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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (25 January 2024) | Viewed by 12331

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Dr. Barbara Manconi

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Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, Cagliari, Italy
Interests: proteomics; mass spectrometry; biomarker discovery; PTMs characterization; saliva
Special Issues, Collections and Topics in MDPI journals

Dr. Tiziana Cabras

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Guest Editor

Biomedical Section–Proteomics Unit, Department of Life and Environmental Sciences, Cagliari State University, Cagliari, Italy
Interests: proteomics; biomarker discovery; mass spectrometry; post-translational modifications; salivary proteomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recently, saliva has arisen as a biological matrix with huge potential beyond its applications in oral health. It is an incredibly complex biofluid which plays a critical role in normal human physiology and pathology. There has been long-standing interest in saliva for its uses in non-invasive biomarker discovery, human health monitoring, human microbiome analysis, and, more recently, for disease surveillance of the SARS-CoV-2 pandemic. Saliva omics is a field with broad profiling that includes, but is not limited to, proteomics and metabolomics, transcriptomics, extracellular vesicle profiling, miRNAs, salivary microbiomes and meta-proteomics.

This Special Issue plans to offer an overview of recent advances in omics technologies in diverse areas of salivary biomedical research, with special emphasis on proteomics-based biomarker discovery. Since the analysis of proteoforms, as biochemical indicators of health or disease, has a longstanding history in biomedical research, descriptions of Post-Translational Modifications of salivary proteins are also welcome.

For this Issue, we invite you and your colleagues to submit an original research article or comprehensive review article related to this field.

Dr. Barbara Manconi
Dr. Tiziana Cabras
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

saliva
proteomics
metabolomics
metaproteomics
microbiomics
transcriptomics
mass-spectrometry
biomarkers
PTMs

Related Special Issue

Omics Sciences for Salivary Diagnostics 2.0 in International Journal of Molecular Sciences

Published Papers (10 papers)

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Research

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17 pages, 3865 KiB

Open AccessArticle

Long-Term Exposure to Supraphysiological Levels of Testosterone Impacts Rat Submandibular Gland Proteome

by João Valente-Santos, Rui Vitorino, Cláudia Sousa-Mendes, Paula Oliveira, Bruno Colaço, Ana I. Faustino-Rocha, Maria João Neuparth, Adelino Leite-Moreira, José Alberto Duarte, Rita Ferreira and Francisco Amado

Int. J. Mol. Sci. 2024, 25(1), 550; https://doi.org/10.3390/ijms25010550 - 31 Dec 2023

Viewed by 949

Abstract

The salivary glands play a central role in the secretion of saliva, whose composition and volume affect oral and overall health. A lesser-explored dimension encompasses the possible changes in salivary gland proteomes in response to fluctuations in sex hormone levels. This study aimed to examine the effects of chronic exposure to testosterone on salivary gland remodeling, particularly focusing on proteomic adaptations. Therefore, male Wistar rats were implanted with subcutaneous testosterone-releasing devices at 14 weeks of age. Their submandibular glands were histologically and molecularly analyzed 47 weeks later. The results underscored a significant increase in gland mass after testosterone exposure, further supported by histologic evidence of granular duct enlargement. Despite increased circulating sex hormones, there was no detectable shift in the tissue levels of estrogen alpha and androgen receptors. GeLC-MS/MS and subsequent bioinformatics identified 308 proteins in the submandibular glands, 12 of which were modulated by testosterone. Of note was the pronounced upregulation of Klk3 and the downregulation of Klk6 and Klk7 after testosterone exposure. Protein–protein interaction analysis with the androgen receptor suggests that Klk3 is a potential target of androgenic signaling, paralleling previous findings in the prostate. This exploratory analysis sheds light on the response of salivary glands to testosterone exposure, providing proteome-level insights into the associated weight and histological changes. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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13 pages, 2630 KiB

Open AccessArticle

Salivary Lipids of Patients with Non-Small Cell Lung Cancer Show Perturbation with Respect to Plasma

by Bo Young Hwang, Jae Won Seo, Can Muftuoglu, Ufuk Mert, Filiz Guldaval, Milad Asadi, Haydar Soydaner Karakus, Tuncay Goksel, Ali Veral, Ayse Caner and Myeong Hee Moon

Int. J. Mol. Sci. 2023, 24(18), 14264; https://doi.org/10.3390/ijms241814264 - 19 Sep 2023

Viewed by 881

Abstract

A comprehensive lipid profile was analyzed in patients with non-small cell lung cancer (NSCLC) using nanoflow ultrahigh-performance liquid chromatography–electrospray ionization–tandem mass spectrometry. This study investigated 297 and 202 lipids in saliva and plasma samples, respectively, comparing NSCLC patients to healthy controls. Lipids with significant changes (>2-fold, p < 0.05) were further analyzed in each sample type. Both saliva and plasma exhibited similar lipid alteration patterns in NSCLC, but saliva showed more pronounced changes. Total triglycerides (TGs) increased (>2–3-fold) in plasma and saliva samples. Three specific TGs (50:2, 52:5, and 54:6) were significantly increased in NSCLC for both sample types. A common ceramide species (d18:1/24:0) and phosphatidylinositol 38:4 decreased in both plasma and saliva by approximately two-fold. Phosphatidylserine 36:1 was selectively detected in saliva and showed a subsequent decrease, making it a potential biomarker for predicting lung cancer. We identified 27 salivary and 10 plasma lipids as candidate markers for NSCLC through statistical evaluations. Moreover, this study highlights the potential of saliva in understanding changes in lipid metabolism associated with NSCLC. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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12 pages, 2576 KiB

Open AccessArticle

Effects of Denture Treatment on Salivary Metabolites: A Pilot Study

by Narumi Ichigaya, Norishige Kawanishi, Takuya Adachi, Masahiro Sugimoto, Katsuhiko Kimoto and Noriyuki Hoshi

Int. J. Mol. Sci. 2023, 24(18), 13959; https://doi.org/10.3390/ijms241813959 - 11 Sep 2023

Viewed by 1180

Abstract

Symptoms of oral discomfort such as dry mouth are common in older people wearing dentures. Such symptoms are mainly treated symptomatically. Many of these symptoms are related to saliva, and associations with salivary volume have been reported. Although denture treatment improves symptoms by increasing the amount of saliva, the effects on salivary components remain unclear. This study aimed to investigate the effects of denture treatment on salivary metabolite changes based on salivary metabolome analyses. We enrolled 21 patients requiring denture treatment. At the first visit, and after completion of denture treatment, saliva outflow was measured under resting and stimulated conditions, samples for salivary metabolite analysis were collected, and masticatory efficiency was tested. In all participants, masticatory efficiency increased after denture treatment. Moreover, the amounts of resting and stimulated saliva were increased. Using salivary metabolome analysis, 61 salivary metabolites were detected. Substantial concentration changes were observed for 4 and 21 metabolites in resting and stimulated saliva, respectively. The four metabolites common to both saliva tests had significantly lower concentrations after treatment. These results suggest that the improvement in masticatory function by dentures is related not only to salivary secretion volume, but also to salivary metabolite composition. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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16 pages, 3561 KiB

Open AccessArticle

Non-Coding RNA in Salivary Extracellular Vesicles: A New Frontier in Sjögren’s Syndrome Diagnostics?

by Tanya Cross, Kari Bente Foss Haug, Berit Sletbakk Brusletto, Stine Kamilla Ommundsen, Anne-Marie Siebke Trøseid, Trude Aspelin, Ole Kristoffer Olstad, Hans Christian Dalsbotten Aass, Hilde Kanli Galtung, Tor Paaske Utheim, Janicke Liaaen Jensen and Reidun Øvstebø

Int. J. Mol. Sci. 2023, 24(17), 13409; https://doi.org/10.3390/ijms241713409 - 29 Aug 2023

Cited by 3 | Viewed by 1101

Abstract

Sjögren’s syndrome is an autoimmune rheumatic disease characterized by inflammation of the salivary and lacrimal glands, often manifesting as dry mouth and dry eyes. To simplify diagnostics of primary Sjögren’s syndrome (pSS), a non-invasive marker is needed. The aim of the study was to compare the RNA content of salivary extracellular vesicles (EVs) between patients with pSS and healthy controls using microarray technology. Stimulated whole saliva was collected from 11 pSS patients and 11 age-matched controls. EV-RNA was isolated from the saliva samples using a Qiagen exoRNeasy Midi Kit and analyzed using Affymetrix Clariom D™ microarrays. A one-way ANOVA test was used to compare the mean signal values of each transcript between the two groups. A total of 9307 transcripts, coding and non-coding RNA, were detected in all samples. Of these transcripts, 1475 showed statistically significant differential abundance between the pSS and the control groups, generating two distinct EV-RNA patterns. In particular, tRNAs were downregulated in pSS patients, with the transcript tRNA-Ile-AAT-2-1 showing a 2-fold difference, and a promise as a potential biomarker candidate. This study therein demonstrates the potential for using salivary EV-RNA in pSS diagnostics. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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23 pages, 7527 KiB

Open AccessArticle

Combined Salivary Proteome Profiling and Machine Learning Analysis Provides Insight into Molecular Signature for Autoimmune Liver Diseases Classification

by Giulia Guadalupi, Cristina Contini, Federica Iavarone, Massimo Castagnola, Irene Messana, Gavino Faa, Simona Onali, Luchino Chessa, Rui Vitorino, Francisco Amado, Giacomo Diaz, Barbara Manconi, Tiziana Cabras and Alessandra Olianas

Int. J. Mol. Sci. 2023, 24(15), 12207; https://doi.org/10.3390/ijms241512207 - 30 Jul 2023

Viewed by 1224

Abstract

Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases that target the liver and have a wide spectrum of presentation. A global overview of quantitative variations on the salivary proteome in presence of these two pathologies is investigated in this study. The acid-insoluble salivary fraction of AIH and PBC patients, and healthy controls (HCs), was analyzed using a gel-based bottom-up proteomic approach combined with a robust machine learning statistical analysis of the dataset. The abundance of Arginase, Junction plakoglobin, Desmoplakin, Hexokinase-3 and Desmocollin-1 decreased, while that of BPI fold-containing family A member 2 increased in AIHp compared to HCs; the abundance of Gelsolin, CD14, Tumor-associated calcium signal transducer 2, Clusterin, Heterogeneous nuclear ribonucleoproteins A2/B1, Cofilin-1 and BPI fold-containing family B member 2 increased in PBCp compared to HCs. The abundance of Hornerin decreased in both AIHp and PBCp with respect to HCs and provided an area under the ROC curve of 0.939. Machine learning analysis confirmed the feasibility of the salivary proteome to discriminate groups of subjects based on AIH or PBC occurrence as previously suggested by our group. The topology-based functional enrichment analysis performed on these potential salivary biomarkers highlights an enrichment of terms mostly related to the immune system, but also with a strong involvement in liver fibrosis process and with antimicrobial activity. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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Review

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20 pages, 5473 KiB

Open AccessReview

by Galina Laputková, Ivan Talian and Vladimíra Schwartzová

Int. J. Mol. Sci. 2023, 24(23), 16745; https://doi.org/10.3390/ijms242316745 - 25 Nov 2023

Viewed by 962

Abstract

The objective was to evaluate the current evidence regarding the etiology of medication-related osteonecrosis of the jaw (MRONJ). This study systematically reviewed the literature by searching PubMed, Web of Science, and ProQuest databases for genes, proteins, and microRNAs associated with MRONJ from the earliest records through April 2023. Conference abstracts, letters, review articles, non-human studies, and non-English publications were excluded. Twelve studies meeting the inclusion criteria involving exposure of human oral mucosa, blood, serum, saliva, or adjacent bone or periodontium to anti-resorptive or anti-angiogenic agents were analyzed. The Cochrane Collaboration risk assessment tool was used to assess the quality of the studies. A total of 824 differentially expressed genes/proteins (DEGs) and 22 microRNAs were extracted for further bioinformatic analysis using Cytoscape, STRING, BiNGO, cytoHubba, MCODE, and ReactomeFI software packages and web-based platforms: DIANA mirPath, OmicsNet, and miRNet tools. The analysis yielded an interactome consisting of 17 hub genes and hsa-mir-16-1, hsa-mir-21, hsa-mir-23a, hsa-mir-145, hsa-mir-186, hsa-mir-221, and hsa-mir-424. A dominance of cytokine pathways was observed in both the cluster of hub DEGs and the interactome of hub genes with dysregulated miRNAs. In conclusion, a panel of genes, miRNAs, and related pathways were found, which is a step toward understanding the complexity of the disease. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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21 pages, 837 KiB

Open AccessReview

Mass Spectrometry-Based Proteomics for Discovering Salivary Biomarkers in Periodontitis: A Systematic Review

by Hongying Hu and Wai Keung Leung

Int. J. Mol. Sci. 2023, 24(19), 14599; https://doi.org/10.3390/ijms241914599 - 27 Sep 2023

Viewed by 1480

Abstract

Periodontitis is one of the primary causes of tooth loss, and is also related to various systemic diseases. Early detection of this condition is crucial when it comes to preventing further oral damage and the associated health complications. This study offers a systematic review of the literature published up to April 2023, and aims to clearly explain the role of proteomics in identifying salivary biomarkers for periodontitis. Comprehensive searches were conducted on PubMed and Web of Science to shortlist pertinent studies. The inclusion criterion was those that reported on mass spectrometry-driven proteomic analyses of saliva samples from periodontitis cohorts, while those on gingivitis or other oral diseases were excluded. An assessment for risk of bias was carried out using the Newcastle–Ottawa Scale and Quality Assessment of Diagnostic Accuracy Studies or the NIH quality assessment tool, and a meta-analysis was performed for replicable candidate biomarkers, i.e., consistently reported candidate biomarkers (in specific saliva samples, and periodontitis subgroups, reported in ≥2 independent cohorts/reports) were identified. A Gene Ontology enrichment analysis was conducted using the Database for Annotation, Visualization, and Integrated Discovery bioinformatics resources, which consistently expressed candidate biomarkers, to explore the predominant pathway wherein salivary biomarkers consistently manifested. Of the 15 studies included, 13 were case–control studies targeting diagnostic biomarkers for periodontitis participants (periodontally healthy/diseased, n = 342/432), while two focused on biomarkers responsive to periodontal treatment (n = 26 participants). The case–control studies were considered to have a low risk of bias, while the periodontitis treatment studies were deemed fair. Summary estimate and confidence/credible interval, etc. determination for the identified putative salivary biomarkers could not be ascertained due to the low number of studies in each case. The results from the included case–control studies identified nine consistently expressed candidate biomarkers (from nine studies with 230/297 periodontally healthy/diseased participants): (i) those that were upregulated: alpha-amylase, serum albumin, complement C3, neutrophil defensin, profilin-1, and S100-P; and (ii) those that were downregulated: carbonic anhydrase 6, immunoglobulin J chain, and lactoferrin. All putative biomarkers exhibited consistent regulation patterns. The implications of the current putative marker proteins identified were reviewed, with a focus on their potential roles in periodontitis diagnosis and pathogenesis, and as putative therapeutic targets. Although in its early stages, mass spectrometry-based salivary periodontal disease biomarker proteomics detection appeared promising. More mass spectrometry-based proteomics studies, with or without the aid of already available clinical biochemical approaches, are warranted to aid the discovery, identification, and validation of periodontal health/disease indicator molecule(s). Protocol registration number: CRD42023447722; supported by RD-02-202410 and GRF17119917. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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16 pages, 2184 KiB

Open AccessReview

Oral Infection, Oral Pathology and Salivary Diagnostics of Mpox Disease: Relevance in Dentistry and OMICs Perspectives

by Marcelo Augusto Garcia-Junior, Bruno Silva Andrade, Marco Guevara-Vega, Igor Santana de Melo, Thúlio M. Cunha, Ana Carolina Gomes Jardim and Robinson Sabino-Silva

Int. J. Mol. Sci. 2023, 24(18), 14362; https://doi.org/10.3390/ijms241814362 - 21 Sep 2023

Viewed by 1247

Abstract

In this narrative review, we aim to point out the close relationship between mpox virus (MPXV) infection and the role of saliva as a diagnostic tool for mpox, considering the current molecular approach and in the perspective of OMICs application. The MPXV uses the host cell’s rough endoplasmic reticulum, ribosomes, and cytoplasmic proteins to replicate its genome and synthesize virions for cellular exit. The presence of oral mucosa lesions associated with mpox infection is one of the first signs of infection; however, current diagnostic tools find it difficult to detect the virus before the rashes begin. MPXV transmission occurs through direct contact with an infected lesion and infected body fluids, including saliva, presenting a potential use of this fluid for diagnostic purposes. Currently available diagnostic tests for MPXV detection are performed either by real-time quantitative PCR (RT-qPCR) or ELISA, which presents several limitations since they are invasive tests. Despite current clinical trials with restricted sample size, MPXV DNA was detected in saliva with a sensitivity of 85%–100%. In this context, the application of transcriptomics, metabolomics, lipidomics, or proteomics analyses coupled with saliva can identify novel disease biomarkers. Thus, it is important to note that the identification and quantification of salivary DNA, RNA, lipid, protein, and metabolite can provide novel non-invasive biomarkers through the use of OMICs platforms aiding in the early detection and diagnosis of MPXV infection. Untargeted mass spectrometry (MS)-based proteomics reveals that some proteins also expressed in saliva were detected with greater expression differences in blood plasma when comparing mpox patients and healthy subjects, suggesting a promising alternative to be applied in screening or diagnostic platforms for mpox salivary diagnostics coupled to OMICs. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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33 pages, 2239 KiB

Open AccessReview

The Post-Translational Modifications of Human Salivary Peptides and Proteins Evidenced by Top-Down Platforms

by Irene Messana, Barbara Manconi, Tiziana Cabras, Mozhgan Boroumand, Maria Teresa Sanna, Federica Iavarone, Alessandra Olianas, Claudia Desiderio, Diana Valeria Rossetti, Federica Vincenzoni, Cristina Contini, Giulia Guadalupi, Antonella Fiorita, Gavino Faa and Massimo Castagnola

Int. J. Mol. Sci. 2023, 24(16), 12776; https://doi.org/10.3390/ijms241612776 - 14 Aug 2023

Viewed by 1209

Abstract

In this review, we extensively describe the main post-translational modifications that give rise to the multiple proteoforms characterized to date in the human salivary proteome and their potential role. Most of the data reported were obtained by our group in over twenty-five years of research carried out on human saliva mainly by applying a top-down strategy. In the beginning, we describe the products generated by proteolytic cleavages, which can occur before and after secretion. In this section, the most relevant families of salivary proteins are also described. Next, we report the current information concerning the human salivary phospho-proteome and the limited news available on sulfo-proteomes. Three sections are dedicated to the description of glycation and enzymatic glycosylation. Citrullination and N- and C-terminal post-translational modifications (PTMs) and miscellaneous other modifications are described in the last two sections. Results highlighting the variation in the level of some proteoforms in local or systemic pathologies are also reviewed throughout the sections of the manuscript to underline the impact and relevance of this information for the development of new diagnostic biomarkers useful in clinical practice. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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10 pages, 957 KiB

Open AccessBrief Report

Saliva microRNA Profile in Children with and without Severe SARS-CoV-2 Infection

by Steven D. Hicks, Dongxiao Zhu, Rhea Sullivan, Nirupama Kannikeswaran, Kathleen Meert, Wei Chen, Srinivasan Suresh and Usha Sethuraman

Int. J. Mol. Sci. 2023, 24(9), 8175; https://doi.org/10.3390/ijms24098175 - 03 May 2023

Viewed by 1400

Abstract

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) may impair immune modulating host microRNAs, causing severe disease. Our objectives were to determine the salivary miRNA profile in children with SARS-CoV-2 infection at presentation and compare the expression in those with and without severe outcomes. Children <18 years with SARS-CoV-2 infection evaluated at two hospitals between March 2021 and February 2022 were prospectively enrolled. Severe outcomes included respiratory failure, shock or death. Saliva microRNAs were quantified with RNA sequencing. Data on 197 infected children (severe = 45) were analyzed. Of the known human miRNAs, 1606 (60%) were measured and compared across saliva samples. There were 43 miRNAs with ≥2-fold difference between severe and non-severe cases (adjusted p-value < 0.05). The majority (31/43) were downregulated in severe cases. The largest between-group differences involved miR-4495, miR-296-5p, miR-548ao-3p and miR-1273c. These microRNAs displayed enrichment for 32 gene ontology pathways including viral processing and transforming growth factor beta and Fc-gamma receptor signaling. In conclusion, salivary miRNA levels are perturbed in children with severe COVID-19, with the majority of miRNAs being down regulated. Further studies are required to validate and determine the utility of salivary miRNAs as biomarkers of severe COVID-19. Full article

(This article belongs to the Special Issue Omics Sciences for Salivary Diagnostics)

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