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Wang J, Xue M, Hu Y, Li J, Li Z, Wang Y. Proteomic Insights into Osteoporosis: Unraveling Diagnostic Markers of and Therapeutic Targets for the Metabolic Bone Disease. Biomolecules 2024; 14:554. [PMID: 38785961 PMCID: PMC11118602 DOI: 10.3390/biom14050554] [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: 03/29/2024] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
Osteoporosis (OP), a prevalent skeletal disorder characterized by compromised bone strength and increased susceptibility to fractures, poses a significant public health concern. This review aims to provide a comprehensive analysis of the current state of research in the field, focusing on the application of proteomic techniques to elucidate diagnostic markers and therapeutic targets for OP. The integration of cutting-edge proteomic technologies has enabled the identification and quantification of proteins associated with bone metabolism, leading to a deeper understanding of the molecular mechanisms underlying OP. In this review, we systematically examine recent advancements in proteomic studies related to OP, emphasizing the identification of potential biomarkers for OP diagnosis and the discovery of novel therapeutic targets. Additionally, we discuss the challenges and future directions in the field, highlighting the potential impact of proteomic research in transforming the landscape of OP diagnosis and treatment.
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Affiliation(s)
- Jihan Wang
- Xi’an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, China; (J.W.)
| | - Mengju Xue
- School of Medicine, Xi’an International University, Xi’an 710077, China
| | - Ya Hu
- Department of Medical College, Hunan Polytechnic of Environment and Biology, Hengyang 421000, China
| | - Jingwen Li
- Xi’an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, China; (J.W.)
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518057, China
| | - Zhenzhen Li
- Xi’an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, China; (J.W.)
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518057, China
| | - Yangyang Wang
- School of Electronics and Information, Northwestern Polytechnical University, Xi’an 710129, China
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Verma A, Patel R, Mahale A, Thorat RV, Rath SL, Sridhar E, Moiyadi A, Srivastava S. Multitarget Potential Drug Candidates for High-Grade Gliomas Identified by Multiple Reaction Monitoring Coupled with In Silico Drug Repurposing. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:59-75. [PMID: 38320249 DOI: 10.1089/omi.2023.0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
High-grade gliomas (HGGs) are extremely aggressive primary brain tumors with high mortality rates. Despite notable progress achieved by clinical research and biomarkers emerging from proteomics studies, efficacious drugs and therapeutic targets are limited. This study used targeted proteomics, in silico molecular docking, and simulation-based drug repurposing to identify potential drug candidates for HGGs. Importantly, we performed multiple reaction monitoring (MRM) on differentially expressed proteins with putative roles in the development and progression of HGGs based on our previous work and the published literature. Furthermore, in silico molecular docking-based drug repurposing was performed with a customized library of FDA-approved drugs to identify multitarget-directed ligands. The top drug candidates such as Pazopanib, Icotinib, Entrectinib, Regorafenib, and Cabozantinib were explored for their drug-likeness properties using the SwissADME. Pazopanib exhibited binding affinities with a maximum number of proteins and was considered for molecular dynamic simulations and cell toxicity assays. HGG cell lines showed enhanced cytotoxicity and cell proliferation inhibition with Pazopanib and Temozolomide combinatorial treatment compared to Temozolomide alone. To the best of our knowledge, this is the first study combining MRM with molecular docking and simulation-based drug repurposing to identify potential drug candidates for HGG. While the present study identified five multitarget-directed potential drug candidates, future clinical studies in larger cohorts are crucial to evaluate the efficacy of these molecular candidates. The research strategy and methodology used in the present study offer new avenues for innovation in drug discovery and development which may prove useful, particularly for cancers with low cure rates.
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Affiliation(s)
- Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rushda Patel
- Sinhgad College of Pharmacy, Savitribai Phule Pune University, Pune, India
| | - Atharva Mahale
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Rujuta Vijay Thorat
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Epari Sridhar
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Aliasgar Moiyadi
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Halder A, Biswas D, Chauhan A, Saha A, Auromahima S, Yadav D, Nissa MU, Iyer G, Parihari S, Sharma G, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S. A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors. Clin Proteomics 2023; 20:41. [PMID: 37770851 PMCID: PMC10540342 DOI: 10.1186/s12014-023-09426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Meningiomas are the most prevalent primary brain tumors. Due to their increasing burden on healthcare, meningiomas have become a pivot of translational research globally. Despite many studies in the field of discovery proteomics, the identification of grade-specific markers for meningioma is still a paradox and requires thorough investigation. The potential of the reported markers in different studies needs further verification in large and independent sample cohorts to identify the best set of markers with a better clinical perspective. METHODS A total of 53 fresh frozen tumor tissue and 51 serum samples were acquired from meningioma patients respectively along with healthy controls, to validate the prospect of reported differentially expressed proteins and claimed markers of Meningioma mined from numerous manuscripts and knowledgebases. A small subset of Glioma/Glioblastoma samples were also included to investigate inter-tumor segregation. Furthermore, a simple Machine Learning (ML) based analysis was performed to evaluate the classification accuracy of the list of proteins. RESULTS A list of 15 proteins from tissue and 12 proteins from serum were found to be the best segregator using a feature selection-based machine learning strategy with an accuracy of around 80% in predicting low grade (WHO grade I) and high grade (WHO grade II and WHO grade III) meningiomas. In addition, the discriminant analysis could also unveil the complexity of meningioma grading from a segregation pattern, which leads to the understanding of transition phases between the grades. CONCLUSIONS The identified list of validated markers could play an instrumental role in the classification of meningioma as well as provide novel clinical perspectives in regard to prognosis and therapeutic targets.
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Affiliation(s)
- Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Aparna Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Adrita Saha
- Motilal Nehru National Institute of Technology, Allahabad, 211004, UP, India
| | - Shreeman Auromahima
- Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Deeksha Yadav
- CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, New Delhi, 110025, India
| | - Mehar Un Nissa
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Gayatri Iyer
- Koita Centre for Digital Health, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shashwati Parihari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, India
| | | | - Graham Roy Ball
- Medical Technology Research Centre, Anglia Ruskin University, Cambridge Campus, East Rd, Cambridge, CB1 1PT, UK
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 185 Berry St., Suite 290, San Francisco, CA, 94107, USA.
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Nevárez-Ramírez AJ, Guzmán-Ortiz AL, Cortes-Reynosa P, Perez-Salazar E, Jaimes-Ortega GA, Valle-Rios R, Marín-Hernández Á, Rodríguez-Zavala JS, Ruiz-May E, Castrejón-Flores JL, Quezada H. Shotgun Proteomics of Co-Cultured Leukemic and Bone Marrow Stromal Cells from Different Species as a Preliminary Approach to Detect Intercellular Protein Transfer. Proteomes 2023; 11:proteomes11020015. [PMID: 37092456 PMCID: PMC10123657 DOI: 10.3390/proteomes11020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cellular interactions within the bone marrow microenvironment modulate the properties of subsets of leukemic cells leading to the development of drug-resistant phenotypes. The intercellular transfer of proteins and organelles contributes to this process but the set of transferred proteins and their effects in the receiving cells remain unclear. This study aimed to detect the intercellular protein transfer from mouse bone marrow stromal cells (OP9 cell line) to human T-lymphoblasts (CCRF-CEM cell line) using nanoLC-MS/MS-based shotgun proteomics in a 3D co-culture system. After 24 h of co-culture, 1513 and 67 proteins from human and mouse origin, respectively, were identified in CCRF-CEM cells. The presence of mouse proteins in the human cell line, detected by analyzing the differences in amino acid sequences of orthologous peptides, was interpreted as the result of intercellular transfer. The transferred proteins might have contributed to the observed resistance to vincristine, methotrexate, and hydrogen peroxide in the co-cultured leukemic cells. Our results suggest that shotgun proteomic analyses of co-cultured cells from different species could be a simple option to get a preliminary survey of the proteins exchanged among interacting cells.
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Affiliation(s)
- Abraham Josué Nevárez-Ramírez
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
- Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna, Mexico City 07340, Mexico
| | - Ana Laura Guzmán-Ortiz
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
| | - Pedro Cortes-Reynosa
- Departamento de Biología Celular, CINVESTAV-IPN, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Eduardo Perez-Salazar
- Departamento de Biología Celular, CINVESTAV-IPN, Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Gustavo Alberto Jaimes-Ortega
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Circuito interior, Av. Universidad 3000, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Ricardo Valle-Rios
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Circuito interior, Av. Universidad 3000, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano 1, Belisario Domínguez—Sección XVI, Mexico City 14080, Mexico
| | - José S. Rodríguez-Zavala
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano 1, Belisario Domínguez—Sección XVI, Mexico City 14080, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa 91073, Mexico
| | - José Luis Castrejón-Flores
- Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna, Mexico City 07340, Mexico
| | - Héctor Quezada
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Dr. Márquez 162, Doctores, Mexico City 06720, Mexico
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Li C, Xiao J, Wu S, Liu L, Zeng X, Zhao Q, Zhang Z. Clinical application of serum-based proteomics technology in human tumor research. Anal Biochem 2023; 663:115031. [PMID: 36580994 DOI: 10.1016/j.ab.2022.115031] [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: 10/28/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 12/27/2022]
Abstract
The rapid development of proteomics technology in the past decades has led to further human understanding of tumor research, and in some ways, the technology plays a very important supporting role in the early detection of tumors. Human serum has been shown to contain a variety of proteins closely related to life activities, and the dynamic change in proteins can often reflect the physiological and pathological conditions of the body. Serum has the advantage of easy extraction, so the application of proteomics technology in serum has become a hot spot and frontier area for the study of malignant tumors. However, there are still many difficulties in the standardized use of proteomic technologies, which inevitably limit the clinical application of proteomic technologies due to the heterogeneity of human proteins leading to incomplete whole proteome populations, in addition to most serum protein markers being now not highly specific in aiding the early detection of tumors. Nevertheless, further development of proteomics technologies will greatly increase our understanding of tumor biology and help discover more new tumor biomarkers with specificity that will enable medical technology.
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Affiliation(s)
- Chen Li
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Juan Xiao
- Department of Otorhinolaryngology, The Second Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Shihua Wu
- Department of Pathology, The Second Hospital of Shaoyang College, Hunan, Shaoyang, 422000, Hunan Province, China
| | - Lu Liu
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Xuemei Zeng
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China
| | - Qiang Zhao
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China.
| | - Zhiwei Zhang
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China; Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China.
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Chantada-Vázquez MDP, Bravo SB, Barbosa-Gouveia S, Alvarez JV, Couce ML. Proteomics in Inherited Metabolic Disorders. Int J Mol Sci 2022; 23:ijms232314744. [PMID: 36499071 PMCID: PMC9740208 DOI: 10.3390/ijms232314744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Inherited metabolic disorders (IMD) are rare medical conditions caused by genetic defects that interfere with the body's metabolism. The clinical phenotype is highly variable and can present at any age, although it more often manifests in childhood. The number of treatable IMDs has increased in recent years, making early diagnosis and a better understanding of the natural history of the disease more important than ever. In this review, we discuss the main challenges faced in applying proteomics to the study of IMDs, and the key advances achieved in this field using tandem mass spectrometry (MS/MS). This technology enables the analysis of large numbers of proteins in different body fluids (serum, plasma, urine, saliva, tears) with a single analysis of each sample, and can even be applied to dried samples. MS/MS has thus emerged as the tool of choice for proteome characterization and has provided new insights into many diseases and biological systems. In the last 10 years, sequential window acquisition of all theoretical fragmentation spectra mass spectrometry (SWATH-MS) has emerged as an accurate, high-resolution technique for the identification and quantification of proteins differentially expressed between healthy controls and IMD patients. Proteomics is a particularly promising approach to help obtain more information on rare genetic diseases, including identification of biomarkers to aid early diagnosis and better understanding of the underlying pathophysiology to guide the development of new therapies. Here, we summarize new and emerging proteomic technologies and discuss current uses and limitations of this approach to identify and quantify proteins. Moreover, we describe the use of proteomics to identify the mechanisms regulating complex IMD phenotypes; an area of research essential to better understand these rare disorders and many other human diseases.
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Affiliation(s)
- Maria del Pilar Chantada-Vázquez
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Susana B. Bravo
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Sofía Barbosa-Gouveia
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - José V. Alvarez
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - María L. Couce
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
- Correspondence: ; Tel.: +349-81-951-100
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Surrogate peptide selection and internal standardization for accurate quantification of endogenous proteins. Bioanalysis 2022; 14:949-961. [PMID: 36017716 DOI: 10.4155/bio-2022-0071] [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: 11/17/2022] Open
Abstract
Relative quantification techniques have dominated the field of proteomics. However, biomarker discovery, mathematical model development and studies on transporter-mediated drug disposition still need absolute quantification of proteins. The quality of data of trace-level protein quantification is solely dependent on the specific selection of surrogate peptides. Selection of surrogate peptides has a major impact on the accuracy of the method. In this article, the advanced approaches for selection of surrogate peptides, which can provide absolute quantification of the proteins are discussed. In addition, internal standardization, which accounts for variations in the quantitation process to achieve absolute protein quantification is discussed.
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9
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Guerrero L, Paradela A, Corrales FJ. Targeted Proteomics for Monitoring One-Carbon Metabolism in Liver Diseases. Metabolites 2022; 12:metabo12090779. [PMID: 36144184 PMCID: PMC9501948 DOI: 10.3390/metabo12090779] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Liver diseases cause approximately 2 million deaths per year worldwide and had an increasing incidence during the last decade. Risk factors for liver diseases include alcohol consumption, obesity, diabetes, the intake of hepatotoxic substances like aflatoxin, viral infection, and genetic determinants. Liver cancer is the sixth most prevalent cancer and the third in mortality (second in males). The low survival rate (less than 20% in 5 years) is partially explained by the late diagnosis, which remarks the need for new early molecular biomarkers. One-carbon metabolism integrates folate and methionine cycles and participates in essential cell processes such as redox homeostasis maintenance and the regulation of methylation reactions through the production of intermediate metabolites such as cysteine and S-Adenosylmethionine. One-carbon metabolism has a tissue specific configuration, and in the liver, the participating enzymes are abundantly expressed—a requirement to maintain hepatocyte differentiation. Targeted proteomics studies have revealed significant differences in hepatocellular carcinoma and cirrhosis, suggesting that monitoring one-carbon metabolism enzymes can be useful for stratification of liver disease patients and to develop precision medicine strategies for their clinical management. Here, reprogramming of one-carbon metabolism in liver diseases is described and the role of mass spectrometry to follow-up these alterations is discussed.
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Affiliation(s)
- Laura Guerrero
- Centro Nacional de Biotecnología (CNB), CSIC. C/Darwin 3, 28049 Madrid, Spain
| | - Alberto Paradela
- Centro Nacional de Biotecnología (CNB), CSIC. C/Darwin 3, 28049 Madrid, Spain
| | - Fernando J. Corrales
- Centro Nacional de Biotecnología (CNB), CSIC. C/Darwin 3, 28049 Madrid, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-585-46-96
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10
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Gan J, Zeng X, Wang X, Wu Y, Lei P, Wang Z, Yang C, Hu Z. Effective Diagnosis of Prostate Cancer Based on mRNAs From Urinary Exosomes. Front Med (Lausanne) 2022; 9:736110. [PMID: 35402423 PMCID: PMC8983915 DOI: 10.3389/fmed.2022.736110] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 03/01/2022] [Indexed: 12/16/2022] Open
Abstract
Background Novel non-invasive biomarkers are urgently required to improve the diagnostic sensitivity and specificity of prostate cancer (PCa). Therefore, the diagnostic value of following candidate genes (ERG, PCA3, ARV7, PSMA, CK19, and EpCAM) were estimated by testing mRNAs from urinary exosomes of patients with primary PCa. Methods Exosomes were obtained using size-exclusion chromatography (SEC), out of which RNAs were extracted, then analyzed by quantitative reverse transcription-polymerase chain reaction according to manufacturer's protocol. Results The expression of urinary exosomal ERG, PCA3, PSMA, CK19, and EpCAM were significantly increased in patients with PCa compared with healthy males. In addition, the levels of urinary exosomal ERG, ARV7, and PSMA were intimately correlated with the Gleason score in PCa patients (P < 0.05). The receiver operating characteristic curves (ROCs) showed that urinary exosomal ERG, PCA3, PSMA, CK19, and EpCAM were able to distinguish patients with PCa from healthy individuals with the area under the curve (AUC) of 0.782, 0.783, 0.772, 0.731, and 0.739, respectively. Urinary exosomal PCA3 and PSMA distinguished PCa patients from healthy individuals with an AUC of 0.870. Combination of urinary exosomal PCA3, PSMA with serum PSA and PI-RADS achieved higher AUC compared with PSA alone (0.914 and 0.846, respectively). Kaplan-Meier curves demonstrated that PCA3, ARV7, and EpCAM were associated in androgen-deprivation therapy (ADT) failure time which is defined as from the initiation of ADT in hormone-sensitive stage to the development of castration-resistant prostate cancer. Conclusion These findings suggested that mRNAs from urinary exosomes have the potential in serving as novel and non-invasive indicators for PCa diagnosis and prediction.
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Affiliation(s)
- Jiahua Gan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ya Wu
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, China
| | - Ping Lei
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunguang Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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11
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Luo H, Ge H. Application of Proteomics in the Discovery of Radiosensitive Cancer Biomarkers. Front Oncol 2022; 12:852791. [PMID: 35280744 PMCID: PMC8904368 DOI: 10.3389/fonc.2022.852791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/04/2022] [Indexed: 12/21/2022] Open
Abstract
Radiation therapy remains an important component of cancer treatment. Gene-encoded proteins were the actual executors of cellular functions. Proteomic was a novel technology that can systematically analysis protein composition and measure their levels of change, this was a high throughput method, and were the import tools in the post genomic era. In recent years, rapid progress of proteomic have been made in the study of cancer mechanism, diagnosis, and treatment. This article elaborates current advances and future directions of proteomics in the discovery of radiosensitive cancer biomarkers.
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Affiliation(s)
- Hui Luo
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong Ge
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
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12
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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13
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Development of a multiplex mass spectrometry method for simultaneous quantification of urinary proteins related to respiratory health. Sci Rep 2021; 11:10107. [PMID: 33980897 PMCID: PMC8115669 DOI: 10.1038/s41598-021-89068-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/16/2021] [Indexed: 02/03/2023] Open
Abstract
Respiratory health of children is a health priority. Club cell protein (CC16) is an interesting biomarker of lung diseases and adverse effects towards the airway epithelium integrity. Osteopontin (OPN) and nuclear factor-kappa B (NF-κB) also play a role in respiratory health. The use of urine as biomarker source is useful in studies involving children but necessitates proper adjustment for physiological confounders influencing the urinary excretion, potentially characterized with beta-2-microglobulin (β2M), retinol binding protein 4 (RBP4) or myoglobin (MYO), as well as adjustment for possible renal dysfunction, characterized by human serum albumin (HSA). The simultaneous quantification of all these proteins in urine could facilitate children's health monitoring. A multiple reaction monitoring method (MRM) was developed and validated for the relative quantification of the seven mentioned urinary proteins. A total of nine proteotypic peptides were selected and used for the relative quantification of the seven proteins. The MRM method was completely validated for all proteins and partially for OPN. LOQ's ranged from 0.3 to 42.8 ng/ml, a good reproducibility and a good linearity were obtained across the analytical measurement range (r2 > 0.98). The method yielded varying correlations (r2 of 0.78, 0.71, 0.34 and 0.15 for CC16, β2M, RBP4 and HSA respectively) with available immunoassay data. It also allowed the identification and successful quantification of β2M and RBP4 as a protein candidate for adjustment of renal handling and dysfunction. All proteins were detected in the urine samples except for MYO and NF-κB. Our validated MRM-method is able to simultaneously quantify in urine biomarkers of airway epithelium integrity and biomarkers of variation in renal function and urinary dilution. This will allow to investigate further in future studies if urine can be used as a good surrogate source for biomarkers of airway epithelium integrity, and to understand the complex relationship between cause and effect in children's respiratory health monitoring.
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Wu J, Wang W, Chen Z, Xu F, Zheng Y. Proteomics applications in biomarker discovery and pathogenesis for abdominal aortic aneurysm. Expert Rev Proteomics 2021; 18:305-314. [PMID: 33840337 DOI: 10.1080/14789450.2021.1916473] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Abdominal aortic aneurysm (AAA) is a common, complex, and life-threatening disease. Currently, the pathogenesis of AAA is not well understood. No biomarkers or specific drugs are available for AAA in clinical applications. Proteomics is a powerful tool in biomarker discovery, exploration of pathogenesis, and drug target identification.Areas covered: We review the application of mass spectrometry-based proteome analysis in AAA patients within the last ten years. Differentially expressed proteins associated with AAA were identified in multiple sample sources, including vascular tissue, intraluminal thrombus, tissue secretome, blood, and cells. Some potential disease biomarkers, pathogenic mechanisms, or therapeutic targets for AAA were discovered using proteome analysis. The challenges and prospects of proteomics applied to AAA are also discussed.Expert opinion: Since most of the previous proteomic studies used relatively small sample sizes, some promising biomarkers need to be validated in multicenter cohorts to accelerate their clinical application. With the rapid development of mass spectrometry technology, modification-specific proteomics and multi-omics research in the future will enhance our understanding of the pathogenesis of AAA and promote biomarker discovery and drug development for clinical translation.
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Affiliation(s)
- Jianqiang Wu
- Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Wang
- Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhaoran Chen
- Department of Geriatrics, Medical Health Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Fang Xu
- Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuehong Zheng
- Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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15
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Vinaiphat A, Low JK, Yeoh KW, Chng WJ, Sze SK. Application of Advanced Mass Spectrometry-Based Proteomics to Study Hypoxia Driven Cancer Progression. Front Oncol 2021; 11:559822. [PMID: 33708620 PMCID: PMC7940826 DOI: 10.3389/fonc.2021.559822] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer is one of the largest contributors to the burden of chronic disease in the world and is the second leading cause of death globally. It is associated with episodes of low-oxygen stress (hypoxia or ischemia/reperfusion) that promotes cancer progression and therapeutic resistance. Efforts have been made in the past using traditional proteomic approaches to decipher oxygen deprivation stress-related mechanisms of the disease initiation and progression and to identify key proteins as a therapeutic target for the treatment and prevention. Despite the potential benefits of proteomic in translational research for the discovery of new drugs, the therapeutic outcome with this approach has not met expectations in clinical trials. This is mainly due to the disease complexity which possess a multifaceted molecular pathology. Therefore, novel strategies to identify and characterize clinically important sets of modulators and molecular events for multi-target drug discovery are needed. Here, we review important past and current studies on proteomics in cancer with an emphasis on recent pioneered labeling approaches in mass spectrometry (MS)-based systematic quantitative analysis to improve clinical success. We also discuss the results of the selected innovative publications that integrate advanced proteomic technologies (e.g. MALDI-MSI, pSILAC/SILAC/iTRAQ/TMT-LC-MS/MS, MRM-MS) for comprehensive analysis of proteome dynamics in different biosystems, including cell type, cell species, and subcellular proteome (i.e. secretome and chromatome). Finally, we discuss the future direction and challenges in the application of these technological advancements in mass spectrometry within the context of cancer and hypoxia.
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Affiliation(s)
- Arada Vinaiphat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jee Keem Low
- Department of Surgery, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kheng Wei Yeoh
- Department of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Hematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Liu M, Eckersall PD, Mrljak V, Horvatić A, Guillemin N, Galan A, Köster L, French A. Novel biomarkers in cats with congestive heart failure due to primary cardiomyopathy. J Proteomics 2020; 226:103896. [PMID: 32652222 DOI: 10.1016/j.jprot.2020.103896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/10/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022]
Abstract
The pathogenesis of feline cardiomyopathy and congestive heart failure (CHF) requires further understanding. In this study, we assessed serum proteome change in feline CHF, aiming to identify novel biomarker for both research and clinical use. The study comprised 15 cats in CHF, 5 cats in preclinical cardiomyopathy and 15 cats as healthy controls. Serum proteome profiles were obtained by tandem mass tag labelling followed by mass spectrometry. Protein concentrations in CHF cats were compared with healthy controls. Western blot was performed for proteomic validation. Correlations were assessed between the altered proteins in CHF and clinical variables in cats with cardiomyopathy to evaluate protein-cardiac association. Bioinformatic analysis was employed to identify pathophysiological pathways involved in feline CHF. Sixteen serum proteins were significantly different between CHF and healthy control cats (P < .05). These included serine protease inhibitors, apolipoproteins and other proteins associated with inflammation and coagulation. Clinical parameters from cats with cardiomyopathy significantly correlated with the altered proteins (P < .05). Bioinformatic analysis identified 13 most relevant functional profiles in feline CHF, which mostly associated with extracellular matrix organization and metabolism. Data are available via ProteomeXchange with identifier PXD017761. SIGNIFICANCE: Cardiomyopathies affect both cats and humans, and they can cause serious consequence such as congestive heart failure (CHF). To date, the pathophysiological mechanism of CHF is not fully understood. In this study, for the first time, we used a proteomic approach combined with bioinformatic analysis to evaluate serum protein change in cats with CHF. Results indicate systemic inflammation, coagulation protein changes, innate immunity and extracellular matrix remodeling are involved in feline CHF, which are largely comparable with findings in previous human studies. Our study provides new insights into CHF and cardiomyopathy in cats, and the identified novel biomarkers and pathophysiological pathways provide valuable information for future studies.
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Affiliation(s)
- Mengmeng Liu
- Small Animal Hospital, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - P David Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK; Laboratory for Proteomics, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Vladimir Mrljak
- Laboratory for Proteomics, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Anita Horvatić
- Laboratory for Proteomics, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Nicolas Guillemin
- Laboratory for Proteomics, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Asier Galan
- Laboratory for Proteomics, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Liza Köster
- Department of Small Animal Clinical Sciences, University of Tennessee, Knoxville, TN, USA
| | - Anne French
- Ross University School of Veterinary Medicine, Basseterre, St Kitts & Nevis, West Indies.
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17
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Liang A, Qin W, Zhang M, Gao F, Zhao C, Gao Y. Profiling tear proteomes of patients with unilateral relapsed Behcet's disease-associated uveitis using data-independent acquisition proteomics. PeerJ 2020; 8:e9250. [PMID: 32596040 PMCID: PMC7307566 DOI: 10.7717/peerj.9250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose To explore whether unilateral relapse of Bechet’s disease-associated uveitis (BDU) causes differences in the tear proteome between the diseased and the contralateral quiescent eye and potential tear biomarkers for uveitis recurrence and disease monitoring. Method To minimize interindividual variations, bilateral tear samples were collected from the same patient (n = 15) with unilateral relapse of BDU. A data-independent acquisition (DIA) strategy was used to identify proteins that differed between active and quiescent eyes. Results A total of 1,797 confident proteins were identified in the tear samples, of which 381 (21.2%) were also highly expressed in various tissues and organs. Fifty-one (2.8%) proteins differed in terms of expression between tears in active and quiescent eyes, 9 (17.6%) of which were functionally related to immunity or inflammation. Alpha-1-acid glycoprotein 1 (fold change = 3.2, p = 0.007) was increased and Annexin A1 (fold change = −1.7, p < 0.001) was decreased in the tears of the active BDU eye compared to the contralateral quiescent eye. Conclusions A substantial amount of confident proteins were detected in the tears of BDU patients, including proteins that were deferentially expressed in the uveitis-relapsed eyes and the contralateral quiescent eyes. Some of these identified tear proteins play important roles in immune and inflammatory processes. Tear proteome might be a good source of biomarkers for uveitis.
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Affiliation(s)
- Anyi Liang
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Weiwei Qin
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China.,Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, China
| | - Meifen Zhang
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Gao
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Chan Zhao
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, China
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Makridakis M, Kontostathi G, Petra E, Stroggilos R, Lygirou V, Filip S, Duranton F, Mischak H, Argiles A, Zoidakis J, Vlahou A. Multiplexed MRM-based protein quantification of putative prognostic biomarkers for chronic kidney disease progression in plasma. Sci Rep 2020; 10:4815. [PMID: 32179759 PMCID: PMC7076027 DOI: 10.1038/s41598-020-61496-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/29/2020] [Indexed: 12/28/2022] Open
Abstract
Current diagnostic measures for Chronic Kidney Disease (CKD) include detection of reduced estimated glomerular filtration rate (eGFR) and albuminuria, which have suboptimal accuracies in predicting disease progression. The disease complexity and heterogeneity underscore the need for multiplex quantification of different markers. The goal of this study was to determine the association of six previously reported CKD-associated plasma proteins [B2M (Beta-2-microglobulin), SERPINF1 (Pigment epithelium-derived factor), AMBP (Protein AMBP), LYZ (Lysozyme C), HBB (Hemoglobin subunit beta) and IGHA1 (Immunoglobulin heavy constant alpha 1)], as measured in a multiplex format, with kidney function, and outcome. Antibody-free, multiple reaction monitoring mass spectrometry (MRM) assays were developed, characterized for their analytical performance, and used for the analysis of 72 plasma samples from a patient cohort with longitudinal follow-up. The MRM significantly correlated (Rho = 0.5–0.9) with results from respective ELISA. Five proteins [AMBP, B2M, LYZ, HBB and SERPINF1] were significantly associated with eGFR, with the three former also associated with unfavorable outcome. The combination of these markers provided stronger associations with outcome (p < 0.0001) compared to individual markers. Collectively, our study describes a multiplex assay for absolute quantification and verification analysis of previously described putative CKD prognostic markers, laying the groundwork for further use in prospective validation studies.
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Affiliation(s)
- Manousos Makridakis
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Georgia Kontostathi
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Eleni Petra
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Rafael Stroggilos
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Szymon Filip
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | | | | | | | - Jerome Zoidakis
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece.
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19
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Kontostathi G, Makridakis M, Zoidakis J, Vlahou A. Applications of multiple reaction monitoring targeted proteomics assays in human plasma. Expert Rev Mol Diagn 2019; 19:499-515. [PMID: 31057016 DOI: 10.1080/14737159.2019.1615448] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Multiple (or selected) reaction monitoring-mass spectrometry (MRM/SRM) is a targeted proteomic method that can be used for relative and absolute quantification. Multiple reports exist supporting the potential of the approach in proteomic biomarker validation. Areas covered: To get an overview of the applications of MRM in protein quantification in plasma, a search in MedLine/PubMed was performed using the keywords: 'MRM/SRM plasma proteomic/proteomics/proteome'. The retrieved studies were further filtered to focus on disease biomarkers and the main results are summarized. Expert opinion: MRM is increasingly employed for the quantification of both well-established but also newly discovered putative biomarkers and occasionally their post-translationally modified forms in plasma. Fractionation is regularly required for the detection of low abundance proteins. Standardized procedures to facilitate assay establishment and marker quantification have been proposed and, in few cases, implemented. Nevertheless, in most cases, absolute quantification is not performed. To advance, multiple technical issues including the regular use of standard labeled peptides and appropriate quality controls to monitor assay performance should be considered. Additionally, clinical aspects involving careful study design to address biomarker clinical use should also be considered.
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Affiliation(s)
- Georgia Kontostathi
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Manousos Makridakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Jerome Zoidakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Antonia Vlahou
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
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20
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Critselis E, Rava M, Marquez M, Lygirou V, Chatzicharalambous D, Liapi P, Lichtinghagen R, Brand K, Cecchini L, Vlahou A, Malats N, Zoidakis J. Diagnostic and Prognostic Performance of Secreted Protein Acidic and Rich in Cysteine (SPARC) Assay for Detecting Primary and Recurrent Urinary Bladder Cancer. Proteomics Clin Appl 2019; 13:e1800148. [DOI: 10.1002/prca.201800148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/03/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Elena Critselis
- Proteomics Laboratory, Biotechnology DivisionBiomedical Research Foundation of the Academy of Athens Athens 11527 Greece
| | - Marta Rava
- Genetic and Molecular Epidemiology GroupSpanish National Cancer Research Centre (Centro Nacional de Investigaciones Oncologicas) Madrid and CIBERONC 28029 Spain
| | - Mirari Marquez
- Genetic and Molecular Epidemiology GroupSpanish National Cancer Research Centre (Centro Nacional de Investigaciones Oncologicas) Madrid and CIBERONC 28029 Spain
| | - Vasiliki Lygirou
- Proteomics Laboratory, Biotechnology DivisionBiomedical Research Foundation of the Academy of Athens Athens 11527 Greece
| | - Despoina Chatzicharalambous
- Proteomics Laboratory, Biotechnology DivisionBiomedical Research Foundation of the Academy of Athens Athens 11527 Greece
| | - Panagiota Liapi
- Proteomics Laboratory, Biotechnology DivisionBiomedical Research Foundation of the Academy of Athens Athens 11527 Greece
| | - Ralph Lichtinghagen
- Institute of Clinical ChemistryHannover Medical School Hannover 30625 Germany
| | - Korbinian Brand
- Institute of Clinical ChemistryHannover Medical School Hannover 30625 Germany
| | | | - Antonia Vlahou
- Proteomics Laboratory, Biotechnology DivisionBiomedical Research Foundation of the Academy of Athens Athens 11527 Greece
| | - Nuria Malats
- Genetic and Molecular Epidemiology GroupSpanish National Cancer Research Centre (Centro Nacional de Investigaciones Oncologicas) Madrid and CIBERONC 28029 Spain
| | - Jerome Zoidakis
- Proteomics Laboratory, Biotechnology DivisionBiomedical Research Foundation of the Academy of Athens Athens 11527 Greece
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Kontostathi G, Makridakis M, Bitsika V, Tsolakos N, Vlahou A, Zoidakis J. Development and Validation of Multiple Reaction Monitoring (MRM) Assays for Clinical Applications. Methods Mol Biol 2019; 1959:205-223. [PMID: 30852825 DOI: 10.1007/978-1-4939-9164-8_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Selected/multiple reaction monitoring-mass spectrometry (SRM/MRM) is an analytical method that is frequently combined to the use of stable isotope-labeled standard (SIS) peptides for absolute protein quantification. The application of SRM/MRM is a relatively recent development in the proteomics field for analysis of biological samples (plasma, urine, cell/tissue lysates) targeting to a large extent biomarker validation. Although MRM generally by-passes the use of antibodies (being linked to sub-optimal assay specificity in many cases), bioanalytical validation of MRM protocols has not been robustly applied because of sensitivity issues, in contrary to antibody-based methods. In this chapter, we will discuss the points that should be addressed for MRM method development in clinical proteomics applications.
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Affiliation(s)
| | | | - Vasiliki Bitsika
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Jerome Zoidakis
- Biomedical Research Foundation Academy of Athens, Athens, Greece.
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22
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Aydindogan E, Penque D, Zoidakis J. Systematic review on recent potential biomarkers of chronic obstructive pulmonary disease. Expert Rev Mol Diagn 2018; 19:37-45. [DOI: 10.1080/14737159.2018.1559054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eda Aydindogan
- Department of Biochemistry, Institute of Natural Sciences, Ege University, Izmir, Turkey
| | - Deborah Penque
- Laboratory of Proteomics, Human Genetics Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal
- ToxOmics- Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jerome Zoidakis
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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Latosinska A, Frantzi M, Merseburger AS, Mischak H. Promise and Implementation of Proteomic Prostate Cancer Biomarkers. Diagnostics (Basel) 2018; 8:diagnostics8030057. [PMID: 30158500 PMCID: PMC6174350 DOI: 10.3390/diagnostics8030057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/26/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022] Open
Abstract
Prostate cancer is one of the most commonly diagnosed malignancy and the fifth leading cause of cancer mortality in men. Despite the broad use of prostate-specific antigen test that resulted in an increase in number of diagnosed cases, disease management needs to be improved. Proteomic biomarkers alone and or in combination with clinical and pathological risk calculators are expected to improve on decreasing the unnecessary biopsies, stratify low risk patients, and predict response to treatment. To this end, significant efforts have been undertaken to identify novel biomarkers that can accurately discriminate between indolent and aggressive cancer forms and indicate those men at high risk for developing prostate cancer that require immediate treatment. In the era of “big data” and “personalized medicine” proteomics-based biomarkers hold great promise to provide clinically applicable tools, as proteins regulate all biological functions, and integrate genomic information with the environmental impact. In this review article, we aim to provide a critical assessment of the current proteomics-based biomarkers for prostate cancer and their actual clinical applicability. For that purpose, a systematic review of the literature published within the last 10 years was performed using the Web of Science Database. We specifically discuss the potential and prospects of use for diagnostic, prognostic and predictive proteomics-based biomarkers, including both body fluid- and tissue-based markers.
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Affiliation(s)
| | - Maria Frantzi
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany.
| | - Axel S Merseburger
- Department of Urology, University Clinic of Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany.
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Frantzi M, Latosinska A, Kontostathi G, Mischak H. Clinical Proteomics: Closing the Gap from Discovery to Implementation. Proteomics 2018; 18:e1700463. [PMID: 29785737 DOI: 10.1002/pmic.201700463] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/10/2018] [Indexed: 12/15/2022]
Abstract
Clinical proteomics, the application of proteome analysis to serve a clinical purpose, represents a major field in the area of proteome research. Over 1000 manuscripts on this topic are published each year, with numbers continuously increasing. However, the anticipated outcome, the transformation of the reported findings into improvements in patient management, is not immediately evident. In this article, the value and validity of selected clinical proteomics findings are investigated, and it is assessed how far implementation has progressed. A main conclusion from this assessment is that to achieve implementation, well-powered clinical studies are required in the appropriate population, addressing a specific clinical need and with a clear context-of-use. Efforts toward implementation, to be feasible, must be supported by the key players in science: publishers and funders. The authors propose a change on objectives, from additional discovery studies toward studies aiming at validation of the plethora of potential biomarkers that have been described, to demonstrate practical value of clinical proteomics. All elements required, potential biomarkers, technologies, and bio-banked samples are available (based on today's literature), hence a change in focus from discovery toward validation and application is not only urgently necessary, but also possible based on resources available today.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Hannover, 30659, Germany
| | | | - Georgia Kontostathi
- Department of Biotechnology, Biomedical Research Foundation Academy of Athens, Athens, 11527, Greece
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Naß J, Efferth T. Insights into apoptotic proteins in chemotherapy: quantification techniques and informing therapy choice. Expert Rev Proteomics 2018; 15:413-429. [DOI: 10.1080/14789450.2018.1468755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Janine Naß
- Department of Pharmaceutical Biology, Institute of Biochemistry and Pharmacy, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Biochemistry and Pharmacy, Johannes Gutenberg University, Mainz, Germany
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26
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Breaking the ice: urine proteomics of medullary sponge kidney disease. Kidney Int 2018; 91:281-283. [PMID: 28087010 DOI: 10.1016/j.kint.2016.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 10/13/2016] [Indexed: 11/23/2022]
Abstract
Urinary proteomics is a promising tool for biomarker investigation, particularly in complex kidney diseases. Fabris and colleagues report that urinary laminin subunit alpha-2 is a potential diagnostic marker of medullary sponge kidney (MSK) disease by using a label-free quantitative proteomics platform and a clinically compatible enzyme-linked immunosorbent assay. The neglected issue of stone pathogenesis was also evidenced. This commentary discusses several considerations in biomarker validation, and how urinary proteomics breaks new ground in MSK research.
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Quantitation of peptides from non-invasive skin tapings using isotope dilution and tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1084:132-140. [PMID: 29601982 DOI: 10.1016/j.jchromb.2018.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 01/10/2023]
Abstract
Previous work from our laboratories utilized a novel skin taping method and mass spectrometry-based proteomics to discover clinical biomarkers of skin conditions; these included atopic dermatitis, Staphylococcus aureus colonization, and eczema herpeticum. While suitable for discovery purposes, semi-quantitative proteomics is generally time-consuming and expensive. Furthermore, depending on the method used, discovery-based proteomics can result in high variation and inadequate sensitivity to detect low abundant peptides. Therefore, we strove to develop a rapid, sensitive, and reproducible method to quantitate disease-related proteins from skin tapings. We utilized isotopically-labeled peptides and tandem mass spectrometry to obtain absolute quantitation values on 14 peptides from 7 proteins; these proteins had shown previous importance in skin disease. The method demonstrated good reproducibility, dynamic range, and linearity (R2 > 0.993) when n = 3 standards were analyzed across 0.05-2.5 pmol. The method was used to determine if differences exist between skin proteins in a small group of atopic versus non-atopic individuals (n = 12). While only minimal differences were found, peptides were detected in all samples and exhibited good correlation between peptides for 5 of the 7 proteins (R2 = 0.71-0.98). This method can be applied to larger cohorts to further establish the relationships of these proteins to skin disease.
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Van Raemdonck GA, Osbak KK, Van Ostade X, Kenyon CR. Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis. F1000Res 2018; 7:336. [PMID: 30519456 PMCID: PMC6248270 DOI: 10.12688/f1000research.13964.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Current syphilis diagnostic strategies are lacking a sensitive manner of directly detecting
Treponema pallidum antigens. A diagnostic test that could directly detect
T. pallidum antigens in individuals with syphilis would be of considerable clinical utility, especially for the diagnosis of reinfections and for post-treatment serological follow-up. Methods: In this study, 11 candidate
T. pallidum biomarker proteins were chosen according to their physiochemical characteristics,
T. pallidum specificity and predicted abundance. Thirty isotopically labelled proteotypic surrogate peptides (hPTPs) were synthesized and incorporated into a scheduled multiple reaction monitoring assay. Protein extracts from undepleted/unenriched plasma (N = 18) and urine (N = 4) samples from 18 individuals with syphilis in various clinical stages were tryptically digested, spiked with the hPTP mixture and analysed with a triple quadruple mass spectrometer. Results: No endogenous PTPs corresponding to the eleven candidate biomarkers were detected in any samples analysed. To estimate the Limit of Detection (LOD) of a comparably sensitive mass spectrometer (LTQ-Orbitrap), two dilution series of rabbit cultured purified
T. pallidum were prepared in PBS. Polyclonal anti-
T. pallidum antibodies coupled to magnetic Dynabeads were used to enrich one sample series; no LOD improvement was found compared to the unenriched series. The estimated LOD of MS instruments is 300
T. pallidum/ml in PBS. Conclusions: Biomarker protein detection likely failed due to the low (femtomoles/liter) predicted concentration of
T. pallidum proteins. Alternative sample preparation strategies may improve the detectability of
T. pallidum proteins in biofluids.
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Affiliation(s)
- Geert A Van Raemdonck
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, 2000, Belgium.,Laboratory for Protein Science, Proteomics and Epigenetic Signalling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, 2610, Belgium
| | - Kara K Osbak
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, 2000, Belgium
| | - Xaveer Van Ostade
- Laboratory for Protein Science, Proteomics and Epigenetic Signalling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, 2610, Belgium
| | - Chris R Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, 2000, Belgium.,Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, 7925, South Africa
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Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN. Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine. Proteomics Clin Appl 2018; 12:e1700135. [DOI: 10.1002/prca.201700135] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/16/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Jarrod J. Sandow
- Walter and Eliza Hall Institute, Department of Medical Biology; University of Melbourne; Parkville VIC Australia
| | - Adam Rainczuk
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Giuseppe Infusini
- Walter and Eliza Hall Institute, Department of Medical Biology; University of Melbourne; Parkville VIC Australia
| | - Ming Makanji
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Maree Bilandzic
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Amy L. Wilson
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | | | - Peter G. Stanton
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
| | - Daniel Garama
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Daniel Gough
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
| | - Thomas W. Jobling
- Obstetrics and Gynaecology; Monash Medical Centre; Clayton VIC Australia
| | - Andrew I. Webb
- Walter and Eliza Hall Institute, Department of Medical Biology; University of Melbourne; Parkville VIC Australia
| | - Andrew N. Stephens
- Department of Molecular and Translational Sciences; Monash University; VIC Australia
- Centre for Cancer Research; Hudson Institute of Medical Research; VIC Australia
- Epworth Research Institute; Epworth HealthCare; Richmond VIC Australia
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Szigyarto CAK, Spitali P. Biomarkers of Duchenne muscular dystrophy: current findings. Degener Neurol Neuromuscul Dis 2018; 8:1-13. [PMID: 30050384 PMCID: PMC6053903 DOI: 10.2147/dnnd.s121099] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Numerous biomarkers have been unveiled in the rapidly evolving biomarker discovery field, with an aim to improve the clinical management of disorders. In rare diseases, such as Duchenne muscular dystrophy, this endeavor has created a wealth of knowledge that, if effectively exploited, will benefit affected individuals, with respect to health care, therapy, improved quality of life and increased life expectancy. The most promising findings and molecular biomarkers are inspected in this review, with an aim to provide an overview of currently known biomarkers and the technological developments used. Biomarkers as cells, genetic variations, miRNAs, proteins, lipids and/or metabolites indicative of disease severity, progression and treatment response have the potential to improve development and approval of therapies, clinical management of DMD and patients’ life quality. We highlight the complexity of translating research results to clinical use, emphasizing the need for biomarkers, fit for purpose and describe the challenges associated with qualifying biomarkers for clinical applications.
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Affiliation(s)
- Cristina Al-Khalili Szigyarto
- Division of Proteomics, School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden, .,Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden,
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands,
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31
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Malchow S, Loosse C, Sickmann A, Lorenz C. Quantification of Cardiovascular Disease Biomarkers in Human Platelets by Targeted Mass Spectrometry. Proteomes 2017; 5:proteomes5040031. [PMID: 29140295 PMCID: PMC5748566 DOI: 10.3390/proteomes5040031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/07/2017] [Accepted: 11/13/2017] [Indexed: 01/01/2023] Open
Abstract
Platelets are known to be key players in thrombosis and hemostasis, contributing to the genesis and progression of cardiovascular diseases. Due to their pivotal role in human physiology and pathology, platelet function is regulated tightly by numerous factors which have either stimulatory or inhibitory effects. A variety of factors, e.g., collagen, fibrinogen, ADP, vWF, thrombin, and thromboxane promote platelet adhesion and aggregation by utilizing multiple intracellular signal cascades. To quantify platelet proteins for this work, a targeted proteomics workflow was applied. In detail, platelets are isolated and lyzed, followed by a tryptic protein digest. Subsequently, a mix of stable isotope-labeled peptides of interesting biomarker proteins in concentrations ranging from 0.1 to 100 fmol is added to 3 μg digest. These peptides are used as an internal calibration curve to accurately quantify endogenous peptides and corresponding proteins in a pooled platelet reference sample by nanoLC-MS/MS with parallel reaction monitoring. In order to assure a valid quantification, limit of detection (LOD) and limit of quantification (LOQ), as well as linear range, were determined. This quantification of platelet activation and proteins by targeted mass spectrometry may enable novel diagnostic strategies in the detection and prevention of cardiovascular diseases.
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Affiliation(s)
- Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany.
| | - Christina Loosse
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany.
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany.
| | - Christin Lorenz
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany.
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32
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Tang Y, Cawthraw S, Bagnall MC, Gielbert AJ, Woodward MJ, Petrovska L. Identification of temperature regulated factors of Campylobacter jejuni and their potential roles in virulence. AIMS Microbiol 2017; 3:885-898. [PMID: 31294195 PMCID: PMC6604965 DOI: 10.3934/microbiol.2017.4.885] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/24/2017] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni is the major cause of bacterial gastroenteritis in man, while it is generally regarded as a commensal of the avian gut. Consumption and handling of contaminated poultry meat products are major risk factors for human infection. The body temperature in man (37 °C) and chickens (42 °C) differ markedly, and differential gene regulation and protein expression at different temperatures may in part explain the behaviour in the two hosts. We performed proteomics analyses with C. jejuni cells grown at 37 °C and 42 °C. Time-of-flight mass spectrometry (Q-Tof) analysis was carried out after samples were digested with the Filter-Aided Sample Preparation (FASP) method and peptides were fractionated by strong anion exchanges. Differentially regulated proteins were identified by Mascot and Scaffold analyses. Triple quadrupole (QQQ) mass spectrometer analysis confirmed that a total of 33 proteins were differentially regulated between 37 °C and 42 °C. Several upregulated proteins were selected for their corresponding gene knock-out mutants to be tested for their virulence in the Galleria mellonella model. To correlate with other tissue/animal models, the GADH mutant was selected for its reduced ability to colonize chickens. At 37 °C, the mutants of outer membrane protein Omp50 and Chaperone GroEL significantly increased virulence; while at 42 °C, the mutants of YceI, Omp50, and GADH reduced virulence against Galleria mellonella compared with the wild type strains. The results of current and previous studies indicate that GADH is a virulent factor in G. mellonella and a colonization factor in chickens. The workflow of this study may prove a new way to identify stress related virulent factors. The implications of these findings are discussed for pathogenesis in the model and other hosts.
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Affiliation(s)
- Yue Tang
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Shaun Cawthraw
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Mary C Bagnall
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Adriana J Gielbert
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Martin J Woodward
- Food and Nutritional Sciences, University of Reading, Whiteknights, Reading RG6 6AP, UK
| | - Liljana Petrovska
- Animal and Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
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Xu Y, Qin S, An T, Tang Y, Huang Y, Zheng L. MiR-145 detection in urinary extracellular vesicles increase diagnostic efficiency of prostate cancer based on hydrostatic filtration dialysis method. Prostate 2017; 77:1167-1175. [PMID: 28617988 DOI: 10.1002/pros.23376] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/18/2017] [Indexed: 12/27/2022]
Abstract
BACKGROUND Extracellular vesicles (EVs) can be detected in body fluids and may serve as disease biomarkers. Increasing evidence suggests that circulating miRNAs in serum and urine may be potential non-invasive biomarkers for prostate cancer (PCa). In the present study, we aimed to investigate whether hydrostatic filtration dialysis (HFD) is suitable for urinary EVs (UEVs) isolation and whether such reported PCa-related miRNAs can be detected in UEVs as PCa biomarkers. METHODS To analyze EVs miRNAs, we searched for an easy and economic method to enrich EVs from urine samples. We compared the efficiency of HFD method and conventional ultracentrifugation (UC) in isolating UEVs. Subsequently, UEVs were isolated from patients with PCa, patients with benign prostate hyperplasia (BPH) and healthy individuals. Differential expression of four PCa-related miRNAs (miR-572, miR-1290, miR-141, and miR-145) were measured in UEVs and paired serum EVs using SYBR Green-based quantitative reverse transcription-polymerase chain reaction (qRT-PCR). RESULTS The overall performance of HFD was similar to UC. In miRNA yield, both HFD and UC can meet the needs of further analysis. The level of miR-145 in UEVs was significantly increased in patients with PCa compared with the patients with BPH (P = 0.018). In addition, significant increase was observed in miR-145 levels when patients with Gleason score ≥8 tumors compared with Gleason score ≤7 (P = 0.020). Receiver-operating characteristic curve (ROC) revealed that miR-145 in UEVs combined with serum PSA could differentiate PCa from BPH better than PSA alone (AUC 0.863 and AUC 0.805, respectively). In serum EVs, four miRNAs were significantly higher in patients with PCa than with BPH. CONCLUSION HFD is appropriate for UEVs isolation and miRNA analysis when compared with conventional UC. miR-145 in UEVs is upregulated from PCa patients compared BPH patients and healthy controls. We suggest the potential use of UEVs miR-145 as a biomarker of PCa.
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Affiliation(s)
- Yong Xu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sihua Qin
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Taixue An
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yueting Tang
- Department of Clinical Laboratory, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Yiyao Huang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Beger R, Yu LR, Daniels J, Mattes W. Exploratory biomarkers: Analytical approaches and their implications. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH. Current trends in quantitative proteomics - an update. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:319-341. [PMID: 28418607 DOI: 10.1002/jms.3932] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 05/11/2023]
Abstract
Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics. In writing this current paper, we realized that, today, we have an even wider selection of potential tools for quantitative proteomics. These tools include new derivatization reagents, novel sampling formats, new types of analyzers and scanning techniques, and recently developed software to assist in assay development and data analysis. In this review article, we will discuss these innovative methods, and their current and potential applications in proteomics. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- H Li
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Han
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Pan
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - T Liu
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C E Parker
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
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Magalhães P, Schanstra JP, Carrick E, Mischak H, Zürbig P. Urinary biomarkers for renal tract malformations. Expert Rev Proteomics 2016; 13:1121-1129. [PMID: 27791437 DOI: 10.1080/14789450.2016.1254555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Renal tract malformations (RTMs) are congenital anomalies of the kidneys and urinary tract, which are the major cause of end-stage renal disease in children. Using immunoassay-based approaches (ELISA, western blot), individual urinary proteins including transforming growth factor β, tumor necrosis factor and monocyte attractant proteins 1 were found to be associated to RTMs. However, only mass spectrometry (MS) based methods leading to the identification of panels of protein-based markers composed of fragments of the extracellular matrix allowed the prediction of progression of RTMs and its complications. Areas covered: In this review, we summarized relevant studies identified in "Pubmed" using the keywords "urinary biomarkers" and "proteomics" and "renal tract malformations" or "hydronephrosis" or "ureteropelvic junction obstruction" or "posterior urethral valves" or "vesicoureteral reflux". These publications represent studies on potential protein-based biomarkers, either individually or combined in panels, of RTMs in human and animal models. Expert commentary: Successful use in the clinic of these protein-based biomarkers will need to involve larger scale studies to reach sufficient power. Improved performance will potentially come from combining immunoassay- and MS-based markers.
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Affiliation(s)
- Pedro Magalhães
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,b Department of Pediatric Nephrology, Hannover Medical School , Hannover , Germany
| | - Joost P Schanstra
- c Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease , Toulouse , France.,d Université Toulouse III Paul-Sabatier , Toulouse , France
| | - Emma Carrick
- e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Harald Mischak
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Petra Zürbig
- a Mosaiques Diagnostics GmbH , Hannover , Germany
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37
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Wang L, Skotland T, Berge V, Sandvig K, Llorente A. Exosomal proteins as prostate cancer biomarkers in urine: From mass spectrometry discovery to immunoassay-based validation. Eur J Pharm Sci 2016; 98:80-85. [PMID: 27664330 DOI: 10.1016/j.ejps.2016.09.023] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 01/04/2023]
Abstract
Exosomes have recently appeared as a novel source of non-invasive cancer biomarkers since tumor-specific molecules can be found in exosomes isolated from biological fluids. We have previously analyzed the proteome of urinary exosomes by mass spectrometry, and identified proteins differentially expressed in prostate cancer patients compared to healthy males. Since mass spectrometry is so far not commonly used in clinical laboratories, we have here investigated whether antibody-based methods such as Western blot or ELISA can be used to validate the use of the identified proteins as prostate cancer biomarkers. Western blot experiments designed to detect flotillin 2, TMEM256, Rab3B and LAMTOR1 showed that the level of these proteins was higher in urinary exosomes from prostate cancer patients compared to healthy males. Furthermore, a receiver operating characteristic curve of flotillin 2 in samples from 16 controls and 16 patients showed an area under the curve of 0.91, and 88% sensitivity at a threshold set to give 94% specificity. In addition, ELISA-based detection of flotillin 2 and PARK7 showed that the combination of these proteins was able to distinguish prostate cancer patients and healthy controls with 68% sensitivity and 93% specificity. Several promising biomarkers identified by mass spectrometry could not be evaluated by Western blot or ELISA due to their low exosomal amount and/or lack of good antibodies. In conclusion, our results show that several urinary exosomal proteins identified as prostate cancer biomarkers by mass spectrometry have a high diagnostic value also when analyzed by immunology-based methods, thus bringing these biomarkers closer to a potential clinical use.
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Affiliation(s)
- Ling Wang
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Tore Skotland
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Viktor Berge
- Department of Urology, Oslo University Hospital, 0586 Oslo, Norway
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway; Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway.
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Pena MJ, Mischak H, Heerspink HJL. Proteomics for prediction of disease progression and response to therapy in diabetic kidney disease. Diabetologia 2016; 59:1819-31. [PMID: 27344310 PMCID: PMC4969331 DOI: 10.1007/s00125-016-4001-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/13/2016] [Indexed: 12/31/2022]
Abstract
The past decade has resulted in multiple new findings of potential proteomic biomarkers of diabetic kidney disease (DKD). Many of these biomarkers reflect an important role in the (patho)physiology and biological processes of DKD. Situations in which proteomics could be applied in clinical practice include the identification of individuals at risk of progressive kidney disease and those who would respond well to treatment, in order to tailor therapy for those at highest risk. However, while many proteomic biomarkers have been discovered, and even found to be predictive, most lack rigorous external validation in sufficiently powered studies with renal endpoints. Moreover, studies assessing short-term changes in the proteome for therapy-monitoring purposes are lacking. Collaborations between academia and industry and enhanced interactions with regulatory agencies are needed to design new, sufficiently powered studies to implement proteomics in clinical practice.
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Affiliation(s)
- Michelle J Pena
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, the Netherlands
| | - Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Hiddo J L Heerspink
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, the Netherlands.
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39
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von Zur Mühlen C, Koeck T, Schiffer E, Sackmann C, Zürbig P, Hilgendorf I, Reinöhl J, Rivera J, Zirlik A, Hehrlein C, Mischak H, Bode C, Peter K. Urine proteome analysis as a discovery tool in patients with deep vein thrombosis and pulmonary embolism. Proteomics Clin Appl 2016; 10:574-84. [PMID: 26898369 DOI: 10.1002/prca.201500105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 12/15/2015] [Accepted: 02/08/2016] [Indexed: 02/03/2023]
Abstract
PURPOSE Early and accurate detection of deep vein thrombosis (DVT) is an important clinical need. Based on the hypothesis that urinary peptides may hold information on DVT in conjunction with pulmonary embolism (PE), the study was aimed at identifying such peptide biomarkers using capillary electrophoresis coupled mass spectrometry. EXPERIMENTAL DESIGN Patients with symptoms of unprovoked/idiopathic DVT and/or PE were examined by doppler-sonography or angio-computed tomography. Urinary proteome analysis allowed for identification of respective peptide biomarkers. To confirm their biological relevance, we induced PE in mice and assessed human ex vivo thrombi. RESULTS We identified 62 urinary peptides as DVT-specific biomarkers, i.e. fragments of collagen type I and a fragment of fibrinogen β-chain. The presence of fibrinogen α/β in the acute thrombus, and collagen type I and osteopontin in the older, organized thrombus was demonstrated. The classifier DVT62 established through support vector machine (SVM) modeling based on the 62 identified peptides was validated in an independent cohort of 47 subjects (six cases and 41 controls) with a sensitivity of 100% and specificity of 83%. CONCLUSIONS AND CLINICAL RELEVANCE Urine proteome analysis enabled the detection of DVT-specific peptides, which were validated in human and mouse tissue. Furthermore, it allowed for the establishment of an urinary-proteome based classifier that is relatively specific for DVT. The data provide the basis for assessment of these biomarkers in a prospective clinical study.
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Affiliation(s)
| | | | | | - Christine Sackmann
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | | | - Ingo Hilgendorf
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Jochen Reinöhl
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Jennifer Rivera
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Andreas Zirlik
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Christoph Hehrlein
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,BHF Glasgow Cardiovascular Research, University of Glasgow, UK
| | - Christoph Bode
- Department of Cardiology and Angiology I, University Heart Center Freiburg, Freiburg, Germany
| | - Karlheinz Peter
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
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