Feasibility of the salivary transcriptome as a novel biomarker in determining disease susceptibility

Hidayat, Mohd Faizal Hafez; Milne, Trudy; Cullinan, M. P.; Seymour, G. J.

doi:10.1111/jre.12522

Cited by 5 publications

(7 citation statements)

References 30 publications

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“…This limitation might have been caused by the total amount of mRNA detected from the whole saliva being less than that detected from the tissue samples, due to the nature of saliva and limitations of the present analytical technology ( Figure 5 ). The present results are in agreement with those of a previous study showing only small amounts of total RNA, with wide variations and contamination from bacterial sources, in microarray analyses of samples taken from patients with chronic periodontitis [ 29 ]. Salivary mRNA is stabilized by interactions with salivary proteins and apoptotic bodies [ 30 ], and RNases and proteases from microbial/human sources can rapidly degrade mRNA.…”

Section: Discussionsupporting

confidence: 93%

Transcriptomic profiles and their correlations in saliva and gingival tissue biopsy samples from periodontitis and healthy patients

Jeon

Kook

Choi

et al. 2020

J Periodontal Implant Sci

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Purpose This study was conducted to analyze specific RNA expression profiles in gingival tissue and saliva samples in periodontitis patients and healthy individuals, and to determine their correlations in light of the potential use of microarray-based analyses of saliva samples as a periodontal monitoring tool. Methods Gingival tissue biopsies and saliva samples from 22 patients (12 with severe periodontitis and 10 with a healthy periodontium) were analyzed using transcriptomic microarray analysis. Differential gene expression was assessed, and pathway and clustering analyses were conducted for the samples. The correlations between the results for the gingival tissue and saliva samples were analyzed at both the gene and pathway levels. Results There were 621 differentially expressed genes (DEGs; 320 upregulated and 301 downregulated) in the gingival tissue samples of the periodontitis group, and 154 DEGs (44 upregulated and 110 downregulated) in the saliva samples. Nine of these genes overlapped between the sample types. The periodontitis patients formed a distinct cluster group based on gene expression profiles for both the tissue and saliva samples. Database for Annotation, Visualization and Integrated Discovery analysis revealed 159 enriched pathways from the tissue samples of the periodontitis patients, as well as 110 enriched pathways In the saliva samples. Thirty-four pathways overlapped between the sample types. Conclusions The present results indicate the possibility of using the salivary transcriptome to distinguish periodontitis patients from healthy individuals. Further work is required to enhance the extraction of available RNA from saliva samples.

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Section: Discussionsupporting

confidence: 93%

Transcriptomic profiles and their correlations in saliva and gingival tissue biopsy samples from periodontitis and healthy patients

Jeon

Kook

Choi

et al. 2020

J Periodontal Implant Sci

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“…However, RNA present considerable stabilization challenges due to its susceptibility to spontaneous phosphodiester bond cleavage and because of degradation by several microbial and human degrading agents, such as ribonucleases (RNases), that are present in saliva. 122,123 The overall stability of salivary RNA depends upon different factors, including RNA purity and origin, collection method, preconditioning steps, and storage. 124 A possible protocol for reliable sampling and detection of salivary DNA and RNA includes the collection of saliva on ice, on-site centrifugation at 4 °C to collect saliva supernatant, addition to the supernatant of a mix of inhibitors targeting enzymatic activities, and storage at −80 °C for long-term sample preservation.…”

Section: Methods For Sampling and Collecting Salivamentioning

confidence: 99%

“…On another front, salivary RNA can be used for disease diagnosis and to evaluate the presence of potential microbial and viral infections, although human RNA is less stable than the viral and microbial counterparts due to the activity of endonucleases. , In addition, using salivary RNA over DNA is advantageous since it makes it possible to detect not only the presence of a gene but also the level of its expression (Figure b). However, RNA present considerable stabilization challenges due to its susceptibility to spontaneous phosphodiester bond cleavage and because of degradation by several microbial and human degrading agents, such as ribonucleases (RNases), that are present in saliva. , …”

Section: Stabilization Approaches For Salivary Biomarkersmentioning

confidence: 99%

“…The preprocessing time varies and can reach up to 24 h before analysis for some stabilizing saliva kits, which may be an issue when high throughput is needed . Sample stability can be achieved for various periods, ranging from days to up to one month at room temperature, or even longer at lower temperatures (−20, −80 °C). ,,, The effectiveness of stabilization may affect not only the storage period but also the yield and the quality of the extracted RNA. − ,, Stabilizing solutions are usually provided in collection tubes. This type of collection device can be extremely useful during daily clinical operations, as the stabilizing effect starts immediately during sample collection.…”

Section: Stabilization Approaches For Salivary Biomarkersmentioning

confidence: 99%

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Stabilization of Salivary Biomarkers

d'Amone

Matzeu

Omenetto

2021

ACS Biomater. Sci. Eng.

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The use of saliva as a diagnostic biofluid has been increasing in recent years, thanks to the identification and validation of new biomarkers and improvements in test accuracy, sensitivity, and precision that enable the development of new noninvasive and cost-effective devices. However, the lack of standardized methods for sample collection, treatment, and storage contribute to the overall variability and lack of reproducibility across analytical evaluations. Furthermore, the instability of salivary biomarkers after sample collection hinders their translation into commercially available technologies for noninvasive monitoring of saliva in home settings. The present review aims to highlight the status of research on the challenges of collecting and using diagnostic salivary samples, emphasizing the methodologies used to preserve relevant proteins, hormones, genomic, and transcriptomic biomarkers during sample handling and analysis.

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“…This is a disadvantage for studying disease states, which are affected more by gene expression and the biochemical outputs of the microbiome than the taxonomic identity of the microorganisms. This has already been demonstrated in several gut and oral microbiome studies [30,31] The lack of comprehensive taxonomic classifications and the inability to investigate gene expression has limited the utility of the conventional methodologies (16S and metagenomics) in investigating the role of the saliva microbiome and human transcriptome in health and disease [32]. This is particularly apparent in the context of microbial functions, which have been shown to be more informative in disease states than taxonomy alone [30].…”

Section: Introductionmentioning

confidence: 99%

A clinically validated human saliva metatranscriptomic test for global systems biology studies

Toma

Cai

Ogundijo

et al. 2021

Preprint

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We report here the development of a high throughput, automated, inexpensive, and clinically validated saliva metatranscriptome test that requires less than 100 microliters of saliva. The RNA in the samples is preserved at the time of collection. Samples can then be stored and transported at ambient temperatures for up to 28 days without significantly affecting the test results. Another important feature of the sample preservative is that it inactivates all classes of pathogens, enabling safe transportation globally. Given the unique set of convenience, low cost, safety, and technical performance, this saliva metatranscriptomic test can be integrated into longitudinal, global scale, systems biology studies that will lead to an accelerated development of precision medicine diagnostic and therapeutic tools. This report describes an important improvement to saliva transcriptome analysis. While current methods are complicated and expensive, the method reported here includes at-home sample collection, global shipping at ambient temperatures and pathogen inactivation at the point of collection; it uses fully automated, clinically validated and licensed laboratory and bioinformatic analyses.

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Feasibility of the salivary transcriptome as a novel biomarker in determining disease susceptibility

Cited by 5 publications

References 30 publications

Transcriptomic profiles and their correlations in saliva and gingival tissue biopsy samples from periodontitis and healthy patients

Transcriptomic profiles and their correlations in saliva and gingival tissue biopsy samples from periodontitis and healthy patients

Stabilization of Salivary Biomarkers

A clinically validated human saliva metatranscriptomic test for global systems biology studies

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