Implications of salivary proteomics in drug discovery and development: a focus on cancer drug discovery

Review Insights on Salivary Proteomics Biomarkers in Oral Cancer Detection and Diagnosis

Early detection is crucial for the treatment and prognosis of oral cancer, a potentially lethal condition. Tumor markers are abnormal biological byproducts produced by malignant cells that may be found and analyzed in a variety of bodily fluids, including saliva. Early detection and appropriate treatment can increase cure rates to 80-90% and considerably improve quality of life by reducing the need for costly, incapacitating medicines. Salivary diagnostics has drawn the interest of many researchers and has been proven to be an effective tool for both medication monitoring and the diagnosis of several systemic diseases. Since researchers are now searching for biomarkers in saliva, an accessible bodily fluid, for noninvasive diagnosis of oral cancer, measuring tumor markers in saliva is an interesting alternative to blood testing for early identification, post-treatment monitoring, and monitoring high-risk lesions. New molecular markers for oral cancer detection, treatment, and prognosis have been found as a result of developments in the fields of molecular biology and salivary proteomics. The numerous salivary tumor biomarkers and how they relate to oral cancer and pre-cancer are covered in this article. We are optimistic that salivary protein biomarkers may one day be discovered for the clinical detection of oral cancer because of the rapid advancement of proteomic technology.

Reshaping de Novo Protein Switches into Bioresponsive Materials for Biomarker, Toxin, and Viral Detection

De novo designed protein switches are powerful tools to specifically and sensitively detect diverse targets with simple chemiluminescent readouts. Finding an appropriate material host for de novo designed protein switches without altering their thermodynamics while preserving their intrinsic stability over time would enable the development of a variety of sensing formats to monitor exposure to pathogens, toxins, and for disease diagnosis. Here, a de novo protein-biopolymer hybrid that maintains the detection capabilities induced by the conformational change of the incorporated proteins in response to analytes of interest is generated in multiple, shelf-stable material formats without the need of refrigerated storage conditions. A set of functional demonstrator devices including personal protective equipment such as masks and laboratory gloves, free-standing films, air quality monitors, and wearable devices is presented to illustrate the versatility of the approach. Such formats are designed to be responsive to human epidermal growth factor receptor (HER2), anti-hepatitis B (HBV) antibodies, Botulinum neurotoxin B (BoNT/B), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This combination of form and function offers wide opportunities for ubiquitous sensing in multiple environments by enabling a large class of bio-responsive interfaces of broad utility.

Salivary Biomarkers in Lung Cancer

A very low percentage of lung cancer (LC) cases are discovered at an early and treatable stage of the disease, leading to an abysmally low 5-year survival rate. This underscores the immediate necessity for improved diagnostic, prognostic, and predictive biomarkers for LC. Biopsied lung tissue, blood, and plasma are common sources used for LC diagnosis and monitoring of the disease. A growing number of studies have reported saliva to be a useful biological sample for early and noninvasive detection of oral and systemic diseases. Nevertheless, salivary biomarker discovery remains underresearched. Here, we have compiled the available literature to provide an overview of the current understanding of salivary markers for LC detection and provided perspectives for future clinical significance. Valuable markers with diagnostic and prognostic potentials in LC have been discovered in saliva, including metabolic (catalase activity, triene conjugates, and Schiff bases), inflammatory (interleukin 10, C-X-C motif chemokine ligand 10), proteomic (haptoglobin, zinc-α-2-glycoprotein, and calprotectin), genomic (epidermal growth factor receptor), and microbial candidates (Veillonella and Streptococcus). In combination, with each other and with other established screening methods, these salivary markers could be useful for improving early detection of the disease and ultimately improve the survival odds of LC patients. The existing literature suggests that saliva is a promising biological sample for identification and validation of biomarkers in LC, but how saliva can be utilized most effectively in a clinical setting for LC management is still under investigation.

More Accurate Oral Cancer Screening with Fewer Salivary Biomarkers

Signal detection and Bayesian inferential tools were applied to salivary biomarkers to improve screening accuracy and efficiency in detecting oral squamous cell carcinoma (OSCC). Potential cancer biomarkers are identified by significant differences in assay concentrations, receiver operating characteristic areas under the curve (AUCs), sensitivity, and specificity. However, the end goal is to report to individual patients their risk of having disease given positive or negative test results. Likelihood ratios (LRs) and Bayes factors (BFs) estimate evidential support and compile biomarker information to optimize screening accuracy. In total, 26 of 77 biomarkers were mentioned as having been tested at least twice in 137 studies and published in 16 summary papers through 2014. Studies represented 10 212 OSCC and 25 645 healthy patients. The measure of biomarker and panel information value was number of biomarkers needed to approximate 100% positive predictive value (PPV). As few as 5 biomarkers could achieve nearly 100% PPV for a disease prevalence of 0.2% when biomarkers were ordered from highest to lowest LR. When sequentially interpreting biomarker tests, high specificity was more important than test sensitivity in achieving rapid convergence toward a high PPV. Biomarkers ranked from highest to lowest LR were more informative and easier to interpret than AUC or Youden index. The proposed method should be applied to more recently published biomarker data to test its screening value.

Salivary Biomarkers Associated With Bone Deterioration in Patients With Medication-Related Osteonecrosis of the Jaws

PURPOSE

The purpose of this study was to investigate the use of saliva as a medium for the identification of biomarkers associated with bone resorption and formation. The authors hypothesized that biomarkers, such as N-telopeptide of type I collagen (NTX) and bone-specific alkaline phosphatase (B-AP), could be identified in saliva. They further hypothesized that there would be a difference between these biomarkers in the saliva of patients with medication-relation osteonecrosis of the jaws (MRONJ) and those who have no risk factors for the development of MRONJ.

PATIENTS AND METHODS

This case-and-control study compared 2 salivary biomarkers, NTX and B-AP, in a group of patients with MRONJ and a control group. The predictor variable was the presence or absence of the disease (MRONJ or control group); the outcome variables were the levels of the 2 salivary biomarkers, NTX and B-AP. Saliva samples from 20 patients with a diagnosis of MRONJ and 14 control participants who were comparable to the study group with no history of antiresorptive medication use were collected. The saliva samples were analyzed using 2 commercially available assays for NTX and B-AP to evaluate for levels of each marker. A 2-tailed t test for 2 groups of unequal distribution was used for statistical analysis, with P values less than .05 considered statistically.

RESULTS

The 2 biomarkers, NTX and B-AP, were detected in saliva samples from the MRONJ and control groups. A statistically significant difference was found in the levels of NTX in saliva of patients with MRONJ compared with the control participants (P = .0067).

CONCLUSIONS

In this exploratory study, the 2 bone deterioration biomarkers (NTX and B-AP) were detected in saliva. There was a statistical difference in the levels of salivary NTX between patients with MRONJ and controls. Saliva evaluation could provide a novel method to detect, diagnose, stage, and potentially guide treatment decisions and monitor outcomes for patients with MRONJ in the future.

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.

Proteomic analysis of human saliva from lung cancer patients using two-dimensional difference gel electrophoresis and mass spectrometry

Lung cancer is often asymptomatic or causes only nonspecific symptoms in its early stages. Early detection represents one of the most promising approaches to reduce the growing lung cancer burden. Human saliva is an attractive diagnostic fluid because its collection is less invasive than that of tissue or blood. Profiling of proteins in saliva over the course of disease progression could reveal potential biomarkers indicative of oral or systematic diseases, which may be used extensively in future medical diagnostics. There were 72 subjects enrolled in this study for saliva sample collection according to the approved protocol. Two-dimensional difference gel electrophoresis combined with MS was the platform for salivary proteome separation, quantification, and identification from two pooled samples. Candidate proteomic biomarkers were verified and prevalidated by using immunoassay methods. There were 16 candidate protein biomarkers discovered by two-dimensional difference gel electrophoresis and MS. Three proteins were further verified in the discovery sample set, prevalidation sample set, and lung cancer cell lines. The discriminatory power of these candidate biomarkers in lung cancer patients and healthy control subjects can reach 88.5% sensitivity and 92.3% specificity with AUC = 0.90. This preliminary data report demonstrates that proteomic biomarkers are present in human saliva when people develop lung cancer. The discriminatory power of these candidate biomarkers indicate that a simple saliva test might be established for lung cancer clinical screening and detection.

iTRAQ™ labeling coupled with LC-MALDI mass spectrometry for monitoring temporal response of colorectal cancer cells to butyrate treatment

Mass spectrometry (MS)-based quantitative proteomics plays important roles in drug discovery. In this chapter, we describe a stable isotope labeling technique which employs 4-plex iTRAQ(™) isobaric reagents coupled with two-dimensional (2-D) liquid chromatography (LC) and MALDI-TOF/TOF MS, for a temporal study of HCT-116 colon carcinoma cells treated with butyrate. Butyrate is a short-chain fatty acid fermentation by-product of fiber that can induce temporal cell maturation, from the early phase of growth arrest, to differentiation, and to the activation of apoptotic cascades. Our quantitative proteomics study uncovered several integrated cellular processes and pathways involved in growth arrest, apoptosis, and metastasis. Selected protein targets are validated by real-time PCR and western blotting.

Saliva: diagnostics and therapeutic perspectives

For the past two decades, salivary diagnostic approaches have been developed to monitor oral diseases such as periodontal diseases and to assess caries risk. Recently, the combination of emerging biotechnologies and salivary diagnostics has extended the range of saliva-based diagnostics from the oral cavity to the whole physiologic system as most compounds found in blood are also present in saliva. Accordingly, saliva can reflect the physiologic state of the body, including emotional, endocrinal, nutritional and metabolic variations and acts as a source for the monitoring of oral and also systemic health. This review presents an update on the status of saliva diagnostics and delves into their applications to the discovery of biomarkers for cancer detection and therapeutic applications. Translating scientific findings of nucleic acids, proteins and metabolites in body fluids to clinical applications is a cumbersome and challenging journey. Our research group is pursuing the biology of salivary analytes and the development of technologies for detection of distinct biomarkers with high sensitivity and specificity. The avenue of saliva diagnostics incorporating transcriptomic, proteomic and metabolomic findings will enable us to connect salivary molecular analytes to monitor therapies, therapeutic outcomes, and finally disease progression in cancer.

Mass spectrometry-based clinical proteomics: head-and-neck cancer biomarkers and drug-targets discovery

Mass spectrometry (MS)-based proteomics is a rapidly developing technology for both qualitative and quantitative analyses of proteins, and investigations into protein posttranslational modifications, subcellular localization, and interactions. Recent advancements in MS have made tremendous impact on the throughput and comprehensiveness of cancer proteomics, paving the way to unraveling deregulated cellular pathway networks in human malignancies. In turn, this knowledge is rapidly being translated into the discovery of novel potential cancer markers (PCMs) and targets for molecular therapeutics. Head-and-neck cancer is one of the most morbid human malignancies with an overall poor prognosis and severely compromised quality of life. Early detection and novel therapeutic strategies are urgently needed for more effective disease management. The characterizations of protein profiles of head-and-neck cancers and non-malignant tissues, with unprecedented sensitivity and precision, are providing technology platforms for identification of novel PCMs and drug targets. Importantly, low-abundance proteins are being identified and characterized, not only from the tumor tissues, but also from bodily fluids (plasma, saliva, and urine) in a high-throughput and unbiased manner. This review is a critical appraisal of recent advances in MS-based proteomic technologies and platforms for facilitating the discovery of biomarkers and novel drug targets in head-and-neck cancer. A major challenge in the discovery and verification of these cancer biomarkers is the typically limited availability of well-characterized and adequately stored clinical samples in tumor and sera banks, collected using recommended procedures, and with detailed information on clinical, pathological parameters, and follow-up. Most biomarker discovery studies use limited number of clinical samples and verification of cancer markers in large number of samples is beyond the scope of a single laboratory. The validation of these potential markers in large sample cohorts in multicentric studies is needed for their translation from the bench to the bedside.

Salivary markers for oral cancer detection

Oral cancer refers to all malignancies that arise in the oral cavity, lips and pharynx, with 90% of all oral cancers being oral squamous cell carcinoma. Despite the recent treatment advances, oral cancer is reported as having one of the highest mortality ratios amongst other malignancies and this can much be attributed to the late diagnosis of the disease. Saliva has long been tested as a valuable tool for drug monitoring and the diagnosis systemic diseases among which oral cancer. The new emerging technologies in molecular biology have enabled the discovery of new molecular markers (DNA, RNA and protein markers) for oral cancer diagnosis and surveillance which are discussed in the current review.

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

OBJECTIVE

Saliva is a biofluid that can be obtained from individuals without supervision by health care providers. To maximize this clinical advantage, it is highly desirable to have a global salivary analyte stabilizer for proteins, RNA and DNA at ambient temperature.

DESIGN

Whole saliva, saliva supernatant and saliva filtrate (5.0 microm) were treated with RPS at room temperature (RT) for up to 6 days and then subjected to SDS-PAGE. Immunoblotting of beta-actin and cystatin C were used to evaluate protein stability. For salivary DNA/RNA, whole saliva was incubated with RPS at RT for up to 10 weeks. After extracting total DNA/RNA in samples at week 0, 2, 6 and 10, DNA stability was assayed by chromosome 18 DNA qPCR and RNA stability by beta-actin mRNA RT-qPCR.

RESULTS

beta-actin completely degraded in all types of saliva samples after 6-day incubation at RT. However, 24.0%, 91.4% and 89.3% of beta-actin remained intact with RPS for whole saliva, saliva supernatant and filtrate, respectively. Similarly, 70.3% of cystatin C in supernatant remained intact in the presence of RPS. For salivary DNA/RNA, the cycle threshold (Ct) values showed no significant change for chromosome 18 DNA and beta-actin mRNA in RPS-incubated saliva during the 10-week time course while significant increase in Ct values were observed in controls without RPS for both beta-actin mRNA and DNA.

CONCLUSIONS

RPS provided effective concurrent stabilization to salivary DNA/RNA in whole saliva for up to 10 weeks and proteins in saliva filtrate for 6 days at RT. We also achieved separation of saliva supernatant from cellular elements by a simple filtration step (bypassing the need for centrifugation).

Innovations, challenges and future prospects of oncoproteomics

Oncoproteomics is playing an increasingly important role in the diagnosis and management of cancer as well as in the development of personalized treatment of cancer. Innovative proteomic technologies relevant to cancer are described briefly, which are helping in the understanding of mechanism of drug resistance in cancer and will provide some leads to improve the management. Most important of these are nanoproteomics, i.e. application of nanobiotechnology to proteomics is playing an important role in nanooncology. Examples of some cancers will be given to point out the challenges and future prospects of oncoproteomics including those involving translation of technologies from the bench to the bedside.

arNOX activity of saliva as a non-invasive measure of coenzyme Q10 response in human trials

arNOX is a coenzyme Q10-inhibited, aging-related ECTO-NOX protein of the cell surface also present in sera. It is capable of superoxide generation measured as superoxide dismutase-inhibited reduction of ferricytochrome c and is a potential contributor to atherogenic risk. Here, we report an arNOX activity of saliva of older individuals also inhibited by coenzyme Q10. The activity first appears after age 30 to a near maximum at about age 55. Those surviving beyond age 55 usually have reduced arNOX activities. Our studies demonstrate significant (25 to 30%) reduction of arNOX levels with coenzyme Q10 supplementation of 60 mg (2 x 30 mg) per day for 28 days. Activity correlated with age. Response to coenzyme Q10 increased with age being greatest between ages 60 and 65. Saliva arNOX levels varied in a regular pattern throughout the day so it was important that samples be collected at approximately the same time each day for comparative purposes. The coenzyme Q10 response was reversible and within 12 h after the last intake of coenzyme Q10, the salivary arNOX levels returned to base line. The findings suggest that salivary arNOX provides a convenient and non-invasive method to monitor arNOX levels in clinical coenzyme Q10 intervention trials with the response levels paralleling those seen with serum and cellular arNOX.