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Mizuno H, Murakami N. Multi-omics Approach in Kidney Transplant: Lessons Learned from COVID-19 Pandemic. CURRENT TRANSPLANTATION REPORTS 2023; 10:173-187. [PMID: 38152593 PMCID: PMC10751044 DOI: 10.1007/s40472-023-00410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2023] [Indexed: 12/29/2023]
Abstract
Purpose of Review Multi-omics approach has advanced our knowledge on transplantation-associated clinical outcomes, such as acute rejection and infection, and emerging omics data are becoming available in kidney transplant and COVID-19. Herein, we discuss updated findings of multi-omics data on kidney transplant outcomes, as well as COVID-19 and kidney transplant. Recent Findings Transcriptomics, proteomics, and metabolomics revealed various inflammation pathways associated with kidney transplantation-related outcomes and COVID-19. Although multi-omics data on kidney transplant and COVID-19 is limited, activation of innate immune pathways and suppression of adaptive immune pathways were observed in the active phase of COVID-19 in kidney transplant recipients. Summary Multi-omics analysis has led us to a deeper exploration and a more comprehensive understanding of key biological pathways in complex clinical settings, such as kidney transplantation and COVID-19. Future multi-omics analysis leveraging multi-center biobank collaborative will further advance our knowledge on the precise immunological responses to allograft and emerging pathogens.
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Affiliation(s)
- Hiroki Mizuno
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
- Dvision of Nephrology and Rheumatology, Toranomon Hospital, Tokyo, Japan
| | - Naoka Murakami
- Transplant Research Center, Division of Renal Medicine, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 305, Boston, MA 02115, USA
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Soltani F, Kaartinen MT. Transglutaminases in fibrosis-overview and recent advances. Am J Physiol Cell Physiol 2023; 325:C885-C894. [PMID: 37642242 DOI: 10.1152/ajpcell.00322.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Transglutaminases (TGs) are a family of protein cross-linking enzymes that are capable of stiffening and insolubilizing proteins and creating protein networks, and thereby altering biological functions of proteins. Their role in fibrosis progression has been widely investigated with a focus on kidney, lung, liver, and heart where activity is triggered by various stimuli including hypoxia, inflammation, and hyperglycemia. TG2 has been considered one of the key enzymes in the pathogenesis of fibrosis mainly through transforming growth factor beta (TGF-beta) signaling and matrix cross-linking mechanisms. Although TG2 has been most widely studied in this context, the involvement of other TGs, TG1 and Factor XIII-A (FXIII-A), is beginning to emerge. This mini-review highlights the major steps taken in the TG and fibrosis research and summarizes the most recent advances and contributions of TG2, TG1, and FXIII-A to the progression of fibrosis in various animal models. Also, their mechanisms of action as well as therapeutic prospects are discussed.
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Affiliation(s)
- Fatemeh Soltani
- Division of Experimental Medicine, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Mari T Kaartinen
- Division of Experimental Medicine, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences (Biomedical Sciences), McGill University, Montreal, Quebec, Canada
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3
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Patent highlights December 2021-January 2022. Pharm Pat Anal 2022; 11:89-96. [PMID: 35861046 DOI: 10.4155/ppa-2022-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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Thangaraj SS, Thiesson HC, Svenningsen P, Stubbe J, Palarasah Y, Bistrup C, Jensen BL, Mortensen LA. Mineralocorticoid receptor blockade with spironolactone has no direct effect on plasma IL-17A and injury markers in urine from kidney transplant patients. Am J Physiol Renal Physiol 2021; 322:F138-F149. [PMID: 34894724 DOI: 10.1152/ajprenal.00104.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Kidney transplantation is associated with increased risk of cardiovascular morbidity. Interleukin-17A (IL-17A) mediates kidney injury. Aldosterone promotes T-helper-17 (Th-17) lymphocyte differentiation and IL-17A production through the mineralocorticoid receptor (MR). In this exploratory, post-hoc substudy, it was hypothesized that 1-year intervention with the MR antagonist spironolactone lowers IL-17A and related cytokines and reduces epithelial injury in kidney transplant recipients. Plasma and urine samples were obtained from kidney transplant recipients from a double-blind randomized clinical trial testing spironolactone (n=39) versus placebo (n=41). Plasma concentrations of cytokines IFN-γ, IL-17A, TNF-α, IL-6, IL-1β, and IL-10 were determined before and after 1-year treatment. Urine calbindin, clusterin, KIM-1, osteoactivin, TFF3, and VEGF/creatinine ratios were analyzed. Blood pressure and plasma aldosterone concentration at inclusion did not relate to plasma cytokines and injury markers. None of the cytokines changed in plasma after spironolactone intervention. Plasma IL-17A increased in the placebo group. Spironolactone induced an increase in plasma K+ (0.4 ± 0.4 mmol/L). This increase did not correlate with plasma IL-17A or urine calbindin and TFF3 changes. Ongoing treatment at inclusion with angiotensin-converting-enzyme inhibitor and/or angiotensin II receptor blockers was not associated with changed levels of IL-17A and injury markers and had no effect on the response to spironolactone. Urinary calbindin and TFF3 decreased in the spironolactone group with no difference in between-group analyses. In conclusion, irrespective of ongoing ANGII inhibition, spironolactone has no effect on plasma IL-17A and related cytokines or urinary injury markers in kidney transplant recipients.
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Affiliation(s)
- Sai Sindhu Thangaraj
- Department of Cardiovascular and Renal Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Helle Charlotte Thiesson
- Department of Nephrology, Odense University Hospital, Odense C, Denmark.,Department of Clinical Research, Faculty of Health Science, University of Southern Denmark
| | - Per Svenningsen
- Department of Cardiovascular and Renal Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Jane Stubbe
- Department of Cardiovascular and Renal Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Yaseelan Palarasah
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of southern Denmark, Odense C, Denmark
| | - Claus Bistrup
- Department of Nephrology, Odense University Hospital, Odense C, Denmark.,Department of Clinical Research, Faculty of Health Science, University of Southern Denmark
| | - Boye L Jensen
- Department of Cardiovascular and Renal Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
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Proteomics and Nucleotide Profiling as Tools for Biomarker and Drug Target Discovery. Int J Mol Sci 2021; 22:ijms222011031. [PMID: 34681691 PMCID: PMC8537915 DOI: 10.3390/ijms222011031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
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Steffensen LB, Iversen XES, Hansen RS, Jensen PS, Thorsen ASF, Lindholt JS, Riber LPS, Beck HC, Rasmussen LM. Basement membrane proteins in various arterial beds from individuals with and without type 2 diabetes mellitus: a proteome study. Cardiovasc Diabetol 2021; 20:182. [PMID: 34496837 PMCID: PMC8428091 DOI: 10.1186/s12933-021-01375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Basement membrane (BM) accumulation is a hallmark of micro-vessel disease in diabetes mellitus (DM). We previously reported marked upregulation of BM components in internal thoracic arteries (ITAs) from type 2 DM (T2DM) patients by mass spectrometry. Here, we first sought to determine if BM accumulation is a common feature of different arteries in T2DM, and second, to identify other effects of T2DM on the arterial proteome. METHODS Human arterial samples collected during heart and vascular surgery from well-characterized patients and stored in the Odense Artery Biobank were analysed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We included ascending thoracic aortas (ATA) (n = 10 (type 2 DM, T2DM) and n = 10 (non-DM)); laser capture micro-dissected plaque- and media compartments from carotid plaques (n = 10 (T2DM) and n = 9 (non-DM)); and media- and adventitia compartments from ITAs (n = 9 (T2DM) and n = 7 (non-DM)). RESULTS We first extended our previous finding of BM accumulation in arteries from T2DM patients, as 7 of 12 pre-defined BM proteins were significantly upregulated in bulk ATAs consisting of > 90% media. Although less pronounced, BM components tended to be upregulated in the media of ITAs from T2DM patients, but not in the neighbouring adventitia. Overall, we did not detect effects on BM proteins in carotid plaques or in the plaque-associated media. Instead, complement factors, an RNA-binding protein and fibrinogens appeared to be regulated in these tissues from T2DM patients. CONCLUSION Our results suggest that accumulation of BM proteins is a general phenomenon in the medial layer of non-atherosclerotic arteries in patients with T2DM. Moreover, we identify additional T2DM-associated effects on the arterial proteome, which requires validation in future studies.
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Affiliation(s)
- Lasse Bach Steffensen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark.,Unit of Cardiovascular and Renal Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Xenia Emilie Sinding Iversen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Rasmus Søgaard Hansen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Pia Søndergaard Jensen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Anne-Sofie Faarvang Thorsen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Jes Sanddal Lindholt
- Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark.,Department of Cardiac, Thoracic, and Vascular Surgery, Odense University Hospital, Odense, Denmark
| | - Lars Peter Schødt Riber
- Department of Cardiac, Thoracic, and Vascular Surgery, Odense University Hospital, Odense, Denmark
| | - Hans Christian Beck
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark
| | - Lars Melholt Rasmussen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense, Denmark. .,Centre for Individualized Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark.
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Abstract
Interstitial fibrosis with tubule atrophy (IF/TA) is the response to virtually any sustained kidney injury and correlates inversely with kidney function and allograft survival. IF/TA is driven by various pathways that include hypoxia, renin-angiotensin-aldosterone system, transforming growth factor (TGF)-β signaling, cellular rejection, inflammation and others. In this review we will focus on key pathways in the progress of renal fibrosis, diagnosis and therapy of allograft fibrosis. This review discusses the role and origin of myofibroblasts as matrix producing cells and therapeutic targets in renal fibrosis with a particular focus on renal allografts. We summarize current trends to use multi-omic approaches to identify new biomarkers for IF/TA detection and to predict allograft survival. Furthermore, we review current imaging strategies that might help to identify and follow-up IF/TA complementary or as alternative to invasive biopsies. We further discuss current clinical trials and therapeutic strategies to treat kidney fibrosis.Supplemental Visual Abstract; http://links.lww.com/TP/C141.
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Rocchetti MT, Rascio F, Castellano G, Fiorentino M, Netti GS, Spadaccino F, Ranieri E, Gallone A, Gesualdo L, Stallone G, Pontrelli P, Grandaliano G. Altered Phosphorylation of Cytoskeleton Proteins in Peripheral Blood Mononuclear Cells Characterizes Chronic Antibody-Mediated Rejection in Kidney Transplantation. Int J Mol Sci 2020; 21:ijms21186509. [PMID: 32899575 PMCID: PMC7556000 DOI: 10.3390/ijms21186509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022] Open
Abstract
Chronic antibody-mediated rejection (CAMR) is the major cause of kidney transplant failure. The molecular mechanisms underlying this event are still poorly defined and this lack of knowledge deeply influences the potential therapeutic strategies. The aim of our study was to analyze the phosphoproteome of peripheral blood mononuclear cells (PBMCs), to identify cellular signaling networks differentially activated in CAMR. Phosphoproteins isolated from PBMCs of biopsy proven CAMR, kidney transplant recipients with normal graft function and histology and healthy immunocompetent individuals, have been investigated by proteomic analysis. Phosphoproteomic results were confirmed by Western blot and PBMCs’ confocal microscopy analyses. Overall, 38 PBMCs samples were analyzed. A differential analysis of PBMCs’ phosphoproteomes revealed an increase of lactotransferrin, actin-related protein 2 (ARPC2) and calgranulin-B in antibody-mediated rejection patients, compared to controls. Increased expression of phosphorylated ARPC2 and its correlation to F-actin filaments were confirmed in CAMR patients. Our results are the first evidence of altered cytoskeleton organization in circulating immune cells of CAMR patients. The increased expression of phosphorylated ARPC2 found in the PBMCs of our patients, and its association with derangement of F-actin filaments, might suggest that proteins regulating actin dynamics in immune cells could be involved in the mechanism of CAMR of kidney grafts.
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Affiliation(s)
- Maria Teresa Rocchetti
- Clinical Pathology Unit and Center for Molecular Medicine, Department of Medical and Surgical Sciences, Faculty of Medicine, University of Foggia, 71122 Foggia, Italy; (M.T.R.); (F.R.); (G.S.N.); (F.S.); (E.R.)
| | - Federica Rascio
- Clinical Pathology Unit and Center for Molecular Medicine, Department of Medical and Surgical Sciences, Faculty of Medicine, University of Foggia, 71122 Foggia, Italy; (M.T.R.); (F.R.); (G.S.N.); (F.S.); (E.R.)
| | - Giuseppe Castellano
- Nephrology Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, Faculty of Medicine University of Foggia, 71122 Foggia, Italy; (G.C.); (G.S.)
| | - Marco Fiorentino
- Nephrology Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, Faculty of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.F.); (L.G.)
| | - Giuseppe Stefano Netti
- Clinical Pathology Unit and Center for Molecular Medicine, Department of Medical and Surgical Sciences, Faculty of Medicine, University of Foggia, 71122 Foggia, Italy; (M.T.R.); (F.R.); (G.S.N.); (F.S.); (E.R.)
| | - Federica Spadaccino
- Clinical Pathology Unit and Center for Molecular Medicine, Department of Medical and Surgical Sciences, Faculty of Medicine, University of Foggia, 71122 Foggia, Italy; (M.T.R.); (F.R.); (G.S.N.); (F.S.); (E.R.)
| | - Elena Ranieri
- Clinical Pathology Unit and Center for Molecular Medicine, Department of Medical and Surgical Sciences, Faculty of Medicine, University of Foggia, 71122 Foggia, Italy; (M.T.R.); (F.R.); (G.S.N.); (F.S.); (E.R.)
| | - Anna Gallone
- Experimental Biology, Department of Basic Medical Sciences, Neuroscience and Sense Organs, Faculty of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Loreto Gesualdo
- Nephrology Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, Faculty of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.F.); (L.G.)
| | - Giovanni Stallone
- Nephrology Dialysis and Transplantation Unit, Department of Medical and Surgical Sciences, Faculty of Medicine University of Foggia, 71122 Foggia, Italy; (G.C.); (G.S.)
| | - Paola Pontrelli
- Experimental Biology, Department of Emergency and Organ Transplantation, Faculty of Medicine, University of Bari “Aldo Moro”, 70124 Bari, Italy
- Correspondence: ; Tel.: +39-08-05-478-868
| | - Giuseppe Grandaliano
- Nephrology Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy;
- Department of Translational Medicine and Surgery, Faculty of Medicine, Catholic University of the Sacred Heart, 00168 Rome, Italy
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Malone AF, Wu H, Fronick C, Fulton R, Gaut JP, Humphreys BD. Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant. J Am Soc Nephrol 2020; 31:1977-1986. [PMID: 32669324 DOI: 10.1681/asn.2020030326] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In solid organ transplantation, donor-derived immune cells are assumed to decline with time after surgery. Whether donor leukocytes persist within kidney transplants or play any role in rejection is unknown, however, in part because of limited techniques for distinguishing recipient from donor cells. METHODS Whole-exome sequencing of donor and recipient DNA and single-cell RNA sequencing (scRNA-seq) of five human kidney transplant biopsy cores distinguished immune cell contributions from both participants. DNA-sequence comparisons used single nucleotide variants (SNVs) identified in the exome sequences across all samples. RESULTS Analysis of expressed SNVs in the scRNA-seq data set distinguished recipient versus donor origin for all 81,139 cells examined. The leukocyte donor/recipient ratio varied with rejection status for macrophages and with time post-transplant for lymphocytes. Recipient macrophages displayed inflammatory activation whereas donor macrophages demonstrated antigen presentation and complement signaling. Recipient-origin T cells expressed cytotoxic and proinflammatory genes consistent with an effector cell phenotype, whereas donor-origin T cells appeared quiescent, expressing oxidative phosphorylation genes. Finally, both donor and recipient T cell clones within the rejecting kidney suggested lymphoid aggregation. The results indicate that donor-origin macrophages and T cells have distinct transcriptional profiles compared with their recipient counterparts, and that donor macrophages can persist for years post-transplantation. CONCLUSIONS Analysis of single nucleotide variants and their expression in single cells provides a powerful novel approach to accurately define leukocyte chimerism in a complex organ such as a transplanted kidney, coupled with the ability to examine transcriptional profiles at single-cell resolution.
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Affiliation(s)
- Andrew F Malone
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Robert Fulton
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri .,Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
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