Exploring the Epigenetic Landscape—Insights from Epigenomics in Periodontitis and Stress-related Health Implications: A Review

Immune System Dynamics: From Innate to Adaptive Responses to Genetic Regulations and Disease Pathways

The immune system orchestrates a complex interplay between innate and adaptive responses to combat invading microorganisms. Foundational components of this intricate defense mechanism encompass both inherent (innate) and acquired (adaptive) factors.⁷ In response to stressful situations, the anterior hypothalamus activates the hypothalamus–pituitary–adrenal (HPA) axis, initiating a cascade of hormonal events. Corticotropin-releasing hormone and arginine vasopressin are secreted, targeting the pituitary gland, ultimately leading to the release of adrenocorticotrophic hormone and cortisol. Notably, cortisol, a glucocorticoid hormone, plays a crucial role in modulating immune responses.⁸

Within the realm of immune responses, external triggers, such as bacterial substances, activate signaling pathways in cells. This activation prompts the binding of transcription factors to DNA regions known as promoters and enhancers, initiating the transcription process and activating specific genes. The genetic constitution of an individual contributes significantly to immune response diversity, involving polygenic interactions and concurrent variations at different genetic locations.⁹ Genetic changes, whether mutations, polymorphisms, or modifications in the DNA sequence, can alter transcription factor binding sites within the DNA’s promoter region, influencing the speed and extent of gene expression.¹⁰ The intricate control of gene expression spans chromatin structures, transcription factors, and posttranscriptional alterations, including ribonucleic acid (RNA) splicing, messenger RNA (mRNA) polyadenylation, and the involvement of regulatory molecules such as microRNA and long noncoding RNAs.¹¹ Chronic inflammatory conditions like periodontitis exhibit particular target tissues where inflammation leads to tissue damage.¹² This integration of genetic regulations into immune system dynamics underscores the complexity of disease pathways and emphasizes the need for a comprehensive understanding to advance therapeutic interventions. Figure 1 illustrates the complex interplay among external stressors, epigenetic modifications, genetics, immunity, inflammation, and periodontitis, showcasing the influence of stress on the immune response and epigenetic changes.

Molecular Choreography: Decoding Epigenetic Mechanisms

Coined by Waddington, “epigenetics” elucidates gene-phenotype cause-and-effect relationships.^13,14 Heritable changes in gene expression involve DNA methylation, chromatin modifications, imprinting changes, and noncoding RNA, constituting key mechanisms.^15,17 Epigenomes, influenced by stress, diet, and maternal care, dictate molecular changes and cell responsiveness.¹⁸ The epigenetic process begins with an “epigenetic initiator,” shaping chromatin interactions and guiding modifications independently of environmental cues.¹⁹ Additionally, the “epigenetic maintainer,” represented by histone acetyltransferases and DNA methyltransferases, forms binding site complexes upon the initiator’s activation. These maintainers induce modifications in histone amino acids and DNA cytosines, culminating in distinctive epigenomes that define cellular states and responsiveness to environmental factors.²⁰ The “epigenetic code” concept emerges from specific patterns, their significance, and guiding pathways.^21,28 DNA methylation involves gene silencing through modifications on amino acid tails, forming heritable epigenetic marks.^29,30 H3-H4 tetramer stability allows diverse modifications on histone tails.^31,32 Noncoding RNA, proposed to regulate gene expression, lacks an open reading frame, inhibiting expression through interactions with RNA molecules.³³Figure 2 illustrates the epigenetic exposome, depicting external influences on gene functions, including repression of transposable elements and gene silencing pathways. The schematic outlines a three-stage mechanism—epigenator, epigenetic initiator, and epigenetic maintainer, providing a comprehensive view of epigenetic regulation.

Periodontal Disease as an Epidisease with Significant Epigenetic Component: A Stride in the Direction of Better Understanding Periodontitis

Periodontitis is the inflammation of the gingival tissues caused by bacteria, leading to tissue and bone loss.¹² According to the 2016 Global Burden of Disease Study, severe periodontal disease was ranked as the 11th most prevalent health condition worldwide.³⁴ Periodontal disease was found to have a global prevalence ranging from 20 to 50%.³⁵ From 1990 to 2010, there was a significant increase of 57.3% in the global burden of periodontal disease.³⁶

Epithelial cells in the oral cavity encounter diverse bacteria, initiating signaling pathways that trigger complex inflammatory responses influenced by both genetic and environmental factors.² Similar to other chronic diseases, periodontal disease is now seen as a multifactorial condition, as evidenced by twin and family studies and recent genome-wide association studies³⁷ researchers have estimated the heritability of periodontal disease to be in the range of 30–50%. Researchers observed that individuals with periodontitis tend to exhibit a similar pattern of early tooth loss as one of their parents.^38,39

Genetic and Epigenetic Insights into Periodontal Disease: Moving Beyond Pathogen-centric Approaches

The study conducted by Chatzopoulos et al. on a Caucasian population with chronic periodontal disease concluded that genetic variations in interleukin-6 (IL-6)—572 G/C and IL-10-592 C/A polymorphisms, both individually and in combination, did not exhibit a significant influence on the outcomes of nonsurgical periodontal therapy. Despite the presence of distinct genotypes, there were no statistically significant associations observed with clinical parameters after therapy, suggesting that these genetic polymorphisms may not be substantial predictors of treatment outcomes in this population.^40,41 Hernández et al. study⁴² revealed 81 differentially hypermethylated genes and 21 differentially hypomethylated genes in patients with periodontitis compared to gingivally healthy controls. Notably, the intersection analysis highlighted three specific genes—zinc finger protein 718 (ZNF718) and Homeobox A4 (HOXA4) were differentially hypermethylated, while ZFP57 was differentially hypomethylated in individuals with periodontitis. The functional enrichment analysis of differentially methylated genes revealed immune-related ontologies such as “detection of a bacterium” and “antigen processing and presentation,” suggesting a potential link between altered DNA methylation patterns in peripheral leukocytes and immune processes in periodontitis. Kurushima et al. study⁴³ focused on self-reported indicators, associating specific DNA methylation changes with periodontal traits, validated in buccal and adipose tissues. Collectively, these studies contribute valuable insights into periodontal disease at the epigenetic level, suggesting potential biomarkers, and personalized treatment avenues. This emphasizes the need for a multifaceted approach beyond pathogen targeting for effective disease management.

Evidence of Epigenetic Alterations and their Role in Development of Periodontal Disease: A Shifting Trend from Genetics to Epigenetics

The landscape of periodontal disease research underwent a significant transformation in the 1990s when the first evidence emerged, linking genetics to the development of periodontitis. This shift marked a departure from a purely genetic focus to an exploration of epigenetic mechanisms, introducing concepts of susceptibility and predisposition.^44,45 Notable studies by Loos and Velden et al.,⁴⁶ and Michalowicz et al.,⁴⁷ provided crucial insights into the hereditary aspects of periodontitis. Loos and Velden, investigated the impact of sibling relationships on periodontal health, revealing a substantial siblingship effect on various clinical parameters. Michalowicz et al., in their assessment of 110 adult twins, highlighted those genetics appeared to be the root cause of familial aggregation.

Despite these genetic underpinnings, the complex interplay of genetic and environmental factors prompted a transition toward investigating epigenetic mechanisms.^48,49 The field of epigenetics, considered a new frontier in dentistry, explores molecular mechanisms such as chromatin remodeling and selective gene activation or inactivation, offering a nuanced understanding of the pathogenesis of infectious and inflammatory diseases.⁵⁰

Recognizing the intricacies of periodontitis, studies emphasized the role of both genetic and epigenetic factors, revealing varying susceptibility among individuals sharing the same microbial infection. The association between periodontal conditions and environmental factors, such as dietary habits and systemic diseases, remains an area of exploration, emphasizing the dynamic nature of epigenetic information responsive to environmental conditions.

The transition from genetics to epigenetics was underscored by advances in sequencing technology, enabling high-throughput DNA analysis. Studies like those by De Souza et al.⁵¹ provided insights into DNA methylation variations in immune-related genes, shedding light on their potential influence on periodontitis prognosis.

Further exploration into the gender-related distinctions in DNA methylation was presented by Li et al.,⁵² their use of pyrosequencing revealed a positive correlation between matrix metalloproteinase-9 (MMP-9) cytosine-phosphate-guanine islands methylation levels and chronic periodontitis severity. Additionally, they observed lower MMP-9 methylation in female patients but higher tissue inhibitor of metalloproteinase-1 (TIMP-1) methylation, with TIMP-1 methylation decreasing with age.

Martins et al.⁵³ delved into the impact of lipopolysaccharides on histone modifications in oral epithelial cells. They identified potential epigenetic mechanisms involving DNA methylation and histone acetylation during dysbiosis, suggesting a delicate molecular balance between these processes. Although further characterization is needed, targeting these epigenetic mechanisms may offer therapeutic insights for periodontitis.

Zhu et al.⁵⁴ provided critical insights into the role of the long noncoding RNA associated with periodontitis (lncR-APDC) in periodontitis. Their work, involving lncR-APDC knockout mice with induced experimental periodontitis, demonstrated exacerbated bone loss, disrupted cytokine regulation, altered immune cell proportions, and increased trefoil factor family 2 expression, highlighting the RNA’s critical role and therapeutic potential in periodontitis.

This evolving trend from genetics to epigenetics signifies a paradigm shift in understanding the intricate molecular mechanisms influencing the development of periodontal disease. Epigenetic alterations, as evidenced by various studies, present a dynamic and responsive framework that extends beyond static genetic information, offering new avenues for therapeutic interventions in periodontitis.

What are the Contributing Factors to Immune Fitness Dysregulation in Periodontitis?

The disruption of immune balance in periodontitis results from a combination of various risk factors. The causal factors for periodontitis can be grouped into five categories—subgingival bacterial biofilm, genetics and epigenetic changes, lifestyle factors, systemic illnesses, and miscellaneous factors. In older individuals, pathobionts are a significant influence on periodontitis, while younger patients, like those with early-onset periodontitis, are more closely linked to genetic factors.⁵⁵ Epigenetic alterations and genetic mutations that occur over a lifetime can additionally influence an individual’s vulnerability to periodontitis.

Chronic Stress and its Detrimental Impact on Physiological Process

Stress is the body’s response to challenging life situations, influenced by factors like the stressor’s duration, intensity, and controllability, as well as the individual’s age and gender.^56,57 From a Darwinian perspective, a person’s parental stress history significantly influences their descendants’ resilience.⁵⁸ Stress-related memories are retained at the cellular level in brain regions like the hippocampus, highlighting the importance of past experiences. Neurons may preserve memories of stressful experiences through epigenetic mechanisms, including DNA methylation and histone modification.

The Impact of Chronic Stress on Periodontal Health: Mechanisms and Indirect Effects

Stress, a recognized trigger for mental and neurological disorders, exerts a profound impact on the epigenome and is implicated in an increased risk of periodontitis. The multifaceted mechanisms through which stress influences the periodontium encompass both indirect and direct pathways. Indirectly, stress instigates behavioral and lifestyle changes, such as heightened smoking, increased alcohol consumption, unhealthy dietary patterns, suboptimal oral hygiene practices, and diminished adherence to dental care recommendations. Simultaneously, stress directly impacts periodontal health by reshaping saliva composition, influencing gingival blood circulation, and modulating the host immune response.⁵⁹

The intricate connection between stress and periodontal health stems from its influence on the immune response and health-related behaviors. Stress elevates the production of neuroendocrine hormones, including glucocorticoids and catecholamines, which detrimentally affect immune functions. This includes reductions in lymphocyte populations and natural killer cell activity, rendering individuals more susceptible to infections and contributing to the degradation of periodontal tissues.⁶⁰

Insights from studies conducted on experimental animal models suggest that persistent stress may induce vascular inflammation, evidenced by an increase in circulating proinflammatory cytokines.⁶¹

Hilgert et al. observed a positive association between higher salivary cortisol levels and increased probing pocket depths and attachment loss in a previous study.⁶² Cakmak et al., found elevated salivary and gingival crevicular fluid (GCF) cortisol levels in groups with aggressive and chronic periodontitis compared to a healthy cohort.⁶³ Jaiswal et al., explored the relationship between self-assessed stress levels and serum cortisol values, revealing a positive correlation with chronic periodontitis.⁶⁴ Mousavijazi et al., investigated the connection between stress disorders and heightened levels of inflammatory mediators in periodontal disease, highlighting the significant role of stress in triggering inflammatory processes, as reflected in increased crevicular IL-1B levels in both aggressive and chronic periodontitis groups.⁶⁵ Goyal et al., delved into the impact of psychosocial stress on periodontal health, establishing significant correlations between cortisol levels and clinical parameters in chronic periodontitis and stressed subjects. The study underscores stress as a potential contributor to periodontal disease.⁶⁶

Genomic Stress Response and Its Epigenetic Influence

Epigenetics explains why individuals with similar genetic backgrounds can have varying disease susceptibility and coping abilities. Epigenetics encompasses both temporary and enduring gene expression changes not directly encoded in DNA, shaping how cells react at a molecular level.^19,67 Epigenetic mechanisms, including DNA methylation and histone modifications, play a key role in regulating gene expression during stress, whether it’s a prolonged or rapid response.⁶⁸ Epigenetics is particularly important in synaptic plasticity, memory formation, cognitive processes, and the development of stress-related traits and behavioral adjustments in response to chronic stress.⁶⁹

Stress Markers and Receptors in Oral Cavity

Periodontal tissues contain glucocorticoid receptors that react to glucocorticoids released from the HPA axis. It has been shown that keratinocytes have the ability to directly react to adrenocorticotropic hormone and generate the glucocorticoid cortisol. This production can lead to localized immunosuppressive and anti-inflammatory effects,⁷⁰ which encompass the inhibition of T lymphocyte formation⁷¹ and the inhibition of macrophage⁷² and natural killer cell functions.⁷³

Stress and periodontal diseases have been studied through blood, saliva, and GCF. Catecholamines affect immune functions, influencing proinflammatory cytokines and inhibiting lymphocyte proliferation and natural killer cell activity.

Chromogranin A (CgA), an acidic secretory glycoprotein, is stored and released with catecholamines from the adrenal medulla and by sympathetic nerve endings and submandibular gland cells. It’s the precursor of bioactive peptides like catestatin, which may contribute to inflammation.

Salivary α-amylase (sAA) reflects sympathetic nervous system activity in response to stress and has antimicrobial properties. Neuropeptides like substance P-mediate neurogenic inflammation, initiating and sustaining inflammation by stimulating proinflammatory cytokine production.

Gallacher and Petersen reported that heightened concentrations of cortisol and β-endorphin might have significantly upregulated the expression of MMP-1, -2, -7, and -11, along with TIMP-1 in human gingival fibroblasts. This suggested mechanism could contribute to the increased periodontal breakdown associated with psychosocial stress status.⁷⁴

Shared Pathways: Unveiling Common Biomarkers between Stress and Periodontitis

The intricate interplay between psychosocial stress and periodontitis reveals shared pathways mediated by a range of biomarkers. Cohen-Cole et al., have implicated proinflammatory cytokines such as IL-1 and IL-6, identified in the GCF, as potential bridges linking stress to periodontal disease.⁷⁵ Additionally, cortisol, a well-established stress hormone, demonstrates associations with clinical periodontal parameters, including pocket depth and bleeding on probing, highlighting its role in the stress-periodontitis nexus. Salivary markers, such as CgA, cortisol, sAA, and β-endorphin, offer insights into the physiological responses to stress in the context of periodontal health. Moreover, the dysregulation of the HPA axis, autonomic nervous system, and central nervous system may influence the immune and inflammatory responses, contributing to the vulnerability of periodontal tissues to pathogenic microorganisms.⁷⁶ These shared pathways underscore the complexity of the relationship between stress and periodontitis, shedding light on potential common biomarkers that warrant further exploration.

Challenges of Epigenetic Study

Studying genetic polymorphisms for periodontitis is challenging because variations associated with the disease in one population, like Caucasians, may not hold the same associations in different racial or ethnic groups, such as Asians, Brazilians, and Africans.⁴⁵

Numerous investigations have indicated that the DNA methylation markers identified in peripheral tissues often lack precision in predicting the DNA methylation patterns found in the brain.⁷⁷

Currently, most literature doesn’t distinguish between DNA methylation and hydroxymethylation, and common assays measure both modifications together. Future research should explore these modifications simultaneously for a more comprehensive understanding.

Using animal models and in vitro studies can be challenging when applying findings to patients due to the impact of environmental factors and significant individual disparities in epigenomic patterns. To establish a dependable benchmark, it’s essential to conduct in-depth analyses with well-organized and controlled conditions. A comprehensive understanding of epigenomic, gene expression, and phenotype profiles related to target diseases is crucial for effective mapping efforts. Additionally, developing user-friendly software for managing large datasets is essential for practical research implementation across various fields.⁷⁸

Personalized Periodontics

Personalized periodontics is an innovative approach that considers variations in genetics, environment, lifestyle, and behavior among individuals. Diagnostic testing is often used to determine the most effective treatments based on factors like genetics or various analyzes encompassing epidemiology, sociology, molecular biology, physiology, or cellular studies.

Stress and allostatic load are gaining importance in personalized periodontics research. Repeated exposure to stressors leads to systemic effects, known as “allostatic load.”

Cutting-edge sequencing technologies and bioinformatics tools have accelerated the evolution of “omics” profiling, advancing the concept of personalized medicine.⁷⁸ Recent advances in genomics allow for the study of complex interaction effects in individuals with multiple health conditions.

To achieve personalized medicine, it’s crucial to analyze multi-omics datasets, including genome, epigenome, transcriptome, metabolome, microbiome, proteome, and more. Effective collaboration between bioinformaticians, scientists, and clinicians is essential for this effort.⁷⁸