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Lo Faro ML, Rozenberg K, Huang H, Maslau S, Bonham S, Fischer R, Kessler B, Leuvenink H, Sharples E, Lindeman JH, Ploeg R. Kidney Tissue Proteome Profiles in Short Versus Long Duration of Delayed Graft Function - A Pilot Study in Donation After Circulatory Death Donors. Kidney Int Rep 2024; 9:1473-1483. [PMID: 38707804 PMCID: PMC11068965 DOI: 10.1016/j.ekir.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Delayed graft function (DGF) is often defined as the need for dialysis treatment in the first week after a kidney transplantation. This definition, though readily applicable, is generic and unable to distinguish between "types" of DGF or time needed to recover function that may also significantly affect longer-term outcomes. We aimed to profile biological pathways in donation after circulatory death (DCD) kidney donors that correlate with DGF and different DGF durations. Methods A total of N = 30 DCD kidney biopsies were selected from the UK Quality in Organ Donation (QUOD) biobank and stratified according to DGF duration (immediate function, IF n = 10; "short-DGF" (1-6 days), SDGF n = 10; "long-DGF" (7-22 days), LDGF n = 10). Samples were matched for donor and recipient demographics and analyzed by label-free quantitative (LFQ) proteomics, yielding identification of N = 3378 proteins. Results Ingenuity pathway analysis (IPA) on differentially abundant proteins showed that SDGF kidneys presented upregulation of stress response pathways, whereas LDGF presented impaired response to stress, compared to IF. LDGF showed extensive metabolic deficits compared to IF and SDGF. Conclusion DCD kidneys requiring dialysis only in the first week posttransplant present acute cellular injury at donation, alongside repair pathways upregulation. In contrast, DCD kidneys requiring prolonged dialysis beyond 7 days present minimal metabolic and antioxidant responses, suggesting that current DGF definitions might not be adequate in distinguishing different patterns of injury in donor kidneys contributing to DGF.
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Affiliation(s)
- M. Letizia Lo Faro
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford Biomedical Research Centre, Oxford, UK
| | - Kaithlyn Rozenberg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford Biomedical Research Centre, Oxford, UK
| | - Honglei Huang
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Biomedical Research Centre, Oxford, UK
| | - Sergei Maslau
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | - Rutger Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford Transplant Centre, Churchill Hospital, Oxford, UK
- Oxford Biomedical Research Centre, Oxford, UK
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Nørregaard R, Mutsaers HAM, Frøkiær J, Kwon TH. Obstructive nephropathy and molecular pathophysiology of renal interstitial fibrosis. Physiol Rev 2023; 103:2827-2872. [PMID: 37440209 PMCID: PMC10642920 DOI: 10.1152/physrev.00027.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023] Open
Abstract
The kidneys play a key role in maintaining total body homeostasis. The complexity of this task is reflected in the unique architecture of the organ. Ureteral obstruction greatly affects renal physiology by altering hemodynamics, changing glomerular filtration and renal metabolism, and inducing architectural malformations of the kidney parenchyma, most importantly renal fibrosis. Persisting pathological changes lead to chronic kidney disease, which currently affects ∼10% of the global population and is one of the major causes of death worldwide. Studies on the consequences of ureteral obstruction date back to the 1800s. Even today, experimental unilateral ureteral obstruction (UUO) remains the standard model for tubulointerstitial fibrosis. However, the model has certain limitations when it comes to studying tubular injury and repair, as well as a limited potential for human translation. Nevertheless, ureteral obstruction has provided the scientific community with a wealth of knowledge on renal (patho)physiology. With the introduction of advanced omics techniques, the classical UUO model has remained relevant to this day and has been instrumental in understanding renal fibrosis at the molecular, genomic, and cellular levels. This review details key concepts and recent advances in the understanding of obstructive nephropathy, highlighting the pathophysiological hallmarks responsible for the functional and architectural changes induced by ureteral obstruction, with a special emphasis on renal fibrosis.
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Affiliation(s)
- Rikke Nørregaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Renal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Jørgen Frøkiær
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Tae-Hwan Kwon
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Taegu, Korea
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Kozawa S, Yokoyama H, Urayama K, Tejima K, Doi H, Takagi S, Sato TN. Latent disease similarities and therapeutic repurposing possibilities uncovered by multi-modal generative topic modeling of human diseases. BIOINFORMATICS ADVANCES 2023; 3:vbad047. [PMID: 37123453 PMCID: PMC10133403 DOI: 10.1093/bioadv/vbad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/14/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023]
Abstract
Motivation Human diseases are characterized by multiple features such as their pathophysiological, molecular and genetic changes. The rapid expansion of such multi-modal disease-omics space provides an opportunity to re-classify diverse human diseases and to uncover their latent molecular similarities, which could be exploited to repurpose a therapeutic-target for one disease to another. Results Herein, we probe this underexplored space by soft-clustering 6955 human diseases by multi-modal generative topic modeling. Focusing on chronic kidney disease and myocardial infarction, two most life-threatening diseases, unveiled are their previously underrecognized molecular similarities to neoplasia and mental/neurological-disorders, and 69 repurposable therapeutic-targets for these diseases. Using an edit-distance-based pathway-classifier, we also find molecular pathways by which these targets could elicit their clinical effects. Importantly, for the 17 targets, the evidence for their therapeutic usefulness is retrospectively found in the pre-clinical and clinical space, illustrating the effectiveness of the method, and suggesting its broader applications across diverse human diseases. Availability and implementation The code reported in this article is available at: https://github.com/skozawa170301ktx/MultiModalDiseaseModeling. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Satoshi Kozawa
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- ERATO Sato-Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Hirona Yokoyama
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- V-iCliniX Laboratory, Nara Medical University, Nara 634-8521, Japan
| | - Kyoji Urayama
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- ERATO Sato-Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Kengo Tejima
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- ERATO Sato-Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Hotaka Doi
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
- V-iCliniX Laboratory, Nara Medical University, Nara 634-8521, Japan
| | - Shunki Takagi
- Karydo TherapeutiX, Inc., Kyoto 619-0288, Japan
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan
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Wei J, Alfajaro MM, Hanna RE, DeWeirdt PC, Strine MS, Lu-Culligan WJ, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Gasque V, de Miguel F, Chen H, Oguntuyo K, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach B, Politi K, van Dijk D, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.16.155101. [PMID: 32869025 PMCID: PMC7457610 DOI: 10.1101/2020.06.16.155101] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-β signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ruth E. Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter C. DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Madison S. Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - William J. Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Vincent R. Graziano
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Cameron O. Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jennifer S. Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Madeleine C. Mankowski
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Fernando de Miguel
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Huacui Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Robert C. Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benhur Lee
- Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - David van Dijk
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Matthew D. Simon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
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Shimoda H, Doi S, Nakashima A, Sasaki K, Doi T, Masaki T. Inhibition of the H3K4 methyltransferase MLL1/WDR5 complex attenuates renal senescence in ischemia reperfusion mice by reduction of p16 INK4a. Kidney Int 2019; 96:1162-1175. [PMID: 31570196 DOI: 10.1016/j.kint.2019.06.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/19/2022]
Abstract
Renal function declines with aging and is pathologically characterized by chronic inflammation and fibrosis. Renal senescence is induced not only by aging but also by various stimuli, including ischemia reperfusion injury. Recently, the accumulation of p16INK4a-positive cells in the kidney has been considered a molecular feature of renal senescence, with the p16INK4a gene reportedly regulated by mixed-lineage leukemia 1 (MLL1)/WD-40 repeat protein 5 (WDR5)-mediated histone 3 lysine 4 trimethylation (H3K4me3). Here, we determined whether inhibition of MLL1/WDR5 activity attenuates renal senescence, inflammation, and fibrosis in mice with ischemia reperfusion injury and in cultured rat renal fibroblasts. MM-102 or OICR-9429, both MLL1/WDR5 protein-protein interaction inhibitors, and small interfering RNA (siRNA) for MLL1 or WDR5 suppressed the expression of p16INK4a in mice with ischemia reperfusion injury, accompanied by downregulation of H3K4me3 expression. MM-102 attenuated renal fibrosis and inflammation in the kidney of mice with ischemia reperfusion injury. Moreover, in vitro study showed that transforming growth factor-β1 induced the expression of MLL1, WDR5, H3K4me3, and p16INK4a. Finally, chromatin immunoprecipitation identified the p16INK4a promoter at an H3K4me3 site in renal fibroblasts. Thus, our findings show that H3K4me3 inhibition ameliorates ischemia reperfusion-induced renal senescence along with fibrosis and inflammation.
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Affiliation(s)
- Hironori Shimoda
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Shigehiro Doi
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan.
| | - Ayumu Nakashima
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Kensuke Sasaki
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Toshiki Doi
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan
| | - Takao Masaki
- Department of Nephrology, Hiroshima University Hospital, Hiroshima, Japan.
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