Comparative profiling of human saliva by intact protein LC/ESI-TOF mass spectrometry

Starch treatment improves the salivary proteome for subject identification purposes

Identification of subjects, including perpetrators, is one of the most crucial goals of forensic science. Saliva is among the most common biological fluids found at crime scenes, containing identifiable components. DNA has been the most prominent identifier to date, but its analysis can be complex due to low DNA yields and issues preserving its integrity at the crime scene. Proteins are emerging as viable candidates for subject identification. Previous work has shown that the salivary proteome of the least-abundant proteins may be helpful for subject identification, but more optimized techniques are needed. Among them is removing the most abundant proteins, such as salivary α-amylase. Starch treatment of saliva samples elicited the removal of this enzyme and that of glycosylated, low-molecular-weight proteins, proteases, and immunoglobulins, resulting in a saliva proteome profile enriched with a subset of proteins, allowing a more reliable and nuanced subject identification.

Salivary Proteome Profile of Women during Fertile Phase of Menstrual Cycle as Characterized by Mass Spectrometry

Objectives:

Ovulation is such a critical physiological process that its noninvasive detection based on salivary constituents has several advantages in humans. Hence, the present study is proposed to identify the ovulatory-specific proteins in saliva in order to detect ovulation phase.

Materials and Methods:

Samples were collected from women volunteers. The procedure adopted was approved by the Institutional Human Ethical Committee (DM/2014/101/38), Bharathidasan University. The saliva samples were collected from thirty healthy female volunteers, with a prior written consent. One-way analysis of variance was used to calculate protein concentration and band intensity using SPSS 16 software (SPSS Inc., Cary, NC, USA). The salivary protein expression pattern during different phases of menstrual cycle was analyzed using gel-based high resolution-liquid chromatography-mass spectrometry/mass spectrometry and matrix-assisted laser desorption ionization-time of flight/time of flight. Further, bioinformatics tools were adopted to annotate the proteins identified at various phases of menstrual cycle.

Results:

As many as 530 proteins showed up in the saliva during ovulatory phase, whereas there were only 251 proteins identified during postovulatory phase. The functional annotation of salivary proteins revealed that the proteins got assigned to the class of “extracellular proteins” which are concerned with regulatory functions. The 16 unique and/or differentially expressed protein spots appeared during ovulatory phase, among which Cystatin-S, Prolactin-inducible protein, Cystatin-A, Cystatin-SN, BPI fold-containing family A member 2, Alpha-tubulin N-acetyltransferase 1, Carbonic anhydrase-6, Protein LEG1 homolog, Hemoglobin subunit beta, and Pancreatic alpha-amylase were identified.

Conclusion:

Total salivary proteome profile has been listed with respect to various phases of menstrual cycle. Among the protein listed, Cystatin-S offers a biomarker protein and/or indicator of ovulatory phase. However, extensive validation is required before arriving to a candidate bio-marker protein.

Proteomic analysis of whole saliva in chronic periodontitis

Periodontitis is a chronic inflammatory disease resulting from a dysbiosis of the dental biofilm and a dysregulated host response in susceptible individuals. It is characterized by periodontal attachment destruction, bone resorption and eventual tooth loss. Salivary biomarkers have been sought to predict and prevent periodontitis. This comparative study analyzed the salivary proteome of individuals with chronic periodontitis (CP) and periodontal health (PH) and correlated specific proteins with clinical parameters of disease by using mass spectrometry. Stimulated whole saliva was obtained 10 PH and 30 CP patients and pooled into 5 healthy control samples and 15 CP samples. After precipitation with TCA, samples were digested enzymatically with trypsin and analyzed by a LTQ Orbitrap Velos equipped with a nanoelectrospray ion source. A wide range of salivary proteins of various functions was significantly reduced in CP individuals, whereas salivary acidic proline-rich phosphoprotein, submaxillary gland androgen-regulated protein, histatin-1, fatty acid binding protein, thioredoxin and cystatin-SA were predominant in diseased patients and correlated significantly with signs of periodontal attachment loss and inflammation. In conclusion, few specific salivary proteins were associated with CP. These findings may contribute to the identification of disease indicators or signatures for the improvement of periodontal diagnosis. SIGNIFICANCE: Periodontitis is a chronic inflammatory disease that results in periodontal attachment destruction, bone resorption and eventual tooth loss. Salivary biomarkers have been sought to predict periodontitis. The analysis of the salivary proteome of individuals with chronic periodontitis indicated that several proteins of various functions were significantly reduced in these individuals, except for salivary acidic proline-rich phosphoprotein, submaxillary gland androgen-regulated protein, histatin, fatty acid binding protein, thioredoxin and cystatin. Differences in salivary proteome profiles between periodontal health and periodontitis may contribute to the identification of disease indicators and to the improvement of periodontal diagnosis and treatment.

Targeted Proteomics Guided by Label-free Quantitative Proteome Analysis in Saliva Reveal Transition Signatures from Health to Periodontal Disease

Periodontal diseases are among the most prevalent worldwide, but largely silent, chronic diseases. They affect the tooth-supporting tissues with multiple ramifications on life quality. Their early diagnosis is still challenging, due to lack of appropriate molecular diagnostic methods. Saliva offers a non-invasively collectable reservoir of clinically relevant biomarkers, which, if utilized efficiently, could facilitate early diagnosis and monitoring of ongoing disease. Despite several novel protein markers being recently enlisted by discovery proteomics, their routine diagnostic application is hampered by the lack of validation platforms that allow for rapid, accurate and simultaneous quantification of multiple proteins in large cohorts. Here we carried out a pipeline of two proteomic platforms; firstly, we applied open ended label-free quantitative (LFQ) proteomics for discovery in saliva (n = 67, including individuals with health, gingivitis, and periodontitis), followed by selected-reaction monitoring (SRM)-targeted proteomics for validation in an independent cohort (n = 82). The LFQ platform led to the discovery of 119 proteins with at least 2-fold significant difference between health and disease. The 65 proteins chosen for the subsequent SRM platform included 50 functionally related proteins derived from the significantly enriched processes of the LFQ data, 11 from literature-mining, and four house-keeping ones. Among those, 60 were reproducibly quantifiable proteins (92% success rate), represented by a total of 143 peptides. Machine-learning modeling led to a narrowed-down panel of five proteins of high predictive value for periodontal diseases with maximum area under the receiver operating curve >0.97 (higher in disease: Matrix metalloproteinase-9, Ras-related protein-1, Actin-related protein 2/3 complex subunit 5; lower in disease: Clusterin, Deleted in Malignant Brain Tumors 1). This panel enriches the pool of credible clinical biomarker candidates for diagnostic assay development. Yet, the quantum leap brought into the field of periodontal diagnostics by this study is the application of the biomarker discovery-through-verification pipeline, which can be used for validation in further cohorts.

The Saliva Proteome of Dogs: Variations Within and Between Breeds and Between Species

Saliva is a complex multifunctional fluid that bathes the oral cavity to assist in soft and hard tissue maintenance, lubrication, buffering, defense against microbes, and initiating digestion of foods. It has been extensively characterized in humans but its protein composition in dogs remains poorly characterized, yet saliva composition could explain (patho) physiological differences between individuals, breeds and with humans. This pilot discovery study aimed to characterize canine saliva from two breeds, Labrador retrievers and Beagles, and to compare this with human saliva using quantitative mass spectrometry. The analysis demonstrated considerable inter-individual variation and difference between breeds; however these were small in comparison to the differences between species. Functional mapping suggested roles of detected proteins similar to those found in human saliva with the exception of the initiation of digestion as salivary amylase was lacking or at very low abundance in canine saliva samples. Many potential anti-microbial proteins were detected agreeing with the notion that the oral cavity is under continuous microbial challenge.

Salivary protein changes in response to acute stress in medical residents performing advanced clinical simulations: a pilot proteomics study

CONTEXT

Quantitative changes of salivary proteins due to acute stress were detected.

OBJECTIVE

To explore protein markers of stress in saliva of eight medical residents who performed emergency medicine simulations.

MATERIALS AND METHODS

Saliva was collected before the simulations, after the simulations, and following morning upon waking. Proteins were separated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), identified by mass spectrometry (MS), and relatively quantified by densitometry.

RESULTS

Salivary alpha-amylase and S-type cystatins significantly increased, while the ∼26 kDa and low-molecular weight (MW) (<10 kDa) SDS-PAGE bands exhibited changes after stress.

DISCUSSION AND CONCLUSION

Alpha-amylase and cystatins are potential salivary markers of acute stress, but further validation should be performed using larger sample populations.

The Denture-Associated Oral Microbiome in Health and Stomatitis

Denture stomatitis is a prevalent inflammatory condition of the mucosal tissue in denture wearers that is triggered by microorganisms. While Candida has been extensively studied for its role in stomatitis etiology, the bacterial component largely remains to be investigated. Our data show that certain types of bacteria are significantly associated with denture health and disease. Furthermore, the bacterial communities residing on the teeth and dentures of the same person are similar to each other independently of the surface, and thus, denture health could impact the maintenance of remaining teeth and vice versa.

While investigation of the microbiome on natural oral surfaces has generated a wealth of information, few studies have examined the microbial communities colonizing dentures and their relationship to oral health. To address this knowledge gap, we characterized the bacterial community associated with dentures and remaining teeth in healthy individuals and patients with denture stomatitis. The microbiome compositions of matched denture and tooth plaque samples of 10 healthy individuals and 9 stomatitis patients were determined by 16S rRNA gene pyrosequencing. The microbial communities colonizing dentures and remaining teeth in health and disease were very similar to each other. Matched denture and tooth samples from the same individuals shared a significantly higher percentage of identical phylotypes than random pairs of samples from different study participants. Despite these overall similarities, several bacterial phylotypes displayed discrete health- and stomatitis-associated denture colonization, while others were distinct in health and disease independently of the surface. Certain phylotypes exhibited differential colonization of dentures and teeth independently of denture health status. In conclusion, denture and natural tooth surfaces in health and stomatitis harbor similar bacterial communities. Individual-related rather than surface-specific factors play a significant role in the bacterial phylotype composition colonizing dentures and teeth. This individual-specific mutual influence on denture and tooth surface colonization could be an important factor in maintaining oral health in denture wearers. Discrete differences in colonization patterns for distinct genera and phylotypes warrant further studies regarding their potential involvement or utility as specific indicators of health and disease development in denture-wearing individuals.

IMPORTANCE Denture stomatitis is a prevalent inflammatory condition of the mucosal tissue in denture wearers that is triggered by microorganisms. While Candida has been extensively studied for its role in stomatitis etiology, the bacterial component largely remains to be investigated. Our data show that certain types of bacteria are significantly associated with denture health and disease. Furthermore, the bacterial communities residing on the teeth and dentures of the same person are similar to each other independently of the surface, and thus, denture health could impact the maintenance of remaining teeth and vice versa.

Quantitative analysis of the intra- and inter-subject variability of the whole salivary proteome

BACKGROUND AND OBJECTIVE

Interest in human saliva is increasing for disease-specific biomarker discovery studies. However, protein composition of whole saliva can grossly vary with physiological and environmental factors over time and it comprises human as well as bacterial proteins.

MATERIAL AND METHODS

We compared intra- and inter-subject variabilities using complementary gel-based (two-dimensional difference gel electrophoresis, 2-D DIGE) and gel-free (liquid chromatography tandem mass spectrometry, LC-MS/MS) proteomics profiling of saliva. Unstimulated whole saliva of four subjects was examined at three different time-points (08.00 h, 12.00 h and 17.00 h) and variability of the saliva proteome was analyzed on two successive days by LC-MS/MS.

RESULTS

In the 2-D DIGE experiment, the median coefficient of variation (CV) for intra-subject variability was significantly lower (CV of 0.39) than that for inter-subject variability (CV of 0.57; CV of technical replicates 0.17). LC-MS/MS data confirmed the significantly lower variation within subjects over time (CV of 0.37) than the inter-subject variability (CV of 0.53; CV of technical replicates 0.11), and that the inter-subject variability was not time-dependent.

CONCLUSION

Both techniques revealed similar trends of variations on technical, intra- and inter-subject level but provided peptide and protein focused information and should thus be used as complementary approaches. The data presented indicate that 2-D DIGE as well as LC-MS/MS approaches are suitable for biomarker screening in saliva.

The human salivary proteome: a critical overview of the results obtained by different proteomic platforms

The development of new separation techniques and different mass spectrometry instrumental devices, as well as the great availability of specific reactants, offers ample choice to scientists for carrying out high-throughput proteomic studies and being competitive in the field today. However, the different options available often do not provide comparable results, which can be linked to factors such as the strategy adopted, the nature of the sample and the instrumental availability. In this critical review, the results obtained so far in the study of human saliva by different proteomic approaches will be compared and discussed.

Induced sputum: a window to lung pathology

Sputum is recognized as a sampling method for the monitoring and assessment of chronic lung diseases such as asthma, COPD (chronic obstructive pulmonary disease) and cystic fibrosis. Sputum samples the central airways and its protein components (e.g. mucins and cytokines), cellular components (e.g. eosinophils and neutrophils) and microbiological components (e.g. viruses and bacteria) can be used as markers of disease severity, exacerbation, susceptibility or progression. This paper describes the basic constituents of induced sputum and how these influence the quantification and identification of novel biomarkers of chronic lung diseases using techniques such as proteomics.

The proteome of the human parotid gland secretion in elderly with and without root caries

OBJECTIVE

Saliva is important for oral health, including the prevention of dental decay. The purpose of the present work was to indicate whether the parotid gland has altered function in the elderly, particularly in terms of proteins secreted, and whether its functional status could be associated with the presence of root caries.

MATERIAL AND METHODS

Ductal parotid gland secretion was obtained from 51 individuals: 21 elderly with carious roots (Patients), 20 elderly (Controls), and 10 adults (Young) without root caries. Pooled aliquots were analyzed by liquid chromatography/tandem mass spectrometry to yield lists of major proteins present in the three groups.

RESULTS

Approximately 200 unique proteins were detected, of which 73 were identified repeatedly with high confidence and therefore included in the comparison. Some of the differences observed, when comparing Patients with respectively elderly Controls and the Young, resembled changes found in patients with Sjogren's syndrome, a condition associated with dental decay. Other changes involved proteins that are likely to impact on the oral microbiota, such as the absence of dermcidin and the presence of collagen in Patients. Cystatin S, a putative indicator of caries, was present at a higher level in Patients.

CONCLUSIONS

Parotid function tends to change upon aging, with possible consequences as to caries activity. However, analyses of individual samples revealed considerable variations in protein patterns.

Quantitative mass spectrometry as a tool for nutritional proteomics

The goal of nutritional science is to determine the effect of dietary components. Proteomics has emerged as a method to study proteins on a large scale. The proteomic information gathered from a sample, whether a biological fluid, cell, or tissue, includes not only the identities of proteins present but also their quantities and posttranslational modifications. Recent advances in mass spectrometry make it possible to accurately measure concentrations of thousands of proteins derived from such complex biological samples. Quantitative data will provide increased understanding of the dynamic changes in the proteome induced by dietary components.