and disease, including insights into diabetic kidney disease (DKD). However, despite the interest and the technological advances, the study of individual cells in DKD is not a new concept. Many clinicians and researchers who work within the DKD space may be familiar with experimental techniques that actually involve the study of individual cells, but may be unfamiliar with newer scRNA-seq technology. Here, with the goal of improving accessibility to the single-cell field, we provide a primer on single-cell studies with a focus on DKD. We situate the technology in its historical context and provide a brief explanation of the common aspects of the different technologies available. Then we review some of the most important recent studies of kidney (patho)biology that have taken advantage of scRNA-seq techniques, before emphasizing the new insights into the molecular pathogenesis of DKD gleaned with these techniques. Finally, we highlight common pitfalls and limitations of scRNA-seq methods and we look toward the future to how single-cell experiments may be incorporated into the study of DKD and how to interpret the findings of these experiments.
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Affiliation(s)
- Harmandeep Kaur
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, 6-151 61 Queen Street East, Toronto, ON, M5C 2T2, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michael's Hospital, 6-151 61 Queen Street East, Toronto, ON, M5C 2T2, Canada.
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33
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Kuppe C, Perales-Patón J, Saez-Rodriguez J, Kramann R. Experimental and computational technologies to dissect the kidney at the single-cell level. Nephrol Dial Transplant 2020; 37:628-637. [PMID: 33332571 DOI: 10.1093/ndt/gfaa233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
The field of single-cell technologies, in particular single-cell genomics with transcriptomics and epigenomics, and most recently single-cell proteomics, is rapidly growing and holds promise to advance our understanding of organ homoeostasis and disease, and facilitate the identification of novel therapeutic targets and biomarkers. This review offers an introduction to these technologies. In addition, as the size and complexity of the data require sophisticated computational methods for analysis and interpretation, we will also provide an overview of these methods and summarize the single-cell literature specifically pertaining to the kidney.
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Affiliation(s)
- Christoph Kuppe
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Javier Perales-Patón
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Rafael Kramann
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
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34
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Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy. Cell Rep 2020; 33:108525. [PMID: 33357427 DOI: 10.1016/j.celrep.2020.108525] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/07/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
IgA nephropathy (IgAN) is the leading cause of kidney failure due to an incomplete understanding of its pathogenesis. We perform single-cell RNA sequencing (RNA-seq) on kidneys and CD14+ peripheral blood mononuclear cells (PBMCs) collected from IgAN and normal samples. In IgAN, upregulation of JCHAIN in mesangial cells provides insight into the trigger mechanism for the dimerization and deposition of IgA1 in situ. The pathological mesangium also demonstrates a prominent inflammatory signature and increased cell-cell communication with other renal parenchymal cells and immune cells, suggesting disease progress from the mesangium to the entire kidney. Specific gene expression of kidney-resident macrophages and CD8+ T cells further indicates abnormal regulation associated with proliferation and inflammation. A transitional cell type among intercalated cells with fibrosis signatures is identified, suggesting an adverse outcome of interstitial fibrosis. Altogether, we systematically analyze the molecular events in the onset and progression of IgAN, providing a promising landscape for disease treatment.
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35
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Sigdel TK, Piehowski PD, Roy S, Liberto J, Hansen JR, Swensen AC, Zhao R, Zhu Y, Rashmi P, Schroeder A, Damm I, Sur S, Luo J, Yang Y, Qian WJ, Sarwal MM. Near-Single-Cell Proteomics Profiling of the Proximal Tubular and Glomerulus of the Normal Human Kidney. Front Med (Lausanne) 2020; 7:499. [PMID: 33072769 PMCID: PMC7533534 DOI: 10.3389/fmed.2020.00499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/21/2020] [Indexed: 01/21/2023] Open
Abstract
Molecular assessments at the single cell level can accelerate biological research by providing detailed assessments of cellular organization and tissue heterogeneity in both disease and health. The human kidney has complex multi-cellular states with varying functionality, much of which can now be completely harnessed with recent technological advances in tissue proteomics at a near single-cell level. We discuss the foundational steps in the first application of this mass spectrometry (MS) based proteomics method for analysis of sub-sections of the normal human kidney, as part of the Kidney Precision Medicine Project (KPMP). Using ~30-40 laser captured micro-dissected kidney cells, we identified more than 2,500 human proteins, with specificity to the proximal tubular (PT; n = 25 proteins) and glomerular (Glom; n = 67 proteins) regions of the kidney and their unique metabolic functions. This pilot study provides the roadmap for application of our near-single-cell proteomics workflow for analysis of other renal micro-compartments, on a larger scale, to unravel perturbations of renal sub-cellular function in the normal kidney as well as different etiologies of acute and chronic kidney disease.
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Affiliation(s)
- Tara K. Sigdel
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Paul D. Piehowski
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Sudeshna Roy
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Juliane Liberto
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Joshua R. Hansen
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Adam C. Swensen
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Priyanka Rashmi
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Andrew Schroeder
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Izabella Damm
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Swastika Sur
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Jinghui Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Yingbao Yang
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Wei-Jun Qian
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Minnie M. Sarwal
- Division of MultiOrgan Transplantation, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
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36
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Buchanan S, Combet E, Stenvinkel P, Shiels PG. Klotho, Aging, and the Failing Kidney. Front Endocrinol (Lausanne) 2020; 11:560. [PMID: 32982966 PMCID: PMC7481361 DOI: 10.3389/fendo.2020.00560] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Klotho has been recognized as a gene involved in the aging process in mammals for over 30 years, where it regulates phosphate homeostasis and the activity of members of the fibroblast growth factor (FGF) family. The α-Klotho protein is the receptor for Fibroblast Growth Factor-23 (FGF23), regulating phosphate homeostasis and vitamin D metabolism. Phosphate toxicity is a hallmark of mammalian aging and correlates with diminution of Klotho levels with increasing age. As such, modulation of Klotho activity is an attractive target for therapeutic intervention in the diseasome of aging; in particular for chronic kidney disease (CKD), where Klotho has been implicated directly in the pathophysiology. A range of senotherapeutic strategies have been developed to directly or indirectly influence Klotho expression, with varying degrees of success. These include administration of exogenous Klotho, synthetic and natural Klotho agonists and indirect approaches, via modulation of the foodome and the gut microbiota. All these approaches have significant potential to mitigate loss of physiological function and resilience accompanying old age and to improve outcomes within the diseasome of aging.
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Affiliation(s)
- Sarah Buchanan
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Emilie Combet
- School of Medicine, Dentistry & Nursing, Human Nutrition, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Peter Stenvinkel
- Division of Renal Medicine M99, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Paul G. Shiels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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37
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Shangguan Y, Li C, Lin H, Ou M, Tang D, Dai Y, Yan Q. Application of single-cell RNA sequencing in embryonic development. Genomics 2020; 112:4547-4551. [PMID: 32781204 DOI: 10.1016/j.ygeno.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Embryonic development is a complex process that is regulated by a series of precise cellular behaviours. The limited number of cells in the early stages of embryonic development represents a challenge for studying early gene regulation and maintaining cell sternness. Single-cell sequencing is a new technology for high-throughput sequencing analysis at the single-cell level that not only reflects the heterogeneity between cells but also reveals gene expression characteristics in different cells from limited samples. Currently, the widespread application of single-cell RNA sequencing technology is gradually changing our understanding of disease pathogenesis. This article reviews the application of single-cell RNA sequencing in embryonic development in recent years and provides innovative ideas for research on embryonic development and the treatment of diseases related to embryonic development.
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Affiliation(s)
- Yu Shangguan
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Chunhong Li
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Hua Lin
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China
| | - Minglin Ou
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China
| | - Donge Tang
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China.
| | - Yong Dai
- Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China; Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen 518020, China.
| | - Qiang Yan
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China; Organ transplantion center of Guilin 924st Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin, Guangxi 541002, China.
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38
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Li H, Humphreys BD. Surveying the human single-cell landscape. Kidney Int 2020; 98:1385-1387. [PMID: 32679106 DOI: 10.1016/j.kint.2020.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/24/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St Louis, Missouri, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St Louis, Missouri, USA; Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.
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39
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Zheng G, Xie ZY, Wang P, Wu YF, Shen HY. Recent advances of single-cell RNA sequencing technology in mesenchymal stem cell research. World J Stem Cells 2020; 12:438-447. [PMID: 32742561 PMCID: PMC7360991 DOI: 10.4252/wjsc.v12.i6.438] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are multipotent stromal cells with great potential for clinical applications. However, little is known about their cell heterogeneity at a single-cell resolution, which severely impedes the development of MSC therapy. In this review, we focus on advances in the identification of novel surface markers and functional subpopulations of MSCs made by single-cell RNA sequencing and discuss their participation in the pathophysiology of stem cells and related diseases. The challenges and future directions of single-cell RNA sequencing in MSCs are also addressed in this review.
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Affiliation(s)
- Guan Zheng
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, Guangdong Province, China
| | - Zhong-Yu Xie
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, Guangdong Province, China
| | - Peng Wang
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, Guangdong Province, China
| | - Yan-Feng Wu
- Center for Biotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong Province, China
| | - Hui-Yong Shen
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, Guangdong Province, China
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40
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Wu H, Humphreys BD. Single Cell Sequencing and Kidney Organoids Generated from Pluripotent Stem Cells. Clin J Am Soc Nephrol 2020; 15:550-556. [PMID: 31992574 PMCID: PMC7133134 DOI: 10.2215/cjn.07470619] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Methods to differentiate human pluripotent stem cells into kidney organoids were first introduced about 5 years ago, and since that time, the field has grown substantially. Protocols are producing increasingly complex three-dimensional structures, have been used to model human kidney disease, and have been adapted for high-throughput screening. Over this same time frame, technologies for massively parallel, single-cell RNA sequencing (scRNA-seq) have matured. Now, both of these powerful approaches are being combined to better understand how kidney organoids can be applied to the understanding of kidney development and disease. There are several reasons why this is a synergistic combination. Kidney organoids are complicated and contain many different cell types of variable maturity. scRNA-seq is an unbiased technology that can comprehensively categorize cell types, making it ideally suited to catalog all cell types present in organoids. These same characteristics also make scRNA-seq a powerful approach for quantitative comparisons between protocols, batches, and pluripotent cell lines as it becomes clear that reproducibility and quality can vary across all three variables. Lineage trajectories can be reconstructed using scRNA-seq data, enabling the rational adjustment of differentiation strategies to promote maturation of desired kidney cell types or inhibit differentiation of undesired off-target cell types. Here, we review the ways that scRNA-seq has been successfully applied in the organoid field and predict future applications for this powerful technique. We also review other developing single-cell technologies and discuss how they may be combined, using "multiomic" approaches, to improve our understanding of kidney organoid differentiation and usefulness in modeling development, disease, and toxicity testing.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine; and
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine; and
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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41
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Sealfon RSG, Mariani LH, Kretzler M, Troyanskaya OG. Machine learning, the kidney, and genotype-phenotype analysis. Kidney Int 2020; 97:1141-1149. [PMID: 32359808 PMCID: PMC8048707 DOI: 10.1016/j.kint.2020.02.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 01/13/2020] [Accepted: 02/06/2020] [Indexed: 01/23/2023]
Abstract
With biomedical research transitioning into data-rich science, machine learning provides a powerful toolkit for extracting knowledge from large-scale biological data sets. The increasing availability of comprehensive kidney omics compendia (transcriptomics, proteomics, metabolomics, and genome sequencing), as well as other data modalities such as electronic health records, digital nephropathology repositories, and radiology renal images, makes machine learning approaches increasingly essential for analyzing human kidney data sets. Here, we discuss how machine learning approaches can be applied to the study of kidney disease, with a particular focus on how they can be used for understanding the relationship between genotype and phenotype.
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Affiliation(s)
- Rachel S G Sealfon
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Laura H Mariani
- Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA.
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA; Department of Computer Science, Princeton University, Princeton, New Jersey, USA.
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42
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Perretta-Tejedor N, Jafree DJ, Long DA. Endothelial-epithelial communication in polycystic kidney disease: Role of vascular endothelial growth factor signalling. Cell Signal 2020; 72:109624. [PMID: 32243961 DOI: 10.1016/j.cellsig.2020.109624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022]
Abstract
Whereas targeting the cyst epithelium and its molecular machinery has been the prevailing clinical strategy for polycystic kidney disease, the endothelium, including blood vasculature and lymphatics, is emerging as an important player in this disorder. In this Review, we provide an overview of the structural and functional alterations to blood vasculature and lymphatic vessels in the polycystic kidney. We also discuss evidence for vascular endothelial growth factor signalling, otherwise critical for endothelial cell development and maintenance, as being a fundamental molecular pathway in polycystic kidney disease and a potential therapeutic target for modulating cyst expansion.
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Affiliation(s)
- Nuria Perretta-Tejedor
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Daniyal J Jafree
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK; UCL MB/PhD Programme, Faculty of Medical Sciences, University College London, London, UK
| | - David A Long
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, London, UK.
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43
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Kidney and organoid single-cell transcriptomics: the end of the beginning. Pediatr Nephrol 2020; 35:191-197. [PMID: 30607565 PMCID: PMC6609508 DOI: 10.1007/s00467-018-4177-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/01/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies are increasingly being applied to reveal cellular heterogeneity in kidney development and disease. In just the last year, multiple scRNA-seq datasets have been generated from kidney organoids, developing mouse and human kidney, adult kidney, and kidney cancer. The data generated enables a much deeper understanding of biological processes within and between cells. It has also elucidated unforeseen cell lineage relationships, defined the presence of off-target cell types in kidney organoids, and revealed a diverse inflammatory response in a human kidney allograft undergoing rejection. This review summarizes the recent rapid progress in scRNA-seq of the kidney and outlines future directions for single-cell technologies as applied to the kidney.
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44
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Schaub JA, Hamidi H, Subramanian L, Kretzler M. Systems Biology and Kidney Disease. Clin J Am Soc Nephrol 2020; 15:695-703. [PMID: 31992571 PMCID: PMC7269226 DOI: 10.2215/cjn.09990819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The kidney is a complex organ responsible for maintaining multiple aspects of homeostasis in the human body. The combination of distinct, yet interrelated, molecular functions across different cell types make the delineation of factors associated with loss or decline in kidney function challenging. Consequently, there has been a paucity of new diagnostic markers and treatment options becoming available to clinicians and patients in managing kidney diseases. A systems biology approach to understanding the kidney leverages recent advances in computational technology and methods to integrate diverse sets of data. It has the potential to unravel the interplay of multiple genes, proteins, and molecular mechanisms that drive key functions in kidney health and disease. The emergence of large, detailed, multilevel biologic and clinical data from national databases, cohort studies, and trials now provide the critical pieces needed for meaningful application of systems biology approaches in nephrology. The purpose of this review is to provide an overview of the current state in the evolution of the field. Recent successes of systems biology to identify targeted therapies linked to mechanistic biomarkers in the kidney are described to emphasize the relevance to clinical care and the outlook for improving outcomes for patients with kidney diseases.
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Affiliation(s)
- Jennifer A Schaub
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Habib Hamidi
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lalita Subramanian
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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45
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Abstract
Decades of pre-clinical research have revealed biologic pathways that have suggested potential therapies for acute kidney injury (AKI) in experimental models. However, translating these to human AKI has largely yielded disappointing results. Fortunately, recent discoveries in AKI molecular mechanisms are providing new opportunities for early detection and novel interventions. This review identifies technologies that are revealing the exceptionally complex nature of the normal kidney, the remarkable heterogeneity of the AKI syndrome, and the myriad responses of the kidney to AKI. Based on the current state of the art, novel approaches to improve the bench-to-bedside translation of novel discoveries are proposed. These strategies include the use of unbiased approaches to improve our understanding of human AKI, establishment of irrefutable biologic plausibility for proposed biomarkers and therapies, identification of patients at risk for AKI pre-injury using clinical scores and non-invasive biomarkers, initiation of safe, and effective preventive interventions of pre-injury in susceptible patients, identification of patients who may develop AKI post-injury using electronic triggers, clinical scores, and novel biomarkers, employment of sequential biomarkers to initiate appropriate therapies based on knowledge of the underlying pathophysiology, use of new biomarkers as criteria for enrollment in randomized clinical trials, assessing efficacy, and empowering the drug development process, and early initiation of anti-fibrotic therapies. These strategies are immediately actionable and hold tremendous promise for effective bench-to-bedside translation of novel discoveries that will change the current dismal prognosis of human AKI.
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Affiliation(s)
- Prasad Devarajan
- Department of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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46
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Wilson PC, Humphreys BD. Single-cell genomics and gene editing: implications for nephrology. Nat Rev Nephrol 2019; 15:63-64. [PMID: 30568287 DOI: 10.1038/s41581-018-0094-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Parker C Wilson
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine, St. Louis, MO, USA. .,Department of Developmental Biology, Washington University in Saint Louis School of Medicine, St. Louis, MO, USA.
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47
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Fan Y, Yi Z, D'Agati VD, Sun Z, Zhong F, Zhang W, Wen J, Zhou T, Li Z, He L, Zhang Q, Lee K, He JC, Wang N. Comparison of Kidney Transcriptomic Profiles of Early and Advanced Diabetic Nephropathy Reveals Potential New Mechanisms for Disease Progression. Diabetes 2019; 68:2301-2314. [PMID: 31578193 PMCID: PMC6868471 DOI: 10.2337/db19-0204] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023]
Abstract
To identify the factors mediating the progression of diabetic nephropathy (DN), we performed RNA sequencing of kidney biopsy samples from patients with early DN, advanced DN, and normal kidney tissue from nephrectomy samples. A set of genes that were upregulated at early but downregulated in late DN were shown to be largely renoprotective, which included genes in the retinoic acid pathway and glucagon-like peptide 1 receptor. Another group of genes that were downregulated at early but highly upregulated in advanced DN consisted mostly of genes associated with kidney disease pathogenesis, such as those related to immune response and fibrosis. Correlation with estimated glomerular filtration rate (eGFR) identified genes in the pathways of iron transport and cell differentiation to be positively associated with eGFR, while those in the immune response and fibrosis pathways were negatively associated. Correlation with various histopathological features also identified the association with the distinct gene ontological pathways. Deconvolution analysis of the RNA sequencing data set indicated a significant increase in monocytes, fibroblasts, and myofibroblasts in advanced DN kidneys. Our study thus provides potential molecular mechanisms for DN progression and association of differential gene expression with the functional and structural changes observed in patients with early and advanced DN.
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Affiliation(s)
- Ying Fan
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zhengzi Yi
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vivette D D'Agati
- Department of Pathology, Columbia University Medical Center, New York, NY
| | - Zeguo Sun
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Fang Zhong
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jiejun Wen
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ting Zhou
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ze Li
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Li He
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qunzi Zhang
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Kidney Center at James J. Peters VA Medical Center, Bronx, NY
| | - Niansong Wang
- Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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48
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Tajti F, Kuppe C, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Holland CH, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. A Functional Landscape of CKD Entities From Public Transcriptomic Data. Kidney Int Rep 2019; 5:211-224. [PMID: 32043035 PMCID: PMC7000845 DOI: 10.1016/j.ekir.2019.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/09/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022] Open
Abstract
Introduction To develop effective therapies and identify novel early biomarkers for chronic kidney disease, an understanding of the molecular mechanisms orchestrating it is essential. We here set out to understand how differences in chronic kidney disease (CKD) origin are reflected in gene expression. To this end, we integrated publicly available human glomerular microarray gene expression data for 9 kidney disease entities that account for most of CKD worldwide. Our primary goal was to demonstrate the possibilities and potential on data analysis and integration to the nephrology community. Methods We integrated data from 5 publicly available studies and compared glomerular gene expression profiles of disease with that of controls from nontumor parts of kidney cancer nephrectomy tissues. A major challenge was the integration of the data from different sources, platforms, and conditions that we mitigated with a bespoke stringent procedure. Results We performed a global transcriptome-based delineation of different kidney disease entities, obtaining a transcriptomic diffusion map of their similarities and differences based on the genes that acquire a consistent differential expression between each kidney disease entity and nephrectomy tissue. We derived functional insights by inferring the activity of signaling pathways and transcription factors from the collected gene expression data and identified potential drug candidates based on expression signature matching. We validated representative findings by immunostaining in human kidney biopsies indicating, for example, that the transcription factor FOXM1 is significantly and specifically expressed in parietal epithelial cells in rapidly progressive glomerulonephritis (RPGN) whereas not expressed in control kidney tissue. Furthermore, we found drug candidates by matching the signature on expression of drugs to that of the CKD entities, in particular, the Food and Drug Administration-approved drug nilotinib. Conclusion These results provide a foundation to comprehend the specific molecular mechanisms underlying different kidney disease entities that can pave the way to identify biomarkers and potential therapeutic targets. To facilitate further use, we provide our results as a free interactive Web application: https://saezlab.shinyapps.io/ckd_landscape/. However, because of the limitations of the data and the difficulties in its integration, any specific result should be considered with caution. Indeed, we consider this study rather an illustration of the value of functional genomics and integration of existing data.
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Affiliation(s)
- Ferenc Tajti
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Christoph Kuppe
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Asier Antoranz
- Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.,Department of Testing Services, ProtATonce Ltd., Athens, Greece
| | - Mahmoud M Ibrahim
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Hyojin Kim
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Francesco Ceccarelli
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Christian H Holland
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany
| | - Hannes Olauson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Leonidas G Alexopoulos
- Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.,Department of Testing Services, ProtATonce Ltd., Athens, Greece
| | - Rafael Kramann
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany
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49
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Park J, Liu CL, Kim J, Susztak K. Understanding the kidney one cell at a time. Kidney Int 2019; 96:862-870. [PMID: 31492507 PMCID: PMC6777841 DOI: 10.1016/j.kint.2019.03.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 01/19/2023]
Abstract
A revolution in cellular measurement technology is underway. Whereas prior studies have been able to analyze only the averaged outputs from renal tissue, we now can accurately monitor genome-wide gene expression, regulation, function, cellular history, and cellular interactions in thousands of individual cells in a single experiment. These methods are key drivers in changing our previous morphotype-based organ and disease descriptions to unbiased genomic definitions and therefore improving our understanding of kidney development, homeostasis, and disease.
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Affiliation(s)
- Jihwan Park
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chang Linda Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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50
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Abais-Battad JM, Alsheikh AJ, Pan X, Fehrenbach DJ, Dasinger JH, Lund H, Roberts ML, Kriegel AJ, Cowley AW, Kidambi S, Kotchen TA, Liu P, Liang M, Mattson DL. Dietary Effects on Dahl Salt-Sensitive Hypertension, Renal Damage, and the T Lymphocyte Transcriptome. Hypertension 2019; 74:854-863. [PMID: 31476910 DOI: 10.1161/hypertensionaha.119.12927] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Dahl salt-sensitive (SS) rat is an established model of SS hypertension and renal damage. In addition to salt, other dietary components were shown to be important determinants of hypertension in SS rats. With previous work eliminating the involvement of genetic differences, grain-fed SS rats from Charles River Laboratories (SS/CRL; 5L2F/5L79) were less susceptible to salt-induced hypertension and renal damage compared with purified diet-fed SS rats bred at the Medical College of Wisconsin (SS/MCW; 0.4% NaCl, AIN-76A). With the known role of immunity in hypertension, the present study characterized the immune cells infiltrating SS/MCW and SS/CRL kidneys via flow cytometry and RNA sequencing in T-cells isolated from the blood and kidneys of rats maintained on their respective parental diet or on 3 weeks of high salt (4.0% NaCl, AIN-76A). SS/CRL rats were protected from salt-induced hypertension (116.5±1.2 versus 141.9±14.4 mm Hg), albuminuria (21.7±3.5 versus 162.9±22.2 mg/d), and renal immune cell infiltration compared with SS/MCW. RNA-seq revealed >50% of all annotated genes in the entire transcriptome to be significantly differentially expressed in T-cells isolated from blood versus kidney, regardless of colony or chow. Pathway analysis of significantly differentially expressed genes between low and high salt conditions demonstrated changes related to inflammation in SS/MCW renal T-cells compared with metabolism-related pathways in SS/CRL renal T-cells. These functional and transcriptomic T-cell differences between SS/MCW and SS/CRL show that dietary components in addition to salt may influence immunity and the infiltration of immune cells into the kidney, ultimately impacting susceptibility to salt-induced hypertension and renal damage.
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Affiliation(s)
- Justine M Abais-Battad
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Ammar J Alsheikh
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Xiaoqing Pan
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Daniel J Fehrenbach
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - John Henry Dasinger
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Hayley Lund
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Michelle L Roberts
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Alison J Kriegel
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Allen W Cowley
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Srividya Kidambi
- Department of Medicine (S.K., T.A.K.), Medical College of Wisconsin
| | | | - Pengyuan Liu
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - Mingyu Liang
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
| | - David L Mattson
- From the Department of Physiology (J.M.A.-B., A.J.A., X.P., D.J.F., J.H.D., H.L., M.L.R., A.J.K., A.W.C., P.L., M.L., D.L.M.), Medical College of Wisconsin
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