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Paphussaro W, Roytrakul S, Phaonakrop N, Buthasane W, Rungsipipat A, Tharasanit T, Suriyaphol G. Analysis of serum peptidome profiles of non-metastatic and metastatic feline mammary carcinoma using liquid chromatography-tandem mass spectrometry. BMC Vet Res 2024; 20:280. [PMID: 38951817 PMCID: PMC11218297 DOI: 10.1186/s12917-024-04148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 06/18/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Feline mammary carcinoma (FMC) is a common aggressive and highly metastatic cancer affecting female cats. Early detection is essential for preventing local and distant metastasis, thereby improving overall survival rates. While acquiring molecular data before surgery offers significant potential benefits, the current protein biomarkers for monitoring disease progression in non-metastatic FMC (NmFMC) and metastatic FMC (mFMC) are limited. The objective of this study was to investigate the serum peptidome profiles of NmFMC and mFMC using liquid chromatography-tandem mass spectrometry. A cross-sectional study was conducted to compare serum peptidome profiles in 13 NmFMC, 23 mFMC and 18 healthy cats. The liquid chromatography-tandem mass spectrometry analysis was performed on non-trypsinized samples. RESULTS Out of a total of 8284 expressed proteins observed, several proteins were found to be associated with human breast cancer. In NmFMC, distinctive protein expressions encompassed double-stranded RNA-binding protein Staufen homolog 2 (STAU2), associated with cell proliferation, along with bromodomain adjacent to zinc finger domain 2A (BAZ2A) and gamma-aminobutyric acid type A receptor subunit epsilon (GABRE), identified as potential treatment targets. Paradoxically, positive prognostic markers emerged, such as complement C1q like 3 (C1QL3) and erythrocyte membrane protein band 4.1 (EPB41 or 4.1R). Within the mFMC group, overexpressed proteins associated with poor prognosis were exhibited, including B-cell lymphoma 6 transcription repressor (BCL6), thioredoxin reductase 3 (TXNRD3) and ceruloplasmin (CP). Meanwhile, the presence of POU class 5 homeobox (POU5F1 or OCT4) and laminin subunit alpha 1 (LAMA1), reported as metastatic biomarkers, was noted. CONCLUSION The presence of both pro- and anti-proliferative proteins was observed, potentially indicating a distinctive characteristic of NmFMC. Conversely, proteins associated with poor prognosis and metastasis were noted in the mFMC group.
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Affiliation(s)
- Weejarin Paphussaro
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Center of Excellence for Companion Animal Cancer, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
| | - Anudep Rungsipipat
- Center of Excellence for Companion Animal Cancer, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
| | - Theerawat Tharasanit
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand.
- Center of Excellence for Companion Animal Cancer, Faculty of Veterinary Science, Chulalongkorn University, Henri Dunant Road, Pathumwan, Bangkok, 10330, Thailand.
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2
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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3
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Ledesma M, Todero MF, Maceira L, Prieto M, Vay C, Galas M, López B, Yokobori N, Rearte B. Peptidome profiling for the immunological stratification in sepsis: a proof of concept study. Sci Rep 2022; 12:11469. [PMID: 35794460 PMCID: PMC9259554 DOI: 10.1038/s41598-022-15792-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Sepsis has been called the graveyard of pharmaceutical companies due to the numerous failed clinical trials. The lack of tools to monitor the immunological status in sepsis constrains the development of therapies. Here, we evaluated a test based on whole plasma peptidome acquired by MALDI-TOF-mass spectrometer and machine-learning algorithms to discriminate two lipopolysaccharide-(LPS) induced murine models emulating the pro- and anti-inflammatory/immunosuppression environments that can be found during sepsis. The LPS group was inoculated with a single high dose of LPS and the IS group was subjected to increasing doses of LPS, to induce proinflammatory and anti-inflammatory/immunosuppression profiles respectively. The LPS group showed leukopenia and higher levels of cytokines and tissue damage markers, and the IS group showed neutrophilia, lymphopenia and decreased humoral response. Principal component analysis of the plasma peptidomes formed discrete clusters that mostly coincided with the experimental groups. In addition, machine-learning algorithms discriminated the different experimental groups with a sensitivity of 95.7% and specificity of 90.9%. Data reveal the potential of plasma fingerprints analysis by MALDI-TOF-mass spectrometry as a simple, speedy and readily transferrable method for sepsis patient stratification that would contribute to therapeutic decision-making based on their immunological status.
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Affiliation(s)
- Martín Ledesma
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas "José de San Martín", Facultad de Farmacia y Bioquímica, UBA, Av. Córdoba 2351, C1120, CABA, Argentina.,Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB, CABA, Argentina
| | - María Florencia Todero
- Instituto de Medicina Experimental (IMEX) - CONICET - Academia Nacional de Medicina, Pacheco de Melo 3081, C1425AUM, CABA, Argentina
| | - Lautaro Maceira
- Instituto de Medicina Experimental (IMEX) - CONICET - Academia Nacional de Medicina, Pacheco de Melo 3081, C1425AUM, CABA, Argentina
| | - Mónica Prieto
- Servicio de Bacteriología Especial. Instituto Nacional de Enfermedades Infecciosas (INEI), ANLIS "Dr. C. G. Malbrán", Av. Vélez Sarsfield 563, C1282AFF, CABA, Argentina
| | - Carlos Vay
- Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas "José de San Martín", Facultad de Farmacia y Bioquímica, UBA, Av. Córdoba 2351, C1120, CABA, Argentina
| | - Marcelo Galas
- Special Program of AMR, Communicable Diseases and Environmental Determinants of Health Department, Pan-American Health Organization, 525 23rd St NW, Washington, DC, 20037, USA
| | - Beatriz López
- Departamento de Bacteriología. INEI, ANLIS "Dr. C. G. Malbrán", Av. Vélez Sarsfield 563, C1282AFF, CABA, Argentina
| | - Noemí Yokobori
- Servicio de Micobacterias INEI, ANLIS "Dr. C. G. Malbrán", Av. Vélez Sarsfield 563, C1282AFF, CABA, Argentina.,Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB, CABA, Argentina
| | - Bárbara Rearte
- Instituto de Medicina Experimental (IMEX) - CONICET - Academia Nacional de Medicina, Pacheco de Melo 3081, C1425AUM, CABA, Argentina. .,Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB, CABA, Argentina.
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4
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Piovesana S, Cerrato A, Antonelli M, Benedetti B, Capriotti AL, Cavaliere C, Montone CM, Laganà A. A clean-up strategy for identification of circulating endogenous short peptides in human plasma by zwitterionic hydrophilic liquid chromatography and untargeted peptidomics identification. J Chromatogr A 2019; 1613:460699. [PMID: 31767259 DOI: 10.1016/j.chroma.2019.460699] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 01/03/2023]
Abstract
Short peptides, namely di- tri- and tetra peptides, have been proven to play an important diagnostic role in several diseases. Therefore, the development of an analytical approach for their detection and identification is nowadays an important research goal. This paper describes an analytical procedure able to overcome the issues of short peptide isolation, clean-up and identification in plasma samples. Four different protocols were compared and tested to maximize both recovery and total number of identifications of short circulating plasma endogenous peptides. The purified peptides, coming from the four different tested protocols, were separated by zwitterionic hydrophilic liquid chromatography coupled to high-resolution mass spectrometry with the purpose of accomplishing an untargeted investigation based on suspect screening for short peptides in plasma. In particular, the use of Phree™ Phospholipid removal cartridge in combination with a purification step by solid phase extraction on a graphitized carbon black sorbent allowed the identification of the largest number of amino acid sequences (91 short peptides). The clean-up procedure allowed to tackle the issue of the low abundance of such peptides and their suppression during mass-spectrometric analysis. The results indicated that sample preparation is therefore fundamental for short peptide analysis in plasma samples.
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Affiliation(s)
- Susy Piovesana
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Michela Antonelli
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Barbara Benedetti
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Chiara Cavaliere
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy; CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100 Lecce, Italy
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5
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Fernández-Puente P, González-Rodríguez L, Calamia V, Picchi F, Lourido L, Camacho-Encina M, Oreiro N, Rocha B, Paz-González R, Marina A, García C, Blanco FJ, Ruiz-Romero C. Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers. Mol Cell Proteomics 2019; 18:2018-2028. [PMID: 31352363 PMCID: PMC6773562 DOI: 10.1074/mcp.ra119.001554] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
Osteoarthritis (OA) is a pathology characterized by the loss of articular cartilage. In this study, we performed a peptidomic strategy to identify endogenous peptides (neopeptides) that are released from human osteoarthritic tissue, which may serve as disease markers. With this aim, secretomes of osteoarthritic and healthy articular cartilages obtained from knee and hip were analyzed by shotgun peptidomics. This discovery step led to the identification of 1175 different peptides, corresponding to 101 proteins, as products of the physiological or pathological turnover of cartilage extracellular matrix. Then, a targeted multiple reaction monitoring-mass spectrometry method was developed to quantify the panel of best marker candidates on a larger set of samples (n = 62). Statistical analyses were performed to evaluate the significance of the observed differences and the ability of the neopeptides to classify the tissue. Eight of them were differentially abundant in the media from wounded zones of OA cartilage compared with the healthy tissue (p < 0.05). Three neopeptides belonging to Clusterin and one from Cartilage Oligomeric Matrix Protein showed a disease-dependent decrease specifically in hip OA, whereas two from Prolargin (PRELP) and one from Cartilage Intermediate Layer Protein 1 were significantly increased in samples from knee OA. The release of one peptide from PRELP showed the best metrics for tissue classification (AUC = 0.834). The present study reveals specific neopeptides that are differentially released from knee or hip human osteoarthritic cartilage compared with healthy tissue. This evidences the intervention of characteristic pathogenic pathways in OA and provides a novel panel of peptidic candidates for biomarker development.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers/metabolism
- Cartilage, Articular/cytology
- Cartilage, Articular/metabolism
- Cartilage, Articular/pathology
- Case-Control Studies
- Cells, Cultured
- Chromatography, Liquid
- Culture Media, Conditioned/chemistry
- Extracellular Matrix/metabolism
- Female
- Humans
- Male
- Organ Specificity
- Osteoarthritis, Hip/metabolism
- Osteoarthritis, Hip/pathology
- Osteoarthritis, Knee/metabolism
- Osteoarthritis, Knee/pathology
- Peptides/metabolism
- Proteomics/methods
- Tandem Mass Spectrometry
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Affiliation(s)
- Patricia Fernández-Puente
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain.; Agrupación Estratégica CICA - INIBIC, Universidade da Coruña, 15071 A Coruña, Spain
| | - Lucía González-Rodríguez
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - Valentina Calamia
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - Florencia Picchi
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - Lucía Lourido
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - María Camacho-Encina
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - Natividad Oreiro
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - Beatriz Rocha
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - Rocío Paz-González
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain
| | - Anabel Marina
- Centro de Biología Molecular Severo Ochoa, CSIC. Nicolás Cabrera, 1, 28049 Madrid, Spain
| | - Carlos García
- Centro de Biología Molecular Severo Ochoa, CSIC. Nicolás Cabrera, 1, 28049 Madrid, Spain
| | - Francisco J Blanco
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain.; Departamento de Medicina, Fisioterapia y Ciencias Biomédicas. Universidade da Coruña, 15006 A Coruña, Spain.; RIER-RED de Inflamación y Enfermedades Reumáticas, INIBIC-CHUAC, As Xubias 84, 15006 A Coruña, Spain.
| | - Cristina Ruiz-Romero
- Proteomics Unit-PBR2-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR). Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS. As Xubias, 84, 15006 A Coruña, Spain.; CIBER-BBN Instituto de Salud Carlos III INIBIC-CHUAC As Xubias 84, 15006 A Coruna, Spain.
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6
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Wang JY, Zhao MP. [Fluorescence assay for the detection of apurinic/apyrimidinic endonuclease 1 (APE1) activity in human blood samples]. JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2019; 51:487-492. [PMID: 31209420 DOI: 10.19723/j.issn.1671-167x.2019.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To develop a simple, sensitive and robust method for rapid detection of human apurinic/apyrimidinic endonuclease 1 (APE1) in various biological samples. METHODS An abasic site-containing DNA probe with a sequence of 5'-T*T*C*C*T*C*T(ROX)AGAGXCGTT (BHQ2)C*A*C*T*G*T*AGTTTATA*C*A*G*T*GAATCTCTCTAG*T*C*T-3' ["X" represents AP site; The phosphorothioated nucleotides (at 3' side) are indicated with an asterisk after the nucleotides; ROX is 6-carboxy-X-rhodamine and BHQ2 is Black Hole quencher 2] was synthesized and used for the detection. In the presence of APE1, the DNA probe could be specifically hydrolyzed by the enzyme and release the fluorophore, resulting in strong fluorescence emission. The activity of APE1 was determined according to the rate of increase in fluorescence intensity. In this work, we modified the reaction buffer and significantly improved the performance of the method. Moreover, the method was further extended to measure the contents of APE1 in the protein extraction from peripheral blood mononuclear cells (PBMCs) extracted from human whole blood samples by density gradient centrifugation. The assay was also applied to measure the activity of APE1 in human serum samples. RESULTS With a new reaction buffer composed of 0.04% (V/V) Triton X-100, 50 mmol/L KAc, 20 mmol/L Tris-Ac, 10 mmol/L Mg(Ac)2 and 1 mmol/L dithiothreitol (DTT), the method achieved a detection limit of 0.005 U/mL (3 pg/mL) and a linear response ranging from 6 pg/mL to 1.2 ng/mL. The contents of APE1 in the protein extraction from PBMCs of eight blood samples were measured to be in the range from 0.061 to 0.40 ng/μg protein, with an average of 0.16 ng/μg protein. The recovery was 98%±5% (n=3). The levels of APE1 in the sera from 102 normal individuals (51 male and 51 female, age range: 59-75 years) were observed to be from 0.13 to 0.34 ng/mL, with a recovery of 96%±15% (n=3). CONCLUSION The new fluorescence assay was simple, rapid and sensitive, providing a practical tool to measure the activity of APE1 in serum samples and cell extracts. It also holds great potential in measurement of APE1 in many other biological samples for clinical test and laboratory research.
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Affiliation(s)
- J Y Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - M P Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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7
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Semis M, Gugiu GB, Bernstein EA, Bernstein KE, Kalkum M. The Plethora of Angiotensin-Converting Enzyme-Processed Peptides in Mouse Plasma. Anal Chem 2019; 91:6440-6453. [PMID: 31021607 DOI: 10.1021/acs.analchem.8b03828] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Angiotensin-converting enzyme (ACE) converts angiotensin I into the potent vasoconstrictor angiotensin II, which regulates blood pressure. However, ACE activity is also essential for other physiological functions, presumably through processing of peptides unrelated to angiotensin. The goal of this study was to identify novel natural substrates and products of ACE through a series of mass-spectrometric experiments. This included comparing the ACE-treated and untreated plasma peptidomes of ACE-knockout (KO) mice, validation with select synthetic peptides, and a quantitative in vivo study of ACE substrates in mice with distinct genetic ACE backgrounds. In total, 244 natural peptides were identified ex vivo as possible substrates or products of ACE, demonstrating high promiscuity of the enzyme. ACE prefers to cleave substrates with Phe or Leu at the C-terminal P2' position and Gly in the P6 position. Pro in P1' and Iso in P1 are typical residues in peptides that ACE does not cleave. Several of the novel ACE substrates are known to have biological activities, including a fragment of complement C3, the spasmogenic C3f, which was processed by ACE ex vivo and in vitro. Analyses with N-domain-inactive (NKO) ACE allowed clarification of domain selectivity toward substrates. The in vivo ACE-substrate concentrations in WT, transgenic ACE-KO, NKO, and CKO mice correspond well with the in vitro observations in that higher levels of the ACE substrates were observed when the processing domain was knocked out. This study highlights the vast extent of ACE promiscuity and provides a valuable platform for further investigations of ACE functionality.
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Affiliation(s)
- Margarita Semis
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Gabriel B Gugiu
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States.,Mass Spectrometry & Proteomics Core Facility , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Ellen A Bernstein
- Departments of Biomedical Sciences, Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Kenneth E Bernstein
- Departments of Biomedical Sciences, Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States.,Mass Spectrometry & Proteomics Core Facility , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
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8
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Vitorino R. Digging Deep into Peptidomics Applied to Body Fluids. Proteomics 2019; 18. [PMID: 29251826 DOI: 10.1002/pmic.201700401] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Peptidomics techniques have allowed the identification of thousands of peptides that are derived from proteins in body fluids, despite the considerable challenges behind sample handling, MS-based identification, data analysis, and integration with bioinformatics tools. Body fluids' naturally occurring peptides are known to perform a variety of local and systemic functions; however, its knowledge is limited. Even so, the biological meaning that can be retrieved from peptidomics applied to the identification of disease markers and to the development of therapies using peptides has driven the progresses made in this field. In this review, a comparative analysis of body fluids' peptidome data retrieved from databases and from scientific papers is performed to identify the biological processes modulated by naturally occurring peptides. This integrative analysis highlights several interesting facts, such as the small overlap between blood-derived serum and plasma, which illustrates the impact of sample handling on these fluids peptidome. Urine is the body fluid with more naturally occurring peptides identified so far, most of which are derived from collagens. In saliva, the majority of peptides are originated from extracellular matrix proteins. Cerebrospinal fluid presents a high number of peptides derived from distinct proteins, mostly involved in the regulation of nervous system homeostasis. The lowest number of endogenous peptides was found in tears, most of which present antimicrobial activity. Collectively, data analysis highlights a peptidome signature for each body fluid, which comprehension will certainly help to improve disease management.
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Affiliation(s)
- Rui Vitorino
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Universidade do Porto, Porto, Portugal
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Abstract
The life span of cancer patients can be prolonged with appropriate therapies if detected early. Mass screening for early detection of cancer, however, requires sensitive and specific biomarkers obtainable from body fluids such as blood or urine. To date, most biomarker discovery programs focus on the proteome rather than the endogenous peptidome. It has been long-established that tumor cells and stromal cells produce tumor resident proteases (TRPs) to remodel the surrounding tumor microenvironment in support of tumor progression. In fact, proteolytic products of TRPs have been shown to correlate with malignant behavior. Being of low molecular weight, these unique peptides can pass through the endothelial barrier of the vasculature into the bloodstream. As such, the cancer peptidome has increasingly become a focus for biomarker discovery. In this review, we discuss on the various aspects of the peptidome in cancer biomarker research.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Greening DW, Kapp EA, Simpson RJ. The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome. Enzymes 2017; 42:27-64. [PMID: 29054270 DOI: 10.1016/bs.enz.2017.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases. The identification of circulating peptides in the context of disease constitutes a hitherto source of new clinical biomarkers. The field of peptidomics can be defined as the identification and comprehensive analysis of physiological and pathological peptides. Like proteomics, peptidomics has been advanced by the development of new separation strategies, analytical detection methods such as mass spectrometry, and bioinformatic technologies. Unlike proteomics, peptidomics is targeted toward identifying endogenous protein and peptide fragments, defining proteolytic enzyme substrate specificity, as well as protease cleavage recognition (degradome). Peptidomics employs "top-down proteomics" strategies where mass spectrometry is applied at the proteoform level to analyze intact proteins and large endogenous peptide fragments. With recent advances in prefractionation workflows for separating peptides, mass spectrometry instrumentation, and informatics, peptidomics is an important field that promises to impact on translational medicine. This review covers the current advances in peptidomics, including top-down and imaging mass spectrometry, comprehensive quantitative peptidome analyses (developments in reproducibility and coverage), peptide prefractionation and enrichment workflows, peptidomic data analyses, and informatic tools. The application of peptidomics in cancer biomarker discovery will be discussed.
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Affiliation(s)
- David W Greening
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
| | - Eugene A Kapp
- Systems Biology & Personalised Medicine Division, Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Florey Institute of Neuroscience, Parkville, Victoria, Australia; University of Melbourne, Parkville, Victoria, Australia
| | - Richard J Simpson
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
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