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Miyaki T, Homma N, Kawasaki Y, Kishi M, Yamaguchi J, Kakuta S, Shindo T, Sugiura M, Oliva Trejo JA, Kaneda H, Omotehara T, Takechi M, Negishi-Koga T, Ishijima M, Aoto K, Iseki S, Kitamura K, Muto S, Amagasa M, Hotchi S, Ogura K, Shibata S, Sakai T, Suzuki Y, Ichimura K. Ultrastructural analysis of whole glomeruli using array tomography. J Cell Sci 2024; 137:jcs262154. [PMID: 39171439 DOI: 10.1242/jcs.262154] [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: 03/28/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024] Open
Abstract
The renal glomerulus produces primary urine from blood plasma by ultrafiltration. The ultrastructure of the glomerulus is closely related to filtration function and disease development. The ultrastructure of glomeruli has mainly been evaluated using transmission electron microscopy; however, the volume that can be observed using transmission electron microscopy is extremely limited relative to the total volume of the glomerulus. Consequently, observing structures that exist in only one location in each glomerulus, such as the vascular pole, and evaluating low-density or localized lesions are challenging tasks. Array tomography (AT) is a technique used to analyze the ultrastructure of tissues and cells via scanning electron microscopy of serial sections. In this study, we present an AT workflow that is optimized for observing complete serial sections of the whole glomerulus, and we share several analytical examples that use the optimized AT workflow, demonstrating the usefulness of this approach. Overall, this AT workflow can be a powerful tool for structural and pathological evaluation of the glomerulus. This workflow is also expected to provide new insights into the ultrastructure of the glomerulus and its constituent cells.
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Affiliation(s)
- Takayuki Miyaki
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Nozomi Homma
- Department of Nephrology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Yuto Kawasaki
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Mami Kishi
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Junji Yamaguchi
- Laboratory of Morphology and Image Analysis, Research Core Facilities , Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Soichiro Kakuta
- Laboratory of Morphology and Image Analysis, Research Core Facilities , Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Tomoko Shindo
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo 160-0016, Japan
| | - Makoto Sugiura
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Juan Alejandro Oliva Trejo
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Hisako Kaneda
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Takuya Omotehara
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Masaki Takechi
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Takako Negishi-Koga
- Department of Medicine for Orthopedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Community Medicine and Research for Bone and Joint Diseases, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Muneaki Ishijima
- Department of Medicine for Orthopedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Department of Community Medicine and Research for Bone and Joint Diseases, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kazushi Aoto
- Central Laboratory, Graduate School of Biomedical and Health Sciences , Hiroshima University, Hiroshima 734-8551, Japan
| | - Sachiko Iseki
- Department of Molecular Craniofacial Embryology and Oral Histology, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kosuke Kitamura
- Department of Urology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Satoru Muto
- Department of Urology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Mao Amagasa
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Shiori Hotchi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kanako Ogura
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo 160-0016, Japan
- Division of Microscopic Anatomy, Graduate School of Medical and Dental Sciences , Niigata University, Niigata City 951-8510, Japan
| | - Tatsuo Sakai
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Yusuke Suzuki
- Department of Nephrology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Koichiro Ichimura
- Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
- Laboratory of Morphology and Image Analysis, Research Core Facilities , Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
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Unger Avila P, Padvitski T, Leote AC, Chen H, Saez-Rodriguez J, Kann M, Beyer A. Gene regulatory networks in disease and ageing. Nat Rev Nephrol 2024; 20:616-633. [PMID: 38867109 DOI: 10.1038/s41581-024-00849-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/14/2024]
Abstract
The precise control of gene expression is required for the maintenance of cellular homeostasis and proper cellular function, and the declining control of gene expression with age is considered a major contributor to age-associated changes in cellular physiology and disease. The coordination of gene expression can be represented through models of the molecular interactions that govern gene expression levels, so-called gene regulatory networks. Gene regulatory networks can represent interactions that occur through signal transduction, those that involve regulatory transcription factors, or statistical models of gene-gene relationships based on the premise that certain sets of genes tend to be coexpressed across a range of conditions and cell types. Advances in experimental and computational technologies have enabled the inference of these networks on an unprecedented scale and at unprecedented precision. Here, we delineate different types of gene regulatory networks and their cell-biological interpretation. We describe methods for inferring such networks from large-scale, multi-omics datasets and present applications that have aided our understanding of cellular ageing and disease mechanisms.
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Affiliation(s)
- Paula Unger Avila
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Tsimafei Padvitski
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ana Carolina Leote
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - He Chen
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Martin Kann
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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Madison J, Wilhelm K, Meehan DT, Gratton MA, Vosik D, Samuelson G, Ott M, Fascianella J, Nelson N, Cosgrove D. Ramipril therapy in integrin α1-null, autosomal recessive Alport mice triples lifespan: mechanistic clues from RNA-seq analysis. J Pathol 2024; 262:296-309. [PMID: 38129319 PMCID: PMC10872630 DOI: 10.1002/path.6231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 10/10/2023] [Accepted: 10/29/2023] [Indexed: 12/23/2023]
Abstract
The standard of care for patients with Alport syndrome (AS) is angiotensin-converting enzyme (ACE) inhibitors. In autosomal recessive Alport (ARAS) mice, ACE inhibitors double lifespan. We previously showed that deletion of Itga1 in Alport mice [double-knockout (DKO) mice] increased lifespan by 50%. This effect seemed dependent on the prevention of laminin 211-mediated podocyte injury. Here, we treated DKO mice with vehicle or ramipril starting at 4 weeks of age. Proteinuria and glomerular filtration rates were measured at 5-week intervals. Glomeruli were analyzed for laminin 211 deposition in the glomerular basement membrane (GBM) and GBM ultrastructure was analyzed using transmission electron microscopy (TEM). RNA sequencing (RNA-seq) was performed on isolated glomeruli at all time points and the results were compared with cultured podocytes overlaid (or not) with recombinant laminin 211. Glomerular filtration rate declined in ramipril-treated DKO mice between 30 and 35 weeks. Proteinuria followed these same patterns with normalization of foot process architecture in ramipril-treated DKO mice. RNA-seq revealed a decline in the expression of Foxc2, nephrin (Nphs1), and podocin (Nphs2) mRNAs, which was delayed in the ramipril-treated DKO mice. GBM accumulation of laminin 211 was delayed in ramipril-treated DKO mice, likely due to a role for α1β1 integrin in CDC42 activation in Alport mesangial cells, which is required for mesangial filopodial invasion of the subendothelial spaces of the glomerular capillary loops. Ramipril synergized with Itga1 knockout, tripling lifespan compared with untreated ARAS mice. © 2023 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jacob Madison
- Boys Town National Research Hospital, Omaha, NE, USA
| | - Kevin Wilhelm
- Boys Town National Research Hospital, Omaha, NE, USA
| | | | | | - Denise Vosik
- Boys Town National Research Hospital, Omaha, NE, USA
| | | | - Megan Ott
- Boys Town National Research Hospital, Omaha, NE, USA
| | | | - Noa Nelson
- Boys Town National Research Hospital, Omaha, NE, USA
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Elshani M, Um IH, Leung S, Reynolds PA, Chapman A, Kudsy M, Harrison DJ. Transcription Factor NFE2L1 Decreases in Glomerulonephropathies after Podocyte Damage. Cells 2023; 12:2165. [PMID: 37681897 PMCID: PMC10487238 DOI: 10.3390/cells12172165] [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: 05/19/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023] Open
Abstract
Podocyte cellular injury and detachment from glomerular capillaries constitute a critical factor contributing to kidney disease. Notably, transcription factors are instrumental in maintaining podocyte differentiation and homeostasis. This study explores the hitherto uninvestigated expression of Nuclear Factor Erythroid 2-related Factor 1 (NFE2L1) in podocytes. We evaluated the podocyte expression of NFE2L1, Nuclear Factor Erythroid 2-related Factor 2 (NFE2L2), and NAD(P)H:quinone Oxidoreductase (NQO1) in 127 human glomerular disease biopsies using multiplexed immunofluorescence and image analysis. We found that both NFE2L1 and NQO1 expressions were significantly diminished across all observed renal diseases. Furthermore, we exposed human immortalized podocytes and ex vivo kidney slices to Puromycin Aminonucleoside (PAN) and characterized the NFE2L1 protein isoform expression. PAN treatment led to a reduction in the nuclear expression of NFE2L1 in ex vivo kidney slices and podocytes.
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Affiliation(s)
- Mustafa Elshani
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK (D.J.H.)
- Pathology, Laboratory Medicine, Royal Infirmary of Edinburgh, Little France, Edinburgh EH16 6NA, UK
- NuCana plc, 3 Lochside Way, Edinburgh EH12 9DT, UK
| | - In Hwa Um
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK (D.J.H.)
| | - Steve Leung
- Urology Department, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Paul A. Reynolds
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK (D.J.H.)
| | - Alex Chapman
- Urology Department, Victoria Hospital, Hayfield Road, Kirkcaldy KY2 5AH, UK
| | - Mary Kudsy
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK (D.J.H.)
| | - David J. Harrison
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK (D.J.H.)
- Pathology, Laboratory Medicine, Royal Infirmary of Edinburgh, Little France, Edinburgh EH16 6NA, UK
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Morito N, Usui T, Ishibashi S, Yamagata K. Podocyte-specific Transcription Factors: Could MafB Become a Therapeutic Target for Kidney Disease? Intern Med 2023; 62:11-19. [PMID: 35249929 PMCID: PMC9876710 DOI: 10.2169/internalmedicine.9336-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The increasing number of patients with chronic kidney disease (CKD) is being recognized as an emerging global health problem. Recently, it has become clear that injury and loss of glomerular visceral epithelial cells, known as podocytes, is a common early event in many forms of CKD. Podocytes are highly specialized epithelial cells that cover the outer layer of the glomerular basement membrane. They serve as the final barrier to urinary protein loss through the formation and maintenance of specialized foot-processes and an interposed slit-diaphragm. We previously reported that the transcription factor MafB regulates the podocyte slit diaphragm protein production and transcription factor Tcf21. We showed that the forced expression of MafB was able to prevent CKD. In this review, we discuss recent advances and offer an updated overview of the functions of podocyte-specific transcription factors in kidney biology, aiming to present new perspectives on the progression of CKD and respective therapeutic strategies.
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Affiliation(s)
- Naoki Morito
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Japan
| | - Toshiaki Usui
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Japan
| | - Shun Ishibashi
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Japan
| | - Kunihiro Yamagata
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Japan
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