1
|
Liu L, Chen Y, Li X, Wang J, Yang L. Therapeutic potential: The role of mesenchymal stem cells from diverse sources and their derived exosomes in diabetic nephropathy. Biomed Pharmacother 2024; 175:116672. [PMID: 38677249 DOI: 10.1016/j.biopha.2024.116672] [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: 02/13/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024] Open
Abstract
Diabetic nephropathy (DN) is one of the most common microvascular complications in diabetic patients, with its incidence continuously increasing in recent years. DN causes renal tissue damage and functional decline, expedites the aging process of the kidneys, and may ultimately progress leading to end-stage renal disease, severely impacting the patient's quality of life and prognosis. Mesenchymal stem cells (MSCs) are highly valued for their multipotent differentiation, paracrine functions, immunomodulatory effects, and capacity for tissue repair. Particularly, exosomes (Exo) derived from MSCs (MSCs-Exo) are rich in bioactive molecules and facilitate intercellular communication, participating in various physiological and pathological processes. MSCs and MSCs-Exo, in particular, have been demonstrated to have therapeutic effects in DN treatment research by encouraging tissue repair, fibrosis inhibition, and inflammation reduction. Research has shown that MSCs and MSCs-Exo have therapeutic effects in DN treatment by promoting tissue repair, inhibiting fibrosis, and reducing inflammation. Recent studies underscore the potential of MSCs and MSCs-Exo, highlighting their broad applicability in DN treatment. This review aims to provide a comprehensive summary of the scientific developments in treating DN using MSCs and MSCs-Exo from diverse sources, while also exploring their future therapeutic possibilities in detail.
Collapse
Affiliation(s)
- Lixin Liu
- Departments of Geriatrics, The First Hospital of China Medical University, Shenyang, Liaoning 110001, PR China
| | - Yiman Chen
- Departments of Geriatrics, The First Hospital of China Medical University, Shenyang, Liaoning 110001, PR China
| | - Xuan Li
- Department of Vascular and Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, PR China.
| | - Juan Wang
- Department of Nephrology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, PR China.
| | - Lina Yang
- Departments of Geriatrics, The First Hospital of China Medical University, Shenyang, Liaoning 110001, PR China; Department of International Physical Examination Center, The First Hospital of China Medical University, Shenyang, Liaoning 110001, PR China.
| |
Collapse
|
2
|
Staruschenko A. SGLT2 inhibitors: not every drug has the same effect. Am J Physiol Renal Physiol 2024; 326:F1039-F1040. [PMID: 38695073 DOI: 10.1152/ajprenal.00126.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Affiliation(s)
- Alexander Staruschenko
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida, United States
- Hypertension and Kidney Research Center, University of South FloridaTampa, Florida, United States
- James A. Haley Veterans Hospital, Tampa, Florida, United States
| |
Collapse
|
3
|
Kume S, Packer M. SGLT2 inhibitors act as metabolic transducers to restore healthy nutrient deprivation and surplus signaling in the kidney. Kidney Int 2024; 105:1172-1176. [PMID: 38777403 DOI: 10.1016/j.kint.2024.01.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 05/25/2024]
Affiliation(s)
- Shinji Kume
- Department of Medicine, Shiga University of Medical Science, Ostu, Shiga, Japan.
| | - Milton Packer
- Baylor University Medical Center, Dallas, Texas, USA; Imperial College, London, UK.
| |
Collapse
|
4
|
Gaudet A, Zheng X, Kambham N, Bhalla V. Esm-1 mediates transcriptional polarization associated with diabetic kidney disease. Am J Physiol Renal Physiol 2024; 326:F1016-F1031. [PMID: 38601985 DOI: 10.1152/ajprenal.00419.2023] [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: 12/22/2023] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
Esm-1, endothelial cell-specific molecule-1, is a susceptibility gene for diabetic kidney disease (DKD) and is a secreted proteoglycan, with notable expression in kidney, which attenuates inflammation and albuminuria. However, little is known about Esm1 expression in mature tissues in the presence or absence of diabetes. We utilized publicly available single-cell RNA sequencing data to characterize Esm1 expression in 27,786 renal endothelial cells (RECs) obtained from three mouse and four human databases. We validated our findings using bulk transcriptome data from 20 healthy subjects and 41 patients with DKD and using RNAscope. In both mice and humans, Esm1 is expressed in a subset of all REC types and represents a minority of glomerular RECs. In patients, Esm1(+) cells exhibit conserved enrichment for blood vessel development genes. With diabetes, these cells are fewer in number and shift expression toward chemotaxis pathways. Esm1 correlates with a majority of genes within these pathways, delineating a glomerular transcriptional polarization reflected by the magnitude of Esm1 deficiency. Diabetes correlates with lower Esm1 expression and with changes in the functional characterization of Esm1(+) cells. Thus, Esm1 appears to be a marker for glomerular transcriptional polarization in DKD.NEW & NOTEWORTHY Esm-1 is primarily expressed in glomerular endothelium in humans. Cells expressing Esm1 exhibit a high degree of conservation in the enrichment of genes related to blood vessel development. In the context of diabetes, these cells are reduced in number and show a significant transcriptional shift toward the chemotaxis pathway. In diabetes, there is a transcriptional polarization in the glomerulus that is reflected by the degree of Esm1 deficiency.
Collapse
Affiliation(s)
- Alexandre Gaudet
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Xiaoyi Zheng
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States
| | - Neeraja Kambham
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States
| | - Vivek Bhalla
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States
| |
Collapse
|
5
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
6
|
Nangaku M. SGLT2 inhibitor: 2-way superstar in nephrology? Kidney Int 2024; 105:1176-1177. [PMID: 38777404 DOI: 10.1016/j.kint.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 05/25/2024]
Affiliation(s)
- Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan.
| |
Collapse
|
7
|
Chen XJ, Tang R, Zha J, Zeng L, Zhou L, Liu Z, Yang D, Zeng M, Zhu X, Chen A, Liu H, Chen H, Chen G. A potential defensive role of TIM-3 on T lymphocytes in the inflammatory involvement of diabetic kidney disease. Front Immunol 2024; 15:1365226. [PMID: 38812511 PMCID: PMC11133625 DOI: 10.3389/fimmu.2024.1365226] [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: 01/04/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Objective The aberrant mobilization and activation of various T lymphocyte subpopulations play a pivotal role in the pathogenesis of diabetic kidney disease (DKD), yet the regulatory mechanisms underlying these processes remain poorly understood. Our study is premised on the hypothesis that the dysregulation of immune checkpoint molecules on T lymphocytes disrupts kidney homeostasis, instigates pathological inflammation, and promotes DKD progression. Methods A total of 360 adult patients with DKD were recruited for this study. The expression of immune checkpoint molecules on T lymphocytes was assessed by flow cytometry for peripheral blood and immunofluorescence staining for kidney tissue. Single-cell sequencing (scRNA-seq) data from the kidneys of DKD mouse model were analyzed. Results Patients with DKD exhibited a reduction in the proportion of CD3+TIM-3+ T cells in circulation concurrent with the emergence of significant albuminuria and hematuria (p=0.008 and 0.02, respectively). Conversely, the incidence of infection during DKD progression correlated with an elevation of peripheral CD3+TIM-3+ T cells (p=0.01). Both univariate and multivariate logistic regression analysis revealed a significant inverse relationship between the proportion of peripheral CD3+TIM-3+ T cells and severe interstitial mononuclear infiltration (OR: 0.193, 95%CI: 0.040,0.926, p=0.04). Immunofluorescence assays demonstrated an increase of CD3+, TIM-3+ and CD3+TIM-3+ interstitial mononuclear cells in the kidneys of DKD patients as compared to patients diagnosed with minimal change disease (p=0.03, 0.02 and 0.002, respectively). ScRNA-seq analysis revealed decreased gene expression of TIM3 on T lymphocytes in DKD compared to control. And one of TIM-3's main ligands, Galectin-9 on immune cells showed a decreasing trend in gene expression as kidney damage worsened. Conclusion Our study underscores the potential protective role of TIM-3 on T lymphocytes in attenuating the progression of DKD and suggests that monitoring circulating CD3+TIM3+ T cells may serve as a viable strategy for identifying DKD patients at heightened risk of disease progression.
Collapse
Affiliation(s)
- Xiao-Jun Chen
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Runyan Tang
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Jie Zha
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Li Zeng
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Linshan Zhou
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Zhiwen Liu
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Danyi Yang
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Mengru Zeng
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Xuejing Zhu
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Anqun Chen
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Hong Liu
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Huihui Chen
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Guochun Chen
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Changsha, China
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| |
Collapse
|
8
|
Luo X, Guo J, Deng H, He Z, Wen Y, Si Z, Li J. Unveiling the role of disulfidptosis-related genes in the pathogenesis of non-alcoholic fatty liver disease. Front Immunol 2024; 15:1386905. [PMID: 38812509 PMCID: PMC11133613 DOI: 10.3389/fimmu.2024.1386905] [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: 02/16/2024] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
Backgrounds Non-alcoholic fatty liver disease (NAFLD) presents as a common liver disease characterized by an indistinct pathogenesis. Disulfidptosis is a recently identified mode of cell death. This study aimed to investigate the potential role of disulfidptosis-related genes (DRGs) in the pathogenesis of NAFLD. Methods Gene expression profiles were obtained from the bulk RNA dataset GSE126848 and the single-cell RNA dataset GSE136103, both associated with NAFLD. Our study assessed the expression of DRGs in NAFLD and normal tissues. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were employed to identify the key NAFLD-specific differentially expressed DRGs (DE-DRGs). To explore the biological functions and immune regulatory roles of these key DE-DRGs, we conducted immune infiltration analysis, functional enrichment analysis, consensus clustering analysis, and single-cell differential state analysis. Finally, we validated the expression and biological functions of DRGs in NAFLD patients using histology and RNA-sequencing transcriptomic assays with human liver tissue samples. Results Through the intersection of WGCNA, differentially expressed genes, and DRGs, two key DE-DRGs (DSTN and MYL6) were identified. Immune infiltration analysis indicated a higher proportion of macrophages, T cells, and resting dendritic cells in NAFLD compared to control liver samples. Based on the key DE-DRGs, Two disulfidptosis clusters were defined in GSE126848. Cluster 1, with higher expression of the key DE-DRGs, exhibited increased immune infiltration abundance and was closely associated with oxidative stress and immune regulation compared to cluster 2. High-resolution analysis of mononuclear phagocytes highlighted the potential role of MYL6 in intrahepatic M1 phenotype Kupffer cells in NAFLD patients. Our transcriptome data revealed that the expression levels of the majority of DRGs were significantly increased in NAFLD patients. NAFLD patients exhibit elevated MYL6 correlating with inflammation, oxidative stress, and disease severity, offering promising diagnostic specificity. Conclusion This comprehensive study provides evidence for the association between NAFLD and disulfidptosis, identifying potential target genes and pathways in NAFLD. The identification of MYL6 as a possible treatment target for NAFLD provided a novel understanding of the disease's development.
Collapse
Affiliation(s)
| | | | | | | | | | - Zhongzhou Si
- Department of Liver Transplant, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jiequn Li
- Department of Liver Transplant, The Second Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
9
|
Li H, Li D, Ledru N, Xuanyuan Q, Wu H, Asthana A, Byers LN, Tullius SG, Orlando G, Waikar SS, Humphreys BD. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy. Cell Metab 2024; 36:1105-1125.e10. [PMID: 38513647 PMCID: PMC11081846 DOI: 10.1016/j.cmet.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct kidney anatomical regions. We generated transcriptomes of 446,267 cells and chromatin accessibility profiles of 401,875 cells and developed a package to analyze 408,218 spatially resolved metabolomes. We find that the same cell type, including thin limb, thick ascending limb loop of Henle and principal cells, display distinct transcriptomic, chromatin accessibility, and metabolomic signatures, depending on anatomic location. Surveying metabolism-associated gene profiles revealed non-overlapping metabolic signatures between nephron segments and dysregulated lipid metabolism in diseased proximal tubule (PT) cells. Integrating multimodal omics with clinical data identified PLEKHA1 as a disease marker, and its in vitro knockdown increased gene expression in PT differentiation, suggesting possible pathogenic roles. This study highlights previously underrepresented cellular heterogeneity underlying the human kidney anatomy.
Collapse
Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Qiao Xuanyuan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Amish Asthana
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Lori N Byers
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Stefan G Tullius
- Division of Transplant Surgery and Transplant Surgery Research Laboratory, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Giuseppe Orlando
- Department of Surgery, Atrium Health Wake Forest Baptist, Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
10
|
Dobner S, Tóth F, de Rooij LPMH. A high-resolution view of the heterogeneous aging endothelium. Angiogenesis 2024; 27:129-145. [PMID: 38324119 PMCID: PMC11021252 DOI: 10.1007/s10456-023-09904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024]
Abstract
Vascular endothelial cell (EC) aging has a strong impact on tissue perfusion and overall cardiovascular health. While studies confined to the investigation of aging-associated vascular readouts in one or a few tissues have already drastically expanded our understanding of EC aging, single-cell omics and other high-resolution profiling technologies have started to illuminate the intricate molecular changes underlying endothelial aging across diverse tissues and vascular beds at scale. In this review, we provide an overview of recent insights into the heterogeneous adaptations of the aging vascular endothelium. We address critical questions regarding tissue-specific and universal responses of the endothelium to the aging process, EC turnover dynamics throughout lifespan, and the differential susceptibility of ECs to acquiring aging-associated traits. In doing so, we underscore the transformative potential of single-cell approaches in advancing our comprehension of endothelial aging, essential to foster the development of future innovative therapeutic strategies for aging-associated vascular conditions.
Collapse
Affiliation(s)
- Sarah Dobner
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fanni Tóth
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Laura P M H de Rooij
- The CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| |
Collapse
|
11
|
Tong M, Bai Y, Han X, Kong L, Ren L, Zhang L, Li X, Yao J, Yan B. Single-cell profiling transcriptomic reveals cellular heterogeneity and cellular crosstalk in choroidal neovascularization model. Exp Eye Res 2024; 242:109877. [PMID: 38537669 DOI: 10.1016/j.exer.2024.109877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/01/2024]
Abstract
Choroidal neovascularization (CNV) is a hallmark of neovascular age-related macular degeneration (nAMD) and a major contributor to vision loss in nAMD cases. However, the identification of specific cell types associated with nAMD remains challenging. Herein, we performed single-cell sequencing to comprehensively explore the cellular diversity and understand the foundational components of the retinal pigment epithelium (RPE)/choroid complex. We unveiled 10 distinct cell types within the RPE/choroid complex. Notably, we observed significant heterogeneity within endothelial cells (ECs), fibroblasts, and macrophages, underscoring the intricate nature of the cellular composition in the RPE/choroid complex. Within the EC category, four distinct clusters were identified and EC cluster 0 was tightly associated with choroidal neovascularization. We identified five clusters of fibroblasts actively involved in the pathogenesis of nAMD, influencing fibrotic responses, angiogenic effects, and photoreceptor function. Additionally, three clusters of macrophages were identified, suggesting their potential roles in regulating the progression of nAMD through immunomodulation and inflammation regulation. Through CellChat analysis, we constructed a complex cell-cell communication network, revealing the role of EC clusters in interacting with fibroblasts and macrophages in the context of nAMD. These interactions were found to govern angiogenic effects, fibrotic responses, and inflammatory processes. In summary, this study reveals noteworthy cellular heterogeneity in the RPE/choroid complex and provides valuable insights into the pathogenesis of CNV. These findings will open up potential avenues for deep understanding and targeted therapeutic interventions in nAMD.
Collapse
Affiliation(s)
- Ming Tong
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yun Bai
- College of Information Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoyan Han
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Lingjie Kong
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Ling Ren
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Linyu Zhang
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, 210000, China; The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Xiumiao Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Jin Yao
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, 210000, China; The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210000, China.
| | - Biao Yan
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| |
Collapse
|
12
|
Wang C, Pan Z, Sun L, Li Q. Integrative transcriptomic and proteomic profile revealed inhibition of oxidative phosphorylation and peroxisomes during renal interstitial fibrosis. J Proteomics 2024; 298:105144. [PMID: 38431085 DOI: 10.1016/j.jprot.2024.105144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Effective therapies of chronic kidney disease (CKD) are lacking due to the unclear molecular pathogenesis. Previous single omics-studies have described potential molecular regulation mechanism of CKD only at the level of transcription or translation. Therefore, this study generated an integrated transcriptomic and proteomic profile to provide deep insights into the continuous transcription-translation process during CKD. The comprehensive datasets identified 14,948 transcripts and 6423 proteins, 233 up-regulated and 364 down-regulated common differentially expressed genes of transcriptome and proteome were selected to further combined bioinformatics analysis. The obtained results revealed reactive oxygen species (ROS) metabolism and antioxidant system due to imbalance of mitochondria and peroxisomes were significantly repressed in CKD. Overall, this study presents a valuable multi-omics analysis that sheds light on the molecular mechanisms underlying CKD. SIGNIFICANCE: Chronic kidney disease (CKD) is a progressive and irreversible condition that results in abnormal kidney function and structure, and is ranked 18th among the leading causes of death globally, leading to a significant societal burden. Hence, there is an urgent need for research to detect new, sensitive, and specific biomarkers. Omics-based studies offer great potential to identify underlying disease mechanisms, aid in clinical diagnosis, and develop novel treatment strategies for CKD. Previous studies have mainly focused on the regulation of gene expression or protein synthesis in CKD, thereby compelling us to conduct a meticulous analysis of transcriptomic and proteomic data from the UUO mouse model. Here, we have performed a unified analysis of CKD model by integrating transcriptomes and protein suites for the first time. Our study contributes to a deeper understanding of the pathogenesis of CKD and provides a basis for subsequent disease management and drug development.
Collapse
Affiliation(s)
- Cheng Wang
- Department of Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, PR China
| | - Zhuo Pan
- Department of General Surgery, First People's Hospital of Huzhou, Huzhou, Zhejiang 313000, PR China
| | - Linxiao Sun
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Medical University First Affiliated Hospital, Wenzhou, Zhejiang 325000, PR China
| | - Qiangqiang Li
- Department of General Surgery, the People's Hospital of Yuhuan, Taizhou 317600, Zhejiang, PR China.
| |
Collapse
|
13
|
Clerici S, Podrini C, Stefanoni D, Distefano G, Cassina L, Steidl ME, Tronci L, Canu T, Chiaravalli M, Spies D, Bell TA, Costa AS, Esposito A, D'Alessandro A, Frezza C, Bachi A, Boletta A. Inhibition of asparagine synthetase effectively retards polycystic kidney disease progression. EMBO Mol Med 2024:10.1038/s44321-024-00071-9. [PMID: 38684863 DOI: 10.1038/s44321-024-00071-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
Polycystic kidney disease (PKD) is a genetic disorder characterized by bilateral cyst formation. We showed that PKD cells and kidneys display metabolic alterations, including the Warburg effect and glutaminolysis, sustained in vitro by the enzyme asparagine synthetase (ASNS). Here, we used antisense oligonucleotides (ASO) against Asns in orthologous and slowly progressive PKD murine models and show that treatment leads to a drastic reduction of total kidney volume (measured by MRI) and a prominent rescue of renal function in the mouse. Mechanistically, the upregulation of an ATF4-ASNS axis in PKD is driven by the amino acid response (AAR) branch of the integrated stress response (ISR). Metabolic profiling of PKD or control kidneys treated with Asns-ASO or Scr-ASO revealed major changes in the mutants, several of which are rescued by Asns silencing in vivo. Indeed, ASNS drives glutamine-dependent de novo pyrimidine synthesis and proliferation in cystic epithelia. Notably, while several metabolic pathways were completely corrected by Asns-ASO, glycolysis was only partially restored. Accordingly, combining the glycolytic inhibitor 2DG with Asns-ASO further improved efficacy. Our studies identify a new therapeutic target and novel metabolic vulnerabilities in PKD.
Collapse
Affiliation(s)
- Sara Clerici
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Christine Podrini
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
- The BioArte Ltd, Laboratories at Malta Life Science Park (LS2.1.10, LS2.1.12-LS2.1.15), Triq San Giljan, San Gwann, SGN, 3000, Malta
| | - Davide Stefanoni
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Gianfranco Distefano
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Laura Cassina
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Maria Elena Steidl
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Laura Tronci
- Cogentech SRL Benefit Corporation, 20139, Milan, Italy
- IFOM ETS The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Tamara Canu
- Center for Experimental Imaging (CIS), IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Marco Chiaravalli
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Daniel Spies
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy
- Center for Omics Sciences (COSR), IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | | | - Ana Sh Costa
- MRC, Cancer Unit Cambridge, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Matterworks, Inc, 444 Somerville Avenue, Somerville, MA, 02143, USA
| | - Antonio Esposito
- Center for Experimental Imaging (CIS), IRCCS, San Raffaele Scientific Institute, Milan, Italy
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - Christian Frezza
- Faculty of Medicine and University Hospital Cologne, Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Str. 26-50931, Cologne, Germany
| | - Angela Bachi
- IFOM ETS The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Alessandra Boletta
- Molecular Basis of Cystic Kidney Disorders Unit, Division of Genetics and Cell Biology, IRCCS, San Raffaele Scientific Institute, Milan, Italy.
| |
Collapse
|
14
|
Li X, Zou J, Lin A, Chi J, Hao H, Chen H, Liu Z. Oxidative Stress, Endothelial Dysfunction, and N-Acetylcysteine in Type 2 Diabetes Mellitus. Antioxid Redox Signal 2024. [PMID: 38497734 DOI: 10.1089/ars.2023.0524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Significance: Cardiovascular diseases (CVDs) remain the leading cause of morbidity and mortality globally. Endothelial dysfunction is closely associated with the development and progression of CVDs. Patients with diabetes mellitus (DM) especially type 2 DM (T2DM) exhibit a significant endothelial cell (EC) dysfunction with substantially increased risk for CVDs. Recent Advances: Excessive reactive oxygen species (ROS) and oxidative stress are important contributing factors to EC dysfunction and subsequent CVDs. ROS production is significantly increased in DM and is critically involved in the development of endothelial dysfunction in diabetic patients. In this review, efforts are made to discuss the role of excessive ROS and oxidative stress in the pathogenesis of endothelial dysfunction and the mechanisms for excessive ROS production and oxidative stress in T2DM. Critical Issues: Although studies with diabetic animal models have shown that targeting ROS with traditional antioxidant vitamins C and E or other antioxidant supplements provides promising beneficial effects on endothelial function, the cardiovascular outcomes of clinical studies with these antioxidant supplements have been inconsistent in diabetic patients. Future Directions: Preclinical and limited clinical data suggest that N-acetylcysteine (NAC) treatment may improve endothelial function in diabetic patients. However, well-designed clinical studies are needed to determine if NAC supplementation would effectively preserve endothelial function and improve the clinical outcomes of diabetic patients with reduced cardiovascular morbidity and mortality. With better understanding on the mechanisms of ROS generation and ROS-mediated endothelial damages/dysfunction, it is anticipated that new selective ROS-modulating agents and effective personalized strategies will be developed for the management of endothelial dysfunction in DM.
Collapse
Affiliation(s)
- Xin Li
- Department of Endocrinology, Ningbo No. 2 Hospital, Ningbo, China
| | - Junyong Zou
- Department of Respiratory Medicine, Ningbo No. 2 Hospital, Ningbo, China
| | - Aiping Lin
- Center for Precision Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Jingshu Chi
- Center for Precision Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Hong Hao
- Center for Precision Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Hong Chen
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zhenguo Liu
- Center for Precision Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, Missouri, USA
| |
Collapse
|
15
|
Zhong D, Chen J, Qiao R, Song C, Hao C, Zou Y, Bai M, Su W, Yang B, Sun D, Jia Z, Sun Y. Genetic or pharmacologic blockade of mPGES-2 attenuates renal lipotoxicity and diabetic kidney disease by targeting Rev-Erbα/FABP5 signaling. Cell Rep 2024; 43:114075. [PMID: 38583151 DOI: 10.1016/j.celrep.2024.114075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
Diabetic kidney disease (DKD) is one of the most common complications of diabetes, and no specific drugs are clinically available. We have previously demonstrated that inhibiting microsomal prostaglandin E synthase-2 (mPGES-2) alleviated type 2 diabetes by enhancing β cell function and promoting insulin production. However, the involvement of mPGES-2 in DKD remains unclear. Here, we aimed to analyze the association of enhanced mPGES-2 expression with impaired metabolic homeostasis of renal lipids and subsequent renal damage. Notably, global knockout or pharmacological blockage of mPGES-2 attenuated diabetic podocyte injury and tubulointerstitial fibrosis, thereby ameliorating lipid accumulation and lipotoxicity. These findings were further confirmed in podocyte- or tubule-specific mPGES-2-deficient mice. Mechanistically, mPGES-2 and Rev-Erbα competed for heme binding to regulate fatty acid binding protein 5 expression and lipid metabolism in the diabetic kidney. Our findings suggest a potential strategy for treating DKD via mPGES-2 inhibition.
Collapse
Affiliation(s)
- Dandan Zhong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Jingshuo Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Ranran Qiao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China; Public Experimental Research Center of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Chang Song
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China; Public Experimental Research Center of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Chang Hao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China; Public Experimental Research Center of Xuzhou Medical University, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Yingying Zou
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China
| | - Mi Bai
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Wen Su
- Department of Pathophysiology, Shenzhen University, Shenzhen 518060, China; Shenzhen University Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Baoxue Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing, China; State Key Laboratory of Vascular Homeostasis and Remodeling, Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Dong Sun
- Department of Nephrology, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, Jiangsu 221002, China.
| | - Zhanjun Jia
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China; Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China.
| | - Ying Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu 221004, P.R. China.
| |
Collapse
|
16
|
Lee LE, Doke T, Mukhi D, Susztak K. The key role of altered tubule cell lipid metabolism in kidney disease development. Kidney Int 2024:S0085-2538(24)00252-7. [PMID: 38614389 DOI: 10.1016/j.kint.2024.02.025] [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: 02/26/2023] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 04/15/2024]
Abstract
Kidney epithelial cells have very high energy requirements, which are largely met by fatty acid oxidation. Complex changes in lipid metabolism are observed in patients with kidney disease. Defects in fatty acid oxidation and increased lipid uptake, especially in the context of hyperlipidemia and proteinuria, contribute to this excess lipid build-up and exacerbate kidney disease development. Recent studies have also highlighted the role of increased de novo lipogenesis in kidney fibrosis. The defect in fatty acid oxidation causes energy starvation. Increased lipid uptake, synthesis, and lower fatty acid oxidation can cause toxic lipid build-up, reactive oxygen species generation, and mitochondrial damage. A better understanding of these metabolic processes may open new treatment avenues for kidney diseases by targeting lipid metabolism.
Collapse
Affiliation(s)
- Lauren E Lee
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Penn-Children's Hospital of Philadelphia Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Tomohito Doke
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Penn-Children's Hospital of Philadelphia Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Dhanunjay Mukhi
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Penn-Children's Hospital of Philadelphia Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Penn-Children's Hospital of Philadelphia Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
17
|
Zhou AX, Jeansson M, He L, Wigge L, Tonelius P, Tati R, Cederblad L, Muhl L, Uhrbom M, Liu J, Björnson Granqvist A, Lerman LO, Betsholtz C, Hansen PBL. Renal Endothelial Single-Cell Transcriptomics Reveals Spatiotemporal Regulation and Divergent Roles of Differential Gene Transcription and Alternative Splicing in Murine Diabetic Nephropathy. Int J Mol Sci 2024; 25:4320. [PMID: 38673910 PMCID: PMC11050020 DOI: 10.3390/ijms25084320] [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: 03/01/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Endothelial cell (EC) injury is a crucial contributor to the progression of diabetic kidney disease (DKD), but the specific EC populations and mechanisms involved remain elusive. Kidney ECs (n = 5464) were collected at three timepoints from diabetic BTBRob/ob mice and non-diabetic littermates. Their heterogeneity, transcriptional changes, and alternative splicing during DKD progression were mapped using SmartSeq2 single-cell RNA sequencing (scRNAseq) and elucidated through pathway, network, and gene ontology enrichment analyses. We identified 13 distinct transcriptional EC phenotypes corresponding to different kidney vessel subtypes, confirmed through in situ hybridization and immunofluorescence. EC subtypes along nephrons displayed extensive zonation related to their functions. Differential gene expression analyses in peritubular and glomerular ECs in DKD underlined the regulation of DKD-relevant pathways including EIF2 signaling, oxidative phosphorylation, and IGF1 signaling. Importantly, this revealed the differential alteration of these pathways between the two EC subtypes and changes during disease progression. Furthermore, glomerular and peritubular ECs also displayed aberrant and dynamic alterations in alternative splicing (AS), which is strongly associated with DNA repair. Strikingly, genes displaying differential transcription or alternative splicing participate in divergent biological processes. Our study reveals the spatiotemporal regulation of gene transcription and AS linked to DKD progression, providing insight into pathomechanisms and clues to novel therapeutic targets for DKD treatment.
Collapse
Affiliation(s)
- Alex-Xianghua Zhou
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Marie Jeansson
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
- Department of Immunology, Genetics and Pathology, Uppsala University, 753 10 Uppsala, Sweden
| | - Liqun He
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
- Department of Immunology, Genetics and Pathology, Uppsala University, 753 10 Uppsala, Sweden
| | - Leif Wigge
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden
| | - Pernilla Tonelius
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Ramesh Tati
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Linda Cederblad
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Lars Muhl
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
| | - Martin Uhrbom
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
| | - Jianping Liu
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
| | - Anna Björnson Granqvist
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Lilach O. Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA;
| | - Christer Betsholtz
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
- Department of Immunology, Genetics and Pathology, Uppsala University, 753 10 Uppsala, Sweden
| | - Pernille B. L. Hansen
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| |
Collapse
|
18
|
Gyarmati G, Shroff UN, Riquier-Brison A, Desposito D, Ju W, Stocker SD, Izuhara A, Deepak S, Becerra Calderon A, Burford JL, Kadoya H, Moon JY, Chen Y, Rinschen MM, Ahmadi N, Lau L, Biemesderfer D, James AW, Minichiello L, Zlokovic BV, Gill IS, Kretzler M, Peti-Peterdi J. Neuronally differentiated macula densa cells regulate tissue remodeling and regeneration in the kidney. J Clin Invest 2024; 134:e174558. [PMID: 38598837 PMCID: PMC11142747 DOI: 10.1172/jci174558] [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: 08/14/2023] [Accepted: 04/09/2024] [Indexed: 04/12/2024] Open
Abstract
Tissue regeneration is limited in several organs, including the kidney, contributing to the high prevalence of kidney disease globally. However, evolutionary and physiological adaptive responses and the presence of renal progenitor cells suggest an existing remodeling capacity. This study uncovered endogenous tissue remodeling mechanisms in the kidney that were activated by the loss of body fluid and salt and regulated by a unique niche of a minority renal cell type called the macula densa (MD). Here, we identified neuronal differentiation features of MD cells that sense the local and systemic environment and secrete angiogenic, growth, and extracellular matrix remodeling factors, cytokines and chemokines, and control resident progenitor cells. Serial intravital imaging, MD nerve growth factor receptor and Wnt mouse models, and transcriptome analysis revealed cellular and molecular mechanisms of these MD functions. Human and therapeutic translation studies illustrated the clinical potential of MD factors, including CCN1, as a urinary biomarker and therapeutic target in chronic kidney disease. The concept that a neuronally differentiated key sensory and regulatory cell type responding to organ-specific physiological inputs controls local progenitors to remodel or repair tissues may be applicable to other organs and diverse tissue-regenerative therapeutic strategies.
Collapse
Affiliation(s)
- Georgina Gyarmati
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Urvi Nikhil Shroff
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Anne Riquier-Brison
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Dorinne Desposito
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Wenjun Ju
- Division of Nephrology, Department of Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Sean D. Stocker
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Audrey Izuhara
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Sachin Deepak
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Alejandra Becerra Calderon
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - James L. Burford
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Hiroyuki Kadoya
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Ju-Young Moon
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Yibu Chen
- USC Libraries Bioinformatics Service, University of Southern California, Los Angeles, California, USA
| | - Markus M. Rinschen
- Center for Molecular Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Nariman Ahmadi
- Institute of Urology, Catherine and Joseph Aresty Department of Urology, University of Southern California, Los Angeles, California, USA
| | - Lester Lau
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois, USA
| | - Daniel Biemesderfer
- Section of Nephrology and Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Aaron W. James
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Berislav V. Zlokovic
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| | - Inderbir S. Gill
- Institute of Urology, Catherine and Joseph Aresty Department of Urology, University of Southern California, Los Angeles, California, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - János Peti-Peterdi
- Department of Physiology and Neuroscience and Department of Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
19
|
Ni XY, Feng XJ, Wang ZH, Zhang Y, Little PJ, Cao Y, Xu SW, Tang LQ, Weng JP. Empagliflozin and liraglutide ameliorate HFpEF in mice via augmenting the Erbb4 signaling pathway. Acta Pharmacol Sin 2024:10.1038/s41401-024-01265-0. [PMID: 38589689 DOI: 10.1038/s41401-024-01265-0] [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: 10/24/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Heart failure with preserved ejection fraction (HFpEF) is closely associated with metabolic derangement. Sodium glucose cotransporter-2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP-1RA) exert anti-HFpEF effects, but the underlying mechanisms remain unclear. In this study, we explored the anti-HFpEF effects of empagliflozin and liraglutide and the underlying molecular mechanisms in a mouse model of HFpEF. This model was established by high-fat diet (HFD) feeding plus Nω-nitro-L-arginine methyl ester (L-NAME) treatment. The mice were treated with empagliflozin (20 mg·kg-1·d-1, i.g.) or liraglutide (0.3 mg·kg-1·d-1, i.p.) or their combination for 4 weeks. At the end of the experimental protocol, cardiac function was measured using ultrasound, then mice were euthanized and heart, liver, and kidney tissues were collected. Nuclei were isolated from frozen mouse ventricular tissue for single-nucleus RNA-sequencing (snRNA-seq). We showed that administration of empagliflozin or liraglutide alone or in combination significantly improved diastolic function, ameliorated cardiomyocyte hypertrophy and cardiac fibrosis, as well as exercise tolerance but no synergism was observed in the combination group. Furthermore, empagliflozin and/or liraglutide lowered body weight, improved glucose metabolism, lowered blood pressure, and improved liver and kidney function. After the withdrawal of empagliflozin or liraglutide for 1 week, these beneficial effects tended to diminish. The snRNA-seq analysis revealed a subcluster of myocytes, in which Erbb4 expression was down-regulated under HFpEF conditions, and restored by empagliflozin or liraglutide. Pseudo-time trajectory analysis and cell-to-cell communication studies confirmed that the Erbb4 pathway was a prominent pathway essential for both drug actions. In the HFpEF mouse model, both empagliflozin and liraglutide reversed Erbb4 down-regulation. In rat h9c2 cells, we showed that palmitic acid- or high glucose-induced changes in PKCα and/or ERK1/2 phosphorylation at least in part through Erbb4. Collectively, the single-cell atlas reveals the anti-HFpEF mechanism of empagliflozin and liraglutide, suggesting that Erbb4 pathway represents a new therapeutic target for HFpEF. Effects and mechanisms of action of empagliflozin and liraglutide in HFpEF mice. HFpEF was induced with a high-fat diet and L-NAME for 15 weeks, and treatment with empagliflozin and liraglutide improved the HFpEF phenotype. Single nucleus RNA sequencing (snRNA-seq) was used to reveal the underlying mechanism of action of empagliflozin and liraglutide.
Collapse
Affiliation(s)
- Xia-Yun Ni
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230036, China
- Department of Pharmacy, The First Affiliated Hospital of University of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, 230001, China
| | - Xiao-Jun Feng
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230036, China
- Department of Pharmacy, The First Affiliated Hospital of University of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, 230001, China
| | - Zhi-Hua Wang
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230036, China
| | - Yang Zhang
- Department of Pharmacy, The First Affiliated Hospital of University of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, 230001, China
| | - Peter J Little
- School of Pharmacy, University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, 4102, Australia
| | - Yang Cao
- Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, 230022, China
| | - Suo-Wen Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230036, China.
| | - Li-Qin Tang
- Department of Pharmacy, The First Affiliated Hospital of University of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, 230001, China.
| | - Jian-Ping Weng
- Department of Endocrinology, Institute of Endocrine and Metabolic Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230036, China.
| |
Collapse
|
20
|
van Raalte DH, Bjornstad P, Cherney DZI, de Boer IH, Fioretto P, Gordin D, Persson F, Rosas SE, Rossing P, Schaub JA, Tuttle K, Waikar SS, Heerspink HJL. Combination therapy for kidney disease in people with diabetes mellitus. Nat Rev Nephrol 2024:10.1038/s41581-024-00827-z. [PMID: 38570632 DOI: 10.1038/s41581-024-00827-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Diabetic kidney disease (DKD), defined as co-existing diabetes and chronic kidney disease in the absence of other clear causes of kidney injury, occurs in approximately 20-40% of patients with diabetes mellitus. As the global prevalence of diabetes has increased, DKD has become highly prevalent and a leading cause of kidney failure, accelerated cardiovascular disease, premature mortality and global health care expenditure. Multiple pathophysiological mechanisms contribute to DKD, and single lifestyle or pharmacological interventions have shown limited efficacy at preserving kidney function. For nearly two decades, renin-angiotensin system inhibitors were the only available kidney-protective drugs. However, several new drug classes, including sodium glucose cotransporter-2 inhibitors, a non-steroidal mineralocorticoid antagonist and a selective endothelin receptor antagonist, have now been demonstrated to improve kidney outcomes in people with type 2 diabetes mellitus. In addition, emerging preclinical and clinical evidence of the kidney-protective effects of glucagon-like-peptide-1 receptor agonists has led to the prospective testing of these agents for DKD. Research and clinical efforts are geared towards using therapies with potentially complementary efficacy in combination to safely halt kidney disease progression. As more kidney-protective drugs become available, the outlook for people living with DKD should improve in the next few decades.
Collapse
Affiliation(s)
- Daniël H van Raalte
- Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, VUMC, Amsterdam, The Netherlands.
- Diabetes Center, Amsterdam University Medical Centers, VUMC, Amsterdam, The Netherlands.
- Research Institute for Cardiovascular Sciences, VU University, Amsterdam, The Netherlands.
| | - Petter Bjornstad
- University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - David Z I Cherney
- Department of Medicine, Division of Nephrology, Toronto General Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Ian H de Boer
- Division of Nephrology and Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Paola Fioretto
- Department of Medicine, University of Padua, Unit of Medical Clinic 3, Padua, Italy
| | - Daniel Gordin
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Sylvia E Rosas
- Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Jennifer A Schaub
- Nephrology Division, Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine Tuttle
- Providence Medical Research Center, Providence Inland Northwest Health, Spokane, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Spokane and Seattle, Washington, USA
- Nephrology Division, Kidney Research Institute and Institute of Translational Health Sciences, University of Washington, Spokane and Seattle, Washington, USA
| | - Sushrut S Waikar
- Section of Nephrology, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Hiddo J L Heerspink
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- The George Institute for Global Health, Sydney, New South Wales, Australia
| |
Collapse
|
21
|
Shen Y, Lotenberg K, Zaworski J, Broeker KAE, Vasseur F, Louedec L, Placier S, Frère P, Verpont MC, Galichon P, Buob D, Hadchouel J, Terzi F, Chatziantoniou C, Calmont A. Neuropilin-1 regulates renin synthesis in juxtaglomerular cells. J Physiol 2024; 602:1815-1833. [PMID: 38381008 DOI: 10.1113/jp285422] [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: 11/14/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Renin is the key enzyme of the systemic renin-angiotensin-aldosterone system, which plays an essential role in regulating blood pressure and maintaining electrolyte and extracellular volume homeostasis. Renin is mainly produced and secreted by specialized juxtaglomerular (JG) cells in the kidney. In the present study, we report for the first time that the conserved transmembrane receptor neuropilin-1 (NRP1) participates in the development of JG cells and plays a key role in renin production. We used the myelin protein zero-Cre (P0-Cre) to abrogate Nrp1 constitutively in P0-Cre lineage-labelled cells of the kidney. We found that the P0-Cre precursor cells differentiate into renin-producing JG cells. We employed a lineage-tracing strategy combined with RNAscope quantification and metabolic studies to reveal a cell-autonomous role for NRP1 in JG cell function. Nrp1-deficient animals displayed abnormal levels of tissue renin expression and failed to adapt properly to a homeostatic challenge to sodium balance. These findings provide new insights into cell fate decisions and cellular plasticity operating in P0-Cre-expressing precursors and identify NRP1 as a novel key regulator of JG cell maturation. KEY POINTS: Renin is a centrepiece of the renin-angiotensin-aldosterone system and is produced by specialized juxtaglomerular cells (JG) of the kidney. Neuropilin-1 (NRP1) is a conserved membrane-bound receptor that regulates vascular and neuronal development, cancer aggressiveness and fibrosis progression. We used conditional mutagenesis and lineage tracing to show that NRP1 is expressed in JG cells where it regulates their function. Cell-specific Nrp1 knockout mice present with renin paucity in JG cells and struggle to adapt to a homeostatic challenge to sodium balance. The results support the versatility of renin-producing cells in the kidney and may open new avenues for therapeutic approaches.
Collapse
Affiliation(s)
- Yunzhu Shen
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Kenza Lotenberg
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Jeremy Zaworski
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | | | - Florence Vasseur
- Institut Necker Enfants Malades, Growth and Signalling departement, Université Paris Cité, INSERM U1151, CNRS UMR 8253, Paris, France
| | - Liliane Louedec
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Sandrine Placier
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Perrine Frère
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Marie-Christine Verpont
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Pierre Galichon
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - David Buob
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Juliette Hadchouel
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Fabiola Terzi
- Institut Necker Enfants Malades, Growth and Signalling departement, Université Paris Cité, INSERM U1151, CNRS UMR 8253, Paris, France
| | - Christos Chatziantoniou
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| | - Amélie Calmont
- Sorbonne Université, INSERM, Unité mixte de Recherche 1155, Kidney Research Centre, Hôpital Tenon, Paris, France
| |
Collapse
|
22
|
Su Y, Yu Z, Yang Y, Wong KC, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307280. [PMID: 38380499 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.
Collapse
Affiliation(s)
- Yanchi Su
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| |
Collapse
|
23
|
Su XT, Reyes JV, Lackey AE, Demirci H, Bachmann S, Maeoka Y, Cornelius RJ, McCormick JA, Yang CL, Jung HJ, Welling PA, Nelson JW, Ellison DH. Enriched Single-Nucleus RNA-Sequencing Reveals Unique Attributes of Distal Convoluted Tubule Cells. J Am Soc Nephrol 2024; 35:426-440. [PMID: 38238903 PMCID: PMC11000721 DOI: 10.1681/asn.0000000000000297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/17/2023] [Indexed: 01/24/2024] Open
Abstract
SIGNIFICANCE STATEMENT High-resolution single-nucleus RNA-sequencing data indicate a clear separation between primary sites of calcium and magnesium handling within distal convoluted tubule (DCT). Both DCT1 and DCT2 express Slc12a3, but these subsegments serve distinctive functions, with more abundant magnesium-handling genes along DCT1 and more calcium-handling genes along DCT2. The data also provide insight into the plasticity of the distal nephron-collecting duct junction, formed from cells of separate embryonic origins. By focusing/changing gradients of gene expression, the DCT can morph into different physiological cell states on demand. BACKGROUND The distal convoluted tubule (DCT) comprises two subsegments, DCT1 and DCT2, with different functional and molecular characteristics. The functional and molecular distinction between these segments, however, has been controversial. METHODS To understand the heterogeneity within the DCT population with better clarity, we enriched for DCT nuclei by using a mouse line combining "Isolation of Nuclei Tagged in specific Cell Types" and sodium chloride cotransporter-driven inducible Cre recombinase. We sorted the fluorescently labeled DCT nuclei using Fluorescence-Activated Nucleus Sorting and performed single-nucleus transcriptomics. RESULTS Among 25,183 DCT cells, 75% were from DCT1 and 25% were from DCT2. In addition, there was a small population (<1%) enriched in proliferation-related genes, such as Top2a , Cenpp , and Mki67 . Although both DCT1 and DCT2 expressed sodium chloride cotransporter, magnesium transport genes were predominantly expressed along DCT1, whereas calcium, electrogenic sodium, and potassium transport genes were more abundant along DCT2. The transition between these two segments was gradual, with a transitional zone in which DCT1 and DCT2 cells were interspersed. The expression of the homeobox genes by DCT cells suggests that they develop along different trajectories. CONCLUSIONS Transcriptomic analysis of an enriched rare cell population using a genetically targeted approach clarifies the function and classification of distal cells. The DCT segment is short, can be separated into two subsegments that serve distinct functions, and is speculated to derive from different origins during development.
Collapse
Affiliation(s)
- Xiao-Tong Su
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Jeremiah V. Reyes
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Anne E. Lackey
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Hasan Demirci
- Department of Anatomy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Bachmann
- Department of Anatomy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yujiro Maeoka
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Ryan J. Cornelius
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - James A. McCormick
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Chao-Ling Yang
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Hyun Jun Jung
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paul A. Welling
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonathan W. Nelson
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - David H. Ellison
- Division of Hypertension and Nephrology, School of Medicine, Oregon Health & Science University, Portland, Oregon
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon
- Renal Section, VA Portland Healthcare System, Portland, Oregon
| |
Collapse
|
24
|
Chen J, Zhang Q, Guo J, Gu D, Liu J, Luo P, Bai Y, Chen J, Zhang X, Nie S, Chen C, Feng Y, Wang J. Single-cell transcriptomics reveals the ameliorative effect of rosmarinic acid on diabetic nephropathy-induced kidney injury by modulating oxidative stress and inflammation. Acta Pharm Sin B 2024; 14:1661-1676. [PMID: 38572101 PMCID: PMC10985035 DOI: 10.1016/j.apsb.2024.01.003] [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: 10/16/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 04/05/2024] Open
Abstract
Diabetic nephropathy (DN) is a severe complication of diabetes, characterized by changes in kidney structure and function. The natural product rosmarinic acid (RA) has demonstrated therapeutic effects, including anti-inflammation and anti-oxidative-stress, in renal damage or dysfunction. In this study, we characterized the heterogeneity of the cellular response in kidneys to DN-induced injury and RA treatment at single cell levels. Our results demonstrated that RA significantly alleviated renal tubular epithelial injury, particularly in the proximal tubular S1 segment and on glomerular epithelial cells known as podocytes, while attenuating the inflammatory response of macrophages, oxidative stress, and cytotoxicity of natural killer cells. These findings provide a comprehensive understanding of the mechanisms by which RA alleviates kidney damage, oxidative stress, and inflammation, offering valuable guidance for the clinical application of RA in the treatment of DN.
Collapse
Affiliation(s)
- Junhui Chen
- National Pharmaceutical Engineering Center for Solid Preparation of Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, China
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Qian Zhang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, China
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jinan Guo
- Department of Urology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China
| | - Di Gu
- Department of Urology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China
| | - Jing Liu
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Piao Luo
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, China
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yunmeng Bai
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Jiayun Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, China
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xinzhou Zhang
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, China
| | - Sheng Nie
- Department of Nephrology, Nanfang Hospital, the First Affiliated Hospital of Southern Medical University, Guangzhou 510515, China
| | - Chunbo Chen
- Department of Critical Care Medicine, Shenzhen People's Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Yulin Feng
- National Pharmaceutical Engineering Center for Solid Preparation of Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, China
| | - Jigang Wang
- National Pharmaceutical Engineering Center for Solid Preparation of Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang 330006, China
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen 518020, China
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
- State Key Laboratory for Quality Esurance 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
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| |
Collapse
|
25
|
Kim JI, Imaizumi K, Thete MV, Hudacova Z, Jurjuţ O, Amin ND, Scherrer G, Paşca SP. Human assembloid model of the ascending neural sensory pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584539. [PMID: 38559133 PMCID: PMC10979925 DOI: 10.1101/2024.03.11.584539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The ascending somatosensory pathways convey crucial information about pain, touch, itch, and body part movement from peripheral organs to the central nervous system. Despite a significant need for effective therapeutics modulating pain and other somatosensory modalities, clinical translation remains challenging, which is likely related to species-specific features and the lack of in vitro models to directly probe and manipulate this polysynaptic pathway. Here, we established human ascending somatosensory assembloids (hASA)- a four-part assembloid completely generated from human pluripotent stem cells that integrates somatosensory, spinal, diencephalic, and cortical organoids to model the human ascending spinothalamic pathway. Transcriptomic profiling confirmed the presence of key cell types in this circuit. Rabies tracing and calcium imaging showed that sensory neurons connected with dorsal spinal cord projection neurons, which ascending axons further connected to thalamic neurons. Following noxious chemical stimulation, single neuron calcium imaging of intact hASA demonstrated coordinated response, while four-part concomitant extracellular recordings and calcium imaging revealed synchronized activity across the assembloid. Loss of the sodium channel SCN9A, which causes pain insensitivity in humans, disrupted synchrony across the four-part hASA. Taken together, these experiments demonstrate the ability to functionally assemble the essential components of the human sensory pathway. These findings could both accelerate our understanding of human sensory circuits and facilitate therapeutic development.
Collapse
|
26
|
Chen S, Huang W, Wan Q, Tang Z, Li X, Zeng F, Zheng S, Li Z, Liu X. Investigation of the acute pathogenesis of spondyloarthritis/HLA-B27-associated anterior uveitis based on genome-wide association analysis and single-cell transcriptomics. J Transl Med 2024; 22:271. [PMID: 38475831 DOI: 10.1186/s12967-024-05077-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Patients with spondyloarthritis (SpA)/HLA-B27-associated acute anterior uveitis (AAU) experience recurring acute flares, which pose significant visual and financial challenges. Despite established links between SpA and HLA-B27-associated AAU, the exact mechanism involved remains unclear, and further understanding is needed for effective prevention and treatment. METHODS To investigate the acute pathogenesis of SpA/HLA-B27-associated AAU, Mendelian randomization (MR) and single-cell transcriptomic analyses were employed. The MR incorporated publicly available protein quantitative trait locus data from previous studies, along with genome-wide association study data from public databases. Causal relationships between plasma proteins and anterior uveitis were assessed using two-sample MR. Additionally, colocalization analysis was performed using Bayesian colocalization. Single-cell transcriptome analysis utilized the anterior uveitis dataset from the Gene Expression Omnibus (GEO) database. Dimensionality reduction, clustering, transcription factor analysis, pseudotime analysis, and cell communication analysis were subsequently conducted to explore the underlying mechanisms involved. RESULTS Mendelian randomization analysis revealed that circulating levels of AIF1 and VARS were significantly associated with a reduced risk of developing SpA/HLA-B27-associated AAU, with AIF1 showing a robust correlation with anterior uveitis onset. Colocalization analysis supported these findings. Single-cell transcriptome analysis showed predominant AIF1 expression in myeloid cells, which was notably lower in the HLA-B27-positive group. Pseudotime analysis revealed dendritic cell terminal positions in differentiation branches, accompanied by gradual decreases in AIF1 expression. Based on cell communication analysis, CD141+CLEC9A+ classic dendritic cells (cDCs) and the APP pathway play crucial roles in cellular communication in the Spa/HLA-B27 group. CONCLUSIONS AIF1 is essential for the pathogenesis of SpA/HLA-B27-associated AAU. Myeloid cell differentiation into DCs and decreased AIF1 levels are also pivotal in this process.
Collapse
Affiliation(s)
- Shuming Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Weidi Huang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Qiaoqian Wan
- Department of Anaesthesiology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zichun Tang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Xie Li
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Fang Zeng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Shuyan Zheng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China
| | - Zhuo Li
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China.
- Hunan Provincial Key Laboratory of Critical Quality Attribute of Cell Therapy Products, Changsha, 410011, Hunan, China.
| | - Xiao Liu
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, 410011, Hunan, China.
| |
Collapse
|
27
|
Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Wick B, Haeussler M, Li Z, Molla G, Satija R, Zhou W, Cao J. A Panoramic View of Cell Population Dynamics in Mammalian Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.583001. [PMID: 38496474 PMCID: PMC10942312 DOI: 10.1101/2024.03.01.583001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different life stages, sexes, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion. Our panoramic analysis uncovered temporally structured, organ- and lineage-specific shifts of cellular dynamics during lifespan progression. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.
Collapse
Affiliation(s)
- Zehao Zhang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Chloe Schaefer
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Weirong Jiang
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Ziyu Lu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Abdulraouf Abdulraouf
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The Tri-Institutional M.D-Ph.D Program, New York, NY, USA
| | - Brittney Wick
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Zhuoyan Li
- New York Genome Center, New York, NY, USA
| | | | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| |
Collapse
|
28
|
Komaru Y, Ning L, Lama C, Suresh A, Kefaloyianni E, Miller MJ, Herrlich A. Sterile kidney tissue injury induces neutrophil swarming in lung alveolar capillaries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582396. [PMID: 38464306 PMCID: PMC10925262 DOI: 10.1101/2024.02.27.582396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Sterile tissue injury, such as by acute kidney injury, is common in the clinic and frequently associated with respiratory compromise and hypoxemia. We previously described signaling components released by the injured kidney that drive a remote inflammatory response in the lung. How this caused the resultant hypoxemia remained unclear. Here, we report that sterile kidney tissue injury induces rapid intravascular "neutrophil train" formation in lung capillaries, a novel form of neutrophil swarming. Rapid swarming is enhanced by decreased deformability of circulating neutrophils that impedes their lung capillary passage. Classical lung monocytes are required for neutrophil train formation and release CXCL2 to attract and retain stiffened neutrophils in lung capillaries which reduces capillary perfusion. We thus discovered a novel feature of kidney-lung crosstalk after sterile kidney tissue injury, capillary perfusion deficits that lead to reduced oxygenation despite proper alveolar function and ventilation, unlike in infectious inflammatory lung processes, such as bacterial pneumonia.
Collapse
|
29
|
Curaj A, Vanholder R, Loscalzo J, Quach K, Wu Z, Jankowski V, Jankowski J. Cardiovascular Consequences of Uremic Metabolites: an Overview of the Involved Signaling Pathways. Circ Res 2024; 134:592-613. [PMID: 38422175 DOI: 10.1161/circresaha.123.324001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The crosstalk of the heart with distant organs such as the lung, liver, gut, and kidney has been intensively approached lately. The kidney is involved in (1) the production of systemic relevant products, such as renin, as part of the most essential vasoregulatory system of the human body, and (2) in the clearance of metabolites with systemic and organ effects. Metabolic residue accumulation during kidney dysfunction is known to determine cardiovascular pathologies such as endothelial activation/dysfunction, atherosclerosis, cardiomyocyte apoptosis, cardiac fibrosis, and vascular and valvular calcification, leading to hypertension, arrhythmias, myocardial infarction, and cardiomyopathies. However, this review offers an overview of the uremic metabolites and details their signaling pathways involved in cardiorenal syndrome and the development of heart failure. A holistic view of the metabolites, but more importantly, an exhaustive crosstalk of their known signaling pathways, is important for depicting new therapeutic strategies in the cardiovascular field.
Collapse
Affiliation(s)
- Adelina Curaj
- Institute of Molecular Cardiovascular Research, RWTH Aachen University, Germany (A.C., K.Q., Z.W., V.J., J.J.)
| | - Raymond Vanholder
- Department of Internal Medicine and Pediatrics, Nephrology Section, University Hospital, Ghent, Belgium (R.V.)
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.L.)
| | - Kaiseng Quach
- Institute of Molecular Cardiovascular Research, RWTH Aachen University, Germany (A.C., K.Q., Z.W., V.J., J.J.)
| | - Zhuojun Wu
- Institute of Molecular Cardiovascular Research, RWTH Aachen University, Germany (A.C., K.Q., Z.W., V.J., J.J.)
| | - Vera Jankowski
- Institute of Molecular Cardiovascular Research, RWTH Aachen University, Germany (A.C., K.Q., Z.W., V.J., J.J.)
| | - Joachim Jankowski
- Institute of Molecular Cardiovascular Research, RWTH Aachen University, Germany (A.C., K.Q., Z.W., V.J., J.J.)
- Experimental Vascular Pathology, Cardiovascular Research Institute Maastricht, University of Maastricht, the Netherlands (J.J.)
- Aachen-Maastricht Institute for Cardiorenal Disease, RWTH Aachen University, Aachen, Germany (J.J.)
| |
Collapse
|
30
|
Hu X, Chen S, Ye S, Chen W, Zhou Y. New insights into the role of immunity and inflammation in diabetic kidney disease in the omics era. Front Immunol 2024; 15:1342837. [PMID: 38487541 PMCID: PMC10937589 DOI: 10.3389/fimmu.2024.1342837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 03/17/2024] Open
Abstract
Diabetic kidney disease (DKD) is becoming the leading cause of chronic kidney disease, especially in the industrialized world. Despite mounting evidence has demonstrated that immunity and inflammation are highly involved in the pathogenesis and progression of DKD, the underlying mechanisms remain incompletely understood. Substantial molecules, signaling pathways, and cell types participate in DKD inflammation, by integrating into a complex regulatory network. Most of the studies have focused on individual components, without presenting their importance in the global or system-based processes, which largely hinders clinical translation. Besides, conventional technologies failed to monitor the different behaviors of resident renal cells and immune cells, making it difficult to understand their contributions to inflammation in DKD. Recently, the advancement of omics technologies including genomics, epigenomics, transcriptomics, proteomics, and metabolomics has revolutionized biomedical research, which allows an unbiased global analysis of changes in DNA, RNA, proteins, and metabolites in disease settings, even at single-cell and spatial resolutions. They help us to identify critical regulators of inflammation processes and provide an overview of cell heterogeneity in DKD. This review aims to summarize the application of multiple omics in the field of DKD and emphasize the latest evidence on the interplay of inflammation and DKD revealed by these technologies, which will provide new insights into the role of inflammation in the pathogenesis of DKD and lead to the development of novel therapeutic approaches and diagnostic biomarkers.
Collapse
Affiliation(s)
- Xinrong Hu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Sixiu Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Siyang Ye
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| | - Yi Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province, Guangzhou, China
| |
Collapse
|
31
|
Chan KW, Kwong ASK, Tsui PN, Chan GCW, Choi WF, Yiu WH, Cheung SCY, Wong MMY, Zhang ZJ, Tan KCB, Lao L, Lai KN, Tang SCW. Add-on astragalus in type 2 diabetes and chronic kidney disease: A multi-center, assessor-blind, randomized controlled trial. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155457. [PMID: 38810556 DOI: 10.1016/j.phymed.2024.155457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/03/2024] [Accepted: 02/14/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND Diabetes leads to chronic kidney disease (CKD) and kidney failure, requiring dialysis or transplantation. Astragalus, a common herbal medicine and US pharmacopeia-registered food ingredient, is shown kidney protective by retrospective and preclinical data but with limited long-term prospective clinical evidence. This trial aimed to assess the effectiveness of astragalus on kidney function decline in macroalbuminuric diabetic CKD patients. METHODS This randomized, assessor-blind, standard care-controlled, multi-center clinical trial randomly assigned 118 patients with estimated glomerular filtration rate (eGFR) of 30-90 ml/min/1.73m2 and urinary albumin-to-creatinine ratio (UACR) of 300-5000 mg/g from 7 public outpatient clinics and the community in Hong Kong between July 2018 and April 2022 to add-on oral astragalus granules (15 gs of raw herbs daily equivalent) or to continue standard care alone as control for 48 weeks. Primary outcomes were the slope of change of eGFR (used for sample size calculation) and UACR of the intention-to-treat population. Secondary outcomes included endpoint blood pressures, biochemistry, biomarkers, concomitant drug change and adverse events. (ClinicalTrials.gov: NCT03535935) RESULTS: During the 48-week period, the estimated difference in the slope of eGFR decline was 4.6 ml/min/1.73m2 per year (95 %CI: 1.5 to 7.6, p = 0.003) slower with astragalus. For UACR, the estimated inter-group proportional difference in the slope of change was insignificant (1.14, 95 %CI: 0.85 to 1.52, p = 0.392). 117 adverse events from 31 astragalus-treated patients and 41 standard care-controlled patients were documented. The 48-week endpoint systolic blood pressure was 7.9 mmHg lower (95 %CI: -12.9 to -2.8, p = 0.003) in the astragalus-treated patients. 113 (96 %) and 107 (91 %) patients had post-randomization and endpoint primary outcome measures, respectively. CONCLUSION In patients with type 2 diabetes, stage 2 to 3 CKD and macroalbuminuria, add-on astragalus for 48 weeks further stabilized kidney function on top of standard care.
Collapse
Affiliation(s)
- Kam Wa Chan
- Division of Nephrology, Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Alfred Siu Kei Kwong
- Department of Family Medicine and Primary Healthcare, Hospital Authority Hong Kong West Cluster, Hong Kong Special Administrative Region, China
| | - Pun Nang Tsui
- Department of Family Medicine and Primary Healthcare, Hospital Authority Hong Kong East Cluster, Hong Kong Special Administrative Region, China
| | - Gary Chi Wang Chan
- Division of Nephrology, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Wing Fai Choi
- School of Chinese Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wai Han Yiu
- Division of Nephrology, Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Simon Chi Yuen Cheung
- Division of Nephrology, Department of Medicine, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, China
| | - Michelle Man Ying Wong
- Department of Family Medicine and Primary Healthcare, Hospital Authority Hong Kong East Cluster, Hong Kong Special Administrative Region, China
| | - Zhang-Jin Zhang
- School of Chinese Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kathryn Choon Beng Tan
- Division of Endocrinology, Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lixing Lao
- School of Chinese Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Virginia University of Integrative Medicine, VA, USA
| | - Kar Neng Lai
- Division of Nephrology, Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sydney Chi Wai Tang
- Division of Nephrology, Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
| |
Collapse
|
32
|
Tomita-Yagi A, Ozeki-Okuno N, Watanabe-Uehara N, Komaki K, Umehara M, Sawada-Yamauchi H, Minamida A, Sunahara Y, Matoba Y, Nakamura I, Nakata T, Nakai K, Ida T, Yamashita N, Kamezaki M, Kirita Y, Taniguchi T, Konishi E, Matoba S, Tamagaki K, Kusaba T. The importance of proinflammatory failed-repair tubular epithelia as a predictor of diabetic kidney disease progression. iScience 2024; 27:109020. [PMID: 38357667 PMCID: PMC10865398 DOI: 10.1016/j.isci.2024.109020] [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: 07/27/2023] [Revised: 11/17/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
The immense public health burden of diabetic kidney disease (DKD) has led to an increase in research on the pathophysiology of advanced DKD. The present study focused on the significance of proinflammatory vascular cell adhesion molecule 1 (VCAM1)+ tubules in DKD progression. A retrospective cohort study of DKD patients showed that the percentage of VCAM1+ tubules in kidney samples was correlated with poor renal outcomes. We established an advanced DKD model by partial resection of the kidneys of db/db mice and demonstrated that it closely resembled the human advanced DKD phenotype, with tissue hypoxia, tubular DNA damage, tissue inflammation, and high tubular VCAM1 expression. Luseogliflozin ameliorated tissue hypoxia and proinflammatory responses, including VCAM1+ expression, in tubules. These findings suggest the potential of tubular VCAM1 as a histological marker for poor DKD outcomes. SGLT2 inhibitors may attenuate tissue hypoxia and subsequent tissue inflammation in advanced DKD, thereby ameliorating tubular injury.
Collapse
Affiliation(s)
- Aya Tomita-Yagi
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Natsuko Ozeki-Okuno
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Noriko Watanabe-Uehara
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazumi Komaki
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Minato Umehara
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroko Sawada-Yamauchi
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Atsushi Minamida
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yasuto Sunahara
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yayoi Matoba
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Itaru Nakamura
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohiro Nakata
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kunihiro Nakai
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoharu Ida
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Noriyuki Yamashita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Michitsugu Kamezaki
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takuya Taniguchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eiichi Konishi
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Keiichi Tamagaki
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tetsuro Kusaba
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| |
Collapse
|
33
|
Wu H, Dixon EE, Xuanyuan Q, Guo J, Yoshimura Y, Debashish C, Niesnerova A, Xu H, Rouault M, Humphreys BD. High resolution spatial profiling of kidney injury and repair using RNA hybridization-based in situ sequencing. Nat Commun 2024; 15:1396. [PMID: 38360882 PMCID: PMC10869771 DOI: 10.1038/s41467-024-45752-8] [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: 05/08/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024] Open
Abstract
Emerging spatially resolved transcriptomics technologies allow for the measurement of gene expression in situ at cellular resolution. We apply direct RNA hybridization-based in situ sequencing (dRNA HybISS, Cartana part of 10xGenomics) to compare male and female healthy mouse kidneys and the male kidney injury and repair timecourse. A pre-selected panel of 200 genes is used to identify cell state dynamics patterns during injury and repair. We develop a new computational pipeline, CellScopes, for the rapid analysis, multi-omic integration and visualization of spatially resolved transcriptomic datasets. The resulting dataset allows us to resolve 13 kidney cell types within distinct kidney niches, dynamic alterations in cell state over the course of injury and repair and cell-cell interactions between leukocytes and kidney parenchyma. At late timepoints after injury, C3+ leukocytes are enriched near pro-inflammatory, failed-repair proximal tubule cells. Integration of snRNA-seq dataset from the same injury and repair samples also allows us to impute the spatial localization of genes not directly measured by dRNA HybISS.
Collapse
Affiliation(s)
- Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Qiao Xuanyuan
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Juanru Guo
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | | | | | - Hao Xu
- 10X Genomics, Pleasanton, CA, USA
- Aplex Bio AB, Solna, Sweden
| | | | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
34
|
Ledru N, Wilson PC, Muto Y, Yoshimura Y, Wu H, Li D, Asthana A, Tullius SG, Waikar SS, Orlando G, Humphreys BD. Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing. Nat Commun 2024; 15:1291. [PMID: 38347009 PMCID: PMC10861555 DOI: 10.1038/s41467-024-45706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/31/2024] [Indexed: 02/15/2024] Open
Abstract
Renal proximal tubule epithelial cells have considerable intrinsic repair capacity following injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and assumes a proinflammatory and profibrotic phenotype that may promote fibrosis and chronic kidney disease. The healthy to failed repair change is marked by cell state-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq sequencing offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We develop a regularized regression approach to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generate a single nucleus multiomic dataset from seven adult human kidney samples and apply our method to study drivers of a failed injury response associated with kidney disease. We demonstrate that our approach is a highly effective tool for predicting key cis- and trans-regulatory elements underpinning the healthy to failed repair transition and use it to identify NFAT5 as a driver of the maladaptive proximal tubule state.
Collapse
Affiliation(s)
- Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Parker C Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Amish Asthana
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Stefan G Tullius
- Division of Transplant Surgery and Transplant Surgery Research Laboratory, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Giuseppe Orlando
- Department of Surgery, Wake Forest Baptist Medical Center; Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
35
|
Bock F, Dong X, Li S, Viquez OM, Sha E, Tantengco M, Hennen EM, Plosa E, Ramezani A, Brown KL, Whang YM, Terker AS, Arroyo JP, Harrison DG, Fogo A, Brakebusch CH, Pozzi A, Zent R. Rac1 promotes kidney collecting duct repair by mechanically coupling cell morphology to mitotic entry. SCIENCE ADVANCES 2024; 10:eadi7840. [PMID: 38324689 PMCID: PMC10849615 DOI: 10.1126/sciadv.adi7840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Prolonged obstruction of the ureter, which leads to injury of the kidney collecting ducts, results in permanent structural damage, while early reversal allows for repair. Cell structure is defined by the actin cytoskeleton, which is dynamically organized by small Rho guanosine triphosphatases (GTPases). In this study, we identified the Rho GTPase, Rac1, as a driver of postobstructive kidney collecting duct repair. After the relief of ureteric obstruction, Rac1 promoted actin cytoskeletal reconstitution, which was required to maintain normal mitotic morphology allowing for successful cell division. Mechanistically, Rac1 restricted excessive actomyosin activity that stabilized the negative mitotic entry kinase Wee1. This mechanism ensured mechanical G2-M checkpoint stability and prevented premature mitotic entry. The repair defects following injury could be rescued by direct myosin inhibition. Thus, Rac1-dependent control of the actin cytoskeleton integrates with the cell cycle to mediate kidney tubular repair by preventing dysmorphic cells from entering cell division.
Collapse
Affiliation(s)
- Fabian Bock
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Hospital, Tennessee Valley Healthcare System, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xinyu Dong
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shensen Li
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olga M. Viquez
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric Sha
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Tantengco
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elizabeth M. Hennen
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Erin Plosa
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alireza Ramezani
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, USA
- Department of Physics and Astronomy, University of California, Riverside, CA, USA
| | - Kyle L. Brown
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Young Mi Whang
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew S. Terker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Juan Pablo Arroyo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Hospital, Tennessee Valley Healthcare System, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David G. Harrison
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Agnes Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cord H. Brakebusch
- Biotech Research Center, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Ambra Pozzi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Hospital, Tennessee Valley Healthcare System, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Physiology and Molecular Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Roy Zent
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Hospital, Tennessee Valley Healthcare System, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| |
Collapse
|
36
|
Lei Y, Liang X, Sun Y, Yao T, Gong H, Chen Z, Gao Y, Wang H, Wang R, Huang Y, Yang T, Yu M, Liu L, Yi CX, Wu QF, Kong X, Xu X, Liu S, Zhang Z, Liu T. Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus. Cell Metab 2024; 36:438-453.e6. [PMID: 38325338 DOI: 10.1016/j.cmet.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/27/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
The hypothalamus plays a crucial role in the progression of obesity and diabetes; however, its structural complexity and cellular heterogeneity impede targeted treatments. Here, we profiled the single-cell and spatial transcriptome of the hypothalamus in obese and sporadic type 2 diabetic macaques, revealing primate-specific distributions of clusters and genes as well as spatial region, cell-type-, and gene-feature-specific changes. The infundibular (INF) and paraventricular nuclei (PVN) are most susceptible to metabolic disruption, with the PVN being more sensitive to diabetes. In the INF, obesity results in reduced synaptic plasticity and energy sensing capability, whereas diabetes involves molecular reprogramming associated with impaired tanycytic barriers, activated microglia, and neuronal inflammatory response. In the PVN, cellular metabolism and neural activity are suppressed in diabetic macaques. Spatial transcriptomic data reveal microglia's preference for the parenchyma over the third ventricle in diabetes. Our findings provide a comprehensive view of molecular changes associated with obesity and diabetes.
Collapse
Affiliation(s)
- Ying Lei
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Xian Liang
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yunong Sun
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Ting Yao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University School of Medicine, Xi'an, Shanxi 710063, China
| | - Hongyu Gong
- School of Life Sciences, Institues of Biomedical Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Zhenhua Chen
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanqing Gao
- Jiangsu Provincial Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Hui Wang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yunqi Huang
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Tao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Miao Yu
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Longqi Liu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China
| | - Chun-Xia Yi
- Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, the Netherlands
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingxing Kong
- School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Xun Xu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China.
| | - Shiping Liu
- BGI-Research, Hangzhou 310012, China; BGI-Research, Shenzhen 518103, China.
| | - Zhi Zhang
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Tiemin Liu
- State Key Laboratory of Genetic Engineering, Department of Endocrinology and Metabolism, Human Phenome Institute, Institute of Metabolism and Integrative Biology, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; School of Life Sciences, Fudan University, Shanghai 200438, China; School of Life Sciences, Institues of Biomedical Sciences, Inner Mongolia University, Hohhot 010000, China.
| |
Collapse
|
37
|
Li Y, Ma S, Wang Z, Shi M, Zeng R, Yao Y. Gclc as a Marker for Injured Distal Nephron in Ischemia-Reperfusion Induced Acute Kidney Injury. J Inflamm Res 2024; 17:527-540. [PMID: 38313210 PMCID: PMC10838515 DOI: 10.2147/jir.s451402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/18/2024] [Indexed: 02/06/2024] Open
Abstract
Purpose The distal nephron of kidney plays a pivotal role in advancing acute kidney injury (AKI). Understanding the role of distal nephrons in AKI and identifying markers of injured distal nephrons are critical to comprehending the mechanism of renal injury and identifying novel therapeutic targets. Methods We analyzed single-cell RNA sequencing (scRNA-seq) data from mice with AKI induced by ischemia-reperfusion (IR), unilateral ureteral obstruction (UUO), cisplatin (CP), sodium oxalate (SO) and lipopolysaccharide (LPS). Additionally, we analyzed renal transcriptomics samples for AKI. Subsequently, we validated the effectiveness of targeting the biomarker Gclc in vitro and in vivo through metabolomics and immunofluorescence. Results The LOH-Inj and DCT-Inj subtypes were identified through scRNA-seq. Compared to normal distal nephrons, the injured distal nephrons exhibited higher levels of ferroptosis, pro-inflammation, and fibrosis. The expression of ferroptosis-related gene Gclc were high in various AKI models. Furthermore, Gclc was exclusively expressed in the distal nephron and upregulated in the injury subtype. To confirm our findings, we suppressed GCLC expression in the kidneys, resulting to aggravated IR-induced AKI. Inhibition of Gclc promoted damage to primarily renal tubular epithelial cells by promoting inflammatory infiltration, inhibiting glutathione metabolism and exacerbating oxidative stress. Conclusion Our research findings suggest that Gclc is a potential marker for injured distal nephron.
Collapse
Affiliation(s)
- Yinzheng Li
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Shulin Ma
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Zheng Wang
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Mengxia Shi
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Rui Zeng
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, 430030, People's Republic of China
- NHC Key Laboratory of Organ Transplantation, Wuhan, 430030, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, 430030, People's Republic of China
| | - Ying Yao
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
- Department of Nutrition, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| |
Collapse
|
38
|
Cohen C, Mhaidly R, Croizer H, Kieffer Y, Leclere R, Vincent-Salomon A, Robley C, Anglicheau D, Rabant M, Sannier A, Timsit MO, Eddy S, Kretzler M, Ju W, Mechta-Grigoriou F. WNT-dependent interaction between inflammatory fibroblasts and FOLR2+ macrophages promotes fibrosis in chronic kidney disease. Nat Commun 2024; 15:743. [PMID: 38272907 PMCID: PMC10810789 DOI: 10.1038/s41467-024-44886-z] [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: 03/06/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Chronic kidney disease (CKD) is a public health problem driven by myofibroblast accumulation, leading to interstitial fibrosis. Heterogeneity is a recently recognized characteristic in kidney fibroblasts in CKD, but the role of different populations is still unclear. Here, we characterize a proinflammatory fibroblast population (named CXCL-iFibro), which corresponds to an early state of myofibroblast differentiation in CKD. We demonstrate that CXCL-iFibro co-localize with macrophages in the kidney and participate in their attraction, accumulation, and switch into FOLR2+ macrophages from early CKD stages on. In vitro, macrophages promote the switch of CXCL-iFibro into ECM-secreting myofibroblasts through a WNT/β-catenin-dependent pathway, thereby suggesting a reciprocal crosstalk between these populations of fibroblasts and macrophages. Finally, the detection of CXCL-iFibro at early stages of CKD is predictive of poor patient prognosis, which shows that the CXCL-iFibro population is an early player in CKD progression and demonstrates the clinical relevance of our findings.
Collapse
Affiliation(s)
- Camille Cohen
- Institut Curie, Stress and Cancer Laboratory, Equipe labélisée par la Ligue Nationale contre le Cancer, PSL Research University, 26, rue d'Ulm, F-75248, Paris, France
- Inserm, U830, 26, rue d'Ulm, Paris, F-75005, France
| | - Rana Mhaidly
- Institut Curie, Stress and Cancer Laboratory, Equipe labélisée par la Ligue Nationale contre le Cancer, PSL Research University, 26, rue d'Ulm, F-75248, Paris, France
- Inserm, U830, 26, rue d'Ulm, Paris, F-75005, France
| | - Hugo Croizer
- Institut Curie, Stress and Cancer Laboratory, Equipe labélisée par la Ligue Nationale contre le Cancer, PSL Research University, 26, rue d'Ulm, F-75248, Paris, France
- Inserm, U830, 26, rue d'Ulm, Paris, F-75005, France
| | - Yann Kieffer
- Institut Curie, Stress and Cancer Laboratory, Equipe labélisée par la Ligue Nationale contre le Cancer, PSL Research University, 26, rue d'Ulm, F-75248, Paris, France
- Inserm, U830, 26, rue d'Ulm, Paris, F-75005, France
| | - Renaud Leclere
- Department of Diagnostic and Theragnostic Medicine, Institut Curie Hospital Group, 26, rue d'Ulm, F-75248, Paris, France
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theragnostic Medicine, Institut Curie Hospital Group, 26, rue d'Ulm, F-75248, Paris, France
| | - Catherine Robley
- Institut Curie, Stress and Cancer Laboratory, Equipe labélisée par la Ligue Nationale contre le Cancer, PSL Research University, 26, rue d'Ulm, F-75248, Paris, France
- Inserm, U830, 26, rue d'Ulm, Paris, F-75005, France
| | - Dany Anglicheau
- Department of Nephrology and Kidney Transplantation, Necker Hospital, AP-HP, Paris Cité University, Inserm U1151, 149 rue de Sèvres, 75015, Paris, France
| | - Marion Rabant
- Department of Pathology, Necker Hospital, AP-HP, Paris Cité University, 149 rue de Sèvres, 75015, Paris, France
| | - Aurélie Sannier
- Department of Pathology, AP-HP, Bichat-Claude Bernard Hospital, Paris Cité University, Inserm, U1148, 46, rue Henri Huchard, 75877, Paris, France
| | - Marc-Olivier Timsit
- Department of Urology, Européen George Pompidou Hospital, APHP, Paris Cité University, Paris, France
| | - Sean Eddy
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Wenjun Ju
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Fatima Mechta-Grigoriou
- Institut Curie, Stress and Cancer Laboratory, Equipe labélisée par la Ligue Nationale contre le Cancer, PSL Research University, 26, rue d'Ulm, F-75248, Paris, France.
- Inserm, U830, 26, rue d'Ulm, Paris, F-75005, France.
| |
Collapse
|
39
|
Sourris KC, Ding Y, Maxwell SS, Al-Sharea A, Kantharidis P, Mohan M, Rosado CJ, Penfold SA, Haase C, Xu Y, Forbes JM, Crawford S, Ramm G, Harcourt BE, Jandeleit-Dahm K, Advani A, Murphy AJ, Timmermann DB, Karihaloo A, Knudsen LB, El-Osta A, Drucker DJ, Cooper ME, Coughlan MT. Glucagon-like peptide-1 receptor signaling modifies the extent of diabetic kidney disease through dampening the receptor for advanced glycation end products-induced inflammation. Kidney Int 2024; 105:132-149. [PMID: 38069998 DOI: 10.1016/j.kint.2023.09.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/16/2023] [Accepted: 09/25/2023] [Indexed: 01/07/2024]
Abstract
Glucagon like peptide-1 (GLP-1) is a hormone produced and released by cells of the gastrointestinal tract following meal ingestion. GLP-1 receptor agonists (GLP-1RA) exhibit kidney-protective actions through poorly understood mechanisms. Here we interrogated whether the receptor for advanced glycation end products (RAGE) plays a role in mediating the actions of GLP-1 on inflammation and diabetic kidney disease. Mice with deletion of the GLP-1 receptor displayed an abnormal kidney phenotype that was accelerated by diabetes and improved with co-deletion of RAGE in vivo. Activation of the GLP-1 receptor pathway with liraglutide, an anti-diabetic treatment, downregulated kidney RAGE, reduced the expansion of bone marrow myeloid progenitors, promoted M2-like macrophage polarization and lessened markers of kidney damage in diabetic mice. Single cell transcriptomics revealed that liraglutide induced distinct transcriptional changes in kidney endothelial, proximal tubular, podocyte and macrophage cells, which were dominated by pathways involved in nutrient transport and utilization, redox sensing and the resolution of inflammation. The kidney-protective action of liraglutide was corroborated in a non-diabetic model of chronic kidney disease, the subtotal nephrectomised rat. Thus, our findings identify a novel glucose-independent kidney-protective action of GLP-1-based therapies in diabetic kidney disease and provide a valuable resource for exploring the cell-specific kidney transcriptional response ensuing from pharmacological GLP-1R agonism.
Collapse
Affiliation(s)
- Karly C Sourris
- Department of Diabetes, Monash University, Central Clinical School, Alfred Research Alliance, Melbourne, Victoria, Australia; Diabetes Complications Division, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia.
| | - Yi Ding
- Diabetes Complications Division, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia; Diabetes Complications Research, Novo Nordisk, Måløv, Denmark
| | - Scott S Maxwell
- Epigenetics in Human Health and Disease Program, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | - Annas Al-Sharea
- Haematopoiesis and Leukocyte Biology, Division of Immunometabolism, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | - Phillip Kantharidis
- Department of Diabetes, Monash University, Central Clinical School, Alfred Research Alliance, Melbourne, Victoria, Australia
| | - Muthukumar Mohan
- Department of Diabetes, Monash University, Central Clinical School, Alfred Research Alliance, Melbourne, Victoria, Australia
| | - Carlos J Rosado
- Department of Diabetes, Monash University, Central Clinical School, Alfred Research Alliance, Melbourne, Victoria, Australia
| | - Sally A Penfold
- Diabetes Complications Division, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | - Claus Haase
- Diabetes Complications Research, Novo Nordisk, Måløv, Denmark
| | - Yangsong Xu
- Haematopoiesis and Leukocyte Biology, Division of Immunometabolism, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | - Josephine M Forbes
- Mater Research Institute, the University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Simon Crawford
- Monash Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Georg Ramm
- Monash Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Brooke E Harcourt
- Murdoch Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Karin Jandeleit-Dahm
- Department of Diabetes, Monash University, Central Clinical School, Alfred Research Alliance, Melbourne, Victoria, Australia
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science and Li Ka Shing Knowledge Institute, St. Michaels Hospital, Toronto, Ontario, Canada
| | - Andrew J Murphy
- Haematopoiesis and Leukocyte Biology, Division of Immunometabolism, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | | | - Anil Karihaloo
- Novo Nordisk Research Center Seattle, Inc., Seattle, Washington, USA
| | | | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
| | - Daniel J Drucker
- Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Mark E Cooper
- Department of Diabetes, Monash University, Central Clinical School, Alfred Research Alliance, Melbourne, Victoria, Australia
| | - Melinda T Coughlan
- Department of Diabetes, Monash University, Central Clinical School, Alfred Research Alliance, Melbourne, Victoria, Australia; Diabetes Complications Division, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University Parkville Campus, Parkville, Victoria, Australia.
| |
Collapse
|
40
|
Eun M, Kim D, Shin SI, Yang HO, Kim KD, Choi SY, Park S, Kim DK, Jeong CW, Moon KC, Lee H, Park J. Chromatin accessibility analysis and architectural profiling of human kidneys reveal key cell types and a regulator of diabetic kidney disease. Kidney Int 2024; 105:150-164. [PMID: 37925023 DOI: 10.1016/j.kint.2023.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/22/2023] [Accepted: 09/25/2023] [Indexed: 11/06/2023]
Abstract
Diabetes is the leading cause of kidney disease that progresses to kidney failure. However, the key molecular and cellular pathways involved in diabetic kidney disease (DKD) pathogenesis are largely unknown. Here, we performed a comparative analysis of adult human kidneys by examining cell type-specific chromatin accessibility by single-nucleus ATAC-seq (snATAC-seq) and analyzing three-dimensional chromatin architecture via high-throughput chromosome conformation capture (Hi-C method) of paired samples. We mapped the cell type-specific and DKD-specific open chromatin landscape and found that genetic variants associated with kidney diseases were significantly enriched in the proximal tubule- (PT) and injured PT-specific open chromatin regions in samples from patients with DKD. BACH1 was identified as a core transcription factor of injured PT cells; its binding target genes were highly associated with fibrosis and inflammation, which were also key features of injured PT cells. Additionally, Hi-C analysis revealed global chromatin architectural changes in DKD, accompanied by changes in local open chromatin patterns. Combining the snATAC-seq and Hi-C data identified direct target genes of BACH1, and indicated that BACH1 binding regions showed increased chromatin contact frequency with promoters of their target genes in DKD. Thus, our multi-omics analysis revealed BACH1 target genes in injured PTs and highlighted the role of BACH1 as a novel regulator of tubular inflammation and fibrosis.
Collapse
Affiliation(s)
- Minho Eun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Donggun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hyun Oh Yang
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea
| | - Sin Young Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sehoon Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Wook Jeong
- Department of Urology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
| |
Collapse
|
41
|
Shen W, Yuan L, Cheng F, Wu Z, Li X. SRSF7 is a promising prognostic biomarker in hepatocellular carcinoma and is associated with immune infiltration. Genes Genomics 2024; 46:49-64. [PMID: 37985547 DOI: 10.1007/s13258-023-01463-w] [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: 07/19/2023] [Accepted: 09/30/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Previous studies indicate that the splicing process, regulated by the cellular machinery of tumors (spliceosome), undergoes alterations, leading to oncogenic splicing events associated with the progression of tumors towards aggressiveness. However, the role of serine/arginine-rich splicing factor 7 (SRSF7) in hepatocellular carcinoma (HCC) and the tumor microenvironment (TME) remains unclear. METHODS This study was aimed to explore the role and clinical significance of SRSF7 in HCC. By conducting functional analysis and gene set enrichment analysis, it was discovered that SRSF7 contributes to multiple pathways associated with immune response and tumor advancement. Further experiments verified that silencing of SRSF7 obviously inhibits progression of HCC. RESULTS Aberrant expression of SRSF7, which were referred as an independent prognostic risk factor, effectively predicts the prognosis of patients with HCC. Functional and gene enrichment analyses revealed that SRSF7 is linked with multiple immune and tumor progression-related pathways, including the B cell receptor signaling pathway, positive regulation of leukocyte and immunoglobulin receptor binding cell activation, nuclear division, membrane invagination, cell cycle, as well as mTOR signaling pathway. Furthermore, increased SRSF7 expression was associated with tumor-infiltrating inflammatory cells (CD4+, monocytes/macrophages, CD8 + and endothelial). Additionally, multiple immune checkpoint genes were markedly positively related to SRSF7. The efficiency of SRSF7 in predicting immunomodulator and chemokine responses were also assessed in microenvironment. Moreover, in vitro analyses demonstrated that knockdown of SRSF7 suppressed the malignant evolution of HCC possibly by deactivating the PI3K/AKT/mTOR signaling. CONCLUSION The role of SRSF7 in the tumor microenvironment has been successfully assessed. It may be a valid bio-index for predicting the HCC prognosis, thereby guiding individualized immunotherapy for cancer.
Collapse
Affiliation(s)
- Wei Shen
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
| | - Lebin Yuan
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Fei Cheng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Zhao Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Xiaodong Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| |
Collapse
|
42
|
Mukhi D, Li L, Liu H, Doke T, Kolligundla LP, Ha E, Kloetzer K, Abedini A, Mukherjee S, Wu J, Dhillon P, Hu H, Guan D, Funai K, Uehara K, Titchenell PM, Baur JA, Wellen KE, Susztak K. ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules. J Clin Invest 2023; 134:e172963. [PMID: 38051585 PMCID: PMC10866669 DOI: 10.1172/jci172963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Worldwide, over 800 million people are affected by kidney disease, yet its pathogenesis remains elusive, hindering the development of novel therapeutics. In this study, we used kidney-specific expression of quantitative traits and single-nucleus open chromatin analysis to show that genetic variants linked to kidney dysfunction on chromosome 20 target the acyl-CoA synthetase short-chain family 2 (ACSS2). By generating ACSS2-KO mice, we demonstrated their protection from kidney fibrosis in multiple disease models. Our analysis of primary tubular cells revealed that ACSS2 regulated de novo lipogenesis (DNL), causing NADPH depletion and increasing ROS levels, ultimately leading to NLRP3-dependent pyroptosis. Additionally, we discovered that pharmacological inhibition or genetic ablation of fatty acid synthase safeguarded kidney cells against profibrotic gene expression and prevented kidney disease in mice. Lipid accumulation and the expression of genes related to DNL were elevated in the kidneys of patients with fibrosis. Our findings pinpoint ACSS2 as a critical kidney disease gene and reveal the role of DNL in kidney disease.
Collapse
Affiliation(s)
- Dhanunjay Mukhi
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Lingzhi Li
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Hongbo Liu
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Tomohito Doke
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Lakshmi P. Kolligundla
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Eunji Ha
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Konstantin Kloetzer
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Amin Abedini
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Sarmistha Mukherjee
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Junnan Wu
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Poonam Dhillon
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Hailong Hu
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
| | - Dongyin Guan
- Division of Endocrinology, Baylor College of Medicine, Houston, Texas, USA
| | - Katsuhiko Funai
- Diabetes and Metabolism Research Center, University of Utah, Salt Lake City, Utah, USA
| | - Kahealani Uehara
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul M. Titchenell
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph A. Baur
- Institutes for Diabetes, Obesity and Metabolism
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathryn E. Wellen
- Department of Cancer Biology
- Abramson Family Cancer Research Institute, and
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division
- Institutes for Diabetes, Obesity and Metabolism
- Department of Genetics, and
- Penn-CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
43
|
Azushima K, Kovalik JP, Yamaji T, Ching J, Chng TW, Guo J, Liu JJ, Nguyen M, Sakban RB, George SE, Tan PH, Lim SC, Gurley SB, Coffman TM. Abnormal lactate metabolism is linked to albuminuria and kidney injury in diabetic nephropathy. Kidney Int 2023; 104:1135-1149. [PMID: 37843477 DOI: 10.1016/j.kint.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 10/17/2023]
Abstract
Diabetic nephropathy (DN) is characterized by abnormal kidney energy metabolism, but its causes and contributions to DN pathogenesis are not clear. To examine this issue, we carried out targeted metabolomics profiling in a mouse model of DN that develops kidney disease resembling the human disorder. We found a distinct profile of increased lactate levels and impaired energy metabolism in kidneys of mice with DN, and treatment with an angiotensin-receptor blocker (ARB) reduced albuminuria, attenuated kidney pathology and corrected many metabolic abnormalities, restoring levels of lactate toward normal while increasing kidney ATP content. We also found enhanced expression of lactate dehydrogenase isoforms in DN. Expression of both the LdhA and LdhB isoforms were significantly increased in kidneys of mice, and treatment with ARB significantly reduced their expression. Single-cell sequencing studies showed specific up-regulation of LdhA in the proximal tubule, along with enhanced expression of oxidative stress pathways. There was a significant correlation between albuminuria and lactate in mice, and also in a Southeast Asian patient cohort consisting of individuals with type 2 diabetes and impaired kidney function. In the individuals with diabetes, this association was independent of ARB and angiotensin-converting enzyme inhibitor use. Furthermore, urinary lactate levels predicted the clinical outcomes of doubling of serum creatinine or development of kidney failure, and there was a significant correlation between urinary lactate levels and biomarkers of tubular injury and epithelial stress. Thus, we suggest that kidney metabolic disruptions leading to enhanced generation of lactate contribute to the pathogenesis of DN and increased urinary lactate levels may be a potential biomarker for risk of kidney disease progression.
Collapse
Affiliation(s)
- Kengo Azushima
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore; Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Japan Society for the Promotion of Science, Tokyo, Japan
| | - Jean-Paul Kovalik
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Takahiro Yamaji
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore; Department of Medical Science and Cardiorenal Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Jianhong Ching
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Tze Wei Chng
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Jing Guo
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | - Mien Nguyen
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Rashidah Binte Sakban
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Simi E George
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore; Diabetes Centre, Khoo Teck Puat Hospital, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Lee Kong Chian School of Medicine, Singapore; Nanyang Technological University, Singapore
| | - Susan B Gurley
- Department of Medicine, Division of Nephrology and Hypertension, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Thomas M Coffman
- Cardiovascular and Metabolic Disorders Signature Research Program, Duke-NUS Medical School, Singapore; Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.
| |
Collapse
|
44
|
Kanasaki K. The aberrant glycolysis in kidney proximal tubule: potential therapeutic target for DKD. Kidney Int 2023; 104:1056-1059. [PMID: 37981426 DOI: 10.1016/j.kint.2023.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 11/21/2023]
Abstract
The presence of glycolysis in kidney proximal tubule has been long debated. However, recent reports suggest that aberrant glycolysis is induced in pathologic conditions and may play a critical role in kidney damage. Azushima et al. provided additional evidence that the accumulation of glycolysis-derived lactate could be the clue to understanding the pathogenesis of diabetic kidney disease.
Collapse
Affiliation(s)
- Keizo Kanasaki
- Department of Internal Medicine 1, Faculty of Medicine, Shimane University, Izumo, Japan.
| |
Collapse
|
45
|
Westerhof LM, Noonan J, Hargrave KE, Chimbayo ET, Cheng Z, Purnell T, Jackson MR, Borcherding N, MacLeod MKL. Multifunctional cytokine production marks influenza A virus-specific CD4 T cells with high expression of survival molecules. Eur J Immunol 2023; 53:e2350559. [PMID: 37490492 PMCID: PMC10947402 DOI: 10.1002/eji.202350559] [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: 05/08/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/27/2023]
Abstract
Cytokine production by memory T cells is a key mechanism of T cell mediated protection. However, we have limited understanding of the persistence of cytokine producing T cells during memory cell maintenance and secondary responses. We interrogated antigen-specific CD4 T cells using a mouse influenza A virus infection model. Although CD4 T cells detected using MHCII tetramers declined in lymphoid and non-lymphoid organs, we found similar numbers of cytokine+ CD4 T cells at days 9 and 30 in the lymphoid organs. CD4 T cells with the capacity to produce cytokines expressed higher levels of pro-survival molecules, CD127 and Bcl2, than non-cytokine+ cells. Transcriptomic analysis revealed a heterogeneous population of memory CD4 T cells with three clusters of cytokine+ cells. These clusters match flow cytometry data and reveal an enhanced survival signature in cells capable of producing multiple cytokines. Following re-infection, multifunctional T cells expressed low levels of the proliferation marker, Ki67, whereas cells that only produce the anti-viral cytokine, interferon-γ, were more likely to be Ki67+ . Despite this, multifunctional memory T cells formed a substantial fraction of the secondary memory pool. Together these data indicate that survival rather than proliferation may dictate which populations persist within the memory pool.
Collapse
Affiliation(s)
| | - Jonathan Noonan
- Baker Heart and Diabetes Institute & Baker Department of Cardiometabolic HealthUniversity of MelbourneMelbourneAustralia
| | | | - Elizabeth T. Chimbayo
- School of Infection and ImmunityUniversity of GlasgowGlasgowUK
- Malawi Liverpool Wellcome CentreBlantyreMalawi
| | - Zhiling Cheng
- School of Infection and ImmunityUniversity of GlasgowGlasgowUK
| | - Thomas Purnell
- School of Infection and ImmunityUniversity of GlasgowGlasgowUK
| | | | | | | |
Collapse
|
46
|
Zhou J, Abedini A, Balzer MS, Shrestha R, Dhillon P, Liu H, Hu H, Susztak K. Unified Mouse and Human Kidney Single-Cell Expression Atlas Reveal Commonalities and Differences in Disease States. J Am Soc Nephrol 2023; 34:1843-1862. [PMID: 37639336 PMCID: PMC10631616 DOI: 10.1681/asn.0000000000000217] [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: 03/09/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
SIGNIFICANCE STATEMENT Mouse models have been widely used to understand kidney disease pathomechanisms and play an important role in drug discovery. However, these models have not been systematically analyzed and compared. The authors characterized 18 different mouse kidney disease models at both bulk and single-cell gene expression levels and compared single-cell gene expression data from diabetic kidney disease (DKD) mice and from patients with DKD. Although single cell-level gene expression changes were mostly model-specific, different disease models showed similar changes when compared at a pathway level. The authors also found that changes in fractions of cell types are major drivers of bulk gene expression differences. Although the authors found only a small overlap of single cell-level gene expression changes between the mouse DKD model and patients, they observed consistent pathway-level changes. BACKGROUND Mouse models have been widely used to understand kidney disease pathomechanisms and play an important role in drug discovery. However, these models have not been systematically analyzed and compared. METHODS We analyzed single-cell RNA sequencing data (36 samples) and bulk gene expression data (42 samples) from 18 commonly used mouse kidney disease models. We compared single-nucleus RNA sequencing data from a mouse diabetic kidney disease model with data from patients with diabetic kidney disease and healthy controls. RESULTS We generated a uniformly processed mouse single-cell atlas containing information for nearly 300,000 cells, identifying all major kidney cell types and states. Our analysis revealed that changes in fractions of cell types are major drivers of differences in bulk gene expression. Although gene expression changes at the single-cell level were mostly model-specific, different disease models showed similar changes when compared at a pathway level. Tensor decomposition analysis highlighted the important changes in proximal tubule cells in disease states. Specifically, we identified important alterations in expression of metabolic and inflammation-associated pathways. The mouse diabetic kidney disease model and patients with diabetic kidney disease shared only a small number of conserved cell type-specific differentially expressed genes, but we observed pathway-level activation patterns conserved between mouse and human diabetic kidney disease samples. CONCLUSIONS This study provides a comprehensive mouse kidney single-cell atlas and defines gene expression commonalities and differences in disease states in mice. The results highlight the key role of cell heterogeneity in driving changes in bulk gene expression and the limited overlap of single-cell gene expression changes between animal models and patients, but they also reveal consistent pathway-level changes.
Collapse
Affiliation(s)
- Jianfu Zhou
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael S. Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rojesh Shrestha
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Poonam Dhillon
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hailong Hu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Kidney Innovation Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
47
|
Han G, Yan D, Sun Z, Fang J, chang X, Wilson L, Liu Y. Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses. RESEARCH SQUARE 2023:rs.3.rs-3384541. [PMID: 37886581 PMCID: PMC10602069 DOI: 10.21203/rs.3.rs-3384541/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive. Results Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power. Conclusion In our idiopathic pulmonary fibrosis (IPF) case study, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.
Collapse
Affiliation(s)
- Gang Han
- Epidemiology & Biostatistics, 212 Adriance Lab Rd, 1266 TAMU College Station, TX 77843
| | - Dongyan Yan
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Zhe Sun
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Jiyuan Fang
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Xinyue chang
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Lucas Wilson
- Epidemiology & Biostatistics, 212 Adriance Lab Rd, 1266 TAMU College Station, TX 77843
| | - Yushi Liu
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| |
Collapse
|
48
|
Naas S, Schiffer M, Schödel J. Hypoxia and renal fibrosis. Am J Physiol Cell Physiol 2023; 325:C999-C1016. [PMID: 37661918 DOI: 10.1152/ajpcell.00201.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Renal fibrosis is the final stage of most progressive kidney diseases. Chronic kidney disease (CKD) is associated with high comorbidity and mortality. Thus, preventing fibrosis and thereby preserving kidney function increases the quality of life and prolongs the survival of patients with CKD. Many processes such as inflammation or metabolic stress modulate the progression of kidney fibrosis. Hypoxia has also been implicated in the pathogenesis of renal fibrosis, and oxygen sensing in the kidney is of outstanding importance for the body. The dysregulation of oxygen sensing in the diseased kidney is best exemplified by the loss of stimulation of erythropoietin production from interstitial cells in the fibrotic kidney despite anemia. Furthermore, hypoxia is present in acute or chronic kidney diseases and may affect all cell types present in the kidney including tubular and glomerular cells as well as resident immune cells. Pro- and antifibrotic effects of the transcription factors hypoxia-inducible factors 1 and 2 have been described in a plethora of animal models of acute and chronic kidney diseases, but recent advances in sequencing technologies now allow for novel and deeper insights into the role of hypoxia and its cell type-specific effects on the progression of renal fibrosis, especially in humans. Here, we review existing literature on how hypoxia impacts the development and progression of renal fibrosis.
Collapse
Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
49
|
Pohl L, Schiessl IM. Endothelial cell plasticity in kidney fibrosis and disease. Acta Physiol (Oxf) 2023; 239:e14038. [PMID: 37661749 DOI: 10.1111/apha.14038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/29/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023]
Abstract
Renal endothelial cells demonstrate an impressive remodeling potential during angiogenic sprouting, vessel repair or while transitioning into mesenchymal cells. These different processes may play important roles in both renal disease progression or regeneration while underlying signaling pathways of different endothelial cell plasticity routes partly overlap. Angiogenesis contributes to wound healing after kidney injury and pharmaceutical modulation of angiogenesis may home a great therapeutic potential. Yet, it is not clear whether any differentiated endothelial cell can proliferate or whether regenerative processes are largely controlled by resident or circulating endothelial progenitor cells. In the glomerular compartment for example, a distinct endothelial progenitor cell population may remodel the glomerular endothelium after injury. Endothelial-to-mesenchymal transition (EndoMT) in the kidney is vastly documented and often associated with endothelial dysfunction, fibrosis, and kidney disease progression. Especially the role of EndoMT in renal fibrosis is controversial. Studies on EndoMT in vivo determined possible conclusions on the pathophysiological role of EndoMT in the kidney, but whether endothelial cells really contribute to kidney fibrosis and if not what other cellular and functional outcomes derive from EndoMT in kidney disease is unclear. Sequencing data, however, suggest no participation of endothelial cells in extracellular matrix deposition. Thus, more in-depth classification of cellular markers and the fate of EndoMT cells in the kidney is needed. In this review, we describe different signaling pathways of endothelial plasticity, outline methodological approaches and evidence for functional and structural implications of angiogenesis and EndoMT in the kidney, and eventually discuss controversial aspects in the literature.
Collapse
Affiliation(s)
- Layla Pohl
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | |
Collapse
|
50
|
Fan K, Yuan S, Zhou M, Yu Y, Guo J, Fang L, Zhou C, Cui P, Zhang S, Li R, Wang Z, Zhong L, Zeng L. Enhanced Biohomogeneous Composite Membrane-Encapsulated Nanoplatform with Podocyte Targeting for Precise and Safe Treatment of Diabetic Nephropathy. ACS NANO 2023; 17:18037-18054. [PMID: 37713364 DOI: 10.1021/acsnano.3c04671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
Diabetic nephropathy (DN), associated with high mobility and disability, is the leading cause of end-stage kidney disease worldwide. Dysfunction of the mammalian target of the rapamycin (mTOR) pathway and reactive oxygen species (ROS) activation in the glomeruli is the main hypnosis for DN progression. However, the use of mTOR inhibitors for DN treatment remains controversial. In this study, we built a multifunctional selective mechanistic target of rapamycin complex 1 (mTORC1) inhibiting nanoplatform (naming as ESC-HCM-B) that targets the release of mTOR and ROS inhibitors near podocytes, aiming to confirm whether combination therapy is an alternative method for DN treatment. The results showed that ESC-HCM-B achieved high drug loading because of the core mesoporous silica nanoparticles (MSNPs), and the enhanced biohomogeneous composite membrane endowed ESC-HCM-B with the characteristics of avoiding immune phagocytosis, automatic valve-type slow-release drug, and high stability. In vitro, the nanoplatform showed high efficiency in podocyte targeting but no significant cytotoxicity or apoptotic promotion. In particular, the quantum dots carried by ESC-HCM-B further amplified the effect of "nanoenzyme"; this mechanism reduced the ROS level in podocytes induced by high glucose, protected mitochondrial damage, and restored mitochondrial energy metabolism. In vivo, the nanoplatform specifically targeted the glomerular and podocyte regions of the kidney. After treatment, the nanoplatform significantly reduced urinary protein levels and delayed glomerulosclerosis in DN rats. This nanoplatform provides a safe and effective strategy for DN treatment.
Collapse
Affiliation(s)
- Kui Fan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
- Institute of Ultrasound Imaging, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Shiyi Yuan
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
- Department of Nephrology, Chongqing Yongchuan District People's Hospital, Chongqing, 402160, China
| | - Mi Zhou
- Department of Biochemistry and Molecular Biology, Army Medical University, Chongqing, 400038, China
| | - Yuan Yu
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Jing Guo
- Radiation Oncology Center, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China
| | - Liang Fang
- Department of Nephrology, Yongchuan Hospital of Chongqing Medical University, Chongqing, 402160, China
| | - Chanjuan Zhou
- Department of Nephrology, Yongchuan Hospital of Chongqing Medical University, Chongqing, 402160, China
| | - Peijin Cui
- Chongqing Key Laboratory of Cerebral Vascular Disease Research, Yongchuan Hospital of Chongqing Medical University, Chongqing, 402160, China
| | - Siliang Zhang
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Rong Li
- Department of Nephrology, Guangyuan Central Hospital, Guanyuan, 628000, China
| | - Zhigang Wang
- Institute of Ultrasound Imaging, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Ling Zhong
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Li Zeng
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| |
Collapse
|