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Umapathy VR, Natarajan PM, Swamikannu B. Review Insights on Salivary Proteomics Biomarkers in Oral Cancer Detection and Diagnosis. Molecules 2023; 28:5283. [PMID: 37446943 PMCID: PMC10343386 DOI: 10.3390/molecules28135283] [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: 05/19/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Early detection is crucial for the treatment and prognosis of oral cancer, a potentially lethal condition. Tumor markers are abnormal biological byproducts produced by malignant cells that may be found and analyzed in a variety of bodily fluids, including saliva. Early detection and appropriate treatment can increase cure rates to 80-90% and considerably improve quality of life by reducing the need for costly, incapacitating medicines. Salivary diagnostics has drawn the interest of many researchers and has been proven to be an effective tool for both medication monitoring and the diagnosis of several systemic diseases. Since researchers are now searching for biomarkers in saliva, an accessible bodily fluid, for noninvasive diagnosis of oral cancer, measuring tumor markers in saliva is an interesting alternative to blood testing for early identification, post-treatment monitoring, and monitoring high-risk lesions. New molecular markers for oral cancer detection, treatment, and prognosis have been found as a result of developments in the fields of molecular biology and salivary proteomics. The numerous salivary tumor biomarkers and how they relate to oral cancer and pre-cancer are covered in this article. We are optimistic that salivary protein biomarkers may one day be discovered for the clinical detection of oral cancer because of the rapid advancement of proteomic technology.
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Affiliation(s)
- Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Thai Moogambigai Dental College and Hospital, Dr. M.G.R. Educational and Research Institute, Chennai 600107, Tamil Nadu, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Centre of Medical and Bio-Allied Health Sciences and Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Bhuminathan Swamikannu
- Department of Prosthodontics, Sree Balaji Dental College and Hospital, BIHER University, Pallikaranai, Chennai 600100, Tamil Nadu, India;
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Savinov SS, Anisimov AA. Effect of Conditions for Sampling of Human Saliva on the Results of Determination of Macro- and Micronutrients. JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1134/s1061934820040139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Houghton JW, Yong JT, Carpenter G, Bartlett D, Moazzez R, O'Toole S. Differences in the Natural Enamel Surface and Acquired Enamel Pellicle following Exposure to Citric or Hydrochloric Acid. Caries Res 2020; 54:226-233. [PMID: 31962317 DOI: 10.1159/000504746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 11/13/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES The aim of this study was to investigate variations in the interaction between enamel, that is, the acquired enamel pellicle (AEP) and citric or hydrochloric acid. MATERIALS AND METHODS A 24-h AEP was formed on natural enamel specimens (n = 40) from pooled whole mouth human saliva. Samples were randomly allocated to citric (0.3%, pH 3.2) or hydrochloric (HCl) acid (0.01 M, pH 2.38) exposure for 30 or 300 s. The total protein concentration (TPC), and phosphorous and calcium concentrations of the pellicle were determined before and after acid exposure, and again after re-immersion in saliva. Surface roughness and tandem scanning confocal microscopy imaging were used to assess enamel changes. RESULTS After 300 s of citric acid exposure, the mean ± SD TPC reduced from 5.1 ± 1.1 to 3.5 ± 1.1 mg/mL (p < 0.05). In contrast, after 300 s of HCl exposure, the mean TPC did not reduce significantly from baseline (6.6 ± 1.1 to 5.7 ± 0.7 mg/mL) but was significantly reduced in the reformed pellicle to 4.9 ± 1.2 mg/mL (p < 0.001). This reduction occurred after significant release of calcium and phosphorous from the enamel surface (p < 0.001). Thirty seconds of exposure to either acid had no obvious effect on the AEP. The surface roughness of the enamel decreased after acid exposure but no differences between groups was observed. CONCLUSIONS These findings indicate that citric acid interacted with proteins in the AEP upon contact, offering enamel protection. In contrast, HCl appeared to bypass the pellicle, and reduced protein was observed only after changes in the enamel chemical composition.
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Affiliation(s)
- Jack William Houghton
- Centre for Host Microbe-Interactions, King's College London Faculty of Dental, Oral and Craniofacial Sciences, London, United Kingdom,
| | - Jing Teng Yong
- Centre for Clinical, Oral and Translational Sciences, King's College London Faculty of Dental, Oral and Craniofacial Sciences, London, United Kingdom
| | - Guy Carpenter
- Centre for Host Microbe-Interactions, King's College London Faculty of Dental, Oral and Craniofacial Sciences, London, United Kingdom
| | - David Bartlett
- Centre for Clinical, Oral and Translational Sciences, King's College London Faculty of Dental, Oral and Craniofacial Sciences, London, United Kingdom
| | - Rebecca Moazzez
- Centre for Clinical, Oral and Translational Sciences, King's College London Faculty of Dental, Oral and Craniofacial Sciences, London, United Kingdom
| | - Saoirse O'Toole
- Centre for Clinical, Oral and Translational Sciences, King's College London Faculty of Dental, Oral and Craniofacial Sciences, London, United Kingdom
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Amado F, Calheiros-Lobo MJ, Ferreira R, Vitorino R. Sample Treatment for Saliva Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:23-56. [DOI: 10.1007/978-3-030-12298-0_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Maes E, Oeyen E, Boonen K, Schildermans K, Mertens I, Pauwels P, Valkenborg D, Baggerman G. The challenges of peptidomics in complementing proteomics in a clinical context. MASS SPECTROMETRY REVIEWS 2019; 38:253-264. [PMID: 30372792 DOI: 10.1002/mas.21581] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Naturally occurring peptides, including growth factors, hormones, and neurotransmitters, represent an important class of biomolecules and have crucial roles in human physiology. The study of these peptides in clinical samples is therefore as relevant as ever. Compared to more routine proteomics applications in clinical research, peptidomics research questions are more challenging and have special requirements with regard to sample handling, experimental design, and bioinformatics. In this review, we describe the issues that confront peptidomics in a clinical context. After these hurdles are (partially) overcome, peptidomics will be ready for a successful translation into medical practice.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Food and Bio-Based Products, AgResearch Ltd., Lincoln, New Zealand
| | - Eline Oeyen
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Karin Schildermans
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Patrick Pauwels
- Molecular Pathology Unit, Department of Pathology, Antwerp University Hospital, Edegem, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Center for Statistics, Hasselt University, Diepenbeek, Belgium
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
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Hicks SD, Jacob P, Middleton FA, Perez O, Gagnon Z. Distance running alters peripheral microRNAs implicated in metabolism, fluid balance, and myosin regulation in a sex-specific manner. Physiol Genomics 2018; 50:658-667. [PMID: 29883262 DOI: 10.1152/physiolgenomics.00035.2018] [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] [Indexed: 12/14/2022] Open
Abstract
Microribonucleic acids (miRNAs) mediate adaptive responses to exercise and may serve as biomarkers of exercise intensity/capacity. Expression of miRNAs is altered in skeletal muscle, plasma, and saliva following exertion. Women display unique physiologic responses to endurance exercise, and miRNAs respond to pathologic states in sex-specific patterns. However sex-specific miRNA responses to exercise remain unexplored. This study utilized high-throughput RNA sequencing to measure changes in salivary RNA expression among 25 collegiate runners following a single long-distance run. RNA concentrations in pre- and post-run saliva was assessed through alignment and quantification of 4,694 miRNAs and 27,687 mRNAs. Pair-wise Wilcoxon rank-sum test identified miRNAs with significant [false discovery rate (FDR) < 0.05] post-run changes. Associations between miRNA levels and predicted mRNA targets were explored with Pearson correlations. Differences in miRNA patterns between men ( n = 13) and women ( n = 12) were investigated with two-way analysis of variance. Results revealed 122 salivary miRNAs with post-run changes. The eight miRNAs with the largest changes were miR-3671, miR-5095 (downregulated); and miR-7154-3p, miR-200b-5p, miR-5582-3p, miR-6859-3p, miR-6751-5p, miR-4419a (upregulated). Predicted mRNA targets for these miRNAs represented 15 physiologic processes, including glycerophospholipid metabolism (FDR = 0.042), aldosterone-regulated sodium reabsorption (FDR = 0.049), and arrhythmogenic ventricular cardiomyopathy (FDR = 0.018). Twenty-six miRNA/mRNA pairs had associated changes in post-run levels. Three miRNAs (miR-4675, miR-6745, miR-6746-3p) demonstrated sex-specific responses to exercise. Numerous salivary miRNAs change in response to endurance running and target the expression of genes involved in metabolism, fluid balance, and musculoskeletal adaptations. A subset of miRNAs may differentiate the metabolic response to exercise in men and women.
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Affiliation(s)
- Steven D Hicks
- Department of Pediatrics, Penn State College of Medicine , Hershey, Pennsylvania
| | - Paige Jacob
- Department of Biology, Marist College , Poughkeepsie, New York
| | - Frank A Middleton
- Departments of Neuroscience, Physiology, Molecular Biology, Pediatrics, and Psychiatry/Behavioral Sciences, Institute for Human Performance, State University of New York Upstate Medical University , Syracuse, New York
| | - Omar Perez
- Department of Biology, Marist College , Poughkeepsie, New York
| | - Zofia Gagnon
- Department of Biology, Marist College , Poughkeepsie, New York
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Helmerhorst EJ, Dawes C, Oppenheim FG. The complexity of oral physiology and its impact on salivary diagnostics. Oral Dis 2017; 24:363-371. [PMID: 28922514 DOI: 10.1111/odi.12780] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Saliva contains biomarkers for systemic as well as oral diseases. This study was undertaken to assess the variability in the sources of such biomarkers (plasma, cells) and attempted to identify saliva deterioration markers in order to improve saliva diagnostic outcomes. MATERIALS AND METHODS Inter- and intrasubject variations in salivary gingival crevicular fluid levels were determined by measuring salivary albumin and transferrin levels. The purity of collected glandular secretions was determined by bacterial culture, and the variability in epithelial cell numbers by cell counting and optical density measurement. Saliva sample deterioration markers were identified by RP-HPLC and LC-ESI-MS/MS. RESULTS Tenfold variations were observed in plasma-derived albumin and transferrin levels, emphasizing the need for biomarker normalization with respect to plasma contributions to saliva. Epithelial cell levels varied 50-fold in samples collected before and after a meal. Salivary fungal levels varied within subjects and among subjects from 0 to >1,000 colony-forming units per milliliter. In saliva samples incubated for various time intervals at 37°C, five peptides were identified that steadily increased in intensity over time and which could be explored as "deterioration markers." CONCLUSION Taking saliva characteristics appropriately into account will help realize the promise that this body fluid is suitable to be exploited for reliable healthcare monitoring and surveillance.
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Affiliation(s)
- E J Helmerhorst
- Department of Molecular and Cell Biology, Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, USA
| | - C Dawes
- Department of Oral Biology, University of Manitoba, Winnipeg, MB, Canada
| | - F G Oppenheim
- Department of Molecular and Cell Biology, Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, USA.,Department of Periodontology, Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, USA
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WANG Y, WU L, XU JL, LI SM, LIU N, JIANG L. Effect of Reproducibility of Nano-liquid Chromatography- Mass Spectrometry on Analysis of Urinary Peptidomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61044-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Marvin RK, Saepoo MB, Ye S, White DB, Liu R, Hensley K, Rega P, Kazan V, Giovannucci DR, Isailovic D. Salivary protein changes in response to acute stress in medical residents performing advanced clinical simulations: a pilot proteomics study. Biomarkers 2017; 22:372-382. [PMID: 28055279 DOI: 10.1080/1354750x.2017.1279215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Quantitative changes of salivary proteins due to acute stress were detected. OBJECTIVE To explore protein markers of stress in saliva of eight medical residents who performed emergency medicine simulations. MATERIALS AND METHODS Saliva was collected before the simulations, after the simulations, and following morning upon waking. Proteins were separated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), identified by mass spectrometry (MS), and relatively quantified by densitometry. RESULTS Salivary alpha-amylase and S-type cystatins significantly increased, while the ∼26 kDa and low-molecular weight (MW) (<10 kDa) SDS-PAGE bands exhibited changes after stress. DISCUSSION AND CONCLUSION Alpha-amylase and cystatins are potential salivary markers of acute stress, but further validation should be performed using larger sample populations.
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Affiliation(s)
- Rachel K Marvin
- a Department of Chemistry and Biochemistry , University of Toledo , Toledo , OH , USA
| | | | - Simiao Ye
- c Department of Mathematics and Statistics , University of Toledo , Toledo , OH , USA
| | - Donald B White
- c Department of Mathematics and Statistics , University of Toledo , Toledo , OH , USA
| | - Rong Liu
- c Department of Mathematics and Statistics , University of Toledo , Toledo , OH , USA
| | - Kenneth Hensley
- d Department of Pathology , University of Toledo, Toledo , OH, USA
| | - Paul Rega
- e Department of Emergency Medicine , University of Toledo , Toledo , OH , USA
| | - Viviane Kazan
- e Department of Emergency Medicine , University of Toledo , Toledo , OH , USA
| | | | - Dragan Isailovic
- a Department of Chemistry and Biochemistry , University of Toledo , Toledo , OH , USA
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XU JL, HONG XY, LI SM, WANG Y. Study of Frozen Storage Conditions Impacting on Salivary Peptidomic by High Resolution Tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60980-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Savinov SS, Anisimov AA, Drobyshev AI. Problems and optimization of sampling, storage, and sample preparation in the determination of the trace element composition of human saliva. JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1134/s1061934816080128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Gualtero DF, Suarez Castillo A. Biomarkers in saliva for the detection of oral squamous cell carcinoma and their potential use for early diagnosis: a systematic review. Acta Odontol Scand 2015; 74:170-7. [PMID: 26577643 DOI: 10.3109/00016357.2015.1110249] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Objective To determine the capacity of salivary biomarkers in the early diagnosis of oral squamous cell carcinoma. Study design A systematic review of the literature was performed based on the English titles listed in the PubMed, EBSCO, Cochrane, Science Direct, ISI web Science and SciELO databases using the following search descriptors: Oral cancer, diagnosis, biomarkers, saliva and oral squamous cell carcinoma. Abstracts and full-text articles were assessed independently by two reviewers. International checklists for assessment of methodological quality were used. Levels of evidence and grades of recommendation through the Scottish Intercollegiate Guidelines Network (SIGN) template were recognized. The units of analysis were identified through a reference matrix. Results Through the research strategy and after application of different filters and considering choosing criteria, six studies were obtained for analysis. Salivary biomarkers for oral cancer most frequently found were mRNA and proteins for IL-8, CD44, MMP-1 and MMP-3. New peptide-biomarkers such as Cyfra 21-1 and ZNF510 were found. ZNF 510 was the only biomarker which increased in the population with tumour stage T1 + T2 and T3 + T4. Only one study showed a sensitivity and specificity of 96% when the biomarker ZNF 510 is employed to discriminate early and late tumour stages. Conclusions There is no sufficient scientific evidence to support the capacity of the identified salivary biomarkers for the early diagnosis of oral cancer (sub-clinical stages of the pathogenic period before cancer phenotypes are manifested). Salivary biomarkers, however, may be employed to discriminate between healthy and cancer patients.
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Affiliation(s)
- Diego F Gualtero
- a Dental Sciences Research Group , Institución Universitaria Colegios De Colombia (UNICOC) School of Dentistry , Bogotá , D.C , Colombia
- b Unit of Basic Oral Investigation-UIBO, School of Dentistry , El Bosque University , Bogota , D.C , Colombia
| | - Angela Suarez Castillo
- a Dental Sciences Research Group , Institución Universitaria Colegios De Colombia (UNICOC) School of Dentistry , Bogotá , D.C , Colombia
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Examination of salivary proteins as biomarkers of pathological conditions. Literature review. CURRENT ISSUES IN PHARMACY AND MEDICAL SCIENCES 2015. [DOI: 10.12923/j.2084-980x/26.1/a.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Saliva is universally available biofluid, easy to collect. Comprehensive analysis and identification of the proteomic content of human saliva may contribute to the understanding of oral pathophysiology and provide a foundation for the recognition of potential biomarkers of human disease. These features make it an ideal biological material for the early detection of many diseases of different origin, and enable non-invasive diagnostics. The presence of protein markers in saliva was found with usage of capillary electrophoresis and mass spectrometry.
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Trindade F, Amado F, Gomes PS, Vitorino R. endoProteoFASP: A novel FASP approach to profile salivary peptidome and disclose salivary proteases. Talanta 2015; 132:486-93. [DOI: 10.1016/j.talanta.2014.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/11/2014] [Accepted: 09/13/2014] [Indexed: 12/13/2022]
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Assessment of pre-analytical and analytical variables affecting peptidome profiling of gingival crevicular fluid by MALDI-TOF mass spectrometry. Clin Chim Acta 2014; 437:120-8. [DOI: 10.1016/j.cca.2014.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 06/24/2014] [Accepted: 07/16/2014] [Indexed: 12/26/2022]
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Boylan KL, Afiuni-Zadeh S, Geller MA, Hickey K, Griffin TJ, Pambuccian SE, Skubitz AP. A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics. Clin Proteomics 2014; 11:30. [PMID: 25097468 PMCID: PMC4106909 DOI: 10.1186/1559-0275-11-30] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/21/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The proteomic analysis of body fluids is a growing technology for the identification of protein biomarkers of disease. Given that Papanicolaou tests (Pap tests) are routinely performed on over 30 million women annually in the U.S. to screen for cervical cancer, we examined the residual Pap test fluid as a source of protein for analysis by mass spectrometry (MS). In the liquid-based Pap test, cervical cells are collected from the ectocervix and placed into an alcohol-based fixative prior to staining and pathologic examination. We hypothesized that proteins shed by cells of the female genital tract can be detected in the Pap test fixative by MS-based proteomic techniques. We examined the feasibility of using residual fluid from discarded Pap tests with cytologically "normal" results to optimize sample preparation for MS analysis. The protein composition of the cell-free Pap test fluid was determined by silver staining of sodium dodecyl sulfate -polyacrylamide gels, and the abundance of serum proteins was examined by Western immunoblot using an antibody against human serum albumin. Both pooled and individual samples were trypsin digested and analyzed by two-dimensional MS/MS. Proteins were identified by searching against the Human Uniprot database, and characterized for localization, function and relative abundance. RESULTS The average volume of the residual Pap test fluid was 1.5 ml and the average protein concentration was 0.14 mg/ml. By Western immunoblot we showed that the amount of albumin in each sample was significantly reduced compared to normal serum. By MS/MS, we identified 714 unique proteins in pooled Pap test samples and an average of 431 proteins in individual samples. About 40% of the proteins identified were extracellular or localized to the plasma membrane. Almost 20% of the proteins identified were involved in immunity and defense, characteristic of the healthy cervical-vaginal proteome. By merging the protein sets from the individual and pooled Pap test samples, we created a "Normal Pap test Core Proteome" consisting of 153 proteins. CONCLUSIONS Residual Pap test fluid contains a sufficient amount of protein for analysis by MS and represents a valuable biospecimen source for the identification of protein biomarkers for gynecological diseases.
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Affiliation(s)
- Kristin Lm Boylan
- Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 395, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
| | - Somaieh Afiuni-Zadeh
- Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 395, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
| | - Melissa A Geller
- Department of Obstetrics, Gynecology, and Women's Health, Division of Gynecologic Oncology, University of Minnesota, Minneapolis, MN, USA
| | - Kayla Hickey
- Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 395, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | | | - Amy Pn Skubitz
- Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 395, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
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Van Riper SK, de Jong EP, Higgins L, Carlis JV, Griffin TJ. Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN). J Proteome Res 2014; 13:1281-92. [PMID: 24571364 PMCID: PMC3993879 DOI: 10.1021/pr400866r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Researchers are increasingly turning to label-free MS1 intensity-based quantification strategies within HPLC-ESI-MS/MS workflows to reveal biological variation at the molecule level. Unfortunately, HPLC-ESI-MS/MS workflows using these strategies produce results with poor repeatability and reproducibility, primarily due to systematic bias and complex variability. While current global normalization strategies can mitigate systematic bias, they fail when faced with complex variability stemming from transient stochastic events during HPLC-ESI-MS/MS analysis. To address these problems, we developed a novel local normalization method, proximity-based intensity normalization (PIN), based on the analysis of compositional data. We evaluated PIN against common normalization strategies. PIN outperforms them in dramatically reducing variance and in identifying 20% more proteins with statistically significant abundance differences that other strategies missed. Our results show the PIN enables the discovery of statistically significant biological variation that otherwise is falsely reported or missed.
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Affiliation(s)
- Susan K Van Riper
- Department of Biomedical Informatics and Computational Biology, University of Minnesota Rochester , 111 South Broadway, Rochester, Minnesota 55904, United States
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Vitorino R, Ferreira R, Caseiro A, Amado F. Salivary Peptidomics Targeting Clinical Applications. COMPREHENSIVE ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-62650-9.00009-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Thanakun S, Watanabe H, Thaweboon S, Izumi Y. An effective technique for the processing of saliva for the analysis of leptin and adiponectin. Peptides 2013; 47:60-5. [PMID: 23851006 DOI: 10.1016/j.peptides.2013.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/14/2013] [Accepted: 06/14/2013] [Indexed: 02/07/2023]
Abstract
The recovery of protein from saliva has been extensively investigated as a method to monitor health. The aim of this study was to compare filtration and centrifugation as two methods of saliva processing necessary for determining the levels of salivary leptin and adiponectin. Thirty-seven healthy patients (median age of 45 years; range 35-73) participated in the study. Unstimulated whole saliva was collected by a drooling technique. An aliquot was filtered using a Millex-Millipore(®) (0.45μm PVDF Dura Pore membrane) syringe and a second aliquot was centrifuged at 15000×g for 15min at 4°C. Leptin and adiponectin levels were analyzed using an ELISA kit for serum (RayBio(®), GA, USA) with minor modifications. Leptin and adiponectin levels following the filtration technique yielded comparable results with those after centrifugation. Correlation was observed between filtered and centrifuged salivary leptin levels ((r=0.9155; 95% CI 0.8362-0.9573; p<0.0001) with concordance correlation coefficient k 0.9114 (95% CI 0.8332-0.9539)). Less correlation was observed for adiponectin ((r=0.5718; 95% CI 0.3041-0.7558; p=0.0002) with concordance correlation coefficient k 0.5586 (95% CI 0.2977-0.7419)). Using a Bland-Altman plot, similar measurements for both adipocytokines were observed with mean difference within a 95% CI, and interpreted as no systematic differences between the two processing techniques. This study showed that filtration is an alternative saliva processing technique to retrieve supernatant for protein analysis. Filtered saliva yielded leptin and adiponectin concentrations comparable with those obtained from centrifuged saliva.
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Affiliation(s)
- S Thanakun
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.
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Thomadaki K, Bosch J, Oppenheim F, Helmerhorst E. The diagnostic potential of salivary protease activities in periodontal health and disease. Oral Dis 2013; 19:781-8. [PMID: 23379269 DOI: 10.1111/odi.12069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/25/2012] [Accepted: 12/26/2012] [Indexed: 11/27/2022]
Abstract
Periodontal disease is characterised by proteolytic processes involving enzymes that are released by host immune cells and periodontal bacteria. These enzymes, when detectable in whole saliva, may serve as valuable diagnostic markers for disease states and progression. Because the substrate specificities of salivary proteases in periodontal health and disease are poorly characterised, we probed these activities using several relevant substrates: (i) gelatin and collagen type IV; (ii) the Arg/Lys-rich human salivary substrate histatin-5; and (iii) a histatin-derived synthetic analog benzyloxycarbonyl-Arg-Gly-Tyr-Arg-methyl cumaryl amide (Z-RGYR-MCA). Substrate degradation was assessed in gel (zymography) and in solution. Whole saliva supernatant enzyme activities directed at gelatin, quantified from the 42 kDa, 92 kDa and 130 kDa bands in the zymograms, were 1.3, 1.4 and 2.0-fold higher, respectively, in the periodontal patient group (P < 0.01), consistent with enhanced activities observed towards collagen type IV. On the other hand, histatin 5 degraded equally fast in healthy and periodontal patients' whole saliva supernatant samples (P > 0.10). Likewise, the hydrolysis rates of the Z-RGYR-MCA substrate were the same in the healthy and periodontal patient groups (P > 0.10). In conclusion, gelatinolytic/collagenolytic activities but not trypsin-like activities in human saliva differentiate health from periodontal disease and may thus provide an adjuvant to diagnosis for monitoring disease activity.
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Affiliation(s)
- K Thomadaki
- Department of Periodontology and Oral Biology, Henry M. Goldman School of Dental Medicine, Boston, MA, USA
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22
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Zheng J, Dixon RA, Li L. Development of isotope labeling LC-MS for human salivary metabolomics and application to profiling metabolome changes associated with mild cognitive impairment. Anal Chem 2012; 84:10802-11. [PMID: 23150892 DOI: 10.1021/ac3028307] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Saliva is a readily available biofluid that may contain metabolites of interest for diagnosis and prognosis of diseases. In this work, a differential (13)C/(12)C isotope dansylation labeling method, combined with liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS), is described for quantitative profiling of the human salivary metabolome. New strategies are presented to optimize the sample preparation and LC-MS detection processes. The strategies allow the use of as little of 5 μL of saliva sample as a starting material to determine the concentration changes of an average of 1058 ion pairs or putative metabolites in comparative saliva samples. The overall workflow consists of several steps including acetone-induced protein precipitation, (12)C-dansylation labeling of the metabolites, and LC-UV measurement of the total concentration of the labeled metabolites in individual saliva samples. A pooled sample was prepared from all the individual samples and labeled with (13)C-dansylation to serve as a reference. Using this metabolome profiling method, it was found that compatible metabolome results could be obtained after saliva samples were stored in tubes normally used for genetic material collection at room temperature, -20 °C freezer, and -80 °C freezer over a period of 1 month, suggesting that many saliva samples already collected in genomic studies could become a valuable resource for metabolomics studies, although the effect of much longer term of storage remains to be determined. Finally, the developed method was applied for analyzing the metabolome changes of two different groups: normal healthy older adults and comparable older adults with mild cognitive impairment (MCI). Top-ranked 18 metabolites successfully distinguished the two groups, among which seven metabolites were putatively identified while one metabolite, taurine, was definitively identified.
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Affiliation(s)
- Jiamin Zheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Effects of the UK Biobank collection protocol on potential biomarkers in saliva. Int J Epidemiol 2012; 41:1786-97. [DOI: 10.1093/ije/dys166] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Salivary proteomics in biomedical research. Clin Chim Acta 2012; 415:261-5. [PMID: 23146870 DOI: 10.1016/j.cca.2012.11.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 11/02/2012] [Accepted: 11/04/2012] [Indexed: 12/26/2022]
Abstract
Proteins that are important indicators of physiological or pathological states, can provide information for the identification of early and differential markers for disease. Saliva, contains an abundance of proteins, offers an easy, inexpensive, safe, and non-invasive approach for disease detection, and possesses a high potential to revolutionize the diagnostics. Discovery of salivary biomarkers could be used to scrutinize health and disease surveillance. The impact of human saliva proteome analysis in the search for clinically relevant disease biomarkers will be realized through advances made using proteomic technologies. The advancements of emerging proteomic techniques have benefited biomarker research to the point where saliva is now recognized as an excellent diagnostic medium for the detection of disease. This review presents an overview of the value of saliva as a credible diagnostic tool and we aim to summarize the proteomic technologies currently used for global analysis of saliva proteins and to elaborate on the application of saliva proteomics to the discovery of disease biomarkers, and discuss some of the critical challenges and perspectives in this field.
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Amado FML, Ferreira RP, Vitorino R. One decade of salivary proteomics: current approaches and outstanding challenges. Clin Biochem 2012; 46:506-17. [PMID: 23103441 DOI: 10.1016/j.clinbiochem.2012.10.024] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/13/2012] [Accepted: 10/16/2012] [Indexed: 12/12/2022]
Abstract
Efforts have been made in the last decade towards the complete characterization of saliva proteome using gel-based and gel-free approaches. The combination of these strategies resulted in the increment of the dynamic range of saliva proteome, which yield in the identification of more than 3,000 different protein species. Comparative protein profiling using isotope labeling and label free approaches has been used for the identification of novel biomarkers for oral and related diseases. Although progresses have been made in saliva proteome characterization, the comparative profiling in different pathophysiological conditions is still at the beginning if compared to other bodily fluids. The potential biomarkers identified so far lack specificity once common differentially expressed proteins were detected in the saliva of patients with distinct diseases. In addition, recent research works focused on saliva peptidome profiling already allowed a better understanding of peptides' physiological role in oral cavity. This review provides an overview of the major achievements in saliva proteomics giving emphasis to methodological concerns related with saliva collection, treatment and analysis, as well as the main advantages and pitfalls underlying salivary proteomic strategies and potential clinical outcomes.
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Affiliation(s)
- Francisco M L Amado
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal.
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Vitorino R, Guedes S, Manadas B, Ferreira R, Amado F. Toward a standardized saliva proteome analysis methodology. J Proteomics 2012; 75:5140-65. [PMID: 22809520 DOI: 10.1016/j.jprot.2012.05.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 05/26/2012] [Accepted: 05/30/2012] [Indexed: 01/01/2023]
Abstract
The present study aimed the evaluation of saliva sample pre-treatment, in particular the sample clearance usually performed by centrifugation, to the contribution of salivary proteome and peptidome. Using in-gel and off-gel approaches, a large content of salivary proteins was detected in the pellet fraction that is usually discarded. In addition, chaotropic/detergent treatment in combination with sonication, before the centrifugation step, resulted in salivary complex disruption and consequently in the extraction of high amounts of proteins. Based on this data, we suggest the use of urea/detergent with sonication as a standard saliva sample pre-treatment procedure. We also described a procedure to extract salivary peptides which can be performed even after saliva sample treatment with chaotropic/detergents. In overall, we reported for the first time the contribution of the pellet fraction to the whole saliva proteome. iTRAQ analysis highlighted a higher number of different peptides as well as distinct quantities of each protein class when after sample treatment with urea and sonication, acetone precipitation followed by solubilization with acetonitrile/HCl was performed.
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Affiliation(s)
- Rui Vitorino
- QOPNA, Mass spectrometry center, Department of Chemistry, University of Aveiro, Portugal.
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Vitorino R, Barros AS, Caseiro A, Ferreira R, Amado F. Evaluation of different extraction procedures for salivary peptide analysis. Talanta 2012; 94:209-15. [DOI: 10.1016/j.talanta.2012.03.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/03/2012] [Accepted: 03/12/2012] [Indexed: 01/05/2023]
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