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Preetam S, Mondal S, Priya S, Bora J, Ramniwas S, Rustagi S, Qusty NF, Alghamdi S, Babalghith AO, Siddiqi A, Malik S. Targeting tumour markers in ovarian cancer treatment. Clin Chim Acta 2024; 559:119687. [PMID: 38663473 DOI: 10.1016/j.cca.2024.119687] [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: 03/10/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
Ovarian cancers (OC) are the most common, lethal, and stage-dependent cancers at the global level, specifically in female patients. Targeted therapies involve the administration of drugs that specifically target the alterations in tumour cells responsible for their growth, proliferation, and metastasis, with the aim of treating particular patients. Presently, within the realm of gynaecological malignancies, specifically in breast and OCs, there exist various prospective therapeutic targets encompassing tumour-intrinsic signalling pathways, angiogenesis, homologous-recombination deficit, hormone receptors, and immunologic components. Breast cancers are often detected in advanced stages, primarily due to the lack of a reliable screening method. However, various tumour markers have been extensively researched and employed to evaluate the condition, progression, and effectiveness of medication treatments for this ailment. The emergence of recent technological advancements in the domains of bioinformatics, genomics, proteomics, and metabolomics has facilitated the exploration and identification of hitherto unknown biomarkers. The primary objective of this comprehensive review is to meticulously investigate and analyze both established and emerging methodologies employed in the identification of tumour markers associated with OC.
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Affiliation(s)
- Subham Preetam
- Department of Robotics and Mechatronics Engineering, Daegu Gyeongbuk Institute of Science & Technology (DGIST) Dalseong-gun, Daegu 42988, South Korea.
| | - Sagar Mondal
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
| | - Swati Priya
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
| | - Jutishna Bora
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
| | - Seema Ramniwas
- University Center for Research and Development, Department of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, India.
| | - Sarvesh Rustagi
- School of Applied and Life Sciences, Uttaranchal University, 248007 Dehradun, Uttarakhand, India.
| | - Naeem F Qusty
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Saad Alghamdi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Ahmad O Babalghith
- Medical Genetics Department, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Abdullah Siddiqi
- Department of Clinical Laboratory, Makkah Park Clinics, Makkah, Saudi Arabia.
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand 834001, India.
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Pietkiewicz D, Zaborowski MP, Jaz K, Matuszewska E, Światły-Błaszkiewicz A, Kluz T, Kokot ZJ, Nowak-Markwitz E, Matysiak J. Serum Proteomic Profiles of Patients with High and Low Risk of Endometrial Cancer Recurrence. Int J Mol Sci 2023; 24:14528. [PMID: 37833976 PMCID: PMC10572223 DOI: 10.3390/ijms241914528] [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: 08/01/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Endometrial cancer is the most common gynecological cancer worldwide. Classifying endometrial cancer into low- or high-risk groups based on the following features is recommended: tumor grade, lymphovascular space invasion, myometrial involvement, and non-endometrioid histology. Despite the recent progress in molecular profiling of endometrial cancer, a substantial group of patients are misclassified based on the current criteria. This study aimed to identify proteins that could be used as biomarkers for the stratification of endometrial cancer patients into low- or high-risk groups. The proteomic analysis of serum samples from endometrial cancer patients was performed using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The data were then analyzed using chemometric algorithms to identify potential biomarkers. Nineteen precursor ions were identified as fragments of eighteen proteins which included (1) connective tissue matrix proteins, (2) cytoskeletal proteins, and (3) innate immune system molecules and stress proteins. These biomarkers could be used to stratify the high- and low-risk patients, thus enabling more precise treatment decisions.
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Affiliation(s)
- Dagmara Pietkiewicz
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 3 Rokietnicka Street, 60-806 Poznan, Poland; (E.M.); (J.M.)
| | - Mikołaj Piotr Zaborowski
- Gynecologic Oncology Department, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland; (M.P.Z.); (K.J.); (E.N.-M.)
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Kamila Jaz
- Gynecologic Oncology Department, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland; (M.P.Z.); (K.J.); (E.N.-M.)
| | - Eliza Matuszewska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 3 Rokietnicka Street, 60-806 Poznan, Poland; (E.M.); (J.M.)
| | - Agata Światły-Błaszkiewicz
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089 Bydgoszcz, Poland;
| | - Tomasz Kluz
- Department of Gynaecology, Gynaecologic Oncology and Obstetrics, Institute of Medical Sciences, Medical College of Rzeszow University, Rejtana 16c Street, 35-959 Rzeszow, Poland;
| | - Zenon J. Kokot
- Faculty of Health Sciences, Calisia University, 13 Kaszubska Street, 62-800 Kalisz, Poland;
| | - Ewa Nowak-Markwitz
- Gynecologic Oncology Department, Poznan University of Medical Sciences, 33 Polna Street, 60-535 Poznan, Poland; (M.P.Z.); (K.J.); (E.N.-M.)
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 3 Rokietnicka Street, 60-806 Poznan, Poland; (E.M.); (J.M.)
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Kaya ZZ, Serdar M, Aksungar F, Kilercik M, Serteser M, Baykal AT. Rapid detection of serum free light chains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:132-140. [PMID: 36734073 DOI: 10.1177/14690667231153616] [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: 06/18/2023]
Abstract
Introduction: Serum free light chain (FLC) measurements are increasingly prominent for patients with plasma cell disorders (PCDs) in screening, prognostic stratification, and monitoring therapy responses. Objectives: We aimed to develop a sensitive, reliable, and accurate method for diagnosing PCDs that can notably decrease the time and cost of current methods. Methods: Here, we present a novel approach for FLC measurement using immunoenrichment on micro-affinity chromatography in combination with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) detection. In this study, serum free kappa (κ) and free lambda (λ) light chain (LC) levels in the serum of 105 patients were compared between the nephelometric serum FLC quantification and MALDI-TOF MS detection. Results: Cohen's kappa coefficient between the MALDI-TOF MS-based method and the FLC assay revealed an almost perfect agreement in the case of normal (negative) results (κ = 0.92; 95% confidence interval (CI): 0.837 to 0.968) and a good agreement in the case of increased (positive) results (κ = 0.76; 95% CI: 0.608 to 0.870). In Spearman's correlation analysis, the best correlation was found between serum free κ/λ ratios (r = 0.628, 0.496 to 0.732; p <0.0001). Our method showed sensitivity (92.5%) and specificity (76.3%) for discrimination between the κ/λ FLC ratio compared to the serum FLC assay. Conclusion: The proposed method can significantly contribute to diagnosing and monitoring PCDs as it can significantly be time-saving, cost-effective in FLC measurement.
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Affiliation(s)
- Zelal Zuhal Kaya
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Muhittin Serdar
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Fehime Aksungar
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Meltem Kilercik
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Medical Biochemistry, Acibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Mustafa Serteser
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Medical Biochemistry, Acibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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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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5
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Changes in Serum Protein-Peptide Patterns in Atopic Children Allergic to Plant Storage Proteins. Int J Mol Sci 2023; 24:ijms24021804. [PMID: 36675318 PMCID: PMC9861933 DOI: 10.3390/ijms24021804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Next to cow's milk and eggs, plant foods, i.e., legumes, tree nuts and cereal grains, most often sensitise atopic children. Storage proteins constitutes the most relevant protein fraction of plant foods, causing primary sensitisation. They exhibit strong allergenic properties and immunogenicity. Our goal was to analyse sensitisation to 26 plant storage proteins in a group of 76 children aged 0-5 years with chronic symptoms of atopic dermatitis using Allergy Explorer ALEX2 and to discover changes in serum protein-peptide patterns in allergic patients with the use of MALDI-TOF-MS. We reported that 25% of children were allergic to 2S albumins, 19.7% to 7S globulins, 13.2% to 11S globulins and 1.3% to cereal prolamins. The most common allergenic molecules were Ara h 1 (18.4%), Ara h 2 (17.1%), Ara h 6 (15.8%) and Ara h 3 (11.8%) from peanuts, and the mean serum sIgE concentrations in allergic patients were 10.93 kUA/L, 15.353 kUA/L, 15.359 kUA/L and 9.038 kUA/L, respectively. In children allergic to storage proteins compared to the other patients (both allergic and non-allergic), the cell cycle control protein 50A, testis-expressed sequence 13B, DENN domain-containing protein 5A and SKI family transcriptional corepressor 2 were altered. Our results indicate that the IgE-mediated allergy to storage proteins is a huge problem in a group of young, atopic children, and show the potential of proteomic analysis in the prediction of primary sensitisation to plant foods. It is the next crucial step for understanding the molecular consequences of allergy to storage proteins.
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Kartsova LA, Bessonova EA, Deev VA, Kolobova EA. Current Role of Modern Chromatography with Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy in the Investigation of Biomarkers of Endometriosis. Crit Rev Anal Chem 2023:1-24. [PMID: 36625278 DOI: 10.1080/10408347.2022.2156770] [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: 01/11/2023]
Abstract
Endometriosis has a wide range of clinical manifestations, and the disease course is unpredictable, making the diagnosis a challenging task. Despite significant advances in the pathophysiology of endometriosis and various proposed theories, the exact etiology is not fully understood and is still unknown. The most commonly used biomarker of endometriosis is CA-125, however, it is nonspecific and is applied for cancers diagnosis. Therefore, the development of reliable noninvasive diagnostic tests for the early diagnosis of endometriosis remains one of the top priorities. Omics technologies are very promising approaches for constructing diagnostic models and biomarker discovery. Their use can greatly facilitate the study of such a complex disease as endometriosis. Nowadays, powerful analytical platforms commonly used in omics, such as gas and liquid chromatography with mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy, have proven to be a promising tools for biomarker discovery. The aim of this review is to summarize the various features of the analytical approaches, practical challenges and features of gas and liquid chromatography with MS and NMR spectroscopy (including sample processing protocols, technological advancements, and methodology) used for profiling of metabolites, lipids, peptides and proteins in physiological fluids and tissues from patients with endometriosis. In addition, this report devotes special attention to the issue of how comprehensive analyses of these profiles can effectively contribute to the study of endometriosis. The search query included reports published between 2012 and 2022 years in PubMed, Web-of-Science, SCOPUS, Science Direct.
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Affiliation(s)
| | | | | | - Ekaterina Alekseevna Kolobova
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
- The Federal State Institute of Public Health 'The Nikiforov Russian Center of Emergency and Radiation Medicine', The Ministry of Russian Federation for Civil Defence, Emergencies and Elimination of Consequences of Natural Disasters, St. Petersburg, Russia
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Utilizing MALDI-TOF MS and LC-MS/MS to access serum peptidome-based biomarkers in canine oral tumors. Sci Rep 2022; 12:21641. [PMID: 36517562 PMCID: PMC9750994 DOI: 10.1038/s41598-022-26132-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Tumors frequently found in dogs include canine oral tumors, either cancerous or noncancerous. The bloodstream is an important route for tumor metastasis, particularly for late-stage oral melanoma (LOM) and late-stage oral squamous cell carcinoma (LOSCC). The present study aimed to investigate serum peptidome-based biomarkers of dogs with early-stage oral melanoma, LOM, LOSCC, benign oral tumors, chronic periodontitis and healthy controls, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography tandem mass spectrometry. A principal component analysis plot showed distinct clusters among all groups. Four peptides were identified, including peptidyl-prolyl cis-trans isomerase FKBP4 isoform X2 (FKBP4), steroid hormone receptor ERR1 (ESRRA or ERRA), immunoglobulin superfamily member 10 (IGSF10) and ATP-binding cassette subfamily B member 5 (ABCB5). FKBP4, ESRRA and ABCB5 were found to be overexpressed in both LOM and LOSCC, whereas IGSF10 expression was markedly increased in LOSCC only. These four proteins also played a crucial role in numerous pathways of cancer metastasis and showed a strong relationship with chemotherapy drugs. In conclusion, this study showed rapid screening of canine oral tumors using serum and MALDI-TOF MS. In addition, potential serum peptidome-based biomarker candidates for LOM and LOSCC were identified.
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Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022; 10:proteomes10040035. [PMID: 36278695 PMCID: PMC9590004 DOI: 10.3390/proteomes10040035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Immunohistochemistry (IHC) is still widely used as a morphology-based assay for in situ analysis of target proteins as specific tumor antigens. However, as a very heterogeneous collection of neoplastic diseases, breast cancer (BC) requires an accurate identification and characterization of larger panels of candidate biomarkers, beyond ER, PR, and HER2 proteins, for diagnosis and personalized treatment, without the limited availability of antibodies that are required to identify specific proteins. Top-down, middle-down, and bottom-up mass spectrometry (MS)-based proteomics approaches complement traditional histopathological tissue analysis to examine expression, modification, and interaction of hundreds to thousands of proteins simultaneously. In this review, we discuss the proteomics-based identification of dysregulated proteins in BC that are essential for the following issues: discovery and validation of new biomarkers by analysis of solid and liquid/non-invasive biopsies, cell lines, organoids and xenograft models; identification of panels of biomarkers for early detection and accurate discrimination between cancer, benign and normal tissues; identification of subtype-specific and stage-specific protein expression profiles in BC grading and measurement of disease progression; characterization of new subtypes of BC; characterization and quantitation of post-translational modifications (PTMs) and aberrant protein-protein interactions (PPI) involved in tumor development; characterization of the global remodeling of BC tissue homeostasis, diagnosis and prognostic information; and deciphering of molecular functions, biological processes and mechanisms through which the dysregulated proteins cause tumor initiation, invasion, and treatment resistance.
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Wang F, Wang ZR, Ding XS, Yang H, Guo Y, Su H, Wan XR, Wang LJ, Jiang XY, Xu YH, Chen F, Cui W, Feng FZ. Combining serum peptide signatures with International Federation of Gynecology and Obstetrics (FIGO) risk score to predict the outcomes of patients with gestational trophoblastic neoplasia (GTN) after first-line chemotherapy. Front Oncol 2022; 12:982806. [PMID: 36338720 PMCID: PMC9634134 DOI: 10.3389/fonc.2022.982806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/06/2022] [Indexed: 11/21/2022] Open
Abstract
Background Gestational trophoblastic neoplasia (GTN) is a group of clinically rare tumors that develop in the uterus from placental tissue. Currently, its satisfactory curability derives from the timely and accurately classification and refined management for patients. This study aimed to discover biomarkers that could predict the outcomes of GTN patients after first-line chemotherapy. Methods A total of 65 GTN patients were included in the study. Patients were divided into the good or poor outcome group and the clinical characteristics of the patients in the two groups were compared. Furthermore, the serum peptide profiles of all patients were uncovered by using weak cation exchange magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Feature peaks were identified by three machine learning algorithms and then models were constructed and compared using five machine learning methods. Additionally, liquid chromatography mass spectrometry was used to identify the feature peptides. Results Multivariate logistic regression analysis showed that the International Federation of Gynecology and Obstetrics (FIGO) risk score was associated with poor outcomes. Eight feature peaks (m/z =1287, 2042, 2862, 2932, 2950, 3240, 3277 and 6626) were selected for model construction and validation by the three algorithms. Based on the panel combining FIGO risk score and peptide serum signatures, the neural network (nnet) model showed promising performance in both the training (AUC=0.9635) and validation (AUC=0.8788) cohorts. Peaks at m/z 2042, 2862, 2932, 3240 were identified as the partial sequences of transthyretin, fibrinogen alpha chain (FGA), beta-globin and FGA, respectively. Conclusion We combined FIGO risk score and serum peptide signatures using the nnet method to construct the model which can accurately predict outcome of GTN patients after first-line chemotherapy. With this model, patients can be further classified and managed, and those with poor predicted outcomes can be given more attention for developing treatment failure.
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Affiliation(s)
- Fei Wang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zi-ran Wang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xue-song Ding
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hua Yang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ye Guo
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hao Su
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xi-run Wan
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li-juan Wang
- Department of Gynecological Oncology, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xiang-yang Jiang
- Department of Obstetrics and Gynecology, Shanxi Provincial People’s Hospital, Xian, China
| | - Yan-hua Xu
- Department of Obstetrics and Gynecology, Jinan Maternity and Child Health Care Hospital, Jinan, China
| | - Feng Chen
- Department of Clinical Laboratory, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Cui
- Department of Clinical Laboratory, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Wei Cui, ; Feng-zhi Feng,
| | - Feng-zhi Feng
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- *Correspondence: Wei Cui, ; Feng-zhi Feng,
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Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research. Molecules 2022; 27:molecules27196196. [PMID: 36234736 PMCID: PMC9570737 DOI: 10.3390/molecules27196196] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein–protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide “molecular pictures”, which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.
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Huh S, Kang C, Park JE, Nam D, Kim SI, Seol A, Choi K, Hwang D, Yu MH, Chung HH, Lee SW, Kang UB. Novel Diagnostic Biomarkers for High-Grade Serous Ovarian Cancer Uncovered by Data-Independent Acquisition Mass Spectrometry. J Proteome Res 2022; 21:2146-2159. [PMID: 35939567 DOI: 10.1021/acs.jproteome.2c00218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) represents the major histological type of ovarian cancer, and the lack of effective screening tools and early detection methods significantly contributes to the poor prognosis of HGSOC. Currently, there are no reliable diagnostic biomarkers for HGSOC. In this study, we performed liquid chromatography data-independent acquisition tandem mass spectrometry (MS) on depleted serum samples from 26 HGSOC cases and 24 healthy controls (HCs) to discover potential HGSOC diagnostic biomarkers. A total of 1,847 proteins were identified across all samples, among which 116 proteins showed differential expressions between HGSOC patients and HCs. Network modeling showed activations of coagulation and complement cascades, platelet activation and aggregation, neutrophil extracellular trap formation, toll-like receptor 4, insulin-like growth factor, and transforming growth factor β signaling, as well as suppression of lipoprotein assembly and Fc gamma receptor activation in HGSOC. Based on the network model, we prioritized 28 biomarker candidates and validated 18 of them using targeted MS assays in an independent cohort. Predictive modeling showed a sensitivity of 1 and a specificity of 0.91 in the validation cohort. Finally, in vitro functional assays on four potential biomarkers (FGA, VWF, ARHGDIB, and SERPINF2) suggested that they may play an important role in cancer cell proliferation and migration in HGSOC. All raw data were deposited in PRIDE (PXD033169).
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Affiliation(s)
- Sunghyun Huh
- Bertis R&D Division, Bertis Inc., Seongnam-si, Gyeonggi-do 13605, Republic of Korea
| | - Chaewon Kang
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Ji Eun Park
- Bertis R&D Division, Bertis Inc., Seongnam-si, Gyeonggi-do 13605, Republic of Korea
| | - Dowoon Nam
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Se Ik Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Aeran Seol
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Obstetrics and Gynecology, Korea University Medical Center, Seoul 02843, Republic of Korea
| | - Kyerim Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Bioinformatics Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Myeong-Hee Yu
- Bertis R&D Division, Bertis Inc., Seongnam-si, Gyeonggi-do 13605, Republic of Korea
| | - Hyun Hoon Chung
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sang-Won Lee
- Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
| | - Un-Beom Kang
- Bertis R&D Division, Bertis Inc., Seongnam-si, Gyeonggi-do 13605, Republic of Korea
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12
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Tarfeen N, Nisa KU, Nisa Q. MALDI-TOF MS: application in diagnosis, dereplication, biomolecule profiling and microbial ecology. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9340741 DOI: 10.1007/s43538-022-00085-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized scientific research over the past few decades and has provided a unique platform in ongoing technological developments. Undoubtedly, there has been a bloom chiefly in the field of biological sciences with this emerging technology, and has enabled researchers to generate critical data in the field of disease diagnoses, drug development, dereplication. It has received well acceptance in the field of microbial identification even at strain level, as well as diversified field like biomolecule profiling (proteomics and lipidomics) has evolved tremendously. Additionally, this approach has received a lot more attention over conventional technologies due to its high throughput, speed, and cost effectiveness. This review aims to provide a detailed insight regarding the application of MALDI-TOF MS in the context of medicine, biomolecule profiling, dereplication, and microbial ecology. In general, the expansion in the application of this technology and new advancements it has made in the field of science and technology has been highlighted.
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13
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Tsai H, Phinney BS, Grigorean G, Salemi MR, Rashidi HH, Pepper J, Tran NK. Identification of Endogenous Peptides in Nasal Swab Transport Media used in MALDI-TOF-MS Based COVID-19 Screening. ACS OMEGA 2022; 7:17462-17471. [PMID: 35600141 PMCID: PMC9113002 DOI: 10.1021/acsomega.2c01864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS) based diagnostic detection of 2019 novel coronavirus infectious disease (COVID-19) has been postulated to be a useful alternative to classical PCR based diagnostics. These MS based approaches have the potential to be both rapid and sensitive and can be done on-site without requiring a dedicated laboratory or depending on constrained supply chains (i.e., reagents and consumables). Matrix-assisted laser desorption ionization (MALDI)-time-of-flight (TOF) MS has a long and established history of microorganism detection and systemic disease assessment. Previously, we have shown that automated machine learning (ML) enhanced MALDI-TOF-MS screening of nasal swabs can be both sensitive and specific for COVID-19 detection. The underlying molecules responsible for this detection are generally unknown nor are they required for this automated ML platform to detect COVID-19. However, the identification of these molecules is important for understanding both the mechanism of detection and potentially the biology of the underlying infection. Here, we used nanoscale liquid chromatography tandem MS to identify endogenous peptides found in nasal swab saline transport media to identify peptides in the same the mass over charge (m/z) values observed by the MALDI-TOF-MS method. With our peptidomics workflow, we demonstrate that we can identify endogenous peptides and endogenous protease cut sites. Further, we show that SARS-CoV-2 viral peptides were not readily detected and are highly unlikely to be responsible for the accuracy of MALDI based SARS-CoV-2 diagnostics. Further analysis with more samples will be needed to validate our findings, but the methodology proves to be promising.
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Affiliation(s)
- Helen Tsai
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Brett S. Phinney
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Gabriela Grigorean
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Michelle R. Salemi
- Proteomics
Core, University of California, Davis, 451 E. Health Sciences Dr., Davis, California 95616, United States
| | - Hooman H. Rashidi
- Department
of Pathology and Laboratory Medicine, University
of California, Davis, 4400 V St., Sacramento, California 95817, United States
| | - John Pepper
- SpectraPass,
LLC, 1980 Festival Plaza,
Suite 770, Las Vegas, Nevada 89135, United States
- Allegiant
Air, 1201 North Town
Center Drive, Las Vegas, Nevada 89144, United
States
| | - Nam K. Tran
- Department
of Pathology and Laboratory Medicine, University
of California, Davis, 4400 V St., Sacramento, California 95817, United States
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14
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Gutaj P, Matysiak J, Matuszewska E, Jaskiewicz K, Kamińska D, Światły-Błaszkiewicz A, Szczapa T, Kalantarova A, Gajecka M, Wender-Ozegowska E. Maternal serum proteomic profiles of pregnant women with type 1 diabetes. Sci Rep 2022; 12:8696. [PMID: 35610262 PMCID: PMC9130255 DOI: 10.1038/s41598-022-12221-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Despite improvement in the care of diabetes over the years, pregnancy complicated by type 1 diabetes (T1DM) is still associated with adverse maternal and neonatal outcomes. To date, proteomics studies have been conducted to identify T1DM biomarkers in non-pregnant women, however, no studies included T1DM pregnant women. In this study serum proteomic profiling was conducted in pregnant women with T1DM in the late third trimester. Serum samples were collected from 40 women with T1DM and 38 healthy controls within 3 days before delivery at term pregnancy. Significant differences between serum proteomic patterns were revealed, showing discriminative peaks for complement C3 and C4-A, kininogen-1, and fibrinogen alpha chain. Quantification of selected discriminative proteins by ELISA kits was also performed. The serum concentration of kininogen-1 was significantly lower in women with T1DM than in controls. There were no significant differences in serum concentrations of complement C3 and complement C4-A between study groups. These data indicate that pregnant women with T1DM have a distinct proteomic profile involving proteins in the coagulation and inflammatory pathways. However, their utility as biomarkers of pregnancy complications in women with T1DM warrants further investigation.
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Affiliation(s)
- Paweł Gutaj
- Department of Reproduction, Poznan University of Medical Sciences, 61-701, Poznan, Poland.
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Eliza Matuszewska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Katarzyna Jaskiewicz
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 61-701, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Dorota Kamińska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Agata Światły-Błaszkiewicz
- Department of Inorganic and Analytical Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089, Bydgoszcz, Poland
| | - Tomasz Szczapa
- Department of Neonatology, Neonatal Biophysical Monitoring and Cardiopulmonary Therapies Research Unit, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | | | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 61-701, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Ewa Wender-Ozegowska
- Department of Reproduction, Poznan University of Medical Sciences, 61-701, Poznan, Poland
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15
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Salivary Proteome, Inflammatory, and NETosis Biomarkers in Older Adult Practitioners and Nonpractitioners of Physical Exercise. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3725056. [PMID: 35502212 PMCID: PMC9056209 DOI: 10.1155/2022/3725056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/22/2022] [Indexed: 11/18/2022]
Abstract
Since aging has been associated with increased production of inflammatory biomarkers, the ability to monitor older adults repeatedly is highly desirable, and saliva is an interesting biofluid for the search of biomarkers, as it is easily accessible in a noninvasive manner. However, given the incipient knowledge of salivary biomarkers in aging and its relationship to physical exercise, the present study is aimed at evaluating the protein expression and the levels of inflammatory and NETosis biomarkers in the saliva of practitioners (PE) and nonpractitioners (NPE) of physical exercise older adults. Six (6) practitioner and 4 nonpractitioner older adults were enrolled in this study. Unstimulated whole saliva was collected for analysis of the proteome by label-free mass spectrometry, as well as of the inflammatory status by evaluation of C-reactive protein (CRP), vascular endothelial growth factor (VEGF), and cytokines (TNF-α, interleukin- (IL-) 1β, and IL-8), while NETosis was assessed by myeloperoxidase (MPO) and neutrophil elastase. Regarding oral health, the decayed, missing, and filled teeth (DMF-T) index, bleeding on probing, suppuration, and probing depth measurement (mm) were evaluated. In addition, functional capacity was investigated using the General Physical Fitness Index (GPFI). In relation to the proteome analysis, 93 and 143 proteins were found exclusively in the PE and NPE groups, respectively; 224 proteins were common to both groups. Among these proteins, 10 proteins showed statistical difference (
) between the groups: alpha-2-macroglobulin, component 3 of the complement, serotransferrin, and protein soluble in brain acid 1 were less expressed, while lactotransferrin, alpha-amylase 1, S100-A8, S100-A9, lactoperoxidase, and galectin-3 binding protein were more expressed in the PE group. No differences between groups were observed in the analysis of inflammatory and NETosis biomarkers. This study shows the potential utility of saliva for detecting protein biomarkers in a noninvasive biological sample of the elderly population.
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16
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Liu J, Tang N, Liu N, Lei P, Wang F. Echinacoside inhibits the proliferation, migration, invasion and angiogenesis of ovarian cancer cells through PI3K/AKT pathway. J Mol Histol 2022; 53:493-502. [PMID: 35325326 DOI: 10.1007/s10735-022-10073-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/08/2022] [Indexed: 12/24/2022]
Abstract
Echinacoside is a group of natural compounds extracted from medicinal plants Cistanche and Echinacea, which has neuroprotective, antiaging, immunomodulatory and anticancer effects, but its specific role and mechanism in tumor remains partially unclear. To our knowledge, it was the first time to reported the effect of Echinacoside in ovarian cancer. Colony formation, TUNEL staining, Transwell and tube formation assays were conducted to analyze the proliferation, apoptosis, invasion and tube formation abilities of serous ovarian carcinoma cells (SKOV3 and OVCAR-3), respectively. The expressions of apoptosis-, invasion- and PI3K/AKT pathway-related proteins were measured by western blotting. In addition, PI3K agonist (740Y-P) was used to assess the regulatory effect of Echinacoside on PI3K/AKT signaling in ovarian cancer. Finally, the anti-tumor effect of Echinacoside on SKOV3-xenografted mice was evaluated by xenograft tumor mouse model. Our results demonstrated Echinacoside concentration-dependently reduced the proliferation, migration and angiogenesis of ovarian cancer cells, whereas promoted apoptosis. Moreover, western blotting revealed that Echinacoside suppressed the growth of ovarian cancer cells by downregulating the phosphorylation levels of PI3K, AKT and mTOR, which could be partially reversed by 740Y-P. Further, in vivo results showed that Echinacoside could effectively alleviate the tumor growth of xenograft mice, accompanied by the decrease of PI3K/AKT signaling. In general, our results demonstrate that Echinacoside could reduce the ovarian cancer progression through inhibition of PI3K/AKT pathway, suggesting that Echinacoside may be a new treatment option for ovarian cancer.
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Affiliation(s)
- Juan Liu
- Department of Gynecology, Weinan Maternal and Child Health Hospital, No. 114, Dongfeng Street, Weinan, 714000, Shaanxi, China
| | - Ni Tang
- Department of Gynecology, Weinan Maternal and Child Health Hospital, No. 114, Dongfeng Street, Weinan, 714000, Shaanxi, China
| | - Ni Liu
- Department of Gynecology, Weinan Maternal and Child Health Hospital, No. 114, Dongfeng Street, Weinan, 714000, Shaanxi, China
| | - Panpan Lei
- Department of Gynecology, Weinan Maternal and Child Health Hospital, No. 114, Dongfeng Street, Weinan, 714000, Shaanxi, China
| | - Fang Wang
- Department of Gynecology, Weinan Maternal and Child Health Hospital, No. 114, Dongfeng Street, Weinan, 714000, Shaanxi, China.
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17
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A Rapid and Affordable Screening Tool for Early-Stage Ovarian Cancer Detection Based on MALDI-ToF MS of Blood Serum. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Ovarian cancer is a worldwide health issue that grows at a rate of almost 250,000 new cases every year. Its early detection is key for a good prognosis and even curative surgery. However, current medical examination methods and tests have been inefficient in detecting ovarian cancer at the early stage, leading to preventable death. So far, new screening tests based on molecular biomarker analysis techniques have not resulted in any substantial improvement in early-stage diagnosis and increased survival. Thus, whilst there remains clear potential to improve outcomes through early detection, novel approaches are needed. Here, we postulated that MALDI-ToF-mass-spectrometry-based tests can be a solution for effective screening of ovarian cancer. In this retrospective cohort study, we generated and analyzed the mass spectra of 181 serum samples of women with and without ovarian cancer. Using bioinformatics pipelines for analysis, including predictive modeling and machine learning, we found distinct mass spectral patterns composed of 9–20 key combinations of peak intensity or peak enrichment features for each stage of ovarian cancer. Based on a scoring algorithm and obtained patterns, the optimal sensitivity for detecting each stage of cancer was 95–97% with a specificity of 97%. Scoring all algorithms simultaneously could detect all stages of ovarian cancer at 99% sensitivity and 92% specificity. The results further demonstrate that the matrix and mass range analyzed played a key role in improving the mass spectral data quality and diagnostic power. Altogether, with the results reported here and increasing evidence of the MS assay’s diagnostic accuracy and instrument robustness, it has become imminent to consider MS in the clinical application for ovarian cancer screening.
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18
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Kaya ZZ, Tuzuner MB, Sahin B, Akgun E, Aksungar F, Koca S, Serdar M, Sahin S, Cinar N, Karsidag S, Hanagasi HA, Kilercik M, Serteser M, K Baykal AT. Kappa/Lambda light-chain typing in Alzheimer's Disease. Curr Alzheimer Res 2022; 19:84-93. [PMID: 35100957 DOI: 10.2174/1567205019666220131101334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/14/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alzheimer's disease is a progressive neurodegenerative disorder characterized by memory loss and cognitive impairment. The diagnosis of Alzheimer's disease according to symptomatic events is still a puzzling task. Developing a biomarker-based, low-cost, and high-throughput test, readily applicable in clinical laboratories, dramatically impacts the rapid and reliable detection of the disease. OBJECTIVE This study aimed to develop an accurate, sensitive, and reliable screening tool for diagnosing Alzheimer's disease, which can significantly reduce the cost and time of existing methods. METHODS We have employed a MALDI-TOF-MS-based methodology combined with a microaffinity chromatogra Results: We observed a statistically significant difference in the kappa light chain over lambda light chain (κLC/LC) ratios between patients with AD and controls (% 95 CI: -0.547 to -0.269, p<0.001). Our method demonstrated higher sensitivity (100.00%) and specificity (71.43%) for discrimination between AD and controls. CONCLUSION We have developed a high-throughput screening test with a novel sample enrichment method for determining κLC/LC ratios associated with AD diagnosis. Following further validation, we believe our test has a potential for clinical laboratories.
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Affiliation(s)
- Zelal Zuhal Kaya
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | - Betul Sahin
- cibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Emel Akgun
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- cibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Fehime Aksungar
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- cibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Sebile Koca
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Muhittin Serdar
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Sevki Sahin
- Maltepe University, School of Medicine, Department of Neurology, Istanbul, Turkey
| | - Nilgun Cinar
- Maltepe University, School of Medicine, Department of Neurology, Istanbul, Turkey
| | - Sibel Karsidag
- Maltepe University, School of Medicine, Department of Neurology, Istanbul, Turkey
| | - Hasmet Ayhan Hanagasi
- istanbul University, Istanbul Medical Faculty, Department of Neurology, Istanbul, Turkey
| | - Meltem Kilercik
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- cibadem Labmed Clinical Laboratories, Istanbul, Turkey; 3 Maltepe University, School of Medicine, Department of Neurology, Istanbul, Turkey
| | - Mustafa Serteser
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- cibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Ahmet Tari K Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- cibadem Labmed Clinical Laboratories, Istanbul, Turkey
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19
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MALDI-TOF MS Characterisation of the Serum Proteomic Profile in Insulin-Resistant Normal-Weight Individuals. Nutrients 2021; 13:nu13113853. [PMID: 34836106 PMCID: PMC8620204 DOI: 10.3390/nu13113853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 12/02/2022] Open
Abstract
Insulin resistance (IR) is one of the most common metabolic disorders worldwide and is involved in the development of diseases, such as diabetes and cardiovascular diseases, affecting civilisations. The possibility of understanding the molecular mechanism and searching for new biomarkers useful in assessing IR can be achieved through modern research techniques such as proteomics. This study assessed the protein–peptide profile among normal-weight patients with IR to understand the mechanisms and to define new risk biomarkers. The research involved 21 IR and 43 healthy, normal-weight individuals, aged 19–65. Serum proteomic patterns were obtained using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The proposed methodology identified six proteins differentiating normal weight IR and insulin sensitive individuals. They were fibrinogen alpha chain, serum albumin, kininogen-1, complement C3, serotransferrin, and Ig gamma-1 chain, which could potentially be related to inflammation. However, further investigation is required to confirm their correlation with IR.
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20
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Ye M, Lin Y, Pan S, Wang ZW, Zhu X. Applications of Multi-omics Approaches for Exploring the Molecular Mechanism of Ovarian Carcinogenesis. Front Oncol 2021; 11:745808. [PMID: 34631583 PMCID: PMC8497990 DOI: 10.3389/fonc.2021.745808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022] Open
Abstract
Ovarian cancer ranks as the fifth most common cause of cancer-related death in females. The molecular mechanisms of ovarian carcinogenesis need to be explored in order to identify effective clinical therapies for ovarian cancer. Recently, multi-omics approaches have been applied to determine the mechanisms of ovarian oncogenesis at genomics (DNA), transcriptomics (RNA), proteomics (proteins), and metabolomics (metabolites) levels. Multi-omics approaches can identify some diagnostic and prognostic biomarkers and therapeutic targets for ovarian cancer, and these molecular signatures are beneficial for clarifying the development and progression of ovarian cancer. Moreover, the discovery of molecular signatures and targeted therapy strategies could noticeably improve the prognosis of ovarian cancer patients.
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Affiliation(s)
- Miaomiao Ye
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yibin Lin
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shuya Pan
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhi-Wei Wang
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xueqiong Zhu
- Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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21
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Oliveira T, Thaysen-Andersen M, Packer NH, Kolarich D. The Hitchhiker's guide to glycoproteomics. Biochem Soc Trans 2021; 49:1643-1662. [PMID: 34282822 PMCID: PMC8421054 DOI: 10.1042/bst20200879] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is one of the most common post-translational modifications that are essential for cell function across all domains of life. Changes in glycosylation are considered a hallmark of many diseases, thus making glycoproteins important diagnostic and prognostic biomarker candidates and therapeutic targets. Glycoproteomics, the study of glycans and their carrier proteins in a system-wide context, is becoming a powerful tool in glycobiology that enables the functional analysis of protein glycosylation. This 'Hitchhiker's guide to glycoproteomics' is intended as a starting point for anyone who wants to explore the emerging world of glycoproteomics. The review moves from the techniques that have been developed for the characterisation of single glycoproteins to technologies that may be used for a successful complex glycoproteome characterisation. Examples of the variety of approaches, methodologies, and technologies currently used in the field are given. This review introduces the common strategies to capture glycoprotein-specific and system-wide glycoproteome data from tissues, body fluids, or cells, and a perspective on how integration into a multi-omics workflow enables a deep identification and characterisation of glycoproteins - a class of biomolecules essential in regulating cell function.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | | | - Nicolle H. Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
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22
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Senent Y, Ajona D, González-Martín A, Pio R, Tavira B. The Complement System in Ovarian Cancer: An Underexplored Old Path. Cancers (Basel) 2021; 13:3806. [PMID: 34359708 PMCID: PMC8345190 DOI: 10.3390/cancers13153806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer is one of the most lethal gynecological cancers. Current therapeutic strategies allow temporary control of the disease, but most patients develop resistance to treatment. Moreover, although successful in a range of solid tumors, immunotherapy has yielded only modest results in ovarian cancer. Emerging evidence underscores the relevance of the components of innate and adaptive immunity in ovarian cancer progression and response to treatment. Particularly, over the last decade, the complement system, a pillar of innate immunity, has emerged as a major regulator of the tumor microenvironment in cancer immunity. Tumor-associated complement activation may support chronic inflammation, promote an immunosuppressive microenvironment, induce angiogenesis, and activate cancer-related signaling pathways. Recent insights suggest an important role of complement effectors, such as C1q or anaphylatoxins C3a and C5a, and their receptors C3aR and C5aR1 in ovarian cancer progression. Nevertheless, the implication of these factors in different clinical contexts is still poorly understood. Detailed knowledge of the interplay between ovarian cancer cells and complement is required to develop new immunotherapy combinations and biomarkers. In this context, we discuss the possibility of targeting complement to overcome some of the hurdles encountered in the treatment of ovarian cancer.
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Affiliation(s)
- Yaiza Senent
- Translational Oncology Group, Program in Solid Tumors, Cima University of Navarra, 31008 Pamplona, Spain; (Y.S.); (A.G.-M.); (R.P.); (B.T.)
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdISNA), 31008 Pamplona, Spain
| | - Daniel Ajona
- Translational Oncology Group, Program in Solid Tumors, Cima University of Navarra, 31008 Pamplona, Spain; (Y.S.); (A.G.-M.); (R.P.); (B.T.)
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdISNA), 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Antonio González-Martín
- Translational Oncology Group, Program in Solid Tumors, Cima University of Navarra, 31008 Pamplona, Spain; (Y.S.); (A.G.-M.); (R.P.); (B.T.)
- Department of Oncology, Clinica Universidad de Navarra, 28027 Madrid, Spain
| | - Ruben Pio
- Translational Oncology Group, Program in Solid Tumors, Cima University of Navarra, 31008 Pamplona, Spain; (Y.S.); (A.G.-M.); (R.P.); (B.T.)
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdISNA), 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Beatriz Tavira
- Translational Oncology Group, Program in Solid Tumors, Cima University of Navarra, 31008 Pamplona, Spain; (Y.S.); (A.G.-M.); (R.P.); (B.T.)
- Navarra Institute for Health Research (IdISNA), 31008 Pamplona, Spain
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
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Martínez-Rodríguez F, Limones-González JE, Mendoza-Almanza B, Esparza-Ibarra EL, Gallegos-Flores PI, Ayala-Luján JL, Godina-González S, Salinas E, Mendoza-Almanza G. Understanding Cervical Cancer through Proteomics. Cells 2021; 10:1854. [PMID: 34440623 PMCID: PMC8391734 DOI: 10.3390/cells10081854] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/05/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022] Open
Abstract
Cancer is one of the leading public health issues worldwide, and the number of cancer patients increases every day. Particularly, cervical cancer (CC) is still the second leading cause of cancer death in women from developing countries. Thus, it is essential to deepen our knowledge about the molecular pathogenesis of CC and propose new therapeutic targets and new methods to diagnose this disease in its early stages. Differential expression analysis using high-throughput techniques applied to biological samples allows determining the physiological state of normal cells and the changes produced by cancer development. The cluster of differential molecular profiles in the genome, the transcriptome, or the proteome is analyzed in the disease, and it is called the molecular signature of cancer. Proteomic analysis of biological samples of patients with different grades of cervical intraepithelial neoplasia (CIN) and CC has served to elucidate the pathways involved in the development and progression of cancer and identify cervical proteins associated with CC. However, several cervical carcinogenesis mechanisms are still unclear. Detecting pathologies in their earliest stages can significantly improve a patient's survival rate, prognosis, and recurrence. The present review is an update on the proteomic study of CC.
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Affiliation(s)
- Fátima Martínez-Rodríguez
- Microbiology Department, Basic Science Center, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico;
| | | | - Brenda Mendoza-Almanza
- Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98068, Mexico; (B.M.-A.); (E.L.E.-I.); (P.I.G.-F.)
| | - Edgar L. Esparza-Ibarra
- Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98068, Mexico; (B.M.-A.); (E.L.E.-I.); (P.I.G.-F.)
| | - Perla I. Gallegos-Flores
- Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas 98068, Mexico; (B.M.-A.); (E.L.E.-I.); (P.I.G.-F.)
| | - Jorge L. Ayala-Luján
- Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico; (J.L.A.-L.); (S.G.-G.)
| | - Susana Godina-González
- Academic Unit of Chemical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico; (J.L.A.-L.); (S.G.-G.)
| | - Eva Salinas
- Microbiology Department, Basic Science Center, Autonomous University of Aguascalientes, Aguascalientes 20100, Mexico;
| | - Gretel Mendoza-Almanza
- Master in Biomedical Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico;
- National Council of Science and Technology, Autonomous University of Zacatecas, Zacatecas 98000, Mexico
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Detection of Hepatocellular Carcinoma in a High-Risk Population by a Mass Spectrometry-Based Test. Cancers (Basel) 2021; 13:cancers13133109. [PMID: 34206321 PMCID: PMC8268628 DOI: 10.3390/cancers13133109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Liver cancer is one of the most common causes of cancer worldwide, but unfortunately, current technology has a limited ability to detect it early in high-risk patients. This study investigates a machine learning algorithm based on protein levels in the blood that can be used to help with diagnosis. The test shows promising results, especially in patients with smaller tumors and compared to current blood detection tests. This research suggests an important role in the future for machine learning algorithm-based blood detection tests. Abstract Hepatocellular carcinoma (HCC) is one of the fastest growing causes of cancer-related death. Guidelines recommend obtaining a screening ultrasound with or without alpha-fetoprotein (AFP) every 6 months in at-risk adults. AFP as a screening biomarker is plagued by low sensitivity/specificity, prompting interest in discovering alternatives. Mass spectrometry-based techniques are promising in their ability to identify potential biomarkers. This study aimed to use machine learning utilizing spectral data and AFP to create a model for early detection. Serum samples were collected from three separate cohorts, and data were compiled to make Development, Internal Validation, and Independent Validation sets. AFP levels were measured, and Deep MALDI® analysis was used to generate mass spectra. Spectral data were input into the VeriStrat® classification algorithm. Machine learning techniques then classified each sample as “Cancer” or “No Cancer”. Sensitivity and specificity of the test were >80% to detect HCC. High specificity of the test was independent of cause and severity of underlying disease. When compared to AFP, there was improved cancer detection for all tumor sizes, especially small lesions. Overall, a machine learning algorithm incorporating mass spectral data and AFP values from serum samples offers a novel approach to diagnose HCC. Given the small sample size of the Independent Validation set, a further independent, prospective study is warranted.
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Association between Venom Immunotherapy and Changes in Serum Protein-Peptide Patterns. Vaccines (Basel) 2021; 9:vaccines9030249. [PMID: 33809001 PMCID: PMC8001044 DOI: 10.3390/vaccines9030249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 01/25/2023] Open
Abstract
Venom immunotherapy (VIT) is administered to allergic patients to reduce the risk of dangerous systemic reactions following an insect sting. To better understand the mechanism of this treatment and its impact on the human organism, we analysed serum proteomic patterns obtained at five time-points from Hymenoptera-venom-allergic patients undergoing VIT. For statistical analyses, patients were additionally divided into two groups (high responders and low responders) according to serum sIgG4 levels. VIT was found to be associated with changes in seven proteins: the fibrinogen alpha chain, complement C4-A, complement C3, filamin-B, kininogen-1, myosin-9 and inter-alpha-trypsin inhibitor heavy chain H1. The number of discriminative m/z (mass-to-charge ratio) features increased up to the 90th day of VIT, which may be associated with the development of immunity after the administration of increased venom doses. It may also suggest that during VIT, there may occur processes involved not only in protein synthesis but also in protein degradation (caused by proteolytic venom components). The results are consistent with measured serum sIgG4 levels, which increased from 2.04 mgA/I at baseline to 7.25 mgA/I at 90 days. Moreover, the major proteomic changes were detected separately in the high responder group. This may suggest that changes in protein–peptide profiles reflect the actual response to VIT.
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Lung cancer: progression of heat shock protein 70 in association with flap endonuclease 1 protein. 3 Biotech 2021; 11:141. [PMID: 33708464 DOI: 10.1007/s13205-020-02598-3] [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: 09/29/2020] [Accepted: 12/17/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is one of the leading causes of cancer deaths worldwide and existing approaches are not enough to manage, and hence, it is important to concentrate on new drug strategies. This study was aimed to identify the interacting partner of Flap endonuclease 1 (FEN1) and its role in cancer treatment. We identified a new FEN1 interacting partner confirmed it as Heat Shock Protein 70 (HSP 70), and its effect on FEN1 expression, in vitro. Additionally, we found that the 5-Fluorouracil's (5-FU) function was significantly improved when used in combination with HSP 70 inhibitor (KNK 437). The findings are interesting, elucidating the synergistic mechanism between two compounds which helps to develop a novel management strategy for over-expressed FEN1 in the lung. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02598-3.
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Chen X, Sun J, Wang X, Yuan Y, Cai L, Xie Y, Fan Z, Liu K, Jiao X. A Meta-Analysis of Proteomic Blood Markers of Colorectal Cancer. Curr Med Chem 2021; 28:1176-1196. [PMID: 32338203 DOI: 10.2174/0929867327666200427094054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/23/2020] [Accepted: 03/24/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Early diagnosis will significantly improve the survival rate of colorectal cancer (CRC); however, the existing methods for CRC screening were either invasive or inefficient. There is an emergency need for novel markers in CRC's early diagnosis. Serum proteomics has gained great potential in discovering novel markers, providing markers that reflect the early stage of cancer and prognosis prediction of CRC. In this paper, the results of proteomics of CRC studies were summarized through a meta-analysis in order to obtain the diagnostic efficiency of novel markers. METHODS A systematic search on bibliographic databases was performed to collect the studies that explore blood-based markers for CRC applying proteomics. The detection and validation methods, as well as the specificity and sensitivity of the biomarkers in these studies, were evaluated. Newcastle- Ottawa Scale (NOS) case-control studies version was used for quality assessment of included studies. RESULTS Thirty-four studies were selected from 751 studies, in which markers detected by proteomics were summarized. In total, fifty-nine proteins were classified according to their biological function. The sensitivity, specificity, or AUC varied among these markers. Among them, Mammalian STE20-like protein kinase 1/ Serine threonine kinase 4 (MST1/STK4), S100 calcium-binding protein A9 (S100A9), and Tissue inhibitor of metalloproteinases 1 (TIMP1) were suitable for effect sizes merging, and their diagnostic efficiencies were recalculated after merging. MST1/STK4 obtained a sensitivity of 68% and a specificity of 78%. S100A9 achieved a sensitivity of 72%, a specificity of 83%, and an AUC of 0.88. TIMP1 obtained a sensitivity of 42%, a specificity of 88%, and an AUC of 0.71. CONCLUSION MST1/STK4, S100A9, and TIMP1 showed excellent performance for CRC detection. Several other markers also presented optimized diagnostic efficacy for CRC early detection, but further verification is still needed before they are suitable for clinical use. The discovering of more efficient markers will benefit CRC treatment.
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Affiliation(s)
- Xiang Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xue Wang
- Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yanxuan Xie
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Zhiqiang Fan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Kaixi Liu
- Shantou Central Hospital, Shantou, Guangdong 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
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Young ED, Manley SJ, Beadnell TC, Shearin AE, Sasaki K, Zimmerman R, Kauffman E, Vivian CJ, Parasuram A, Iwakuma T, Grandgenett PM, Hollingsworth MA, O'Neil M, Welch DR. Suppression of pancreatic cancer liver metastasis by secretion-deficient ITIH5. Br J Cancer 2021; 124:166-175. [PMID: 33024269 PMCID: PMC7782545 DOI: 10.1038/s41416-020-01093-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Previously, we identified ITIH5 as a suppressor of pancreatic ductal adenocarcinoma (PDAC) metastasis in experimental models. Expression of ITIH5 correlated with decreased cell motility, invasion and metastasis without significant inhibition of primary tumour growth. Here, we tested whether secretion of ITIH5 is required to suppress liver metastasis and sought to understand the role of ITIH5 in human PDAC. METHODS We expressed mutant ITIH5 with deletion of the N-terminal secretion sequence (ITIH5Δs) in highly metastatic human PDAC cell lines. We used a human tissue microarray (TMA) to compare ITIH5 levels in uninvolved pancreas, primary and metastatic PDAC. RESULTS Secretion-deficient ITIH5Δs was sufficient to suppress liver metastasis. Similar to secreted ITIH5, expression of ITIH5Δs was associated with rounded cell morphology, reduced cell motility and reduction of liver metastasis. Expression of ITIH5 is low in both human primary PDAC and matched metastases. CONCLUSIONS Metastasis suppression by ITIH5 may be mediated by an intracellular mechanism. In human PDAC, loss of ITIH5 may be an early event and ITIH5-low PDAC cells in primary tumours may be selected for liver metastasis. Further defining the ITIH5-mediated pathway in PDAC could establish future therapeutic exploitation of this biology and reduce morbidity and mortality associated with PDAC metastasis.
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Affiliation(s)
- Eric D Young
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sharon J Manley
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Thomas C Beadnell
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Alexander E Shearin
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ken Sasaki
- Department of Digestive Surgery, Breast and Thyroid Surgery, Kagoshima University, Kagoshima, Japan
| | - Rosalyn Zimmerman
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Evan Kauffman
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Carolyn J Vivian
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Aishwarya Parasuram
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Tomoo Iwakuma
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Paul M Grandgenett
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Maura O'Neil
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Danny R Welch
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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Definition and Independent Validation of a Proteomic-Classifier in Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12092519. [PMID: 32899818 PMCID: PMC7564837 DOI: 10.3390/cancers12092519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The heterogeneity of epithelial ovarian cancer and its associated molecular biological characteristics are continuously integrated in the development of therapy guidelines. In a next step, future therapy recommendations might also be able to focus on the patient’s systemic status, not only the tumor’s molecular pattern. Therefore, new methods to identify and validate host-related biomarkers need to be established. Using mass spectrometry, we developed and independently validated a blood-based proteomic classifier, stratifying epithelial ovarian cancer patients into good and poor survival groups. We also determined an age dependence of the prognostic performance of this classifier and its association with important biological processes. This work highlights that, just like molecular markers of the tumor itself, the systemic condition of a patient (partly reflected in proteomic patterns) also influences survival and therapy response and could therefore be integrated into future processes of therapy planning. Abstract Mass-spectrometry-based analyses have identified a variety of candidate protein biomarkers that might be crucial for epithelial ovarian cancer (EOC) development and therapy response. Comprehensive validation studies of the biological and clinical implications of proteomics are needed to advance them toward clinical use. Using the Deep MALDI method of mass spectrometry, we developed and independently validated (development cohort: n = 199, validation cohort: n = 135) a blood-based proteomic classifier, stratifying EOC patients into good and poor survival groups. We also determined an age dependency of the prognostic performance of this classifier, and our protein set enrichment analysis showed that the good and poor proteomic phenotypes were associated with, respectively, lower and higher levels of complement activation, inflammatory response, and acute phase reactants. This work highlights that, just like molecular markers of the tumor itself, the systemic condition of a patient (partly reflected in proteomic patterns) also influences survival and therapy response in a subset of ovarian cancer patients and could therefore be integrated into future processes of therapy planning.
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Ding D, Chen M, Xiao X, Cao P, Li S. Novel serum peptide model revealed by MALDI-TOF-MS and its diagnostic value in early bladder cancer. Int J Biol Markers 2020; 35:59-66. [PMID: 32701013 DOI: 10.1177/1724600820935473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Bladder cancer is the ninth most common cancer worldwide and has high morbidity and mortality. We aimed to search for potential serum peptide biomarkers and establish a diagnostic model for early bladder cancer. METHODS A total of 67 bladder cancer patients and 64 healthy volunteers were randomly divided into a training set and testing set 1. There were 30 hematuria patients used as testing set 2. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on weak cation exchange magnetic beads was used to obtain and analyze the serum peptide profiles between bladder cancer patients and healthy volunteers in the training set. Serum peptide diagnostic model through a k-nearest neighbor algorithm, was established and validated, and significantly differentially expressed protein biomarkers were ultimately identified. RESULTS We constructed a diagnostic model containing five peptides (m/z 1954.9, m/z 2081.0, m/z 3938.3, m/z 3946.5, and m/z 4268.8). In the training set, the area under the curve (AUC) value of the five-peptide model was 0.923, and the sensitivity and specificity was 93.75% and 96.77%, respectively. In testing set 1, the sensitivity and specificity was 91.43% and 90.91%, respectively, and the specificity of testing set 2 was 73.33%. For early-stage bladder cancer, the sensitivity and specificity was 92.31% and 93.75%, respectively; the sensitivity of early low-grade bladder cancer was 90.00%; and the AUC value was 0.944. CONCLUSION The five-peptide diagnostic model established in this study had high sensitivity and specificity, especially in the diagnosis of early bladder cancer, and could differentiate between healthy volunteers and hematuria patients.
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Affiliation(s)
- Dapeng Ding
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Mingying Chen
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Xiaoguang Xiao
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Penglong Cao
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Shijun Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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Li K, Pei Y, Wu Y, Guo Y, Cui W. Performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in diagnosis of ovarian cancer: a systematic review and meta-analysis. J Ovarian Res 2020; 13:6. [PMID: 31924227 PMCID: PMC6954560 DOI: 10.1186/s13048-019-0605-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND To evaluate the diagnostic performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for ovarian cancer. PATIENTS AND METHODS A thorough research was conducted in PubMed, Web of Science and Embase (until November 2018) to identify studies evaluating the accuracy of MALDI-TOF-MS for ovarian cancer. Using Meta-Disc1.4, Review Manager 5.3 and Stata 15.1 software to analyze the pooled results: sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and 95% confidence intervals (CI). The summary receiver operating characteristic curves (SROC) and area under the curve (AUC) show the overall performance of MALDI-TOF-MS. RESULTS Eighteen studies were included in the meta-analysis. Methodological quality analysis of the included studies showed that these articles were at low risk of bias and applicability concerns in total. Summary estimates of the diagnostic parameters were as follows: sensitivity, 0.77 (95% CI: 0.73-0.80); specificity, 0.72 (95% CI: 0.70-0.74), PLR, 2.80 (95% CI: 2.41-3.24); NLR, 0.30 (95% CI: 0.22-0.40) and DOR, 10.71 (95% CI: 7.81-14.68). And the AUC was 0.8336. Egger's test showed no significant publication bias in this meta-analysis. CONCLUSION In conclusion, MALDI-TOF-MS shows a good ability for diagnosing ovarian cancer. Further evaluation and optimization of standardized procedures are necessary for complete relying on MALDI-TOF-MS to diagnose ovarian cancer.
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Affiliation(s)
- Kexin Li
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yuqing Pei
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yue Wu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yi Guo
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wei Cui
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Matuszewska E, Matysiak J, Bręborowicz A, Olejniczak K, Kycler Z, Kokot ZJ, Matysiak J. Proteomic features characterization of Hymenoptera venom allergy. Allergy Asthma Clin Immunol 2019; 15:77. [PMID: 31798646 PMCID: PMC6881982 DOI: 10.1186/s13223-019-0387-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 11/05/2019] [Indexed: 02/06/2023] Open
Abstract
Background Hymenoptera venom allergy is one of the most frequent causes of anaphylaxis. In its most severe form, the reaction to wasp and honey bee stings may be life-threatening. Therefore, immediate and proper diagnosis of venom allergy and implementation of suitable therapy are extremely important. Broadening the knowledge on the mechanism of the allergic reaction may contribute to the improvement of both diagnostic and treatment methods. Thus, this study aimed to discover changes in protein expression in serum of patients allergic to Hymenoptera (wasp and honeybee) venom and to point out proteins and peptides involved in the allergic inflammation. Methods Serum proteomic patterns typical to allergic patients and healthy volunteers were obtained with MALDI-TOF (matrix-assisted laser desorption/ionization-time of flight) mass spectrometer. The spectra were processed, analyzed and compared using advanced bioinformatics tools. The discriminative peaks were subjected to identification with liquid chromatography coupled with tandem mass spectrometry. Results This methodology allowed for the identification of four features differentiating between allergy and control groups. They were: fibrinogen alpha chain, coagulation factor XIII chain A, complement C4-A, and inter-alpha-trypsin inhibitor heavy chain H4. All of these proteins are involved in allergic inflammatory response. Conclusions Extending the knowledge of the Hymenoptera venom sensitization will contribute to the development of novel, sensitive and specific methods for quick and unambiguous allergy diagnosis. Understanding the basis of the allergy at the proteomic level will support the improvement of preventive and therapeutic measures.
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Affiliation(s)
- Eliza Matuszewska
- 1Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland
| | - Joanna Matysiak
- Medical Faculty, Higher Vocational State School, 13 Kaszubska Street, 62-800 Kalisz, Poland
| | - Anna Bręborowicz
- 3Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna Street, 60-572 Poznan, Poland
| | - Katarzyna Olejniczak
- 3Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna Street, 60-572 Poznan, Poland
| | - Zdzisława Kycler
- 3Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, 27/33 Szpitalna Street, 60-572 Poznan, Poland
| | - Zenon J Kokot
- 1Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland
| | - Jan Matysiak
- 1Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland
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Monedeiro F, Pomastowski P, Milanowski M, Ligor T, Buszewski B. Monitoring of Bactericidal Effects of Silver Nanoparticles Based on Protein Signatures and VOC Emissions from Escherichia coli and Selected Salivary Bacteria. J Clin Med 2019; 8:E2024. [PMID: 31752439 PMCID: PMC6912796 DOI: 10.3390/jcm8112024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 01/13/2023] Open
Abstract
Escherichia coli and salivary Klebsiella oxytoca and Staphylococcus saccharolyticus were subjected to different concentrations of silver nanoparticles (AgNPs), namely: 12.5, 50, and 100 µg mL-1. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) spectra were acquired after specified periods: 0, 1, 4, and 12 h. For study of volatile metabolites, headspace solid-phase microextraction coupled to gas chromatography/mass spectrometry (HS-SPME-GC-MS) was employed-AgNPs were added to bacteria cultures and the headspace was analyzed immediately and after 12 h of incubation. Principal components analysis provided discrimination between clusters of protein profiles belonging to different strains. Canonical correlation, network analysis, and multiple linear regression approach revealed that dimethyl disulfide, dimethyl trisulfide, 2-heptanone, and dodecanal (related to the metabolism of sulfur-containing amino acids and fatty acids synthesis) are exemplary molecular indicators, whose response variation deeply correlated to the interaction with bacteria. Therefore, such species can serve as biomarkers of the agent's effectiveness. The present investigation pointed out that the used approaches can be useful in the monitoring of response to therapeutic treatment based on AgNPs. Furthermore, biochemical mechanisms enrolled in the bactericidal action of nanoparticles can be applied in the development of new agents with enhanced properties.
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Affiliation(s)
- Fernanda Monedeiro
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
- Department of Chemistry, Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto CEP 14040-901, Brazil
| | - Paweł Pomastowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Maciej Milanowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Tomasz Ligor
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland; (F.M.); (P.P.); (M.M.); (T.L.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
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Ciocan-Cartita CA, Jurj A, Buse M, Gulei D, Braicu C, Raduly L, Cojocneanu R, Pruteanu LL, Iuga CA, Coza O, Berindan-Neagoe I. The Relevance of Mass Spectrometry Analysis for Personalized Medicine through Its Successful Application in Cancer "Omics". Int J Mol Sci 2019; 20:ijms20102576. [PMID: 31130665 PMCID: PMC6567119 DOI: 10.3390/ijms20102576] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
Mass spectrometry (MS) is an essential analytical technology on which the emerging omics domains; such as genomics; transcriptomics; proteomics and metabolomics; are based. This quantifiable technique allows for the identification of thousands of proteins from cell culture; bodily fluids or tissue using either global or targeted strategies; or detection of biologically active metabolites in ultra amounts. The routine performance of MS technology in the oncological field provides a better understanding of human diseases in terms of pathophysiology; prevention; diagnosis and treatment; as well as development of new biomarkers; drugs targets and therapies. In this review; we argue that the recent; successful advances in MS technologies towards cancer omics studies provides a strong rationale for its implementation in biomedicine as a whole.
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Affiliation(s)
- Cristina Alexandra Ciocan-Cartita
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Ancuța Jurj
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Mihail Buse
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Diana Gulei
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Roxana Cojocneanu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Lavinia Lorena Pruteanu
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Cristina Adela Iuga
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hațieganu" University of Medicine and Pharmacy, 6 Louis Pasteur Street, 400349 Cluj-Napoca.
| | - Ovidiu Coza
- Department of Oncology, "Iuliu Hațieganu" University of Medicine and Pharmacy, 34-36 Republicii Street, 400015 Cluj-Napoca, Romania.
- Department of Radiotherapy with High Energies and Brachytherapy, Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, 400015 Cluj-Napoca.
| | - Ioana Berindan-Neagoe
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
- Department of Functional Genomics and Experimental Pathology, Ion Chiricuțǎ Oncology Institute, 34-36 Republicii Street, 400015 Cluj-Napoca.
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Wide spectrum targeted metabolomics identifies potential ovarian cancer biomarkers. Life Sci 2019; 222:235-244. [PMID: 30853626 DOI: 10.1016/j.lfs.2019.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 02/06/2023]
Abstract
AIMS Despite of almost a hundred years of research on cancer metabolism, the biological background of cancerogenesis and cancer-related reprogramming of metabolism remains not fully understood. In order to comprehensively and effectively diagnose and treat the deadliest diseases, the mechanisms underlying these diseases have to be discovered urgently. Among the gynecological malignancies, ovarian cancer is the most common cause of death. The aim of the study was to search for potential cancer-related differences in concentrations of metabolites and interactions between them in serum of women with ovarian cancer and benign ovarian tumor in comparison with healthy controls using targeted metabolomics. These metabolites might serve as biomarkers in the future. MAIN METHODS We used wide spectrum targeted metabolomics to evaluate serum concentrations of metabolites related to ovarian cancer and compared them against benign ovarian tumors and healthy controls. The measurements were performed using high performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry technique in highly-selective multiple reaction monitoring mode. KEY FINDINGS In this study we confirmed our previous findings about the role of histidine and citrulline in ovarian cancer as well as we indicated new lipid compounds (lysoPC a C16:1, PC aa C32:2, PC aa C34:4 and PC aa C 36:6) potentially involved in cancer metabolism. SIGNIFICANCES We indicated interesting interactions between metabolites for further in-depth research which could potentially serve as clinically useful biomarkers in future. Moreover, the presented work attempts to visualize a possible 3D-network of relationships between the molecules found to be related to ovarian malignancy.
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Swiatly A, Plewa S, Matysiak J, Kokot ZJ. Mass spectrometry-based proteomics techniques and their application in ovarian cancer research. J Ovarian Res 2018; 11:88. [PMID: 30270814 PMCID: PMC6166298 DOI: 10.1186/s13048-018-0460-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/20/2018] [Indexed: 12/26/2022] Open
Abstract
Ovarian cancer has emerged as one of the leading cause of gynecological malignancies. So far, the measurement of CA125 and HE4 concentrations in blood and transvaginal ultrasound examination are essential ovarian cancer diagnostic methods. However, their sensitivity and specificity are still not sufficient to detect disease at the early stage. Moreover, applied treatment may appear to be ineffective due to drug-resistance. Because of a high mortality rate of ovarian cancer, there is a pressing need to develop innovative strategies leading to a full understanding of complicated molecular pathways related to cancerogenesis. Recent studies have shown the great potential of clinical proteomics in the characterization of many diseases, including ovarian cancer. Therefore, in this review, we summarized achievements of proteomics in ovarian cancer management. Since the development of mass spectrometry has caused a breakthrough in systems biology, we decided to focus on studies based on this technique. According to PubMed engine, in the years 2008-2010 the number of studies concerning OC proteomics was increasing, and since 2010 it has reached a plateau. Proteomics as a rapidly evolving branch of science may be essential in novel biomarkers discovery, therapy decisions, progression predication, monitoring of drug response or resistance. Despite the fact that proteomics has many to offer, we also discussed some limitations occur in ovarian cancer studies. Main difficulties concern both complexity and heterogeneity of ovarian cancer and drawbacks of the mass spectrometry strategies. This review summarizes challenges, capabilities, and promises of the mass spectrometry-based proteomics techniques in ovarian cancer management.
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Affiliation(s)
- Agata Swiatly
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Szymon Plewa
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Jan Matysiak
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
| | - Zenon J. Kokot
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznań, Poland
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Greco V, Piras C, Pieroni L, Ronci M, Putignani L, Roncada P, Urbani A. Applications of MALDI-TOF mass spectrometry in clinical proteomics. Expert Rev Proteomics 2018; 15:683-696. [PMID: 30058389 DOI: 10.1080/14789450.2018.1505510] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics. Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD). Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.
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Affiliation(s)
- Viviana Greco
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
| | - Cristian Piras
- c Dipartimento di Medicina Veterinaria , Università degli studi di Milano , Milano , Italy
| | - Luisa Pieroni
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy
| | - Maurizio Ronci
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy.,e Department of Medical, Oral and Biotechnological Sciences , University "G. D'Annunzio" of Chieti-Pescara , Chieti , Italy
| | - Lorenza Putignani
- f Unit of Parasitology Bambino Gesù Children's Hospital , IRCCS , Rome , Italy.,g Unit of Human Microbiome , Bambino Gesù Children's Hospital, IRCCS , Rome , Italy
| | - Paola Roncada
- h Dipartimento di Scienze della Salute , Università degli studi "Magna Græcia" di Catanzaro , Catanzaro , Italy
| | - Andrea Urbani
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
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Understanding Ovarian Cancer: iTRAQ-Based Proteomics for Biomarker Discovery. Int J Mol Sci 2018; 19:ijms19082240. [PMID: 30065196 PMCID: PMC6121953 DOI: 10.3390/ijms19082240] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Despite many years of studies, ovarian cancer remains one of the top ten cancers worldwide. Its high mortality rate is mainly due to lack of sufficient diagnostic methods. For this reason, our research focused on the identification of blood markers whose appearance would precede the clinical manifestation of the disease. ITRAQ-tagging (isobaric Tags for Relative and Absolute Quantification) coupled with mass spectrometry technology was applied. Three groups of samples derived from patients with: ovarian cancer, benign ovarian tumor, and healthy controls, were examined. Mass spectrometry analysis allowed for highlighting the dysregulation of several proteins associated with ovarian cancer. Further validation of the obtained results indicated that five proteins (Serotransferrin, Amyloid A1, Hemopexin, C-reactive protein, Albumin) were differentially expressed in ovarian cancer group. Interestingly, the addition of Albumin, Serotransferrin, and Amyloid A1 to CA125 (cancer antigen 125) and HE4 (human epididymis protein4) improved the diagnostic performance of the model discriminating between benign and malignant tumors. Identified proteins shed light on the molecular signaling pathways that are associated with ovarian cancer development and should be further investigated in future studies. Our findings indicate five proteins with a strong potential to use in a multimarker test for screening and detection of ovarian cancer.
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Bareke H, Akbuga J. Complement system's role in cancer and its therapeutic potential in ovarian cancer. Scand J Immunol 2018; 88:e12672. [PMID: 29734524 DOI: 10.1111/sji.12672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/30/2018] [Indexed: 12/31/2022]
Abstract
Cancer immunotherapy is a strong candidate for the long-awaited new edition to standard cancer therapies. For an effective immunotherapy, it is imperative to delineate the players of antitumour immune response. As an important innate immune system effector mechanism, complement is highly likely to play a substantial role in cancer immunity. Studies suggest that there may be two different "states of complement" that show opposing effects on cancer cells; a complement profile that has antitumour effects with low expression of membrane-bound complement regulator proteins (mCRPs), lytic membrane attack complex (MAC) concentration and moderate C5a concentration, and a complement profile that has protumour effects with high expression of mCRPs, sublytic MAC and high concentrations of C5a. One of the cancers that urgently require innovative therapeutic approaches is ovarian cancer, and complement has a potential to be a good target for this purpose. A combinatorial approach where the complement cascade is fine-tuned by inhibiting some of its activities while promoting the others can prove to be a fruitful approach. Herein, we will briefly discuss the cancer-immune system interaction and then present a discussion of complement system's role in tumour immunity and its therapeutic potential for ovarian cancer immunotherapy.
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Affiliation(s)
- H Bareke
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey.,Faculty of Pharmacy, Girne American University, Kyrenia, North Cyprus, Turkey
| | - J Akbuga
- Faculty of Pharmacy, Girne American University, Kyrenia, North Cyprus, Turkey
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Identification of MST1 as a potential early detection biomarker for colorectal cancer through a proteomic approach. Sci Rep 2017; 7:14265. [PMID: 29079854 PMCID: PMC5660227 DOI: 10.1038/s41598-017-14539-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 10/12/2017] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is a common malignant neoplasm worldwide. It is important to identify new biomarkers for the early detection of CRC. In this study, magnetic beads and the Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) platform were used to analyse CRC and healthy control (HC) serum samples. The CRC diagnosis pattern was established to have a specificity of 94.7% and sensitivity of 92.3% in a blind test. The candidate biomarker serine/threonine kinase 4 (STK4, also known as MST1) was identified by Tandem mass spectrometry (MS/MS) and verified with western blotting and enzyme-linked immunosorbent assay (ELISA). The results indicated that there was a higher concentration of MST1 in HC subjects than stage I CRC patients for the early detection of CRC and a lower concentration in stage IV patients than in other CRC patients. The sensitivity and specificity of MST1 combined with carcinoembryonic antigen (CEA) and faecal occult blood test (FOBT) in diagnosis of colorectal cancer were 92.3% and 100%, respectively. Additionally, low MST1 expression was associated with the poor prognosis. These results illustrate that MST1 is a potential biomarker for early detection, prognosis and prediction of distant metastasis of CRC.
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