Mass spectrometry-based salivary proteomics for the discovery of head and neck squamous cell carcinoma. Pathol Oncol Res. 2012;18:623-628. [PMID: 22350791 DOI: 10.1007/s12253-011-9486-4]

Salivaomics in head and neck cancer

Salivaomics is a promising method for the early detection and monitoring of head and neck cancer (HNC). By analyzing salivary proteomics, RNA, and DNA, it identifies biomarkers that distinguish HNC patients from healthy individuals. Saliva's non-invasive, easily collectible nature and affordability make it an advantageous screening tool. Multiomics approaches, which explore genetic mutations, gene expression patterns, protein profiles, and metabolite levels, provide a comprehensive molecular perspective that enhances clinical applicability. The approaches enhance the precision of diagnoses, enable the development and application of targeted therapies, and contribute to the overall advancement of personalized medicine. Despite its potential, larger-scale studies are essential for validating biomarkers, and assessing sensitivity, accuracy, and specificity in detecting HNC. This review highlights salivaomics' potential as a non-invasive, accessible biological sample for early disease detection in HNC and underscores the value of multiomics in advancing this research. Salivaomics offers significant insights into the underlying mechanisms of HNC, enabling the discovery of robust, non-invasive biomarkers for improved disease management.

Pleomorphic adenoma and carcinoma ex-pleomorphic adenoma tumorigenesis: A proteomic analysis

OBJECTIVES

To conduct a comprehensive proteomic analysis of normal salivary gland tissue, pleomorphic adenoma (PA), and carcinoma ex-pleomorphic adenoma (CXPA), and validate the proteomic findings using immunohistochemistry.

METHODS

Six normal salivary gland tissues, seven PA and seven CXPA samples underwent laser microdissection followed by liquid chromatography coupled to mass spectrometry. Protein identification and quantification were performed using MaxQuant software. Statistical analysis and functional enrichment were conducted using the Perseus platform and STRING tool, respectively. Immunohistochemistry was used for validation.

RESULTS

Comparative proteomic analysis revealed 2680 proteins across the three tissue types, with 799 significantly altered between groups. Translocation protein SEC63 homolog, Annexin A6 and Biglycan were up-regulated in CXPA compared to PA. Decorin was markedly up-regulated in both PA and CXPA compared to normal salivary gland (log2 fold changes of 7.58 and 7.38, respectively). Validation confirmed elevated levels of Biglycan and Decorin in the extracellular matrix of CXPA compared to PA.

CONCLUSIONS

Proteomic analysis identified differential protein expression patterns associated with malignant transformation of PA into CXPA. Findings indicate a crucial role for extracellular matrix proteins, specifically Biglycan and Decorin, in the tumorigenic progression of PA and CXPA.

Salivary Antioxidant Capacity and Magnesium in Generalized Anxiety Disorder

Generalized anxiety disorder (GAD) is a prevalent disorder. The search for biomarkers may contribute to new knowledge about molecular pathogenesis and treatment. Since oxidative stress and micronutrient imbalance play a key role in the development of mental disorders, we aimed to study salivary antioxidant capacity and magnesium in patients with GAD in an anxiety model of solving problems with increasing complexity. The study subgroup consisted of 15 patients with GAD, and 17 healthy volunteers of the same age made up the control subgroup. Participants took a test with six levels of difficulty, which included false feedback. In this test, the participants were asked to remember the colors of balloons and react when the color changed. The reaction time, the number of correct answers, as well as biochemical parameters such as the antioxidant capacity of saliva and salivary magnesium, were assessed. There was no difference in the results of the quest between the subgroups; however, anxious participants spent more time at the moment of experimental frustration due to incorrect feedback and additional negative psycho-emotional load. Antioxidant capacity did not differ between the subgroups both before and after the experimental session. Average antioxidant capacity also did not change significantly at the endpoint of the experiment. However, the endpoint antioxidant capacity correlated negatively with the reaction time in anxious patients in the second block (where the false feedback as a frustrating factor appeared). Magnesium was initially significantly higher in the group of anxious participants and decreased at the experiment endpoint; in healthy patients, there were no changes in salivary magnesium at the endpoint. In conclusion, the compensatory potential of oxidative metabolism and magnesium in patients with GAD was spent with additional psycho-emotional stress, in contrast to healthy individuals, but it was sufficient to avoid exhaustion during experimental frustrating exposure.

Analysis of the saliva metabolic signature in patients with primary Sjögren’s syndrome

Background

The saliva metabolome has been applied to explore disease biomarkers. In this study we characterized the metabolic profile of primary Sjögren’s syndrome (pSS) patients and explored metabolomic biomarkers.

Methods

This work presents a liquid chromatography-mass spectrometry-based metabolomic study of the saliva of 32 patients with pSS and 38 age- and sex-matched healthy adults. Potential pSS saliva metabolite biomarkers were explored using test group saliva samples (20 patients with pSS vs. 25 healthy adults) and were then verified by a cross-validation group (12 patients with pSS vs. 13 healthy adults).

Results

Metabolic pathways, including tryptophan metabolism, tyrosine metabolism, carbon fixation, and aspartate and asparagine metabolism, were found to be significantly regulated and related to inflammatory injury, neurological cognitive impairment and the immune response. Phenylalanyl-alanine was discovered to have good predictive ability for pSS, with an area under the curve (AUC) of 0.87 in the testing group (validation group: AUC = 0.75).

Conclusion

Our study shows that salivary metabolomics is a useful strategy for differential analysis and biomarker discovery in pSS.

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

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

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.

Serum, plasma and saliva biomarkers for head and neck cancer

INTRODUCTION

Head and neck squamous cell carcinoma (HNSCC) encompasses tumors arising from several locations (oral and nasal cavities, paranasal sinuses, salivary glands, pharynx, and larynx) and currently stands as the sixth most common cancer worldwide. The most important risk factors identified so far are tobacco and alcohol consumption, and, for a subgroup of HNSCCs, infection with high-risk types of human papillomavirus (HPV). Despite several improvements in the treatment of these tumors in the last decades, overall survival rates have only improved marginally, mainly due to the advanced clinical stage at diagnosis and the high rates of treatment failure associated with this late diagnosis. Areas covered: This review will focus on the feasibility of evaluating molecular-based biomarkers (mRNA, microRNA, lncRNA, DNA methylation and protein expression) in body fluids (serum, plasma, and saliva) as markers for diagnosis, prognosis, and surveillance. Expert commentary: The potential use of those markers in the clinical setting would allow for early diagnosis, prediction of treatment response, improvement in treatment selection and provide disease monitoring for early detection of tumor recurrence. It can ultimately be translated into better survival rates and improved quality of life for HNSCC patients.

Comparative proteomic analysis of the influence of gender and acid stimulation on normal human saliva using LC/MS/MS

PURPOSE

Human saliva is an important source for disease biomarker discovery. This study is to investigate the influence of gender and acid stimulation on the normal human salivary proteome.

EXPERIMENTAL DESIGN

Unstimulated and acid-stimulated saliva samples from 5 males and 5 females were labeled with 4-plex iTRAQ and analyzed by 2-DLC MS/MS. By bioinformatics analysis the gender and acid stimulation related proteins were defined. According to protein annotation the important proteins were validated by multiple reaction monitor analysis.

RESULTS

A total of 1770 proteins were identified, and 82 proteins in unstimulated saliva were found to be gender-specific, mainly associated with immune function, metabolism and inflammation. However, no gender-specific proteins were found in acid-stimulated saliva. In addition, 182 and 307 differential proteins were found to be acid stimulation-specific in male samples and female samples, respectively, mainly participated in the process of cellular movement, immune function and inflammatory response. Besides, it was found that acid stimulation caused more significant alteration and played a more important role in the human salivary proteome than gender. Gender-specific (IGHG2 and TIMP1) and acid stimulation (PERL, ENOA, ACTB, B4E022 and CALL3) related proteins were validated by MRM analysis.

CONCLUSIONS AND CLINICAL RELEVANCE

The results indicate that gender differences exist in the unstimulated salivary proteome, and the influence of acid stimulation on the salivary proteome was more significant than that of gender. The above results may be helpful for salivary proteome research in the future.

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

BACKGROUND

Cutaneous squamous cell carcinoma (cSCC) is a common type of skin cancer but there are no comprehensive proteomic studies on this entity.

MATERIALS AND METHODS

We employed liquid chromatography coupled with tandem mass spectrometry (MS/MS) using formalin-fixed paraffin-embedded (FFPE) cSCC material to study the tumor and normal skin tissue proteomes. Ingenuity Pathway Analysis (IPA) was used to interpret the role of altered proteins in cSCC pathophysiology. Results were validated using the Human Protein Atlas and Oncomine database in silico.

RESULTS

Of 1,310 unique proteins identified, expression of an average of 144 and 88 proteins were significantly (p<0.05) increased and decreased, respectively, in the tumor samples compared to their normal counterparts. IPA analysis revealed disruptions in proteins associated with cell proliferation, apoptosis, and migration. In silico analysis confirmed that proteins corresponding to 12 antibodies, and genes corresponding to 18 proteins were differentially expressed between the two categories, validating our proteomic measurements.

CONCLUSION

Label-free MS-based proteomics is useful for analyzing FFPE cSCC tissues.

Proteomic study of benign and malignant pleural effusion

BACKGROUND

Lung adenocarcinoma can easily cause malignant pleural effusion which was difficult to discriminate from benign pleural effusion. Now there was no biomarker with high sensitivity and specificity for the malignant pleural effusion.

PURPOSE

This study used proteomics technology to acquire and analyze the protein profiles of the benign and malignant pleural effusion, to seek useful protein biomarkers with diagnostic value and to establish the diagnostic model.

METHODS

We chose the weak cationic-exchanger magnetic bead (WCX-MB) to purify peptides in the pleural effusion, used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to obtain peptide expression profiles from the benign and malignant pleural effusion samples, established and validated the diagnostic model through a genetic algorithm (GA) and finally identified the most promising protein biomarker.

RESULTS

A GA diagnostic model was established with spectra of 3930.9 and 2942.8 m/z in the training set including 25 malignant pleural effusion and 26 benign pleural effusion samples, yielding both 100 % sensitivity and 100 % specificity. The accuracy of diagnostic prediction was validated in the independent testing set with 58 malignant pleural effusion and 34 benign pleural effusion samples. Blind evaluation was as follows: the sensitivity was 89.6 %, specificity 88.2 %, PPV 92.8 %, NPV 83.3 % and accuracy 89.1 % in the independent testing set. The most promising peptide biomarker was identified successfully: Isoform 1 of caspase recruitment domain-containing protein 9 (CARD9), with 3930.9 m/z, was decreased in the malignant pleural effusion.

CONCLUSIONS

This model is suitable to discriminate benign and malignant pleural effusion and CARD9 can be used as a new peptide biomarker.

Differences in the whole saliva baseline proteome profile associated with development of oral mucositis in head and neck cancer patients undergoing radiotherapy

Oral mucositis (OM) is a common, painful and often treatment-limiting side effect of radiotherapy (RT) for head and neck cancer (HNC) patients. Unstimulated saliva was collected before the first radiotherapy application in 50 HNC patients. 41 out of 50 patients developed OM (grade III) during radiotherapy, of which 14 patients even displayed an early OM (grade III) at a low radiation dose of 30Gy. Nine patients did not develop OM (grade III). Using an LC-MS/MS approach 5323 tryptic peptides were assigned to 487 distinct proteins (≥2 peptides) in the data set. The levels of 48 proteins differed significantly (p<0.05) between patients developing OM or not. 17 proteins displayed increased levels (≥1.3-fold) and 31 proteins decreased in level in OM, respectively. Furthermore, using partial least square analysis protein patterns could be used to distinguish subjects which did not develop grade III OM even after 70Gy total dose (n=9) and those displaying early OM (grade III at <30Gy total dose, n=14). Using leave one out cross validation 37 of 41 patients (90%) developing OM could be correctly assigned indicating that prognostic proteome signatures may help identify patients that should be specifically monitored to increase overall effectiveness of RT treatment.

Biological sample collection for clinical proteomics: existing SOPs

Proteomic study of clinical samples aims at the better understanding of physiological and pathological conditions, as well as the discovery of diagnostic and prognostic markers for the latter. Quantitative and/or qualitative variations of body fluid proteome may reflect health- or disease-associated events connected to the adjacent or distant body regions of the fluid production/secretion/excretion and/or systemic reactions to the presence of disease. Sample collection and preparation is a critical step in order to obtain useful and valid information in clinical proteomics analysis. In this chapter, we present the current protocols and guidelines for human body fluid collection and storage, prior to proteomic analysis. A variety of body fluids that are currently being used in proteomic analysis and have potential interest in clinical practice are presented including blood plasma and serum, urine, cerebrospinal fluid, cerumen, nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma. With no doubt these body fluids differ in the extent of their application in clinical proteomics investigations, hence in some cases the presented SOPs are established following more extensive testing (e.g., plasma, serum, urine, CSF) than others (nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma). However, even in these latter cases, the presented protocols were reported by at least two independent groups according to the literature. We hope they can thus serve as a reliable guide for sample collection based on our current knowledge in the field and excellent starting points for proteomics investigators. It should also be pointed that variations to these protocols exist and their further refinement in the future is foreseen following the evolution of the proteomics technologies.

Salivary biomarkers indicate obstructive sleep apnea patients with cardiovascular diseases

Although obstructive sleep apnea (OSA) patients are at high risk of developing cardiovascular disease (CVD), only a small proportion is currently diagnosed. To explore and identify the differentially expressed proteins/peptides of OSA patients with CVDs, a mass spectrometry-based salivary analysis was performed. In our study, eleven peaks were observed differentially expressed in saliva from the non-CVD and CVD groups. Five masses mass peaks (1594.1, 1673.7, 1196.6, 1290.5, and 1447.0 Da) showed an upregulated trend in the CVD group, whereas six mass peaks (3038.6, 2164.3, 2301.4, 3195.0, 2628.4, and 1721.9 Da) were downregulated in the CVD group. In addition, the alpha-2-HS-glycoprotein (AHSG) levels in saliva were verified to be decreased in CVD group compared to non-CVD group. Analysis of the salivary peptidome provides a promising approach to screening for novel biomarkers before further identification, and may contribute to early diagnosis of CVD patients with OSA.

Top-down analytical platforms for the characterization of the human salivary proteome

Comprehensive analysis and characterization of the human salivary proteome is an important step towards the possible use of saliva for diagnostic and prognostic purposes. The contribution of the different sources to whole saliva, and the evaluation of individual variability and physiological modifications have been investigated by top-down proteomic approaches, disclosing the faceted and complex profile of the human salivary proteome. All this information is essential to develop saliva protein biomarkers. In this Review the major results obtained in the field by top-down platforms, and the improvements required to allow a more complete picture, will be discussed.

Identification of human tissue kallikrein 6 as a potential marker of laryngeal cancer based on the relevant secretory/releasing protein database

OBJECTIVE

This study was aimed to create a large-scale laryngeal cancer relevant secretory/releasing protein database and further discover candidate biomarkers.

METHODS

Primary tissue cultures were established using tumor tissues and matched normal mucosal tissues collected from four laryngeal cancer patients. Serum-free conditioned medium (CM) samples were collected. These samples were then sequentially processed by SDS-PAGE separation, trypsin digestion, and LC-MS/MS analysis. The candidates in the database were validated by ELISA using plasma samples from laryngeal cancer patients, benign patients, and healthy individuals.

RESULTS

Combining MS data from the tumor tissues and normal tissues, 982 proteins were identified in total; extracellular proteins and cell surface proteins accounted for 15.0% and 4.3%, respectively. According to stringent criteria, 49 proteins were selected as candidates worthy of further validation. Of these, human tissue kallikrein 6 (KLK6) was verified. The level of KLK6 was significantly increased in the plasma samples from the cancer cohort compared to the benign and healthy cohorts and moreover showed a slight decrease in the postoperative plasma samples in comparison to the preoperative plasma samples.

CONCLUSIONS

This laryngeal cancer-derived protein database provides a promising repository of candidate blood biomarkers for laryngeal cancer. The diagnostic potential of KLK6 deserves further investigation.

Potential role of Anxa1 in cancer

The annexins are a well-known, closely related, multigene superfamily of Ca2+-regulated, phospholipid-dependent, membrane-binding proteins. As a member of the annexins, Anxa1 participates in a variety of important biological processes, such as cellular transduction, membrane aggregation, inflammation, phagocytosis, proliferation, differentiation and apoptosis. Accumulated evidence has indicated that Anxa1 deregulations are associated with the development, invasion, metastasis, occurrence and drug resistance of cancers. The research evidence in recent years indicates that Anxa1 might specifically function either as a tumor suppressor or a tumor promoter candidate for certain cancers depending on the particular type of tumor cells/tissues. This article summarizes the associations between Anxa1 and malignant tumors, as well as potential action mechanisms. Anxa1 has the potential to be used in the future as a biomarker for the diagnosis, treatment and prognosis of certain tumors.

Laser ionization mass spectrometry in oral squamous cell carcinoma

Biomarker research in oral squamous cell carcinoma (OSCC) aims for screening/early diagnosis and in predicting its recurrence, metastasis and overall prognosis. This article reviews the current molecular perspectives and diagnosis of oral cancer with proteomics using matrix-assisted laser desorption ionization (MALDI) and surface-enhanced laser desorption ionization (SELDI) mass spectrometry (MS). This method shows higher sensitivity, accuracy, reproducibility and ability to handle complex tissues and biological fluid samples. However, the data interpretation tools of contemporary mass spectrometry still warrant further improvement. Based on the data available with laser-based mass spectrometry, biomarkers of OSCC are classified as (i) diagnosis and prognosis, (ii) secretory, (iii) recurrence and metastasis, and (iv) drug targets. Majority of these biomarkers are involved in cell homeostasis and are either physiologic responders or enzymes. Therefore, proteins directly related to tumorigenesis have more diagnostic value. Salivary secretory markers are another group that offers a favourable and easy strategy for non-invasive screening and early diagnosis in oral cancer. Key molecular inter-related pathways in oral carcinogenesis are also intensely researched with software analysis to facilitate targeted drug therapeutics. The review suggested the need for incorporating 'multiple MS or tandem approaches' and focusing on a 'group of biomarkers' instead of single protein entities, for making early diagnosis and treatment for oral cancer a reality.

Annexin-A1 protein and its relationship to cortisol in human saliva

Salivary cortisol is commonly used as a clinical biomarker of endocrine status and also as a marker of psychosocial stress. Annexin-A1 (AnxA1) is an anti-inflammatory protein whose expression is modulated by glucocorticoids. Our principal objectives were to (i) detect the presence of and (ii) measure AnxA1 protein in whole human saliva and to (iii) investigate whether salivary cortisol and AnxA1 are correlated in healthy humans. A total of 37 healthy participants (male and female) were used in the study. Saliva was collected using salivette tubes. Salivary cortisol and AnxA1 protein were sampled at between 3 and 6 time points over 24h and measured for cortisol and AnxA1 protein using specific ELISA's. The presence of salivary AnxA1 protein was confirmed by Western blotting. AnxA1 protein is detectable in whole human saliva, as detected by Western blot analysis and ELISA. A diurnal rhythm was evident in both salivary cortisol (P<0.01) and AnxA1 (P<0.01) and was defined as a significant difference in time 0 (waking) samples compared to 'bed' (2300 h) samples. AnxA1 protein did not exhibit an awakening response (P>0.05), whereas salivary cortisol was significantly elevated between time 0 and 30 min post waking (P<0.001). AnxA1 protein correlates positively with salivary cortisol, indicating that cortisol is most likely a regulator of AnxA1 in human saliva.

Secretome analysis using a hollow fiber culture system for cancer biomarker discovery

Secreted proteins, collectively referred to as the secretome, were suggested as valuable biomarkers in disease diagnosis and prognosis. However, some secreted proteins from cell cultures are difficult to detect because of their intrinsically low abundance; they are frequently masked by the released proteins from lysed cells and the substantial amounts of serum proteins used in culture medium. The hollow fiber culture (HFC) system is a commercially available system composed of small fibers sealed in a cartridge shell; cells grow on the outside of the fiber. Recently, because this system can help cells grow at a high density, it has been developed and applied in a novel analytical platform for cell secretome collection in cancer biomarker discovery. This article focuses on the advantages of the HFC system, including the effectiveness of the system for collection of secretomes, and reviews the process of cell secretome collection by the HFC system and proteomic approaches to discover cancer biomarkers. The HFC system not only provides a high-density three-dimensional (3D) cell culture system to mimic tumor growth conditions in vivo but can also accommodate numerous cells in a small volume, allowing secreted proteins to be accumulated and concentrated. In addition, cell lysis rates can be greatly reduced, decreasing the amount of contamination by abundant cytosolic proteins from lysed cells. Therefore, the HFC system is useful for preparing a wide range of proteins from cell secretomes and provides an effective method for collecting higher amounts of secreted proteins from cancer cells. This article is part of a Special Issue entitled: An Updated Secretome.

Salivary proteomics in biomedical research

Proteins that are important indicators of physiological or pathological states, can provide information for the identification of early and differential markers for disease. Saliva, contains an abundance of proteins, offers an easy, inexpensive, safe, and non-invasive approach for disease detection, and possesses a high potential to revolutionize the diagnostics. Discovery of salivary biomarkers could be used to scrutinize health and disease surveillance. The impact of human saliva proteome analysis in the search for clinically relevant disease biomarkers will be realized through advances made using proteomic technologies. The advancements of emerging proteomic techniques have benefited biomarker research to the point where saliva is now recognized as an excellent diagnostic medium for the detection of disease. This review presents an overview of the value of saliva as a credible diagnostic tool and we aim to summarize the proteomic technologies currently used for global analysis of saliva proteins and to elaborate on the application of saliva proteomics to the discovery of disease biomarkers, and discuss some of the critical challenges and perspectives in this field.

One decade of salivary proteomics: current approaches and outstanding challenges

Efforts have been made in the last decade towards the complete characterization of saliva proteome using gel-based and gel-free approaches. The combination of these strategies resulted in the increment of the dynamic range of saliva proteome, which yield in the identification of more than 3,000 different protein species. Comparative protein profiling using isotope labeling and label free approaches has been used for the identification of novel biomarkers for oral and related diseases. Although progresses have been made in saliva proteome characterization, the comparative profiling in different pathophysiological conditions is still at the beginning if compared to other bodily fluids. The potential biomarkers identified so far lack specificity once common differentially expressed proteins were detected in the saliva of patients with distinct diseases. In addition, recent research works focused on saliva peptidome profiling already allowed a better understanding of peptides' physiological role in oral cavity. This review provides an overview of the major achievements in saliva proteomics giving emphasis to methodological concerns related with saliva collection, treatment and analysis, as well as the main advantages and pitfalls underlying salivary proteomic strategies and potential clinical outcomes.

Advances in proteomics of digestive juices for the diagnosis of digestive system malignancies

Body fluid proteomic analysis is a new technology and strategy for disease diagnosis and treatment. Blood is the most commonly used specimen in body fluid proteomics, but as a systemic fluid, it has limitations because of complex composition and low abundance of disease-related proteins. In contrast, local body fluids are closest to the lesions, contain more pathological information, and therefore are more valuable in clinical proteomics. In the digestive system, there are a variety of body fluids which are considered potential reservoirs of biomarkers for their quality and quantity of proteins will alter during lesions occurring in corresponding organs. In recent years, more and more clinical proteomic analyses of saliva, gastric juice, bile and pancreatic juice has been reported and the proteins related to digestive cancers have been found, and some proteins show application potentials in cancer diagnosis. However, the proteomic analyses of digestive juices are facing technical challenges in terms of the reproducibility of results and standardization of specimen handling.