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Kim SY, Choi YY, Kwon EJ, Seo S, Kim WY, Park SH, Park S, Chin HJ, Na KY, Kim S. Characterizing Glomerular Barrier Dysfunction with Patient-Derived Serum in Glomerulus-on-a-Chip Models: Unveiling New Insights into Glomerulonephritis. Int J Mol Sci 2024; 25:5121. [PMID: 38791159 PMCID: PMC11121116 DOI: 10.3390/ijms25105121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/29/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Glomerulonephritis (GN) is characterized by podocyte injury or glomerular filtration dysfunction, which results in proteinuria and eventual loss of kidney function. Progress in studying the mechanism of GN, and developing an effective therapy, has been limited by the absence of suitable in vitro models that can closely recapitulate human physiological responses. We developed a microfluidic glomerulus-on-a-chip device that can recapitulate the physiological environment to construct a functional filtration barrier, with which we investigated biological changes in podocytes and dynamic alterations in the permeability of the glomerular filtration barrier (GFB) on a chip. We also evaluated the potential of GN-mimicking devices as a model for predicting responses to human GN. Glomerular endothelial cells and podocytes successfully formed intact monolayers on opposite sides of the membrane in our chip device. Permselectivity analysis confirmed that the chip was constituted by a functional GFB that could accurately perform differential clearance of albumin and dextran. Reduction in cell viability resulting from damage was observed in all serum-induced GN models. The expression of podocyte-specific marker WT1 was also decreased. Albumin permeability was increased in most models of serum-induced IgA nephropathy (IgAN) and membranous nephropathy (MN). However, sera from patients with minimal change disease (MCD) or lupus nephritis (LN) did not induce a loss of permeability. This glomerulus-on-a-chip system may provide a platform of glomerular cell culture for in vitro GFB in formation of a functional three-dimensional glomerular structure. Establishing a disease model of GN on a chip could accelerate our understanding of pathophysiological mechanisms of glomerulopathy.
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Affiliation(s)
- Shin Young Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (S.Y.K.); (Y.Y.C.); (W.Y.K.); (S.H.P.)
| | - Yun Yeong Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (S.Y.K.); (Y.Y.C.); (W.Y.K.); (S.H.P.)
| | - Eun Jeong Kwon
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; (E.J.K.); (S.P.); (K.Y.N.)
| | - Seungwan Seo
- Osong Medical Innovation Foundation, Cheongju-si 28161, Republic of Korea; (S.S.); (H.J.C.)
| | - Wan Young Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (S.Y.K.); (Y.Y.C.); (W.Y.K.); (S.H.P.)
| | - Sung Hyuk Park
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (S.Y.K.); (Y.Y.C.); (W.Y.K.); (S.H.P.)
| | - Seokwoo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; (E.J.K.); (S.P.); (K.Y.N.)
| | - Ho Jun Chin
- Osong Medical Innovation Foundation, Cheongju-si 28161, Republic of Korea; (S.S.); (H.J.C.)
| | - Ki Young Na
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; (E.J.K.); (S.P.); (K.Y.N.)
| | - Sejoong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si 13620, Republic of Korea; (S.Y.K.); (Y.Y.C.); (W.Y.K.); (S.H.P.)
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; (E.J.K.); (S.P.); (K.Y.N.)
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2
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Brandt S, Bernhardt A, Häberer S, Wolters K, Gehringer F, Reichardt C, Krause A, Geffers R, Kahlfuß S, Jeron A, Bruder D, Lindquist JA, Isermann B, Mertens PR. Comparative Analysis of Acute Kidney Injury Models and Related Fibrogenic Responses: Convergence on Methylation Patterns Regulated by Cold Shock Protein. Cells 2024; 13:367. [PMID: 38474331 DOI: 10.3390/cells13050367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/02/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Fibrosis is characterized by excessive extracellular matrix formation in solid organs, disrupting tissue architecture and function. The Y-box binding protein-1 (YB-1) regulates fibrosis-related genes (e.g., Col1a1, Mmp2, and Tgfβ1) and contributes significantly to disease progression. This study aims to identify fibrogenic signatures and the underlying signaling pathways modulated by YB-1. METHODS Transcriptomic changes associated with matrix gene patterns in human chronic kidney diseases and murine acute injury models were analyzed with a focus on known YB-1 targets. Ybx1-knockout mouse strains (Ybx1ΔRosaERT+TX and Ybx1ΔLysM) were subjected to various kidney injury models. Fibrosis patterns were characterized by histopathological staining, transcriptome analysis, qRT-PCR, methylation analysis, zymography, and Western blotting. RESULTS Integrative transcriptomic analyses revealed that YB-1 is involved in several fibrogenic signatures related to the matrisome, the WNT, YAP/TAZ, and TGFß pathways, and regulates Klotho expression. Changes in the methylation status of the Klotho promoter by specific methyltransferases (DNMT) are linked to YB-1 expression, extending to other fibrogenic genes. Notably, kidney-resident cells play a significant role in YB-1-modulated fibrogenic signaling, whereas infiltrating myeloid immune cells have a minimal impact. CONCLUSIONS YB-1 emerges as a master regulator of fibrogenesis, guiding DNMT1 to fibrosis-related genes. This highlights YB-1 as a potential target for epigenetic therapies interfering in this process.
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Affiliation(s)
- Sabine Brandt
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Anja Bernhardt
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Saskia Häberer
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Katharina Wolters
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Fabian Gehringer
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Charlotte Reichardt
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Anna Krause
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Robert Geffers
- Genome Analytics Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Sascha Kahlfuß
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Andreas Jeron
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Research Group Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Dunja Bruder
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Research Group Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Jonathan A Lindquist
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig University, 04103 Leipzig, Germany
| | - Peter R Mertens
- Clinic of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke University, 39120 Magdeburg, Germany
- Medical Faculty, Health Campus Immunology, Infectiology and Inflammation (GCI-3), Otto-von-Guericke University, 39120 Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University, 39120 Magdeburg, Germany
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Gipson DS, Wang CS, Salmon E, Gbadegesin R, Naik A, Sanna-Cherchi S, Fornoni A, Kretzler M, Merscher S, Hoover P, Kidwell K, Saleem M, Riella L, Holzman L, Jackson A, Olabisi O, Cravedi P, Freedman BS, Himmelfarb J, Vivarelli M, Harder J, Klein J, Burke G, Rheault M, Spino C, Desmond HE, Trachtman H. FSGS Recurrence Collaboration: Report of a Symposium. GLOMERULAR DISEASES 2024; 4:1-10. [PMID: 38348154 PMCID: PMC10859699 DOI: 10.1159/000535138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/30/2023] [Indexed: 02/15/2024]
Affiliation(s)
- Debbie S. Gipson
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Chia-Shi Wang
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Eloise Salmon
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Rasheed Gbadegesin
- Department of Medicine, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Abhijit Naik
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Paul Hoover
- Department of Medicine, Harvard University, Cambridge, MA, USA
| | - Kelley Kidwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Moin Saleem
- Translational Health Sciences, University of Bristol, Bristol, UK
| | - Leonardo Riella
- Department of Medicine, Harvard University, Cambridge, MA, USA
| | - Lawrence Holzman
- Department of Internal Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Paolo Cravedi
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Marina Vivarelli
- Department of Pediatric Subspecialties, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Jennifer Harder
- Department of Internal Medicine, University of Louisville, Louisville, KY, USA
| | - Jon Klein
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - George Burke
- Department of Surgery, University of Miami, Miami, FL, USA
| | - Michelle Rheault
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Cathie Spino
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Hailey E. Desmond
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Howard Trachtman
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
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4
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Rhode H, Lüse A, Tautkus B, Nabity M, John-Kroegel U, Weigel F, Dost A, Schitke J, Metzing O, Böckhaus J, Rubel D, Kiess W, Gross O. Urinary Protein-Biomarkers Reliably Indicate Very Early Kidney Damage in Children With Alport Syndrome Independently of Albuminuria and Inflammation. Kidney Int Rep 2023; 8:2778-2793. [PMID: 38106579 PMCID: PMC10719601 DOI: 10.1016/j.ekir.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/25/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction Alport syndrome (AS) is a hereditary type IV collagen disease. It starts shortly after birth, without clinical symptoms, and progresses to end-stage kidney disease early in life. The earlier therapy starts, the more effectively end-stage kidney disease can be delayed. Clearly then, to ensure preemptive therapy, early diagnosis is an essential prerequisite. Methods To provide early diagnosis, we searched for protein biomarkers (BMs) by mass spectrometry in dogs with AS stage 0. At this very early stage, we identified 74 candidate BMs. Of these, using commercial enzyme-linked immunosorbent assays (ELISAs), we evaluated 27 in dogs and 28 in children, 50 with AS and 104 healthy controls. Results Most BMs from blood appeared as fractions of multiple variants of the same protein, as shown by their chromatographic distribution before mass spectrometry. Blood samples showed only minor differences because ELISAs rarely detect disease-specific variants. However, in urine , several proteins, individually or in combination, were promising indicators of very early and preclinical kidney injury. The BMs with the highest sensitivity and specificity were collagen type XIII, hyaluronan binding protein 2 (HABP2), and complement C4 binding protein (C4BP). Conclusion We generated very strong candidate BMs by our approach of first examining preclinical AS in dogs and then validating these BMs in children at early stages of disease. These BMs might serve for screening purposes for AS before the onset of kidney damage and therefore allow preemptive therapy.
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Affiliation(s)
- Heidrun Rhode
- Institute of Biochemistry I, Jena University Hospital, Jena, Germany
| | - Alexandra Lüse
- Institute of Biochemistry I, Jena University Hospital, Jena, Germany
| | - Bärbel Tautkus
- Institute of Biochemistry I, Jena University Hospital, Jena, Germany
| | - Mary Nabity
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, USA
| | | | | | - Axel Dost
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - Julia Schitke
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - Oliver Metzing
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - Jan Böckhaus
- Clinics for Nephrology and Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | - Diana Rubel
- Clinics for Nephrology and Rheumatology, University Medical Center Göttingen, Göttingen, Germany
| | - Wieland Kiess
- Hospital for Children and Adolescents, University of Leipzig, Liebigstr. 20a, 04103 Leipzig, Germany
| | - Oliver Gross
- Clinics for Nephrology and Rheumatology, University Medical Center Göttingen, Göttingen, Germany
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5
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Kavuru V, Senger RS, Robertson JL, Choudhury D. Analysis of urine Raman spectra differences from patients with diabetes mellitus and renal pathologies. PeerJ 2023; 11:e14879. [PMID: 36874959 PMCID: PMC9979830 DOI: 10.7717/peerj.14879] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/20/2023] [Indexed: 03/03/2023] Open
Abstract
Background Chronic kidney disease (CKD) poses a major public health burden. Diabetes mellitus (DM) is one of the major causes of CKD. In patients with DM, it can be difficult to differentiate diabetic kidney disease (DKD) from other causes of glomerular damage; it should not be assumed that all DM patients with decreased eGFR and/or proteinuria have DKD. Renal biopsy is the standard for definitive diagnosis, but other less invasive methods may provide clinical benefit. As previously reported, Raman spectroscopy of CKD patient urine with statistical and chemometric modeling may provide a novel, non-invasive methodology for discriminating between renal pathologies. Methods Urine samples were collected from renal biopsied and non-biopsied patients presenting with CKD secondary to DM and non-diabetic kidney disease. Samples were analyzed by Raman spectroscopy, baselined with the ISREA algorithm, and subjected to chemometric modeling. Leave-one-out cross-validation was used to assess the predictive capabilities of the model. Results This proof-of-concept study consisted of 263 samples, including renal biopsied, non-biopsied diabetic and non-diabetic CKD patients, healthy volunteers, and the Surine™ urinalysis control. Urine samples of DKD patients and those with immune-mediated nephropathy (IMN) were distinguished from one another with 82% sensitivity, specificity, positive-predictive value (PPV), and negative-predictive value (NPV). Among urine samples from all biopsied CKD patients, renal neoplasia was identified in urine with 100% sensitivity, specificity, PPV, and NPV, and membranous nephropathy was identified with 66.7% sensitivity, 96.4% specificity, 80.0% PPV, and 93.1% NPV. Finally, DKD was identified among a population of 150 patient urine samples containing biopsy-confirmed DKD, other biopsy-confirmed glomerular pathologies, un-biopsied non-diabetic CKD patients (no DKD), healthy volunteers, and Surine™ with 36.4% sensitivity, 97.8% specificity, 57.1% PPV, and 95.1% NPV. The model was used to screen un-biopsied diabetic CKD patients and identified DKD in more than 8% of this population. IMN in diabetic patients was identified among a similarly sized and diverse population with 83.3% sensitivity, 97.7% specificity, 62.5% PPV, and 99.2% NPV. Finally, IMN in non-diabetic patients was identified with 50.0% sensitivity, 99.4% specificity, 75.0% PPV, and 98.3% NPV. Conclusions Raman spectroscopy of urine with chemometric analysis may be able to differentiate between DKD, IMN, and other glomerular diseases. Future work will further characterize CKD stages and glomerular pathology, while assessing and controlling for differences in factors such as comorbidities, disease severity, and other lab parameters.
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Affiliation(s)
- Varun Kavuru
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States.,University Hospital at University of Virginia Medical Center, Charlottesville, VA, United States
| | - Ryan S Senger
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States.,DialySensors, Inc., Blacksburg, VA, United States
| | - John L Robertson
- DialySensors, Inc., Blacksburg, VA, United States.,Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States
| | - Devasmita Choudhury
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States.,Salem Veteran Affairs Health Care System, Salem, VA, United States
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6
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Lausecker F, Lennon R, Randles MJ. The kidney matrisome in health, aging, and disease. Kidney Int 2022; 102:1000-1012. [PMID: 35870643 DOI: 10.1016/j.kint.2022.06.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]
Abstract
Dysregulated extracellular matrix is the hallmark of fibrosis, and it has a profound impact on kidney function in disease. Furthermore, perturbation of matrix homeostasis is a feature of aging and is associated with declining kidney function. Understanding these dynamic processes, in the hope of developing therapies to combat matrix dysregulation, requires the integration of data acquired by both well-established and novel technologies. Owing to its complexity, the extracellular proteome, or matrisome, still holds many secrets and has great potential for the identification of clinical biomarkers and drug targets. The molecular resolution of matrix composition during aging and disease has been illuminated by cutting-edge mass spectrometry-based proteomics in recent years, but there remain key questions about the mechanisms that drive altered matrix composition. Basement membrane components are particularly important in the context of kidney function; and data from proteomic studies suggest that switches between basement membrane and interstitial matrix proteins are likely to contribute to organ dysfunction during aging and disease. Understanding the impact of such changes on physical properties of the matrix, and the subsequent cellular response to altered stiffness and viscoelasticity, is of critical importance. Likewise, the comparison of proteomic data sets from multiple organs is required to identify common matrix biomarkers and shared pathways for therapeutic intervention. Coupled with single-cell transcriptomics, there is the potential to identify the cellular origin of matrix changes, which could enable cell-targeted therapy. This review provides a contemporary perspective of the complex kidney matrisome and draws comparison to altered matrix in heart and liver disease.
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Affiliation(s)
- Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Michael J Randles
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester, UK.
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Cummins TD, Korte EA, Bhayana S, Merchant ML, Barati MT, Smoyer WE, Klein JB. Advances in proteomic profiling of pediatric kidney diseases. Pediatr Nephrol 2022; 37:2255-2265. [PMID: 35220505 PMCID: PMC9398920 DOI: 10.1007/s00467-022-05497-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 01/22/2023]
Abstract
Chronic kidney disease (CKD) can progress to kidney failure and require dialysis or transplantation, while early diagnosis can alter the course of disease and lead to better outcomes in both pediatric and adult patients. Significant CKD comorbidities include the manifestation of cardiovascular disease, heart failure, coronary disease, and hypertension. The pathogenesis of chronic kidney diseases can present as subtle and especially difficult to distinguish between different glomerular pathologies. Early detection of adult and pediatric CKD and detailed mechanistic understanding of the kidney damage can be helpful in delaying or curtailing disease progression via precise intervention toward diagnosis and prognosis. Clinically, serum creatinine and albumin levels can be indicative of CKD, but often are a lagging indicator only significantly affected once kidney function has severely diminished. The evolution of proteomics and mass spectrometry technologies has begun to provide a powerful research tool in defining these mechanisms and identifying novel biomarkers of CKD. Many of the same challenges and advances in proteomics apply to adult and pediatric patient populations. Additionally, proteomic analysis of adult CKD patients can be transferred directly toward advancing our knowledge of pediatric CKD as well. In this review, we highlight applications of proteomics that have yielded such biomarkers as PLA2R, SEMA3B, and other markers of membranous nephropathy as well as KIM-1, MCP-1, and NGAL in lupus nephritis among other potential diagnostic and prognostic markers. The potential for improving the clinical toolkit toward better treatment of pediatric kidney diseases is significantly aided by current and future development of proteomic applications.
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Affiliation(s)
- Timothy D Cummins
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA.
| | - Erik A Korte
- Bluewater Diagnostics, Mount Washington, KY, USA
| | - Sagar Bhayana
- Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Michael L Merchant
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA
| | - Michelle T Barati
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA
| | - William E Smoyer
- Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Jon B Klein
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA
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8
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Martin CE, Phippen NJ, Keyvani Chahi A, Tilak M, Banerjee SL, Lu P, New LA, Williamson CR, Platt MJ, Simpson JA, Krendel M, Bisson N, Gingras AC, Jones N. Complementary Nck1/2 Signaling in Podocytes Controls α Actinin-4-Mediated Actin Organization, Adhesion, and Basement Membrane Composition. J Am Soc Nephrol 2022; 33:1546-1567. [PMID: 35906089 PMCID: PMC9342632 DOI: 10.1681/asn.2021101343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/26/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Maintenance of the kidney filtration barrier requires coordinated interactions between podocytes and the underlying glomerular basement membrane (GBM). GBM ligands bind podocyte integrins, which triggers actin-based signaling events critical for adhesion. Nck1/2 adaptors have emerged as essential regulators of podocyte cytoskeletal dynamics. However, the precise signaling mechanisms mediated by Nck1/2 adaptors in podocytes remain to be fully elucidated. METHODS We generated podocytes deficient in Nck1 and Nck2 and used transcriptomic approaches to profile expression differences. Proteomic techniques identified specific binding partners for Nck1 and Nck2 in podocytes. We used cultured podocytes and mice deficient in Nck1 and/or Nck2, along with podocyte injury models, to comprehensively verify our findings. RESULTS Compound loss of Nck1/2 altered expression of genes involved in actin binding, cell adhesion, and extracellular matrix composition. Accordingly, Nck1/2-deficient podocytes showed defects in actin organization and cell adhesion in vitro, with podocyte detachment and altered GBM morphology present in vivo. We identified distinct interactomes for Nck1 and Nck2 and uncovered a mechanism by which Nck1 and Nck2 cooperate to regulate actin bundling at focal adhesions via α actinin-4. Furthermore, loss of Nck1 or Nck2 resulted in increased matrix deposition in vivo, with more prominent defects in Nck2-deficient mice, consistent with enhanced susceptibility to podocyte injury. CONCLUSION These findings reveal distinct, yet complementary, roles for Nck proteins in regulating podocyte adhesion, controlling GBM composition, and sustaining filtration barrier integrity.
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Affiliation(s)
- Claire E Martin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Noah J Phippen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ava Keyvani Chahi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Manali Tilak
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Sara L Banerjee
- Division of Oncology, Centre de Recherche du Centre Hospitalier Universitaire de Quebec-Laval University, Quebec City, Quebec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, Quebec, Canada
| | - Peihua Lu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura A New
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Casey R Williamson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Mathew J Platt
- Department of Human Health and Nutritional Science, University of Guelph, Guelph, Ontario, Canada
| | - Jeremy A Simpson
- Department of Human Health and Nutritional Science, University of Guelph, Guelph, Ontario, Canada
| | - Mira Krendel
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York
| | - Nicolas Bisson
- Division of Oncology, Centre de Recherche du Centre Hospitalier Universitaire de Quebec-Laval University, Quebec City, Quebec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Quebec City, Quebec, Canada.,PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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9
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Adeva-Andany MM, Carneiro-Freire N. Biochemical composition of the glomerular extracellular matrix in patients with diabetic kidney disease. World J Diabetes 2022; 13:498-520. [PMID: 36051430 PMCID: PMC9329837 DOI: 10.4239/wjd.v13.i7.498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/19/2022] [Accepted: 06/26/2022] [Indexed: 02/06/2023] Open
Abstract
In the glomeruli, mesangial cells produce mesangial matrix while podocytes wrap glomerular capillaries with cellular extensions named foot processes and tether the glomerular basement membrane (GBM). The turnover of the mature GBM and the ability of adult podocytes to repair injured GBM are unclear. The actin cytoskeleton is a major cytoplasmic component of podocyte foot processes and links the cell to the GBM. Predominant components of the normal glomerular extracellular matrix (ECM) include glycosaminoglycans, proteoglycans, laminins, fibronectin-1, and several types of collagen. In patients with diabetes, multiorgan composition of extracellular tissues is anomalous, including the kidney, so that the constitution and arrangement of glomerular ECM is profoundly altered. In patients with diabetic kidney disease (DKD), the global quantity of glomerular ECM is increased. The level of sulfated proteoglycans is reduced while hyaluronic acid is augmented, compared to control subjects. The concentration of mesangial fibronectin-1 varies depending on the stage of DKD. Mesangial type III collagen is abundant in patients with DKD, unlike normal kidneys. The amount of type V and type VI collagens is higher in DKD and increases with the progression of the disease. The GBM contains lower amount of type IV collagen in DKD compared to normal tissue. Further, genetic variants in the α3 chain of type IV collagen may modulate susceptibility to DKD and end-stage kidney disease. Human cellular models of glomerular cells, analyses of human glomerular proteome, and improved microscopy procedures have been developed to investigate the molecular composition and organization of the human glomerular ECM.
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10
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Boger M, Bennewitz K, Wohlfart DP, Hausser I, Sticht C, Poschet G, Kroll J. Comparative Morphological, Metabolic and Transcriptome Analyses in elmo1−/−, elmo2−/−, and elmo3−/− Zebrafish Mutants Identified a Functional Non-Redundancy of the Elmo Proteins. Front Cell Dev Biol 2022; 10:918529. [PMID: 35874819 PMCID: PMC9304559 DOI: 10.3389/fcell.2022.918529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
The ELMO protein family consists of the homologues ELMO1, ELMO2 and ELMO3. Several studies have shown that the individual ELMO proteins are involved in a variety of cellular and developmental processes. However, it has poorly been understood whether the Elmo proteins show similar functions and act redundantly. To address this question, elmo1−/−, elmo2−/− and elmo3−/− zebrafish were generated and a comprehensive comparison of the phenotypic changes in organ morphology, transcriptome and metabolome was performed in these mutants. The results showed decreased fasting and increased postprandial blood glucose levels in adult elmo1−/−, as well as a decreased vascular formation in the adult retina in elmo1−/−, but an increased vascular formation in the adult elmo3−/− retina. The phenotypical comparison provided few similarities, as increased Bowman space areas in adult elmo1−/− and elmo2−/− kidneys, an increased hyaloid vessel diameter in elmo1−/− and elmo3−/− and a transcriptional downregulation of the vascular development in elmo1−/−, elmo2−/−, and elmo3−/− zebrafish larvae. Besides this, elmo1−/−, elmo2−/−, and elmo3−/− zebrafish exhibited several distinct changes in the vascular and glomerular structure and in the metabolome and the transcriptome. Especially, elmo3−/− zebrafish showed extensive differences in the larval transcriptome and an impaired survivability. Together, the data demonstrated that the three zebrafish Elmo proteins regulate not only similar but also divergent biological processes and mechanisms and show a low functional redundancy.
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Affiliation(s)
- Mike Boger
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katrin Bennewitz
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Philipp Wohlfart
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ingrid Hausser
- Institute of Pathology IPH, EM Lab, Heidelberg University Hospital, Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Jens Kroll
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- *Correspondence: Jens Kroll,
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11
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Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics 2022; 21:100254. [PMID: 35654359 PMCID: PMC9256833 DOI: 10.1016/j.mcpro.2022.100254] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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Affiliation(s)
- Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
| | - Thomas P Conrads
- Inova Women's Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marc Vidal
- Department of Genetics, Harvard University, Cambridge, Massachusetts, USA
| | - Christine Vogel
- New York University Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - David R Walt
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Wyss Institute at Harvard University, Boston, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
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12
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Abdollahzadeh F, Khoshdel-Rad N, Moghadasali R. Kidney development and function: ECM cannot be ignored. Differentiation 2022; 124:28-42. [DOI: 10.1016/j.diff.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 11/03/2022]
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13
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Kruse ARS, Spraggins JM. Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. Front Physiol 2022; 13:837773. [PMID: 35222094 PMCID: PMC8874197 DOI: 10.3389/fphys.2022.837773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
The kidney functions through the coordination of approximately one million multifunctional nephrons in 3-dimensional space. Molecular understanding of the kidney has relied on transcriptomic, proteomic, and metabolomic analyses of kidney homogenate, but these approaches do not resolve cellular identity and spatial context. Mass spectrometry analysis of isolated cells retains cellular identity but not information regarding its cellular neighborhood and extracellular matrix. Spatially targeted mass spectrometry is uniquely suited to molecularly characterize kidney tissue while retaining in situ cellular context. This review summarizes advances in methodology and technology for spatially targeted mass spectrometry analysis of kidney tissue. Profiling technologies such as laser capture microdissection (LCM) coupled to liquid chromatography tandem mass spectrometry provide deep molecular coverage of specific tissue regions, while imaging technologies such as matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) molecularly profile regularly spaced tissue regions with greater spatial resolution. These technologies individually have furthered our understanding of heterogeneity in nephron regions such as glomeruli and proximal tubules, and their combination is expected to profoundly expand our knowledge of the kidney in health and disease.
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Affiliation(s)
- Angela R. S. Kruse
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Jeffrey M. Spraggins,
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14
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Han Y, Wu J, Gong Z, Zhou Y, Li H, Chen Y, Qian Q. Identification and development of the novel 7-genes diagnostic signature by integrating multi cohorts based on osteoarthritis. Hereditas 2022; 159:10. [PMID: 35093162 PMCID: PMC8801091 DOI: 10.1186/s41065-022-00226-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/29/2021] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
A chronic progressive degenerative joint disease, such as osteoarthritis (OA) is positively related to age. The medical economy is facing a major burden, because of the high disability rate seen in patients with OA. Therefore, to prevent and treat OA, exploring the diagnostic biomarkers of OA will be of great significance.
Methods
Differentially expressed genes (DEGs) were obtained from the Gene Expression Omnibus database using the RobustRankAggreg R package, and a protein–protein interaction network was constructed. The module was obtained from Cytoscape, and the four algorithms of degree, MNC, closeness, and MCC in CytoHubba were used to identify the hub genes. A diagnostic model was constructed using Support Vector Machines (SVM), and the ability of the model to predict was evaluated by other cohorts.
Results
From normal and OA samples, 136 DEGs were identified, out of which 45 were downregulated in the normal group and 91 were upregulated in the OA group. These genes were associated with the extracellular matrix-receptor interactions, the PI3K-Akt signaling pathway, and the protein digestion and absorption pathway, as per a functional enrichment analysis. Finally, we identified the 7 hub genes (COL6A3, COL1A2, COL1A1, MMP2, COL3A1, POST, and FN1). These genes have important roles and are widely involved in the immune response, apoptosis, inflammation, and bone development. These 7 genes were used to construct a diagnostic model by SVM, and it performed well in different cohorts. Additionally, we verified the methylation expression of these hub genes.
Conclusions
The 7-genes signature can be used for the diagnosis of OA and can provide new ideas in the clinical decision-making for patients with OA.
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15
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Caster DJ, Merchant ML. Collagen Remodeling Biomarkers in Lupus Nephritis. KIDNEY360 2021; 2:1395-1398. [PMID: 35373099 PMCID: PMC8786132 DOI: 10.34067/kid.0004732021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/18/2021] [Indexed: 02/04/2023]
Affiliation(s)
- Dawn J. Caster
- Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, Kentucky
| | - Michael L. Merchant
- Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, Kentucky
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16
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Williams S, Charest J, Pollak M, Subramanian BK. Bioengineering Strategies To Develop Podocyte Culture Systems. TISSUE ENGINEERING PART B-REVIEWS 2021; 28:938-948. [PMID: 34541902 PMCID: PMC9419930 DOI: 10.1089/ten.teb.2021.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Unraveling the complex behavior of healthy and disease podocytes by analyzing the changes in their unique arrangement of foot processes, slit diaphragm and the 3D morphology is a long-standing goal in kidney-glomerular research. The complexities surrounding the podocytes' accessibility in animal models and growing evidence of differences between humans and animal systems have compelled researchers to look for alternate approaches to study podocyte behaviors. With the advent of bioengineered models, an increasingly powerful and diverse set of tools is available to develop novel podocyte culture systems. This review discusses the pertinence of various culture models of podocytes to study podocyte mechanisms in both normal physiology and disease conditions. While no one in vitro system comprehensively recapitulates podocytes' in vivo architecture, we emphasize how the existing systems can be exploited to answer targeted questions on podocyte structure and function. We highlight the distinct advantages and limitations of using these models to study podocyte behaviors and screen therapeutics. Finally, we discuss various considerations and potential engineering strategies for developing next-generation complex 3D culture models for studying podocyte behaviors in vitro.
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Affiliation(s)
- Sarah Williams
- Beth Israel Deaconess Medical Center, 1859, Boston, Massachusetts, United States;
| | - Joseph Charest
- Draper Laboratory, Biomedical Engineering, 555 Technology Square, Cambridge, Massachusetts, United States, 02139;
| | - Martin Pollak
- Beth Israel Deaconess Medical Center, 1859, Boston, Massachusetts, United States;
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17
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Roye Y, Bhattacharya R, Mou X, Zhou Y, Burt MA, Musah S. A Personalized Glomerulus Chip Engineered from Stem Cell-Derived Epithelium and Vascular Endothelium. MICROMACHINES 2021; 12:967. [PMID: 34442589 PMCID: PMC8400556 DOI: 10.3390/mi12080967] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 01/13/2023]
Abstract
Progress in understanding kidney disease mechanisms and the development of targeted therapeutics have been limited by the lack of functional in vitro models that can closely recapitulate human physiological responses. Organ Chip (or organ-on-a-chip) microfluidic devices provide unique opportunities to overcome some of these challenges given their ability to model the structure and function of tissues and organs in vitro. Previously established organ chip models typically consist of heterogenous cell populations sourced from multiple donors, limiting their applications in patient-specific disease modeling and personalized medicine. In this study, we engineered a personalized glomerulus chip system reconstituted from human induced pluripotent stem (iPS) cell-derived vascular endothelial cells (ECs) and podocytes from a single patient. Our stem cell-derived kidney glomerulus chip successfully mimics the structure and some essential functions of the glomerular filtration barrier. We further modeled glomerular injury in our tissue chips by administering a clinically relevant dose of the chemotherapy drug Adriamycin. The drug disrupts the structural integrity of the endothelium and the podocyte tissue layers, leading to significant albuminuria as observed in patients with glomerulopathies. We anticipate that the personalized glomerulus chip model established in this report could help advance future studies of kidney disease mechanisms and the discovery of personalized therapies. Given the remarkable ability of human iPS cells to differentiate into almost any cell type, this work also provides a blueprint for the establishment of more personalized organ chip and 'body-on-a-chip' models in the future.
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Affiliation(s)
- Yasmin Roye
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; (Y.R.); (R.B.); (X.M.); (Y.Z.); (M.A.B.)
| | - Rohan Bhattacharya
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; (Y.R.); (R.B.); (X.M.); (Y.Z.); (M.A.B.)
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC 27708, USA
| | - Xingrui Mou
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; (Y.R.); (R.B.); (X.M.); (Y.Z.); (M.A.B.)
| | - Yuhao Zhou
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; (Y.R.); (R.B.); (X.M.); (Y.Z.); (M.A.B.)
| | - Morgan A. Burt
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; (Y.R.); (R.B.); (X.M.); (Y.Z.); (M.A.B.)
| | - Samira Musah
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA; (Y.R.); (R.B.); (X.M.); (Y.Z.); (M.A.B.)
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC 27708, USA
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27708, USA
- Department of Cell Biology, Duke University, Durham, NC 27708, USA
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18
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Sobreiro‐Almeida R, Quinteira R, Neves NM. Renal Regeneration: The Role of Extracellular Matrix and Current ECM-Based Tissue Engineered Strategies. Adv Healthc Mater 2021; 10:e2100160. [PMID: 34137210 DOI: 10.1002/adhm.202100160] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/29/2021] [Indexed: 12/15/2022]
Abstract
Natural extracellular matrices (ECM) are currently being studied as an alternative source for organ transplantation or as new solutions to treat kidney injuries, which can evolve to end-stage renal disease, a life devastating condition. This paper provides an overview on the current knowledge in kidney ECM and its usefulness on future investigations. The composition and structure of kidney ECM is herein associated with its intrinsic capacity of remodeling and repair after insult. Moreover, it provides a deeper insight on altered ECM components during disease. The use of decellularized kidney matrices is discussed in the second part of the review, with emphasis on how these matrices contribute to tissue-specific differentiation of embryonic, pluripotent, and other stem cells. The evolution on the field toward different uses of xenogeneic ECM as a biological scaffold material is discussed, namely the major outcomes on whole kidney recellularization and its in vivo implantation. At last, the recent literature on the use of processed kidney decellularized ECM to produce diverse biomaterial substrates, such as hydrogels, membranes, and bioinks are reviewed, with emphasis on future perspectives of its translation into the clinic.
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Affiliation(s)
- Rita Sobreiro‐Almeida
- 3B's Research Group I3Bs–Research Institute on Biomaterials, Biodegradables and Biomimetics University of Minho Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco Guimarães 4805‐017 Portugal
- ICVS/3B's–PT Government Associate Laboratory Braga/Guimarães Portugal
| | - Rita Quinteira
- 3B's Research Group I3Bs–Research Institute on Biomaterials, Biodegradables and Biomimetics University of Minho Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco Guimarães 4805‐017 Portugal
- ICVS/3B's–PT Government Associate Laboratory Braga/Guimarães Portugal
| | - Nuno M. Neves
- 3B's Research Group I3Bs–Research Institute on Biomaterials, Biodegradables and Biomimetics University of Minho Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, Barco Guimarães 4805‐017 Portugal
- ICVS/3B's–PT Government Associate Laboratory Braga/Guimarães Portugal
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19
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Randles MJ, Lausecker F, Kong Q, Suleiman H, Reid G, Kolatsi-Joannou M, Davenport B, Tian P, Falcone S, Potter P, Van Agtmael T, Norman JT, Long DA, Humphries MJ, Miner JH, Lennon R. Identification of an Altered Matrix Signature in Kidney Aging and Disease. J Am Soc Nephrol 2021; 32:1713-1732. [PMID: 34049963 PMCID: PMC8425653 DOI: 10.1681/asn.2020101442] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Accumulation of extracellular matrix in organs and tissues is a feature of both aging and disease. In the kidney, glomerulosclerosis and tubulointerstitial fibrosis accompany the decline in function, which current therapies cannot address, leading to organ failure. Although histologic and ultrastructural patterns of excess matrix form the basis of human disease classifications, a comprehensive molecular resolution of abnormal matrix is lacking. METHODS Using mass spectrometry-based proteomics, we resolved matrix composition over age in mouse models of kidney disease. We compared the changes in mice with a global characterization of human kidneymatrix during aging and to existing kidney disease datasets to identify common molecular features. RESULTS Ultrastructural changes in basement membranes are associated with altered cell adhesion and metabolic processes and with distinct matrix proteomes during aging and kidney disease progression in mice. Within the altered matrix, basement membrane components (laminins, type IV collagen, type XVIII collagen) were reduced and interstitial matrix proteins (collagens I, III, VI, and XV; fibrinogens; and nephronectin) were increased, a pattern also seen in human kidney aging. Indeed, this signature of matrix proteins was consistently modulated across all age and disease comparisons, and the increase in interstitial matrix was also observed in human kidney disease datasets. CONCLUSIONS This study provides deep molecular resolution of matrix accumulation in kidney aging and disease, and identifies a common signature of proteins that provides insight into mechanisms of response to kidney injury and repair.
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Affiliation(s)
- Michael J. Randles
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Qingyang Kong
- Department of Renal Medicine, University College London, London, United Kingdom
| | - Hani Suleiman
- Renal Division, Washington University School of Medicine, Saint Louis, Missouri
| | - Graeme Reid
- Department of Histopathology, Manchester Royal Infirmary, Manchester University Hospitals National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Maria Kolatsi-Joannou
- Developmental Biology and Cancer Programme, Great Ormond Institute of Child Health, University College London, London, United Kingdom
| | - Bernard Davenport
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Pinyuan Tian
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sara Falcone
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Paul Potter
- Department Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Tom Van Agtmael
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jill T. Norman
- Department of Renal Medicine, University College London, London, United Kingdom
| | - David A. Long
- Developmental Biology and Cancer Programme, Great Ormond Institute of Child Health, University College London, London, United Kingdom
| | - Martin J. Humphries
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jeffrey H. Miner
- Renal Division, Washington University School of Medicine, Saint Louis, Missouri
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Paediatric Nephrology, Royal Manchester Children’s Hospital, Manchester University Hospitals National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
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20
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Lipp SN, Jacobson KR, Hains DS, Schwarderer AL, Calve S. 3D Mapping Reveals a Complex and Transient Interstitial Matrix During Murine Kidney Development. J Am Soc Nephrol 2021; 32:1649-1665. [PMID: 33875569 PMCID: PMC8425666 DOI: 10.1681/asn.2020081204] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/20/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The extracellular matrix (ECM) is a network of proteins and glycosaminoglycans that provides structural and biochemical cues to cells. In the kidney, the ECM is critical for nephrogenesis; however, the dynamics of ECM composition and how it relates to 3D structure during development is unknown. METHODS Using embryonic day 14.5 (E14.5), E18.5, postnatal day 3 (P3), and adult kidneys, we fractionated proteins based on differential solubilities, performed liquid chromatography-tandem mass spectrometry, and identified changes in ECM protein content (matrisome). Decellularized kidneys were stained for ECM proteins and imaged in 3D using confocal microscopy. RESULTS We observed an increase in interstitial ECM that connects the stromal mesenchyme to the basement membrane (TNXB, COL6A1, COL6A2, COL6A3) between the embryo and adult, and a transient elevation of interstitial matrix proteins (COL5A2, COL12A1, COL26A1, ELN, EMID1, FBN1, LTBP4, THSD4) at perinatal time points. Basement membrane proteins critical for metanephric induction (FRAS1, FREM2) were highest in abundance in the embryo, whereas proteins necessary for integrity of the glomerular basement membrane (COL4A3, COL4A4, COL4A5, LAMB2) were more abundant in the adult. 3D visualization revealed a complex interstitial matrix that dramatically changed over development, including the perinatal formation of fibrillar structures that appear to support the medullary rays. CONCLUSION By correlating 3D ECM spatiotemporal organization with global protein abundance, we revealed novel changes in the interstitial matrix during kidney development. This new information regarding the ECM in developing kidneys offers the potential to inform the design of regenerative scaffolds that can guide nephrogenesis in vitro.
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Affiliation(s)
- Sarah N. Lipp
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
- Medical Scientist/Engineer Training Program, Indiana University, Indianapolis, Indiana
| | - Kathryn R. Jacobson
- Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana
| | - David S. Hains
- Department of Pediatrics, School of Medicine, Indiana University, Riley Children’s Hospital, Indianapolis, Indiana
| | - Andrew L. Schwarderer
- Department of Pediatrics, School of Medicine, Indiana University, Riley Children’s Hospital, Indianapolis, Indiana
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
- Interdisciplinary Life Science Program, Purdue University, West Lafayette, Indiana
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado
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21
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Taylor DA, Kren SM, Rhett K, Robertson MJ, Morrissey J, Rodriguez OE, Virk H, Chacon-Alberty L, Curty da Costa E, Mesquita FCP, Sampaio LC, Hochman-Mendez C. Characterization of perfusion decellularized whole animal body, isolated organs, and multi-organ systems for tissue engineering applications. Physiol Rep 2021; 9:e14817. [PMID: 34184419 PMCID: PMC8239446 DOI: 10.14814/phy2.14817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/07/2023] Open
Abstract
To expand the application of perfusion decellularization beyond isolated single organs, we used the native vasculature of adult and neonatal rats to systemically decellularize the organs of a whole animal in situ. Acellular scaffolds were generated from kidney, liver, lower limb, heart‐lung system, and a whole animal body, demonstrating that perfusion decellularization technology is applicable to any perfusable tissue, independent of age. Biochemical and histological analyses demonstrated that organs and organ systems (heart‐lung pair and lower limb) were successfully decellularized, retaining their extracellular matrix (ECM) structure and organ‐specific composition, as evidenced by differences in organ‐specific scaffold stiffness. Altogether, we demonstrated that organs, organ systems and whole animal bodies can be perfusion decellularized while retaining ECM components and biomechanics.
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Affiliation(s)
| | - Stefan M Kren
- Lillehei Heart Institute, Univeristy of Minnesota, USA
| | - Katrina Rhett
- Department of Physical Therapy and Occupational Therapy, Idaho State University, USA
| | | | | | | | - Hassan Virk
- Division of Infectious Diseases, University of Texas, Houston, USA
| | | | | | | | - Luiz C Sampaio
- Center for Advanced Cardiopulmonary Therapies and Transplantation, University of Texas Health Science Center, Houston, USA
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22
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García-Vence M, Chantada-Vazquez MDP, Sosa-Fajardo A, Agra R, Barcia de la Iglesia A, Otero-Glez A, García-González M, Cameselle-Teijeiro JM, Nuñez C, Bravo JJ, Bravo SB. Protein Extraction From FFPE Kidney Tissue Samples: A Review of the Literature and Characterization of Techniques. Front Med (Lausanne) 2021; 8:657313. [PMID: 34055835 PMCID: PMC8158658 DOI: 10.3389/fmed.2021.657313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Most tissue biopsies from patients in hospital environments are formalin-fixed and paraffin-embedded (FFPE) for long-term storage. This fixation process produces a modification in the proteins called “crosslinks”, which improves protein stability necessary for their conservation. Currently, these samples are mainly used in clinical practice for performing immunohistochemical analysis, since these modifications do not suppose a drawback for this technique; however, crosslinks difficult the protein extraction process. Accordingly, these modifications make the development of a good protein extraction protocol necessary. Due to the specific characteristics of each tissue, the same extraction buffers or deparaffinization protocols are not equally effective in all cases. Therefore, it is necessary to obtain a specific protocol for each tissue. The present work aims to establish a deparaffinization and protein extraction protocol from FFPE kidney samples to obtain protein enough of high quality for the subsequent proteomic analysis. Different deparaffination, protocols and protein extraction buffers will be tested in FFPE kidney samples. The optimized conditions will be applied in the identification by LC-MS/MS analysis of proteins extracted from 5, 10, and 15 glomeruli obtained through the microdissection of FFPE renal samples.
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Affiliation(s)
- Maria García-Vence
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Maria Del Pilar Chantada-Vazquez
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain.,Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain
| | - Ana Sosa-Fajardo
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit, Brussels, Belgium
| | - Rebeca Agra
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Ana Barcia de la Iglesia
- Nephrology Laboratory, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Alfonso Otero-Glez
- Nephrology Service, University Clinical Hospital of Ourense (CHOU), Orense, Spain
| | - Miguel García-González
- Nephrology Laboratory, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - José M Cameselle-Teijeiro
- Department of Pathology, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Santiago, Spain
| | - Cristina Nuñez
- Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain
| | - Juan J Bravo
- Nephrology Service, University Clinical Hospital of Vigo (Alvaro Cunqueiro-CHUVI), Vigo, Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
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23
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Differentiating Staphylococcus infection-associated glomerulonephritis and primary IgA nephropathy: a mass spectrometry-based exploratory study. Sci Rep 2020; 10:17179. [PMID: 33057112 PMCID: PMC7560901 DOI: 10.1038/s41598-020-73847-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/18/2020] [Indexed: 01/18/2023] Open
Abstract
Staphylococcus infection-associated glomerulonephritis (SAGN) and primary IgA nephropathy (IgAN) are separate disease entities requiring different treatment approaches. However, overlapping histologic features may cause a diagnostic dilemma. An exploratory proteomic study to identify potential distinguishing biomarkers was performed on formalin fixed paraffin embedded kidney biopsy tissue, using mass spectrometry (HPLC–MS/MS) (n = 27) and immunohistochemistry (IHC) (n = 64), on four main diagnostic groups—SAGN, primary IgAN, acute tubular necrosis (ATN) and normal kidney (baseline transplant biopsies). Spectral counts modeled as a negative binomial distribution were used for statistical comparisons and in silico pathway analysis. Analysis of variance techniques were used to compare groups and the ROC curve to evaluate classification algorithms. The glomerular proteomes of SAGN and IgAN showed remarkable similarities, except for significantly higher levels of monocyte/macrophage proteins in SAGN—mainly lysozyme and S100A9. This finding was confirmed by IHC. In contrast, the tubulointerstitial proteomes were markedly different in IgAN and SAGN, with a lower abundance of metabolic pathway proteins and a higher abundance of extracellular matrix proteins in SAGN. The stress protein transglutaminase-2 (TGM2) was also significantly higher in SAGN. IHC of differentially-expressed glomerular and tubulointerstitial proteins can be used to help discriminate between SAGN and IgAN in ambiguous cases.
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Rinschen MM, Saez-Rodriguez J. The tissue proteome in the multi-omic landscape of kidney disease. Nat Rev Nephrol 2020; 17:205-219. [PMID: 33028957 DOI: 10.1038/s41581-020-00348-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Kidney research is entering an era of 'big data' and molecular omics data can provide comprehensive insights into the molecular footprints of cells. In contrast to transcriptomics, proteomics and metabolomics generate data that relate more directly to the pathological symptoms and clinical parameters observed in patients. Owing to its complexity, the proteome still holds many secrets, but has great potential for the identification of drug targets. Proteomics can provide information about protein synthesis, modification and degradation, as well as insight into the physical interactions between proteins, and between proteins and other biomolecules. Thus far, proteomics in nephrology has largely focused on the discovery and validation of biomarkers, but the systematic analysis of the nephroproteome can offer substantial additional insights, including the discovery of mechanisms that trigger and propagate kidney disease. Moreover, proteome acquisition might provide a diagnostic tool that complements the assessment of a kidney biopsy sample by a pathologist. Such applications are becoming increasingly feasible with the development of high-throughput and high-coverage technologies, such as versatile mass spectrometry-based techniques and protein arrays, and encourage further proteomics research in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Department of Chemistry, Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research, La Jolla, CA, USA.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
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25
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Bingham GC, Lee F, Naba A, Barker TH. Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology. Matrix Biol 2020; 91-92:152-166. [DOI: 10.1016/j.matbio.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
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26
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Merchant ML, Barati MT, Caster DJ, Hata JL, Hobeika L, Coventry S, Brier ME, Wilkey DW, Li M, Rood IM, Deegens JK, Wetzels JF, Larsen CP, Troost JP, Hodgin JB, Mariani LH, Kretzler M, Klein JB, McLeish KR. Proteomic Analysis Identifies Distinct Glomerular Extracellular Matrix in Collapsing Focal Segmental Glomerulosclerosis. J Am Soc Nephrol 2020; 31:1883-1904. [PMID: 32561683 DOI: 10.1681/asn.2019070696] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/13/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The mechanisms leading to extracellular matrix (ECM) replacement of areas of glomerular capillaries in histologic variants of FSGS are unknown. This study used proteomics to test the hypothesis that glomerular ECM composition in collapsing FSGS (cFSGS) differs from that of other variants. METHODS ECM proteins in glomeruli from biopsy specimens of patients with FSGS not otherwise specified (FSGS-NOS) or cFSGS and from normal controls were distinguished and quantified using mass spectrometry, verified and localized using immunohistochemistry (IHC) and confocal microscopy, and assessed for gene expression. The analysis also quantified urinary excretion of ECM proteins and peptides. RESULTS Of 58 ECM proteins that differed in abundance between cFSGS and FSGS-NOS, 41 were more abundant in cFSGS and 17 in FSGS-NOS. IHC showed that glomerular tuft staining for cathepsin B, cathepsin C, and annexin A3 in cFSGS was significantly greater than in other FSGS variants, in minimal change disease, or in membranous nephropathy. Annexin A3 colocalized with cathepsin B and C, claudin-1, phosphorylated ERK1/2, and CD44, but not with synaptopodin, in parietal epithelial cells (PECs) infiltrating cFSGS glomeruli. Transcripts for cathepsins B and C were increased in FSGS glomeruli compared with normal controls, and urinary excretion of both cathepsins was significantly greater in cFSGS compared with FSGS-NOS. Urinary excretion of ECM-derived peptides was enhanced in cFSGS, although in silico analysis did not identify enhanced excretion of peptides derived from cathepsin B or C. CONCLUSIONS ECM differences suggest that glomerular sclerosis in cFSGS differs from that in other FSGS variants. Infiltration of activated PECs may disrupt ECM remodeling in cFSGS. These cells and their cathepsins may be therapeutic targets.
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Affiliation(s)
- Michael L Merchant
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Michelle T Barati
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Dawn J Caster
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Jessica L Hata
- Pathology Department, Norton Children's Hospital, Louisville, Kentucky
| | - Liliane Hobeika
- Division of Nephrology, Department of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Susan Coventry
- Pathology Department, Norton Children's Hospital, Louisville, Kentucky
| | - Michael E Brier
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Daniel W Wilkey
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Ming Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Ilse M Rood
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen K Deegens
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jack F Wetzels
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Jonathan P Troost
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey B Hodgin
- Division of Pathology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Laura H Mariani
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jon B Klein
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky.,Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky
| | - Kenneth R McLeish
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
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27
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Bousalis D, Lacko CS, Hlavac N, Alkassis F, Wachs RA, Mobini S, Schmidt CE, Kasahara H. Extracellular Matrix Disparities in an Nkx2-5 Mutant Mouse Model of Congenital Heart Disease. Front Cardiovasc Med 2020; 7:93. [PMID: 32548129 PMCID: PMC7272573 DOI: 10.3389/fcvm.2020.00093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 12/19/2022] Open
Abstract
Congenital heart disease (CHD) affects almost one percent of all live births. Despite diagnostic and surgical reparative advances, the causes and mechanisms of CHD are still primarily unknown. The extracellular matrix plays a large role in cell communication, function, and differentiation, and therefore likely plays a role in disease development and pathophysiology. Cell adhesion and gap junction proteins, such as integrins and connexins, are also essential to cellular communication and behavior, and could interact directly (integrins) or indirectly (connexins) with the extracellular matrix. In this work, we explore disparities in the expression and spatial patterning of extracellular matrix, adhesion, and gap junction proteins between wild type and Nkx2-5 +/R52G mutant mice. Decellularization and proteomic analysis, Western blotting, histology, immunostaining, and mechanical assessment of embryonic and neonatal wild type and Nkx2-5 mutant mouse hearts were performed. An increased abundance of collagen IV, fibronectin, and integrin β-1 was found in Nkx2-5 mutant neonatal mouse hearts, as well as increased expression of connexin 43 in embryonic mutant hearts. Furthermore, a ventricular noncompaction phenotype was observed in both embryonic and neonatal mutant hearts, as well as spatial disorganization of ECM proteins collagen IV and laminin in mutant hearts. Characterizing such properties in a mutant mouse model provides valuable information that can be applied to better understanding the mechanisms of congenital heart disease.
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Affiliation(s)
- Deanna Bousalis
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Christopher S Lacko
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Nora Hlavac
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Fariz Alkassis
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, United States
| | - Rebecca A Wachs
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Sahba Mobini
- Instituto de Micro y Nanotecnología, IMN-CNM, CSIC (CEI UAM+CSIC), Madrid, Spain.,Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Christine E Schmidt
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, United States
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28
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Tang SW, Tong WY, Pang SW, Voelcker NH, Lam YW. Deconstructing, Replicating, and Engineering Tissue Microenvironment for Stem Cell Differentiation. TISSUE ENGINEERING PART B-REVIEWS 2020; 26:540-554. [PMID: 32242476 DOI: 10.1089/ten.teb.2020.0044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One of the most crucial components of regenerative medicine is the controlled differentiation of embryonic or adult stem cells into the desired cell lineage. Although most of the reported protocols of stem cell differentiation involve the use of soluble growth factors, it is increasingly evident that stem cells also undergo differentiation when cultured in the appropriate microenvironment. When cultured in decellularized tissues, for instance, stem cells can recapitulate the morphogenesis and functional specialization of differentiated cell types with speed and efficiency that often surpass the traditional growth factor-driven protocols. This suggests that the tissue microenvironment (TME) provides stem cells with a holistic "instructive niche" that harbors signals for cellular reprogramming. The translation of this into medical applications requires the decoding of these signals, but this has been hampered by the complexity of TME. This problem is often addressed by a reductionist approach, in which cells are exposed to substrates decorated with simple, empirically designed geometries, textures, and chemical compositions ("bottom-up" approach). Although these studies are invaluable in revealing the basic principles of mechanotransduction mechanisms, their physiological relevance is often uncertain. This review examines the recent progress of an alternative, "top-down" approach, in which the TME is treated as a holistic biological entity. This approach is made possible by recent advances in systems biology and fabrication technologies that enable the isolation, characterization, and reconstitution of TME. It is hoped that these new techniques will elucidate the nature of niche signals so that they can be extracted, replicated, and controlled. This review summarizes these emerging techniques and how the data they generated are changing our view on TME. Impact statement This review summarizes the current state of art of the understanding of instructive niche in the field of tissue microenvironment. Not only did we survey the use of different biochemical preparations as stimuli of stem cell differentiation and summarize the recent effort in dissecting the biochemical composition of these preparations, through the application of extracellular matrix (ECM) arrays and proteomics, but we also introduce the use of open-source, high-content immunohistochemistry projects in contributing to the understanding of tissue-specific composition of ECM. We believe this review would be highly useful for our peer researching in the same field. "Mr. Tulkinghorn is always the same… so oddly out of place and yet so perfectly at home." -Charles Dickens, Bleak House.
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Affiliation(s)
- Sze Wing Tang
- Department of Chemistry, City University of Hong Kong, Hong Kong, Hong Kong
| | - Wing Yin Tong
- Melbourne Center for Nanofabrication, Victorian Node of the Australian National Fabrication, Clayton, Australia.,Drug Delivery Disposition & Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Stella W Pang
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, Hong Kong
| | - Nicolas H Voelcker
- Melbourne Center for Nanofabrication, Victorian Node of the Australian National Fabrication, Clayton, Australia.,Drug Delivery Disposition & Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Yun Wah Lam
- Department of Chemistry, City University of Hong Kong, Hong Kong, Hong Kong
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29
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Bukosza EN, Kornauth C, Hummel K, Schachner H, Huttary N, Krieger S, Nöbauer K, Oszwald A, Razzazi Fazeli E, Kratochwill K, Aufricht C, Szénási G, Hamar P, Gebeshuber CA. ECM Characterization Reveals a Massive Activation of Acute Phase Response during FSGS. Int J Mol Sci 2020; 21:ijms21062095. [PMID: 32197499 PMCID: PMC7139641 DOI: 10.3390/ijms21062095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 12/19/2022] Open
Abstract
The glomerular basement membrane (GBM) and extra-cellular matrix (ECM) are essential to maintain a functional interaction between the glomerular podocytes and the fenestrated endothelial cells in the formation of the slit diaphragm for the filtration of blood. Dysregulation of ECM homeostasis can cause Focal segmental glomerulosclerosis (FSGS). Despite this central role, alterations in ECM composition during FSGS have not been analyzed in detail yet. Here, we characterized the ECM proteome changes in miR-193a-overexpressing mice, which suffer from FSGS due to suppression of Wilms' tumor 1 (WT1). By mass spectrometry we identified a massive activation of the acute phase response, especially the complement and fibrinogen pathways. Several protease inhibitors (ITIH1, SERPINA1, SERPINA3) were also strongly increased. Complementary analysis of RNA expression data from both miR-193a mice and human FSGS patients identified additional candidate genes also mainly involved in the acute phase response. In total, we identified more than 60 dysregulated, ECM-associated genes with potential relevance for FSGS progression. Our comprehensive analysis of a murine FSGS model and translational comparison with human data offers novel targets for FSGS therapy.
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Affiliation(s)
- Eva Nora Bukosza
- Institute of Translational Medicine, Semmelweis University Budapest, Tűzoltó u 37-47, 1094 Budapest, Hungary; (E.N.B.); (G.S.); (P.H.)
- Clinical Institute for Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (C.K.); (H.S.); (N.H.); (S.K.); (A.O.)
| | - Christoph Kornauth
- Clinical Institute for Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (C.K.); (H.S.); (N.H.); (S.K.); (A.O.)
- Clinical Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Karin Hummel
- Vetcore Facility for Research, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (K.H.); (K.N.); (E.R.F.)
| | - Helga Schachner
- Clinical Institute for Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (C.K.); (H.S.); (N.H.); (S.K.); (A.O.)
| | - Nicole Huttary
- Clinical Institute for Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (C.K.); (H.S.); (N.H.); (S.K.); (A.O.)
| | - Sigurd Krieger
- Clinical Institute for Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (C.K.); (H.S.); (N.H.); (S.K.); (A.O.)
| | - Katharina Nöbauer
- Vetcore Facility for Research, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (K.H.); (K.N.); (E.R.F.)
| | - André Oszwald
- Clinical Institute for Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (C.K.); (H.S.); (N.H.); (S.K.); (A.O.)
| | - Ebrahim Razzazi Fazeli
- Vetcore Facility for Research, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (K.H.); (K.N.); (E.R.F.)
| | - Klaus Kratochwill
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1210 Vienna, Austria;
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1210 Vienna, Austria;
| | - Christoph Aufricht
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1210 Vienna, Austria;
| | - Gabor Szénási
- Institute of Translational Medicine, Semmelweis University Budapest, Tűzoltó u 37-47, 1094 Budapest, Hungary; (E.N.B.); (G.S.); (P.H.)
| | - Peter Hamar
- Institute of Translational Medicine, Semmelweis University Budapest, Tűzoltó u 37-47, 1094 Budapest, Hungary; (E.N.B.); (G.S.); (P.H.)
| | - Christoph A. Gebeshuber
- Clinical Institute for Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria; (C.K.); (H.S.); (N.H.); (S.K.); (A.O.)
- Correspondence: ; Tel.: +43-1-40400-51840
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Lin MH, Pope BD, Sasaki T, Keeley DP, Sherwood DR, Miner JH. Mammalian hemicentin 1 is assembled into tracks in the extracellular matrix of multiple tissues. Dev Dyn 2020; 249:775-788. [PMID: 32035013 DOI: 10.1002/dvdy.159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/20/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hemicentins (HMCNs) are a family of extracellular matrix proteins first identified in Caenorhabditis elegans, with two orthologs (HMCN1 and 2) in vertebrates. In worms, HMCN is deposited at specific sites where it forms long, fine tracks that link two tissues by connecting adjacent basement membranes (BMs). By generating CRISPR/Cas9-mediated Hmcn1 and Hmcn2 knockout mice, we tested the hypothesis that HMCNs perform similar functions in mammals. RESULTS Hmcn1 -/- mice were viable and fertile. Using new, knockout mouse-validated HMCN1 antibodies, HMCN1 was detected in wild-type mice as fine tracks along the BM of hair and whisker follicles, in the sclera of the eyes, and in the lumen of some lymphoid conduits. It was also observed in the mesangial matrix of the kidney glomerulus. However, HMCN1 deficiency did not affect the functions of these tissues, including adherence of coat hairs and whiskers, the sieving function of lymphoid conduits, or the immune response to injected antigens. HMCN2 deficiency did not lead to any discernible phenotypes on its own or when combined with HMCN1 deficiency. CONCLUSION That Hmcn1 -/- , Hmcn2 -/- , and Hmcn1/2 double knockout mice did not display any overt phenotypes implicates compensation by other members of the fibulin family.
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Affiliation(s)
- Meei-Hua Lin
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bill D Pope
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Takako Sasaki
- Department of Biochemistry II, Oita University, Oita, Japan
| | - Daniel P Keeley
- Department of Biology, Regeneration Next, Duke University, Durham, North Carolina, USA
| | - David R Sherwood
- Department of Biology, Regeneration Next, Duke University, Durham, North Carolina, USA
| | - Jeffrey H Miner
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
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Paunas FTI, Finne K, Leh S, Osman TAH, Marti HP, Berven F, Vikse BE. Characterization of glomerular extracellular matrix in IgA nephropathy by proteomic analysis of laser-captured microdissected glomeruli. BMC Nephrol 2019; 20:410. [PMID: 31726998 PMCID: PMC6854890 DOI: 10.1186/s12882-019-1598-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/23/2019] [Indexed: 12/29/2022] Open
Abstract
Background IgA nephropathy (IgAN) involves mesangial matrix expansion, but the proteomic composition of this matrix is unknown. The present study aimed to characterize changes in extracellular matrix in IgAN. Methods In the present study we used mass spectrometry-based proteomics in order to quantitatively compare protein abundance between glomeruli of patients with IgAN (n = 25) and controls with normal biopsy findings (n = 15). Results Using a previously published paper by Lennon et al. and cross-referencing with the Matrisome database we identified 179 extracellular matrix proteins. In the comparison between IgAN and controls, IgAN glomeruli showed significantly higher abundance of extracellular matrix structural proteins (e.g periostin, vitronectin, and extracellular matrix protein 1) and extracellular matrix associated proteins (e.g. azurocidin, myeloperoxidase, neutrophil elastase, matrix metalloproteinase-9 and matrix metalloproteinase 2). Periostin (fold change 3.3) and azurocidin (3.0) had the strongest fold change between IgAN and controls; periostin was also higher in IgAN patients who progressed to ESRD as compared to patients who did not. Conclusion IgAN is associated with widespread changes of the glomerular extracellular matrix proteome. Proteins important in glomerular sclerosis or inflammation seem to be most strongly increased and periostin might be an important marker of glomerular damage in IgAN.
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Affiliation(s)
- Flavia Teodora Ioana Paunas
- Department of Medicine, Haugesund Hospital, Haugesund, Norway. .,Department of Clinical Medicine, University of Bergen, Bergen, Norway.
| | - Kenneth Finne
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | | | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Frode Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Bjørn Egil Vikse
- Department of Medicine, Haugesund Hospital, Haugesund, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
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Exploring the extracellular matrix in health and disease using proteomics. Essays Biochem 2019; 63:417-432. [DOI: 10.1042/ebc20190001] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023]
Abstract
Abstract
The extracellular matrix (ECM) is a complex assembly of hundreds of proteins that constitutes the scaffold of multicellular organisms. In addition to providing architectural and mechanical support to the surrounding cells, it conveys biochemical signals that regulate cellular processes including proliferation and survival, fate determination, and cell migration. Defects in ECM protein assembly, decreased ECM protein production or, on the contrary, excessive ECM accumulation, have been linked to many pathologies including cardiovascular and skeletal diseases, cancers, and fibrosis. The ECM thus represents a potential reservoir of prognostic biomarkers and therapeutic targets. However, our understanding of the global protein composition of the ECM and how it changes during pathological processes has remained limited until recently.
In this mini-review, we provide an overview of the latest methodological advances in sample preparation and mass spectrometry-based proteomics that have permitted the profiling of the ECM of now dozens of normal and diseased tissues, including tumors and fibrotic lesions.
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Li QK, Pavlovich CP, Zhang H, Kinsinger CR, Chan DW. Challenges and opportunities in the proteomic characterization of clear cell renal cell carcinoma (ccRCC): A critical step towards the personalized care of renal cancers. Semin Cancer Biol 2019; 55:8-15. [PMID: 30055950 PMCID: PMC6624650 DOI: 10.1016/j.semcancer.2018.06.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 12/28/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer, comprising approximately 75% of all kidney tumors. Recent the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) studies have significantly advanced the molecular characterization of RCC and facilitated the development of targeted therapies. Such advances have improved the median survival of patients with advanced disease from less than 10 months prior to 2004 to 30 months by 2011. However, approximately 30% of localized ccRCC patients will nevertheless develop recurrence or metastasis after surgical resection of their tumor. Therefore, it is critical to further analyze potential tumor-associated proteins and their profiles during disease progression. Over the past decade, tremendous effort has been focused on the study of molecular pathways, including genomics, transcriptomics, and proteomics in order to identify potential molecular biomarkers, as well as to facilitate early detection, monitor tumor progression and uncover potentially therapeutic targets. In this review, we focus on recent advances in the proteomic analysis of ccRCC, current strategies and challenges, and perspectives in the field. This insight will highlight the discovery of tumor-associated proteins, and their potential clinical impact on personalized precision-based care in ccRCC.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, United States.
| | - Christian P Pavlovich
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, United States
| | - Hui Zhang
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, United States
| | | | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, United States
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Srivastava S, Merchant M, Rai A, Rai SN. Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2019; 12:48-55. [PMID: 32148359 PMCID: PMC7059694 DOI: 10.35248/0974-276x.19.12.496] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
INTRODUCTION The quantitative measurements based on liquid chromatography (LC) coupled with mass spectrometry (MS) often suffer from the problem of missing values and data heterogeneity from technical variability. We considered a proteomics data set generated from human kidney biopsy material to investigate the technical effects of sample preparation and the quantitative MS. METHODS We studied the effect of tissue storage methods (TSMs) and tissue extraction methods (TEMs) on data analysis. There are two TSMs: frozen (FR) and FFPE (formalin-fixed paraffin embedded); and three TEMs: MAX, TX followed by MAX and SDS followed by MAX. We assessed the impact of different strategies to analyze the data while considering heterogeneity and MVs. We have used analysis of variance (ANOVA) model to study the effects due to various sources of variability. RESULTS AND CONCLUSION We found that the FFPE TSM is better than the FR TSM. We also found that the one-step TEM (MAX) is better than those of two-steps TEMs. Furthermore, we found the imputation method is a better approach than excluding the proteins with MVs or using unbalanced design.
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Affiliation(s)
- Sudhir Srivastava
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, Kentucky, United States of America
| | - Michael Merchant
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Pharmacology & Toxicology, University of Louisville, Louisville, Kentucky, United States of America
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shesh N. Rai
- Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, Kentucky, United States of America
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Corresponding author: Shesh N. Rai, Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, United States of America, Tel: + 502-852-4030; Fax: + 502-852-7979;
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Keeley DP, Sherwood DR. Tissue linkage through adjoining basement membranes: The long and the short term of it. Matrix Biol 2019; 75-76:58-71. [PMID: 29803937 PMCID: PMC6252152 DOI: 10.1016/j.matbio.2018.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 01/01/2023]
Abstract
Basement membranes (BMs) are thin dense sheets of extracellular matrix that surround most tissues. When the BMs of neighboring tissues come into contact, they usually slide along one another and act to separate tissues and organs into distinct compartments. However, in certain specialized regions, the BMs of neighboring tissues link, helping to bring tissues together. These BM connections can be transient, such as during tissue fusion events in development, or long-term, as with adult tissues involved with filtration, including the blood brain barrier and kidney glomerulus. The transitory nature of these connections in development and the complexity of tissue filtration systems in adults have hindered the understanding of how juxtaposed BMs fasten together. The recent identification of a BM-BM adhesion system in C. elegans, termed B-LINK (BM linkage), however, is revealing cellular and extracellular matrix components of a nascent tissue adhesion system. We discuss insights gained from studying the B-LINK tissue adhesion system in C. elegans, compare this adhesion with other BM-BM connections in Drosophila and vertebrates, and outline important future directions towards elucidating this fascinating and poorly understood mode of adhesion that joins neighboring tissues.
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Affiliation(s)
- Daniel P Keeley
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA
| | - David R Sherwood
- Department of Biology, Regeneration Next, Duke University, Box 90338, Durham, NC 27708, USA.
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Späth MR, Bartram MP, Palacio-Escat N, Hoyer KJR, Debes C, Demir F, Schroeter CB, Mandel AM, Grundmann F, Ciarimboli G, Beyer A, Kizhakkedathu JN, Brodesser S, Göbel H, Becker JU, Benzing T, Schermer B, Höhne M, Burst V, Saez-Rodriguez J, Huesgen PF, Müller RU, Rinschen MM. The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury. Kidney Int 2018; 95:333-349. [PMID: 30522767 DOI: 10.1016/j.kint.2018.08.037] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 01/18/2023]
Abstract
Acute kidney injury (AKI) leads to significant morbidity and mortality; unfortunately, strategies to prevent or treat AKI are lacking. In recent years, several preconditioning protocols have been shown to be effective in inducing organ protection in rodent models. Here, we characterized two of these interventions-caloric restriction and hypoxic preconditioning-in a mouse model of cisplatin-induced AKI and investigated the underlying mechanisms by acquisition of multi-layered omic data (transcriptome, proteome, N-degradome) and functional parameters in the same animals. Both preconditioning protocols markedly ameliorated cisplatin-induced loss of kidney function, and caloric restriction also induced lipid synthesis. Bioinformatic analysis revealed mRNA-independent proteome alterations affecting the extracellular space, mitochondria, and transporters. Interestingly, our analyses revealed a strong dissociation of protein and RNA expression after cisplatin treatment that showed a strong correlation with the degree of damage. N-degradomic analysis revealed that most posttranscriptional changes were determined by arginine-specific proteolytic processing. This included a characteristic cisplatin-activated complement signature that was prevented by preconditioning. Amyloid and acute-phase proteins within the cortical parenchyma showed a similar response. Extensive analysis of disease-associated molecular patterns suggested that transcription-independent deposition of amyloid P-component serum protein may be a key component in the microenvironmental contribution to kidney damage. This proof-of-principle study provides new insights into the pathogenesis of cisplatin-induced AKI and the molecular mechanisms underlying organ protection by correlating phenotypic and multi-layered omics data.
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Affiliation(s)
- Martin R Späth
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Malte P Bartram
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Nicolàs Palacio-Escat
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen, Germany
| | - K Johanna R Hoyer
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Cedric Debes
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Christina B Schroeter
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Amrei M Mandel
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Franziska Grundmann
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Giuliano Ciarimboli
- Department of Experimental Nephrology, University Hospital of Münster, Münster, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Department of Pathology, Centre for Blood Research, The University of British Columbia, British Columbia, Vancouver, Canada; Laboratory Medicine, Department of Chemistry, The University of British Columbia, British Columbia, Vancouver, Canada
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Heike Göbel
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Jan U Becker
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany
| | - Volker Burst
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- COMBINE-Joint Research Center for Computational Biomedicine RWTH Aachen University, Aachen, Germany; Faculty of Medicine Bioquant, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.
| | - Markus M Rinschen
- Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany.
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Looker HC, Merchant ML, Rane MJ, Nelson RG, Kimmel PL, Rovin BH, Klein JB, Mauer M. Urine inositol pentakisphosphate 2-kinase and changes in kidney structure in early diabetic kidney disease in type 1 diabetes. Am J Physiol Renal Physiol 2018; 315:F1484-F1492. [PMID: 30132343 DOI: 10.1152/ajprenal.00183.2018] [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: 11/22/2022] Open
Abstract
We examined the association of urine inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPP2K) with the presence and progression of diabetic kidney disease (DKD) lesions. Urine IPP2K was measured at baseline by quantitative liquid chromatography-mass spectrometry in 215 participants from the Renin-Angiotensin System Study who had type 1 diabetes and were normoalbuminuric and normotensive with normal or increased glomerular filtration rate (GFR). Urine IPP2K was detectable in 166 participants. Participants with IPP2K below the limit of quantification (LOQ) were assigned concentrations of LOQ/√2. All concentrations were then standardized to urine creatinine (Cr) concentration. Kidney morphometric data were available from biopsies at baseline and after 5 yr. Relationships of IPP2K/Cr with morphometric variables were assessed by linear regression after adjustment for age, sex, diabetes duration, hemoglobin A1c, mean arterial pressure, treatment assignment, and, for longitudinal analyses, baseline structure. Baseline mean age was 29.7 yr, mean diabetes duration 11.2 yr, median albumin excretion rate 5.0 μg/min, and mean iohexol GFR 129 ml·min-1·1.73m-2. Higher IPP2K/Cr was associated with higher baseline peripheral glomerular total filtration surface density [Sv(PGBM/glom), tertile 3 vs. tertile 1 β = 0.527, P = 0.011] and with greater preservation of Sv(PGBM/glom) after 5 yr ( tertile 3 vs. tertile 1 β = 0.317, P = 0.013). Smaller increases in mesangial fractional volume ( tertile 3 vs. tertile 1 β = -0.578, P = 0.018) were observed after 5 yr in men with higher urine IPP2K/Cr concentrations. Higher urine IPP2K/Cr is associated with less severe kidney lesions at baseline and with preservation of kidney structure over 5 yr in individuals with type 1 diabetes and no clinical evidence of DKD at baseline.
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Affiliation(s)
- Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases , Phoenix, Arizona
| | - Michael L Merchant
- Division of Nephrology and Hypertension, University of Louisville , Louisville, Kentucky
| | - Madhavi J Rane
- Department of Biochemistry and Molecular Genetics, University of Louisville , Louisville, Kentucky
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases , Phoenix, Arizona
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases , Bethesda, Maryland
| | - Brad H Rovin
- Division of Nephrology, Ohio State University , Columbus, Ohio
| | - Jon B Klein
- Department of Medicine, University of Louisville , Louisville, Kentucky
| | - Michael Mauer
- Division of Renal Diseases and Hypertension, University of Minnesota , Minneapolis, Minnesota
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Cellular and molecular mechanisms of kidney fibrosis. Mol Aspects Med 2018; 65:16-36. [PMID: 29909119 DOI: 10.1016/j.mam.2018.06.002] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/12/2018] [Indexed: 12/14/2022]
Abstract
Renal fibrosis is the final pathological process common to any ongoing, chronic kidney injury or maladaptive repair. It is considered as the underlying pathological process of chronic kidney disease (CKD), which affects more than 10% of world population and for which treatment options are limited. Renal fibrosis is defined by excessive deposition of extracellular matrix, which disrupts and replaces the functional parenchyma that leads to organ failure. Kidney's histological structure can be divided into three main compartments, all of which can be affected by fibrosis, specifically termed glomerulosclerosis in glomeruli, interstitial fibrosis in tubulointerstitium and arteriosclerosis and perivascular fibrosis in vasculature. In this review, we summarized the different appearance, cellular origin and major emerging processes and mediators of fibrosis in each compartment. We also depicted and discussed the challenges in translation of anti-fibrotic treatment to clinical practice and discuss possible solutions and future directions.
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Klein JB, A Knepper M. Protein Mass Spectrometry Made Simple. J Am Soc Nephrol 2018; 29:1585-1587. [PMID: 29724882 DOI: 10.1681/asn.2018030244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Jon B Klein
- University of Louisville School of Medicine and Robley Rex Veterans Administration Medical Center, Louisville, Kentucky; and
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Merchant ML, Brier ME, Slaughter MS, Klein JB, McLeish KR. Biomarker enhanced risk prediction for development of AKI after cardiac surgery. BMC Nephrol 2018; 19:102. [PMID: 29720115 PMCID: PMC5930948 DOI: 10.1186/s12882-018-0902-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/22/2018] [Indexed: 01/18/2023] Open
Abstract
Background Acute kidney injury (AKI) is a common post-cardiac surgery complication and influences patient morbidity and prognosis. This study was designed to identify preoperative candidate urine biomarkers in patients undergoing cardiac surgery. Methods A prospective cohort study of adults undergoing cardiac surgery at increased risk for AKI at a single hospital between July 2010 and September 2012 was performed. The primary outcome was the development of AKI, defined as an absolute serum creatinine (SCr) level increase ≥ 0.5 mg/dL or a ≥ 50% relative increase within 72 h of surgery. A secondary outcome was development of AKI defined by Kidney Disease Improving Global Outcomes (KDIGO). Urine collected by voiding within 4 h prior to surgery was used for proteomic analysis and confirmatory enzyme linked immunosorbent assays (ELISAs) studies. Biomarkers were tested for AKI-prediction using Cox and Snell R2, area under the receiver operating curve (AUROC), and percent of corrected classifications. To evaluate the added effect of each candidate biomarker on AKI discrimination, receiver operator characteristic (ROC) curves, integrated discrimination improvement (IDI), and net reclassification improvement (NRI) were calculated. Results Forty-seven of 755 patients met screening criteria including 15 with AKI. Proteomic analysis identified 29 proteins with a significant ≥2-fold change. Confirmatory ELISA measurements of five candidate markers showed urinary complement factor B (CFB) and histidine rich glycoprotein (HRG) concentrations were significantly increased in patients with AKI. By multivariate analysis, NRI, and IDI the addition of CFB and HRG to the standard clinical assessment significantly improved risk prediction for the primary outcome. Only HRG was a significant predictor in the 21 patients with AKI defined by KDIGO criteria. Conclusions Pre-operative urine measurement of CFB or HRG significantly enhanced the current post-surgery AKI risk stratification for more restrictive definition of AKI. HRG, but not CFB or clinical risk stratification, predicted AKI defined by KDIGO. The ability of these biomarkers to predict risk for dialysis-requiring AKI or death could not be reliably assessed in our study due to a small number of patients with either outcome. Electronic supplementary material The online version of this article (10.1186/s12882-018-0902-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael L Merchant
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Donald Baxter Research Building, Rm 204C, 570 S. Preston Street, Louisville, KY, 40202, USA.
| | - Michael E Brier
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Donald Baxter Research Building, Rm 204C, 570 S. Preston Street, Louisville, KY, 40202, USA
| | - Mark S Slaughter
- Cardiovascular and Thoracic Surgery, University of Louisville School of Medicine, Louisville, USA
| | - Jon B Klein
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Donald Baxter Research Building, Rm 204C, 570 S. Preston Street, Louisville, KY, 40202, USA.,Robley Rex VAMC, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kenneth R McLeish
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Donald Baxter Research Building, Rm 204C, 570 S. Preston Street, Louisville, KY, 40202, USA.,Robley Rex VAMC, University of Louisville School of Medicine, Louisville, KY, USA
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Baba SP, Zhang D, Singh M, Dassanayaka S, Xie Z, Jagatheesan G, Zhao J, Schmidtke VK, Brittian KR, Merchant ML, Conklin DJ, Jones SP, Bhatnagar A. Deficiency of aldose reductase exacerbates early pressure overload-induced cardiac dysfunction and autophagy in mice. J Mol Cell Cardiol 2018; 118:183-192. [PMID: 29627295 PMCID: PMC6205513 DOI: 10.1016/j.yjmcc.2018.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 12/21/2022]
Abstract
Pathological cardiac hypertrophy is associated with the accumulation of lipid peroxidation-derived aldehydes such as 4-hydroxy-trans-2-nonenal (HNE) and acrolein in the heart. These aldehydes are metabolized via several pathways, of which aldose reductase (AR) represents a broad-specificity route for their elimination. We tested the hypothesis that by preventing aldehyde removal, AR deficiency accentuates the pathological effects of transverse aortic constriction (TAC). We found that the levels of AR in the heart were increased in mice subjected to TAC for 2 weeks. In comparison with wild-type (WT), AR-null mice showed lower ejection fraction, which was exacerbated 2 weeks after TAC. Levels of atrial natriuretic peptide and myosin heavy chain were higher in AR-null than in WT TAC hearts. Deficiency of AR decreased urinary levels of the acrolein metabolite, 3-hydroxypropylmercapturic acid. Deletion of AR did not affect the levels of the other aldehyde-metabolizing enzyme - aldehyde dehydrogenase 2 in the heart, or its urinary product - (N-Acetyl-S-(2-carboxyethyl)-l-cystiene). AR-null hearts subjected to TAC showed increased accumulation of HNE- and acrolein-modified proteins, as well as increased AMPK phosphorylation and autophagy. Superfusion with HNE led to a greater increase in p62, LC3II formation, and GFP-LC3-II punctae formation in AR-null than WT cardiac myocytes. Pharmacological inactivation of JNK decreased HNE-induced autophagy in AR-null cardiac myocytes. Collectively, these results suggest that during hypertrophy the accumulation of lipid peroxidation derived aldehydes promotes pathological remodeling via excessive autophagy, and that metabolic detoxification of these aldehydes by AR may be essential for maintaining cardiac function during early stages of pressure overload.
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Affiliation(s)
- Shahid P Baba
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States.
| | - Deqing Zhang
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Mahavir Singh
- Department of Physiology, University of Louisville, Louisville, KY, United States
| | - Sujith Dassanayaka
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Zhengzhi Xie
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Ganapathy Jagatheesan
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Jingjing Zhao
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Virginia K Schmidtke
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Kenneth R Brittian
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Michael L Merchant
- Divisions of Nephrology and Hypertension and the Institute of Molecular Cardiology, University of Louisville, Louisville, KY, United States
| | - Daniel J Conklin
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Steven P Jones
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
| | - Aruni Bhatnagar
- Diabetes and Obesity Center, University of Louisville, Louisville, KY, United States
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Salmon CR, Giorgetti APO, Paes Leme AF, Domingues RR, Kolli TN, Foster BL, Nociti FH. Microproteome of dentoalveolar tissues. Bone 2017; 101:219-229. [PMID: 28527949 DOI: 10.1016/j.bone.2017.05.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/12/2017] [Accepted: 05/15/2017] [Indexed: 01/18/2023]
Abstract
Proteomic analysis of extracellular matrices (ECM) of dentoalveolar tissues can provide insights into developmental, pathological, and reparative processes. However, targeted dissection of mineralized tissues, dental cementum (DC), alveolar bone (AB), and dentin (DE), presents technical difficulties. We demonstrate an approach combining EDTA decalcification and laser capture microdissection (LCM), followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), to analyze proteome profiles of these tissues. Using the LCM-LC-MS/MS approach, a total of 243 proteins was identified from all tissues, 193 proteins in DC, 147 in AB, and 135 proteins DE. Ninety proteins (37% of total) were common to all tissues, whereas 52 proteins (21%) were overlapping in only two. Also, 101 (42%) proteins were exclusively detected in DC (60), AB (15), or DE (26). Identification in all tissues of expected ECM proteins including collagen alpha-1(I) chain (COL1A1), collagen alpha-1(XII) chain (COL12A1), biglycan (BGN), asporin (ASPN), lumican (LUM), and fibromodulin (FMOD), served to validate the approach. Principal component analysis (PCA) and hierarchical clustering identified a high degree of similarity in DC and AB proteomes, whereas DE presented a distinct dataset. Exclusively and differentially identified proteins were detected from all three tissues. The protein-protein interaction network (interactome) of DC was notable for its inclusion of several indicators of metabolic function (e.g. mitochondrial proteins, protein synthesis, and calcium transport), possibly reflecting cementocyte activity. The DE proteome included known and novel mineralization regulators, including matrix metalloproteinase 20 (MMP-20), 5' nucleotidase (NT5E), and secreted phosphoprotein 24 (SPP-24 or SPP-2). Application of the LCM-LC-MS/MS approach to dentoalveolar tissues would be of value in many experimental designs, including developmental studies of transgenic animals, investigation of treatment effects, and identification of novel regenerative factors.
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Affiliation(s)
- Cristiane R Salmon
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil
| | - Ana Paula O Giorgetti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil
| | - Adriana F Paes Leme
- National Biosciences Laboratory, Brazilian Synchrotron Light Laboratory, Campinas, SP, Brazil
| | - Romênia R Domingues
- National Biosciences Laboratory, Brazilian Synchrotron Light Laboratory, Campinas, SP, Brazil
| | - Tamara N Kolli
- Biosciences Division, College of Dentistry, Ohio State University, Columbus, OH, United States
| | - Brian L Foster
- Biosciences Division, College of Dentistry, Ohio State University, Columbus, OH, United States
| | - Francisco H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil.
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Abstract
The phospholipase A2 receptor (PLA2R) and thrombospondin type-1 domain-containing 7A (THSD7A) are the two major autoantigens in primary membranous nephropathy (MN), and define two molecular subclasses of this disease. Both proteins are large transmembrane glycoproteins expressed by the podocyte, and both induce IgG4-predominant humoral immune responses that produce circulating autoantibodies that can be used clinically for diagnostic and monitoring purposes. The biologic roles of these proteins remain speculative, although several features of THSD7A suggest a role in adhesion. PLA2R-associated MN was initially found to associate with risk alleles within HLA-DQA1, but subsequent studies have shifted the focus to the HLA-DRB locus. Three distinct humoral epitope-containing regions have been defined within the extracellular portion of PLA2R, and it appears that the number of targeted epitopes may determine disease severity. Although similar information is not yet available for THSD7A-associated MN, this form of MN may have a unique association with malignancy. Finally, it appears likely that other autoantigens in primary MN exist. Although protocols similar to those that identified PLA2R and THSD7A may be successful in the identification of novel antigenic targets in MN, newer techniques such as laser-capture mass spectrometry or protein arrays may be helpful as well.
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Affiliation(s)
- Laurence H Beck
- Renal Section, Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts
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Klein JB. Applying proteomics to detect early signs of chronic kidney disease: where has the magic gone? Expert Rev Proteomics 2017; 14:387-390. [PMID: 28363249 DOI: 10.1080/14789450.2017.1315303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jon B Klein
- a Division of Nephrology and Hypertension , University of Louisville School of Medicine , Louisville , KY , USA
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