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Shaheed SU, McGivern H, Oliveira M, Snashall C, Sutton CW, Tam KH, Knight S, Abbas SH, Kers J, Cross S, Ploeg R, Hunter J. Research biopsies in kidney transplantation: an evaluation of surgical techniques and optimal tissue mass allowing molecular and histological analyses. Clin Proteomics 2024; 21:55. [PMID: 39271970 PMCID: PMC11401365 DOI: 10.1186/s12014-024-09508-2] [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: 07/18/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Research biopsies have great potential to advance scientific knowledge by helping to establish predictors of favourable or unfavourable outcomes in kidney transplantation. We evaluated punch and core biopsies of different sizes to determine the optimal size for clinical use. METHODS A total of 54 punch biopsies and 18 core needle biopsies were retrieved by three transplant surgeons. Each surgeon obtained three separate 2 mm, 3 mm and 4 mm punch biopsy samples and three 23 mm (length) core needle biopsies from two pig kidneys. RESULTS 4 mm punch biopsies yielded the greatest amount of protein (2.11 ± 0.41 mg) with good reproducibility between surgeons and biopsy types (Coefficient of Variation ∼ 22.13%). All surgeons found 2 mm biopsies technically challenging to obtain and sample processing was difficult due to the sample size. Shotgun proteomics identified 3853 gene products with no significant difference in the quantitative proteome of 2 mm and 3 mm punch biopsies. However, the expression of 158 Kidney enriched genes, was higher in bigger and deeper 4 mm punch and core needle biopsies compared to 2 mm biopsy. Only 80% of 2 mm biopsies demonstrated the presence of glomeruli, whereas glomeruli were present in 100% of all other biopsy sizes. CONCLUSIONS The 2 mm punch biopsy has been shown to be challenging to use and frequently provides inadequate tissue for histology and proteomics while 3 mm research biopsies were the smallest size that were technically obtainable with adequate tissue for molecular studies.
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Affiliation(s)
- Sadr Ul Shaheed
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Hannah McGivern
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Bodleian Health Care Libraries, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - Marta Oliveira
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - Corinna Snashall
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
| | - Chris W Sutton
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Ka Ho Tam
- Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Simon Knight
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Syed Hussain Abbas
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Jesper Kers
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Pathology, Leiden Transplant Center, Leiden University Medical Center, Leiden, Netherlands
| | - Sarah Cross
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - Rutger Ploeg
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
| | - James Hunter
- Nuffield Department of Surgical Sciences and Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Headley Way, Headington, Oxford, OX3 9BQ, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
- National QUOD Biobank Consortium with NHS Blood and Transplant, Bradford, UK
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van Duijl TT, Soonawala D, de Fijter JW, Ruhaak LR, Cobbaert CM. Rational selection of a biomarker panel targeting unmet clinical needs in kidney injury. Clin Proteomics 2021; 18:10. [PMID: 33618665 PMCID: PMC7898424 DOI: 10.1186/s12014-021-09315-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/30/2021] [Indexed: 12/01/2022] Open
Abstract
The pipeline of biomarker translation from bench to bedside is challenging and limited biomarkers have been adopted to routine clinical care. Ideally, biomarker research and development should be driven by unmet clinical needs in health care. To guide researchers, clinical chemists and clinicians in their biomarker research, the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) has developed a structured questionnaire in which the clinical gaps in current clinical pathways are identified and desirable performance specifications are predefined. In kidney injury, the high prevalence of the syndrome acute kidney injury (AKI) in the hospital setting has a significant impact on morbidity, patient survival and health care costs, but the use of biomarkers indicating early kidney injury in daily patient care remains limited. Routinely, medical labs measure serum creatinine, which is a functional biomarker, insensitive for detecting early kidney damage and cannot distinguish between renal and prerenal AKI. The perceived unmet clinical needs in kidney injury were identified through the EFLM questionnaire. Nephrologists within our tertiary care hospital emphasized that biomarkers are needed for (1) early diagnosis of in-hospital AKI after a medical insult and in critically ill patients, (2) risk stratification for kidney injury prior to a scheduled (elective) intervention, (3) kidney injury monitoring in patients scheduled to receive nephrotoxic medication and after kidney transplantation and (4) differentiation between prerenal AKI and structural kidney damage. The biomarker search and selection strategy resulted in a rational selection of an eleven-protein urinary panel for kidney injury that target these clinical needs. To assess the clinical utility of the proposed biomarker panel in kidney injury, a multiplexed LC-MS test is now in development for the intended translational research.
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Affiliation(s)
- T T van Duijl
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| | - D Soonawala
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Haga Teaching Hospital, The Hague, The Netherlands
| | - J W de Fijter
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
| | - L R Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - C M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Postzone E2-P, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
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3
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Prikryl P, Satrapova V, Frydlova J, Hruskova Z, Zima T, Tesar V, Vokurka M. Mass spectrometry-based proteomic exploration of the small urinary extracellular vesicles in ANCA-associated vasculitis in comparison with total urine. J Proteomics 2020; 233:104067. [PMID: 33307252 DOI: 10.1016/j.jprot.2020.104067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 11/29/2020] [Indexed: 01/07/2023]
Abstract
ANCA-associated vasculitis (AAV) is a rare, but potentially severe autoimmune disease, even nowadays displaying increased mortality and morbidity. Finding early biomarkers of activity and prognosis is thus very important. Small extracellular vesicles (EVs) isolated from urine can be considered as a non-invasive source of biomarkers. We evaluated several protocols for urinary EV isolation. To eliminate contaminating non-vesicular proteins due to AAV associated proteinuria we used proteinase K treatment. We investigated the differences in proteomes of small EVs of patients with AAV compared to healthy controls by label-free LC-MS/MS. In parallel, we performed an analogous proteomic analysis of urine samples from identical patients. The study results showed significant differences and similarities in both EV and urine proteome, the latter one being highly affected by proteinuria. Using bioinformatics tools we explored differentially changed proteins and their related pathways with a focus on the pathophysiology of AAV. Our findings indicate significant regulation of Golgi enzymes, such as MAN1A1, which can be involved in T cell activation by N-glycans glycosylation and may thus play a key role in pathogenesis and diagnosis of AAV. SIGNIFICANCE: The present study explores for the first time the changes in proteomes of small extracellular vesicles and urine of patients with renal ANCA-associated vasculitis compared to healthy controls by label-free LC-MS/MS. Isolation of vesicles from proteinuric urine samples has been modified to minimize contamination by plasma proteins and to reduce co-isolation of extraluminal proteins. Differentially changed proteins and their related pathways with a role in the pathophysiology of AAV were described and discussed. The results could be helpful for the research of potential biomarkers in renal vasculitis associated with ANCA.
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Affiliation(s)
- Petr Prikryl
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Satrapova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jana Frydlova
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Zdenka Hruskova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Tomas Zima
- Institute of Clinical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Vladimir Tesar
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Martin Vokurka
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic.
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4
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Louzao-Martinez L, van Dijk CG, Xu YJ, Korn A, Bekker NJ, Brouwhuis R, Nicese MN, Demmers JA, Goumans MJT, Masereeuw R, Duncker DJ, Verhaar MC, Cheng C. A proteome comparison between human fetal and mature renal extracellular matrix identifies EMILIN1 as a regulator of renal epithelial cell adhesion. Matrix Biol Plus 2019; 4:100011. [PMID: 33543009 PMCID: PMC7852202 DOI: 10.1016/j.mbplus.2019.100011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/08/2019] [Accepted: 07/18/2019] [Indexed: 12/27/2022] Open
Abstract
Cell-based approaches using tissue engineering and regenerative medicine to replace damaged renal tissue with 3D constructs is a promising emerging therapy for kidney disease. Besides living cells, a template provided by a scaffold based on biomaterials and bioactive factors is needed for successful kidney engineering. Nature's own template for a scaffolding system is the extracellular matrix (ECM). Research has focused on mapping the mature renal ECM; however, the developing fetal ECM matches more the active environment required in 3D renal constructs. Here, we characterized the differences between the human fetal and mature renal ECM using spectrometry-based proteomics of decellularized tissue. We identified 99 different renal ECM proteins of which the majority forms an overlapping core, but also includes proteins enriched in either the fetal or mature ECM. Relative protein quantification showed a significant dominance of EMILIN1 in the fetal ECM. We functionally tested the role of EMILIN1 in the ECM using a novel methodology that permits the reliable anchorage of native cell-secreted ECM to glass coverslips. Depletion of EMILIN1 from the ECM layer using siRNA mediated knock-down technologies does not affect renal epithelial cell growth, but does promote migration. Lack of EMILIN1 in the ECM layer reduces the adhesion strength of renal epithelial cells, shown by a decrease in focal adhesion points and associated stress fibers. We showed in this study the importance of a human renal fetal and mature ECM catalogue for identifying promising ECM components that have high implementation potential in scaffolds for 3D renal constructs. Proteomics revealed the differences between the renal fetal and mature extracellular matrix. EMILIN1 has a significant dominance in the fetal extracellular matrix. EMILIN1 depletion from the extracellular matrix reduces the adhesion strength and promotes migration of renal epithelial cells.
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Affiliation(s)
- Laura Louzao-Martinez
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Christian G.M. van Dijk
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Yan Juan Xu
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Amber Korn
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Nicolaas J. Bekker
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Romi Brouwhuis
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Maria Novella Nicese
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | | | | | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht, the Netherlands
| | - Dirk J. Duncker
- Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, the Netherlands
| | - Marianne C. Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
| | - Caroline Cheng
- Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands
- Experimental Cardiology, Department of Cardiology, Erasmus University Medical Center, the Netherlands
- Corresponding author at: Department of Nephrology and Hypertension, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, the Netherlands, Experimental Cardiology, Thoraxcenter, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, the Netherlands.
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5
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Recent progress in mass spectrometry proteomics for biomedical research. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1093-1113. [DOI: 10.1007/s11427-017-9175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022]
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6
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Diedrich B, Dengjel J. Insights into autosomal dominant polycystic kidney disease by quantitative mass spectrometry-based proteomics. Cell Tissue Res 2017; 369:41-51. [DOI: 10.1007/s00441-017-2617-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/21/2017] [Indexed: 12/12/2022]
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7
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Impact and influence of “omics” technology on hyper tension studies. Int J Cardiol 2017; 228:1022-1034. [DOI: 10.1016/j.ijcard.2016.11.179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/06/2016] [Indexed: 12/14/2022]
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8
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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.
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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.
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Papadopoulos T, Krochmal M, Cisek K, Fernandes M, Husi H, Stevens R, Bascands JL, Schanstra JP, Klein J. Omics databases on kidney disease: where they can be found and how to benefit from them. Clin Kidney J 2016; 9:343-52. [PMID: 27274817 PMCID: PMC4886900 DOI: 10.1093/ckj/sfv155] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023] Open
Abstract
In the recent decades, the evolution of omics technologies has led to advances in all biological fields, creating a demand for effective storage, management and exchange of rapidly generated data and research discoveries. To address this need, the development of databases of experimental outputs has become a common part of scientific practice in order to serve as knowledge sources and data-sharing platforms, providing information about genes, transcripts, proteins or metabolites. In this review, we present omics databases available currently, with a special focus on their application in kidney research and possibly in clinical practice. Databases are divided into two categories: general databases with a broad information scope and kidney-specific databases distinctively concentrated on kidney pathologies. In research, databases can be used as a rich source of information about pathophysiological mechanisms and molecular targets. In the future, databases will support clinicians with their decisions, providing better and faster diagnoses and setting the direction towards more preventive, personalized medicine. We also provide a test case demonstrating the potential of biological databases in comparing multi-omics datasets and generating new hypotheses to answer a critical and common diagnostic problem in nephrology practice. In the future, employment of databases combined with data integration and data mining should provide powerful insights into unlocking the mysteries of kidney disease, leading to a potential impact on pharmacological intervention and therapeutic disease management.
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Affiliation(s)
- Theofilos Papadopoulos
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Magdalena Krochmal
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece; Institute for Molecular Cardiovascular Research, Universitätsklinikum RWTH Aachen, Aachen, Germany
| | | | - Marco Fernandes
- BHF Glasgow Cardiovascular Research Centre , University of Glasgow , Glasgow , UK
| | - Holger Husi
- BHF Glasgow Cardiovascular Research Centre , University of Glasgow , Glasgow , UK
| | - Robert Stevens
- School of Computer Science , University of Manchester , Manchester , UK
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
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L'Imperio V, Smith A, Chinello C, Pagni F, Magni F. Proteomics and glomerulonephritis: A complementary approach in renal pathology for the identification of chronic kidney disease related markers. Proteomics Clin Appl 2016; 10:371-83. [DOI: 10.1002/prca.201500075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/16/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022]
Affiliation(s)
| | - Andrew Smith
- Department of Health Sciences; University Milan Bicocca; Monza Italy
| | - Clizia Chinello
- Department of Health Sciences; University Milan Bicocca; Monza Italy
| | - Fabio Pagni
- Department of Pathology; University Milan Bicocca; Monza Italy
| | - Fulvio Magni
- Department of Health Sciences; University Milan Bicocca; Monza Italy
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11
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Zhou T, Sha J, Guo X. The need to revisit published data: A concept and framework for complementary proteomics. Proteomics 2015; 16:6-11. [PMID: 26552962 DOI: 10.1002/pmic.201500170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/26/2015] [Accepted: 11/04/2015] [Indexed: 12/14/2022]
Abstract
Tandem proteomic strategies based on large-scale and high-resolution mass spectrometry have been widely applied in various biomedical studies. However, protein sequence databases and proteomic software are continuously updated. Proteomic studies should not be ended with a stable list of proteins. It is necessary and beneficial to regularly revise the results. Besides, the original proteomic studies usually focused on a limited aspect of protein information and valuable information may remain undiscovered in the raw spectra. Several studies have reported novel findings by reanalyzing previously published raw data. However, there are still no standard guidelines for comprehensive reanalysis. In the present study, we proposed the concept and draft framework for complementary proteomics, which are aimed to revise protein list or mine new discoveries by revisiting published data.
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Affiliation(s)
- Tao Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P. R. China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P. R. China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P. R. China
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12
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Magdeldin S, Hirao Y, Elguoshy A, Xu B, Zhang Y, Fujinaka H, Yamamoto K, Yates JR, Yamamoto T. A proteomic glimpse into human ureter proteome. Proteomics 2015; 16:80-4. [PMID: 26442468 PMCID: PMC4737284 DOI: 10.1002/pmic.201500214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/31/2015] [Accepted: 09/28/2015] [Indexed: 12/18/2022]
Abstract
Urine has evolved as one of the most important biofluids in clinical proteomics due to its noninvasive sampling and its stability. Yet, it is used in clinical diagnostics of several disorders by detecting changes in its components including urinary protein/polypeptide profile. Despite the fact that majority of proteins detected in urine are primarily originated from the urogenital (UG) tract, determining its precise source within the UG tract remains elusive. In this article, we performed a comprehensive analysis of ureter proteome to assemble the first unbiased ureter dataset. Next, we compared these data to urine, urinary exosome, and kidney mass spectrometric datasets. Our result concluded that among 2217 nonredundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, the ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. All MS data have been deposited in the ProteomeXchange with identifier PXD002620 (http://proteomecentral.proteomexchange.org/dataset/PXD002620).
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Affiliation(s)
- Sameh Magdeldin
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan.,Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismaïlia, Egypt.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Amr Elguoshy
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan.,Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Bo Xu
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Ying Zhang
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Hidehiko Fujinaka
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Tadashi Yamamoto
- Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
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Karimi P, Shahrokni A, Ranjbar MRN. Implementation of proteomics for cancer research: past, present, and future. Asian Pac J Cancer Prev 2015; 15:2433-8. [PMID: 24761843 DOI: 10.7314/apjcp.2014.15.6.2433] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cancer is the leading cause of the death, accounts for about 13% of all annual deaths worldwide. Many different fields of science are collaborating together studying cancer to improve our knowledge of this lethal disease, and find better solutions for diagnosis and treatment. Proteomics is one of the most recent and rapidly growing areas in molecular biology that helps understanding cancer from an omics data analysis point of view. The human proteome project was officially initiated in 2008. Proteomics enables the scientists to interrogate a variety of biospecimens for their protein contents and measure the concentrations of these proteins. Current necessary equipment and technologies for cancer proteomics are mass spectrometry, protein microarrays, nanotechnology and bioinformatics. In this paper, we provide a brief review on proteomics and its application in cancer research. After a brief introduction including its definition, we summarize the history of major previous work conducted by researchers, followed by an overview on the role of proteomics in cancer studies. We also provide a list of different utilities in cancer proteomics and investigate their advantages and shortcomings from theoretical and practical angles. Finally, we explore some of the main challenges and conclude the paper with future directions in this field.
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Affiliation(s)
- Parisa Karimi
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA E-mail :
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Habuka M, Fagerberg L, Hallström BM, Kampf C, Edlund K, Sivertsson Å, Yamamoto T, Pontén F, Uhlén M, Odeberg J. The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling. PLoS One 2014; 9:e116125. [PMID: 25551756 PMCID: PMC4281243 DOI: 10.1371/journal.pone.0116125] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/02/2014] [Indexed: 12/22/2022] Open
Abstract
To understand renal functions and disease, it is important to define the molecular constituents of the various compartments of the kidney. Here, we used comparative transcriptomic analysis of all major organs and tissues in the human body, in combination with kidney tissue micro array based immunohistochemistry, to generate a comprehensive description of the kidney-specific transcriptome and proteome. A special emphasis was placed on the identification of genes and proteins that were elevated in specific kidney subcompartments. Our analysis identified close to 400 genes that had elevated expression in the kidney, as compared to the other analysed tissues, and these were further subdivided, depending on expression levels, into tissue enriched, group enriched or tissue enhanced. Immunohistochemistry allowed us to identify proteins with distinct localisation to the glomeruli (n = 11), proximal tubules (n = 120), distal tubules (n = 9) or collecting ducts (n = 8). Among the identified kidney elevated transcripts, we found several proteins not previously characterised or identified as elevated in kidney. This description of the kidney specific transcriptome and proteome provides a resource for basic and clinical research to facilitate studies to understand kidney biology and disease.
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Affiliation(s)
- Masato Habuka
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan
| | - Linn Fagerberg
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn M. Hallström
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karolina Edlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Sivertsson
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Tadashi Yamamoto
- Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jacob Odeberg
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Medicine, Karolinska Institutet and Centre for Hematology, Karolinska University Hospital, Stockholm, Sweden
- * E-mail:
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15
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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.
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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
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16
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Proteomic analysis of glomeruli from streptozotocin-induced diabetic rats. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-014-0184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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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.
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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
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18
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Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL. State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res 2013; 13:60-75. [PMID: 24261998 DOI: 10.1021/pr4010037] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The kidney, urine, and plasma proteomes are intimately related: proteins and metabolic waste products are filtered from the plasma by the kidney and excreted via the urine, while kidney proteins may be secreted into the circulation or released into the urine. Shotgun proteomics data sets derived from human kidney, urine, and plasma samples were collated and processed using a uniform software pipeline, and relative protein abundances were estimated by spectral counting. The resulting PeptideAtlas builds yielded 4005, 2491, and 3553 nonredundant proteins at 1% FDR for the kidney, urine, and plasma proteomes, respectively - for kidney and plasma, the largest high-confidence protein sets to date. The same pipeline applied to all available human data yielded a 2013 Human PeptideAtlas build containing 12,644 nonredundant proteins and at least one peptide for each of ∼14,000 Swiss-Prot entries, an increase over 2012 of ∼7.5% of the predicted human proteome. We demonstrate that abundances are correlated between plasma and urine, examine the most abundant urine proteins not derived from either plasma or kidney, and consider the biomarker potential of proteins associated with renal decline. This analysis forms part of the Biology and Disease-driven Human Proteome Project (B/D-HPP) and is a contribution to the Chromosome-centric Human Proteome Project (C-HPP) special issue.
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