Standardization of a protocol for shotgun proteomic analysis of saliva

Proteomic analysis of stimulated saliva in gastroesophageal reflux disease patients with and without erosive tooth wear: Observational study

OBJECTIVE

To evaluate the difference in the proteomic profile of stimulated saliva in patients with gastroesophageal reflux disease (GERD) with (GE) and without (GNE) erosive tooth wear (ETW), regarding both human and bacterial proteins.

METHODS

Stimulated saliva (SS) was collected from 16 patients (8/group). Samples were centrifuged at 4.500 g for 15 min under refrigeration to remove all debris. The supernatant from each saliva sample was taken and frozen at -80 °C. After extracting the proteins, they were submitted to reverse phase liquid chromatography and mass spectrometry (nLC-ESI-MS/MS). Label-free proteomic quantification was performed using Protein Lynx Global Service (PLGS) software (p < 0.05) for human and bacterial proteins.

RESULTS

In total, 67 human proteins were common for GNE and GE groups. GNE group presented, compared to GE group, increase in proteins that confer antimicrobial and acid resistant properties, such as cystatins, histatin and immunoglobulins. However, GNE group had a marked decrease in subunits of hemoglobin (α, β and delta). Regarding bacterial proteins, for SS, 7 and 10 unique proteins were identified in the GE and GNE groups, respectively. They are related to protein synthesis and energy metabolism and interact with human proteins typically found in saliva and supramolecular complexes of the acquired pellicle.

CONCLUSIONS

Our data indicate that the stimulation of the salivary flow increases acid resistant and antimicrobial proteins in saliva, which might protect against ETW.

CLINICAL SIGNIFICANCE

This pioneer study showed important differences in the human and bacterial proteome of SS in patients with GERD with or without ETW.

Salivary proteomic profile of young healthy subjects

Background: The incidence of noncommunicable diseases (NCDs) has been rapidly ramped up worldwide. Hence, there is an urgent need to non-invasively detect NCDs possibly by exploiting saliva as a 'liquid biopsy' to identify biomarkers of the health status. Since, the absence of standardized procedures of collection/analysis and the lack of normal ranges makes the use of saliva still tricky, our purpose was to outline a salivary proteomic profile which features healthy individuals. Methods: We collected saliva samples from 19 young blood donors as reference population and the proteomic profile was investigated through mass-spectrometry. Results: We identified 1,004 proteins of whose 243 proteins were shared by all subjects. By applying a data clustering approach, we found a set of six most representative proteins across all subjects including Coronin-1A, F-actin-capping protein subunit alpha, Immunoglobulin J chain, Prosaposin, 78 kDa glucose-regulated protein and Heat shock 70 kDa protein 1A and 1B. Conclusion: All of these proteins are involved in immune system activation, cellular stress responses, proliferation, and invasion thus suggesting their use as biomarkers in patients with NCDs.

The Multifarious Functions of Leukotrienes in Bone Metabolism

Leukotrienes (LTs) are derived from arachidonic acid metabolism by the 5-lipoxygenase (5-LO) enzyme. The production of LTs is stimulated in the pathogenesis of rheumatoid arthritis (RA), osteoarthritis, and periodontitis, with a relevant contribution to bone resorption. However, its role in bone turnover, particularly the suppression of bone formation by modulating the function of osteoclasts and osteoblasts, remains unclear. We investigated the effects of LTs on bone metabolism and their impact on osteogenic differentiation and osteoclastogenesis using a 5-LO knockout (KO) mouse model. Results from micro-computed tomography (μCT) analysis of femur from 8-week-old 5-LO-deficient mice showed increased cortical bone and medullary region in females and males and decreased trabecular bone in females. In the vertebra, we observed increased marrow area in both females and males 5-LO KO and decreased trabecular bone only in females 5-LO KO. Immunohistochemistry (IHC) analysis showed higher levels of osteogenic markers tissue-nonspecific alkaline phosphatase (TNAP) and osteopontin (OPN) and lower expression of osteoclastogenic marker tartrate-resistant acid phosphatase (TRAP) in the femurs of 5-LO KO mice versus wild-type (WT). Alkaline phosphatase activity and mineralization assay results showed that the 5-LO absence enhances osteoblasts differentiation and mineralization but decreases the proliferation. Alkaline phosphatase (ALP), Bglap, and Sp7 gene expression were higher in 5-LO KO osteoblasts compared to WT cells. Eicosanoids production was higher in 5-LO KO osteoblasts except for thromboxane 2, which was lower in 5-LO-deficient mice. Proteomic analysis identified the downregulation of proteins related to adenosine triphosphate (ATP) metabolism in 5-LO KO osteoblasts, and the upregulation of transcription factors such as the adaptor-related protein complex 1 (AP-1 complex) in long bones from 5-LO KO mice leading to an increased bone formation pattern in 5-LO-deficient mice. We observed enormous differences in the morphology and function of osteoclasts with reduced bone resorption markers and impaired osteoclasts in 5-LO KO compared to WT osteoclasts. Altogether, these results demonstrate that the absence of 5-LO is related to the greater osteogenic profile. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Is There a Difference in the Proteomic Profile of Stimulated and Unstimulated Saliva Samples from Pregnant Women with/without Obesity and Periodontitis?

This study aimed to compare the proteomic profile of stimulated and unstimulated saliva samples from pregnant women with/without obesity and periodontitis. Pregnant women were allocated into four groups: with obesity and periodontitis (OP); with obesity but without periodontitis (OWP); with normal BMI but with periodontitis (NP); with normal BMI and without periodontitis (NWP). Stimulated saliva (SS) and unstimulated saliva (US) samples were collected, and salivary proteins were extracted and individually processed by proteomic analysis (nLC-ESI-MS/MS). Proteins involved with the immune response process, antioxidant activity, and retina homeostasis were decreased or absent in SS samples from all groups (i.e., Antileukoproteinase, Lysozyme C, Alpha-2-macroglobulin-like protein 1, Heat shock proteins-70 kDa 1-like, 1A, 1B, 6, Heat shock-related 70 kDa protein 2, Putative Heat shock 70 kDa protein 7, Heat shock cognate 71 kDa). Additionally, proteins related to the carbohydrate metabolic process and glycolytic and glucose metabolic process were absent in SS, mainly from OP and OWP (i.e., Frutose-bisphosphate aldose A, Glusoce-6-phosphate isomerase, Pyruvate kinase). Saliva stimulation decreased important proteins involved with immune response and inflammation process in all groups. Unstimulated salivary samples seem to be the best choice for the proteomic approach in pregnant women.

Saliva proteomic profile of early childhood caries and caries-free children

OBJECTIVE

Saliva plays an important antimicrobial role and it is related to the pathogenesis of early childhood caries (ECC). The aim of this study was to compare the proteomic profile of unstimulated saliva of children aged 3-5 years who had ECC and caries-free (CF) children.

MATERIALS AND METHODS

After the saliva collection from 20 children (ECC: n = 10; CF: n = 10), the samples were processed for proteomic analysis on a mass spectrometer.

RESULTS

1638 proteins were identified, of which 355 were present in both groups. A total of 579 proteins were exclusively identified in the CF group and included Leucine-rich alpha-2-glycoprotein, Protein S100-A5, Protein S100-A8 and Mucin-2. Moreover, 704 proteins were exclusively identified in the ECC group, including Enamelin. The differential expression analysis revealed that 112 proteins were up-regulated in the CF group. Among these proteins, we highlighted Hemoglobin subunit gamma-1 (343-fold increase), gamma-2 (336-fold increase) and alpha (40-fold increase).

CONCLUSIONS

The proteomic profile of the saliva varied substantially between the groups. Hemoglobin subunit gamma-1, gamma-2 and alpha may play a protective role in children with ECC. These proteins should be evaluated in future studies, because they may be possible good candidates to be included in anti-caries dental products.

Teeth with acute apical abscess vs. teeth with chronic apical periodontitis: a quantitative and qualitative proteomic analysis

OBJECTIVE

To quantitatively and qualitatively analyze the proteomic profile of teeth with acute apical abscesses (AAA) compared with teeth with chronic apical periodontitis (CAP) and to correlate the expression of detected human proteins with their main biological functions.

MATERIALS AND METHODS

Samples were obtained from root canals of 9 patients diagnosed with AAA and 9 with CAP. Samples were analyzed by reversed-phase liquid chromatography coupled to mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in protein expression were calculated using the t-test (p < 0.05).

RESULTS

In total, 246 human proteins were identified from all samples. Proteins exclusively found in the AAA group were mainly associated with the immunoinflammatory response and oxidative stress response. In the quantitative analysis, 17 proteins were upregulated (p < 0.05) in the AAA group, including alpha-1-acid glycoprotein, hemopexin, fibrinogen gamma chain, and immunoglobulin. Additionally, 61 proteins were downregulated (p < 0.05), comprising cathepsin G, moesin, gelsolin, and transketolase. Most of the proteins were from the extracellular matrix, cytoplasm, and nucleus.

CONCLUSIONS

The common proteins between the groups were mainly associated with the immune response at both expression levels. Upregulated proteins mostly belonged to the acute-phase proteins, while the downregulated proteins were associated with DNA/RNA regulation and repair, and structural function.

CLINICAL RELEVANCE

The host response is directly related to the development of apical abscesses. Thus, understanding the behavior of human proteins against the endodontic pathogens involved in this condition might contribute to the study of new approaches related to the treatment of this disease.

Salivary protein candidates for biomarkers of oral disorders in people with a crack cocaine use disorder

The use of cocaine and its main derivative, crack, can cause some systemic effects that may lead to the development of some oral disorders. To assess the oral health of people with a crack cocaine use disorder and identify salivary protein candidates for biomarkers of oral disorders. A total of 40 volunteers hospitalized for rehabilitation for crack cocaine addiction were enrolled; nine were randomly selected for proteomic analysis. Intraoral examination, report of DMFT, gingival and plaque index, xerostomia, and non-stimulated saliva collection were performed. A list of proteins identified was generated from the UniProt database and manually revised. The mean age (n=40) was 32 (±8.88; 18-51) years; the mean DMFT index was 16±7.70; the mean plaque and gingival index were 2.07±0.65 and 2.12±0.64, respectively; and 20 (50%) volunteers reported xerostomia. We identified 305 salivary proteins (n=9), of which 23 were classified as candidate for biomarkers associated with 14 oral disorders. The highest number of candidates for biomarkers was associated with carcinoma of head and neck (n=7) and nasopharyngeal carcinoma (n=7), followed by periodontitis (n=6). People with a crack cocaine use disorder had an increased risk of dental caries and gingival inflammation; less than half had oral mucosal alterations, and half experienced xerostomia. As possible biomarkers for 14 oral disorders, 23 salivary proteins were identified. Oral cancer and periodontal disease were the most often associated disorders with biomarkers.

Label-Free Quantitative Proteomic Analysis Reveals Inflammatory Pattern Associated with Obesity and Periodontitis in Pregnant Women

Obesity and pregnancy may have synergistic effects on periodontal condition, and proteomics could be an ideal approach to highlight the pathophysiological mechanisms associated with these outcomes. This study analyzed the salivary proteomics related to obesity and periodontitis in women during pregnancy (T1) and after delivery (T2). Initially, 126 women were recruited and forty were allocated into groups: with obesity and periodontitis (OP); with obesity, but without periodontitis (OWP); with normal BMI, but with periodontitis (NP); with normal BMI and without periodontitis (NWP). Whole-mouth saliva was collected in T1 and T2, and proteins were extracted and individually processed by label-free proteomics (nLC-ESI-MS/MS). The up-regulations of Heat shock 70 kDa protein 1A, 1B, and 1-like were related to both obesity and periodontitis, separately. Albumin and Thioredoxin were up-regulated in periodontitis cases, while Cystatins (mainly S, SA, SN) and Lactotransferrin were down-regulated. The high abundances of Submaxillary gland androgen-regulated protein 3B, Protein S100-A8, Matrix metalloproteinase-9, Heat shock 70 kDa protein 2 and 6, Putative Heat shock 70 kDa protein 7, Heat shock 71 kDa protein, Haptoglobin and Plastin-1 were significant in the combination of obesity and periodontitis. Obesity and periodontitis remarkably altered the proteome of the saliva during pregnancy with substantial alterations after delivery.

Proteomic analysis of infected root canals with apical periodontitis in patients with type 2 diabetes mellitus: A cross-sectional study

AIM

This study aimed to quantitatively and qualitatively determine the proteomic profile of apical periodontitis (AP) in type 2 diabetes mellitus (T2DM) patients in comparison with systemically noncompromised patients and to correlate the protein expression of both groups with their biological functions.

METHODOLOGY

The sample consisted of 18 patients with asymptomatic AP divided into two groups according to the presence of T2DM: diabetic group-patients with T2DM (n = 9) and control group-systemically healthy patients (n = 9). After sample collection, the root canal samples were prepared for proteomic analysis using reverse-phase liquid chromatography-mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in protein expression between groups were calculated using t-test (p < .05). Biological functions were analysed using the Homo sapiens UniProt database.

RESULTS

A total of 727 human proteins were identified in all samples. Among them, 124 proteins common to both groups were quantified, out of which 65 proteins from the diabetic group showed significant differences compared with the control: 43 upregulated (p < .05) and 22 downregulated (p < .05) proteins. No significant differences in protein expression were seen for the remaining 59 proteins (p > .05). Most proteins with differences in expression were related to immune/inflammatory response. Neutrophil gelatinase-associated lipocalin, Plastin-2, Lactotransferrin and 13 isoforms of immunoglobulins were upregulated. In contrast, Protein S100-A8, Protein S100-A9, Histone H2B, Neutrophil defensin 1, Neutrophil defensin 3 and Prolactin-inducible protein were downregulated.

CONCLUSIONS

Quantitative differences were demonstrated in the expression of proteins common to diabetic and control groups, mainly related to immune response, oxidative stress, apoptosis and proteolysis. These findings revealed biological pathways that provide the basis to support clinical findings on the relationship between AP and T2DM.

Clinical Proteomics of Biofluids in Haematological Malignancies

Since the emergence of high-throughput proteomic techniques and advances in clinical technologies, there has been a steady rise in the number of cancer-associated diagnostic, prognostic, and predictive biomarkers being identified and translated into clinical use. The characterisation of biofluids has become a core objective for many proteomic researchers in order to detect disease-associated protein biomarkers in a minimally invasive manner. The proteomes of biofluids, including serum, saliva, cerebrospinal fluid, and urine, are highly dynamic with protein abundance fluctuating depending on the physiological and/or pathophysiological context. Improvements in mass-spectrometric technologies have facilitated the in-depth characterisation of biofluid proteomes which are now considered hosts of a wide array of clinically relevant biomarkers. Promising efforts are being made in the field of biomarker diagnostics for haematologic malignancies. Several serum and urine-based biomarkers such as free light chains, β-microglobulin, and lactate dehydrogenase are quantified as part of the clinical assessment of haematological malignancies. However, novel, minimally invasive proteomic markers are required to aid diagnosis and prognosis and to monitor therapeutic response and minimal residual disease. This review focuses on biofluids as a promising source of proteomic biomarkers in haematologic malignancies and a key component of future diagnostic, prognostic, and disease-monitoring applications.

Radiotherapy changes the salivary proteome in head and neck cancer patients: evaluation before, during, and after treatment

OBJECTIVES

Salivary glands are affected during radiotherapy in the head and neck region, leading to a reduction in salivary flow and changes its composition. Besides negatively affecting the oral soft tissues, this can also lead to dental impairment. Thus, we evaluated the effect of radiotherapy in the proteomic profile of the saliva in patients with head and neck cancer (HNC).

MATERIALS AND METHODS

HNC patients had their saliva collected before (BRT), during (2-5 weeks; DRT), and after (3-4 months; ART) radiotherapy. Saliva was also collected from healthy volunteers (control; C). Samples were processed for proteomic analysis.

RESULTS

In total, 1055 proteins were identified, among which 46 were common to all groups, while 86, 86, 286, and 395 were exclusively found in C, BRT, DRT, and ART, respectively. Remarkably, alpha-enolase was increased 35-fold DRT compared with BRT, while proline-rich proteins were decreased. ART there was a 16-fold increase in scaffold attachment factor-B1 and a 3-fold decrease in alpha-enolase and several cystatins. When compared with C, salivary proteins of BRT patients showed increases cystatin-C, lysozyme C, histatin-1, and proline-rich proteins CONCLUSION/CLINICAL REVELANCE: Both HNC and radiotherapy remarkably change the salivary protein composition. Altogether, our results, for the first time, suggest investigating alpha-enolase levels in saliva DRT in future studies as a possible biomarker and strategy to predict the efficiency of the treatment. Moreover, our data provide important insights for designing dental products that are more effective for these patients and contribute to a better understanding of the progressive changes in salivary proteins induced by radiotherapy. Graphical abstract.

Is there difference in the comparative and quantitative salivary proteome between stimulated and unstimulated saliva in head and neck cancer patients treated by radiotherapy?

Stimulation of saliva production is an alternative to improve the quality of life of patients treated by radiotherapy. However, there is no information about changes in the salivary proteome of stimulated and unstimulated saliva in these patients.

OBJECTIVES

Thus, we evaluated the difference in the proteomic profile of stimulated and unstimulated saliva in patients with head and neck cancer (HNC) treated by radiotherapy.

METHODS

Stimulated and unstimulated saliva were collected from 9 patients with HNC before (BRT), during (DRT; 2-5 weeks) and after (ART; 3-4 months) treatment. Healthy patients paired by age and gender also had their saliva collected (C; control group). The stimulated and unstimulated salivary flow were evaluated (p < 0.05). Salivary proteins were extracted and processed for shotgun proteomic analysis.

RESULTS

Significant differences were observed between stimulated and unstimulated salivary flows for C and BRT (p greater than 0.001), but not for DRT and ART. Proteins involved with apoptosis, antibacterial and acid-resistance were decreased in stimulated saliva in comparison to unstimulated saliva DRT and ART. Isoforms of keratins were not identified in control and BRT.

CONCLUSION

there is a marked difference in the protein profile of stimulated and unstimulated salivary flows in HNC patients treated by radiotherapy. In addition, saliva stimulation in patients with HNC decreases important proteins involved with dental protection. The unstimulated salivary flow seems to be the best alternative to search for biomarkers. Our results contribute in an unprecedented way to understand the changes in the salivary proteome of different flows in HNC patients undergoing radiotherapy treatment.

Quantitative proteomic analysis in symptomatic and asymptomatic apical periodontitis

AIM

To quantitatively and qualitatively compare the host proteomic profile in samples of symptomatic and asymptomatic apical periodontitis (AP) using nano-liquid chromatography-electron spray tandem mass spectrometry.

METHODOLOGY

Samples were obtained from 18 patients with radiographically evident AP, divided into symptomatic and asymptomatic groups (nine per group) according to clinical characteristics. After sample collection, protein extraction, purification and quantification of the samples were performed, which were analysed by reverse-phase liquid chromatography coupled to mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in expression of proteins between the groups were calculated using the Monte Carlo algorithm, considering P < 0.05 for down-regulated proteins and 1 - P > 0.95 for up-regulated proteins. Proteins were identified with the embedded ion accounting algorithm in the software and a search of the Homo sapiens UniProt database.

RESULTS

A total of 853 individual human proteins were identified. In the quantitative analysis, common proteins to both groups accounted for 143 proteins. Differences in expression between groups resulted in 51 up-regulated proteins (1 - P > 0.95) in the symptomatic group, including alpha-1-antitrypsin, protein S100-A8, myeloperoxidase, peroxiredoxin and lactotransferrin. This group also had 43 down-regulated proteins (P < 0.05), comprising immunoglobulin, neutrophil defensin, pyruvate kinase and alpha-enolase. The qualitative analysis considered only the exclusive proteins of each group. For the symptomatic group, 318 complete proteins and 29 fragments were identified, such as dedicator of cytokinesis protein, intersectin, prostaglandin, phospholipase DDHD2 and superoxide dismutase. For the asymptomatic group, 326 complete proteins and 37 fragments were identified, including azurocidin, C-reactive protein, collagen alpha, cathepsin, heat shock and laminin.

CONCLUSIONS

Quantitative differences in the expression of common proteins in cases of symptomatic and asymptomatic AP were found, which were mostly related to host immune response in both groups. Exclusive proteins in the symptomatic group were mainly related to the host response to the presence of viruses in endodontic infections, oxidative stress and proteolytic enzymes. The results provide a basis for a better understanding of cellular and molecular pathways involved in AP, establishing specific proteomic profiles for symptomatic and asymptomatic conditions.

Human body-fluid proteome: quantitative profiling and computational prediction

Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.

SWATH-MS Protocols in Human Diseases

Identification of molecular biomarkers for human diseases is one of the most important disciplines in translational science as it helps to elucidate their origin and early progression. Thus, it is a key factor in better diagnosis, prognosis, and treatment. Proteomics can help to solve the problem of sample complexity when the most common primary sample specimens were analyzed: organic fluids of easy access. The latest developments in high-throughput and label-free quantitative proteomics (SWATH-MS), together with more advanced liquid chromatography, have enabled the analysis of large sample sets with the sensitivity and depth needed to succeed in this task. In this chapter, we show different sample processing methods (major protein depletion, digestion, etc.) and a micro LC-SWATH-MS protocol to identify/quantify several proteins in different types of samples (serum/plasma, saliva, urine, tears).

Effect of reduction and alkylation treatment in three different assays used for the measurement of oxytocin in saliva of pigs

Oxytocin is a hormone that is increasingly being used for welfare evaluation in animals. Although several types of samples have been used for oxytocin measurement, saliva can be a suitable option for pigs producing less stress than blood sampling. In this study, 3 different methods for oxytocin measurements, 2 based on alphaLISA technology (one with a monoclonal and other with a polyclonal antibody) and one commercially available kit, were compared in saliva of pigs. These methods were used in saliva samples obtained from female pigs at 3 different days during gestation and lactation, with and without a reduction/alkylation (R/A), which is a procedure for breaking the links between oxytocin and proteins of the sample. The assays showed a different behavior after the R/A procedure, with no significant changes in the oxytocin results in case of the alphaLISA monoclonal method, a significant decrease with the alphaLISA polyclonal method, and a significant increase with the commercial kit. Although all assays showed a similar tendency in detecting the changes in oxytocin during gestation and lactation, they showed changes of different magnitude and statistical signification. This report indicates that different assays can measure different forms of oxytocin present in saliva and can have a different behavior after R/A of the sample and when are used to measure oxytocin in gestation and lactation.

A shotgun proteomic approach reveals novel potential salivary protein biomarkers for asthma

OBJECTIVE

The aim of this study was to determine if there is an association between the salivary protein profile and disease control in asthma.

METHODS

Thirty asthmatic patients (17 adults and 13 children) participated in this study. Saliva samples were collected from healthy subjects, controlled and uncontrolled asthmatics. Individual samples from each group were combined to form a pooled sample, from which proteomic analysis was performed using gel-based quantitative proteomics.

RESULTS

Fourteen out of thirty asthmatics were classified to be controlled asthma. Most of asthmatics received inhaled corticosteroids as the controller medications. SDS-PAGE showed predominant bands at high molecular weight in asthmatic saliva compared to that of the controls. Shotgun proteomic analyses indicated that 193 salivary proteins were expressed in both controlled and uncontrolled asthmatics. They were predicted to associate with proteins involved in pathogenesis of asthma including IL-5, IL-6, MCP-1, VEGF, and periostin and asthma medicines (Cromolyn, Nedocromil, and Theophylline). Nucleoside diphosphate kinase (NME1-NME2) only expressed in controlled asthmatics whereas polycystic kidney and hepatic disease 1 (PKHD1)/fibrocystin, zinc finger protein 263 (ZNF263), uncharacterized LOC101060047 (ENSG00000268865), desmoglein 2 (DSG2) and S100 calcium binding protein A2 (S100A2) were only found in uncontrolled asthma. Therefore, the six proteins were associated with disease control in children and adults with asthma.

CONCLUSION

Our findings suggest that NME1-NME2, PKHD1, ZNF 263, uncharacterized LOC101060047, DSG 2 and S100 A2 in saliva are associated with disease control in asthma.

Salivary Hemoglobin Protects against Erosive Tooth Wear in Gastric Reflux Patients

<b><i>Objective:</i></b> Saliva is the most important biological factor to protect against erosive tooth wear (ETW). Gastroesophageal reflux disease (GERD) patients have an increased risk of ETW due to the frequent presence of intrinsic acids in the oral cavity. Remarkably, not all GERD patients suffer from ETW, which might be due to differences in the composition of the saliva. <b><i>Methods:</i></b> This study compared the proteomic profile of saliva in patients (1) with GERD and ETW (basic erosive wear examination, BEWE, score ≥9; GE group) and (2) with GERD without ETW (BEWE = 0; GNE group) using shotgun label-free quantitative proteomic analysis nLC-ESI-MS/MS. The ability of hemoglobin (Hb) to protect against initial enamel erosion caused by a daily 10-s immersion of enamel specimens in 0.01 M HCl (pH 2.3) for 3 days was evaluated in vitro for proof of concept. Surface hardness change was used as response variable. <b><i>Results:</i></b> The differential expression of Hb subunits was significantly increased in the GNE group versus the GE group, in particular the Hb α-subunit that showed a &#x3e;22-fold increase. Expressions of serum albumin (4.5-fold) and isoforms of cytoskeletal keratin type II (&#x3e;3-fold) were also increased in the GNE group. Proteinase inhibitors, such as α₁-antitrypsin and α₂-macroglobulin, were only identified in the GNE group. In vitro, Hb (1.0 and 4.0 mg/mL) significantly reduced initial enamel erosion compared to a negative control after 3 days. <b><i>Conclusions:</i></b> Our results indicate that many proteins, with special emphasis on Hb, may be involved in the resistance of GERD patients to the occurrence of ETW. These proteins may be candidates for inclusion in dental products to protect against ETW.

Salivary proteome analysis of crack cocaine dependents

OBJECTIVE

Salivary proteomic analysis may help to understand physiopathological changes in crack cocaine dependents. This study aimed to compare the salivary protein profile between crack cocaine dependents and non-drug users.

DESIGN

Nine heavy smokers and alcohol consumers men admitted to rehab due to crack cocaine abuse and nine non-drug users age-matched men were evaluated. Unstimulated whole saliva was collected. Proteomic analysis was performed by mass spectrometer. Data were processed using ProteinLynx GlobalServer software. Results were obtained by searching the Homo sapiens database from the UniProt catalog. The search tool IBI-IMIM was used to identify proteins candidates for biomarkers.

RESULTS

The mean age of crack cocaine and control groups was 36.89 ± 7.78 and 35.78 ± 6.68 years, respectively. 458 salivary proteins were identified in both groups; 305 proteins in the crack cocaine group. Among the 68 proteins presented in both groups, 29 were down-regulated (i.e. "Statherin" and "Transforming growth factor-beta-induced protein ig-h3" were down-regulated at least 10-fold) and 27 up-regulated (i.e. "Negative elongation factor" was up-regulated 19-fold) in the crack cocaine group compared to controls. 90 out of the 458 proteins found in the proteomic analysis were identified as candidates for biomarkers of diseases. Among these, 65 (72.22 %) were detected in the crack cocaine group.

CONCLUSION

Crack cocaine dependents with chronic alcohol and tobacco use have a higher number of proteins in saliva compared to non-drug users. 22.3 % of salivary proteins present in crack cocaine dependents were present in controls; 3.9 % of them were expressed in similar quantity.

Salivary protein candidates for biomarkers of oral disorders in alcohol and tobacco dependents

OBJECTIVES

To evaluate the oral condition of alcohol and tobacco dependents and identify salivary protein candidates for biomarkers of oral disorders.

SUBJECTS AND METHODS

Thirty-three male volunteers were evaluated for alcohol abuse rehabilitation; nine were selected for proteomic analysis. Intraoral examination was performed, and non-stimulated saliva was collected. Salivary proteins were extracted and processed for analysis. A list of proteins identified in saliva was generated from the database and manually revised, obtaining the total number of candidate biomarkers for oral disorders.

RESULTS

The mean age (n = 33) was 42.94 ± 8.61 years. Fourteen (42.4%) subjects presented with 23 oral mucosa changes, and 31 (94%) had dental plaque. A total of 282 proteins were found in saliva (n = 9), of which 26 were identified as candidates for biomarkers of oral disorders. After manual review, 21 proteins were selected. The highest number of candidates for biomarkers was associated with carcinoma of head and neck (n = 10), nasopharyngeal carcinoma (n = 6), and periodontal disease (n = 6).

CONCLUSION

Alcohol and tobacco dependents showed gingival inflammation, and less than half of them showed oral mucosa changes. Twenty-one protein candidates for biomarkers of oral disorders were identified in saliva. The two major oral disorders in number of candidates for biomarkers were head and neck cancer and periodontal disease.

Salivary proteome characterization of alcohol and tobacco dependents

BACKGROUND

Alcohol and substances found in tobacco may alter salivary flow and amount of saliva proteins. This study aimed to compare salivary proteins between alcohol dependent smokers and controls.

METHODS

This is a case-control study with men older than 18 years of age, matched by age. The alcohol-dependent group was composed by heavy smokers and alcohol consumers. Unstimulated whole saliva was collected from all subjects. Analysis of digested peptides was performed in mass spectrometer. Data were processed using ProteinLynx GlobalServer software. Results were obtained by searching theHomo sapiens database from the UniProt catalog. The search tool IBI-IMIM was used to identify candidate proteins for biomarkers.

RESULTS

Alcohol-dependent and control groups were composed of nine participants each, with mean age of 36.89 ± 2.57 and 35.78 ± 1.64 years, respectively. 404 salivary proteins were found in both groups; 282 in the alcohol-dependent. Among the 96 proteins presented in both groups, 32 were up-regulated in the alcohol dependents (i.e. "Hemoglobin subunit beta" and "Forkhead box protein P2" were up-regulated at least 10-fold), 23 were down-regulated (i.e. "Statherin" and "RNA-binding protein 25" were down-regulated at least 10-fold), and 41 presented similar expression in both groups. 71 proteins were candidates for biomarkers of disorders 58 presented in alcohol dependents' saliva. The most common disorders were neoplasms, genetic, cardiovascular, metabolic and glandular diseases.

CONCLUSIONS

Salivary protein profile undergoes strong changes in alcohol and tobacco dependents. 34% of salivary proteins present in alcohol and tobacco dependents were present in controls; 14.5% of them were expressed in similar quantity.