The power of saliva in multi-omics biomarker discovery

What is the significance of the multi-omics biomarker discovery paradigm and the role of the Hurdle.bio platform?

The Hurdle.bio platform enables the transition from a single omics to
a multi-omics framework for biomarker discovery, allowing the integration of different molecular layers to improve our ability to quantify human health and disease. This approach has facilitated the development of novel biomarkers, such as InflammAge, a saliva-based DNA methylation biomarker for systemic chronic inflammation (SCI).¹ InflammAge borrows information from proteomics inflammatory markers and maps it to epigenetic data, ensuring a robust, scalable, and cost-effective method for quantifying a key mechanism of human aging. By combining machine-learning models with large-scale epigenetic datasets, the platform has successfully translated novel diagnostics from conception to global-scale implementation.

What are the main advantages of using saliva as a sample type for biomarker discovery?

Saliva is a source of DNA and RNA, including small, non-coding RNA, and provides a window into the immune system and systemic diseases. This makes saliva suitable for applications in oncology, pharmacogenomics, epigenetics, rare disease testing, and psychiatric genetics, among others.

Saliva collection is minimally invasive, easy to collect and typically provides high participant compliance. Saliva collection solutions such as the Oragene™ and ORAcollect™ devices are designed with the user in mind and robustly tested for ease of use and technical performance.

These devices simplify logistics, allow long-term storage at room temperature, and provide consistent results. Saliva samples collected with an Oragene device yield lower bacterial DNA contamination compared with other oral sampling methods.^2,3 Studies show that up to 74% of the DNA in saliva⁴ comes from immune cells with a smaller proportion (about 15%) from buccal epithelial cells. The portfolio of DNA Genotek Inc. sample collection solutions includes saliva collection devices that are U.S. FDA 510(k) cleared for prescription and direct-to-consumer use, or CE marked to meet EU standards, making them easy to scale across global markets.

What are the requirements for an accessible gold-standard biomarker for systemic chronic inflammation?

An effective biomarker for systemic chronic inflammation should:

• be minimally invasive and widely accessible for routine testing.
• demonstrate stability over time, minimizing fluctuations due to short-term environmental or biological changes.
• be quantifiable using standardized, cost-effective assays, enabling broad adoption.

Saliva collected using DNA Genotek™ Oragene devices meets these criteria by remaining stable at room temperature, making it an ideal sample for DNA methylation analysis using Illumina methylation arrays.

How are DNA methylation (DNAm) proxies used in the context of systemic chronic inflammation (SCI)?

DNA methylation (DNAm) proxies, also known as EpiScores, serve as computationally derived indicators of inflammatory protein or cytokine levels. These are developed using large datasets that contain both protein expression data and matched DNA methylation profiles from the same individuals. Using machine-learning models, well-performing EpiScores can then be integrated to create a composite biomarker of systemic chronic inflammation (SCI) while also providing insight into how different features play a role in each individual.

What is InflammAge, how is it developed and what are the clinical implications of InflammAge acceleration?

InflammAge is a saliva-based epigenetic biomarker for systemic chronic inflammation, trained on chronological age, and is comprised of 42 DNA methylation EpiScore features. The degree of InflammAge acceleration, or the deviation between a person’s chronological age and their InflammAge score, serves as an indicator of inflammatory burden. Individuals with higher InflammAge acceleration were found to have increased blood biomarkers outside reference ranges, a higher mortality risk, and associations with many diseases.¹ Additionally, lifestyle factors such as smoking, alcohol consumption, and diet were significantly associated with InflammAge scores, as observed in a cohort of 18,000 participants.¹ A three-month intervention study demonstrated that participants with elevated InflammAge acceleration successfully reduced their inflammation levels after taking anti-inflammatory supplements.⁵ InflammAge was also lower in patients with Alzheimer’s disease treated with a drug that inhibits inflammatory signaling compared with placebo- treated control group.⁶ These findings highlight InflammAge as a modifiable and actionable biomarker, offering potential for tracking and mitigating inflammation-related health risks through targeted interventions.

What are the key features of Oragene™ saliva collection devices that make them suitable for epigenetic research?

Oragene™ devices ensure the robust collection of high-quality, saliva-derived DNA, making them highly suitable for epigenetic studies. These devices provide proven long-term stability, with saliva samples remaining viable for over a year at room temperature without degradation. Their effectiveness has been validated in both consumer studies and open-label trials conducted
as part of this project, demonstrating their reliability for research and clinical applications. Additionally, studies have confirmed the reproducibility of results obtained from DNA extracted from samples collected using Oragene™ devices, further establishing them as an optimal choice for high-throughput epigenetic research.

What are the key conclusions from the research on saliva-based epigenetic biomarkers?

• Multi-omic approaches enable mapping from proteomic to epigenetic data, leading to stable and reproducible biomarkers.
• Saliva is a powerful tool for developing accessible, minimally invasive, and cost-effective biomarkers across multiple disease domains.
• DNA methylation-based biomarkers, such as InflammAge, provide valuable insights into inflammation-related health risks, with potential for disease risk monitoring, and personalized interventions.

This research underscores the transformative potential of saliva-based epigenetic biomarkers, paving the way for their integration into preventative medicine and personalized healthcare.

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1 Schmunk LJ, Call TP, McCartney DL, et al. (2025). A novel framework to build saliva-based DNA methylation biomarkers: Quantifying systemic chronic inflammation as a case study. Aging Cell, 30, e14444.
2 Feigelson HS, Rodriguez C, Robertson AS, et al. (2001). Determinants of DNA yield and quality from buccal cell samples collected with mouthwash. Cancer Epidemiol. Biomarkers Prev. 10(9):1005-8.
3 García-Closas M, Egan KM, Abruzzo J, et al. (2001). Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. Cancer Epidemiol. Biomarkers Prev. 10(6): 687-96.
4 Thiede C, Prange-Krex G, Freiberg-Richter J, et al. (2000). Buccal swabs but not mouthwash samples can be used to obtain pretransplant DNA fingerprints from recipients of allogeneic bone marrow transplants. Bone Marrow Transplant. 25(5):575-577.
5 McGee, K.C., Sullivan, J., Hazeldine, J. et al. (2024). A combination nutritional supplement reduces DNA methylation age only in older adults with a raised epigenetic age. GeroScience. 46, 4333–4347.
6 Reading C. (2024). Bezisterim Effects on Biological Age, Alzheimer’s Epigenetics, and Neurologic Assessments. https://bioviepharma.com/wp-content/uploads/2024/12/ARDD-Presentation-2024.pdf

Some DNA Genotek Inc. products may not be available in all geographic regions.
Customers must review the labels (RUO or IVD) of sample collection devices and ensure compliance for their intended use.
Oragene™•DISCOVER saliva collection devices are intended for research use only and not for use in diagnostic procedures.
Device/Assay manufacturers must validate the use of Oragene™•Dx and ORAcollect™•Dx for their specific indications for use.

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