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Rao C, Yang F, Lai Z, Chen S, Lu X, Jiang X. Differential expression of peptides serves as an indicator of IgA nephropathy in pediatric patients. Exp Ther Med 2020; 20:67. [PMID: 32963597 PMCID: PMC7490786 DOI: 10.3892/etm.2020.9195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 03/10/2020] [Indexed: 11/05/2022] Open
Abstract
Peptide profiles change significantly with aging and peptide biomarkers discovered in adult patients may not be suitable for the evaluation of pediatric patients. The present study was designed to explore alterations in the serum peptidome profile of pediatric patients with IgA nephropathy (IgAN). A total of 17 children diagnosed with IgAN were recruited as the experimental group, 11 sex-matched healthy children were recruited as a healthy control group and 18 sex-matched children with other glomerular diseases were recruited as a disease control group. Serum peptides of each subject were enriched and analyzed by liquid chromatography with tandem mass spectrometry and the subsequently identified IgAN-specific peptides were evaluated using Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. Subsequently, the function of the IgAN-specific peptides was predicted via sequence comparison with other known functional bioactive peptides. A total of 123 peptides with a fold change >2 (P<0.05) and 48 peptides with a fold change >5 (P<0.05) were identified to be differentially expressed between the pediatric IgAN group and the two other groups. Consequently, two putative peptides that may have bioactive effects in the pathogenesis of IgAN in pediatric patients were identified. The serum peptidome profile of pediatric patients with IgAN was significantly different from the disease control group and the healthy control group. These differentially expressed peptides may serve as biomarkers for the minimally invasive diagnosis of pediatric patients with IgAN. Additionally, the potential bioactive peptides specifically expressed in pediatric IgAN patients that were identified in this study may lay a foundation for exploring new therapies for IgAN, such as the creation of novel peptide drugs.
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Affiliation(s)
- Chunbao Rao
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China.,Scientific Research Center, Children's Hospital of Dongguan, Dongguan, Guangdong 523000, P.R. China
| | - Fan Yang
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zhijun Lai
- Pediatric Intensive Care Unit, Children's Hospital of Dongguan, Dongguan, Guangdong 523000, P.R. China
| | - Sujun Chen
- Pediatric Intensive Care Unit, Children's Hospital of Dongguan, Dongguan, Guangdong 523000, P.R. China
| | - Xiaomei Lu
- Scientific Research Center, Children's Hospital of Dongguan, Dongguan, Guangdong 523000, P.R. China
| | - Xiaoyun Jiang
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
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Chen L, Su W, Chen H, Chen DQ, Wang M, Guo Y, Zhao YY. Proteomics for Biomarker Identification and Clinical Application in Kidney Disease. Adv Clin Chem 2018; 85:91-113. [PMID: 29655463 DOI: 10.1016/bs.acc.2018.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Treatment effectiveness for kidney disease is limited by lack of accuracy, sensitivity, specificity of diagnostic, prognostic, and therapeutic biomarkers. The gold standard test renal biopsy along with serum creatinine and proteinuria is often necessary to establish a diagnosis, particularly in glomerular disease. Proteomics has become a powerful tool for novel biomarker discovery in kidney disease. Novel proteomics offer earlier and more accurate diagnosis of renal pathology than possible with traditional biomarkers such as serum creatinine and urine protein. In addition, proteomic biomarkers could also be useful to choose the most suitable therapeutic targets. This review focuses on the current status of proteomic biomarkers from animal models (5/6 nephrectomy, unilateral ureteral obstruction, and diabetic nephropathy) and human studies (chronic kidney disease, glomerular diseases, transplantation, dialysis, acute and drug-induced kidney injury) to assess relevant findings and clinical usefulness. Current issues and problems related to the discovery, validation, and clinical application of proteomic biomarkers are discussed. We also describe several proteomic strategies highlighting technologic advancements, specimen selection, data processing and analysis. This review might provide help in future proteomic studies to improve the diagnosis and management of kidney disease.
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Affiliation(s)
- Lin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Wei Su
- Baoji Central Hospital, Baoji, China
| | - Hua Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Dan-Qian Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Ming Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Yan Guo
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, United States
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China.
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Zeng J, Wen Q, Rong R, Huang F, Yang Q, Tang X, He F, Huang N, Yu X. Vitamin D-Binding Protein Is a Potential Urinary Biomarker of Irbesartan Treatment Response in Patients with IgA Nephropathy. Genet Test Mol Biomarkers 2016; 20:666-673. [PMID: 27603418 DOI: 10.1089/gtmb.2016.0070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
AIMS The purpose of this study was to identify predictive markers of irbesartan (an angiotensin receptor blocker) treatment response in immunoglobulin A nephropathy (IgAN) patients. METHODS Urine samples were collected both before and after irbesartan treatment in IgAN patients and compared with urine from healthy volunteers. The total urinary protein produced in 24 h was measured to determine therapeutic response. The urinary proteome was evaluated by two-dimensional gel electrophoresis coupled with MALDI-TOF-MS/MS analysis. Western blotting was used to verify protein expression. A receiver operating characteristic curve was used to evaluate the sensitivity and specificity of candidate biomarkers. RESULTS Four differentially expressed proteins were identified as vitamin D-binding proteins (VDPs). Western blot showed that urinary VDPs were significantly elevated in nonresponsive versus responsive IgAN patients. The sensitivity, specificity, and accuracy of urinary VDP as a predictive biomarker of irbesartan nonresponsiveness in IgAN were 65%, 85%, and 75%, respectively. CONCLUSION Our results revealed that urinary VDP might be a useful biomarker for predicting irbesartan treatment response.
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Affiliation(s)
- Jiashun Zeng
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Qiong Wen
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Rong Rong
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Fengxian Huang
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Qiongqiong Yang
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Xueqing Tang
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Feng He
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Naya Huang
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
| | - Xueqing Yu
- 1 Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, People's Republic of China .,2 Key Laboratory of Nephrology, Ministry of Health , Guangzhou, People's Republic of China
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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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Miura Y, Hashii N, Tsumoto H, Takakura D, Ohta Y, Abe Y, Arai Y, Kawasaki N, Hirose N, Endo T. Change in N-Glycosylation of Plasma Proteins in Japanese Semisupercentenarians. PLoS One 2015; 10:e0142645. [PMID: 26559536 PMCID: PMC4641608 DOI: 10.1371/journal.pone.0142645] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/23/2015] [Indexed: 12/26/2022] Open
Abstract
An N-glycomic analysis of plasma proteins was performed in Japanese semisupercentenarians (SSCs) (mean 106.7 years), aged controls (mean 71.6 years), and young controls (mean 30.2 years) by liquid chromatography/mass spectrometry (LC/MS) using a graphitized carbon column. Characteristic N-glycans in SSCs were discriminated using a multivariate analysis; orthogonal projections to latent structures (O-PLS). The results obtained showed that multi-branched and highly sialylated N-glycans as well as agalacto- and/or bisecting N-glycans were increased in SSCs, while biantennary N-glycans were decreased. Since multi-branched and highly sialylated N-glycans have been implicated in anti-inflammatory activities, these changes may play a role in the enhanced chronic inflammation observed in SSCs. The levels of inflammatory proteins, such as CRP, adiponectin, IL-6, and TNF-α, were elevated in SSCs. These results suggested that responses to inflammation may play an important role in extreme longevity and healthy aging in humans. This is the first study to show that the N-glycans of plasma proteins were associated with extreme longevity and healthy aging in humans.
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Affiliation(s)
- Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Daisuke Takakura
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Yuki Ohta
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Yukiko Abe
- Center for Supercentenarian Research, Keio University School of Medicine, Tokyo, Japan
| | - Yasumichi Arai
- Center for Supercentenarian Research, Keio University School of Medicine, Tokyo, Japan
| | - Nana Kawasaki
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, Japan
| | - Nobuyoshi Hirose
- Center for Supercentenarian Research, Keio University School of Medicine, Tokyo, Japan
| | - Tamao Endo
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
- * E-mail:
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Noguchi M, Sato T, Nagai K, Utagawa I, Suzuki I, Arito M, Iizuka N, Suematsu N, Okamoto K, Kato T, Yamaguchi N, Kurokawa MS. Roles of serum fibrinogen α chain-derived peptides in Alzheimer's disease. Int J Geriatr Psychiatry 2014; 29:808-18. [PMID: 24190360 DOI: 10.1002/gps.4047] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/09/2013] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To find a blood biomarker and disease-related peptides in Alzheimer's disease (AD), we comprehensively detected serum peptides. METHODS Ion intensity of serum peptides from 62 AD patients and 82 control subjects was measured by mass spectrometry. RESULTS A total of 157 peptides were detected from 30 AD patients and 30 healthy control (HC) subjects. Sixty out of the 157 peptide profiles discriminated between the AD and HC groups. Sixteen out of the 60 peptides were identified, 10 out of which were fragments of a fibrinogen α chain (FIBA). Among the 10 peptides, four and six peptides were derived from fibrinopeptide A (FPA, Aα1-16) and the C-terminal region of the αC-domain (αCDC, Aα557-610), respectively. The profile of 10 FIBA-derived peptides combined with age discriminated between the two groups with an area under the receiver operating characteristic curve (AUROC) of 0.940. Validation of this model using a testing set of 32 AD patients and 19 HC subjects showed an AUROC of 0.717, sensitivity of 65.6%, and specificity of 73.7% by a cutoff value of 0.56420. Another value, 0.04029, showed sensitivity of 96.9%, suggesting that subjects with values less than 0.04029 rarely possess AD. FPA and αCDC showed increased ion intensity in the AD group compared with the HC group (p < 0.05). CONCLUSIONS The profile of 10 FIBA-derived peptides combined with age would be a candidate biomarker for AD, which facilitates screening of the disease. The significant release of FPA and αCDC may be involved in the aberrant coagulation that leads to vascular damage in AD.
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Affiliation(s)
- Miwa Noguchi
- Department of Neuropsychiatry, St. Marianna University School of Medicine, Kawasaki, Japan
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Hashii N, Harazono A, Kuribayashi R, Takakura D, Kawasaki N. Characterization of N-glycan heterogeneities of erythropoietin products by liquid chromatography/mass spectrometry and multivariate analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:921-932. [PMID: 24623697 DOI: 10.1002/rcm.6858] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 01/26/2014] [Accepted: 01/26/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Glycan heterogeneity on recombinant human erythropoietin (rEPO) product is considered to be one of the critical quality attributes, and similarity tests of glycan heterogeneities are required in the manufacturing process changes and developments of biosimilars. A method for differentiating highly complex and diverse glycosylations is needed to evaluate comparability and biosimilarity among rEPO batches and products manufactured by different processes. METHODS The glycan heterogeneities of nine rEPO products (four innovator products and five biosimilar products) were distinguished by multivariate analysis (MVA) using the peak area ratios of each glycan to the total peak area of glycans in mass spectra obtained by liquid chromatography/mass spectrometry (LC/MS) of N-glycans from rEPOs. RESULTS Principal component analysis (PCA) using glycan profiles obtained by LC/MS proved to be a useful method for differentiating glycan heterogeneities among nine rEPOs. Using PC values as indices, we were able to visualize and digitalize the glycan heterogeneities of each rEPO. The characteristic glycans of each rEPO were also successfully identified by orthogonal partial least-squares discrimination analysis (OPLS-DA), an MVA method, using the glycan profile data. CONCLUSIONS PCA values were useful for evaluating the relative differences among the glycan heterogeneities of rEPOs. The characteristic glycans that contributed to the differentiation were also successfully identified by OPLS-DA. PCA and OPLS-DA based on mass spectrometric data are applicable for distinguishing glycan heterogeneities, which are virtually indistinguishable on rEPO products.
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Affiliation(s)
- Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan
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Pérez V, Juega-Mariño J, Bonjoch A, Negredo E, Clotet B, Romero R, Bonet J. Evaluation of protease inhibitors containing tubes for MS-based plasma peptide profiling studies. J Clin Lab Anal 2014; 28:364-7. [PMID: 24648264 DOI: 10.1002/jcla.21694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Peptide profiling of biological fluids is a promising tool for biomarker discovery. Blood is an ideal entity for proteomic studies but it is subjected to a proteolytic activity that sets up just at the moment of phlebotomy. Intending to prevent this proteolytic activity, tubes containing protease inhibitors (PI) have been developed. In this study, we evaluated the effect on plasma peptide profile of using tubes containing PI and the evolution of this effect over time. METHODS Blood samples from ten subjects were drawn into conventional tubes containing ethylenediaminetetraacetic acid (EDTA) and tubes containing PI. Samples were processed at time "zero" and after 1, 2, 4, and 8 hr. Plasma peptide profiles were analyzed by magnetic bead based technology coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry readout. RESULTS When comparing plasma peptide profile of blood samples collected into tubes containing PI with samples collected into conventional EDTA tubes, differences in the area of 13 peaks were detected at time "zero"; after 8 hr these differences tended to disappear. Moreover, bradykinin and C3- and C4-derived peptides were produced promptly after blood extraction when samples were collected into conventional EDTA tubes, and the use of PI prevented their generation. CONCLUSION Considering that time taken to process blood samples affects their peptide profile and a decrease in PI's effect occurs over time, it may be concluded that the use of tubes containing PI for blood collection may be advantageous in the context of research, but may have some limitations regarding clinical practice.
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Affiliation(s)
- Vanessa Pérez
- Department of Nephrology, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain; Laboratory of Experimental Nephrology, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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Conraux L, Pech C, Guerraoui H, Loyaux D, Ferrara P, Guillemot JC, Meininger V, Pradat PF, Salachas F, Bruneteau G, Le Forestier N, Lacomblez L. Plasma peptide biomarker discovery for amyotrophic lateral sclerosis by MALDI-TOF mass spectrometry profiling. PLoS One 2013; 8:e79733. [PMID: 24224000 PMCID: PMC3818176 DOI: 10.1371/journal.pone.0079733] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 10/03/2013] [Indexed: 12/13/2022] Open
Abstract
The diagnostic of Amyotrophic lateral sclerosis (ALS) remains based on clinical and neurophysiological observations. The actual delay between the onset of the symptoms and diagnosis is about 1 year, preventing early inclusion of patients into clinical trials and early care of the disease. Therefore, finding biomarkers with high sensitivity and specificity remains urgent. In our study, we looked for peptide biomarkers in plasma samples using reverse phase magnetic beads (C18 and C8) and MALDI-TOF mass spectrometry analysis. From a set of ALS patients (n=30) and healthy age-matched controls (n=30), C18- or C8-SVM-based models for ALS diagnostic were constructed on the base of the minimum of the most discriminant peaks. These two SVM-based models end up in excellent separations between the 2 groups of patients (recognition capability overall classes > 97%) and classify blinded samples (10 ALS and 10 healthy age-matched controls) with very high sensitivities and specificities (>90%). Some of these discriminant peaks have been identified by Mass Spectrometry (MS) analyses and correspond to (or are fragments of) major plasma proteins, partly linked to the blood coagulation.
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Affiliation(s)
| | | | | | | | | | | | - Vincent Meininger
- Centre référent maladies Rares, APHP, UPMC, La Salpêtrière Hospital, Paris, France
| | | | - François Salachas
- Centre référent maladies Rares, APHP, UPMC, La Salpêtrière Hospital, Paris, France
| | - Gaëlle Bruneteau
- Centre référent maladies Rares, APHP, UPMC, La Salpêtrière Hospital, Paris, France
| | - Nadine Le Forestier
- Centre référent maladies Rares, APHP, UPMC, La Salpêtrière Hospital, Paris, France
| | - Lucette Lacomblez
- Centre référent maladies Rares, APHP, UPMC, La Salpêtrière Hospital, Paris, France
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A novel differential predict model based on matrix-assisted laser ionization time-of-flight mass spectrometry and serum ferritin for acute graft-versus-host disease. BIOMED RESEARCH INTERNATIONAL 2013; 2013:563751. [PMID: 24195075 PMCID: PMC3806346 DOI: 10.1155/2013/563751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 08/20/2013] [Indexed: 12/12/2022]
Abstract
Clinical diagnosis of acute graft-versus-host disease (aGVHD) mainly depends on clinical manifestation and tissue biopsies, leading to a delayed diagnosis and treatment for aGVHD patients when the early symptom is insignificant. Our objective was to investigate the possibility of prewarning the risk of aGVHD before and after allogeneic hematopoietic stem cell transplantation (allo-HSCT) by serum protein profiling combined with serum ferritin. The difference in polypeptide expression before and after transplantation had been compared by using CLINPROT technology, and serum ferritin levels have been analyzed simultaneously. Through combining serum ferritin and MS spectral data, the diagnosis sensitivity and specificity of our model for prewarning severe aGVHD (III~IV°aGVHD) before transplant all increased to 90.0%, while after transplant, the sensitivity and specificity are 78.3% and 86.4%. Our joint prewarning model could predict the risk of aGVHD, especially severe aGVHD before and after transplant, which also provides a reliable method to the continuous monitoring of the condition of patients.
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Noguchi Y, Kurokawa MS, Okuse C, Matsumoto N, Nagai K, Sato T, Arito M, Suematsu N, Okamoto K, Suzuki M, Itoh F, Kato T. Serum peptides, represented by complement 3f des-arginine, are useful for prediction of the response to pegylated interferon-α plus ribavirin in patients with chronic hepatitis C. Hepatol Res 2013; 43:743-56. [PMID: 23216931 DOI: 10.1111/hepr.12018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 10/08/2012] [Accepted: 10/31/2012] [Indexed: 02/06/2023]
Abstract
AIM Biomarkers predicting sustained virological response (SVR) to pegylated interferon-α plus ribavirin (PEG IFN-α/RBV) were investigated. METHODS Peptides in pretreatment sera from 107 patients with hepatitis C virus (HCV) genotype 1 were comprehensively analyzed by mass spectrometry. Ion intensity of the peptides was used to generate discriminant models between the responders who achieved SVR (R) and the non-responders (NR) to PEG IFN-α/RBV. RESULTS In total, 107 peptides were detected in a training set (n = 23). A discriminant model using a peptide, complement 3f des-arginine (C3f-dR), showed sensitivity of 35% and specificity of 94% for SVR prediction in a testing set (n = 68). In all the R and NR (n = 96), an area under the receiver-operator curve (AUROC) of 0.64 in the C3f-dR model was increased to 0.78 by addition of platelet (PLT) counts (C3f-dR/PLT model). Another model using the 107 peptides (AUROC, 0.77) also showed higher AUROC (0.79) by addition of hemoglobin (Hb), body mass index (BMI) and age (107P/Hb/BMI/Age model). The sensitivity and specificity of the C3f-dR/PLT model were 59% and 88%, and those of the 107P/Hb/BMI/Age model were 70% and 92%, respectively. The C3f-dR/PLT model showed high AUROC (0.82), similar to that of interleukin-28B rs8099917 genotype analysis (0.86) in the 45 tested patients. Prediction by the combination of the C3f-dR/PLT model, the 107P/Hb/BMI/Age model and the rs8099917 genotype analysis was accurate in 44 out of the 45 patients (AUROC, 0.95). CONCLUSION Serum peptides, especially C3f-dR, would be useful predictors for SVR to PEG IFN-α/RBV. The complements may be involved in the HCV elimination.
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Affiliation(s)
- Yohei Noguchi
- Clinical Proteomics and Molecular Medicine, St Marianna University Graduate School of Medicine, Japan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, St Marianna University School of Medicine, Japan
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Konvalinka A, Scholey JW, Diamandis EP. Searching for new biomarkers of renal diseases through proteomics. Clin Chem 2011; 58:353-65. [PMID: 21980170 DOI: 10.1373/clinchem.2011.165969] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Technological advances have resulted in a renaissance of proteomic studies directed at finding markers of disease progression, diagnosis, or responsiveness to therapy. Renal diseases are ideally suited for such research, given that urine is an easily accessible biofluid and its protein content is derived mainly from the kidney. Current renal prognostic markers have limited value, and renal biopsy remains the sole method for establishing a diagnosis. Mass spectrometry instruments, which can detect thousands of proteins at nanomolar (or even femtomolar) concentrations, may be expected to allow the discovery of improved markers of progression, diagnosis, or treatment responsiveness. CONTENT In this review we describe the strengths and limitations of proteomic methods and the drawbacks of existing biomarkers, and provide an overview of opportunities in the field. We also highlight several proteomic studies of biomarkers of renal diseases selected from the plethora of studies performed. SUMMARY It is clear that the field of proteomics has not yet fulfilled its promise. However, ongoing efforts to standardize sample collection and preparation, improve study designs, perform multicenter validations, and create joint industry-regulatory bodies offer promise for the recognition of novel molecules that could change clinical nephrology forever.
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Affiliation(s)
- Ana Konvalinka
- Department of Medicine, Division of Nephrology, University of Toronto, Toronto, Ontario, Canada
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Prunotto M, Ghiggeri G, Bruschi M, Gabbiani G, Lescuyer P, Hocher B, Chaykovska L, Berrera M, Moll S. Renal fibrosis and proteomics: current knowledge and still key open questions for proteomic investigation. J Proteomics 2011; 74:1855-70. [PMID: 21642026 DOI: 10.1016/j.jprot.2011.05.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/27/2011] [Accepted: 05/22/2011] [Indexed: 12/25/2022]
Abstract
Renal tubulo-interstitial fibrosis is a non-specific process, representing the final common pathway for all kidney diseases, irrespective of their initial cause, histological injury, or etiology, leading to gradual expansion of the fibrotic mass which destroys the normal structure of the tissue and results in organ dysfunction and, ultimately, in end-stage organ failure. Proteomic studies of the fibrotic pathophysiological mechanisms have been performed in cell cultures, animal models and human tissues, addressing some of the key issues. This article will review proteomic contribution to the raising current knowledge on renal fibrosis biology and also mention seminal open questions to which proteomic techniques and proteomists could fruitfully contribute.
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Affiliation(s)
- Marco Prunotto
- RenalChild Foundation, G. Gaslini Children Hospital, Genoa, Italy.
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Teunissen CE, Koel-Simmelink MJA, Pham TV, Knol JC, Khalil M, Trentini A, Killestein J, Nielsen J, Vrenken H, Popescu V, Dijkstra CD, Jimenez CR. Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry. Mult Scler 2011; 17:838-50. [PMID: 21505015 DOI: 10.1177/1352458511399614] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Body fluid biomarkers for clinical subtyping and monitoring of disease progression are of considerable interest in multiple sclerosis (MS). Proteomics tools are optimal for the unbiased simultaneous detection of large series of peptides and proteins. OBJECTIVES To identify novel candidate biomarkers discriminating patients with MS from patients with other neurological diseases (OND), and for subtyping of relapsing-remitting (RR), secondary progressive (SP) and primary progressive (PP) MS patients using a high-throughput MALDI-TOF-based mass spectrometry method. METHODS Paired cerebrospinal fluid (CSF) and serum samples of 41 RRMS, 30 SPMS, 13 PPMS patients and 25 patients with OND were analysed. RESULTS Out of a total of 100 detected peptides in CSF and 200 peptides in serum, 11 peptides were differentially regulated in serum and two in CSF between patients with MS and the OND control group. Eleven peptides were differentially regulated in both serum and CSF between relapse-onset MS and PPMS patients. Lastly, four peptides were differentially regulated in serum and two in CSF between RRMS and SPMS patients. Specific peaks regulated in MS were tentatively identified as fragments of secretogranin III and complement C3. The peak intensity of the CSF peptide ion with m/z value 8607.7 correlated to atrophy (r = -0.27, p < 0.005), black hole volumes (r = 0.31, p < 0.008) and total lesion load (r = 0.34, p < 0.003). A serum peptide with m/z value of 872.4 elevated in SPMS correlated to Expanded Disability Status Scale (r = 0.341, p < 0.005) and atrophy (r = -0.286, p < 0.028). CONCLUSIONS Using high-throughput body fluid profiling by MALDI-TOF mass spectrometry, small proteins and peptides were detected as promising candidate biomarkers for diagnosis and disease progression of MS.
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Affiliation(s)
- C E Teunissen
- NUBIN, Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands.
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The Quest for Renal Disease Proteomic Signatures: Where Should We Look? Clin Proteomics 2010. [DOI: 10.1007/s12014-010-9047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Abstract
Renal diseases are prevalent and important. However, despite significant strides in medicine, clinical nephrology still relies on nonspecific and inadequate markers such as serum creatinine and total urine protein for monitoring and diagnosis of renal disease. In case of glomerular renal diseases, biopsy is often necessary to establish the diagnosis. With new developments in proteomics technology, numerous studies have emerged, searching for better markers of kidney disease diagnosis and/or prognosis. Blood, urine, and renal biopsy tissue have been explored as potential sources of biomarkers. Some interesting individual or multiparametric biomarkers have been found; however, none have yet been validated or entered clinical practice. This review focuses on some studies of biomarkers of glomerular renal diseases, as well as addresses the question of which sample type(s) might be most promising in preliminary discovery phases of candidate proteins.
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