A proteomic approach to compare saliva from individuals with and without oral leukoplakia

Targeted Phosphoproteomics of Human Saliva Extracellular Vesicles via Multiple Reaction Monitoring Cubed (MRM3)

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.

Saliva diagnostics: emerging techniques and biomarkers for salivaomics in cancer detection

INTRODUCTION

The pursuit of easy-to-use, non-invasive and inexpensive diagnostics is an urgent task for clinicians and scientists. Saliva is an important component of body fluid with regular changes of contents under various pathophysiological conditions, and the biomarkers identified from saliva shows high application potentials and values in disease diagnostics. This review introduces the latest developments in saliva research, with an emphasis on the detection and application of salivary biomarkers in cancer detection.

AREAS COVERED

Detection of disease-specific biomarkers in saliva samples by existing salivaomic methods can be used to diagnose various human pathological conditions and was introduced in details. This review also covers the saliva collection methods, the analytical techniques as well as the corresponding commercial products, with an aim to describe an holistic process for saliva-based diagnostics.

EXPERT OPINION

Saliva, as a non-invasive and collectable body fluid, can reflect the pathophysiological changes of the human body to a certain extent. Identification of reliable saliva biomarkers can provide a convenient way for cancer detection in clinical applications.

MALDI-TOF/MS Analysis of Non-Invasive Human Urine and Saliva Samples for the Identification of New Cancer Biomarkers

Cancer represents a group of heterogeneous diseases that are a leading global cause of death. Even though mortality has decreased in the past thirty years for different reasons, most patients are still diagnosed at the advanced stage, with limited therapeutic choices and poor outcomes. Moreover, the majority of cancers are detected using invasive painful methods, such as endoscopic biopsy, making the development of non-invasive or minimally invasive methods for the discovery and fast detection of specific biomarkers a crucial need. Among body fluids, a valuable non-invasive alternative to tissue biopsy, the most accessible and least invasive are undoubtedly urine and saliva. They are easily retrievable complex fluids containing a large variety of endogenous compounds that may provide information on the physiological condition of the body. The combined analysis of these fluids with matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF/MS), a reliable and easy-to-use instrumentation that provides information with relatively simple sample pretreatments, could represent the ideal option to rapidly achieve fast early stage diagnosis of tumors and their real-time monitoring. On this basis, the present review summarizes the recently reported applications relevant to the MALDI analysis of human urine and saliva samples.

Recognizing the salivary panomics for the clinical application in oral potentially malignant disorders

Oral cancer arises as a result of multistep carcinogenic progress from precursor lesion to oral squamous cell carcinoma through collective mutational process occur in the stem cells of mucosal epithelium. The detection of such oral potentially malignant disorders (OPMDs)/cancer in subclinical level will greatly improve the prognosis of a patient. The highly specific and sensitive salivary biomarkers have functioned in detection, prediction, surveillance and therapeutic monitoring of the diseases of interest. The aim of the review is to appraise various salivary biomarkers for the clinical utility in OPMDs. An electronic web-supported search was performed via PubMed, ScienceDirect and Google Scholar search engine since the year 2015–2019. A total of 28 research articles were selected for the review after screening and assessment. The various genomic, transcriptomic, proteomic, metabolomic and miscellaneous markers were analyzed and their characteristics and clinical application in OPMD patients were discussed. miR-21, miR-31, miR-84, H3F3A mRNA + IL-8P, matrix metalloproteinase-9, chemerin, tumor necrosis factor-alpha, cytokeratin-10, ornithine + O-hydroxybenzoate + R5F, 8-hydroxy-2-deoxyguanosine, malondialdehyde, Vitamin E and Vitamin C are identified as potential markers for OPMD patients. Scientifically validated, reliable and economical clinical biomarkers in OPMDs would serve as evidence-based treatment from patient point of view. Further longitudinal studies are needed to verify the accuracy and validate the applicability of these diagnostic/prognostic markers. Saliva has been reported as a valuable noninvasive valuable tool in biomarker identification. Recent advancements in salivary biomarker identification techniques lead to various potential biomarkers with precise outcome. The utilization of these biomarkers for the clinical application in OPMDs depends on the feasibility and personal choice of the clinician.

A systematic review of proteomic biomarkers in oral squamous cell cancer

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.

Usefulness of protein-based salivary markers in the diagnosis of oral potentially malignant disorders: A systematic review and meta-analysis

By using a meta-analytical approach, this study aimed to analyse the diagnostic capacity of protein-based biomarkers in saliva for the differential diagnosis of oral potentially malignant disorders (OPMDs) and oral squamous cell carcinoma (OSCC) from healthy individuals as control group (HCG).Articles on protein-based biomarkers in saliva, which provided quantitative expression in individuals with clinical and histopathological diagnosis of OPMD or oral leukoplakia (OL) were considered eligible. Searches were conducted in eight electronic databases. The methodological quality was assessed using the Quality Assessment of Diagnostic Studies tool (QUADAS-2). Functional analysis was also performed. Meta-analyses were performed using the OpenMeta tool (Analyst).Meta-analysis was possible for 4 of the 11 biomarkers studied. Only the carcinoembryonic antigen (CEA) and the soluble fragment of cytokeratin 19 (CYFRA21) were significant for the OSCC/OPMD subgroup, both with a very low heterogeneity. CEA had an OE = 25.854 (CI95%: 13.215-38.492, p< 0.001, I2 = 0) and CYFRA21 had an OE = 9.317 (CI95%: 9.014-9.619, p< 0.001, I2 = 0). For the OPMD/HCG subgroup, only CYFRA21 was significant, with an OE = 3.679 (CI95%: 0.663-6.696, p= 0.017) although with high heterogeneity (I2 = 91.24).The CEA and CYFRA21 markers proved very useful when differentiating OSCC from OPMD. The CYFRA21 was the only protein that was capable of distinguishing between OPMD and healthy controls.

Inhomogeneity of stiffness and density of the extracellular matrix within the leukoplakia of human oral mucosa as potential physicochemical factors leading to carcinogenesis

Oral leukoplakia is a clinical term relating to various morphological lesions, including squamous cell hyperplasia, dysplasia and carcinoma. Leukoplakia morphologically manifested as hyperplasia with epithelial dysplasia is clinically treated as precancerous condition. Nevertheless, there is a lack of good markers indicating the transformation of premalignancies towards cancer. A better understanding of the mechanical environment within the tissues where tumors grow might be beneficial for the development of prevention, diagnostic, and treatment methods in cancer management. Atomic force microscopy (AFM) and immunohistology techniques were used to assess changes in the stiffness and morphology of oral mucosa and leukoplakia samples at different stages of their progression towards cancer. The Young's moduli of the tested leukoplakia samples were significantly higher than those of the surrounding mucus. Robust inhomogeneity of stiffness within leukoplakia samples, reflecting an increase in regeneration and collagen accumulation (increasing density) in the extracellular matrix (ECM), was observed. Within the histologically confirmed cancer samples, Young's moduli were significantly lower than those within the precancerous ones. Inhomogeneous stiffness within leukoplakia might act as "a mechanoagonist" that promotes oncogenesis. In contrast, cancer growth might require the reorganization of tissue structure to create a microenvironment with lower and homogenous stiffness. The immunohistology data collected here indicates that changes in tissue stiffness are achieved by increasing cell/ECM density. The recognition of new markers of premalignancy will aid in the development of new therapies and will expand the diagnostic methods.

Identification of potential glycoprotein biomarkers in oral squamous cell carcinoma using sweet strategies

The prevalence of oral squamous cell carcinoma (OSCC) is high in South and Southeast Asia regions. Most OSCC patients are detected at advanced stages low 5-year survival rates. Aberrant expression of glycosylated proteins was found to be associated with malignant transformation and cancer progression. Hence, identification of cancer-associated glycoproteins could be used as potential biomarkers that are beneficial for diagnosis or clinical management of patients. This study aims to identify the differentially expressed glycoproteins using lectin-based glycoproteomics approaches. Serum samples of 40 patients with OSCC, 10 patients with oral potentially malignant disorder (OPMD), and 10 healthy individuals as control group were subjected to two-dimensional gel electrophoresis (2-DE) coupled with lectin Concanavalin A and Jacalin that specifically bind to N- and O-glycosylated proteins, respectively. Five differentially expressed N- and O-glycoproteins with various potential glycosylation sites were identified, namely N-glycosylated α1-antitrypsin (AAT), α2-HS-glycoprotein (AHSG), apolipoprotein A-I (APOA1), and haptoglobin (HP); as well as O-glycosylated AHSG and clusterin (CLU). Among them, AAT and APOA1 were further validated using enzyme-linked immunosorbent assay (ELISA) (n = 120). It was found that AAT and APOA1 are significantly upregulated in OSCC and these glycoproteins are independent risk factors of OSCC. The clinical utility of AAT and APOA1 as potential biomarkers of OSCC is needed for further evaluation.

Salivary biomarkers in oral squamous cell carcinoma

In disease diagnostics and health surveillance, the use of saliva has potential because its collection is convenient and noninvasive. Over the past two decades, the development of salivary utilization for the early detection of cancer, especially oral cavity and oropharynx cancer has gained the interest of the researcher and clinician. Until recently, the oral cavity and oropharynx cancers are still having a five-year survival rate of 62%, one of the lowest in all major human cancers. More than 90% of oral cancers are oral squamous cell carcinoma (OSCC). Despite the ease of accessing the oral cavity in clinical examination, most OSCC lesions are not diagnosed in the early stage, which is suggested to be the main cause of the low survival rate. Many studies have been performed and reported more than 100 potential saliva biomarkers for OSCC. However, there are still obstacles in figuring out the reliable OSCC salivary biomarkers and the clinical application of the early diagnosis protocol. The current review article discusses the emerging issues and is hoped to raise awareness of this topic in both researchers and clinicians. We also suggested the potential salivary biomarkers that are reliable, specific, and sensitive for the early detection of OSCC.

Biochemical analysis of oral fluids for disease detection

The field of diagnostics using invasive blood testing represents the majority of diagnostic tests used as part of routine health monitoring. The relatively recent introduction of salivary diagnostics has lead to a major paradigm shift in diagnostic analyses. Additionally, in this era of big data, oral fluid testing has shown promising outcomes in a number of fields, particularly the areas of genomics, microbiomics, proteomics, metabolomics, and transcriptomics. Despite the analytical challenges involved in the interpretation of large datasets generated from biochemical studies involving bodily fluids, including saliva, many studies have identified novel oral biomarkers for diagnosing oral and systemic diseases. In this regard, oral biofluids, including saliva, gingival crevicular fluid (GCF), peri-implant crevicular fluid (PICF), dentinal tubular fluid (DTF), are now attracting increasing attention due to their important attributes, such as noninvasive sampling, easy handling, low cost, and more accurate diagnosis of oral diseases. Recently, the utilization of salivary diagnostics to evaluate systemic diseases and monitor general health has increased in popularity among clinicians. Saliva contains a wide range of protein, DNA and RNA biomarkers, which assist in the diagnosis of multiple diseases and conditions, including cancer, cardiovascular diseases (CVD), auto-immune and degenerative diseases, respiratory infections, oral diseases, and microbial (viral, bacterial and fungal) diseases. Moreover, due to its noninvasive nature and ease-of-adoption by children, it is now being used in mass screening programs, oral health-related studies and clinical trials in support of the development of therapeutic agents. The recent advent of highly sensitive technologies, such as next-generation sequencing, mass spectrometry, highly sensitives ELISAs, and homogeneous immunoassays, suggests that even small quantities of salivary biomarkers are able to be assayed accurately, providing opportunities for the development of many future diagnostic applications (including emerging technologies, such as point-of-care and rapid molecular technologies). The present article explores the omics and biochemical compositions of various oral biofluids with important value in diagnostics and monitoring.

Unravelling the Potential of Salivary Volatile Metabolites in Oral Diseases. A Review

Fostered by the advances in the instrumental and analytical fields, in recent years the analysis of volatile organic compounds (VOCs) has emerged as a new frontier in medical diagnostics. VOCs analysis is a non-invasive, rapid and inexpensive strategy with promising potential in clinical diagnostic procedures. Since cellular metabolism is altered by diseases, the resulting metabolic effects on VOCs may serve as biomarkers for any given pathophysiologic condition. Human VOCs are released from biomatrices such as saliva, urine, skin emanations and exhaled breath and are derived from many metabolic pathways. In this review, the potential of VOCs present in saliva will be explored as a monitoring tool for several oral diseases, including gingivitis and periodontal disease, dental caries, and oral cancer. Moreover, the analytical state-of-the-art for salivary volatomics, e.g., the most common extraction techniques along with the current challenges and future perspectives will be addressed unequivocally.

Systems Biology Approaches and Precision Oral Health: A Circadian Clock Perspective

A vast majority of the pathophysiological and metabolic processes in humans are temporally controlled by a master circadian clock located centrally in the hypothalamic suprachiasmatic nucleus of the brain, as well as by specialized peripheral oscillators located in other body tissues. This circadian clock system generates a rhythmical diurnal transcriptional-translational cycle in clock genes and protein expression and activities regulating numerous downstream target genes. Clock genes as key regulators of physiological function and dysfunction of the circadian clock have been linked to various diseases and multiple morbidities. Emerging omics technologies permits largescale multi-dimensional investigations of the molecular landscape of a given disease and the comprehensive characterization of its underlying cellular components (e.g., proteins, genes, lipids, metabolites), their mechanism of actions, functional networks and regulatory systems. Ultimately, they can be used to better understand disease and interpatient heterogeneity, individual profile, identify personalized targetable key molecules and pathways, discover novel biomarkers and genetic alterations, which collectively can allow for a better patient stratification into clinically relevant subgroups to improve disease prediction and prevention, early diagnostic, clinical outcomes, therapeutic benefits, patient's quality of life and survival. The use of “omics” technologies has allowed for recent breakthroughs in several scientific domains, including in the field of circadian clock biology. Although studies have explored the role of clock genes using circadiOmics (which integrates circadian omics, such as genomics, transcriptomics, proteomics and metabolomics) in human disease, no such studies have investigated the implications of circadian disruption in oral, head and neck pathologies using multi-omics approaches and linking the omics data to patient-specific circadian profiles. There is a burgeoning body of evidence that circadian clock controls the development and homeostasis of oral and maxillofacial structures, such as salivary glands, teeth and oral epithelium. Hence, in the current era of precision medicine and dentistry and patient-centered health care, it is becoming evident that a multi-omics approach is needed to improve our understanding of the role of circadian clock-controlled key players in the regulation of head and neck pathologies. This review discusses current knowledge on the role of the circadian clock and the contribution of omics-based approaches toward a novel precision health era for diagnosing and treating head and neck pathologies, with an emphasis on oral, head and neck cancer and Sjögren's syndrome.

Protein-Based Salivary Profiles as Novel Biomarkers for Oral Diseases

The Global Burden of Oral Diseases affects 3.5 billion people worldwide, representing the number of people affected by the burden of untreated dental caries, severe periodontal disease, and edentulism. Thus, much more efforts in terms of diagnostics and treatments must be provided in the fight of these outcomes. In this sense, recently, the study of saliva as biological matrix has been identified as a new landmark initiative in the search of novel and useful biomarkers to prevent and diagnose these conditions. Specifically, saliva is a rich reservoir of different proteins and peptides and accessible due to recent advances in molecular biology and specially in targeted and unbiased proteomics technologies. Nonetheless, emerging barriers are an obstacle to the study of the salivary proteome in an effective way. This review aims at giving an overall perspective of salivary biomarkers identified in several oral diseases by means of molecular biology approaches.

Differentially expressed proteins in positive versus negative HNSCC lymph nodes

Background

Lymph node metastasis is one of the most important prognostic factors in head and neck squamous cell carcinomas (HNSCCs) and critical for delineating their treatment. However, clinical and histological criteria for the diagnosis of nodal status remain limited. In the present study, we aimed to characterize the proteomic profile of lymph node metastasis from HNSCC patients.

Methods

In the present study, we used one- and two-dimensional electrophoresis and mass spectrometry analysis to characterize the proteomic profile of lymph node metastasis from HNSCC.

Results

Comparison of metastatic and non-metastatic lymph nodes showed 52 differentially expressed proteins associated with neoplastic development and progression. The results reinforced the idea that tumors from different anatomical subsites have dissimilar behaviors, which may be influenced by micro-environmental factor including the lymphatic network. The expression pattern of heat shock proteins and glycolytic enzymes also suggested an effect of the lymph node environment in controlling tumor growth or in metabolic reprogramming of the metastatic cell. Our study, for the first time, provided direct evidence of annexin A1 overexpression in lymph node metastasis of head and neck cancer, adding information that may be useful for diagnosing aggressive disease.

Conclusions

In brief, this study contributed to our understanding of the metastatic phenotype of HNSCC and provided potential targets for diagnostic in this group of carcinomas.

Electronic supplementary material

The online version of this article (10.1186/s12920-018-0382-6) contains supplementary material, which is available to authorized users.

Standardization of a protocol for shotgun proteomic analysis of saliva

INTRODUCTION

Saliva contains numerous proteins and peptides, each of them carries a number of biological functions that are very important in maintaining the oral cavity health and also yields information about both local and systemic diseases. Currently, proteomic analysis is the basis for large-scale identification of these proteins and discovery of new biomarkers for distinct diseases.

OBJECTIVE

This study compared methodologies to extract salivary proteins for proteomic analysis.

MATERIAL AND METHODS

Saliva samples were collected from 10 healthy volunteers. In the first test, the necessity for using an albumin and IgG depletion column was evaluated, employing pooled samples from the 10 volunteers. In the second test, the analysis of the pooled samples was compared with individual analysis of one sample. Salivary proteins were extracted and processed for analysis by LC-ESI-MS/MS.

RESULTS

In the first test, we identified only 35 proteins using the albumin and IgG depletion column, while we identified 248 proteins without using the column. In the second test, the pooled sample identified 212 proteins, such as carbonic anhydrase 6, cystatin isoforms, histatins 1 and 3, lysozyme C, mucin 7, protein S100A8 and S100A9, and statherin, while individual analysis identified 239 proteins, among which are carbonic anhydrase 6, cystatin isoforms, histatin 1 and 3, lactotransferrin, lyzozyme C, mucin 7, protein S100A8 and S100A9, serotransferrin, and statherin.

CONCLUSIONS

The standardization of protocol for salivary proteomic analysis was satisfactory, since the identification detected typical salivary proteins, among others. The results indicate that using the column for depletion of albumin and IgG is not necessary and that performing individual analysis of saliva samples is possible.

Salivary biomarkers and proteomics: future diagnostic and clinical utilities

Saliva testing is a non-invasive and inexpensive test that can serve as a source of information useful for diagnosis of disease. As we enter the era of genomic technologies and -omic research, collection of saliva has increased. Recent proteomic platforms have analysed the human salivary proteome and characterised about 3000 differentially expressed proteins and peptides: in saliva, more than 90% of proteins in weight are derived from the secretion of three couples of "major" glands; all the other components are derived from minor glands, gingival crevicular fluid, mucosal exudates and oral microflora. The most common aim of proteomic analysis is to discriminate between physiological and pathological conditions. A proteomic protocol to analyze the whole saliva proteome is not currently available. It is possible distinguish two type of proteomic platforms: top-down proteomics investigates intact naturally-occurring structure of a protein under examination; bottom-up proteomics analyses peptide fragments after pre-digestion (typically with trypsin). Because of this heterogeneity, many different biomarkers may be proposed for the same pathology. The salivary proteome has been characterised in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease Sjögren's syndrome and other autoimmune disorders such as SAPHO, schizophrenia and bipolar disorder, and genetic diseases like Down's Syndrome and Wilson disease. The results of research reported herein suggest that in the near future human saliva will be a relevant diagnostic fluid for clinical diagnosis and prognosis.

Salivary biomarkers for oral cancer and pre-cancer screening: a review

OBJECTIVE

The objective of the study was to conduct a systematic review of the literature assessing potential salivary biomarkers of oral cancer and pre-cancer and discuss emerging issues and challenges in relation to oral cancer and pre-cancer diagnostics.

MATERIALS AND METHODS

Search for articles involved the Medline, PubMed, and EMBASE. Specific terms were used from January 1995 to March 2017 by three experts.

RESULTS

This search collected 270 articles, of which 105 articles such as reviews, case reports, news, letter to editor, etc. in first round and 117 articles such as publications in other languages than English, non-human studies, etc. were excluded. The remaining 48 articles considered analyzing whole saliva as well as specific gland saliva. Thirty-one studies considered oral stimuli such as eating, drinking, and oral hygiene practices for varied periods of time prior to sample collection. The time of collection of saliva was morning in most studies, but the exact time of collection was not mentioned. Three studies showed to have evaluated the whole saliva without centrifugation. Two-dimensional gel electrophoresis and tandem mass spectrometry were the most commonly used methods. Most of the potential salivary biomarkers of oral cancer are salivary proteins.

CONCLUSION

Combination approach of salivary biomarkers could be used as screening tool to improve early detection and diagnostic precision of oral pre-cancer and cancer.

CLINICAL RELEVANCE

The current findings are of importance for clinicians and researchers to mitigate the challenges in salivary-based diagnosis of oral cancer and to evaluate reliable, specific, and sensitive salivary biomarkers for oral pre-cancer and cancer diagnosis.

Salivary proteomics of healthy dogs: An in depth catalog

Objective

To provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups.

Methods

36 healthy dogs without evidence of periodontal disease representing four breed phylogeny groups, based upon single nucleotide polymorphism haplotypes (ancient, herding/sighthound, and two miscellaneous groups). Saliva collected from dogs was pooled by phylogeny group and analyzed using nanoscale liquid chromatography-tandem mass spectrometry. Resulting tandem mass spectra were compared to databases for identification of endogenous peptides and inferred proteins.

Results

2,491 proteins and endogenous peptides were found in the saliva of healthy dogs with no periodontal disease. All dog phylogeny groups’ saliva was rich in proteins and peptides with antimicrobial functions. The ancient breeds group was distinct in that it contained unique proteins and was missing many proteins and peptides present in the other groups.

Conclusions and clinical relevance

Using a sophisticated nanoscale liquid chromatography-tandem mass spectrometry, we were able to identify 10-fold more salivary proteins than previously reported in dogs. Seven of the top 10 most abundant proteins or peptides serve immune functions and many more with various antimicrobial mechanisms were found. This is the most comprehensive analysis of healthy canine saliva to date, and will provide the groundwork for future studies analyzing salivary proteins and endogenous peptides in disease states.

Peroxiredoxin-2 and zinc-alpha-2-glycoprotein as potentially combined novel salivary biomarkers for early detection of oral squamous cell carcinoma using proteomic approaches

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.

Serum, plasma and saliva biomarkers for head and neck cancer

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.

Construction and characterization of the Korean whole saliva proteome to determine ethnic differences in human saliva proteome

As the first step to discover protein disease biomarkers from saliva, global analyses of the saliva proteome have been carried out since the early 2000s, and more than 3,000 proteins have been identified in human saliva. Recently, ethnic differences in the human plasma proteome have been reported, but such corresponding studies on human saliva in this aspect have not been previously reported. Thus, here, in order to determine ethnic differences in the human saliva proteome, a Korean whole saliva (WS) proteome catalogue indexing 480 proteins was built and characterized through nLC-Q-IMS-TOF analyses of WS samples collected from eleven healthy South Korean male adult volunteers for the first time. Identification of 226 distinct Korean WS proteins, not observed in the integrated human saliva protein dataset, and significant gene ontology distribution differences in the Korean WS proteome compared to the integrated human saliva proteome strongly support ethnic differences in the human saliva proteome. Additionally, the potential value of ethnicity-specific human saliva proteins as biomarkers for diseases highly prevalent in that ethnic group was confirmed by finding 35 distinct Korean WS proteins likely to be associated with the top 10 deadliest diseases in South Korea. Finally, the present Korean WS protein list can serve as the first level reference for future proteomic studies including disease biomarker studies on Korean saliva.

Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia

Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.