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Ge L, Liu J, Lin B, Qin X. Progress in understanding primary glomerular disease: insights from urinary proteomics and in-depth analyses of potential biomarkers based on bioinformatics. Crit Rev Clin Lab Sci 2023:1-20. [PMID: 36815270 DOI: 10.1080/10408363.2023.2178378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Chronic kidney disease (CKD) has become a global public health challenge. While primary glomerular disease (PGD) is one of the leading causes of CKD, the specific pathogenesis of PGD is still unclear. Accurate diagnosis relies largely on invasive renal biopsy, which carries risks of bleeding, pain, infection and kidney vein thrombosis. Problems with the biopsy procedure include lack of glomeruli in the tissue obtained, and the sampling site not being reflective of the overall lesion in the kidney. Repeated renal biopsies to monitor disease progression cannot be performed because of the significant risks of bleeding and kidney vein thrombosis. On the other hand, urine collection, a noninvasive method, can be performed repeatedly, and urinary proteins can reflect pathological changes in the urinary system. Advancements in proteomics technologies, especially mass spectrometry, have facilitated the identification of candidate biomarkers in different pathological types of PGD. Such biomarkers not only provide insights into the pathogenesis of PGD but also are important for diagnosis, monitoring treatment, and prognosis. In this review, we summarize the findings from studies that have used urinary proteomics, among other omics screens, to identify potential biomarkers for different types of PGD. Moreover, we performed an in-depth bioinformatic analysis to gain a deeper understanding of the biological processes and protein-protein interaction networks in which these candidate biomarkers may participate. This review, including a description of an integrated analysis method, is intended to provide insights into the pathogenesis, noninvasive diagnosis, and personalized treatment efforts of PGD and other associated diseases.
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Affiliation(s)
- Lili Ge
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Jianhua Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Baoxu Lin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
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Johann DJ, Shin IJ, Roberge A, Laun S, Peterson EA, Liu M, Steliga MA, Muesse J, Emmert-Buck MR, Tangrea MA. Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples. J Histochem Cytochem 2022; 70:643-658. [PMID: 36129255 PMCID: PMC9527476 DOI: 10.1369/00221554221124163] [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: 05/25/2021] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Immunohistochemical (IHC) staining is an established technique for visualizing proteins in tissue sections for research studies and clinical applications. IHC is increasingly used as a targeting strategy for procurement of labeled cells via tissue microdissection, including immunodissection, computer-aided laser dissection (CALD), expression microdissection (xMD), and other techniques. The initial antigen retrieval (AR) process increases epitope availability and improves staining characteristics; however, the procedure can damage DNA. To better understand the effects of AR on DNA quality and quantity in immunodissected samples, both clinical specimens (KRAS gene mutation positive cases) and model system samples (lung cancer patient-derived xenograft tissue) were subjected to commonly employed AR methods (heat induced epitope retrieval [HIER], protease digestion) and the effects on DNA were assessed by Qubit, fragment analysis, quantitative PCR, digital droplet PCR (ddPCR), library preparation, and targeted sequencing. The data showed that HIER resulted in optimal IHC staining characteristics, but induced significant damage to DNA, producing extensive fragmentation and decreased overall yields. However, neither of the AR methods combined with IHC prevented ddPCR amplification of small amplicons and gene mutations were successfully identified from immunodissected clinical samples. The results indicate for the first time that DNA recovered from immunostained slides after standard AR and IHC processing can be successfully employed for genomic mutation analysis via ddPCR and next-generation sequencing (NGS) short-read methods.
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Affiliation(s)
- Donald J. Johann
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ik Jae Shin
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Sarah Laun
- Avoneaux Medical Institute, Baltimore,
Maryland
- Alvin & Lois Lapidus Cancer Institute,
Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, Maryland
| | - Erich A. Peterson
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Meei Liu
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Matthew A. Steliga
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jason Muesse
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Michael A. Tangrea
- Alvin & Lois Lapidus Cancer Institute,
Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, Maryland
- Biology Department, Loyola University
Maryland, Baltimore, Maryland
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Li Y, Yang K, Yuan H, Zhang W, Sui Z, Wang N, Lin H, Zhang L, Zhang Y. Surface Nanosieving Polyether Sulfone Particles with Graphene Oxide Encapsulation for the Negative Isolation toward Extracellular Vesicles. Anal Chem 2021; 93:16835-16844. [PMID: 34889606 DOI: 10.1021/acs.analchem.1c03588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Extracellular vesicles (EVs) contain specific biomarkers for disease diagnosis. Current EV isolation methods are hampered in important biological applications due to their low recovery and purity. Herein, we first present a novel EV negative isolation strategy based on surface nanosieving polyether sulfone particles with graphene oxide encapsulation (SNAPs) by which the coexisting proteins are irreversibly adsorbed by graphene oxide (GO) inside the particles, while EVs with large sizes are excluded from the outside due to the well-defined surface pore sizes (10-40 nm). By this method, the purity of the isolated EVs from urine could be achieved 4.91 ± 1.01e10 particles/μg, 40.9-234 times higher than those obtained by the ultracentrifugation (UC), size-exclusion chromatography (SEC), and PEG-based precipitation. In addition, recovery ranging from 90.4 to 93.8% could be obtained with excellent reproducibility (RSD < 6%). This was 1.8-4.3 times higher than those obtained via SEC and UC, comparable to that obtained by PEG-based precipitation. Taking advantage of this strategy, we further isolated urinary EVs from IgA nephropathy (IgAN) patients and healthy donors for comparative proteome analysis, by which significantly regulated EV proteins were found to distinguish IgAN patients from healthy donors. All of the results indicated that our strategy would provide a new avenue for highly efficient EV isolation to enable many important clinical applications.
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Affiliation(s)
- Yilan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Nan Wang
- The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Hongli Lin
- The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Urinary Protein and Peptide Markers in Chronic Kidney Disease. Int J Mol Sci 2021; 22:ijms222212123. [PMID: 34830001 PMCID: PMC8625140 DOI: 10.3390/ijms222212123] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/21/2022] Open
Abstract
Chronic kidney disease (CKD) is a non-specific type of kidney disease that causes a gradual decline in kidney function (from months to years). CKD is a significant risk factor for death, cardiovascular disease, and end-stage renal disease. CKDs of different origins may have the same clinical and laboratory manifestations but different progression rates, which requires early diagnosis to determine. This review focuses on protein/peptide biomarkers of the leading causes of CKD: diabetic nephropathy, IgA nephropathy, lupus nephritis, focal segmental glomerulosclerosis, and membranous nephropathy. Mass spectrometry (MS) approaches provided the most information about urinary peptide and protein contents in different nephropathies. New analytical approaches allow urinary proteomic-peptide profiles to be used as early non-invasive diagnostic tools for specific morphological forms of kidney disease and may become a safe alternative to renal biopsy. MS studies of the key pathogenetic mechanisms of renal disease progression may also contribute to developing new approaches for targeted therapy.
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Wu Q, Fenton RA. Urinary proteomics for kidney dysfunction: insights and trends. Expert Rev Proteomics 2021; 18:437-452. [PMID: 34187288 DOI: 10.1080/14789450.2021.1950535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introduction: Kidney dysfunction poses a high burden on patients and health care systems. Early detection and accurate prediction of kidney disease progression remains a major challenge. Compared to existing clinical parameters, urinary proteomics has the potential to reveal molecular alterations within the kidney that may alter its function before the onset of clinical symptoms. Thus, urinary proteomics has greater prognostic potential for assessment of kidney dysfunction progression.Areas covered: Advances in urinary proteomics for major causes of kidney dysfunction are discussed. The application of urinary extracellular vesicles for studying kidney dysfunction are discussed. Technological advances in urinary proteomics are discussed. The literature was identified using a database search for titles containing 'proteom*' and 'urin*' and published within the past 5 years. Retrieved literature was manually filtered to retain kidney dysfunctions-related studies.Expert opinion: Despite major advances, diagnosis by urinary proteomics has not been fully applied in any clinical settings. This could be attributed to the complex nature of kidney diseases, in addition to the constraints on study power and feasibility of incorporating mass spectrometry techniques in daily routine analysis. Nevertheless, we are confident that advances in urinary proteomics will soon provide superior insights into kidney disease beyond existing clinical parameters.
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Affiliation(s)
- Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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Jin J, Gong J, Zhao L, Li Y, Wang Y, He Q. iTRAQ-based comparative proteomics analysis reveals specific urinary biomarkers for various kidney diseases. Biomark Med 2020; 14:839-854. [PMID: 32856461 DOI: 10.2217/bmm-2019-0556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/20/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Proteome studies for multiple renal diseases is bare. Methodology & results: Using isobaric tags for relative and absolute quantitation labeling, many differentially expressed proteins (DEPs) were identified in acute kidney injury (AKI), AKI + chronic kidney disease (CKD), diabetic CKD and nondiabetic CKD with or without IgA nephropathy (IgAN). Comparative analysis indicated that 34, 35, 17, 91 and 14 unique DEPs were found in AKI, AKI + CKD, CKD, diabetic CKD and nondiabetic CKD. Compared with nondiabetic CKD with IgAN, 47 unique DEPs were found in that without IgAN. Serum amyloid A1 (SAA1) and hepatocyte growth factor activator were unregulated in AKI and nondiabetic CKD without IgAN, respectively. Regenerating islet-derived protein 3-α (Reg3A) upregulation is associated with AKI and AKI + CKD patients. Conclusion: This research contributes to urinary biomarker discovery from multiple renal diseases.
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Affiliation(s)
- Juan Jin
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Jianguang Gong
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Li Zhao
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Yiwen Li
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Yunguang Wang
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Qiang He
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
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Jiang W, Ma T, Zhang C, Tang X, Xu Q, Meng X, Ma T. Identification of urinary candidate biomarkers of cisplatin-induced nephrotoxicity in patients with carcinoma. J Proteomics 2020; 210:103533. [DOI: 10.1016/j.jprot.2019.103533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/23/2019] [Accepted: 09/19/2019] [Indexed: 10/25/2022]
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Kawata N, Kang D, Aiuchi T, Obama T, Yoshitake O, Shibata T, Takimoto M, Itabe H, Honda K. Proteomics of human glomerulonephritis by laser microdissection and liquid chromatography-tandem mass spectrometry. Nephrology (Carlton) 2019; 25:351-359. [PMID: 31707756 PMCID: PMC7064884 DOI: 10.1111/nep.13676] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/04/2019] [Accepted: 10/13/2019] [Indexed: 12/14/2022]
Abstract
Aim Laser microdissection (LMD) and liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) enable clinicians to analyse proteins from tissue sections. In nephrology, these methods are used to diagnose diseases of abnormal protein deposition, such as amyloidosis, but they are seldom applied to the diagnosis and pathophysiological understanding of human glomerular diseases. Methods Renal biopsy specimens were obtained from five patients with IgA nephropathy (IgAN), five patients with membranous nephropathy (MN) and five kidney transplant donors (as controls). From 10‐μm‐thick sections of formalin‐fixed, paraffin‐embedded specimens, 0.3‐mm2 samples of glomerular tissue were subjected to LMD. The samples were analysed by LC‐MS/MS and investigated clinically and histologically. Results From the control glomeruli, we identified more than 300 types of proteins. In patients with IgAN, we detected significant increases not only in IgA1 and in C3, but also in the factors related to oxidative stress and cell proliferation in comparison to the controls. In patients with MN, levels of IgG1, IgG4, C3, C4a and phospholipase‐A2‐receptor were significantly elevated in comparison to the controls, as were the aforementioned factors related to oxidative stress and cell proliferations detected in IgAN. Conclusion Application of LMD and LC‐MS/MS to renal biopsy specimens enabled us to identify not only pathognomonic proteins for the diagnosis, but also several factors possibly involved in the pathogenesis of human glomerular diseases. This paper examined the possible application of laser microdissection and liquid chromatography‐tandem mass spectrometry to renal biopsy specimens to clarify the pathogenesis of human glomerular diseases.
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Affiliation(s)
- Naoto Kawata
- Department of Anatomy, Showa University School of Medicine, Tokyo, Japan.,Department of Medicine, Division of Nephrology, Showa University Fujigaoka Hospital, Kanagawa, Japan
| | - Dedong Kang
- Department of Anatomy, Showa University School of Medicine, Tokyo, Japan
| | - Toshihiro Aiuchi
- Department of Pharmaceutical Sciences, Division of Biological Chemistry, Showa University School of Pharmacy, Tokyo, Japan
| | - Takashi Obama
- Department of Pharmaceutical Sciences, Division of Biological Chemistry, Showa University School of Pharmacy, Tokyo, Japan
| | - Osamu Yoshitake
- Department of Surgery, Division of General and Gastroenterological Surgery, Showa University School of Medicine, Tokyo, Japan
| | - Takanori Shibata
- Department of Medicine, Division of Nephrology, Showa University School of Medicine, Tokyo, Japan
| | - Masafumi Takimoto
- Department of Pathology, Showa University School of Medicine, Tokyo, Japan
| | - Hiroyuki Itabe
- Department of Pharmaceutical Sciences, Division of Biological Chemistry, Showa University School of Pharmacy, Tokyo, Japan
| | - Kazuho Honda
- Department of Anatomy, Showa University School of Medicine, Tokyo, Japan
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