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Pan Y, Wong CYP, Ma H, Tse RTH, Cheng CKL, Tan M, Chiu PKF, Teoh JYC, Wang X, Ng CF, Zhang L. Quantitative comparison of the renal pelvic urine and bladder urine to examine modifications of the urine proteome by the lower urinary tract. Proteomics Clin Appl 2024; 18:e2300004. [PMID: 37574260 DOI: 10.1002/prca.202300004] [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: 01/13/2023] [Revised: 06/21/2023] [Accepted: 08/04/2023] [Indexed: 08/15/2023]
Abstract
PURPOSE Urine proteome is a valuable reservoir of biomarkers for disease diagnosis and monitoring. Following formation as the plasma filtrate in the kidney, urine is progressively modified by the active reabsorption and secretion of the urinary tract. However, little is known about how the urine proteome changes as it passes along the urinary tract. EXPERIMENTAL DESIGN To investigate this, we compared the proteome composition of the renal pelvis urine (RPU) and individually self-voided bladder urine (BU) collected from seven unilateral urinary tract obstruction male patients by LC-MS/MS screening. To our knowledge, this is the first proteomic comparison of RPU and BU samples from the same individual. RESULTS Overall, RPU and BU proteomes did not exhibit proteins that were exclusively present in all samples of one urine type while in none of the other type. Nonetheless, BU had more overrepresented proteins that were observed at a higher frequency than RPU. Label-free quantitative analyses revealed BU-RPU differential proteins that are enriched in exosomes and extracellular proteins. However, the differences were not significant after corrections for multiple testing. Interestingly, we observed a significant increase of collagen peptides with hydroxyproline modifications in the BU samples, suggesting differences in protein modifications. CONCLUSIONS AND CLINICAL RELEVANCE Our study revealed no substantial differences at the protein level between the BU and RPU samples. Future investigations with expanded cohorts would provide more insights about the urothelial-urinary interactions.
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Affiliation(s)
- Yilin Pan
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
| | - Christine Yim-Ping Wong
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Haiying Ma
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ryan Tsz-Hei Tse
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Carol Ka-Lo Cheng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Miaomiao Tan
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Peter Ka-Fung Chiu
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Jeremy Yuen-Chun Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Fai Ng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Liang Zhang
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
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2
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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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3
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Gao YC, Jiang NN, Qin XJ, Jiang H, Wei LB, Gao JR. High-throughput data on circular RNA reveal novel insights into chronic glomerulonephritis. Genes Genomics 2023; 45:475-490. [PMID: 36264417 DOI: 10.1007/s13258-022-01320-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/27/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs), a unique novel type of RNA, have been widely reported to be involved in physiologic and pathologic processes in humans. However, the exact molecular pathogenesis of circRNAs in chronic glomerulonephritis (CGN) is far from clear. OBJECTIVE This paper aims to evaluate the specific expression profile of circRNAs in renal cortex tissues from Adriamycin-induced CGN rats. METHODS CircRNAs were screened in renal cortex tissues from 3 CGN rats and 3 control rats by using high-throughput sequencing (HTS). Then, 4 circRNAs were selected randomly for verification by quantitative real-time polymerase chain reaction (qRT-PCR). In addition, the differentially expressed (DE) circRNAs were analyzed by bioinformatics methods. RESULTS In total, 31 significantly DE circRNAs were identified, which revealed their potential roles in CGN; in particular, we found that 4 confirmed altered circRNAs (rno-circ-RNAs 689, 3217, 1327, and 5001) might play important roles in the development of CGN. CONCLUSION This study reveals a cluster of circRNAs that are DE in Adriamycin-induced CGN rats, which brings us closer to understanding the pathogenic mechanisms and may provide new potential targets for clinical treatment.
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Affiliation(s)
- Ya-Chen Gao
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, China
| | - Nan-Nan Jiang
- College of Pharmacy, Anhui University of Chinese Medicine, 103 Meishan Road, Hefei, China
| | - Xiu-Juan Qin
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Hui Jiang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Liang-Bing Wei
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Jia-Rong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China.
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4
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Ma Z, Mao C, Jia Y, Yu F, Xu P, Tan Y, Zou QH, Zhou XJ, Kong W, Fu Y. ADAMTS7-Mediated Complement Factor H Degradation Potentiates Complement Activation to Contributing to Renal Injuries. J Am Soc Nephrol 2023; 34:291-308. [PMID: 36735376 PMCID: PMC10103097 DOI: 10.1681/asn.0000000000000004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/31/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The dysfunction of complement factor H (CFH), the main soluble complement negative regulator, potentiates various complement-induced renal injuries. However, insights into the underlying mechanism of CFH dysfunction remain limited. In this study, we investigated whether extracellular protease-mediated degradation accounts for CFH dysfunction in complement-mediated renal injuries. METHODS An unbiased interactome of lupus mice kidneys identified CFH-binding protease. In vitro cleavage assay clarified CFH degradation. Pristane-induced SLE or renal ischemia-reperfusion (I/R) injury models were used in wild-type and ADAMTS7-/- mice. RESULTS We identified the metalloprotease ADAMTS7 as a CFH-binding protein in lupus kidneys. Moreover, the upregulation of ADAMTS7 correlated with CFH reduction in both lupus mice and patients. Mechanistically, ADAMTS7 is directly bound to CFH complement control protein (CCP) 1-4 domain and degraded CCP 1-7 domain through multiple cleavages. In mice with lupus nephritis or renal I/R injury, ADAMTS7 deficiency alleviated complement activation and related renal pathologies, but without affecting complement-mediated bactericidal activity. Adeno-associated virus-mediated CFH silencing compromised these protective effects of ADAMTS7 knockout against complement-mediated renal injuries in vivo. CONCLUSION ADAMTS7-mediated CFH degradation potentiates complement activation and related renal injuries. ADAMTS7 would be a promising anticomplement therapeutic target that does not increase bacterial infection risk.
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Affiliation(s)
- Zihan Ma
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Chenfeng Mao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
- Beijing Institute of Biotechnology, Beijing, China
| | - Yiting Jia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Fang Yu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drugs of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Ying Tan
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Qing-Hua Zou
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Wei Kong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Yi Fu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
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5
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Weeding E, Fava A, Mohan C, Magder L, Goldman D, Petri M. Urine proteomic insights from the belimumab in lupus nephritis trial. Lupus Sci Med 2022; 9:9/1/e000763. [PMID: 36167482 PMCID: PMC9516299 DOI: 10.1136/lupus-2022-000763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Urine proteomic approaches have shown promise in identifying biological pathways in lupus nephritis (LN) which are not captured on renal histopathology or by measurement of proteinuria alone. We investigated how the urine proteome changes with treatment response and with belimumab therapy. METHODS Urine samples from 54 Belimumab International Systemic Lupus Erythematosus-Lupus Nephritis trial participants (all with biopsy-proven LN) were collected at weeks 0, 24 and 52. At each time point, 1000 urinary proteins were quantified using antibody microarrays (Raybiotech Kiloplex), and their abundance was compared in responders (n=31) versus non-responders (n=22) and with belimumab treatment (n=28) versus standard of care therapy (n=26). Response was defined as proteinuria <500 mg/gcreatinine (cr), serum creatinine ≤1.25 times the week 0 value and prednisone ≤10 mg/day at week 52. RESULTS By week 52, CD163 was the urine protein with the most significant difference in abundance between complete responders (median 1.8 pg/mgcr) versus non-responders (median 8.2 pg/mgcr, p=4e-7) regardless of treatment arm. At week 24, five urinary proteins were present at a significantly lower (CD23 and Siglec-5) or higher (AIF, CRELD2 and ROR2) level in the belimumab group. Belimumab therapy was particularly associated with reduction in CD23 between week 0 and week 24 (p=0.0001). CONCLUSIONS Reduction in urinary CD163 was strongly associated with complete renal response, confirming the results of multiple prior studies. Treatment with belimumab can be detected in the urine proteome, and further study is needed to determine whether modulation of CD23-mediated immune enhancement pathways might be implicated in LN treatment response.
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Affiliation(s)
- Emma Weeding
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrea Fava
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Laurence Magder
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Daniel Goldman
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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6
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Sanchez-Martin I, Magalhães P, Ranjzad P, Fatmi A, Richard F, Manh TPV, Saurin AJ, Feuillet G, Denis C, Woolf AS, Schanstra JP, Zürbig P, Caubit X, Fasano L. Haploinsufficiency of the mouse Tshz3 gene leads to kidney defects. Hum Mol Genet 2021; 31:1921-1945. [PMID: 34919690 DOI: 10.1093/hmg/ddab362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/14/2022] Open
Abstract
Renal tract defects and autism spectrum disorder (ASD) deficits represent the phenotypic core of the 19q12 deletion syndrome caused by the loss of one copy of the TSHZ3 gene. While a proportion of Tshz3 heterozygous (Tshz3+/lacZ) mice display ureteral defects, no kidney defects have been reported in these mice. The purpose of this study was to characterize the expression of Tshz3 in adult kidney as well as the renal consequences of embryonic haploinsufficiency of Tshz3 by analyzing the morphology and function of Tshz3 heterozygous adult kidney. Here, we described Tshz3 expression in the smooth muscle and stromal cells lining the renal pelvis, the papilla and glomerular endothelial cells (GEnCs) of the adult kidney as well as in the proximal nephron tubules in neonatal mice. Histological analysis showed that Tshz3+/lacZ adult kidney had an average of 29% fewer glomeruli than wild type kidney. Transmission electron microscopy (TEM) of Tshz3+/lacZ glomeruli revealed a reduced thickness of the glomerular basement membrane and a larger foot process width. Compared to wild type, Tshz3+/lacZ mice showed lower blood urea, phosphates, magnesium and potassium at 2 months of age. At the molecular level, transcriptome analysis identified differentially expressed genes related to inflammatory processes in Tshz3+/lacZ compare to wild type (WT; control) adult kidneys. Lastly, analysis of the urinary peptidome revealed 33 peptides associated with Tshz3+/lacZ adult mice. These results provide the first evidence that in the mouse Tshz3 haploinsufficiency leads to cellular, molecular and functional abnormalities in the adult mouse kidney.
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Affiliation(s)
| | | | - Parisa Ranjzad
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, UK
| | - Ahmed Fatmi
- Aix Marseille Univ, CNRS, IBDM, UMR7288, Marseille, France
| | | | - Thien Phong Vu Manh
- Aix Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | | | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, UK.,Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | - Xavier Caubit
- Aix Marseille Univ, CNRS, IBDM, UMR7288, Marseille, France
| | - Laurent Fasano
- Aix Marseille Univ, CNRS, IBDM, UMR7288, Marseille, France
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7
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Fava A, Rao DA, Mohan C, Zhang T, Rosenberg A, Fenaroli P, Belmont HM, Izmirly P, Clancy R, Monroy Trujillo J, Fine D, Arazi A, Berthier CC, Davidson A, James JA, Diamond B, Hacohen N, Wofsy D, Raychaudhuri S, Apruzzese W, Buyon J, Petri M. Urine Proteomics and Renal Single Cell Transcriptomics Implicate IL-16 in Lupus Nephritis. Arthritis Rheumatol 2021; 74:829-839. [PMID: 34783463 PMCID: PMC9050800 DOI: 10.1002/art.42023] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 10/13/2021] [Accepted: 11/09/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES Current treatments are effective only in 30% of lupus nephritis patients emphasizing the need for novel therapeutic strategies. To develop mechanistic hypotheses and explore novel biomarkers, we analyzed the longitudinal urinary proteomic profiles in patients with lupus nephritis undergoing treatment. METHODS We quantified 1,000 urinary proteins in 30 patients with lupus nephritis at the time of the diagnostic renal biopsy and after 3, 6, and 12 months. The proteins and molecular pathways detected in the urine proteome were then analyzed with respect to baseline clinical features and longitudinal trajectories. The intrarenal expression of candidate biomarkers was evaluated using single cell transcriptomics of renal biopsies from lupus nephritis patients. RESULTS Our analysis revealed multiple biological pathways including chemotaxis, neutrophil activation, platelet degranulation, and extracellular matrix organization that could be noninvasively quantified and monitored in the urine. We identified 237 urinary biomarkers associated with lupus nephritis as compared to controls without SLE. IL-16, CD163, and TGF-β mirrored intrarenal nephritis activity. Response to treatment was paralleled by a reduction of urinary IL-16, a CD4 ligand with proinflammatory and chemotactic properties. Single cell RNA sequencing independently demonstrated that IL16 is the second most expressed cytokine by most infiltrating immune cells in lupus nephritis kidneys. IL-16 producing cells were found at key sites of kidney injury. CONCLUSION Urine proteomics may profoundly change the diagnosis and management of lupus nephritis by noninvasively monitor active intrarenal biological pathways. These findings implicate IL-16 in lupus nephritis pathogenesis designating it as a potentially treatable target and biomarker.
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Affiliation(s)
- Andrea Fava
- Division of Rheumatology, Johns Hopkins University, Baltimore, MD, USA
| | - Deepak A Rao
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Avi Rosenberg
- Division of Renal Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Paride Fenaroli
- Division of Renal Pathology, Johns Hopkins University, Baltimore, MD, USA.,Department of Medicine and Surgery, Nephrology Unit, Parma University Hospital, Parma, Italy
| | | | - Peter Izmirly
- New York University School of Medicine, New York, New York, USA
| | - Robert Clancy
- New York University School of Medicine, New York, New York, USA
| | | | - Derek Fine
- Division of Nephrology, Johns Hopkins University, Baltimore, MD, USA
| | - Arnon Arazi
- Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | | | | | - Judith A James
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Betty Diamond
- Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | | | - David Wofsy
- University of California San Francisco, San Francisco, CA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | - William Apruzzese
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jill Buyon
- New York University School of Medicine, New York, New York, USA
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University, Baltimore, MD, USA
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8
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Genovese F, Akhgar A, Lim SS, Farris AB, Battle M, Cobb J, Sinibaldi D, Karsdal MA, White WI. Collagen Type III and VI Remodeling Biomarkers Are Associated with Kidney Fibrosis in Lupus Nephritis. KIDNEY360 2021; 2:1473-1481. [PMID: 35373114 PMCID: PMC8786137 DOI: 10.34067/kid.0001132021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/18/2021] [Indexed: 02/04/2023]
Abstract
Background Lupus nephritis (LN) occurs in <40% of patients with SLE. Reliable biomarkers of kidney damage are needed to identify patients with SLE at risk of developing LN to improve screening, treat the disease earlier, and halt progression to kidney failure. Novel biomarkers of extracellular matrix remodeling were evaluated as markers of kidney fibrosis and disease activity in patients with LN. Methods Biomarkers of the interstitial collagen type III (PRO-C3) and type VI (PRO-C6) formation and of collagen type III (C3M) degradation were evaluated in the serum and urine of 40 patients with LN, 20 patients with SLE but without LN, 20 healthy controls, and ten biopsy controls (histologic kidney inflammation/damage without SLE). Their association with histologic markers of interstitial fibrosis and tubular atrophy, with inflammatory cell infiltration and with disease activity and chronicity in the patients with LN was assessed. Results Despite PRO-C3 (serum) and PRO-C6 (serum and urine) being significantly elevated in patients with LN compared with healthy controls, the markers did not differentiate patients with LN from those with SLE. C3M (urine) levels were not different in LN compared with the other groups. C3M (urine) strongly correlated and PRO-C6 (serum and urine) inversely correlated with kidney function (eGFR). The biomarkers of interstitial collagen turnover PRO-C6 (serum) and C3M (urine) correlated with histologic markers of interstitial fibrosis, tubular atrophy, and monocyte infiltration. Conclusions Noninvasive collagen turnover biomarkers are promising tools to identify patients with SLE with kidney histologic modifications.
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Affiliation(s)
| | - Ahmad Akhgar
- Clinical Pharmacology and Quantitative Pharmacology, AstraZeneca, Gaithersburg, Maryland
| | - Sung Sam Lim
- Department of Medicine, Division of Rheumatology, Emory University School of Medicine, Atlanta, Georgia
| | - Alton B. Farris
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Monica Battle
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, Atlanta, Georgia
| | - Jason Cobb
- Department of Medicine, Renal Division, Emory University School of Medicine, Atlanta, Georgia
| | - Dominic Sinibaldi
- Biological and Knowledge Analytics, AstraZeneca, Gaithersburg, Maryland
| | | | - Wendy I. White
- Clinical Pharmacology and Quantitative Pharmacology, AstraZeneca, Gaithersburg, Maryland
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9
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Tailliar M, Schanstra JP, Dierckx T, Breuil B, Hanouna G, Charles N, Bascands JL, Dussol B, Vazi A, Chiche L, Siwy J, Faguer S, Daniel L, Daugas E, Jourde-Chiche N. Urinary Peptides as Potential Non-Invasive Biomarkers for Lupus Nephritis: Results of the Peptidu-LUP Study. J Clin Med 2021; 10:jcm10081690. [PMID: 33920017 PMCID: PMC8071029 DOI: 10.3390/jcm10081690] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Lupus nephritis (LN) is a severe manifestation of Systemic Lupus Erythematosus (SLE). The therapeutic strategy relies on kidney biopsy (KB) results. We tested whether urinary peptidome analysis could non-invasively differentiate active from non-active LN. Design: Urinary samples were collected from 93 patients (55 with active LN and 38 with non-active LN), forming a discovery (n = 42) and an independent validation (n = 51) cohort. Clinical characteristics were collected at inclusion and prospectively for 24 months. The urinary peptidome was analyzed by capillary-electrophoresis coupled to mass-spectrometry, comparing active LN to non-active LN, and assessing chronic lesions and response to therapy. The value of previously validated prognostic (CKD273) and differential diagnostic (LN172) signatures was evaluated. Results: Urinary peptides could not discriminate between active and non-active LN or predict early response to therapy. Tubulo-interstitial fibrosis was correlated to the CKD273. The LN172 score identified 92.5% of samples as LN. Few patients developed new-onset CKD. Conclusions: We validated the CKD273 and LN172 classifiers but did not identify a robust signature that could predict active LN and replace KB. The value of urinary peptidome to predict long-term CKD, or renal flares in SLE, remains to be evaluated.
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Affiliation(s)
- Maxence Tailliar
- AP-HM, Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, 13005 Marseille, France; (M.T.); (B.D.)
| | - Joost P. Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Metabolic and Cardiovascular Disease (I2MC), 31432 Toulouse, France; (J.P.S.); (B.B.); (S.F.)
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Tim Dierckx
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium;
| | - Benjamin Breuil
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Metabolic and Cardiovascular Disease (I2MC), 31432 Toulouse, France; (J.P.S.); (B.B.); (S.F.)
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Guillaume Hanouna
- AP-HP, Service de Néphrologie, Hôpital Bichat, DMU VICTOIRE, 75018 Paris, France; (G.H.); (E.D.)
| | - Nicolas Charles
- Centre de Recherche sur l’Inflammation, Université de Paris, INSERM UMRS1149, CNRS ERL8252, Labex INFLAMEX, DHU FIRE, 75890 Paris, France;
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1188-Université de La Réunion, 97490 Saint-Denis, France;
| | - Bertrand Dussol
- AP-HM, Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, 13005 Marseille, France; (M.T.); (B.D.)
- Centre d’Investigation Clinique, CHU Conception, AP-HM, 13005 Marseille, France;
| | - Alain Vazi
- Centre d’Investigation Clinique, CHU Conception, AP-HM, 13005 Marseille, France;
| | - Laurent Chiche
- Médecine Interne, Hôpital Européen, 13003 Marseille, France;
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany;
| | - Stanislas Faguer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Metabolic and Cardiovascular Disease (I2MC), 31432 Toulouse, France; (J.P.S.); (B.B.); (S.F.)
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
- CHU de Toulouse, Service de Néphrologie, 31300 Toulouse, France
| | - Laurent Daniel
- AP-HM, Laboratoire d’Ananatomie Pathologique, Hôpital de la Timone, 13005 Marseille, France;
- Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, INSERM, INRAE, 13005 Marseille, France
| | - Eric Daugas
- AP-HP, Service de Néphrologie, Hôpital Bichat, DMU VICTOIRE, 75018 Paris, France; (G.H.); (E.D.)
- Centre de Recherche sur l’Inflammation, Université de Paris, INSERM UMRS1149, CNRS ERL8252, Labex INFLAMEX, DHU FIRE, 75890 Paris, France;
| | - Noémie Jourde-Chiche
- AP-HM, Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, 13005 Marseille, France; (M.T.); (B.D.)
- Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, INSERM, INRAE, 13005 Marseille, France
- Correspondence:
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10
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Latosinska A, Siwy J, Faguer S, Beige J, Mischak H, Schanstra JP. Value of Urine Peptides in Assessing Kidney and Cardiovascular Disease. Proteomics Clin Appl 2021; 15:e2000027. [PMID: 32710812 DOI: 10.1002/prca.202000027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/18/2020] [Indexed: 12/14/2022]
Abstract
Urinary peptides gained significant attention as potential biomarkers especially in the context of kidney and cardiovascular disease. In this manuscript the recent literature since 2015 on urinary peptide investigation in human kidney and cardiovascular disease is reviewed. The technology most commonly used in this context is capillary electrophoresis coupled mass spectrometry, in part owed to the large database available and the well-defined dataspace. Several studies based on over 1000 subjects are reported in the recent past, especially examining CKD273, a classifier for assessment of chronic kidney disease based on 273 urine peptides. Interestingly, the most abundant urinary peptides are generally collagen fragments, which may have gone undetected for some time as they are typically modified via proline hydroxylation. The data available suggest that urinary peptides specifically depict inflammation and fibrosis, and may serve as a non-invasive tool to assess fibrosis, which appears to be a key driver in kidney and cardiovascular disease. The recent successful completion of the first urinary peptide guided intervention trial, PRIORITY, is expected to further spur clinical application of urinary peptidomics, aiming especially at early detection of chronic diseases, prediction of progression, and prognosis of drug response.
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Affiliation(s)
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Stanislas Faguer
- Département de Néphrologie et Transplantation d'organes, Centre de référence des maladies rénales rares, Centre Hospitalier Universitaire de Toulouse, 1, Avenue Jean Poulhes, Toulouse, 31059, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France
- Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
| | - Joachim Beige
- Department of Nephrology and Kuratorium for Dialysis and Transplantation Renal Unit, Hospital St Georg, Delitzscher Str. 141, 04129, Leipzig, Germany
- Department of Nephrology, Martin-Luther-University Halle/Wittenberg, Universitätsplatz 10, 06108, Halle (Saale), Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France
- Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
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11
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Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE‐MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019; 40:2294-2308. [DOI: 10.1002/elps.201900091] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
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12
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Caster DJ, Merchant ML, Klein JB, Powell DW. Precision medicine in lupus nephritis: can biomarkers get us there? Transl Res 2018; 201:26-39. [PMID: 30179587 PMCID: PMC6415919 DOI: 10.1016/j.trsl.2018.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/04/2018] [Accepted: 08/07/2018] [Indexed: 01/08/2023]
Abstract
Patients with systemic lupus erythematosus frequently develop lupus nephritis (LN), a condition that can lead to end-stage kidney disease. Multiple serum and urine biomarkers for LN have been proposed in recent years, yet none have become incorporated into clinical use. The majority of studies have been single center with significant variability in cohorts, assays, and sample storage, leading to inconclusive results. It has become clear that no single biomarker is likely to be sufficient to diagnose LN, identify flares, and define the response to therapy and prognosis. A more likely scenario is a panel of urine, serum, tissue, and genetic biomarkers. In this review, we summarize traditional and novel biomarkers and discuss how they may be utilized in order to bring precision medicine to clinical practice in LN.
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Affiliation(s)
- Dawn J Caster
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky.
| | - Michael L Merchant
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Jon B Klein
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky
| | - David W Powell
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
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13
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Urinary CE-MS peptide marker pattern for detection of solid tumors. Sci Rep 2018; 8:5227. [PMID: 29588543 PMCID: PMC5869723 DOI: 10.1038/s41598-018-23585-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/09/2018] [Indexed: 01/06/2023] Open
Abstract
Urinary profiling datasets, previously acquired by capillary electrophoresis coupled to mass-spectrometry were investigated to identify a general urinary marker pattern for detection of solid tumors by targeting common systemic events associated with tumor-related inflammation. A total of 2,055 urinary profiles were analyzed, derived from a) a cancer group of patients (n = 969) with bladder, prostate, and pancreatic cancers, renal cell carcinoma, and cholangiocarcinoma and b) a control group of patients with benign diseases (n = 556), inflammatory diseases (n = 199) and healthy individuals (n = 331). Statistical analysis was conducted in a discovery set of 676 cancer cases and 744 controls. 193 peptides differing at statistically significant levels between cases and controls were selected and combined to a multi-dimensional marker pattern using support vector machine algorithms. Independent validation in a set of 635 patients (293 cancer cases and 342 controls) showed an AUC of 0.82. Inclusion of age as independent variable, significantly increased the AUC value to 0.85. Among the identified peptides were mucins, fibrinogen and collagen fragments. Further studies are planned to assess the pattern value to monitor patients for tumor recurrence. In this proof-of-concept study, a general tumor marker pattern was developed to detect cancer based on shared biomarkers, likely indicative of cancer-related features.
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Magalhães P, Pejchinovski M, Markoska K, Banasik M, Klinger M, Švec-Billá D, Rychlík I, Rroji M, Restivo A, Capasso G, Bob F, Schiller A, Ortiz A, Perez-Gomez MV, Cannata P, Sanchez-Niño MD, Naumovic R, Brkovic V, Polenakovic M, Mullen W, Vlahou A, Zürbig P, Pape L, Ferrario F, Denis C, Spasovski G, Mischak H, Schanstra JP. Association of kidney fibrosis with urinary peptides: a path towards non-invasive liquid biopsies? Sci Rep 2017; 7:16915. [PMID: 29208969 PMCID: PMC5717105 DOI: 10.1038/s41598-017-17083-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
Chronic kidney disease (CKD) is a prevalent cause of morbidity and mortality worldwide. A hallmark of CKD progression is renal fibrosis characterized by excessive accumulation of extracellular matrix (ECM) proteins. In this study, we aimed to investigate the correlation of the urinary proteome classifier CKD273 and individual urinary peptides with the degree of fibrosis. In total, 42 kidney biopsies and urine samples were examined. The percentage of fibrosis per total tissue area was assessed in Masson trichrome stained kidney tissues. The urinary proteome was analysed by capillary electrophoresis coupled to mass spectrometry. CKD273 displayed a significant and positive correlation with the degree of fibrosis (Rho = 0.430, P = 0.0044), while the routinely used parameters (glomerular filtration rate, urine albumin-to-creatinine ratio and urine protein-to-creatinine ratio) did not (Rho = -0.222; -0.137; -0.070 and P = 0.16; 0.39; 0.66, respectively). We identified seven fibrosis-associated peptides displaying a significant and negative correlation with the degree of fibrosis. All peptides were collagen fragments, suggesting that these may be causally related to the observed accumulation of ECM in the kidneys. CKD273 and specific peptides are significantly associated with kidney fibrosis; such an association could not be detected by other biomarkers for CKD. These non-invasive fibrosis-related biomarkers can potentially be implemented in future trials.
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Affiliation(s)
- Pedro Magalhães
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Katerina Markoska
- Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Macedonia
| | - Miroslaw Banasik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Marian Klinger
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Dominika Švec-Billá
- 1st Department of Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ivan Rychlík
- 1st Department of Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Merita Rroji
- Department of Nephrology, University Hospital Center "Mother Teresa", Tirana, Albania
| | - Arianna Restivo
- Department of Nephrology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Flaviu Bob
- Department of Nephrology, 'Victor Babes' University of Medicine and Pharmacy, County Emergency Hospital, Timisoara, Romania
| | - Adalbert Schiller
- Department of Nephrology, 'Victor Babes' University of Medicine and Pharmacy, County Emergency Hospital, Timisoara, Romania
| | | | | | | | | | - Radomir Naumovic
- Clinic of Nephrology, Clinical Center of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Voin Brkovic
- Clinic of Nephrology, Clinical Center of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | | | - Lars Pape
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Goce Spasovski
- Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Macedonia
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Cardiovascular and Metabolic Disease, Toulouse, France.
- Université Toulouse III Paul-Sabatier, Toulouse, France.
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