1
|
Kostopoulou E, Kalavrizioti D, Davoulou P, Papachristou E, Sinopidis X, Fouzas S, Dassios T, Gkentzi D, Kyriakou SI, Karatza A, Dimitriou G, Goumenos D, Spiliotis BE, Plotas P, Papasotiriou M. Monocyte Chemoattractant Protein-1 (MCP-1), Activin-A and Clusterin in Children and Adolescents with Obesity or Type-1 Diabetes Mellitus. Diagnostics (Basel) 2024; 14:450. [PMID: 38396489 PMCID: PMC10887959 DOI: 10.3390/diagnostics14040450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/04/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Inflammation plays a crucial role in diabetes and obesity through macrophage activation. Macrophage chemoattractant protein-1 (MCP-1), activin-A, and clusterin are chemokines with known roles in diabetes and obesity. The aim of this study is to investigate their possible diagnostic and/or early prognostic values in children and adolescents with obesity and type-1 diabetes mellitus (T1DM). METHODS We obtained serum samples from children and adolescents with a history of T1DM or obesity, in order to measure and compare MCP-1, activin-A, and clusterin concentrations. RESULTS Forty-three subjects were included in each of the three groups (controls, T1DM, and obesity). MCP-1 values were positively correlated to BMI z-score. Activin-A was increased in children with obesity compared to the control group. A trend for higher values was detected in children with T1DM. MCP-1 and activin-A levels were positively correlated. Clusterin levels showed a trend towards lower values in children with T1DM or obesity compared to the control group and were negatively correlated to renal function. CONCLUSIONS The inflammation markers MCP-1, activin-A, and clusterin are not altered in children with T1DM. Conversely, obesity in children is positively correlated to serum MCP-1 values and characterized by higher activin-A levels, which may reflect an already established systematic inflammation with obesity since childhood.
Collapse
Affiliation(s)
- Eirini Kostopoulou
- Division of Pediatric Endocrinology, Department of Pediatrics, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (E.K.); (B.E.S.)
| | - Dimitra Kalavrizioti
- Department of Nephrology and Kidney Transplantation, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (D.K.); (P.D.); (E.P.); (D.G.); (M.P.)
| | - Panagiota Davoulou
- Department of Nephrology and Kidney Transplantation, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (D.K.); (P.D.); (E.P.); (D.G.); (M.P.)
| | - Evangelos Papachristou
- Department of Nephrology and Kidney Transplantation, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (D.K.); (P.D.); (E.P.); (D.G.); (M.P.)
| | - Xenophon Sinopidis
- Department of Pediatric Surgery, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece;
| | - Sotirios Fouzas
- Department of Pediatrics, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (S.F.); (T.D.); (D.G.); (A.K.); (G.D.)
| | - Theodore Dassios
- Department of Pediatrics, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (S.F.); (T.D.); (D.G.); (A.K.); (G.D.)
| | - Despoina Gkentzi
- Department of Pediatrics, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (S.F.); (T.D.); (D.G.); (A.K.); (G.D.)
| | - Stavroula Ioanna Kyriakou
- Department of Pediatric Surgery, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece;
| | - Ageliki Karatza
- Department of Pediatrics, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (S.F.); (T.D.); (D.G.); (A.K.); (G.D.)
| | - Gabriel Dimitriou
- Department of Pediatrics, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (S.F.); (T.D.); (D.G.); (A.K.); (G.D.)
| | - Dimitrios Goumenos
- Department of Nephrology and Kidney Transplantation, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (D.K.); (P.D.); (E.P.); (D.G.); (M.P.)
| | - Bessie E. Spiliotis
- Division of Pediatric Endocrinology, Department of Pediatrics, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (E.K.); (B.E.S.)
| | - Panagiotis Plotas
- Department of Speech and Language Therapy, School of Health Rehabilitation Sciences, University of Patras, 26504 Patras, Greece;
| | - Marios Papasotiriou
- Department of Nephrology and Kidney Transplantation, University Hospital of Patras, School of Medicine, University of Patras, 26504 Patras, Greece; (D.K.); (P.D.); (E.P.); (D.G.); (M.P.)
| |
Collapse
|
2
|
Tserga A, Saulnier-Blache JS, Palamaris K, Pouloudi D, Gakiopoulou H, Zoidakis J, Schanstra JP, Vlahou A, Makridakis M. Complement Cascade Proteins Correlate with Fibrosis and Inflammation in Early-Stage Type 1 Diabetic Kidney Disease in the Ins2Akita Mouse Model. Int J Mol Sci 2024; 25:1387. [PMID: 38338666 PMCID: PMC10855735 DOI: 10.3390/ijms25031387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Diabetic kidney disease (DKD) is characterized by histological changes including fibrosis and inflammation. Evidence supports that DKD is mediated by the innate immune system and more specifically by the complement system. Using Ins2Akita T1D diabetic mice, we studied the connection between the complement cascade, inflammation, and fibrosis in early DKD. Data were extracted from a previously published quantitative-mass-spectrometry-based proteomics analysis of kidney glomeruli of 2 (early DKD) and 4 months (moderately advanced DKD)-old Ins2Akita mice and their controls A Spearman rho correlation analysis of complement- versus inflammation- and fibrosis-related protein expression was performed. A cross-omics validation of the correlation analyses' results was performed using public-domain transcriptomics datasets (Nephroseq). Tissue sections from 43 patients with DKD were analyzed using immunofluorescence. Among the differentially expressed proteins, the complement cascade proteins C3, C4B, and IGHM were significantly increased in both early and later stages of DKD. Inflammation-related proteins were mainly upregulated in early DKD, and fibrotic proteins were induced in moderately advanced stages of DKD. The abundance of complement proteins with fibrosis- and inflammation-related proteins was mostly positively correlated in early stages of DKD. This was confirmed in seven additional human and mouse transcriptomics DKD datasets. Moreover, C3 and IGHM mRNA levels were found to be negatively correlated with the estimated glomerular filtration rate (range for C3 rs = -0.58 to -0.842 and range for IGHM rs = -0.6 to -0.74) in these datasets. Immunohistology of human kidney biopsies revealed that C3, C1q, and IGM proteins were induced in patients with DKD and were correlated with fibrosis and inflammation. Our study shows for the first time the potential activation of the complement cascade associated with inflammation-mediated kidney fibrosis in the Ins2Akita T1D mouse model. Our findings could provide new perspectives for the treatment of early DKD as well as support the use of Ins2Akita T1D in pre-clinical studies.
Collapse
Affiliation(s)
- Aggeliki Tserga
- Biomedical Research Foundation, Academy of Athens, Department of Biotechnology, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (J.Z.); (A.V.)
| | - Jean Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France; (J.S.S.-B.); (J.P.S.)
- Department of Biology, Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Kostantinos Palamaris
- 1st Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 34400 Athens, Greece; (K.P.); (D.P.); (H.G.)
| | - Despoina Pouloudi
- 1st Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 34400 Athens, Greece; (K.P.); (D.P.); (H.G.)
| | - Harikleia Gakiopoulou
- 1st Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 34400 Athens, Greece; (K.P.); (D.P.); (H.G.)
| | - Jerome Zoidakis
- Biomedical Research Foundation, Academy of Athens, Department of Biotechnology, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (J.Z.); (A.V.)
- Department of Biology, National and Kapodistrian University of Athens, 15701 Zografou, Greece
| | - Joost Peter Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR1297, Institute of Cardiovascular and Metabolic Disease, 31432 Toulouse, France; (J.S.S.-B.); (J.P.S.)
- Department of Biology, Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens, Department of Biotechnology, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (J.Z.); (A.V.)
| | - Manousos Makridakis
- Biomedical Research Foundation, Academy of Athens, Department of Biotechnology, Soranou Efessiou 4, 11527 Athens, Greece; (A.T.); (J.Z.); (A.V.)
| |
Collapse
|
3
|
Viggiano D. Mechanisms of Diabetic Nephropathy Not Mediated by Hyperglycemia. J Clin Med 2023; 12:6848. [PMID: 37959313 PMCID: PMC10650633 DOI: 10.3390/jcm12216848] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Diabetes mellitus (DM) is characterized by the appearance of progressive kidney damage, which may progress to end-stage kidney disease. The control of hyperglycemia is usually not sufficient to halt this progression. The kidney damage is quantitatively and qualitatively different in the two forms of diabetes; the typical nodular fibrosis (Kimmelstiel Wilson nodules) appears mostly in type 1 DM, whereas glomerulomegaly is primarily present in type 2 obese DM. An analysis of the different metabolites and hormones in type 1 and type 2 DM and their differential pharmacological treatments might be helpful to advance the hypotheses on the different histopathological patterns of the kidneys and their responses to sodium/glucose transporter type 2 inhibitors (SGLT2i).
Collapse
Affiliation(s)
- Davide Viggiano
- Department of Translational Medical Sciences, University of Campania, 80131 Naples, Italy
| |
Collapse
|
4
|
Kipp A, Marti HP, Babickova J, Nakken S, Leh S, Halden TAS, Jenssen T, Vikse BE, Åsberg A, Spagnoli G, Furriol J. Glomerular proteomic profiling reveals early differences between preexisting and de novo type 2 diabetes in human renal allografts. BMC Nephrol 2023; 24:254. [PMID: 37626301 PMCID: PMC10464146 DOI: 10.1186/s12882-023-03294-z] [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: 06/28/2022] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Diabetes mellitus (DM), either preexisting or developing after transplantation, remains a crucial clinical problem in kidney transplantation. To obtain insights into the molecular mechanisms underlying PTDM development and early glomerular damage before the development of histologically visible diabetic kidney disease, we comparatively analysed the proteome of histologically normal glomeruli from patients with PTDM and normoglycaemic (NG) transplant recipients. Moreover, to assess specificities inherent in PTDM, we also comparatively evaluated glomerular proteomes from transplant recipients with preexisting type 2 DM (T2DM). METHODS Protocol biopsies were obtained from adult NG, PTDM and T2DM patients one year after kidney transplantation. Biopsies were formalin-fixed and embedded in paraffin, and glomerular cross-sections were microdissected. A total of 4 NG, 7 PTDM and 6 T2DM kidney biopsies were used for the analysis. The proteome was determined by liquid chromatography-tandem mass spectrometry. Relative differences in protein abundance and significantly dysregulated pathways were analysed. RESULTS Proteins involved in cell adhesion, immune response, leukocyte transendothelial filtration, and cell localization and organization were less abundant in glomeruli from PTDM patients than in those from NG patients, and proteins associated with supramolecular fibre organization and protein-containing complex binding were more abundant in PTDM patients. Overall, proteins related to adherens and tight junctions and those related to the immune system, including leukocyte transendothelial migration, were more abundant in NG patients than in transplanted patients with DM, irrespective of the timing of its development. However, proteins included in cell‒cell junctions and adhesion, insulin resistance, and vesicle-mediated transport were all less abundant in PTDM patients than in T2DM patients. CONCLUSIONS The glomerular proteome profile differentiates PTDM from NG and T2DM, suggesting specific pathogenetic mechanisms. Further studies are warranted to validate these results, potentially leading to an improved understanding of PTDM kidney transplant pathophysiology and to the identification of novel biomarkers.
Collapse
Affiliation(s)
- Anne Kipp
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Janka Babickova
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Sigrid Nakken
- 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
| | - Thea A S Halden
- Department of Transplantation Medicine, Oslo University Hospital, Rikshospitalet and University of Oslo, Oslo, Norway
| | - Trond Jenssen
- Department of Transplantation Medicine, Oslo University Hospital, Rikshospitalet and University of Oslo, Oslo, Norway
- Metabolic and Renal Research Group, Faculty of Health Sciences UiT, The Arctic University of Norway, Tromsø, Norway
| | - Bjørn Egil Vikse
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Medicine, Haugesund Hospital, Haugesund, Norway
| | - Anders Åsberg
- Department of Transplantation Medicine, Oslo University Hospital, Rikshospitalet and University of Oslo, Oslo, Norway
- Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Giulio Spagnoli
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Jessica Furriol
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.
- Department of Medicine, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
5
|
Wei L, Han Y, Tu C. Molecular Pathways of Diabetic Kidney Disease Inferred from Proteomics. Diabetes Metab Syndr Obes 2023; 16:117-128. [PMID: 36760602 PMCID: PMC9842482 DOI: 10.2147/dmso.s392888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023] Open
Abstract
Diabetic kidney disease (DKD) affects an estimated 20-40% of type 2 diabetes patients and is among the most prevalent microvascular complications in this patient population, contributing to high morbidity and mortality rates. Currently, changes in albuminuria status are thought to be a primary indicator of the onset or progression of DKD, yet progressive nephropathy and renal impairment can occur in certain diabetic individuals who exhibit normal urinary albumin levels, emphasizing the lack of sensitivity and specificity associated with the use of albuminuria as a biomarker for detecting diabetic kidney disease and predicting DKD risk. According to the study, a non-invasive method for early detection or prediction of DKD may involve combining proteomic analytical techniques such second generation sequencing, mass spectrometry, two-dimensional gel electrophoresis, and other advanced system biology algorithms. Another category of proteins of relevance may now be provided by renal tissue biomarkers. The establishment of reliable proteomic biomarkers of DKD represents a novel approach to improving the diagnosis, prognostic evaluation, and treatment of affected patients. In the present review, a series of protein biomarkers that have been characterized to date are discussed, offering a theoretical foundation for future efforts to aid patients suffering from this debilitating microvascular complication.
Collapse
Affiliation(s)
- Lan Wei
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, People’s Republic of China
| | - Chao Tu
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
- Correspondence: Chao Tu, Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, 213000, People’s Republic of China, Email
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Dooling LJ, Saini K, Anlaş AA, Discher DE. Tissue mechanics coevolves with fibrillar matrisomes in healthy and fibrotic tissues. Matrix Biol 2022; 111:153-188. [PMID: 35764212 PMCID: PMC9990088 DOI: 10.1016/j.matbio.2022.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 12/12/2022]
Abstract
Fibrillar proteins are principal components of extracellular matrix (ECM) that confer mechanical properties to tissues. Fibrosis can result from wound repair in nearly every tissue in adults, and it associates with increased ECM density and crosslinking as well as increased tissue stiffness. Such fibrotic tissues are a major biomedical challenge, and an emerging view posits that the altered mechanical environment supports both synthetic and contractile myofibroblasts in a state of persistent activation. Here, we review the matrisome in several fibrotic diseases, as well as normal tissues, with a focus on physicochemical properties. Stiffness generally increases with the abundance of fibrillar collagens, the major constituent of ECM, with similar mathematical trends for fibrosis as well as adult tissues from soft brain to stiff bone and heart development. Changes in expression of other core matrisome and matrisome-associated proteins or proteoglycans contribute to tissue stiffening in fibrosis by organizing collagen, crosslinking ECM, and facilitating adhesion of myofibroblasts. Understanding how ECM composition and mechanics coevolve during fibrosis can lead to better models and help with antifibrotic therapies.
Collapse
Affiliation(s)
- Lawrence J Dooling
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA
| | - Karanvir Saini
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA
| | - Alişya A Anlaş
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA
| | - Dennis E Discher
- Molecular and Cellular Biophysics Lab, University of Pennsylvania,Philadelphia, PA 19104, USA.
| |
Collapse
|
8
|
Ma J, Bi L, Spurlin J, Lwigale P. Nephronectin-Integrin α8 signaling is required for proper migration of periocular neural crest cells during chick corneal development. eLife 2022; 11:74307. [PMID: 35238772 PMCID: PMC8916771 DOI: 10.7554/elife.74307] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/02/2022] [Indexed: 11/19/2022] Open
Abstract
During development, cells aggregate at tissue boundaries to form normal tissue architecture of organs. However, how cells are segregated into tissue precursors remains largely unknown. Cornea development is a perfect example of this process whereby neural crest cells aggregate in the periocular region prior to their migration and differentiation into corneal cells. Our recent RNA-seq analysis identified upregulation of nephronectin (Npnt) transcripts during early stages of corneal development where its function has not been investigated. We found that Npnt mRNA and protein are expressed by various ocular tissues, including the migratory periocular neural crest (pNC), which also express the integrin alpha 8 (Itgα8) receptor. Knockdown of either Npnt or Itgα8 attenuated cornea development, whereas overexpression of Npnt resulted in cornea thickening. Moreover, overexpression of Npnt variants lacking RGD-binding sites did not affect corneal thickness. Neither the knockdown nor augmentation of Npnt caused significant changes in cell proliferation, suggesting that Npnt directs pNC migration into the cornea. In vitro analyses showed that Npnt promotes pNC migration from explanted periocular mesenchyme, which requires Itgα8, focal adhesion kinase, and Rho kinase. Combined, these data suggest that Npnt augments cell migration into the presumptive cornea extracellular matrix by functioning as a substrate for Itgα8-positive pNC cells.
Collapse
Affiliation(s)
- Justin Ma
- Department of Biosciences, Rice University, Houston, United States
| | - Lian Bi
- Department of Biosciences, Rice University, Houston, United States
| | - James Spurlin
- Department of Biosciences, Rice University, Houston, United States
| | - Peter Lwigale
- Department of Biosciences, Rice University, Houston, United States
| |
Collapse
|
9
|
Clotet-Freixas S, Konvalinka A. Too Little or Too Much? Extracellular Matrix Remodeling in Kidney Health and Disease. J Am Soc Nephrol 2021; 32:1541-1543. [PMID: 34135080 PMCID: PMC8425646 DOI: 10.1681/asn.2021050654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Affiliation(s)
- Sergi Clotet-Freixas
- Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Renal Transplant Program, Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, Ontario, Canada
| | - Ana Konvalinka
- Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Renal Transplant Program, Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, Ontario, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, Alberta, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Nephronectin as a Matrix Effector in Cancer. Cancers (Basel) 2021; 13:cancers13050959. [PMID: 33668838 PMCID: PMC7956348 DOI: 10.3390/cancers13050959] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary The extracellular matrix provides an important scaffold for cells and tissues of multicellular organisms. The scaffold not only provides a secure anchorage point, but also functions as a reservoir for signalling molecules, sequestered and released when necessary. A dysregulated extracellular matrix may therefore modulate cellular behaviour, as seen during cancer progression. The extracellular matrix protein nephronectin was discovered two decades ago and found to regulate important embryonic developmental processes. Loss of either nephronectin or its receptor, integrin α8β1, leads to underdeveloped kidneys. Recent findings show that nephronectin is also dysregulated in breast cancer and plays a role in promoting metastasis. To enable therapeutic intervention, it is important to fully understand the role of nephronectin and its receptors in cancer progression. In this review, we summarise the literature on nephronectin, analyse the structure and domain-related functions of nephronectin and link these functions to potential roles in cancer progression. Abstract The extracellular matrix protein nephronectin plays an important regulatory role during embryonic development, controlling renal organogenesis through integrin α8β1 association. Nephronectin has three main domains: five N-terminal epidermal growth factor-like domains, a linker region harbouring two integrin-binding motifs (RGD and LFEIFEIER), and a C-terminal MAM domain. In this review, we look into the domain-related functions of nephronectin, and tissue distribution and expression. During the last two decades it has become evident that nephronectin also plays a role during cancer progression and in particular metastasis. Nephronectin is overexpressed in both human and mouse breast cancer compared to normal breast tissue where the protein is absent. Cancer cells expressing elevated levels of nephronectin acquire increased ability to colonise distant organs. In particular, the enhancer-motif (LFEIFEIER) which is specific to the integrin α8β1 association induces viability via p38 MAPK and plays a role in colonization. Integrins have long been desired as therapeutic targets, where low efficiency and receptor redundancy have been major issues. Based on the summarised publications, the enhancer-motif of nephronectin could present a novel therapeutic target.
Collapse
|
12
|
Glomerular clusterin expression is increased in diabetic nephropathy and protects against oxidative stress-induced apoptosis in podocytes. Sci Rep 2020; 10:14888. [PMID: 32913257 PMCID: PMC7484791 DOI: 10.1038/s41598-020-71629-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Clusterin, a glycoprotein encoded by the CLU gene, is expressed in many tissues, including the kidney, and clusterin expression is upregulated in the glomeruli of patients with various forms of kidney disease. Here, we investigated the role of clusterin in diabetic nephropathy (DN). In this study, we found that glomerular clusterin expression was increased in both patients with DN and streptozotocin-induced diabetic mice and that it co-localised with the podocyte marker WT1, indicating clusterin is expressed in podocytes. In our in vitro analysis, we found no significant change in CLU mRNA expression in podocytes following stimulation with high glucose and angiotensin II; in contrast, CLU mRNA expression was significantly upregulated following methylglyoxal stimulation. Methylglyoxal treatment also significantly decreased the mRNA expression of the slit diaphragm markers ZO-1 and NEPH1 and significantly increased the mRNA expression of the oxidative stress marker HO-1. Lastly, we showed that pre-incubating podocytes with recombinant human clusterin protein increased podocyte survival, prevented slit diaphragm damage, and reduced oxidative stress‒induced apoptosis following methylglyoxal stimulation. Taken together, our results indicate that glomerular clusterin is upregulated in DN, and this increase in clusterin expression may protect against oxidative stress-induced apoptosis in podocytes, providing a possible new therapeutic target for DN and other kidney diseases.
Collapse
|
13
|
Amarnani A, Capri JR, Souda P, Elashoff DA, Lopez IA, Whitelegge JP, Singh RR. Quantitative Proteomics Using Formalin-fixed, Paraffin-embedded Biopsy Tissues in Inflammatory Disease. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2019; 12:104-112. [PMID: 32431480 PMCID: PMC7236785 DOI: 10.35248/0974-276x.12.19.503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Investigations in human disease pathogenesis have been hampered due to paucity of access to fresh-frozen tissues (FFT) for use in global, data-driven methodologies. As an alternative, formalin-fixed, paraffin-embedded (FFPE) tissues are readily available in pathology banks. However, the use of formalin for fixation can lead to the loss of proteins that appear during inflammation, thus introducing an inherent sample bias. To address this, we compared FF and FFPE tissue proteomics to determine whether FFPE-tissue can be used effectively in inflammatory diseases. METHODS Adjacent kidney slices from lupus nephritic mice were processed as FFPE or FFTs. Their tissue lysates were run together using proteomics workflow involving filter-aided sample preparation, in-solution dimethyl isotope labeling, StageTip fractionation, and nano-LC MS/MS through an Orbitrap XL MS. RESULTS We report a >97% concordance in protein identification between adjacent FFPE and FFTs in murine lupus nephritic kidneys. Specifically, proteins representing pathways, namely, 'systemic lupus erythematosus', 'interferon-α', 'TGF-β', and 'extracellular matrix', were reproducibly quantified between FFPE and FFTs. However, 12%-29% proteins were quantified differently in FFPE compared to FFTs, but the differences were consistent across experiments. In particular, certain proteins represented in pathways, including 'inflammatory response' and 'innate immune system' were quantified less in FFPE than in FFTs. In a pilot study of human FFPE tissues, we identified proteins relevant to pathogenesis in lupus nephritic kidney biopsies compared to control kidneys. CONCLUSION This is the first report of lupus nephritis kidney proteomics using FFPE tissue. We concluded that archived FFPE tissues can be reliably used for proteomic analyses in inflammatory diseases, with a caveat that certain proteins related to immunity and inflammation may be quantified less in FFPE than in FFTs.
Collapse
Affiliation(s)
- Abhimanyu Amarnani
- Department of Head and Neck Surgery, UCLA, Los Angeles, CA 90095, USA
- Department of Medicine/Rheumatology, UCLA, Los Angeles, CA 90095, USA
| | - Joseph R. Capri
- The Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, CA 90024, USA
| | - Puneet Souda
- The Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, CA 90024, USA
| | - David A. Elashoff
- Department of Medicine/Statistics Core, UCLA, Los Angeles, CA 90095, USA
| | - Ivan A. Lopez
- Department of Head and Neck Surgery, UCLA, Los Angeles, CA 90095, USA
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, CA 90024, USA
| | - Ram R. Singh
- Department of Medicine/Rheumatology, UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
- Molecular Toxicology Interdepartmental Program, UCLA, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| |
Collapse
|
14
|
Giusti L, Angeloni C, Lucacchini A. Update on proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2019; 16:513-520. [DOI: 10.1080/14789450.2019.1615452] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Laura Giusti
- School of Pharmacy, University of Camerino, Camerino, Italy
| | | | - Antonio Lucacchini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| |
Collapse
|
15
|
Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics. J Pharm Biomed Anal 2018; 155:125-134. [PMID: 29627729 DOI: 10.1016/j.jpba.2018.03.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 02/07/2023]
Abstract
More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field.
Collapse
|
16
|
Zimmerman SE, Hiremath C, Tsunezumi J, Yang Z, Finney B, Marciano DK. Nephronectin Regulates Mesangial Cell Adhesion and Behavior in Glomeruli. J Am Soc Nephrol 2018; 29:1128-1140. [PMID: 29335243 DOI: 10.1681/asn.2017070752] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/13/2017] [Indexed: 01/03/2023] Open
Abstract
A critical aspect of kidney function occurs at the glomerulus, the capillary network that filters the blood. The glomerular basement membrane (GBM) is a key component of filtration, yet our understanding of GBM interactions with mesangial cells, specialized pericytes that provide structural stability to glomeruli, is limited. We investigated the role of nephronectin (Npnt), a GBM component and known ligand of α8β1 integrin. Immunolocalization and in situ hybridization studies in kidneys of adult mice revealed that nephronectin is produced by podocytes and deposited into the GBM. Conditional deletion of Npnt from nephron progenitors caused a pronounced increase in mesangial cell number and mesangial sclerosis. Nephronectin colocalized with α8β1 integrin to novel, specialized adhesion structures that occurred at sites of mesangial cell protrusion at the base of the capillary loops. Absence of nephronectin disrupted these adhesion structures, leading to mislocalization of α8β1. Podocyte-specific deletion of Npnt also led to mesangial sclerosis in mice. These results demonstrate a novel role for nephronectin and α8β1 integrin in a newly described adhesion complex and begin to uncover the molecular interactions between the GBM and mesangial cells, which govern mesangial cell behavior and may have a role in pathologic states.
Collapse
Affiliation(s)
- Susan E Zimmerman
- Division of Nephrology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Chitkale Hiremath
- Division of Nephrology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jun Tsunezumi
- Division of Nephrology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zhufeng Yang
- Division of Nephrology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Bronwyn Finney
- Division of Nephrology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Denise K Marciano
- Division of Nephrology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| |
Collapse
|
17
|
Tang J, Saito T. Nephronectin Stimulates the Differentiation of MDPC-23 Cells into an Odontoblast-like Phenotype. J Endod 2018; 43:263-271. [PMID: 28132711 DOI: 10.1016/j.joen.2016.10.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 10/18/2016] [Accepted: 10/22/2016] [Indexed: 12/29/2022]
Abstract
INTRODUCTION The present study investigated the in vitro effects of nephronectin (Npnt) on the proliferation, differentiation, and mineralization of a rat odontoblast-like cell line (MDPC-23 cells). METHODS MDPC-23 cells were cultured on Npnt-coated polystyrene or in the presence of soluble Npnt. Cell proliferation was analyzed using a Cell Counting Kit-8 kit (Dojindo, Kumamoto, Japan). Alkaline phosphatase (ALP) activity was quantified using an ALP activity assay. A reverse-transcription polymerase chain reaction was performed to evaluate the messenger RNA (mRNA) expression level of odontogenic markers and integrin(s). Alizarin red staining was conducted to quantify the calcium deposition. RESULTS Soluble Npnt had no adverse effect on the proliferation of MDPC-23 cells, but it exhibited concentration-dependent inhibitory activity toward differentiation. In contrast, coated Npnt promoted cell proliferation dramatically and significantly up-regulated the mRNA expression of odontogenesis-related genes; moreover, mRNA expression of integrin α1, α3, α5, β1, and β5 was found to be augmented. MDPC-23 cells cultured on Npnt-coated polystyrene displayed markedly higher ALP activity as early as day 3 after inoculation. In addition, mineralization was accelerated on Npnt-coated polystyrene. CONCLUSIONS Npnt in its immobilized form enhanced the proliferation of MDPC-23 cells and induced this odontoblastic precursor cell line to differentiate into a mineralizing phenotype.
Collapse
Affiliation(s)
- Jia Tang
- Division of Clinical Cariology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan.
| | - Takashi Saito
- Division of Clinical Cariology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| |
Collapse
|
18
|
Sun Y, Kuek V, Qiu H, Tickner J, Chen L, Wang H, He W, Xu J. The emerging role of NPNT in tissue injury repair and bone homeostasis. J Cell Physiol 2017; 233:1887-1894. [DOI: 10.1002/jcp.26013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 05/15/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Youqiang Sun
- The National Key Discipline and the Orthopedic Laboratory; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
- Department of Orthopedics, First Affiliated Hospital; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
- School of Pathology and Laboratory Medicine; The University of Western Australia; Perth WA Australia
| | - Vincent Kuek
- School of Pathology and Laboratory Medicine; The University of Western Australia; Perth WA Australia
| | - Heng Qiu
- School of Pathology and Laboratory Medicine; The University of Western Australia; Perth WA Australia
| | - Jennifer Tickner
- School of Pathology and Laboratory Medicine; The University of Western Australia; Perth WA Australia
| | - Leilei Chen
- The National Key Discipline and the Orthopedic Laboratory; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
- Department of Orthopedics, First Affiliated Hospital; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
| | - Haibin Wang
- The National Key Discipline and the Orthopedic Laboratory; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
- Department of Orthopedics, First Affiliated Hospital; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
| | - Wei He
- The National Key Discipline and the Orthopedic Laboratory; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
- Department of Orthopedics, First Affiliated Hospital; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
| | - Jiake Xu
- The National Key Discipline and the Orthopedic Laboratory; Guangzhou University of Chinese Medicine; Guangzhou Guangdong P. R. China
- School of Pathology and Laboratory Medicine; The University of Western Australia; Perth WA Australia
| |
Collapse
|
19
|
Müller-Deile J, Dannenberg J, Schroder P, Lin MH, Miner JH, Chen R, Bräsen JH, Thum T, Nyström J, Staggs LB, Haller H, Fiedler J, Lorenzen JM, Schiffer M. Podocytes regulate the glomerular basement membrane protein nephronectin by means of miR-378a-3p in glomerular diseases. Kidney Int 2017; 92:836-849. [PMID: 28476557 DOI: 10.1016/j.kint.2017.03.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/11/2017] [Accepted: 03/02/2017] [Indexed: 01/03/2023]
Abstract
The pathophysiology of many proteinuric kidney diseases is poorly understood, and microRNAs (miRs) regulation of these diseases has been largely unexplored. Here, we tested whether miR-378a-3p is a novel regulator of glomerular diseases. MiR-378a-3p has two predicted targets relevant to glomerular function, the glomerular basement membrane matrix component, nephronectin (NPNT), and vascular endothelial growth factor VEGF-A. In zebrafish (Danio rerio), miR-378a-3p mimic injection or npnt knockdown by a morpholino oligomer caused an identical phenotype consisting of edema, proteinuria, podocyte effacement, and widening of the glomerular basement membrane in the lamina rara interna. Zebrafish vegf-A protein could not rescue this phenotype. However, mouse Npnt constructs containing a mutated 3'UTR region prevented the phenotype caused by miR-378a-3p mimic injection. Overexpression of miR-378a-3p in mice confirmed glomerular dysfunction in a mammalian model. Biopsies from patients with focal segmental glomerulosclerosis and membranous nephropathy had increased miR-378a-3p expression and reduced glomerular levels of NPNT. Thus, miR-378a-3p-mediated suppression of the glomerular matrix protein NPNT is a novel mechanism for proteinuria development in active glomerular diseases.
Collapse
Affiliation(s)
- Janina Müller-Deile
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA.
| | - Jan Dannenberg
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA
| | - Patricia Schroder
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA
| | - Meei-Hua Lin
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey H Miner
- Division of Nephrology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rongjun Chen
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; Imperial College London, National Heart and Lung Institute, London, UK; REBIRTH Excellence Cluster, Hannover Medical School, Hannover, Germany
| | - Jenny Nyström
- Departments of Physiology and Nephrology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Hermann Haller
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Johan M Lorenzen
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany; Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; REBIRTH Excellence Cluster, Hannover Medical School, Hannover, Germany
| | - Mario Schiffer
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany; Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, USA.
| |
Collapse
|
20
|
Pedersen MH, Hood BL, Beck HC, Conrads TP, Ditzel HJ, Leth-Larsen R. Downregulation of antigen presentation-associated pathway proteins is linked to poor outcome in triple-negative breast cancer patient tumors. Oncoimmunology 2017. [PMID: 28638726 DOI: 10.1080/2162402x.2017.1305531] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous subtype with varying disease outcomes. Tumor-infiltrating lymphocytes (TILs) are frequent in TNBC and have been shown to correlate with outcome, suggesting an immunogenic component in this subtype. However, other factors intrinsic to the cancer cells may also influence outcome. To identify proteins and molecular pathways associated with recurrence in TNBC, 34 formalin-fixed paraffin-embedded (FFPE) primary TNBC tumors were investigated by global proteomic profiling using mass spectrometry. Approximately, half of the patients were lymph node-negative and remained free of local or distant metastasis within 10 y follow-up, while the other half developed distant metastasis. Proteomic profiling identified >4,000 proteins, of which 63 exhibited altered expression in primary tumors of recurrence versus recurrence-free patients. Importantly, downregulation of proteins in the major histocompatibility complex (MHC) class I antigen presentation pathways were enriched, including TAP1, TAP2, CALR, HLA-A, ERAP1 and TAPBP, and were associated with significantly shorter recurrence-free and overall survival. In addition, proteins involved in cancer cell proliferation and growth, including GBP1, RAD23B, WARS and STAT1, also exhibited altered expression in primary tumors of recurrence versus recurrence-free patients. The association between the antigen-presentation pathway and outcome were validated in a second sample set of 10 primary TNBC tumors and corresponding metastases using proteomics and in a large public gene expression database of 249 TNBC and 580 basal-like breast cancer cases. Our study demonstrates that downregulation of antigen presentation is a key mechanism for TNBC cells to avoid immune surveillance, allowing continued growth and spread.
Collapse
Affiliation(s)
- Martin H Pedersen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
| | - Brian L Hood
- Womens Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Henry Jackson Foundation for the Advancement of Military Medicine, Annandale, VA, USA
| | - Hans Christian Beck
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Thomas P Conrads
- Womens Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Henry Jackson Foundation for the Advancement of Military Medicine, Annandale, VA, USA
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark.,Department of Oncology, Odense University Hospital, Odense C, Denmark
| | - Rikke Leth-Larsen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense C, Denmark
| |
Collapse
|
21
|
Hobeika L, Barati MT, Caster DJ, McLeish KR, Merchant ML. Characterization of glomerular extracellular matrix by proteomic analysis of laser-captured microdissected glomeruli. Kidney Int 2016; 91:501-511. [PMID: 27988214 DOI: 10.1016/j.kint.2016.09.044] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/14/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
Abnormal extracellular matrix (ECM) remodeling is a prominent feature of many glomerular diseases and is a final common pathway of glomerular injury. However, changes in ECM composition accompanying disease-related remodeling are unknown. The physical properties of ECM create challenges for characterization of composition using standard protein extraction techniques, as the insoluble components of ECM are frequently discarded and many ECM proteins are in low abundance compared to other cell proteins. Prior proteomic studies defining normal ECM composition used a large number of glomeruli isolated from human kidneys retrieved for transplantation or by nephrectomy for cancer. Here we examined the ability to identify ECM proteins by mass spectrometry using glomerular sections compatible with those available from standard renal biopsy specimens. Proteins were classified as ECM by comparison to the Matrisome database and previously identified glomerular ECM proteins. Optimal ECM protein identification resulted from sequential decellularization and protein extraction of 100 human glomerular sections isolated by laser capture microdissection from either frozen or formalin-fixed, paraffin-embedded tissue. In total, 147 ECM proteins were identified, including the majority of structural and GBM proteins previously identified along with a number of matrix and glomerular basement membrane proteins not previously associated with glomeruli. Thus, our study demonstrates the feasibility of proteomic analysis of glomerular ECM from retrieved glomerular sections isolated from renal biopsy tissue and expands the list of known ECM proteins in glomeruli.
Collapse
Affiliation(s)
- Liliane Hobeika
- Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Michelle T Barati
- Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Dawn J Caster
- Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, Kentucky, USA; Robley Rex VAMC, Louisville, Kentucky, USA
| | - Kenneth R McLeish
- Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, Kentucky, USA; Robley Rex VAMC, Louisville, Kentucky, USA
| | - Michael L Merchant
- Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, Kentucky, USA.
| |
Collapse
|
22
|
Conserva F, Gesualdo L, Papale M. A Systems Biology Overview on Human Diabetic Nephropathy: From Genetic Susceptibility to Post-Transcriptional and Post-Translational Modifications. J Diabetes Res 2016; 2016:7934504. [PMID: 26798653 PMCID: PMC4698547 DOI: 10.1155/2016/7934504] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/16/2015] [Accepted: 09/10/2015] [Indexed: 12/19/2022] Open
Abstract
Diabetic nephropathy (DN), a microvascular complication occurring in approximately 20-40% of patients with type 2 diabetes mellitus (T2DM), is characterized by the progressive impairment of glomerular filtration and the development of Kimmelstiel-Wilson lesions leading to end-stage renal failure (ESRD). The causes and molecular mechanisms mediating the onset of T2DM chronic complications are yet sketchy and it is not clear why disease progression occurs only in some patients. We performed a systematic analysis of the most relevant studies investigating genetic susceptibility and specific transcriptomic, epigenetic, proteomic, and metabolomic patterns in order to summarize the most significant traits associated with the disease onset and progression. The picture that emerges is complex and fascinating as it includes the regulation/dysregulation of numerous biological processes, converging toward the activation of inflammatory processes, oxidative stress, remodeling of cellular function and morphology, and disturbance of metabolic pathways. The growing interest in the characterization of protein post-translational modifications and the importance of handling large datasets using a systems biology approach are also discussed.
Collapse
Affiliation(s)
- Francesca Conserva
- Division of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy
- Division of Cardiology and Cardiac Rehabilitation, “S. Maugeri” Foundation, IRCCS, Institute of Cassano Murge, 70020 Cassano delle Murge, Italy
| | - Loreto Gesualdo
- Division of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy
- *Loreto Gesualdo:
| | - Massimo Papale
- Molecular Medicine Center, Section of Nephrology, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| |
Collapse
|
23
|
Harder JL, Hodgin JB, Kretzler M. Integrative Biology of Diabetic Kidney Disease. KIDNEY DISEASES 2015; 1:194-203. [PMID: 26929927 DOI: 10.1159/000439196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND The leading cause of ESRD in the U.S. is diabetic kidney disease (DKD). Despite significant efforts to improve outcomes in DKD, the impact on disease progression has been disappointing. This has prompted clinicians and researchers to search for alternative approaches to identify persons at risk, and to search for more effective therapies to halt progression of DKD. Identification of novel therapies is critically dependent on a more comprehensive understanding of the pathophysiology of DKD, specifically at the molecular level. A more expansive and exploratory view of DKD is needed to complement more traditional research approaches that have focused on single molecules. SUMMARY In recent years, sophisticated research methodologies have emerged within systems biology that should allow for a more comprehensive disease definition of DKD. Systems biology provides an inter-disciplinary approach to describe complex interactions within biological systems including how these interactions influence systems' functions and behaviors. Computational modeling of large, system-wide, quantitative data sets is used to generate molecular interaction pathways, such as metabolic and cell signaling networks. KEY MESSAGES Importantly, interpretation of data generated by systems biology tools requires integration with enhanced clinical research data and validation using model systems. Such an integrative biological approach has already generated novel insights into pathways and molecules involved in DKD. In this review, we highlight recent examples of how combining systems biology with traditional clinical and model research efforts results in an integrative biology approach that has significantly added to the understanding of the complex pathophysiology of DKD.
Collapse
Affiliation(s)
- Jennifer L Harder
- Department of Internal Medicine, the Division of Nephrology, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Department of Internal Medicine, the Division of Nephrology, University of Michigan, Ann Arbor, Michigan ; Department of Bioinformatics and Computational Medicine, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
24
|
Weißer J, Lai ZW, Bronsert P, Kuehs M, Drendel V, Timme S, Kuesters S, Jilg CA, Wellner UF, Lassmann S, Werner M, Biniossek ML, Schilling O. Quantitative proteomic analysis of formalin-fixed, paraffin-embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines. BMC Genomics 2015. [PMID: 26220445 PMCID: PMC4518706 DOI: 10.1186/s12864-015-1768-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most abundant resource of archived human specimens in pathology. Such tissue specimens are emerging as a highly valuable resource for translational proteomic studies. In quantitative proteomic analysis, reductive di-methylation of primary amines using stable isotopic formaldehyde variants is increasingly used due to its robustness and cost-effectiveness. Results In the present study we show for the first time that isotopic amine dimethylation can be used in a straightforward manner for the quantitative proteomic analysis of FFPE specimens without interference from formalin employed in the FFPE process. Isotopic amine dimethylation of FFPE specimens showed equal labeling efficiency as for cryopreserved specimens. For both FFPE and cryopreserved specimens, differential labeling of identical samples yielded highly similar ratio distributions within the expected range for dimethyl labeling. In an initial application, we profiled proteome changes in clear cell renal cell carcinoma (ccRCC) FFPE tissue specimens compared to adjacent non–malignant renal tissue. Our findings highlight increased levels of glyocolytic enzymes, annexins as well as ribosomal and proteasomal proteins. Conclusion Our study establishes isotopic amine dimethylation as a versatile tool for quantitative proteomic analysis of FFPE specimens and underlines proteome alterations in ccRCC. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1768-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- J Weißer
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany. .,Present address: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090, Vienna, Austria.
| | - Z W Lai
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.
| | - P Bronsert
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany. .,Comprehensive Cancer Center Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - M Kuehs
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.
| | - V Drendel
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.
| | - S Timme
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.
| | - S Kuesters
- Clinic for General and Visceral Surgery, University Medical Center Freiburg, Freiburg, Germany.
| | - C A Jilg
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, 79106, Germany.
| | - U F Wellner
- Clinic for General and Visceral Surgery, University Medical Center Freiburg, Freiburg, Germany. .,Present address: Clinic for Surgery, University Clinic of Schleswig-Holstein Campus Lübeck, Lübeck, Germany.
| | - S Lassmann
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104, Freiburg, Germany. .,Comprehensive Cancer Center Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - M Werner
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany. .,Comprehensive Cancer Center Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - M L Biniossek
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.
| | - O Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104, Freiburg, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
25
|
Label-free quantitative proteomic analysis reveals strong involvement of complement alternative and terminal pathways in human glomerular sclerotic lesions. J Proteomics 2015; 123:89-100. [DOI: 10.1016/j.jprot.2015.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 03/02/2015] [Accepted: 03/19/2015] [Indexed: 11/21/2022]
|
26
|
Steiner C, Ducret A, Tille JC, Thomas M, McKee TA, Rubbia-Brandt L, Scherl A, Lescuyer P, Cutler P. Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues. Proteomics 2014; 14:441-51. [PMID: 24339433 PMCID: PMC4265304 DOI: 10.1002/pmic.201300311] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 12/12/2022]
Abstract
Proteomic analysis of tissues has advanced in recent years as instruments and methodologies have evolved. The ability to retrieve peptides from formalin-fixed paraffin-embedded tissues followed by shotgun or targeted proteomic analysis is offering new opportunities in biomedical research. In particular, access to large collections of clinically annotated samples should enable the detailed analysis of pathologically relevant tissues in a manner previously considered unfeasible. In this paper, we review the current status of proteomic analysis of formalin-fixed paraffin-embedded tissues with a particular focus on targeted approaches and the potential for this technique to be used in clinical research and clinical diagnosis. We also discuss the limitations and perspectives of the technique, particularly with regard to application in clinical diagnosis and drug discovery.
Collapse
Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland; Human Protein Sciences Department, University of Geneva, Geneva, Switzerland; Translational Technologies and Bioinformatics, Pharma Research and Early Development, F. Hoffmann-La Roche AG, Basel, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| |
Collapse
|
28
|
Finne K, Vethe H, Skogstrand T, Leh S, Dahl TD, Tenstad O, Berven FS, Reed RK, Vikse BE. Proteomic analysis of formalin-fixed paraffin-embedded glomeruli suggests depletion of glomerular filtration barrier proteins in two-kidney, one-clip hypertensive rats. Nephrol Dial Transplant 2014; 29:2217-27. [PMID: 25129444 PMCID: PMC4240179 DOI: 10.1093/ndt/gfu268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background It is well known that hypertension may cause glomerular damage, but the molecular mechanisms involved are still incompletely understood. Methods In the present study, we used formalin-fixed paraffin-embedded (FFPE) tissue to investigate changes in the glomerular proteome in the non-clipped kidney of two-kidney one-clip (2K1C) hypertensive rats, with special emphasis on the glomerular filtration barrier. 2K1C hypertension was induced in 6-week-old Wistar Hannover rats (n = 6) that were sacrificed 23 weeks later and compared with age-matched sham-operated controls (n = 6). Tissue was stored in FFPE tissue blocks and later prepared on tissue slides for laser microdissection. Glomeruli without severe morphological damage were isolated, and the proteomes were analysed using liquid chromatography–tandem mass spectrometry. Results 2K1C glomeruli showed reduced abundance of proteins important for slit diaphragm complex, such as nephrin, podocin and neph1. The podocyte foot process had a pattern of reduced abundance of transmembrane proteins but unchanged abundances of the podocyte cytoskeletal proteins synaptopodin and α-actinin-4. Lower abundance of important glomerular basement membrane proteins was seen. Possible glomerular markers of damage with increased abundance in 2K1C were transgelin, desmin and acyl-coenzyme A thioesterase 1. Conclusions Microdissection and tandem mass spectrometry could be used to investigate the proteome of isolated glomeruli from FFPE tissue. Glomerular filtration barrier proteins had reduced abundance in the non-clipped kidney of 2K1C hypertensive rats.
Collapse
Affiliation(s)
- Kenneth Finne
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Heidrun Vethe
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Trude Skogstrand
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Tone D Dahl
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Olav Tenstad
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway The Norwegian Multiple Sclerosis National Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Rolf K Reed
- Department of Biomedicine, University of Bergen, Bergen, Norway Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - Bjørn Egil Vikse
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Medicine, Haukeland University Hospital, Bergen, Norway Department of Medicine, Haugesund Hospital, Haugesund, Norway
| |
Collapse
|
29
|
Kosanam H, Thai K, Zhang Y, Advani A, Connelly KA, Diamandis EP, Gilbert RE. Diabetes induces lysine acetylation of intermediary metabolism enzymes in the kidney. Diabetes 2014; 63:2432-9. [PMID: 24677711 DOI: 10.2337/db12-1770] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cells in which insulin is not required for glucose uptake are susceptible to the long-term complications of diabetes. Even in these tissues, however, the major perturbations that would otherwise be engendered by the greatly increased intracellular glucose concentration are mollified by adaptive changes in the enzymes of intermediary metabolism. These include allosteric regulation, product inhibition, and covalent modification as well as alterations in gene transcription. More recently, advances in proteomic technology have shown that reversible acetylation of the ε-amino group of lysine provides an additional means of modulating protein function and, in particular, enzyme activity. Here, we explored the extent of protein acetylation in an organ susceptible to the long-term complications of diabetes, examining the kidneys of rats with streptozotocin-induced diabetes and kidney cells exposed to high glucose. Using high-resolution mass spectrometry coupled with immunoaffinity enrichment, we identified 47 lysine-acetylated proteins in the kidneys of diabetic rats compared with 11 in control kidneys. Bioinformatic interrogation of the acetylome from diabetic animals showed a predominance of metabolic pathway involvement including the citrate acid cycle, glycolysis/gluconeogenesis, and metabolism of branched chain amino acids. Increased lysine acetylation was also noted in mesangial and tubular cells exposed to 25 mmol/L compared with 5.6 mmol/L glucose. These findings highlight acetylation as a posttranslational modification affecting numerous proteins. Current drug discovery efforts to develop small molecule inhibitors and activators of various lysine acetylases and deacetylases offer a new potential strategy to reduce the likelihood of diabetes complications.
Collapse
Affiliation(s)
- Hari Kosanam
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kerri Thai
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Yanling Zhang
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Andrew Advani
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Kim A Connelly
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Richard E Gilbert
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| |
Collapse
|
30
|
MiR-223 downregulation promotes glomerular endothelial cell activation by upregulating importin α4 and α5 in IgA nephropathy. Kidney Int 2014; 85:624-35. [DOI: 10.1038/ki.2013.469] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 09/08/2013] [Accepted: 09/12/2013] [Indexed: 12/14/2022]
|
31
|
Proteomics and diabetic nephropathy: what have we learned from a decade of clinical proteomics studies? J Nephrol 2014; 27:221-8. [PMID: 24567069 DOI: 10.1007/s40620-014-0044-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/15/2013] [Indexed: 02/02/2023]
Abstract
Diabetic nephropathy (DN) has become the most frequent cause of chronic kidney disease worldwide due to the constant increase of the incidence of type 2 diabetes mellitus in developed and developing countries. The understanding of the pathophysiological mechanisms of human diseases through a large-scale characterization of the protein content of a biological sample is the key feature of the proteomics approach to the study of human disease. We discuss the main results of over 10 years of tissue and urine proteomics studies applied to DN in order to understand how far we have come and how far we still have to go before obtaining a full comprehension of the molecular mechanisms involved in the pathogenesis of DN and identifying reliable biomarkers for accurate management of patients.
Collapse
|
32
|
Lennon R, Byron A, Humphries JD, Randles MJ, Carisey A, Murphy S, Knight D, Brenchley PE, Zent R, Humphries MJ. Global analysis reveals the complexity of the human glomerular extracellular matrix. J Am Soc Nephrol 2014; 25:939-51. [PMID: 24436468 DOI: 10.1681/asn.2013030233] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The glomerulus contains unique cellular and extracellular matrix (ECM) components, which are required for intact barrier function. Studies of the cellular components have helped to build understanding of glomerular disease; however, the full composition and regulation of glomerular ECM remains poorly understood. We used mass spectrometry-based proteomics of enriched ECM extracts for a global analysis of human glomerular ECM in vivo and identified a tissue-specific proteome of 144 structural and regulatory ECM proteins. This catalog includes all previously identified glomerular components plus many new and abundant components. Relative protein quantification showed a dominance of collagen IV, collagen I, and laminin isoforms in the glomerular ECM together with abundant collagen VI and TINAGL1. Protein network analysis enabled the creation of a glomerular ECM interactome, which revealed a core of highly connected structural components. More than one half of the glomerular ECM proteome was validated using colocalization studies and data from the Human Protein Atlas. This study yields the greatest number of ECM proteins relative to previous investigations of whole glomerular extracts, highlighting the importance of sample enrichment. It also shows that the composition of glomerular ECM is far more complex than previously appreciated and suggests that many more ECM components may contribute to glomerular development and disease processes. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000456.
Collapse
Affiliation(s)
- Rachel Lennon
- Wellcome Trust Centre for Cell-Matrix Research and Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom;
| | - Adam Byron
- Wellcome Trust Centre for Cell-Matrix Research and
| | | | - Michael J Randles
- Wellcome Trust Centre for Cell-Matrix Research and Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
| | - Alex Carisey
- Wellcome Trust Centre for Cell-Matrix Research and
| | - Stephanie Murphy
- Wellcome Trust Centre for Cell-Matrix Research and Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
| | - David Knight
- Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, and
| | - Paul E Brenchley
- Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
| | - Roy Zent
- Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and Department of Medicine, Veterans Affairs Hospital, Nashville, Tennessee
| | | |
Collapse
|
33
|
Giusti L, Lucacchini A. Proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2013; 10:165-77. [PMID: 23573783 DOI: 10.1586/epr.13.3] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a valuable informational resource of histologically characterized specimens for proteomic studies. In this article, the authors review the advancement performed in the field of FFPE proteomics focusing on formaldehyde treatment and on strategies addressed to obtain the best recovery in the protein/peptide extraction. A variety of approaches have been used to characterize protein tissue extracts, and many efforts have been performed demonstrating the comparability between fresh/frozen and FFPE proteomes. Finally, the authors report and discuss the large numbers of works aimed at developing new strategies and sophisticated platforms in the analysis of FFPE samples to validate known potential biomarkers and to discover new ones.
Collapse
Affiliation(s)
- Laura Giusti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | |
Collapse
|
34
|
Nakatani S, Ishimura E, Mori K, Fukumoto S, Yamano S, Wei M, Emoto M, Wanibuchi H, Inaba M. Nephronectin expression in glomeruli of renal biopsy specimens from various kidney diseases: nephronectin is expressed in the mesangial matrix expansion of diabetic nephropathy. Nephron Clin Pract 2013; 122:114-21. [PMID: 23689482 DOI: 10.1159/000350816] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/19/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In a previous proteomic study, we detected increased expression of nephronectin in the glomeruli from patients with diabetic nephropathy (DN). The aim of the present study was to clarify the usefulness of determining glomerular expression of nephronectin in kidney disease. METHODS We performed immunohistochemical staining for nephronectin in renal biopsy specimens from patients with a variety of kidney diseases (n = 190). The percentage of nephronectin-positive areas in the glomeruli was analyzed using an image analyzer. RESULTS Nephronectin immunoreactivity was clearly, strongly positive in the mesangial expansion and nodular lesions of DN (n = 18), whereas nephronectin immunoreactivity was negative in IgA glomerulonephritis, membranoproliferative glomerulonephritis, lupus nephritis, membranous glomerulonephritis, minor glomerular abnormalities, crescentic glomerulonephritis, and other kidney diseases, such as amyloidosis and light chain deposition disease. Nephronectin was stained weakly in sclerotic lesions, such as focal segmental glomerulosclerosis and hypertensive nephropathy. The percentage of nephronectin-positive areas in the glomeruli from DN patients [15.1 ± 4.7% (n = 18)] was significantly higher than that for other kidney diseases [5.5 ± 3.6% (n = 172)] (p < 0.001). In multiple regression analyses, fasting plasma glucose and hemoglobin A1c were significantly associated with the increase in the percentage of nephronectin-positive areas in the glomeruli (β = 0.23, p < 0.001 and β = 0.16, p = 0.045, respectively). CONCLUSIONS The expression of nephronectin was sufficient to discriminate DN from other kidney diseases with mesangial matrix expansion and nodular lesions. We consider that nephronectin staining could be helpful in the diagnosis of DN.
Collapse
Affiliation(s)
- Shinya Nakatani
- Department of Metabolism, Endocrinology and Molecular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 2013; 45:205-18. [PMID: 23592010 DOI: 10.1007/s00726-013-1494-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a real treasure for retrospective analysis considering the amount of samples present in hospital archives, combined with pathological, clinical, and outcome information available for every sample. Although unlocking the proteome of these tissues is still a challenge, new approaches are being developed. In this review, we summarize the different mass spectrometry platforms that are used in human clinical studies to unravel the FFPE proteome. The different ways of extracting crosslinked proteins and the analytical strategies are pointed out. Also, the pitfalls and challenges concerning the quality of FFPE proteomic approaches are depicted. We also evaluated the potential of these analytical methods for future clinical FFPE proteomics applications.
Collapse
|
36
|
Vincenti DC, Murray GI. The proteomics of formalin-fixed wax-embedded tissue. Clin Biochem 2013; 46:546-51. [DOI: 10.1016/j.clinbiochem.2012.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/06/2012] [Accepted: 10/01/2012] [Indexed: 01/16/2023]
|
37
|
Murray GI. Has the proteome of formalin-fixed wax-embedded tissue been unlocked? Nephrol Dial Transplant 2012; 27:3395-8. [PMID: 22859788 DOI: 10.1093/ndt/gfs342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
38
|
Long DA, Lennon R. The renal archaeologist: digging for clues in archived tissues to understand diabetic kidney disease. Nephrol Dial Transplant 2012; 27:1693-5. [DOI: 10.1093/ndt/gfs025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|