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Bradford STJ, Wu H, Kirita Y, Chen C, Malvin NP, Yoshimura Y, Muto Y, Humphreys BD. Tnik depletion induces inflammation and apoptosis ininjured renal proximal tubule epithelial cells. Am J Physiol Renal Physiol 2024. [PMID: 38482555 DOI: 10.1152/ajprenal.00262.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/05/2024] [Indexed: 04/12/2024] Open
Abstract
In the aftermath of acute kidney injury (AKI), surviving proximal tubule epithelia repopulate injured tubules to promote repair. However, a portion of cells fail to repair (termed Failed Repair Proximal Tubule Cells, FR-PTCs) and exert ongoing proinflammatory and profibrotic effects. To better understand the molecular drivers of the FR-PTC state, we reanalyzed a mouse ischemia-reperfusion injury single nucleus RNA-sequencing (snRNA-seq) atlas to identify Traf2 and Nck Interacting Kinase, Tnik, to be exclusively expressed in FR-PTCs, but not in healthy or acutely injured proximal tubules post AKI (2 and 6 weeks) in mice. We confirmed expression of Tnik protein in injured mouse and human tissues by immunofluorescence. Then, to determine the functional role of Tnik in FR-PTCs, we depleted Tnik using siRNA in two human renal proximal tubule epithelial cell lines (primary and immortalized hRPTECs) and analyzed each by bulk RNA-sequencing. Pathway analysis revealed significant upregulation of inflammatory signaling pathways, while pathways associated with differentiated proximal tubule such as organic acid transport were significantly downregulated. TNIK knockdown drove reduced cell viability and increased apoptosis, including differentially expressed PARP family members, cleaved PARP-1 fragments and increased Annexin V binding to phosphatidylserine. Together, these results indicate that Tnik upregulation in FR-PTCs acts in a compensatory fashion to suppress inflammation and promote proximal tubule epithelial cell survival following injury. Modulating Tnik activity may represent a pro-repair therapeutic strategy after AKI.
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Affiliation(s)
- Shayna T J Bradford
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Haojia Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Yuhei Kirita
- Department of Nephrology, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, Japan
| | - Changfeng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Nicole P Malvin
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Yasuhiro Yoshimura
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Yoshiharu Muto
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Benjamin D Humphreys
- Renal Division, Washington University in St. Louis, St. Louis, MO, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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Wilson PC, Verma A, Yoshimura Y, Muto Y, Li H, Malvin NP, Dixon EE, Humphreys BD. Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease. Genome Biol 2024; 25:36. [PMID: 38287344 PMCID: PMC10823641 DOI: 10.1186/s13059-024-03173-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and chronic kidney disease. RESULTS The likelihood of a cell having LOY varies depending on its location in the nephron. Cortical epithelial cell types have a greater proportion of LOY than medullary or glomerular cell types, which may reflect their proliferative history. Proximal tubule cells are the most abundant cell type in the cortex and are susceptible to hypoxic injury. A subset of these cells acquires a pro-inflammatory transcription and chromatin accessibility profile associated with expression of HAVCR1, VCAM1, and PROM1. These injured epithelial cells have the greatest proportion of LOY and their presence predicts future kidney function decline. Moreover, proximal tubule cells with LOY are more likely to harbor additional large chromosomal gains and express pro-survival pathways. Spatial transcriptomics localizes injured proximal tubule cells to a pro-fibrotic microenvironment where they adopt a secretory phenotype and likely communicate with infiltrating immune cells. CONCLUSIONS We hypothesize that LOY is an indicator of increased DNA damage and potential marker of cellular senescence that can be applied to single-cell datasets in other tissues.
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Affiliation(s)
- Parker C Wilson
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Amit Verma
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole P Malvin
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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Muto Y, Dixon EE, Yoshimura Y, Ledru N, Kirita Y, Wu H, Humphreys BD. Epigenetic reprogramming driving successful and failed repair in acute kidney injury. bioRxiv 2024:2024.01.20.576421. [PMID: 38328130 PMCID: PMC10849487 DOI: 10.1101/2024.01.20.576421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Acute kidney injury (AKI) causes epithelial damage followed by subsequent repair. While successful repair restores kidney function, this process is often incomplete and can lead to chronic kidney disease (CKD) in a process called failed repair. To better understand the epigenetic reprogramming driving this AKI-to-CKD transition we generated a single nucleus multiomic atlas for the full mouse AKI time course, consisting of ~280,000 single nucleus transcriptomes and epigenomes. We reveal cell-specific dynamic alterations in gene regulatory landscapes reflecting especially activation of proinflammatory pathways. We further generated single nucleus multiomic data from four human AKI samples including validation by genome-wide identification of NF-kB binding sites. A regularized regression analysis identifies key regulators involved in both successful and failed repair cell fate, identifying the transcription factor CREB5 as a regulator of both successful and failed tubular repair that also drives proximal tubule cell proliferation after injury. Our interspecies multiomic approach provides a foundation to comprehensively understand cell states in AKI.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E. Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- 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
| | - Yuhei Kirita
- 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
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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Muto Y, Humphreys BD. Leveraging multimodal chromatin profiling to identify a new potential driver of diabetic kidney disease. Kidney Int 2024; 105:25-27. [PMID: 38182297 DOI: 10.1016/j.kint.2023.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 01/07/2024]
Abstract
The 3-dimensional nature of chromatin architecture plays crucial roles in regulating gene expression in development, homeostasis, and disease. Until recently, however, comprehensive chromatin profiling in human kidneys has been lacking. In this issue, Eun and Kim et al. employed a multimodal approach by integrating a single-nucleus assay for transposase-accessible chromatin sequencing, chromatin immunoprecipitation sequencing, and Hi-C (a method to comprehensively detect chromatin interactions) to investigate how the epigenetic landscape is altered in diabetic kidney disease.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
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Yoshimura Y, Muto Y, Omachi K, Miner JH, Humphreys BD. Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids. J Am Soc Nephrol 2023; 34:1672-1686. [PMID: 37488681 PMCID: PMC10561821 DOI: 10.1681/asn.0000000000000197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/08/2023] [Indexed: 07/26/2023] Open
Abstract
SIGNIFICANCE STATEMENT HNF4 genes promote proximal tubule differentiation in mice, but their function in human nephrogenesis is not fully defined. This study uses human pluripotent stem cell (PSC)-derived kidney organoids as a model to investigate HNF4A and HNF4G functions. The loss of HNF4A , but not HNF4G , impaired reabsorption-related molecule expression and microvilli formation in human proximal tubules. Cleavage under targets and release using nuclease (CUT&RUN) sequencing and CRISPR-mediated transcriptional activation (CRISPRa) further confirm that HNF4A directly regulates its target genes. Human kidney organoids provide a good model for studying transcriptional regulation in human kidney development. BACKGROUND The proximal tubule plays a major role in electrolyte homeostasis. Previous studies have shown that HNF4A regulates reabsorption-related genes and promotes proximal tubule differentiation during murine kidney development. However, the functions and gene regulatory mechanisms of HNF4 family genes in human nephrogenesis have not yet been investigated. METHODS We generated HNF4A -knock out (KO), HNF4G -KO, and HNF4A/4G -double KO human pluripotent stem cell lines, differentiated each into kidney organoids, and used immunofluorescence analysis, electron microscopy, and RNA-seq to analyze them. We probed HNF4A-binding sites genome-wide by cleavage under targets and release using nuclease sequencing in both human adult kidneys and kidney organoid-derived proximal tubular cells. Clustered Regularly Interspaced Short Palindromic Repeats-mediated transcriptional activation validated HNF4A and HNF4G function in proximal tubules during kidney organoid differentiation. RESULTS Organoids lacking HNF4A , but not HNF4G , showed reduced expression of transport-related, endocytosis-related, and brush border-related genes, as well as disorganized brush border structure in the apical lumen of the organoid proximal tubule. Cleavage under targets and release using nuclease revealed that HNF4A primarily bound promoters and enhancers of genes that were downregulated in HNF4A -KO, suggesting direct regulation. Induced expression of HNF4A or HNF4G by CRISPR-mediated transcriptional activation drove increased expression of selected target genes during kidney organoid differentiation. CONCLUSIONS This study reveals regulatory mechanisms of HNF4A and HNF4G during human proximal tubule differentiation. The experimental strategy can be applied more broadly to investigate transcriptional regulation in human kidney development.
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Affiliation(s)
- Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Kohei Omachi
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Jeffrey H. Miner
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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Yoshimura Y, Muto Y, Ledru N, Wu H, Omachi K, Miner JH, Humphreys BD. A single-cell multiomic analysis of kidney organoid differentiation. Proc Natl Acad Sci U S A 2023; 120:e2219699120. [PMID: 37155865 DOI: 10.1073/pnas.2219699120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Kidney organoids differentiated from pluripotent stem cells are powerful models of kidney development and disease but are characterized by cell immaturity and off-target cell fates. Comparing the cell-specific gene regulatory landscape during organoid differentiation with human adult kidney can serve to benchmark progress in differentiation at the epigenome and transcriptome level for individual organoid cell types. Using single-cell multiome and histone modification analysis, we report more broadly open chromatin in organoid cell types compared to the human adult kidney. We infer enhancer dynamics by cis-coaccessibility analysis and validate an enhancer driving transcription of HNF1B by CRISPR interference both in cultured proximal tubule cells and also during organoid differentiation. Our approach provides an experimental framework to judge the cell-specific maturation state of human kidney organoids and shows that kidney organoids can be used to validate individual gene regulatory networks that regulate differentiation.
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Affiliation(s)
- Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Kohei Omachi
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Jeffrey H Miner
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
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Zhao ZB, Marschner JA, Iwakura T, Li C, Motrapu M, Kuang M, Popper B, Linkermann A, Klocke J, Enghard P, Muto Y, Humphreys BD, Harris HE, Romagnani P, Anders HJ. Tubular Epithelial Cell HMGB1 Promotes AKI-CKD Transition by Sensitizing Cycling Tubular Cells to Oxidative Stress: A Rationale for Targeting HMGB1 during AKI Recovery. J Am Soc Nephrol 2023; 34:394-411. [PMID: 36857499 PMCID: PMC10103235 DOI: 10.1681/asn.0000000000000024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 10/22/2022] [Indexed: 01/22/2023] Open
Abstract
SIGNIFICANCE STATEMENT Cells undergoing necrosis release extracellular high mobility group box (HMGB)-1, which triggers sterile inflammation upon AKI in mice. Neither deletion of HMGB1 from tubular epithelial cells, nor HMGB1 antagonism with small molecules, affects initial ischemic tubular necrosis and immediate GFR loss upon unilateral ischemia/reperfusion injury (IRI). On the contrary, tubular cell-specific HMGB1 deficiency, and even late-onset pharmacological HMGB1 inhibition, increased functional and structural recovery from AKI, indicating that intracellular HMGB1 partially counters the effects of extracellular HMGB1. In vitro studies indicate that intracellular HMGB1 decreases resilience of tubular cells from prolonged ischemic stress, as in unilateral IRI. Intracellular HMGB1 is a potential target to enhance kidney regeneration and to improve long-term prognosis in AKI. BACKGROUND Late diagnosis is a hurdle for treatment of AKI, but targeting AKI-CKD transition may improve outcomes. High mobility group box-1 (HMGB1) is a nuclear regulator of transcription and a driver of necroinflammation in AKI. We hypothesized that HMGB1 would also modulate AKI-CKD transition in other ways. METHODS We conducted single-cell transcriptome analysis of human and mouse AKI and mouse in vivo and in vitro studies with tubular cell-specific depletion of Hmgb1 and HMGB1 antagonists. RESULTS HMGB1 was ubiquitously expressed in kidney cells. Preemptive HMGB1 antagonism with glycyrrhizic acid (Gly) and ethyl pyruvate (EP) did not affect postischemic AKI but attenuated AKI-CKD transition in a model of persistent kidney hypoxia. Consistently, tubular Hmgb1 depletion in Pax8 rtTA, TetO Cre, Hmgb1fl/fl mice did not protect from AKI, but from AKI-CKD transition. In vitro studies confirmed that absence of HMGB1 or HMGB1 inhibition with Gly and EP does not affect ischemic necrosis of growth-arrested differentiated tubular cells but increased the resilience of cycling tubular cells that survived the acute injury to oxidative stress. This effect persisted when neutralizing extracellular HMGB1 with 2G7. Consistently, late-onset HMGB1 blockade with EP started after the peak of ischemic AKI in mice prevented AKI-CKD transition, even when 2G7 blocked extracellular HMGB1. CONCLUSION Treatment of AKI could become feasible when ( 1 ) focusing on long-term outcomes of AKI; ( 2 ) targeting AKI-CKD transition with drugs initiated after the AKI peak; and ( 3 ) targeting with drugs that block HMGB1 in intracellular and extracellular compartments.
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Affiliation(s)
- Zhi Bo Zhao
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
| | - Julian A. Marschner
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
| | - Takamasa Iwakura
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
| | - Chenyu Li
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
| | - Manga Motrapu
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
| | - Meisi Kuang
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
| | - Bastian Popper
- Biomedical Center, Core Facility Animal Models, LMU München, Munich, Germany
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine 3, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Jan Klocke
- Department of Nephrology and Intensive Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Philipp Enghard
- Department of Nephrology and Intensive Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri
| | - Helena Erlandsson Harris
- Departments of Rheumatology and of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paola Romagnani
- Department of Experimental and Biomedical Sciences "Mario Serio" and Nephrology and Dialysis Unit, Meyer Children's University Hospital, Florence, Italy
| | - Hans-Joachim Anders
- Nephrologisches Zentrum, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, Munich, Germany
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Muto Y, Takeuchi A, Zennami K, Sugihara E, Shiroki R, Saya H, Sumitomo M. Targeting glutamine addiction with potent drug combination therapy for renal cell carcinoma. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)01083-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Takeuchi A, Takeda M, Sugihara E, Muto Y, Nohara S, Tanishima S, Zennami K, Takahara K, Tsukamoto T, Shiroki R, Saya H, Sumitomo M. Comprehensive analysis of copy number variation and sensitivity to targeted therapy in renal cell carcinoma using in-house cancer gene panel testing. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)01081-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Han SK, Muto Y, Wilson PC, Humphreys BD, Sampson MG, Chakravarti A, Lee D. Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model. Proc Natl Acad Sci U S A 2022; 119:e2212810119. [PMID: 36508674 PMCID: PMC9907136 DOI: 10.1073/pnas.2212810119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/28/2022] [Indexed: 12/15/2022] Open
Abstract
Chromatin accessibility assays are central to the genome-wide identification of gene regulatory elements associated with transcriptional regulation. However, the data have highly variable quality arising from several biological and technical factors. To surmount this problem, we developed a sequence-based machine learning method to evaluate and refine chromatin accessibility data. Our framework, gapped k-mer SVM quality check (gkmQC), provides the quality metrics for a sample based on the prediction accuracy of the trained models. We tested 886 DNase-seq samples from the ENCODE/Roadmap projects to demonstrate that gkmQC can effectively identify "high-quality" (HQ) samples with low conventional quality scores owing to marginal read depths. Peaks identified in HQ samples are more accurately aligned at functional regulatory elements, show greater enrichment of regulatory elements harboring functional variants, and explain greater heritability of phenotypes from their relevant tissues. Moreover, gkmQC can optimize the peak-calling threshold to identify additional peaks, especially for rare cell types in single-cell chromatin accessibility data.
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Affiliation(s)
- Seong Kyu Han
- Department of Pediatrics, Division of Nephrology, Boston Children’s Hospital, Boston & Harvard Medical School, Boston, MA02115
- Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA02142
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO63130
| | - Parker C. Wilson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO63130
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO63130
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO63130
| | - Matthew G. Sampson
- Department of Pediatrics, Division of Nephrology, Boston Children’s Hospital, Boston & Harvard Medical School, Boston, MA02115
- Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA02142
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY10016
| | - Dongwon Lee
- Department of Pediatrics, Division of Nephrology, Boston Children’s Hospital, Boston & Harvard Medical School, Boston, MA02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA02115
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Muto Y, Dixon EE, Yoshimura Y, Wu H, Omachi K, Ledru N, Wilson PC, King AJ, Eric Olson N, Gunawan MG, Kuo JJ, Cox JH, Miner JH, Seliger SL, Woodward OM, Welling PA, Watnick TJ, Humphreys BD. Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis. Nat Commun 2022; 13:6497. [PMID: 36310237 PMCID: PMC9618568 DOI: 10.1038/s41467-022-34255-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 10/17/2022] [Indexed: 12/25/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the leading genetic cause of end stage renal disease characterized by progressive expansion of kidney cysts. To better understand the cell types and states driving ADPKD progression, we analyze eight ADPKD and five healthy human kidney samples, generating single cell multiomic atlas consisting of ~100,000 single nucleus transcriptomes and ~50,000 single nucleus epigenomes. Activation of proinflammatory, profibrotic signaling pathways are driven by proximal tubular cells with a failed repair transcriptomic signature, proinflammatory fibroblasts and collecting duct cells. We identify GPRC5A as a marker for cyst-lining collecting duct cells that exhibits increased transcription factor binding motif availability for NF-κB, TEAD, CREB and retinoic acid receptors. We identify and validate a distal enhancer regulating GPRC5A expression containing these motifs. This single cell multiomic analysis of human ADPKD reveals previously unrecognized cellular heterogeneity and provides a foundation to develop better diagnostic and therapeutic approaches.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- 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
| | - Kohei Omachi
- 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
| | - Parker C Wilson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | | | | | | | - Jay J Kuo
- Chinook Therapeutics, Inc., Vancouver, BC, Canada
| | | | - Jeffrey H Miner
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Stephen L Seliger
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Owen M Woodward
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Terry J Watnick
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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13
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Wilson PC, Muto Y, Wu H, Karihaloo A, Waikar SS, Humphreys BD. Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression. Nat Commun 2022; 13:5253. [PMID: 36068241 PMCID: PMC9448792 DOI: 10.1038/s41467-022-32972-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
The proximal tubule is a key regulator of kidney function and glucose metabolism. Diabetic kidney disease leads to proximal tubule injury and changes in chromatin accessibility that modify the activity of transcription factors involved in glucose metabolism and inflammation. Here we use single nucleus RNA and ATAC sequencing to show that diabetic kidney disease leads to reduced accessibility of glucocorticoid receptor binding sites and an injury-associated expression signature in the proximal tubule. We hypothesize that chromatin accessibility is regulated by genetic background and closely-intertwined with metabolic memory, which pre-programs the proximal tubule to respond differently to external stimuli. Glucocorticoid excess has long been known to increase risk for type 2 diabetes, which raises the possibility that glucocorticoid receptor inhibition may mitigate the adverse metabolic effects of diabetic kidney disease.
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Affiliation(s)
- Parker C Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Anil Karihaloo
- Novo Nordisk Research Center Seattle Inc, Seattle, WA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine, Boston Medical Center, Boston, MA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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14
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Ogawa Y, Muto Y, Shimada S, Kawamura T. 585 The effect of topical 5-azacytidine in irritant and allergic contact dermatitis. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Muto Y, Numakura K, Sekine Y, Kobayashi M, Kashima S, Yamamoto R, Koizumi A, Nara T, Saito M, Narita S, Omori Y, Habuchi T. Cancer-associated adipose-derived mesenchymal stem cells promote migration and invasion in kidney cancer. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)01199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Numakura K, Sekine Y, Muto Y, Kobayashi M, Kashima S, Yamamoto R, Koizumi A, Nara T, Saito M, Narita S, Habuchi T. Cortisol regulates adrenaline synthesis via phenylethanolamine N-methyltransferase in surgical specimens of pheochromocytoma. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00708-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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17
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Dixon EE, Wu H, Muto Y, Wilson PC, Humphreys BD. Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model. J Am Soc Nephrol 2022; 33:279-289. [PMID: 34853151 PMCID: PMC8819997 DOI: 10.1681/asn.2021081150] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Single-cell sequencing technologies have advanced our understanding of kidney biology and disease, but the loss of spatial information in these datasets hinders our interpretation of intercellular communication networks and regional gene expression patterns. New spatial transcriptomic sequencing platforms make it possible to measure the topography of gene expression at genome depth. METHODS We optimized and validated a female bilateral ischemia-reperfusion injury model. Using the 10× Genomics Visium Spatial Gene Expression solution, we generated spatial maps of gene expression across the injury and repair time course, and applied two open-source computational tools, Giotto and SPOTlight, to increase resolution and measure cell-cell interaction dynamics. RESULTS An ischemia time of 34 minutes in a female murine model resulted in comparable injury to 22 minutes for males. We report a total of 16,856 unique genes mapped across our injury and repair time course. Giotto, a computational toolbox for spatial data analysis, enabled increased resolution mapping of genes and cell types. Using a seeded nonnegative matrix regression (SPOTlight) to deconvolute the dynamic landscape of cell-cell interactions, we found that injured proximal tubule cells were characterized by increasing macrophage and lymphocyte interactions even 6 weeks after injury, potentially reflecting the AKI to CKD transition. CONCLUSIONS In this transcriptomic atlas, we defined region-specific and injury-induced loss of differentiation markers and their re-expression during repair, as well as region-specific injury and repair transcriptional responses. Lastly, we created an interactive data visualization application for the scientific community to explore these results (http://humphreyslab.com/SingleCell/).
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Affiliation(s)
- Eryn E. Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Parker C. Wilson
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri
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18
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Muto Y, Humphreys BD. Recent advances in lineage tracing for the kidney. Kidney Int 2021; 100:1179-1184. [PMID: 34217781 DOI: 10.1016/j.kint.2021.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/19/2022]
Abstract
Lineage tracing was originally developed by developmental biologists to identify all progeny of a single cell during morphogenesis. More recently this approach has been applied to other fields, including organ homeostasis and recovery from injury. Modern lineage tracing techniques typically rely on reporter gene expression induced by cell-specific DNA recombination. There have been important scientific advances in the last 10 years that have impacted lineage tracing approaches, including intersectional genetics, optical clearing techniques, and the use of sequencing-based genomic lineage tracing. The latter combines CRISPR-Cas9-based genetic scarring with single-cell RNA-sequencing that, in theory, could allow comprehensive reconstruction of a lineage tree for an entire organism. This review summarizes recent advances in lineage tracing technologies and outlines potential applications for kidney research.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA; Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.
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19
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Muto Y, Wilson PC, Ledru N, Wu H, Dimke H, Waikar SS, Humphreys BD. Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney. Nat Commun 2021; 12:2190. [PMID: 33850129 PMCID: PMC8044133 DOI: 10.1038/s41467-021-22368-w] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
The integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney. We demonstrate that snATAC-seq is comparable to snRNA-seq in the assignment of cell identity and can further refine our understanding of functional heterogeneity in the nephron. The majority of differentially accessible chromatin regions are localized to promoters and a significant proportion are closely associated with differentially expressed genes. Cell-type-specific enrichment of transcription factor binding motifs implicates the activation of NF-κB that promotes VCAM1 expression and drives transition between a subpopulation of proximal tubule epithelial cells. Our multi-omics approach improves the ability to detect unique cell states within the kidney and redefines cellular heterogeneity in the proximal tubule and thick ascending limb.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Parker C Wilson
- Department of Pathology and Immunology, 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
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Henrik Dimke
- Department of Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Nephrology, Odense University Hospital, Odense, Denmark
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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20
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Nita A, Muto Y, Katayama Y, Matsumoto A, Nishiyama M, Nakayama KI. The autism-related protein CHD8 contributes to the stemness and differentiation of mouse hematopoietic stem cells. Cell Rep 2021; 34:108688. [PMID: 33535054 DOI: 10.1016/j.celrep.2021.108688] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/26/2020] [Accepted: 12/30/2020] [Indexed: 01/26/2023] Open
Abstract
Chromodomain helicase DNA-binding protein 8 (CHD8) is an ATP-dependent chromatin-remodeling factor that is encoded by the most frequently mutated gene in individuals with autism spectrum disorder. CHD8 is expressed not only in neural tissues but also in many other organs; however, its functions are largely unknown. Here, we show that CHD8 is highly expressed in and maintains the stemness of hematopoietic stem cells (HSCs). Conditional deletion of Chd8 specifically in mouse bone marrow induces cell cycle arrest, apoptosis, and a differentiation block in HSCs in association with upregulation of the expression of p53 target genes. A colony formation assay and bone marrow transplantation reveal that CHD8 deficiency also compromises the stemness of HSCs. Furthermore, additional ablation of p53 rescues the impaired stem cell function and differentiation block of CHD8-deficient HSCs. Our results thus suggest that the CHD8-p53 axis plays a key role in regulation of the stemness and differentiation of HSCs.
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Affiliation(s)
- Akihiro Nita
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yoshiharu Muto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yuta Katayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Masaaki Nishiyama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
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21
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Yamauchi Y, Nita A, Nishiyama M, Muto Y, Shimizu H, Nakatsumi H, Nakayama KI. Skp2 contributes to cell cycle progression in trophoblast stem cells and to placental development. Genes Cells 2020; 25:427-438. [PMID: 32267063 DOI: 10.1111/gtc.12769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 12/29/2022]
Abstract
All trophoblast subtypes of the placenta are derived from trophoblast stem cells (TSCs). TSCs have the capacity to self-renew, but how the proliferation of these cells is regulated in the undifferentiated state has been largely unclear. We now show that the F-box protein Skp2 regulates the proliferation of TSCs and thereby plays a pivotal role in placental development in mice on the C57BL/6 background. The placenta of Skp2-/- mouse embryos on the C57BL/6 background was smaller than that of their Skp2+/+ littermates, with the mutant embryos also manifesting intrauterine growth retardation. Although the Skp2-/- mice were born alive, most of them died before postnatal day 21, presumably as a result of placental defects. Depletion of Skp2 in TSCs cultured in the undifferentiated state resulted in a reduced rate of proliferation and arrest of the cell cycle in G1 phase, indicative of a defect in self-renewal capacity. The cell cycle arrest apparent in Skp2-deficient TSCs was reversed by additional ablation of the cyclin-dependent kinase inhibitor (CKI) p57 but not by that of the CKI p27. Our results thus suggest that Skp2-mediated degradation of p57 is an important determinant of the self-renewal capacity of TSCs during placental development, at least in mice of certain genetic backgrounds.
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Affiliation(s)
- Yuhei Yamauchi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Akihiro Nita
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Masaaki Nishiyama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yoshiharu Muto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Hideyuki Shimizu
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Hirokazu Nakatsumi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, Japan
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22
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Muto Y, Moroishi T, Ichihara K, Nishiyama M, Shimizu H, Eguchi H, Moriya K, Koike K, Mimori K, Mori M, Katayama Y, Nakayama KI. Disruption of FBXL5-mediated cellular iron homeostasis promotes liver carcinogenesis. J Exp Med 2019; 216:950-965. [PMID: 30877170 PMCID: PMC6446870 DOI: 10.1084/jem.20180900] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/15/2019] [Accepted: 02/25/2019] [Indexed: 12/17/2022] Open
Abstract
Hepatocellular iron overload elicited by ablation of the iron-sensing ubiquitin ligase FBXL5 promotes liver carcinogenesis induced by exposure to a chemical carcinogen or hepatitis virus, suggesting that FBXL5 is a previously unrecognized oncosuppressor in liver carcinogenesis in mice. Hepatic iron overload is a risk factor for progression of hepatocellular carcinoma (HCC), although the molecular mechanisms underlying this association have remained unclear. We now show that the iron-sensing ubiquitin ligase FBXL5 is a previously unrecognized oncosuppressor in liver carcinogenesis in mice. Hepatocellular iron overload elicited by FBXL5 ablation gave rise to oxidative stress, tissue damage, inflammation, and compensatory proliferation of hepatocytes and to consequent promotion of liver carcinogenesis induced by exposure to a chemical carcinogen. The tumor-promoting outcome of FBXL5 deficiency in the liver was also found to be effective in a model of virus-induced HCC. FBXL5-deficient mice thus constitute the first genetically engineered mouse model of liver carcinogenesis promoted by iron overload. In addition, dysregulation of FBXL5-mediated cellular iron homeostasis was found to be associated with poor prognosis in human HCC, suggesting that FBXL5 plays a key role in defense against hepatocarcinogenesis.
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Affiliation(s)
- Yoshiharu Muto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Toshiro Moroishi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kazuya Ichihara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Masaaki Nishiyama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hideyuki Shimizu
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kyoji Moriya
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University, Beppu Hospital, Beppu, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yuta Katayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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23
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Ó hAinmhire E, Wu H, Muto Y, Donnelly EL, Machado FG, Fan LX, Chang-Panesso M, Humphreys BD. A conditionally immortalized Gli1-positive kidney mesenchymal cell line models myofibroblast transition. Am J Physiol Renal Physiol 2019; 316:F63-F75. [PMID: 30303712 PMCID: PMC6383201 DOI: 10.1152/ajprenal.00460.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glioma-associated oncogene homolog-1 (Gli1)-positive resident mesenchymal stem cell-like cells are the predominant source of kidney myofibroblasts in fibrosis, but investigating Gli1-positive myofibroblast progenitor activation is hampered by the difficulty of isolating and propagating primary cultures of these cells. Using a genetic strategy with positive and negative selection, we isolated Kidney-Gli1 (KGli1) cells that maintain expression of appropriate mesenchymal stem cell-like cell markers, respond to hedgehog pathway activation, and display robust myofibroblast differentiation upon treatment with transforming growth factor-β (TGF-β). Coculture of KGli1 cells with endothelium stabilizes capillary formation. Single-cell RNA sequencing (scRNA-seq) analysis during differentiation identified autocrine ligand-receptor pair upregulation and a strong focal adhesion pathway signal. This led us to test the serum response factor inhibitor CCG-203971 that potently inhibited TGF-β-induced pericyte-to-myofibroblast transition. scRNA-seq also identified the unexpected upregulation of nerve growth factor (NGF), which we confirmed in two mouse kidney fibrosis models. The Ngf receptor Ntrk1 is expressed in tubular epithelium in vivo, suggesting a novel interstitial-to-tubule paracrine signaling axis. Thus, KGli1 cells accurately model myofibroblast activation in vitro, and the development of this cell line provides a new tool to study resident mesenchymal stem cell-like progenitors in health and disease.
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Affiliation(s)
- Eoghainín Ó hAinmhire
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
| | - Erinn L Donnelly
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
| | - Flavia G Machado
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
| | - Lucy X Fan
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
| | - Monica Chang-Panesso
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
- Department of Developmental Biology, Washington University in Saint Louis School of Medicine , St. Louis, Missouri
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24
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Namikawa K, Mori T, Muto Y, jinnai S, Kage Y, Nakano E, Takahashi A, Yamazaki N. PD-L1 expression and clinical outcome after nivolumab monotherapy in various subtypes of melanoma: A single-institutional retrospective study. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy439.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Namikawa K, Takahashi A, Tsutsumida A, Mori T, Motoi N, Jinnai S, Kage Y, Muto Y, Nakano E, Yamazaki N. Nivolumab for patients with metastatic uveal melanoma previously untreated with ipilimumab: A single-institutional retrospective study. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx667.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Ichida K, Suzuki K, Muto Y, Fukui T, Takayama Y, Futsuhara K, Tsujinaka S, Miyakura Y, Noda H, Rikiyama T. 208P Significance of the difference in size of liver tumors in management of patients with colorectal liver metastases. Ann Oncol 2016. [DOI: 10.1016/s0923-7534(21)00366-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Isomura T, Suzuki S, Origasa H, Hosono A, Suzuki M, Sawada T, Terao S, Muto Y, Koga T. Liver-related safety assessment of green tea extracts in humans: a systematic review of randomized controlled trials. Eur J Clin Nutr 2016; 70:1221-1229. [PMID: 27188915 PMCID: PMC5193539 DOI: 10.1038/ejcn.2016.78] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 03/07/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
There remain liver-related safety concerns, regarding potential hepatotoxicity in humans, induced by green tea intake, despite being supposedly beneficial. Although many randomized controlled trials (RCTs) of green tea extracts have been reported in the literature, the systematic reviews published to date were only based on subjective assessment of case reports. To more objectively examine the liver-related safety of green tea intake, we conducted a systematic review of published RCTs. A systematic literature search was conducted using three databases (PubMed, EMBASE and Cochrane Central Register of Controlled Trials) in December 2013 to identify RCTs of green tea extracts. Data on liver-related adverse events, including laboratory test abnormalities, were abstracted from the identified articles. Methodological quality of RCTs was assessed. After excluding duplicates, 561 titles and abstracts and 119 full-text articles were screened, and finally 34 trials were identified. Of these, liver-related adverse events were reported in four trials; these adverse events involved seven subjects (eight events) in the green tea intervention group and one subject (one event) in the control group. The summary odds ratio, estimated using a meta-analysis method for sparse event data, for intervention compared with placebo was 2.1 (95% confidence interval: 0.5-9.8). The few events reported in both groups were elevations of liver enzymes. Most were mild, and no serious liver-related adverse events were reported. Results of this review, although not conclusive, suggest that liver-related adverse events after intake of green tea extracts are expected to be rare.
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Affiliation(s)
- T Isomura
- Clinical Study Support Inc.,
Nagoya, Japan
- Institute of Medical Science, Tokyo
Medical University, Tokyo, Japan
- Department of Public Health, Nagoya City
University Graduate School of Medical Sciences, Nagoya,
Japan
- Division of Biostatistics and Clinical
Epidemiology, University of Toyama Graduate School of Medicine and Pharmaceutical
Sciences, Toyama, Japan
| | - S Suzuki
- Department of Public Health, Nagoya City
University Graduate School of Medical Sciences, Nagoya,
Japan
| | - H Origasa
- Division of Biostatistics and Clinical
Epidemiology, University of Toyama Graduate School of Medicine and Pharmaceutical
Sciences, Toyama, Japan
| | - A Hosono
- Department of Public Health, Nagoya City
University Graduate School of Medical Sciences, Nagoya,
Japan
| | - M Suzuki
- Clinical Study Support Inc.,
Nagoya, Japan
| | - T Sawada
- Clinical Study Support Inc.,
Nagoya, Japan
| | - S Terao
- Clinical Study Support Inc.,
Nagoya, Japan
| | - Y Muto
- Clinical Study Support Inc.,
Nagoya, Japan
| | - T Koga
- Clinical Study Support Inc.,
Nagoya, Japan
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Nakamura Y, Kitano S, Takahashi A, Tsutsumida A, Namikawa K, Muto I, Ueno M, Muto Y, Yamazaki N. Pretreatment prognostic factors and early markers for outcome in advanced melanoma treated with nivolumab. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw379.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Di Nardo A, Holmes A, Muto Y, Huang E, Preston N, Winkelman W, Gallo R. 281 Doxycycline modified release (MR) capsules improve rosacea clinical outcomes by modifying antimicrobial peptide metabolism: Results of a multicenter, randomized, double blind, placebo controlled study of 170 adults with papulopustular rosacea. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.02.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nita A, Nishiyama M, Muto Y, Nakayama KI. FBXL12 regulates T-cell differentiation in a cell-autonomous manner. Genes Cells 2016; 21:517-24. [DOI: 10.1111/gtc.12360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/14/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Akihiro Nita
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Masaaki Nishiyama
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Yoshiharu Muto
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
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Muto Y, Suzuki K, Ichida K, Takayama Y, Fukui T, Kakizawa N, Watanabe F, Kato T, Saito M, Konishi F, Rikiyama T. P-210 Detection of epithelial-mesenchymal transition in colorectal cancer in consideration of intratumor heterogeneity. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv233.208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Kanai M, Iwanaga T, Hagino N, Muto Y. Retinol-binding protein in tubular proteinuria of patients with Itai-Itai disease. World Rev Nutr Diet 2015; 31:31-6. [PMID: 216161 DOI: 10.1159/000401296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Muto Y, Sakai A, Sakamoto A, Suzuki H. Activation of NK₁ receptors in the locus coeruleus induces analgesia through noradrenergic-mediated descending inhibition in a rat model of neuropathic pain. Br J Pharmacol 2012; 166:1047-57. [PMID: 22188400 DOI: 10.1111/j.1476-5381.2011.01820.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND PURPOSE The locus coeruleus (LC) is a major source of noradrenergic projections to the dorsal spinal cord, and thereby plays an important role in the modulation of nociceptive information. The LC receives inputs from substance P (SP)-containing fibres from other regions, and expresses the NK(1) tachykinin receptor, a functional receptor for SP. In the present study, we investigated the roles of SP in the LC in neuropathic pain. EXPERIMENTAL APPROACH Chronic constriction injury (CCI) of the left sciatic nerve was performed in rats to induce neuropathic pain. After development of neuropathic pain, SP was injected into the LC and the nocifensive behaviours were assessed. The involvement of noradrenergic descending inhibition in SP-induced analgesia was examined by i.t. administration of yohimbine, an α(2) -adrenoceptor antagonist. NK(1) receptor expression in the LC was examined by immunohistochemistry. KEY RESULTS In CCI rats, mechanical allodynia was alleviated by SP injection into the LC. These effects were abolished by prior injection of WIN 51708, an NK(1) receptor antagonist, into the LC or i.t. treatment with yohimbine. NK(1) receptor-like immunoreactivity was observed in noradrenergic neurons throughout the LC in intact rats, and remained unchanged after CCI. CONCLUSION AND IMPLICATIONS SP in the LC exerted analgesic effects on neuropathic pain through NK(1) receptor activation and resulted in facilitation of spinal noradrenergic transmission. Accordingly, manipulation of the SP/NK(1) receptor signalling pathway in the LC may be a promising strategy for effective treatment of neuropathic pain.
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Affiliation(s)
- Y Muto
- Department of Anesthesiology, Nippon Medical School, Tokyo, Japan
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Kusumoto T, Oki E, Hiroshige S, Endo Y, Uchida H, Matsumoto T, Takeuchi H, Matsushima T, Emi Y, Matsuura H, Muto Y, Maehara Y. Efficacy and safety of consecutive chemotherapy treatments for elderly patients with advanced or recurrent gastric cancer. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e14586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kimura H, Takeda K, Tsuruya K, Mukai H, Muto Y, Okuda H, Furusho M, Ueno T, Nakashita S, Miura S, Maeda A, Kondo H. Left ventricular mass index is an independent determinant of diastolic dysfunction in patients on chronic hemodialysis: a tissue Doppler imaging study. Nephron Clin Pract 2010; 117:c67-73. [PMID: 20689327 DOI: 10.1159/000319649] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 03/24/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Diastolic heart failure is the most common clinical form of heart failure. Tissue Doppler imaging (TDI) is often used to quantitate left ventricular (LV) diastolic function. The purpose of this study was to identify the determinant(s) of diastolic dysfunction in patients with end-stage renal disease on hemodialysis (HD), using the TDI method. METHODS The study subjects were 53 patients with end-stage renal disease and preserved LV systolic function on maintenance HD. LV function was assessed by conventional echocardiography. The ratio of early trans-mitral flow velocity to early mitral annular velocity (E/e') was measured by TDI. Patients were stratified into two groups based on E/e' value (≤15 and >15 groups). Arterial stiffness was evaluated by pulse wave velocity and cardio-ankle vascular index. RESULTS Patients of the E/e' >15 group were older (p = 0.025). There were no significant differences in blood pressure, ejection fraction, E/A, deceleration time, and pulse wave velocity between the E/e' >15 and E/e' ≤15 groups. However, there were significant differences in LV mass index (LVMI; p < 0.001) and cardio-ankle vascular index (p = 0.048) between the two groups. Multiple regression analysis identified that LVMI was an independent determinant of E/e' (p = 0.003). CONCLUSIONS Our findings suggest that LVMI is an independent determinant of LV diastolic dysfunction in patients on HD.
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Affiliation(s)
- Hiroshi Kimura
- Department of Nephrology and Kidney Center, Aso-Iizuka Hospital, Iizuka City, Fukuoka, Japan.
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Ito Y, Nakamura T, Saito K, Moriwaki H, Muto Y, Watanabe K, Ueno K. Pathophysiological Role of Intestinal Flora in the Development of Hepatic Encephalopathy, with Special Reference to Floral Alterations Induced by Antimicrobial Agents. Microbial Ecology in Health and Disease 2009. [DOI: 10.3109/08910609209141299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Y. Ito
- First Department of Internal Medicine and Gifu, University School of Medicine, Gifu, 500, Japan
| | - T. Nakamura
- First Department of Internal Medicine and Gifu, University School of Medicine, Gifu, 500, Japan
| | - K. Saito
- First Department of Internal Medicine and Gifu, University School of Medicine, Gifu, 500, Japan
| | - H. Moriwaki
- First Department of Internal Medicine and Gifu, University School of Medicine, Gifu, 500, Japan
| | - Y. Muto
- First Department of Internal Medicine and Gifu, University School of Medicine, Gifu, 500, Japan
| | - K. Watanabe
- Institute of Anaerobic Bacteriology, Gifu University School of Medicine, Gifu, Japan
| | - K. Ueno
- Institute of Anaerobic Bacteriology, Gifu University School of Medicine, Gifu, Japan
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Abstract
Sphingolipid profiles of strains from species of genus Bacteroides, and representative strains from Prevotella and Porphyromonas, were analyzed by thin-layer chromatography and infrared spectrophotometry. Two major types of phosphosphingolipid, ceramide phosphorylethanolamine and ceramide phosphorylglycerol, were detected in B. fragilis, B. ovatus, B. uniformis, B. caccae, B. eggerthii, B. thetaiotaomicron, and B. stercoris, but not in B. merdae, B. distasonis, and B. vulgatus. Strains from the genera Prevotella and Porphyromonas also contained these two sphingolipids. These sphingolipid profiles were conserved within the species tested, and may be useful for differentiation and recognition of relationships within the genera Bacteroides, Prevotella and Porphyromonas.
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Affiliation(s)
- M Kato
- Institute of Anaerobic Bacteriology, Gifu University School of Medicine, Gifu, Japan
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Kusumi E, Arakawa A, Kami M, Kato D, Yuji K, Kishi Y, Murashige N, Miyakoshi S, Ueyama J, Morinaga S, Taniguchi S, Muto Y. Visual disturbance due to retinal edema as a complication of imatinib. Leukemia 2004; 18:1138-9. [PMID: 15085156 DOI: 10.1038/sj.leu.2403364] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Kusumi E, Kami M, Yuji K, Hamaki T, Murashige N, Hori A, Kojima R, Kishi Y, Kim SW, Ueyama J, Miyakoshi S, Tanosaki R, Morinaga S, Mori S, Heike Y, Muto Y, Masuo S, Taniguchi S, Takaue Y. Feasibility of reduced intensity hematopoietic stem cell transplantation from an HLA-matched unrelated donor. Bone Marrow Transplant 2004; 33:697-702. [PMID: 14755317 DOI: 10.1038/sj.bmt.1704425] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To evaluate the feasibility of reduced intensity stem cell transplantation (RIST) with bone marrow from a matched unrelated donor (MUD), we retrospectively investigated 20 patients with hematological disorders who received RIST in the Tokyo SCT consortium from January 2000 to October 2002. The preparative regimens were fludarabine-based (150-180 mg/m(2), n=18) or cladribine-based (0.77 mg/kg, n=2). To enhance engraftment, antithymocyte globulin (ATG) and 4 or 8 Gy total body irradiation (TBI) were added to these regimens in nine and 11 patients, respectively. GVHD prophylaxis was cyclosporine with or without methotrexate. In all, 19 achieved primary engraftment. Three developed graft failure (one primary, two secondary), and five died of treatment-related mortality within 100 days of transplant. Seven of the 19 patients who achieved initial engraftment developed grade II-IV acute GVHD, and seven of 13 patients who survived >100 days developed chronic GVHD. At a median follow-up of 5.5 months, estimated 1-year overall survival was 35%. Compared with a TBI-containing regimen, an ATG-containing regimen was associated with a high risk of graft failure (30 vs 0%, P=0.0737). This study supports the feasibility of RIST from MUD; however, procedure-related toxicities remain significant in its application to patients.
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Affiliation(s)
- E Kusumi
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
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41
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Baba S, Osakabe N, Natsume M, Yasuda A, Muto Y, Hiyoshi K, Takano H, Yoshikawa T, Terao J. Absorption, metabolism, degradation and urinary excretion of rosmarinic acid after intake of Perilla frutescens extract in humans. Eur J Nutr 2004. [DOI: 10.1007/s00394-004-0524-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Kusumi E, Miyakoshi S, Murashige N, Katayama Y, Kim SW, Yuji K, Kami M, Ueyama J, Morinaga S, Masuo S, Taniguchi S, Takaue Y, Muto Y. Successful reduced-intensity stem cell transplantation (RIST) with mismatched cord blood in a 70-year-old patient with severe aplastic anemia (SAA). Bone Marrow Transplant 2003; 32:1111-2. [PMID: 14625587 DOI: 10.1038/sj.bmt.1704310] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Muto Y, Krummel DA, Kambach C, Hernandez H, Robinson CV, Nagai K. Reconstitution of the spliceosomal U1 snRNP from all recombinant subunits and its characterisation by ionspray Q-tof mass-spectrometry. Nucleic Acids Res Suppl 2003:275-6. [PMID: 12836371 DOI: 10.1093/nass/1.1.275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The first important step in pre-mRNA splicing is the recognition of the 5' splice site by the U1 snRNP. It consists of U1 snRNA and 10 protein subunits. We have reconstituted the U1 snRNP from all its ten proteins produced in E. coli and U1 snRNA transcribed in vitro. We have used nano spray time-of-flight (TOF) mass spectrometer in order to characterise the reconstituted U1 snRNP and its sub-assemblies which lack one of more subunits. The reconstituted U1 snRNP and its variants remained intact as multiply charged ions within the mass spectrometer and their mass was determined. By increasing collision energy subparticles are also observed. This method provides information not only about the stoichiometry of subunits within the complex but also about subsets of interacting proteins.
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Affiliation(s)
- Y Muto
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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Tanimoto TE, Kusumi E, Hamaki T, Yuji K, Ueyama J, Miyakoshi S, Morinaga S, Kami M, Kanda Y, Ando T, Yoshihara S, Masuo S, Kim SW, Nakai K, Tobinai K, Tanosaki R, Mineishi S, Takaue Y, Muto Y. High complete response rate after allogeneic hematopoietic stem cell transplantation with reduced-intensity conditioning regimens in advanced malignant lymphoma. Bone Marrow Transplant 2003; 32:131-7. [PMID: 12838276 DOI: 10.1038/sj.bmt.1704118] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The possible advantage of allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a graft-versus-lymphoma effect. We explored the feasibility and efficacy of allo-HSCT with reduced-intensity (RI) regimens in advanced malignant lymphoma (ML). A total of 20 patients with indolent (n=9) or aggressive lymphoma (n=11) received allo-HSCT with an RI regimen (RIST). The preparative regimen consisted of a combination of purine analog and alkylating agent with or without antithymocyte globulin. A total of 11 patients had chemorefractory disease, seven had chemosensitive relapsed disease and two had residual disease. All of the patients received G-CSF-mobilized blood stem cells from HLA-matched siblings. Of the 20 patients, 19 achieved engraftment with acceptable regimen-related toxicities. Seven patients developed grade II-IV acute GVHD and 15 developed chronic GVHD. Of the 15 patients with evaluable disease, 12 achieved a complete response. One died of invasive fusariosis, four subsequently died of GVHD complicated with fungal infection and one died of progressive disease. With a median follow-up of 358 days, the Kaplan-Meier estimates for 1-year overall and progression-free survival were both 70%. The high response rate with low relapse observed in this study suggests that RIST may be an effective alternative curative treatment for patients with advanced ML.
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Affiliation(s)
- T E Tanimoto
- Hematopoietic Stem Cell Transplant Unit, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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Yoshioka S, Suzuki K, Muto Y, Fushihara K, Kanemoto K, Sato E, Ishii H. EF6265: a new synthetic, potent and selective plasma CPB/TAFIa inhibitor. J Thromb Haemost 2003. [DOI: 10.1111/j.1538-7836.2003.tb04431.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yano R, Yap CC, Yamazaki Y, Muto Y, Kishida H, Okada D, Hashikawa T. Sast124, a novel splice variant of syntrophin-associated serine/threonine kinase (SAST), is specifically localized in the restricted brain regions. Neuroscience 2003; 117:373-81. [PMID: 12614677 DOI: 10.1016/s0306-4522(02)00785-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Syntrophin is an adaptor protein that binds signaling molecules to the dystrophin-associated protein complex, which connects extracellular matrix to intracellular cytoskeleton for construction and maintenance of the postsynaptic structures in the neuromuscular junction and the CNS. Among these signaling molecules, a family of microtubule-associated serine/threonine kinases has a unique structural feature with a serine/threonine kinase domain and a postsynaptic density protein-95/discs large/zona occludens-1 domain. In the present study, we identified syntrophin-associated serine/threonine kinase-124, a novel splice variant of the syntrophin-associated serine/threonine kinase which is a member of the microtubule-associated serine/threonine kinases family. Comparing to the original clone (syntrophin-associated serine/threonine kinase-170), syntrophin-associated serine/threonine kinase-124 is truncated just downstream of the postsynaptic density protein-95/discs large/zona occludens-1 domain. Using a monoclonal antibody specifically recognizing syntrophin-associated serine/threonine kinase-124, strong expression of the protein was observed in neurons of the subventricular zone and granule cells of the olfactory bulb, Islands of Calleja, hippocampal dentate gyrus and cerebellum. syntrophin-associated serine/threonine kinase-124 is selectively localized in the nuclei of neurons and distinct from syntrophin-associated serine/threonine kinase-170, which is interacting with syntrophin on the cell surface. Considering the tissue and subcellular distributions of syntrophin-associated serine/threonine kinase-124, it is suggested that syntrophin-associated serine/threonine kinase-124 may have functions in transcriptional regulation for the features commonly shared by these neurons. On the other hand, syntrophin-associated serine/threonine kinase-124 was also localized in glia-like cell bodies in the corpus callosum and fiber bundles in the spinal trigeminal and solitary tracts, suggesting syntrophin-associated serine/threonine kinase-124 may have other functions in these types of cells.
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Affiliation(s)
- R Yano
- Laboratory for Cellular Information Processing, Brain Science Institute, RIKEN, Wako, Saitama351-0198, Japan.
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Yuji K, Kusumi E, Miyakoshi S, Ueyama J, Kami M, Morinaga S, Muto Y. 51 Mismatched unrelated cord blood transplantation following reduced-intensity conditioning regimen (RICBT) in adults with hematological diseases and solid malignancies. Biol Blood Marrow Transplant 2003. [DOI: 10.1016/s1083-8791(03)80052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Yuji K, Hamaki T, Iijima K, Yosihara S, Imataki O, Kojima R, Ueyama J, Kasumi E, Muto Y, Mitani K, Mori S. 173Once and twice filgrastim for allogeneic PBSCmobilization. Biol Blood Marrow Transplant 2003. [DOI: 10.1016/s1083-8791(03)80171-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Baba S, Osakabe N, Natsume M, Muto Y, Takizawa T, Terao J. Absorption and urinary excretion of (-)-epicatechin after administration of different levels of cocoa powder or (-)-epicatechin in rats. J Agric Food Chem 2001; 49:6050-6056. [PMID: 11743807 DOI: 10.1021/jf010965h] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
(-)-Epicatechin is a major polyphenol component of cocoa powder. The absorption and urinary excretion of (-)-epicatechin following administration of different levels of either cocoa powder (150, 750, and 1500 mg/kg) or (-)-epicatechin (1, 5, and 10 mg/kg) were evaluated in rats. Both the sum of plasma (-)-epicatechin metabolites at 1 h postadministration and peak plasma concentrations increased in a dose-dependent fashion. The sum of (-)-epicatechin metabolites in urine, excreted within 18 h postadministration, also increased with dose. Moreover, the sum of (-)-epicatechin metabolites excreted in urine reached the same level in both (-)-epicatechin and cocoa powder administration groups for equivalent amounts of (-)-epicatechin. These results suggest that, in the dose range examined in this study, bioavailability of (-)-epicatechin following administration of either (-)-epicatechin or cocoa powder shows dose dependence and that the various compounds present in cocoa powder have little effect on the bioavailability of (-)-epicatechin in cocoa powder.
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Affiliation(s)
- S Baba
- Functional Foods Research and Development Laboratories, Meiji Seika Kaisha, Ltd., 5-3-1 Chiyoda, Sakado-shi, Saitama 350-0289, Japan.
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