A universal pre-analytic solution for concurrent stabilization of salivary proteins, RNA and DNA at ambient temperature

Effect of Processing Methods of Human Saliva on the Proteomic Profile and Protein-Mediated Biological Processes

The use of saliva as a protein source prior to microbiological and biological assays requires previous processing. However, the effect of these processing methods on the proteomic profile of saliva has not been tested. Stimulated human saliva was collected from eight healthy volunteers. Non-processed saliva was compared with 0.22 μm filtered, 0.45 μm filtered, and pasteurized saliva, by liquid chromatography-mass spectrometry. Data are available via ProteomeXchange with identifier PXD039248. The effect of processed saliva on microbial adhesion was tested using bacterial and fungus species and in biological cell behavior using HaCaT immortalized human keratinocytes. Two hundred and seventy-eight proteins were identified in non-processed saliva, of which 54 proteins (≈19%) were exclusive. Saliva processing reduced identified proteins to 222 (≈80%) for the 0.22 μm group, 219 (≈79%) for the 0.45 μm group, and 201 (≈72%) for the pasteurized saliva, compared to non-processed saliva. The proteomic profile showed similar molecular functions and biological processes. The different saliva processing methods did not alter microbial adhesion (ANOVA, p > 0.05). Interestingly, pasteurized saliva reduced keratinocyte cell viability. Saliva processing methods tested reduced the proteomic profile diversity of saliva but maintained similar molecular functions and biological processes, not interfering with microbial adhesion and cell viability, except for pasteurization, which reduced cell viability.

Saliva profiling with differential scanning calorimetry: A feasibility study with ex vivo samples

Differential scanning calorimetry (DSC) has been used widely to study various biomarkers from blood, less is known about the protein profiles from saliva. The aim of the study was to investigate the use DSC in order to detect saliva thermal profiles and determine the most appropriate sampling procedure to collect and process saliva. Saliva was collected from 25 healthy young individuals and processed using different protocols based on centrifugation and filtering. The most effective protocol was centrifugation at 5000g for 10 min at 4°C followed by filtration through Millex 0.45 μm filter. Prepared samples were transferred to 3 mL calorimetric ampoules and then loaded into TAM48 calibrated to 30°C until analysis. DSC scans were recorded from 30°C to 90°C at a scan rate of 1°C/h with a pre-conditioning the samples to starting temperature for 1 h. The results show that the peak distribution of protein melting points was clearly bimodal, and the majority of peaks appeared between 40–50°C. Another set of peaks is visible between 65°C– 75°C. Additionally, the peak amplitude and area under the peak are less affected by the concentration of protein in the sample than by the individual differences between people. In conclusion, the study shows that with right preparation of the samples, there is a possibility to have thermograms of salivary proteins that show peaks in similar temperature regions between different healthy volunteers.

The transcript integrity index (TII) provides a standard measure of sperm RNA

Standardizing RNA quality is key to interpreting RNA-seq data as a compromised sample can mask the underlying biology. The challenge remains when evaluating RNA quality in samples with high RNA fragmentation. For example, programmed fragmentation and cytoplasmic expulsion, integral to sperm maturation, is a prime example of the complexities of interpreting RNA-seq data, given that fragmentation can be random and\or targeted. To meet this challenge, we developed an algorithm that accurately measures RNA quality in samples with high fragmentation, such as spermatozoa. The integrity of 1,000 previously identified abundant sperm transcripts were independently visualized and evaluated using the Transcript Integrity Index (TII) algorithm to identify intact transcripts. Full-length transcripts from visual and the TII algorithm were evaluated for testis preference in humans using the GTEx tissues database. Samples were then filtered by the Interquartile Range (IQR), identifying those in which the greatest number of transcripts failed to pass the visual or TII thresholds. Transcript lists were overlapped, forming the set of intact transcripts used as TII standards. Each sample was re-evaluated as a function of this TII set of intact transcripts, with poor quality samples identified as those failing in the largest number of transcripts. While ontologically enriched in roles related to spermatogenesis and/or fertilization, samples did not segregate based on birth outcome. The TII algorithm proved an effective means to identify samples of similar quality from sperm, a cell type enriched in biologically fragmented RNAs. The algorithm should facilitate other studies using samples compromised by high levels of RNA fragmentation, such as Formalin-Fixed Paraffin-Embedded samples. Requisite to assessing male health, TII provides a solution to the long-sought-after standard that identifies samples of similar quality.

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.

α1 adrenergic receptors in serum and saliva of patients with oral squamous cell carcinoma

BACKGROUND

Neurotransmitters released from the sympathetic nervous system attach to the adrenergic receptors on the surface of tumoral cells in response to stress, and alter the expression of genes programming cellular activity. This study aimed to assess the expression of α1 adrenergic receptors in the serum and saliva of patients with oral squamous cell carcinoma (OSCC) compared with healthy controls.

MATERIALS AND METHODS

In this case-control study, serum and stimulated and unstimulated saliva samples were collected from 26 OSCC patients and 26 healthy controls. ELISA kits were used for measurement of the serum and salivary levels of α1 adrenergic receptors.

RESULTS

The level of α1 adrenergic receptors was significantly higher in the stimulated and unstimulated saliva of OSCC patients than healthy controls (P = 0.000). However, their serum level was not significantly different between the two groups (P = 0.389). The serum level of α1 adrenergic receptors significantly increased by an increase in OSCC grade. No significant correlation was noted between the serum and salivary levels of α1 adrenergic receptors in OSCC patients. The salivary level of α1 adrenergic receptors was significantly higher in patients with tumors located in the gingiva, compared with other sites.

CONCLUSION

Significantly higher salivary level of α1 adrenergic receptors in OSCC patients compared with healthy controls, and no significant difference in their serum level between the two groups may indirectly indicate the over-expression of these receptors in OSCC cells, compared with normal oral mucosa. Further studies and particularly histological analyses are required to confirm this finding.

Technical Considerations and Protocol Optimization for Neonatal Salivary Biomarker Discovery and Analysis

Non-invasive techniques to monitor and diagnose neonates, particularly those born prematurely, are a long-sought out goal of Newborn Medicine. In recent years, technical advances, combined with increased assay sensitivity, have permitted the high-throughput analysis of multiple biomarkers simultaneously from a single sample source. Multiplexed transcriptomic and proteomic platforms, along with more comprehensive assays such as RNASeq, allow for interrogation of ongoing physiology and pathology in unprecedented ways. In the fragile neonatal population, saliva is an ideal biofluid to assess clinical status serially and offers many advantages over more invasively obtained blood samples. Importantly, saliva samples are amenable to analysis on emerging proteomic and transcriptomic platforms, even at quantitatively limited volumes. However, biomarker targets are often degraded in human saliva, and as a mixed source biofluid containing both human and microbial targets, saliva presents unique challenges for the investigator. Here, we provide insight into technical considerations and protocol optimizations developed in our laboratory to quantify and discover neonatal salivary biomarkers with improved reproducibility and reliability. We will detail insights learned from years of experimentation on neonatal saliva within our laboratory ranging from salivary collection techniques to processing to downstream analyses, highlighting the need for consistency in approach and a global understanding of both the potential benefits and limitations of neonatal salivary biomarker analyses. Importantly, we will highlight the need for robust and stringent research in this population to provide the field with standardized approaches and workflows to impact neonatal care successfully.

Telomerase in saliva: An assistant marker for oral squamous cell carcinoma

Introduction:

Telomerase is a ribonucleoprotein complex responsible for de novo telomere synthesis and addition of telomeric repeats to existing telomeres. Telomerase activity is generally found to be absent in normal tissues. Telomerase is known to be induced upon malignant transformation of human cells.

Method:

In the present study, we analyzed both telomere length and telomerase activity in saliva samples from oral carcinoma patients. The study was done to investigate the presence of telomerase activity in oral squamous cell carcinoma by TRAP assay.

Result:

Telomerase activity was detectable in 79 of 100 human OSCC and 51 of 100 premalignant cases and 8 of 100 normal patients.

Conclusion:

These results indicate that telomerase is activated frequently during the late stage of oral premalignancy and may play a crucial role in OSCC.

Role of Salivary Biomarkers in Oral Cancer Detection

Oral cancers are the sixth most frequent cancer with a high mortality rate. Oral squamous cell carcinoma accounts for more than 90% of all oral cancers. Standard methods used to detect oral cancers remain comprehensive clinical examination, expensive biochemical investigations, and invasive biopsy. The identification of biomarkers from biological fluids (blood, urine, saliva) has the potential of early diagnosis. The use of saliva for early cancer detection in the search for new clinical markers is a promising approach because of its noninvasive sampling and easy collection methods. Human whole-mouth saliva contains proteins, peptides, electrolytes, organic, and inorganic salts secreted by salivary glands and complimentary contributions from gingival crevicular fluids and mucosal transudates. This diagnostic modality in the field of molecular biology has led to the discovery and potential of salivary biomarkers for the detection of oral cancers. Biomarkers are the molecular signatures and indicators of normal biological, pathological process, and pharmacological response to treatment hence may provide useful information for detection, diagnosis, and prognosis of the disease. Saliva's direct contact with oral cancer lesions makes it more specific and potentially sensitive screening tool, whereas more than 100 salivary biomarkers (DNA, RNA, mRNA, protein markers) have already been identified, including cytokines (IL-8, IL-1b, TNF-α), defensin-1, P53, Cyfra 21-1, tissue polypeptide-specific antigen, dual specificity phosphatase, spermidine/spermineN1-acetyltransferase , profilin, cofilin-1, transferrin, and many more. However, further research is still required for the reliability and validation of salivary biomarkers for clinical applications. This chapter provides the latest up-to-date list of known and emerging potential salivary biomarkers for early diagnosis of oral premalignant and cancerous lesions and monitoring of disease activity.

A Review of Salivary Biomarker: A Tool for Early Oral Cancer Diagnosis

The oral squamous cell carcinoma (OSCC) is one of the most common epithelial malignancies with significant morbidity and mortality. Recent observations indicate that the clinical and histological appearance of oral mucosa may not truly depict the damage occurring at the genetic level. This phenotypic and genotypic disparity may account in part for the failure to establish effective screening and surveillance protocols, based on the traditional clinical and microscopic examination. The tumor markers are playing an increasingly important role in cancer detection and management. These laboratory-based tests are potentially useful in screening for early malignancy, aiding in cancer diagnosis, determining prognosis, surveillance following curative surgery for cancer, up-front predicting drug response or resistance, and monitoring therapy in advanced disease. 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 keywords. Abstracts and full-text articles were assessed. This article may help to identify the potential biomarkers for screening and the molecular pathology analysis in the high-risk patients with the OSCC.

Cancer Salivary Biomarkers for Tumours Distant to the Oral Cavity

The analysis of saliva as a diagnostic approach for systemic diseases was proposed just two decades ago, but recently great interest in the field has emerged because of its revolutionary potential as a liquid biopsy and its usefulness as a non-invasive sampling method. Multiple molecules isolated in saliva have been proposed as cancer biomarkers for diagnosis, prognosis, drug monitoring and pharmacogenetic studies. In this review, we focus on the current status of the salivary diagnostic biomarkers for different cancers distant to the oral cavity, noting their potential use in the clinic and their applicability in personalising cancer therapies.

Non-coding RNAs in saliva: emerging biomarkers for molecular diagnostics

Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have reported that saliva body fluid can be useful for discriminating several oral diseases, but also systemic diseases including cancer. Most of these studies revealed messenger RNA (mRNA) and proteomic biomarker signatures rather than specific non-coding RNA (ncRNA) profiles. NcRNAs are emerging as new regulators of diverse biological functions, playing an important role in oncogenesis and tumor progression. Indeed, the small size of these molecules makes them very stable in different body fluids and not as susceptible as mRNAs to degradation by ribonucleases (RNases). Therefore, the development of a non-invasive salivary test, based on ncRNAs profiles, could have a significant applicability to clinical practice, not only by reducing the cost of the health system, but also by benefitting the patient. Here, we summarize the current status and clinical implications of the ncRNAs present in human saliva as a source of biological information.

Salivary extracellular noncoding RNA: emerging biomarkers for molecular diagnostics

Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, nourished by body's vasculature. Although many circulatory molecules (DNA, RNA, and proteins) can also be present in saliva, saliva harbors unique molecular constituents that can be discriminatory for oral and systemic disease screening and detection. Many studies have reported that salivary constituents can discriminate oral diseases (oral cancer and Sjögren's syndrome) and also systemic diseases (lung cancer, breast cancer, pancreatic cancer, and ovarian cancer). Noncoding RNAs (ncRNAs) are emerging new regulators of diverse biological functions, playing important roles in oncogenesis and tumor progression. Indeed, the short size of these molecules makes them stable in different body fluids such as urine, blood, and saliva, being not as susceptible as mRNAs to degradation by RNases. Here, the current status and clinical implications of the ncRNAs present in human saliva are reviewed for translational applications and basic biological research. The development of noninvasive salivary test (based on ncRNAs profiles) for disease detection could have effective applications into the clinical context with a translational significance as emerging molecular biomarkers for non-invasively disease detection, not only by reducing the cost to the health care system but also by benefitting patients.

RNAPro•SAL: a device for rapid and standardized collection of saliva RNA and proteins

The stabilization and processing of salivary transcriptome and proteome biomarkers is a critical challenge due to the ubiquitous nature of nucleases and proteases as well as the inherent instability of these biomarkers. Furthermore, extension of salivary transcriptome and proteome analysis to point-of-care and remote sites requires the availability of self-administered ambient temperature collection and storage tools. To address these challenges, a self-contained whole saliva collection and extraction system, RNAPro•SAL, has been developed that provides rapid ambient temperature collection along with concurrent processing and stabilization of extracellular RNA (exRNA) and proteins. The system was compared to the University of California, Los Angeles (UCLA) standard clinical collection process (standard operating procedure, SOP). Both systems measured total RNA and protein, and exRNA IL-8, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), β-actin and ribosomal protein S9 (RPS9) by qPCR. Proteome analysis was measured by EIA analysis of interleukin-8 (IL-8), and β-actin, as well as total protein. Over 97% of viable cells were removed by both methods. The system compared favorably to the labor-intensive clinical SOP, which requires low-temperature collection and isolation, yielding samples with similar protein and exRNA recovery and stability.

Erosive Effect of Different Soft Drinks on Enamel Surface in vitro: Application of Stylus Profilometry

OBJECTIVE

To assess the erosive potential of various soft drinks by measuring initial pH and titratable acidity (TA) and to evaluate enamel surface roughness using different exposure times.

MATERIALS AND METHODS

The initial pH of the soft drinks (group 1: Coca-Cola; group 2: orange juice; group 3: Cedevita; group 4: Guarana, and group 5: strawberry yoghurt) was measured using a pH meter, and TA was measured by titration with NaOH. Enamel samples (n = 96), cut from unerupted human third molars, were randomly assigned to 6 groups: experimental (groups 1-5) and control (filtered saliva). The samples were exposed to 50 ml of soft drinks for 15, 30 and 60 min, 3 times daily, during 10 days. Between immersions, the samples were kept in filtered saliva. Enamel surface roughness was measured by diamond stylus profilometer using the following roughness parameters: Ra, Rq, Rz, and Ry. Data were analyzed by one-way ANOVA, Tukey's post hoc and Student-Newman-Keuls post hoc tests.

RESULTS

The pH values of the soft drinks ranged from 2.52 (Guarana) to 4.21 (strawberry yoghurt). Orange juice had the highest TA, requiring 5.70 ml of NaOH to reach pH 7.0, whereas Coca-Cola required only 1.87 ml. Roughness parameters indicated that Coca-Cola had the strongest erosion potential during the 15 min of exposure, while Coca-Cola and orange juice were similar during 30- and 60-min exposures. There were no significant differences related to all exposure times between Guarana and Cedevita. Strawberry yoghurt did not erode the enamel surface regardless of the exposure time.

CONCLUSION

All of the tested soft drinks except yoghurt were erosive. Erosion of the enamel surfaces exposed to Coca-Cola, orange juice, Cedevita, and Guarana was directly proportional to the exposure time.

Measurement and validation of the nature of salivary adiponectin

Adiponectin (Ad) is an adipocyte-derived hormone that plays an essential role in regulating insulin sensitivity, inflammation, and atherogenesis. Levels of some hormones in saliva change in a fashion similar to that in plasma in response to a disease or physiological condition. Since saliva is an easy to obtain biological fluid, measurements of salivary hormonal changes are preferred in diagnoses and treatments. Therefore, it was of interest to examine the nature of salivary Ad. While there have been two publications in the literature reporting presence of Ad in human saliva, the nature of salivary Ad has not been characterized. To this end, we investigated the effect of sample dilution on the measurement of Ad in saliva. To our surprise, we observed an increase in measurable level of Ad in saliva on sample dilution. One explanation for this paradoxical observation may be the presence of inhibitor(s) of Ad/anti-Ad binding in saliva that following dilution relieves the inhibitory effect. Working with this hypothesis, we were able to demonstrate the presence of an inhibitor in saliva that co-eluted with the dimeric form of Ad and was capable of inhibiting Ad assay. The presence of such inhibitor(s) may lead to underestimation of Ad in saliva.

An effective technique for the processing of saliva for the analysis of leptin and adiponectin

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.

On the origin and diagnostic use of salivary RNA

Saliva as a diagnostic fluid enables non-invasive sampling, which can be performed even by an untrained person. Saliva is, thus, particularly useful for large population screenings, for children, elderly and whenever repeated samplings are needed. Saliva is a plasma filtrate actively modified by the salivary glands. Saliva could replace some routine blood tests in the future. The sources of salivary RNA include oral epithelial cells and oral micro-organisms. Recent developments suggest that using known salivary RNA markers, it is possible to diagnose diseases such as oral carcinoma and other diseases will be added soon. Salivary RNA can be used to identify oral bacteria and to determine the expression of specific genes. On a systemic level, it provides information about the whole oral transcriptome and microbiome. Despite the small amount of salivary RNA, the issues with its isolation have been overcome. Saliva, thus, contains RNA of sufficient quality and quantity for sensitive and specific analyses. Salivary RNA can provide medically relevant information about oral microbiome, oral carcinoma, but also breast and pancreatic cancer and is, thus, a promising tool for future research and clinical diagnostics.

Salivary biomarker development using genomic, proteomic and metabolomic approaches

The use of saliva as a diagnostic sample provides a non-invasive, cost-efficient method of sample collection for disease screening without the need for highly trained professionals. Saliva collection is far more practical and safe compared with invasive methods of sample collection, because of the infection risk from contaminated needles during, for example, blood sampling. Furthermore, the use of saliva could increase the availability of accurate diagnostics for remote and impoverished regions. However, the development of salivary diagnostics has required technical innovation to allow stabilization and detection of analytes in the complex molecular mixture that is saliva. The recent development of cost-effective room temperature analyte stabilization methods, nucleic acid pre-amplification techniques and direct saliva transcriptomic analysis have allowed accurate detection and quantification of transcripts found in saliva. Novel protein stabilization methods have also facilitated improved proteomic analyses. Although candidate biomarkers have been discovered using epigenetic, transcriptomic, proteomic and metabolomic approaches, transcriptomic analyses have so far achieved the most progress in terms of sensitivity and specificity, and progress towards clinical implementation. Here, we review recent developments in salivary diagnostics that have been accomplished using genomic, transcriptomic, proteomic and metabolomic approaches.

The use of salivary cytokines as a screening tool for oral squamous cell carcinoma : A review of the literature

Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer. The 5-year survival rate has remained below 50% over the last two decades, and new tools for early diagnosis are needed. Saliva has been used for diagnosis of several systemic diseases, and its use for diagnosis of OSCC has been sought extensively. Among the many salivary analytes for diagnosis of OSCC, accumulating evidences indicate the possibility of using salivary cytokines. Overproduction of proinflammatory, proangiogenic cytokines by OSCC cells has been reported, and their role in tumor progression and angiogenesis is well established. However, many inflammatory conditions and immunological diseases could affect the levels of cytokines in serum and saliva. This article has reviewed publications in this matter, and some strengths and weaknesses have been pointed out. Conclusively, large-scale investigations are required for validation of the use of salivary cytokines for diagnosis of OSCC, with consideration to the influential role of periodontal inflammation in their levels.

Salivary diagnostics

Saliva is a noninvasive and accessible biofluid that permits early detection of oral and systemic diseases. Recent scientific and technologic advances have uncovered specific salivary biomarkers for a number of clinical conditions, including cancers, autoimmune diseases, and cardiovascular disorders. The availability of highly sensitive and high-throughput assays such as microarray, mass spectrometry, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and nano-scale sensors that can measure proteins and nucleic acids are poising saliva as an emerging biofluid for translational and clinical applications. This paper will discuss development of salivary biomarkers for the detection of oral and systemic diseases and the translational application of these markers for clinical applications.

Ultrastructural changes in the cemento-enamel junction after vital tooth bleaching with fluoride and fluoride-free agents - a pilot study

Background

The impact of bleaching on the cemento-enamel junction (CEJ) is not well known. Due to frequent sensitivity of the cervical region of teeth after the vital bleaching, the aim of the present study was to evaluate the morphological features of the CEJ of human teeth after application of fluoridated and fluoride-free bleaching agents, as well as post-bleaching fluoridation treatment, by scanning electron microscopy (SEM) analysis.

Material/Methods

Thirty-five extracted permanent human teeth were longitudinally cut, yielding 70 specimens. Thirty specimens were randomly divided into the 3 experimental groups, and 20 specimens, were used as (2) control groups, each: negative (untreated) control group; positive control group treated with 35% hydrogen peroxide; experimental group 1, bleaching with 10% carbamide peroxide (CP); experimental group 2, treatment with a mixture of 10% CP and fluoride; and experimental group 3, treatment with 10% CP and 2% sodium fluoride gel applied 30 minutes after bleaching. Experimental groups were treated 8 h per day for 14 days. The samples were examined by SEM.

Results

The bleaching materials tested caused morphological changes to the surface of the CEJ. There was a statistically significant difference between experimental groups (Kruskal Wallis Test chi-square=11,668; p<0.005). Mean value of experimental group 2 scores showed statistically significant difference from groups 1 and 3.

Conclusions

Bleaching gel with fluorides does not significantly change morphological appearance of the CEJ and represents a better choice than the hard tissue fluoridation process after bleaching.

Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery

BACKGROUND

Proteomic studies in saliva have demonstrated its potential as a diagnostic biofluid, however the salivary peptidome is less studied. Here we study the effects of several sample collection and handling factors on salivary peptide abundance levels.

METHODS

Salivary peptides were isolated using an ultrafiltration device and analyzed by tandem mass spectrometry. A panel of 41 peptides common after various treatments were quantified and normalized. We evaluated the effects of freezing rate of the samples, nutritional status of the donors (fed vs. fasted), and room-temperature sample degradation on peptide abundance levels. Repeatability of our sample processing method and our instrumental analysis method were investigated.

RESULTS

Increased sample freezing rate produced higher levels of peptides. Donor nutritional status had no influence on the levels of measured peptides. No significant difference was detected in donors' saliva following 5, 10 and 15 min of room-temperature degradation. Sample processing and instrumental variability were relatively small, with median CVs of 9.6 and 6.6.

CONCLUSIONS

Peptide abundance levels in saliva are rather forgiving towards variations in sample handling and donor nutritional status. Differences in freezing methods may affect peptide abundance, so consistency in freezing samples is preferred. Our results are valuable for standardizing sample collection and handling methods for peptidomic-based biomarker studies in saliva.

Direct Saliva Transcriptome Analysis

BACKGROUND

Current standard operating procedures for salivary transcriptomic analysis require low temperatures and lengthy mRNA isolation, which substantially hamper its use in the clinic. We developed a streamlined, ambient-temperature processing, stabilization, and storage protocol for clinical analysis of salivary RNA.

METHODS

The direct saliva transcriptome analysis (DSTA) used cell-free saliva supernatant instead of isolated mRNA for saliva transcriptomic detection, and all procedures, including processing, stabilization, and storage of saliva samples, were performed at ambient temperature without a stabilizing reagent. We evaluated this streamlined protocol by comparing the mRNA expression levels of 3 saliva internal reference genes [glyceraldehyde-3-phosphate dehydrogenase (GAPDH); actin, beta (ACTB); and ribosomal protein S9 (RPS9)] to levels measured with standard procedures, and detecting the variation of their expression levels under long-term ambient temperature storage. The clinical utility of DSTA was assessed by use of 7 oral cancer salivary mRNA biomarkers in a clinical study.

RESULTS

Each saliva internal reference gene mRNA showed similar expression levels when assayed by the DSTA or standard procedures, and remained stable under ambient temperature storage for at least 10 weeks without significant degradation (P = 0.918, 0.288, and 0.242 for GAPDH, ACTB, and RPS9, respectively). Compared with standard procedures, the performance characteristics of oral cancer salivary transcriptomic markers were retained as assayed by DSTA after 10 weeks of storage at ambient temperature. These results indicate that the DSTA is a suitable alternative method for saliva transcriptomic analysis and is feasible for use in clinical cancer research applications.

CONCLUSIONS

The streamlined DSTA protocol can impact the saliva-handling method and improve the standard operating procedures for clinical saliva transcriptomic diagnostics.

A review on salivary genomics and proteomics biomarkers in oral cancer

Oral cancer has emerged as an alarming public health problem with increasing incidence and mortality rates all over the world. Therefore, the implementation of newer screening and early detection approaches are of utmost importance which could reduce the morbidity and mortality associated with this disease. Sensitive and specific biomarkers for oral cancer are likely to be most effective for screening, diagnosis, staging and follow-up for this dreaded malignancy. Unlike other deep cancers, oral cancer is located in oral cavity. Hence, the direct contact between saliva and oral cancer lesion makes the measurement of tumor markers in saliva an attractive alternative to serum and tissue testing. The DNA, RNA and protein molecules derived from the living cancer cells can be conveniently obtained from saliva. Thus, salivary biomarkers, a non-invasive alternative to serum and tissue-based biomarkers may be an effective modality for early diagnosis, prognostication and monitoring post therapy status. In the current post-genomic era, various technologies provide opportunities for high-throughput approaches to genomics and proteomics; which have been used to evaluate altered expressions of gene and protein targets in saliva of oral cancer patients. The emerging field of salivary biomarkers has great potentials to prove its clinical significance to combat oral cancer. Hence, we have reviewed importance of several salivary genomics and proteomics biomarkers for oral cancer.

Collection, storage, and processing of saliva samples for downstream molecular applications

Saliva is an ideal translational research tool and diagnostic medium and is being used in novel ways to provide molecular biomarkers for a variety of oral and systemic diseases and conditions. The ability to analyze saliva to monitor health and disease is a highly desirable goal for oral health promotion and research. Saliva has been used to detect caries risk, periodontitis, oral cancer, breast cancer, salivary gland diseases, and systemic disorders such as hepatitis, HIV and HCV. Technology advancement has allowed high-throughput studies to be performed at a scale unrealized previously and is serving to advance the discovery and validation of salivary disease biomarkers. Of course, successful measurement of salivary analytes requires optimal collection, processing, and storage procedures and conditions. This chapter describes protocols for saliva collection, processing, and storage for the molecular analysis of salivary diagnostic constituents.

Transcriptomic analyses of saliva

Salivary biomarkers for diagnostic and prognostic assessments have become increasingly well established in recent years. Salivary mRNA transcriptomic analyses create a new paradigm in the emerging field for noninvasive molecular diagnosis. In this chapter, we will overview the development of sensitive and robust microarray and multiplex quantitative reverse transcriptase-PCR assays for the discovery and validation of mRNA biomarkers in human saliva. Total RNA isolated from human saliva is used for microarray profiling through Human Genome U133 Plus 2.0 and Exon 1.0 ST array platforms. A universal RNA linear amplification strategy was used to amplify RNA from nanogram scale followed by reverse transcription-PCR reaction, cleaned up enzymatically, and validated by quantitative PCR. Further, the integrity of RNA can be analyzed by the Agilent Bioanalyzer and quantified using a Nanodrop microvolume spectrophotometer. Using these invaluable technical tools, one can identify thousands of mRNA species in saliva. These methods indicate that salivary mRNA provides an efficient medium for biomarker discovery in oral and systemic diseases detection.