Proteomic Studies of Saliva: A Proposal for a Standardized Handling of Clinical Samples

The Salivary Transcriptome: A Window into Local and Systemic Gene Expression Patterns

Saliva, a readily available and noninvasive biofluid, has emerged as a promising source for gene expression studies, offering a window into both local and systemic gene expression patterns. The salivary transcriptome and miRNome hold valuable information about the physiological and pathological processes occurring in the oral cavity and throughout the body.This chapter delves into the potential of saliva as a noninvasive sampling method, exploring its utility in gene expression profiling for various applications. It provides an overview of the components contributing to the salivary transcriptome and discusses the challenges associated with salivary RNA analysis. We highlight the applications of salivary gene expression studies in biomarker discovery for oral and systemic diseases.While discussing various saliva collection techniques, here we focus on the procedure for RNA extraction, including microRNA (miRNA) from the OMNIgene™ SALIVA DNA and RNA device, OMR-610 (DNA Genotek Inc., Ottawa, Ontario, Canada). Herein, we provide the detailed methodologies for RNA extraction for salivary transcriptomics and the miRNome, thus providing a resource for researchers interested in leveraging the diagnostic and prognostic potential of saliva for personalized medicine and precision health initiatives.

Shaping the future of oral cancer diagnosis: advances in salivary proteomics

INTRODUCTION

Saliva has gained increasing attention in the quest for disease biomarkers. Because it is a biological fluid that can be collected is an easy, painless, and safe way, it has been increasingly studied for the identification of oral cancer biomarkers. This is particularly important because oral cancer is often diagnosed at late stages with a poor prognosis.

AREAS COVERED

The review addresses the evolution of the experimental approaches used in salivary proteomics studies of oral cancer over the years and outlines advantages and pitfalls related to each one. In addition, examines the current landscape of oral cancer biomarker discovery and translation focusing on salivary proteomic studies. This discussion is based on an extensive literature search (PubMed, Scopus and Google Scholar).

EXPERT OPINION

The introduction of mass spectrometry has revolutionized the study of salivary proteomics. In the future, the focus will be on refining existing methods and introducing powerful experimental techniques such as mass spectrometry with selected reaction monitoring, which, despite their effectiveness, are still underutilized due to their high cost. In addition, conducting studies with larger cohorts and establishing standardized protocols for salivary proteomics are key challenges that need to be addressed in the coming years.

Effects of the Saliva of Patients Undergoing Orthodontic Treatment with Invisalign and Brackets on Human Gingival Fibroblasts and Oral Epithelial Cells

The transient worsening of oral health sometimes accompanies orthodontic treatment (OT), and the extent of this effect might depend on whether the patients are treated with traditional brackets or clear aligners. Saliva is an important tool for monitoring oral health and influences the functional properties of various oral cells. This study aimed to compare the effects of saliva from patients undergoing OT with Invisalign aligners and brackets on human gingival fibroblasts and oral epithelial cells in vitro. Unstimulated saliva was collected from 15 patients treated with Invisalign and 16 patients treated with brackets before and 3 and 6 months after therapy began. The saliva was used to stimulate primary human gingival fibroblasts and the oral epithelial Ca9-22 cell line, and the resulting cell response was investigated. Saliva did not exhibit any toxic effect on investigated cells, as shown by the proliferation/viability assay with the MTT method. In human gingival fibroblasts, saliva increased gene expression of various proinflammatory mediators, such as interleukin (IL)-6, IL-8, and monocyte chemoattractant protein-1, assessed by qPCR. In epithelial cells, saliva increased the production of IL-8 measured by ELISA and decreased gene expression of various proteins involved in the barrier function. During the therapy, the saliva-induced production of IL-8 tended to be decreased, and the saliva-induced decrease in the expression of barrier protein was partially improved. No difference between aligners and brackets was observed in either cell type. Saliva affects the functional properties of oral cells, but this effect is not influenced by the type of OT.

Saliva biomarkers in oral disease

Saliva is a versatile biofluid that contains a wide variety of biomarkers reflecting both physiologic and pathophysiologic states. Saliva collection is noninvasive and highly applicable for tests requiring serial sampling. Furthermore, advances in test accuracy, sensitivity and precision for saliva has improved diagnostic performance as well as the identification of novel markers especially in oral disease processes. These include dental caries, periodontitis, oral squamous cell carcinoma (OSCC) and Sjögren's syndrome (SS). Numerous growth factors, enzymes, interleukins and cytokines have been identified and are the subject of much research investigation. This review highlights current procedures for successful determination of saliva biomarkers including preanalytical factors associated with sampling, storage and pretreatment as well as subsequent analysis. Moreover, it provides an overview of the diagnostic applications of these salivary biomarkers in common oral diseases.

The Influence of (Poly)phenol Intake in Saliva Proteome: Short- and Medium-Term Effects of Apple

The relationship between salivary proteome and dietary habits was studied in previous works, where a relationship between salivary proteins like cystatins and polyphenol/tannin levels in diet was observed. However, it remains to be elucidated if this association results from an effect of polyphenol-rich food ingestion on saliva composition. The aim of this work was to test the effects of apple intake on the saliva proteome, both in the short and medium term (after 4 days of continuous intake). By incubating saliva samples with apple phenolic-rich extract, protein bands containing α-amylase, S-type cystatins, and proline-rich proteins (PRPs) appeared in the fraction that precipitated, showing the potential of these (poly)phenols to precipitate salivary proteins. Among these, it was salivary cystatins that presented changes in their levels both in the saliva samples collected immediately after apple intake and in the ones collected after 4 days of intake of an extra amount of apple. These results support the thought that intake is reflected in the salivary proteome. The effect of a polyphenol-rich food, like the apple, on salivary cystatin levels is in line with results observed in animal models and, due to the involvement of these proteins in oral food perception, it would be interesting to explore in future studies the effect of these changes on sensory perception and acceptance of polyphenol-rich food.

Salivary Huntingtin protein is uniquely associated with clinical features of Huntington's disease

Measuring Huntingtin (HTT) protein in peripheral cells represents an essential step in biomarker discovery for Huntington's Disease (HD), however to date, investigations into the salivary expression of HTT has been lacking. In the current study, we quantified total HTT (tHTT) and mutant HTT (mHTT) protein in matched blood and saliva samples using single molecule counting (SMC) immunoassays: 2B7-D7F7 (tHTT) and 2B7-MW1 (mHTT). Matched samples, and clinical data, were collected from 95 subjects: n = 19 manifest HD, n = 34 premanifest HD (PM), and n = 42 normal controls (NC). Total HTT and mHTT levels were not correlated in blood and saliva. Plasma tHTT was significantly associated with age, and participant sex; whereas salivary mHTT was significantly correlated with age, CAG repeat length and CAP score. Plasma and salivary tHTT did not differ across cohorts. Salivary and plasma mHTT were significantly increased in PM compared to NC; salivary mHTT was also significantly increased in HD compared to NC. Only salivary tHTT and mHTT were significantly correlated with clinical measures. Salivary HTT is uniquely associated with clinical measures of HD and offers significant promise as a relevant, non-invasive HD biomarker. Its use could be immediately implemented into both translational and clinical research applications.

Biofluids manipulation methods for liquid biopsy in minimally-invasive assays

The Liquid Biopsy (LB) is an opportunity for non-invasive diagnosis and prognosis of various diseases. To date, it isn't possible to consider that tissue biopsy can represent a pathology entirety. Then, body fluids are rich in a large number and variety of biomarkers and they can provide information about several diseases.•

Recently, other biological fluids, easy to be collected are rising for their significant content of biomarkers and for the possibility to collect and manipulate them without the intervention of medical staff.

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The management of biological fluids requires suitable storage methods. Temperature, storage time and physical stresses due to sample handling can lead to chemical and physical changes that may induce sample degradation and incorrect analysis.

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The reliability of a diagnostic or screening test depends on its sensitivity and specificity. As the liquid biopsy is a 'snapshot' of a pathophysiological condition, it is crucial that its components do not degrade due to the improper handling of the body fluid.

In this review, some handling methods of Saliva, Urine, Stool, Seminal Fluid, Tears and Sweat samples will be described, as well as protocols to facilitate the analysis of metabolites, nucleic acids, proteins and Extracellular Vesicles (EVs) from those unusual body fluids.

Stabilization of Salivary Biomarkers

The use of saliva as a diagnostic biofluid has been increasing in recent years, thanks to the identification and validation of new biomarkers and improvements in test accuracy, sensitivity, and precision that enable the development of new noninvasive and cost-effective devices. However, the lack of standardized methods for sample collection, treatment, and storage contribute to the overall variability and lack of reproducibility across analytical evaluations. Furthermore, the instability of salivary biomarkers after sample collection hinders their translation into commercially available technologies for noninvasive monitoring of saliva in home settings. The present review aims to highlight the status of research on the challenges of collecting and using diagnostic salivary samples, emphasizing the methodologies used to preserve relevant proteins, hormones, genomic, and transcriptomic biomarkers during sample handling and analysis.

Spectroscopic molecular-fingerprint profiling of saliva

Saliva analysis has been gaining interest as a potential non-invasive source of disease indicative biomarkers due to being a complex biofluid correlating with blood-based constituents on a molecular level. For saliva to cement its usage for analytical applications, it is paramount to gain underpinning molecular knowledge and establish a 'baseline' of the salivary composition in healthy individuals as well as characterize how these factors are impacting its performance as potential analytical biofluid. Here, we have systematically studied the molecular spectral fingerprint of saliva, including the changes associated with gender, age, and time. Via hybrid artificial neural network algorithms and Raman spectroscopy, we have developed a non-destructive molecular profiling approach enabling the assessment of salivary spectral changes yielding the determination of gender and age of the biofluid source. Our classification algorithm successfully identified the gender and age from saliva with high classification accuracy. Discernible spectral molecular 'barcodes' were subsequently constructed for each class and found to primarily stem from amino acid, protein, and lipid changes in saliva. This unique combination of Raman spectroscopy and advanced machine learning techniques lays the platform for a variety of applications in forensics and biosensing.

Childhood Allergy Disease, Early Diagnosis, and the Potential of Salivary Protein Biomarkers

Allergic disease has risen to epidemic proportions since the last decade and is among the most common noncommunicable, chronic diseases in children and adolescents worldwide. Allergic disease usually occurs in early life; thus, early biomarkers of allergic susceptibility are required for preventive measures to high-risk infants which enable early interventions to decrease allergic severity. However, to date, there is no reliable general or specific allergy phenotype detection method that is easy and noninvasive for children. Most reported allergic phenotype detection methods are invasive, such as the skin prick test (SPT), oral food challenge (OFC), and blood test, and many involve not readily accessible biological samples, such as cord blood (CB), maternal blood, or newborn vernix. Saliva is a biological sample that has great potential as a biomarker measurement as it consists of an abundance of biomarkers, such as genetic material and proteins. It is easily accessible, noninvasive, collected via a painless procedure, and an easy bedside screening for real-time measurement of the ongoing human physiological system. All these advantages emphasise saliva as a very promising diagnostic candidate for the detection and monitoring of disease biomarkers, especially in children. Furthermore, protein biomarkers have the advantages as modifiable influencing factors rather than genetic and epigenetic factors that are mostly nonmodifiable factors for allergic disease susceptibility in childhood. Saliva has great potential to replace serum as a biological fluid biomarker in diagnosing clinical allergy. However, to date, saliva is not considered as an established medically acceptable biomarker. This review considers whether the saliva could be suitable biological samples for early detection of allergic risk. Such tools may be used as justification for targeted interventions in early childhood for disease prevention and assisting in reducing morbidity and mortality caused by childhood allergy.

Differentially Expressed Salivary Proteins in Dental Caries Patients

Dental caries is a multifactorial disease mainly caused by cariogenic bacteria commonly found in the oral cavity. Dental caries may cause demineralization of the tooth, cavitation, hypersensitivity, pulp inflammation, and even tooth loss if left untreated. Saliva secreted in the oral cavity can serve as a tool for identification of biomarkers for early detection of diseases. In the present study, differential expression of salivary proteins from 33 dental caries patients was compared with 10 control subjects. The unstimulated saliva was analyzed by 12% SDS-PAGE and two-dimensional gel electrophoresis. Gelatin and casein zymography was performed to check for protease activity. Also, salivary IgAs from both groups were compared by sandwich ELISA technique. Dental caries patient's saliva showed decreased caseinolytic and increased gelatinolytic activity probably due to metalloproteases and cathepsins. Mean salivary levels of sIgA were also significantly higher (p < 0.018) in dental caries saliva samples. The 2D electrophoresis profile of both the groups showed regions on gel with visually detectable alterations in protein expression. The present study is among the few initial studies in the locality for identification of protein differences in saliva from dental caries patients and has demonstrated a good potential to identify alterations. However, a large population-based analysis is required to validate these findings to be translated as a tool for indicative applications.

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.

Prolactin-Induced Protein is a novel biomarker for Keratoconus

PURPOSE

The purpose of the study was to investigate the role of Prolactin-Induced Protein (PIP) as a predictive biomarker for Keratoconus (KC).

PARTICIPANTS

This study included one hundred and forty-seven patients with KC (105 male, 42 female), and sixty healthy controls (27 male, 33 female).

METHODS

Tears, plasma and saliva samples were collected from all participants. In both KC and healthy groups all collected samples were divided into four age subgroups (15-24y), (25-34y), (35-44y) and (45y and up). Samples were analyzed using western blot (WB) and enzyme-linked immunosorbent assay (ELISA). Areas under the receiver operating characteristic curves (AUROCs) were used to evaluate diagnostic accuracy for distinguishing between KC and healthy eyes.

MAIN OUTCOME MEASURES

Difference in PIP protein levels between patients with KC and healthy controls.

RESULTS

Results showed significant downregulation of PIP expression in all three biological fluids on KC patients when compared to healthy controls, independent of age, sex and severity. Since PIP is a hormonal-regulated protein, we also investigated the expression of major sex hormones. We detected significant upregulation in salivary and plasma Dehydroepiandrosterone sulfate (DHEA-S) levels and significant downregulation of estrone and estriol levels, in KC patients compared to healthy controls, independent of sex, age, and KC severity stage. ROC was used to determine the overall predictive accuracy of this protein in KC. Data showed an area under the curve (AUC) for PIP in tears of 0.937 (95%CI: 0.902-0.971), in plasma of 0.928 (95%CI: 0.890-0.968) and in saliva of 0.929 (95%CI: 0.890-0.968).

CONCLUSIONS

Conclusively, our results show that PIP levels are reduced in all three human biological fluids tested, and may independently or in combination with current imaging techniques aid in screening and diagnosis of KC. Our data revealed that PIP levels can potentially differentiate between disease and healthy cases, and PIP levels are stable in relation to KC severity, sex and age. Moreover, alterations in sex hormone levels in correlation with reduced PIP levels in KC provide an intriguing insight in the underlying KC pathophysiology and highlights the role of PIP as a KC biomarker.

Effect of storage on long-term stability of salivary α-amylase, lysozyme, lactate dehydrogenase, calcium and phosphorus in dogs

Research or diagnostic conditions may require the storage of salivary samples for long periods before analysis is processed. The aim of this study was to evaluate the stability of canine salivary α-amylase, lysozyme, lactate dehydrogenase (LDH), and total calcium and phosphorus after storage for 1, 3 and 6 months at -20°C. Available saliva samples were 75 immediately after collection (T0) and 46 at 1 month (T1), 31 at 3 months (T3) and 18 at 6 months (T6) of storage, according to the number of aliquots collected from each saliva sample. Compared to T0, LDH declined by 92.3% after 1 month of storage (P<0.001), whereas lysozyme concentration significantly decreased as storage time increased (-29.3%, -43.4% and -59.1% at T1, T3, and T6 respectively, P<0.001). Amylase maintained basically the same concentration for the entire experimental period, whereas total calcium and phosphorus concentration decreased over time (calcium, P<0.001). Assessing the long-term stability of canine salivary analytes stored at -20°C may have important implications in diagnosis and research.

The effects of collection and storage conditions in the field on salivary testosterone, cortisol, and sIgA values

AIM

To determine if field-typical storage and collection conditions are related to salivary testosterone (T), cortisol (cort) and secretory immunoglobulin A (sIgA) as measured using commercially available kits.

SUBJECTS AND METHODS

This study assessed whether storage time (∼6 months to 1.5 years) at -35 °C impacted levels of the measured biomarkers (n = 10,247 samples). For a sub-set of T samples (n = 2954), we also evaluated the impact of collection conditions, such as time spent at room temperature in participants' homes (0-39 hours) and time spent in coolers (0.3-10 hours) in transit.

RESULTS

T was unrelated to storage and collection variables and there was no evidence of reduced sample fidelity at longer storage times. Cort samples stored at -35 °C for longer had significantly lower values, but the effect was small (β = -0.003 nmol/L/day, SE <0.001, p = 0.005). sIgA trended higher with longer storage at -35 °C (β = 0.84 µg/mL/day, SE = 0.45, p = 0.063). Collection and storage time variables did not improve the fit of any of the models except the one that evaluated cortisol.

CONCLUSIONS

Salivary T was unaffected by extended storage at -35 °C and only a weak relationship was found between storage time and salivary cort or sIgA. Findings underscore the robustness of these biomarkers under field-typical freezer storage conditions.

Assessing a multiplex-targeted proteomics approach for the clinical diagnosis of periodontitis using saliva samples

AIM

The present study focused on the research of new biomarkers based on the liquid chromatography-multiple-reaction monitoring (MRM) proteomic profile in whole saliva of patients with periodontitis compared with periodontal healthy patients.

METHODS

A 30-min multiplexed liquid chromatography-MRM method was used for absolute quantification of 35 plasma biomarkers in saliva from control patients and patients with periodontitis.

RESULTS

Three proteins namely hemopexin, plasminogen and α-fibrinogen were shown to be clearly related to the presence of periodontitis compared with healthy patients. Apolipoprotein H was found to discriminate for the first time chronic and aggressive periodontitis.

CONCLUSION

Our results indicate that this innovative MRM method could be used to screen for periodontitis in clinical environment. Furthermore, apolipoprotein H was found to be a discriminant biomarker of aggressive periodontitis.

One decade of salivary proteomics: current approaches and outstanding challenges

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.

Comparative proteomic analysis of egg white proteins under various storage temperatures

Although the effect of storage temperature was suggested to be a more important factor than that of storage time on changes in unfertilized egg white proteins, no comprehensive analysis of the thermally induced egg white protein changes was carried out. This study presents a proteomic analysis of the changes in unfertilized egg white proteins after 15 days of storage at 4, 20, and 37 °C. Using two-dimensional electrophoresis followed by MALDI-TOF MS/MS, 32 protein spots representing 8 proteins were identified with significant differences in abundance when stored at different temperatures. An accelerated degradation of ovalbumin, possibly resulting from the reduction of antiprotease, was observed after the storage at higher temperature. In addition, an increase in the formation of ovalbumin complexes and a decrease in lipocalin family proteins were detected with increasing storage temperature, which may indicate a thermally promoted change in chicken eggs. The decrease of clusterin during the high-temperature storage was suggested to be an effective biomarker for egg quality evaluation. These findings will give insight into the effects of storage temperature on changes in unfertilized egg white proteins during storage and provide a better understanding of the thermally induced biochemical changes that may affect the egg deteriorative process.

Toward a standardized saliva proteome analysis methodology

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.