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Wei D, Sun J, Luo Z, Zhang G, Liu Y, Zhang H, Xie Z, Gu Z, Tao WA. Targeted Phosphoproteomics of Human Saliva Extracellular Vesicles via Multiple Reaction Monitoring Cubed (MRM 3). Anal Chem 2024; 96:1223-1231. [PMID: 38205554 DOI: 10.1021/acs.analchem.3c04464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Oral squamous cell carcinoma (OSCC) has become a global health problem due to its increasing incidence and high mortality rate. Early intervention through monitoring of the diagnostic biomarker levels during OSCC treatment is critical. Extracellular vesicles (EVs) are emerging surrogates in intercellular communication through transporting biomolecule cargo and have recently been identified as a potential source of biomarkers such as phosphoproteins for many diseases. Here, we developed a multiple reaction monitoring cubed (MRM3) method coupled with a novel sample preparation strategy, extracellular vesicles to phosphoproteins (EVTOP), to quantify phosphoproteins using a minimal amount of saliva (50 μL) samples from OSCC patients with high specificity and sensitivity. Our results established differential patterns in the phosphopeptide content of healthy, presurgery, and postsurgery OSCC patient groups. Notably, we discovered significantly increased salivary phosphorylated alpha-amylase (AMY) in the postsurgery group compared to the presurgery group. We hereby present the first targeted MS method with extremely high sensitivity for measuring endogenous phosphoproteins in human saliva EVs.
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Affiliation(s)
- Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Jie Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuojun Luo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Guiyuan Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Yufeng Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Hao Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuoying Xie
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - W Andy Tao
- Department of Chemistry and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
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Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
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Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
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Kalló G, Bertalan PM, Márton I, Kiss C, Csősz É. Salivary Chemical Barrier Proteins in Oral Squamous Cell Carcinoma-Alterations in the Defense Mechanism of the Oral Cavity. Int J Mol Sci 2023; 24:13657. [PMID: 37686462 PMCID: PMC10487546 DOI: 10.3390/ijms241713657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most frequent types of head and neck cancer. Despite the genetic and environmental risk factors, OSCC is also associated with microbial infections and/or dysbiosis. The secreted saliva serves as the chemical barrier of the oral cavity and, since OSCC can alter the protein composition of saliva, our aim was to analyze the effect of OSCC on the salivary chemical barrier proteins. Publicly available datasets regarding the analysis of salivary proteins from patients with OSCC and controls were collected and examined in order to identify differentially expressed chemical barrier proteins. Network analysis and gene ontology (GO) classification of the differentially expressed chemical barrier proteins were performed as well. One hundred and twenty-seven proteins showing different expression pattern between the OSCC and control groups were found. Protein-protein interaction networks of up- and down-regulated proteins were constructed and analyzed. The main hub proteins (IL-6, IL-1B, IL-8, TNF, APOA1, APOA2, APOB, APOC3, APOE, and HP) were identified and the enriched GO terms were examined. Our study highlighted the importance of the chemical barrier of saliva in the development of OSCC.
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Affiliation(s)
- Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Petra Magdolna Bertalan
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Ildikó Márton
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
| | - Csongor Kiss
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary;
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (P.M.B.); (I.M.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
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Ali MF, Hosein M, Butt S, Siddiqui R. Zinc-alpha 2 glycoprotein a diagnostic Biomarker for early stage oral Squamous Cell Carcinoma. Pak J Med Sci 2023; 39:513-517. [PMID: 36950446 PMCID: PMC10025728 DOI: 10.12669/pjms.39.2.6488] [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: 04/13/2022] [Revised: 12/10/2022] [Accepted: 12/27/2022] [Indexed: 01/27/2023] Open
Abstract
Objectives In this study, we investigated the expression of zinc alpha-2 glycoprotein in oral squamous cell carcinoma tissue samples. Additionally, ascertained its association to the oral cancer stage and subscale parameters (TNM). Methods This observational study was conducted at Ziauddin University from January to December 2020. Using the Open-Epi software, the sample size of 120 oral squamous cell carcinomas was calculated at 95% confidence interval and a 5% margin of error. Ethical approval was taken from the Institutional Ethical Review Committee. Histologically diagnosed cases of oral squamous cell carcinoma were obtained from the Histopathology Department of Ziauddin University, Karachi. Study data was analyzed through SPSS version-20 and p-value ≤0.05 considered as significant. One-way ANOVA and Multiple linear regression were applied for analysis of data. Result In the study, none of the oral squamous cell carcinoma tissue samples from the later stages were stained for ZAG. However 71% (35/49) of the early stage OSCC samples showed positive IHC results for ZAG expression in the cytoplasm. One-way ANOVA indicates that high ZAG expression was significantly associated with smaller tumor size (p<0.001), lymph node involvement (p=0.002), early stages of OSCC (p<0.001) and less differentiated tumor (p=0.001). The site of the tumor was also significantly associated with ZAG staining (p<0.001). Conclusion Zinc alpha-2 glycoprotein expressed in the early stages of oral cancer development so that effective treatment modalities can be planned as per the patient's status. This may also assist a clinician to achieve tumor-free surgical margins and monitor the post treatment outcomes.
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Affiliation(s)
- Mehwish Feroz Ali
- Dr. Mehwish Feroz Ali, BDS, MPhil-Oral Pathology. Assistant Professor, Department of Oral Pathology, Ziauddin University, Karachi, Pakistan
| | - Mervyn Hosein
- Dr. Mervyn Hosein (BDS, FCPS) Principal Ziauddin College of Dentistry, Ziauddin University, Karachi, Pakistan
| | - Saima Butt
- Dr. Saima Akram Butt (BDS, MDS, Head of Oral Pathology Department, Ziauddin College of Dentistry, Karachi, Pakistan
| | - Rehan Siddiqui
- Dr. Rehan Ahmed Siddiqui (PhD), Assistant Professor, Research Department, Ziauddin University, Karachi, Pakistan
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Huang Z, Yang X, Huang Y, Tang Z, Chen Y, Liu H, Huang M, Qing L, Li L, Wang Q, Jie Z, Jin X, Jia B. Saliva - a new opportunity for fluid biopsy. Clin Chem Lab Med 2023; 61:4-32. [PMID: 36285724 DOI: 10.1515/cclm-2022-0793] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022]
Abstract
Saliva is a complex biological fluid with a variety of biomolecules, such as DNA, RNA, proteins, metabolites and microbiota, which can be used for the screening and diagnosis of many diseases. In addition, saliva has the characteristics of simple collection, non-invasive and convenient storage, which gives it the potential to replace blood as a new main body of fluid biopsy, and it is an excellent biological diagnostic fluid. This review integrates recent studies and summarizes the research contents of salivaomics and the research progress of saliva in early diagnosis of oral and systemic diseases. This review aims to explore the value and prospect of saliva diagnosis in clinical application.
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Affiliation(s)
- Zhijie Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Xiaoxia Yang
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yisheng Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Zhengming Tang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yuanxin Chen
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Hongyu Liu
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Mingshu Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Ling Qing
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Li Li
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Qin Wang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Zhuye Jie
- BGI Genomics, BGI-Shenzhen, Shenzhen, P.R. China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, P.R. China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xin Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, P.R. China
| | - Bo Jia
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
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6
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Hsueh PC, Chang KP, Liu HP, Chiang WF, Chan XY, Hung CM, Chu LJ, Wu CC. Development of a salivary autoantibody biomarker panel for diagnosis of oral cavity squamous cell carcinoma. Front Oncol 2022; 12:968570. [DOI: 10.3389/fonc.2022.968570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
Oral cavity squamous cell carcinoma (OSCC) is a destructive disease with increasing incidence. OSCC is usually diagnosed at an advanced stage, which leads to poor outcomes of OSCC patients. Currently, there is a lack of biomarkers with sufficient effectiveness in early diagnosis of OSCC. To ameliorate OSCC screening, we evaluated the performances of salivary autoantibodies (auto-Abs) to nine proteins (ANXA2, CA2, ISG15, KNG1, MMP1, MMP3, PRDX2, SPARC, and HSPA5) as OSCC biomarkers. A multiplexed immunoassay using a fluorescence bead-based suspension array system was established for simultaneous assessment of the salivary levels of the above nine auto-Abs and a known OSCC-associated auto-Ab, anti-p53. Compared to healthy individuals (n = 140), the salivary levels of nine auto-Abs were significantly elevated in OSCC patients (n = 160). Notably, the salivary levels of the 10 auto-Abs in the early-stage OSCC patients (n = 102) were higher than that in the healthy group. Most importantly, utilizing a marker panel consisting of anti-MMP3, anti-PRDX2, anti-SPARC, and anti-HSPA5 for detection of early-stage OSCC achieved a sensitivity of 63.8% with a specificity of 90%. Collectively, herein we established a multiplex auto-Ab platform for OSCC screening, and demonstrated a four-auto-Ab panel which shows clinical applicability for early diagnosis of OSCC.
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7
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Kwon IJ, Jung TY, Son Y, Kim B, Kim SM, Lee JH. Detection of volatile sulfur compounds (VSCs) in exhaled breath as a potential diagnostic method for oral squamous cell carcinoma. BMC Oral Health 2022; 22:268. [PMID: 35778718 PMCID: PMC9250215 DOI: 10.1186/s12903-022-02301-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 06/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background Oral squamous cell carcinoma causes a significant proportion of global cancer morbidity and mortality. The aim of this study is to investigate whether the exhaled breath test can be a new, non-invasive, and effective method for diagnosing oral squamous cell carcinoma. Methods A comparative analysis of exhaled breath between patients with oral squamous cell carcinoma (OSCC) and healthy controls (HC) was performed with the Twin Breasor II™, a simple gas chromatography system. Results Both hydrogen sulfide (H2S) and methyl mercaptan (Ch3SH) were significantly higher in the OSCC group than in the HC group. The total sulfur concentration was also higher in the OSCC group, but there was no significant difference in the ratio of Ch3SH to H2S between the two groups. Using logistic regression, we constructed a new variable with an area under the curve (AUC) of 0.740, 68.0% sensitivity, and 72.0% specificity. Conclusions Exhaled gas analysis via simple gas chromatography can potentially serve as an accessory non-invasive method for OSCC diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12903-022-02301-3.
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Affiliation(s)
- Ik-Jae Kwon
- Department of Oral and Maxillofacial Surgery, Dental Research Institute, School of Dentistry, Seoul National University, 101 Daehakro, Jongnogu, Seoul, 03080, Korea
| | - Tae-Young Jung
- Department of Oral and Maxillofacial Surgery, Busan Paik Hospital, Inje University, Bokji-ro 75, Busanjin-gu, Busan, 47392, Korea
| | - Youjeong Son
- Dental Life Science Research Institute/Innovation Research & Support Center for Dental Science, Seoul National University Dental Hospital, Seoul, 03080, Korea
| | - Bongju Kim
- Dental Life Science Research Institute/Innovation Research & Support Center for Dental Science, Seoul National University Dental Hospital, Seoul, 03080, Korea
| | - Soung-Min Kim
- Department of Oral and Maxillofacial Surgery, Dental Research Institute, School of Dentistry, Seoul National University, 101 Daehakro, Jongnogu, Seoul, 03080, Korea
| | - Jong-Ho Lee
- Department of Oral and Maxillofacial Surgery, Dental Research Institute, School of Dentistry, Seoul National University, 101 Daehakro, Jongnogu, Seoul, 03080, Korea. .,Dental Life Science Research Institute/Innovation Research & Support Center for Dental Science, Seoul National University Dental Hospital, Seoul, 03080, Korea.
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Development of a method for dansylation of metabolites using organic solvent-compatible buffer systems for amine/phenol submetabolome analysis. Anal Chim Acta 2022; 1189:339218. [PMID: 34815039 DOI: 10.1016/j.aca.2021.339218] [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: 08/27/2021] [Revised: 10/17/2021] [Accepted: 10/23/2021] [Indexed: 11/21/2022]
Abstract
Metabolomics, which serves as a readout of biological processes and diseases monitoring, is an informative research area for disease biomarker discovery and systems biology studies. In particular, reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) has become a powerful and popular tool for metabolomics analysis, enabling the detection of most metabolites. Very polar and ionic metabolites, however, are less easily detected because of their poor retention in RP columns. Dansylation of metabolites simplifies the sub-metabolome analysis by reducing its complexity and increasing both hydrophobicity and ionization ability. However, the various metabolite concentrations in clinical samples have a wide dynamic range with highly individual variation in total metabolite amount, such as in saliva. The bicarbonate buffer typically used in dansylation labeling reactions induces solvent stratification, resulting in poor reproducibility, selective sample loss and an increase in false-determined metabolite peaks. In this study, we optimized the dansylation protocol for samples with wide concentration range of metabolites, utilizing diisopropylethylamine (DIPEA) or tri-ethylamine (TEA) in place of bicarbonate buffer, and presented the results of a systemic investigation of the influences of individual processes involved on the overall performance of the protocol. In addition to achieving high reproducibility, substitution of DIPEA or TEA buffer resulted in similar labeling efficiency of most metabolites and more efficient labeling of some metabolites with a higher pKa. With this improvement, compounds that are only present in samples in trace amounts can be detected, and more comprehensive metabolomics profiles can be acquired for biomarker discovery or pathway analysis, making it possible to analyze clinical samples with limited amounts of metabolites.
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Pillai J, Chincholkar T, Dixit R, Pandey M. A systematic review of proteomic biomarkers in oral squamous cell cancer. World J Surg Oncol 2021; 19:315. [PMID: 34711249 PMCID: PMC8555221 DOI: 10.1186/s12957-021-02423-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/06/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Head and neck squamous cell cancer (HNSCC) is the most common cancer associated with chewing tobacco, in the world. As this is divided in to sites and subsites, it does not make it to top 10 cancers. The most common subsite is the oral cancer. At the time of diagnosis, more than 50% of patients with oral squamous cell cancers (OSCC) had advanced disease, indicating the lack of availability of early detection and risk assessment biomarkers. The new protein biomarker development and discovery will aid in early diagnosis and treatment which lead to targeted treatment and ultimately a good prognosis. METHODS This systematic review was performed as per PRISMA guidelines. All relevant studies assessing characteristics of oral cancer and proteomics were considered for analysis. Only human studies published in English were included, and abstracts, incomplete articles, and cell line or animal studies were excluded. RESULTS A total of 308 articles were found, of which 112 were found to be relevant after exclusion. The present review focuses on techniques of cancer proteomics and discovery of biomarkers using these techniques. The signature of protein expression may be used to predict drug response and clinical course of disease and could be used to individualize therapy with such knowledge. CONCLUSIONS Prospective use of these markers in the clinical setting will enable early detection, prediction of response to treatment, improvement in treatment selection, and early detection of tumor recurrence for disease monitoring. However, most of these markers for OSCC are yet to be validated.
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Affiliation(s)
| | | | - Ruhi Dixit
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Manoj Pandey
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India.
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Di Natale C, Battista E, Lettera V, Reddy N, Pitingolo G, Vecchione R, Causa F, Netti PA. Easy Surface Functionalization and Bioconjugation of Peptides as Capture Agents of a Microfluidic Biosensing Platform for Multiplex Assay in Serum. Bioconjug Chem 2021; 32:1593-1601. [PMID: 34114801 PMCID: PMC8382222 DOI: 10.1021/acs.bioconjchem.1c00146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Indexed: 12/11/2022]
Abstract
The development of assays for protein biomarkers in complex matrices is a demanding task that still needs implementation of new approaches. Antibodies as capture agents have been largely used in bioassays but their low stability, low-efficiency production, and cross-reactivity in multiplex approaches impairs their larger applications. Instead, synthetic peptides, even with higher stability and easily adapted amino acid sequences, still remain largely unexplored in this field. Here, we provide a proof-of-concept of a microfluidic device for direct detection of biomarker overexpression. The multichannel microfluidic polydimethylsiloxane (PDMS) device was first derivatized with PAA (poly(acrylic acid)) solution. CRP-1, VEGF-114, and ΦG6 peptides were preliminarily tested to respectively bind the biomarkers, C-reactive protein (CRP), vascular endothelial growth factor (VEGF), and tumor necrosis factor-alpha (TNF-α). Each PDMS microchannel was then respectively bioconjugated with a specific peptide (CRP-1, VEGF-114, or ΦG6) to specifically capture CRP, VEGF, and TNF-α. With such microdevices, a fluorescence bioassay has been set up with sensitivity in the nanomolar range, both in buffered solution and in human serum. The proposed multiplex assay worked with a low amount of sample (25 μL) and detected biomarker overexpression (above nM concentration), representing a noninvasive and inexpensive screening platform.
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Affiliation(s)
- Concetta Di Natale
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Edmondo Battista
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Vincenzo Lettera
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Biopox
srl, Viale Maria Bakunin
12, 80125 Naples, Italy
| | - Narayana Reddy
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Gabriele Pitingolo
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Raffaele Vecchione
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Filippo Causa
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica del Materiali e della Produzione Industriale
(DICMAPI), University “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Paolo Antonio Netti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica del Materiali e della Produzione Industriale
(DICMAPI), University “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
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Sá JDO, Trino LD, Oliveira AK, Lopes AFB, Granato DC, Normando AGC, Santos ES, Neves LX, Carnielli CM, Paes Leme AF. Proteomic approaches to assist in diagnosis and prognosis of oral cancer. Expert Rev Proteomics 2021; 18:261-284. [PMID: 33945368 DOI: 10.1080/14789450.2021.1924685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Oral squamous cell carcinoma (OSCC) ranks among the top 10 leading causes of cancer worldwide, with 5-year survival rate of about 50%, high lymph node metastasis, and relapse rates. The OSCC diagnosis, prognosis, and treatment are mostly based on the clinical TNM classification. There is an urgent need for the discovery of biomarkers and therapeutic targets to assist in the clinical decision-making process.Areas covered: We summarize proteomic studies of the OSCC tumor, immune microenvironment, potential liquid biopsy sites, and post-translational modifications trying to retrieve information in the discovery and verification or (pre)validation phases. The search strategy was based on the combination of MeSH terms and expert refinement.Expert opinion: Untargeted combined with targeted proteomics are strategies that provide reliable and reproducible quantitation of proteins and are the methods of choice of many groups worldwide. Undoubtedly, proteomics has been contributing to the understanding of OSCC progression and uncovers potential candidates as biomarker or therapeutic targets. Nevertheless, none of these targets are available in the clinical practice yet. The scientific community needs to overcome the limitations by investing in robust experimental designs to strengthen the value of the findings, leveraging the translation of knowledge, and further supporting clinical decisions.
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Affiliation(s)
- Jamile De Oliveira Sá
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Luciana Daniele Trino
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ana Karina Oliveira
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ariane Fidelis Busso Lopes
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ana Gabriela Costa Normando
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Erison Santana Santos
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Leandro Xavier Neves
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Carolina Moretto Carnielli
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
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12
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Bian J, Sze YH, Tse DYY, To CH, McFadden SA, Lam CSY, Li KK, Lam TC. SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina. Int J Mol Sci 2021; 22:4721. [PMID: 33946922 PMCID: PMC8124159 DOI: 10.3390/ijms22094721] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Most of the previous myopic animal studies employed a single-candidate approach and lower resolution proteomics approaches that were difficult to detect minor changes, and generated limited systems-wide biological information. Hence, a complete picture of molecular events in the retina involving myopic development is lacking. Here, to investigate comprehensive retinal protein alternations and underlying molecular events in the early myopic stage, we performed a data-independent Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) based proteomic analysis coupled with different bioinformatics tools in pigmented guinea pigs after 4-day lens-induced myopia (LIM). Myopic eyes compared to untreated contralateral control eyes caused significant changes in refractive error and choroid thickness (p < 0.05, n = 5). Relative elongation of axial length and the vitreous chamber depth were also observed. Using pooled samples from all individuals (n = 10) to build a species-specific retinal ion library for SWATH analysis, 3202 non-redundant proteins (with 24,616 peptides) were identified at 1% global FDR. For quantitative analysis, the 10 individual retinal samples (5 pairs) were analyzed using a high resolution Triple-TOF 6600 mass spectrometry (MS) with technical replicates. In total, 37 up-regulated and 21 down-regulated proteins were found significantly changed after LIM treatment (log2 ratio (T/C) > 0.26 or < -0.26; p ≤ 0.05). Data are accepted via ProteomeXchange with identifier PXD025003. Through Ingenuity Pathways Analysis (IPA), "lipid metabolism" was found as the top function associated with the differentially expressed proteins. Based on the protein abundance and peptide sequences, expression patterns of two regulated proteins (SLC6A6 and PTGES2) identified in this pathway were further successfully validated with high confidence (p < 0.05) using a novel Multiple Reaction Monitoring (MRM) assay on a QTRAP 6500+ MS. In summary, through an integrated discovery and targeted proteomic approach, this study serves as the first report to detect and confirm novel retinal protein changes and significant biological functions in the early LIM mammalian guinea pigs. The study provides new workflow and insights for further research to myopia control.
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Affiliation(s)
- Jingfang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Ying-Hon Sze
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Dennis Yan-Yin Tse
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Chi-Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Sally A. McFadden
- School of Psychology, College of Engineering, Science and the Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - King-Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen 518052, China
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13
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Preparation of Tissue Samples for Large-scale Quantitative Mass Spectrometric Analysis. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0495-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Lee JY, Shi T, Petyuk VA, Schepmoes AA, Fillmore TL, Wang YT, Cardoni W, Coppit G, Srivastava S, Goodman JF, Shriver CD, Liu T, Rodland KD. Detection of Head and Neck Cancer Based on Longitudinal Changes in Serum Protein Abundance. Cancer Epidemiol Biomarkers Prev 2020; 29:1665-1672. [PMID: 32532828 DOI: 10.1158/1055-9965.epi-20-0192] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/16/2020] [Accepted: 06/02/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Approximately 85% of the U.S. military active duty population is male and less than 50 years of age, with elevated levels of known risk factors for oropharyngeal squamous cell carcinoma (OPSCC), including smoking, excessive use of alcohol, and greater numbers of sexual partners, and elevated prevalence of human papilloma virus (HPV). Given the recent rise in incidence of OPSCC related to the HPV, the Department of Defense Serum Repository provides an unparalleled resource for longitudinal studies of OPSCC in the military for the identification of early detection biomarkers. METHODS We identified 175 patients diagnosed with OPSCC with 175 matched healthy controls and retrieved a total of 978 serum samples drawn at the time of diagnosis, 2 and 4 years prior to diagnosis, and 2 years after diagnosis. Following immunoaffinity depletion, serum samples were analyzed by targeted proteomics assays for multiplexed quantification of a panel of 146 candidate protein biomarkers from the curated literature. RESULTS Using a Random Forest machine learning approach, we derived a 13-protein signature that distinguishes cases versus controls based on longitudinal changes in serum protein concentration. The abundances of each of the 13 proteins remain constant over time in control subjects. The AUC for the derived Random Forest classifier was 0.90. CONCLUSIONS This 13-protein classifier is highly promising for detection of OPSCC prior to overt symptoms. IMPACT Use of longitudinal samples has significant potential to identify biomarkers for detection and risk stratification.
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Affiliation(s)
- Ju Yeon Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Wayne Cardoni
- Frederick Regional Health System, Frederick, Maryland
| | - George Coppit
- Frederick Regional Health System, Frederick, Maryland
| | - Shiv Srivastava
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Joseph F Goodman
- Division of Otolaryngology, George Washington University, Washington, DC
| | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington. .,Department of Cell Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
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15
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Van Gool A, Corrales F, Čolović M, Krstić D, Oliver-Martos B, Martínez-Cáceres E, Jakasa I, Gajski G, Brun V, Kyriacou K, Burzynska-Pedziwiatr I, Wozniak LA, Nierkens S, Pascual García C, Katrlik J, Bojic-Trbojevic Z, Vacek J, Llorente A, Antohe F, Suica V, Suarez G, t'Kindt R, Martin P, Penque D, Martins IL, Bodoki E, Iacob BC, Aydindogan E, Timur S, Allinson J, Sutton C, Luider T, Wittfooth S, Sammar M. Analytical techniques for multiplex analysis of protein biomarkers. Expert Rev Proteomics 2020; 17:257-273. [PMID: 32427033 DOI: 10.1080/14789450.2020.1763174] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The importance of biomarkers for pharmaceutical drug development and clinical diagnostics is more significant than ever in the current shift toward personalized medicine. Biomarkers have taken a central position either as companion markers to support drug development and patient selection, or as indicators aiming to detect the earliest perturbations indicative of disease, minimizing therapeutic intervention or even enabling disease reversal. Protein biomarkers are of particular interest given their central role in biochemical pathways. Hence, capabilities to analyze multiple protein biomarkers in one assay are highly interesting for biomedical research. AREAS COVERED We here review multiple methods that are suitable for robust, high throughput, standardized, and affordable analysis of protein biomarkers in a multiplex format. We describe innovative developments in immunoassays, the vanguard of methods in clinical laboratories, and mass spectrometry, increasingly implemented for protein biomarker analysis. Moreover, emerging techniques are discussed with potentially improved protein capture, separation, and detection that will further boost multiplex analyses. EXPERT COMMENTARY The development of clinically applied multiplex protein biomarker assays is essential as multi-protein signatures provide more comprehensive information about biological systems than single biomarkers, leading to improved insights in mechanisms of disease, diagnostics, and the effect of personalized medicine.
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Affiliation(s)
- Alain Van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Fernado Corrales
- Functional Proteomics Laboratory, Centro Nacional De Biotecnología , Madrid, Spain
| | - Mirjana Čolović
- Department of Physical Chemistry, "Vinča" Institute of Nuclear Sciences, University of Belgrade , Belgrade, Serbia
| | - Danijela Krstić
- Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade , Belgrade, Serbia
| | - Begona Oliver-Martos
- Neuroimmunology and Neuroinflammation Group. Instituto De Investigación Biomédica De Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario De Málaga , Malaga, Spain
| | - Eva Martínez-Cáceres
- Immunology Division, LCMN, Germans Trias I Pujol University Hospital and Research Institute, Campus Can Ruti, Badalona, and Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma De Barcelona , Cerdanyola Del Vallès, Spain
| | - Ivone Jakasa
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb , Zagreb, Croatia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health , Zagreb, Croatia
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm, IRIG, BGE , Grenoble, France
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Biology, The Cyprus School of Molecular Medicine/The Cyprus Institute of Neurology and Genetics , Nicosia, Cyprus
| | - Izabela Burzynska-Pedziwiatr
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Lucyna Alicja Wozniak
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Stephan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht & Princess Máxima Center for Pediatric Oncology , Utrecht, The Netherlands
| | - César Pascual García
- Materials Research and Technology Department, Luxembourg Institute of Science and Technology (LIST) , Belvaux, Luxembourg
| | - Jaroslav Katrlik
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences , Bratislava, Slovakia
| | - Zanka Bojic-Trbojevic
- Laboratory for Biology of Reproduction, Institute for the Application of Nuclear Energy - INEP, University of Belgrade , Belgrade, Serbia
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital , Oslo, Norway
| | - Felicia Antohe
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Viorel Suica
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Guillaume Suarez
- Center for Primary Care and Public Health (Unisanté), University of Lausanne , Lausanne, Switzerland
| | - Ruben t'Kindt
- Research Institute for Chromatography (RIC) , Kortrijk, Belgium
| | - Petra Martin
- Department of Medical Oncology, Midland Regional Hospital Tullamore/St. James's Hospital , Dublin, Ireland
| | - Deborah Penque
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ines Lanca Martins
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ede Bodoki
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Bogdan-Cezar Iacob
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Eda Aydindogan
- Department of Chemistry, Graduate School of Sciences and Engineering, Koç University , Istanbul, Turkey
| | - Suna Timur
- Institute of Natural Sciences, Department of Biochemistry, Ege University , Izmir, Turkey
| | | | | | - Theo Luider
- Department of Neurology, Erasmus MC , Rotterdam, The Netherlands
| | | | - Marei Sammar
- Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College , Karmiel, Israel
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16
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Zhang Z, Zhang Y, Song S, Yin L, Sun D, Gu J. Recent advances in the bioanalytical methods of polyethylene glycols and PEGylated pharmaceuticals. J Sep Sci 2020; 43:1978-1997. [DOI: 10.1002/jssc.201901340] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Zhi Zhang
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Yuyao Zhang
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Shiwen Song
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Lei Yin
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Research Institute of Translational MedicineThe First Bethune Hospital of Jilin University Changchun P. R. China
| | - Dong Sun
- Department of Biopharmacy, College of Life ScienceJilin University Changchun P. R. China
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education”Yantai University Yantai P. R. China
| | - Jingkai Gu
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
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17
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Sivadasan P, Gupta MK, Sathe G, Sudheendra H, Sunny SP, Renu D, Hari P, Gowda H, Suresh A, Kuriakose MA, Sirdeshmukh R. Salivary proteins from dysplastic leukoplakia and oral squamous cell carcinoma and their potential for early detection. J Proteomics 2020; 212:103574. [DOI: 10.1016/j.jprot.2019.103574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/18/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022]
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18
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Kowalczyk T, Ciborowski M, Kisluk J, Kretowski A, Barbas C. Mass spectrometry based proteomics and metabolomics in personalized oncology. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165690. [PMID: 31962175 DOI: 10.1016/j.bbadis.2020.165690] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/18/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023]
Abstract
Precision medicine (PM) means the customization of healthcare with decisions and practices adjusted to the individual patient. It includes personalized diagnostics, patients' sub-classification, individual treatment selection and the monitoring of its effectiveness. Currently, in oncology, PM is based on the molecular and cellular features of a tumor, its microenvironment and the patient's genetics and lifestyle. Surprisingly, the available targeted therapies were found effective only in a subset of patients. An in-depth understanding of tumor biology is crucial to improve their effectiveness and develop new therapeutic targets. Completion of genetic information with proteomics and metabolomics can give broader knowledge about tumor biology which consequently provides novel biomarkers and indicates new therapeutic targets. Recently, metabolomics and proteomics have extensively been applied in the field of oncology. In the context of PM, human studies, with the use of mass spectrometry (MS) which allows the detection of thousands of molecules in a large number of samples, are the most valuable. Such studies, focused on cancer biomarkers discovery or patients' stratification, are presented in this review. Moreover, the technical aspects of MS-based clinical proteomics and metabolomics are described.
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Affiliation(s)
- Tomasz Kowalczyk
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain.
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Chu HW, Chang KP, Hsu CW, Chang IYF, Liu HP, Chen YT, Wu CC. Identification of Salivary Biomarkers for Oral Cancer Detection with Untargeted and Targeted Quantitative Proteomics Approaches. Mol Cell Proteomics 2019; 18:1796-1806. [PMID: 31253657 PMCID: PMC6731081 DOI: 10.1074/mcp.ra119.001530] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 01/08/2023] Open
Abstract
Oral cavity squamous cell carcinoma (OSCC) is one of the most common cancers worldwide. In Taiwan, OSCC is the fifth leading cause of cancer-related mortality and leads to 2800 deaths per year. The poor outcome of OSCC patients is principally ascribed to the fact that this disease is often advanced at the time of diagnosis, suggesting that early detection of OSCC is urgently needed. Analysis of cancer-related body fluids is one promising approach to identify biomarker candidates of cancers. To identify OSCC biomarkers, salivary proteomes of OSCC patients, individuals with oral potentially malignant disorders (OPMDs), and healthy volunteers were comparatively profiled with isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry (MS). The salivary levels of 67 and 18 proteins in the OSCC group are elevated and decreased compared with that in the noncancerous group (OPMD and healthy groups), respectively. The candidate biomarkers were further selected using the multiple reaction monitoring (MRM)-MS and validated with the immunoassays. More importantly, the higher salivary level of three proteins, complement factor H (CFH), fibrinogen alpha chain (FGA), and alpha-1-antitrypsin (SERPINA1) was correlated with advanced stages of OSCC. Our results indicate that analysis of salivary proteome is a feasible strategy for biomarker discovery, and the three proteins are potential salivary markers for OSCC diagnosis.
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Affiliation(s)
- Hao-Wei Chu
- ‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kai-Ping Chang
- §Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Chia-Wei Hsu
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hao-Ping Liu
- ‖Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ting Chen
- ‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; **Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; ‡‡Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Chih-Ching Wu
- ‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; §Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; §§Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan; ¶¶Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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20
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Gouveia D, Almunia C, Cogne Y, Pible O, Degli-Esposti D, Salvador A, Cristobal S, Sheehan D, Chaumot A, Geffard O, Armengaud J. Ecotoxicoproteomics: A decade of progress in our understanding of anthropogenic impact on the environment. J Proteomics 2019; 198:66-77. [DOI: 10.1016/j.jprot.2018.12.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/19/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022]
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21
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Yu B, Cao W, Zhang C, Xia R, Liu J, Yan M, Chen W. Prediction of lymph node metastasis in oral squamous cell carcinoma based on protein profile. Expert Rev Proteomics 2019; 16:363-373. [PMID: 30779878 DOI: 10.1080/14789450.2019.1584039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Lymph node metastasis leads to high mortality rates of oral squamous cell carcinoma (OSCC). However, it is still controversial to define clinically negative neck (cN0) and positive neck (cN1-3). METHODS We retrieved candidate biomarkers identified by proteomic analysis in OSCC from published works of literature. In training stage, immunohistochemistry (IHC) analysis was used to determine the expression of proteins and logistic regression models with stepwise variable selection were used to identify potential factors that might affect lymph node metastasis and life status. Furthermore, the prediction model was validated in validating stage. RESULTS We screened eight highly expressed proteins related to lymph node metastasis in OSCC and found that the expression levels of SOD2, BST2, CAD, ITGB6, and PRDX4 were significantly elevated in patients with lymph node metastasis compared to the patients without lymph node metastasis. Furthermore, in training and validating stages, the prediction model base on the combination of CAD, SOD2 expression levels, and histopathologic grade was developed and validated in patients with OSCC. CONCLUSIONS Our findings showed that the developed model well predicts the lymph node metastasis and life status in patients with OSCC, independent of TNM stage.
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Affiliation(s)
- Binbin Yu
- a Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital & College of Stomatology , Shanghai Jiao Tong University School of Medicine , Shanghai , China
- b National Clinical Research Center of Stomatology , Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai , China
| | - Wei Cao
- a Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital & College of Stomatology , Shanghai Jiao Tong University School of Medicine , Shanghai , China
- b National Clinical Research Center of Stomatology , Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai , China
| | - Chenping Zhang
- a Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital & College of Stomatology , Shanghai Jiao Tong University School of Medicine , Shanghai , China
- b National Clinical Research Center of Stomatology , Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai , China
| | - Ronghui Xia
- b National Clinical Research Center of Stomatology , Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai , China
- c Department of Oral Pathology, Shanghai Ninth People's Hospital & College of Stomatology , Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Jinlin Liu
- b National Clinical Research Center of Stomatology , Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai , China
| | - Ming Yan
- a Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital & College of Stomatology , Shanghai Jiao Tong University School of Medicine , Shanghai , China
- b National Clinical Research Center of Stomatology , Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai , China
| | - Wantao Chen
- a Department of Oral and Maxillofacial-Head & Neck Oncology, Shanghai Ninth People's Hospital & College of Stomatology , Shanghai Jiao Tong University School of Medicine , Shanghai , China
- b National Clinical Research Center of Stomatology , Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai , China
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22
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Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y. Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery. J Proteome Res 2019; 18:1907-1915. [PMID: 30848925 DOI: 10.1021/acs.jproteome.9b00037] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clinical biomarkers identified by shotgun proteomics require proteins in body fluids or tissues to be enzymatically digested before being separated and sequenced by liquid chromatography-tandem mass spectrometry. How well peptide signals can be resolved and detected is largely dependent on the quality of sample preparation. Conventional approaches such as in-gel, in-solution, and filter-based digestion, despite their extensive implementation by the community, become less appealing due to their unsatisfying protein/peptide recovery rate, lengthy sample processing, and/or lowcost-effectiveness. Suspension trapping has recently been demonstrated as an ultrafast approach for proteomic analysis. Here, for the first time, we extend its application to human salivary proteome analyses. In particular, we present a simple self-assembled glass fiber filter device which can be packed with minimal difficulty, is extremely cost-effective, and maintains the same performance as commercial filters. As a proof-of-principle, we analyzed the whole saliva from 8 healthy individuals as well as a cohort of 10 subjects of oral squamous cell carcinoma (OSCC) patients and non-OSCC subjects. Label-free quantification revealed surprisingly low interindividual variability and several known markers. Our study provides the first evidence of an easy-to-use and low-cost device for clinical proteomics as well as for general proteomic sample preparation.
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Affiliation(s)
- Yi-Han Lin
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Rodrigo Vargas Eguez
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Manolito G Torralba
- J. Craig Venter Institute , 4120 Capricorn Lane , La Jolla , California 92037 , United States
| | - Harinder Singh
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Pawel Golusinski
- Department of Otolaryngology and Maxillofacial Surgery , University of Zielona Gora , Zielona Gora 65-417 , Poland.,Department of Head and Neck Surgery , Poznan University of Medical Sciences, Greater Poland Cancer Centre , Poznan 61-866 , Poland.,Department of Biology and Environmental Studies , Poznan University of Medical Sciences , Poznan 61-701 , Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery , Poznan University of Medical Sciences, Greater Poland Cancer Centre , Poznan 61-866 , Poland
| | - Michal Masternak
- College of Medicine, Burnett School of Biomedical Sciences , University of Central Florida , Orlando , Florida 32827 , United States
| | - Karen E Nelson
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States.,J. Craig Venter Institute , 4120 Capricorn Lane , La Jolla , California 92037 , United States
| | - Marcelo Freire
- J. Craig Venter Institute , 4120 Capricorn Lane , La Jolla , California 92037 , United States
| | - Yanbao Yu
- J. Craig Venter Institute , 9605 Medical Center Drive , Rockville , Maryland 20850 , United States
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23
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Hsiao YC, Chu LJ, Chen YT, Chi LM, Chien KY, Chiang WF, Chang YT, Chen SF, Wang WS, Chuang YN, Lin SY, Chien CY, Chang KP, Chang YS, Yu JS. Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring-Mass Spectrometry. Proteomics Clin Appl 2018; 12. [PMID: 29350471 DOI: 10.1002/prca.201700039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/11/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE Saliva is an attractive sample source for the biomarker-based testing of several diseases, especially oral cancer. Here, we sought to apply multiplexed LC-MRM-MS to precisely quantify 90 disease-related proteins and assess their intra- and interindividual variability in saliva samples from healthy donors. EXPERIMENTAL DESIGN We developed two multiplexed LC-MRM-MS assays for 122 surrogate peptides representing a set of disease-related proteins. Saliva samples were collected from 10 healthy volunteers at three different time points (Day 1 morning and afternoon, and Day 2 morning). Each sample was spiked with a constant amount of a 15 N-labeled protein and analyzed by MRM-MS in triplicate. Quantitative results from LC-MRM-MS were calculated by single-point quantification with reference to a known amount of internal standard (heavy peptide). RESULTS The CVs for assay reproducibility and technical variation were 13 and 11%, respectively. The average concentrations of the 99 successfully quantified proteins ranged from 0.28 ± 0.58 ng mL-1 for profilin-2 (PFN2) to 8.55 ±8.96 μg mL-1 for calprotectin (S100A8). For the 90 proteins detectable in >50% of samples, the average CVs for intraday, interday, intraindividual, and interindividual samples were 38%, 43%, 45%, and 69%, respectively. The fluctuations of most target proteins in individual subjects were found to be within ± twofold. CONCLUSIONS AND CLINICAL RELEVANCE Our study elucidated the intra- and interindividual variability of 90 disease-related proteins in saliva samples from healthy donors. The findings may facilitate the further development of salivary biomarkers for oral and systemic diseases.
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Affiliation(s)
- Yung-Chin Hsiao
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lang-Ming Chi
- Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kun-Yi Chien
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Fan Chiang
- Department of Oral and Maxillofacial Surgery, Chi-Mei Medical Center, Tainan, Taiwan.,School of Dentistry, National Yang Ming University, Taipei, Taiwan
| | - Ya-Ting Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Szu-Fan Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Shun Wang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yao-Ning Chuang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Yu Lin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Yen Chien
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Ping Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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24
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Olkowicz M, Jablonska P, Rogowski J, Smolenski RT. Simultaneous accurate quantification of HO-1, CD39, and CD73 in human calcified aortic valves using multiple enzyme digestion - filter aided sample pretreatment (MED-FASP) method and targeted proteomics. Talanta 2018; 182:492-499. [PMID: 29501184 DOI: 10.1016/j.talanta.2018.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/05/2023]
Abstract
Several proteins such as membrane-associated ectonucleotidases: ecto-5'-nucleotidase (E5NT/CD73) and ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1/CD39), and intracellular heme oxygenase-1 (HO-1) may contribute to protection from inflammation-related diseases such as calcific aortic valve stenosis (CAS). Accurate quantification of these proteins could contribute to better understanding of the disease mechanisms and identification of biomarkers. This report presents development and validation of quantification method for E5NT/CD73, ENTPD1/CD39 and HO-1. The multiplexed targeted proteomic assay involved antibody-free, multiple-enzyme digestion, filter-assisted sample preparation (MED-FASP) strategy and a nanoflow liquid chromatography/mass spectrometry under multiple reaction monitoring mode (LC-MRM/MS). The method developed presented high sensitivity (LLOQ of 5 pg/mL for each of the analytes) and accuracy that ranged from 92.0% to 107.0%, and was successfully applied for the absolute quantification of HO-1, CD39 and CD73 proteins in homogenates of human calcified and non-calcified valves. The absolute CD39 and CD73 concentrations were lower in calcified aortic valves (as compared to non-stenotic ones) and were found to be: 1.16 ± 0.39 vs. 3.15 ± 0.37 pmol/mg protein and 1.94 ± 0.21 vs. 2.39 ± 0.39 pmol/mg protein, respectively, while the quantity of HO-1 was elevated in calcified valves (10.72 ± 1.18 vs. 4.28 ± 0.42 amol/mg protein). These results were consistent but more reproducible as compared to immunoassays. In conclusion, multiplexed quantification of HO-1, CD39 and CD73 proteins by LC-MRM/MS works well in challenging human tissues such as aortic valves. This analysis confirmed the relevance of these proteins in pathogenesis of CAS and could be extended to other biomedical investigations.
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Affiliation(s)
- Mariola Olkowicz
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego St., 60-627 Poznan, Poland.
| | - Patrycja Jablonska
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland
| | - Jan Rogowski
- Department of Cardiac and Vascular Surgery, Medical University of Gdansk, 7 Debinki St., 80-211 Gdansk, Poland
| | - Ryszard T Smolenski
- Department of Biochemistry, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland
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25
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Kailemia MJ, Xu G, Wong M, Li Q, Goonatilleke E, Leon F, Lebrilla CB. Recent Advances in the Mass Spectrometry Methods for Glycomics and Cancer. Anal Chem 2018; 90:208-224. [PMID: 29049885 PMCID: PMC6200424 DOI: 10.1021/acs.analchem.7b04202] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Muchena J. Kailemia
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Frank Leon
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
- Foods for Health Institute, University of California, Davis, CA 95616, USA
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26
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Heawchaiyaphum C, Pientong C, Phusingha P, Vatanasapt P, Promthet S, Daduang J, Teeramatwanich W, Kongyingyoes B, Chuerduangphui J, Ekalaksananan T. Peroxiredoxin-2 and zinc-alpha-2-glycoprotein as potentially combined novel salivary biomarkers for early detection of oral squamous cell carcinoma using proteomic approaches. J Proteomics 2017; 173:52-61. [PMID: 29199150 DOI: 10.1016/j.jprot.2017.11.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/20/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023]
Abstract
No effective screening method is available for oral squamous cell carcinoma (OSCC) that is recognized to influence by environmental factors as well as human papillomavirus (HPV) and Epstein-Barr virus (EBV). Therefore, we sought to identify salivary biomarkers for screening of OSCC with or without HPV and/or EBV infection. Saliva, lesion and oral exfoliated cells were collected from OSCC patients and cancer-free controls (CFCs) and grouped depending on their HPV- and EBV-infection status. Salivary protein was precipitated and subjected to 2-dimensional gel electrophoresis. Differential expression of proteins was identified by mass spectrometry and validated by Western blotting. Distinctive expression patterns of salivary proteins were detected in OSCC as compared with CFCs. Levels of peroxiredoxin-2 (PRDX-2) and zinc-alpha-2-glycoprotein (ZAG) were significantly up-regulated in OSCC cases (p<0.001) relative to CFCs. Similarly, these proteins were also up-regulated in lesion cells compared with oral exfoliated cells (p<0.001). However, the expression patterns of these proteins were not significantly influenced by patient histories (risk factors). In combination, these proteins yielded the highest discriminatory power (AUC=0.999), sensitivity (100%), and specificity (98.77%) in distinguishing the early stages of OSCC. The detection of PRDX-2 combining with ZAG protein could potentially be used as salivary biomarkers for early screening of OSCC. SIGNIFICANCE Our findings demonstrate a useful of combined detection of PRDX-2 and ZAG as a salivary biomarker for the early detection of OSCC.
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Affiliation(s)
- Chukkris Heawchaiyaphum
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand.
| | - Pensiri Phusingha
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Patravoot Vatanasapt
- Department of Otorhinolaryngology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand.
| | - Supannee Promthet
- Department of Epidemiology, Faculty of Public Health, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand.
| | - Jureerut Daduang
- Department of Clinical Chemistry, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand.
| | - Watchareporn Teeramatwanich
- Department of Otorhinolaryngology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Bunkerd Kongyingyoes
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
| | - Jureeporn Chuerduangphui
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand.
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27
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Arantes LMRB, De Carvalho AC, Melendez ME, Lopes Carvalho A. Serum, plasma and saliva biomarkers for head and neck cancer. Expert Rev Mol Diagn 2017; 18:85-112. [PMID: 29134827 DOI: 10.1080/14737159.2017.1404906] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Head and neck squamous cell carcinoma (HNSCC) encompasses tumors arising from several locations (oral and nasal cavities, paranasal sinuses, salivary glands, pharynx, and larynx) and currently stands as the sixth most common cancer worldwide. The most important risk factors identified so far are tobacco and alcohol consumption, and, for a subgroup of HNSCCs, infection with high-risk types of human papillomavirus (HPV). Despite several improvements in the treatment of these tumors in the last decades, overall survival rates have only improved marginally, mainly due to the advanced clinical stage at diagnosis and the high rates of treatment failure associated with this late diagnosis. Areas covered: This review will focus on the feasibility of evaluating molecular-based biomarkers (mRNA, microRNA, lncRNA, DNA methylation and protein expression) in body fluids (serum, plasma, and saliva) as markers for diagnosis, prognosis, and surveillance. Expert commentary: The potential use of those markers in the clinical setting would allow for early diagnosis, prediction of treatment response, improvement in treatment selection and provide disease monitoring for early detection of tumor recurrence. It can ultimately be translated into better survival rates and improved quality of life for HNSCC patients.
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Affiliation(s)
| | | | - Matias Eliseo Melendez
- a Molecular Oncology Research Center , Barretos Cancer Hospital , Barretos - SP , Brazil
| | - André Lopes Carvalho
- a Molecular Oncology Research Center , Barretos Cancer Hospital , Barretos - SP , Brazil
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