SNPs of Fc-gamma receptor genes and chronic periodontitis

Comparison of genetic and epigenetic profiles of periodontitis according to the presence of type 2 diabetes

Type 2 diabetes mellitus (T2DM) and periodontitis (PD) have intricated connections as chronic inflammatory diseases. While the immune response is a key factor that accounts for their association, the underlying mechanisms remain unclear. To gain a deeper understanding of the connection, we conducted research using a multiomics approach. We generated whole genome and methylation profiling array data from the periodontium of PD patients with DM (PDDM) and without DM to confirm genetic and epigenetic changes. Independent bulk and single-cell RNA sequencing data were employed to verify the expression levels of hypo-methylated genes. We observed a gradual rise in C>T base substitutions and hypomethylation in PD and PDDM patients compared with healthy participants. Furthermore, specific genetic and epigenetic alterations were prominently associated with the Fc-gamma receptor-mediated phagocytosis pathway. The upregulation of these genes was confirmed in both the periodontal tissues of PD patients and the pancreatic tissues of T2DM patients. Through single-cell RNA analysis of peripheral blood mononuclear cells, substantial upregulation of Fc-gamma receptors and related genes was particularly identified in monocytes. Our findings suggest that targeting the Fc-gamma signaling pathway in monocytes holds promise as a potential treatment strategy for managing systemic complications associated with diabetes.

Periodontitis Continuum: Antecedents, Triggers, Mediators, and Treatment Strategies

Periodontitis (PD) is a chronic inflammatory disease of the periodontium characterized by the formation of gingival pockets and gingival recession. The local inflammatory environment can lead to the destruction of the extracellular matrix and subsequent bone loss. The pathophysiology of PD involves interactions between genetic predisposition, lifestyle, environmental factors, the oral microbiota condition, systemic health disorders, innate and adaptive immune responses, and various host defenses. The review highlighted the importance of the oral cavity condition in systemic health. Thus, a correlation between harmful oral microbiota and cardiovascular disease (CVD)/diabetes/ arthritis, etc, progressions through inflammation and bacterial translocation was highlighted. Antecedents increase an individual's risk of developing PD, trigger initiate microbe-host immunologic responses, and mediators sustain inflammatory interactions. Generally, this review explores the antecedents, triggers, and mediators along the pathophysiological continuum of PD. An analysis of modern approaches to treating periodontitis, including antibiotics for systemic and local use, was carried out. The potential role of natural ingredients such as herbal extracts, phytoconstituents, propolis, and probiotics in preventing and treating PD was highlighted.

Identifying Oxidative Stress-Related Genes (OSRGs) as Potential Target for Treating Periodontitis Based on Bioinformatics Analysis

BACKGROUND

Periodontitis (PD) is a multifactorial inflammatory disease that is closely associated with periodontopathic bacteria. Numerous studies have demonstrated oxidative stress (OS) contributes to inflammation and is a prime factor in the development of PD. It is imperative to explore the function of newly discovered hub genes associated with OS in the advancement of PD, thereby identifying potential targets for therapeutic intervention.

OBJECTIVES

The goal of the current study was to identify the oxidative-stress-related genes (OSRGs) associated with periodontitis (PD) development using an integrated bioinformatics method.

METHODS

DEGs from GEO gene-expression data were identified using the "limma" package. We obtained OSRGs from GeneCards and utilized a Venn diagram to uncover differentially expressed OSRGs (DEOSRGs). After receiving the DEOSRGs, we employed Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) analytical tools to examine their possible functions and pathways in PD. Receiver operating characteristic (ROC) curves screened for hub genes of PD. RT-qPCR and western blot analysis were used to detect DEOSRG expression in mouse ligature-induced periodontitis gingival tissues.

RESULTS

The investigation identified 273 OSRGs. Based on PPI analysis, we recognized 20 OSRGs as hub genes. GO and KEGG enrichment analysis indicated that these hub genes were predominantly enriched in leukocyte migration, lymphocyte proliferation, and humoral immune response, and associated with leukocyte trans-endothelial migration, cytokine-cytokine receptor interaction, and NF-κB signaling pathway. Following ROC analysis, VCAM1, ITGAM, FCGR3A, IL1A, PECAM1, and VCAM1were identified as PD prognostic gene. RT-qPCR and western blot analyses confirmed that the expression ITGAM, FCGR3A, and PECAM1 were significantly elevated in the gingival tissues obtained from mice.

CONCLUSION

This investigation revealed that ITGAM, FCGR3A, and PECAM1 may have a crucial function in the advancement of PD.

Deep Learning Reveals Key Immunosuppression Genes and Distinct Immunotypes in Periodontitis

Background

Periodontitis is a chronic immuno-inflammatory disease characterized by inflammatory destruction of tooth-supporting tissues. Its pathogenesis involves a dysregulated local host immune response that is ineffective in combating microbial challenges. An integrated investigation of genes involved in mediating immune response suppression in periodontitis, based on multiple studies, can reveal genes pivotal to periodontitis pathogenesis. Here, we aimed to apply a deep learning (DL)-based autoencoder (AE) for predicting immunosuppression genes involved in periodontitis by integrating multiples omics datasets.

Methods

Two periodontitis-related GEO transcriptomic datasets (GSE16134 and GSE10334) and immunosuppression genes identified from DisGeNET and HisgAtlas were included. Immunosuppression genes related to periodontitis in GSE16134 were used as input to build an AE, to identify the top disease-representative immunosuppression gene features. Using K-means clustering and ANOVA, immune subtype labels were assigned to disease samples and a support vector machine (SVM) classifier was constructed. This classifier was applied to a validation set (Immunosuppression genes related to periodontitis in GSE10334) for predicting sample labels, evaluating the accuracy of the AE. In addition, differentially expressed genes (DEGs), signaling pathways, and transcription factors (TFs) involved in immunosuppression and periodontitis were determined with an array of bioinformatics analysis. Shared DEGs common to DEGs differentiating periodontitis from controls and those differentiating the immune subtypes were considered as the key immunosuppression genes in periodontitis.

Results

We produced representative molecular features and identified two immune subtypes in periodontitis using an AE. Two subtypes were also predicted in the validation set with the SVM classifier. Three “master” immunosuppression genes, PECAM1, FCGR3A, and FOS were identified as candidates pivotal to immunosuppressive mechanisms in periodontitis. Six transcription factors, NFKB1, FOS, JUN, HIF1A, STAT5B, and STAT4, were identified as central to the TFs-DEGs interaction network. The two immune subtypes were distinct in terms of their regulating pathways.

Conclusion

This study applied a DL-based AE for the first time to identify immune subtypes of periodontitis and pivotal immunosuppression genes that discriminated periodontitis from the healthy. Key signaling pathways and TF-target DEGs that putatively mediate immune suppression in periodontitis were identified. PECAM1, FCGR3A, and FOS emerged as high-value biomarkers and candidate therapeutic targets for periodontitis.

Th2 cell regulatory and effector molecules single nucleotide polymorphisms and periodontitis

To investigate the association between T helper 2 (Th2) cell regulatory and effector molecules' genetic polymorphisms and periodontitis. Single nucleotide polymorphisms (SNPs) of 11 Th2 cell regulatory or effector molecules genes (CD28, CTLA4, IL4, IL5, IL6, IL9, IL10, IL13, IL4R, GATA3, STAT6, and rs1537415; total 130 SNPs) were studied in Chinese nonsmokers (163 periodontitis-free controls, 141 periodontitis patients) using Sequenom iPlex assays. SNPs potentially associated with periodontitis (adjusted allelic P < 0.1) in this cross-sectional study were further investigated via meta-analysis. Allele G of rs4553808 in promoter of CTLA4 was more frequently detected in periodontitis than controls (P < 0.005), but did not remain significant after age and gender adjustment. Haplotype (GTT) in a block of three CTLA4 SNPs (rs4553808, rs16840252, rs5742909) was significantly associated with periodontitis. Meta-analysis of SNPs identified indicated allele T of CTLA4 rs5742909 (3 studies; 461 control, 369 periodontitis) and allele G of IL6 rs1800796 (18 studies; 2760 control, 2442 periodontitis) were significantly associated with periodontitis (OR = 1.44 and OR = 1.30, respectively). Within limitations of this study, a haplotype of CTLA4 concerning Th2 cell regulation, may be associated with periodontitis in Chinese nonsmokers followed. Meta-analysis indicated rs5742909 of CTLA4 and rs1800796 of IL6 appeared significantly associated with periodontitis.

A comprehensive overview of FCGR3A gene variability by full-length gene sequencing including the identification of V158F polymorphism

The FCGR3A gene encodes for the receptor important for antibody-dependent natural killer cell-mediated cytotoxicity. FCGR3A gene polymorphisms could affect the success of monoclonal antibody therapy. Although polymorphisms, such as the FcγRIIIA-V158F and -48L/R/H, have been studied extensively, an overview of other polymorphisms within this gene is lacking. To provide an overview of FCGR3A polymorphisms, we analysed the 1000 Genomes project database and found a total of 234 polymorphisms within the FCGR3A gene, of which 69%, 16%, and 15% occur in the intron, UTR, and exon regions respectively. Additionally, only 16% of all polymorphisms had a minor allele frequency (MAF) > 0.01. To facilitate (full-length) analysis of FCGR3A gene polymorphism, we developed a FCGR3A gene-specific amplification and sequencing protocol for Sanger sequencing and MinION (Nanopore Technologies). First, we used the Sanger sequencing protocol to study the presence of the V158F polymorphism in 76 individuals resulting in frequencies of 38% homozygous T/T, 7% homozygous G/G and 55% heterozygous. Next, we performed a pilot with both Sanger sequencing and MinION based sequencing of 14 DNA samples which showed a good concordance between Sanger- and MinION sequencing. Additionally, we detected 13 SNPs listed in the 1000 Genome Project, from which 11 had MAF > 0.01, and 10 SNPs were not listed in 1000 Genome Project. In summary, we demonstrated that FCGR3A gene is more polymorphic than previously described. As most novel polymorphisms are located in non-coding regions, their functional relevance needs to be studied in future functional studies.

Polymorphic Regions in Fc Gamma Receptor and Tumor Necrosis Factor-α Genes and Susceptibility to Chronic Periodontitis in a Cohort From South India

BACKGROUND

Polymorphisms in the immunoglobulin G Fc receptor II (FcGR) and tumor necrosis factor-α (TNFA) genes are known to influence pathogenesis and severity of several inflammatory conditions. Association of FcGR and TNFA gene polymorphisms with chronic periodontitis (CP) susceptibility has been found to be diverse among different ethnic populations. Objectives of the present study are to determine association of functional single nucleotide polymorphisms (SNPs) in FcGR and TNF-α genes with CP susceptibility in a cohort from South India.

METHODS

Polymorphisms of: 1) FCGR2A 131His/Arg (rs1801274); 2) FCGR2B 232Ile/Thr (rs1050501); 3) TNFA -1031T/C (rs1799964); and 4) TNFA -863C/A (rs1800630) were analyzed among patients with healthy gingiva (n = 176) and patients with CP (n = 177). Genotyping was performed using allele-specific real-time polymerase chain reaction assay. Association between CP and SNPs was examined by multivariable logistic regression analysis with adjustment for: 1) age; 2) sex; and 3) oral hygiene index (OHI). Epistatic interaction between FcGR polymorphisms and interleukin 1B (IL1B) +3954C/T (rs1143634) was assessed using multifactorial dimensionality reduction analysis.

RESULTS

Among four SNPs analyzed, only FCGR2A 131His/Arg showed significant association with CP in a dominant model (odds ratio: 1.6; 95% confidence interval: 1.028 to 2.530). This significance disappeared after correcting for multiple comparisons using Bonferroni analysis, or after adjusting for age, sex, and OHI. A significant redundant interaction between IL1B +3954 C/T and FCGR2A 131His/Arg was observed.

CONCLUSION

Study results suggest the variant form of the SNP in FCGR2A 131His/Arg, FCGR2B 232Ile/Thr, TNFA -1031T/C, and TNFA -863C/A are not associated with CP susceptibility in the selected cohort from South India.

Oral Infections, Metabolic Inflammation, Genetics, and Cardiometabolic Diseases

Although several epidemiologic studies reported plausible and potentially causal associations between oral infections and cardiometabolic diseases (CMDs), controversy still lingers. This might be due to unrecognized confounding from metabolic inflammation and genetics, both of which alter the immune responses of the host. Low-grade inflammation termed metainflammation is the hallmark of obesity, insulin resistance, type 2 diabetes, and CMDs. According to the common soil theory, the continuum of obesity to CMDs is the same pathology at different time points, and early metainflammations, such as hyperglycemia and obesity, display many adverse cardiometabolic characteristics. Consequently, adipose tissue is now considered a dynamic endocrine organ that expresses many proinflammatory cytokines such as TNF-α, IL-6, plasminogen activator inhibitor 1, and IL-1β. In metainflammation, IL-1β and reactive oxygen species are generated, and IL-1β is a pivotal molecule in the pathogenesis of CMDs. Note that the same cytokines expressed in metainflammation are also reported in oral infections. In metabolic inflammation and oral infections, the innate immune system is activated through pattern recognition receptors-which include transmembrane receptors such as toll-like receptors (TLRs), cytosolic receptors such as nucleotide-binding oligomerization domain-like receptors, and multiprotein complexes called inflammasome. In general, TLR-2s are presumed to recognize lipoteichoic acid of Gram-positive microbes-and TLR-4s, lipopolysaccharide of Gram-negative microbes-while nucleotide-binding oligomerization domain-like receptors detect both Gram-positive and Gram-negative peptidoglycans on the bacterial cell walls. However, a high-fat diet activates TLR-2s, and obesity activates TLR-4s and induces spontaneous increases in serum lipopolysaccharide levels (metabolic endotoxemia). Moreover, genetics controls lipid-related transcriptome and the differentiation of monocyte and macrophages. Additionally, genetics influences CMDs, and this creates a confounding relationship among oral infections, metainflammation, and genetics. Therefore, future studies must elucidate whether oral infections can increase the risk of CMDs independent of the aforementioned confounding factors.

Human FcR polymorphism and disease

Fc receptors play a central role in maintaining the homeostatic balance in the immune system. Our knowledge of the structure and function of these receptors and their naturally occurring polymorphisms, including single nucleotide polymorphisms and/or copy number variations, continues to expand. Through studies of their impact on human biology and clinical phenotype, the contributions of these variants to the pathogenesis, progression, and/or treatment outcome of many diseases that involve immunoglobulin have become evident. They affect susceptibility to bacterial and viral pathogens, constitute as risk factors for IgG or IgE mediated inflammatory diseases, and impact the development of many autoimmune conditions. In this chapter, we will provide an overview of these genetic variations in classical FcγRs, FcRLs, and other Fc receptors, as well as challenges in achieving an accurate and comprehensive understanding of the FcR polymorphisms and genomic architecture.

Epigenetic biomarkers: a step forward for understanding periodontitis

Periodontitis is a common oral disease that is characterized by infection and inflammation of the tooth supporting tissues. While its incidence is highly associated with outgrowth of the pathogenic microbiome, some patients show signs of predisposition and quickly fall into recurrence after treatment. Recent research using genetic associations of candidates as well as genome-wide analysis highlights that variations in genes related to the inflammatory response are associated with an increased risk of periodontitis. Intriguingly, some of the genes are regulated by epigenetic modifications, supposedly established and reprogrammed in response to environmental stimuli. In addition, the treatment with epigenetic drugs improves treatment of periodontitis in a mouse model. In this review, we highlight some of the recent progress identifying genetic factors associated with periodontitis and point to promising approaches in epigenetic research that may contribute to the understanding of molecular mechanisms involving different responses in individuals and the early detection of predispositions that may guide in future oral treatment and disease prevention.

Associations between FCGR2A rs1801274, FCGR3A rs396991, FCGR3B NA1/NA2 polymorphisms and periodontitis: a meta-analysis

The aim of this study was to determine whether the Fcγ receptors (FCGRs) polymorphisms confer susceptibility to periodontitis in ethnically different populations. We did a literature search using PubMed and Embase, and conducted a meta-analysis on the associations between the FCGR2A H131R (rs1801274), FCGR3A F158V (rs396991), and FCGR3B NA1/NA2 polymorphisms and periodontitis using allele contrast, the recessive model, the dominant model, and the homozygote contrast. A total of 17 separate comparisons with 1,421 patients with periodontitis and 1,454 controls, involving six Caucasian, six East Asian, two African and one South Asian population were considered in the meta-analysis. Meta-analysis of the FCGR2A H131R polymorphism showed no association between periodontitis and the FCGR2A R allele (OR=0.987, 95% CI=0.881-1.107, p=0.827). Stratification by ethnicity revealed an association between the RR+RH genotype with periodontitis in Caucasian population (OR=0.624, 95% CI=0.479-0.813, p=4.7×10(-5)), but not in East Asian, and African populations. Meta-analysis of the FCGR3A F158V polymorphism revealed an association between the FCGR3A V allele and periodontitis is in Caucasians (OR=1.457, 95% CI=1.014-2.092, p=0.042), but not in East Asians and Africans. In addition, analysis using the dominant model and homozygote contrast showed the same pattern for the FCGR3A V allele. Meta-analysis of the FCGR3B NA1/NA2 polymorphism using the recessive model revealed a significant association between the NA2/NA2 genotype and periodontitis in aggressive periodontitis (OR=2.853, 95% CI=1.673-4.863, 1.1×10(-5)). This meta-analysis demonstrates that the FCGR2A, and FCGR3A polymorphisms may confer susceptibility to periodontitis in Caucasians, and that the FCGR3B polymorphism may be associated with susceptibility to aggressive periodontitis.

Association of Fcγ receptor IIB polymorphism with cryptococcal meningitis in HIV-uninfected Chinese patients

BACKGROUND

As important regulators of the immune system, the human Fcγ receptors (FcγRs) have been demonstrated to play important roles in the pathogenesis of various infectious diseases. The aim of the present study was to identify the association between FCGR polymorphisms and cryptococcal meningitis.

METHODOLOGY/PRINCIPAL FINDINGS

In this case control genetic association study, we genotyped four functional polymorphisms in low-affinity FcγRs, including FCGR2A 131H/R, FCGR3A 158F/V, FCGR3B NA1/NA2, and FCGR2B 232I/T, in 117 patients with cryptococcal meningitis and 190 healthy controls by multiplex SNaPshot technology. Among the 117 patients with cryptococcal meningitis, 59 had predisposing factors. In patients with cryptococcal meningitis, the FCGR2B 232I/I genotype was over-presented (OR = 1.652, 95% CI [1.02-2.67]; P = 0.039) and the FCGR2B 232I/T genotype was under-presented (OR = 0.542, 95% CI [0.33-0.90]; P = 0.016) in comparison with control group. In cryptococcal meningitis patients without predisposing factors, FCGR2B 232I/I genotype was also more frequently detected (OR = 1.958, 95% CI [1.05-3.66]; P = 0.033), and the FCGR2B 232I/T genotype was also less frequently detected (OR = 0.467, 95% CI [0.24-0.91]; P = 0.023) than in controls. No significant difference was found among FCGR2A 131H/R, FCGR3A 158F/V, and FCGR3B NA1/NA2 genotype frequencies between patients and controls.

CONCLUSION/SIGNIFICANCE

We found for the first time associations between cryptococcal meningitis and FCGR2B 232I/T genotypes, which suggested that FcγRIIB might play an important role in the central nervous system infection by Cryptococcus in HIV-uninfected individuals.

Genetic polymorphism studies in periodontitis and Fcγ receptors

Periodontitis is a complex chronic subgingival plaque-induced inflammatory disease influenced by multiple factors, including genetics, behavior and the environment. Many genetic association studies have been conducted in periodontology. One of the most extensively investigated gene families is the Fcγ receptor gene family, which plays a key role in regulating host immune responses to bacteria. Unlike other genetic polymorphisms reported in periodontology, most Fcγ receptor polymorphisms reported not only have established biological functions but are reported to associate with other autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus. There are, however, few recent reviews summarizing the association of this gene family with periodontitis. This article critically reviews the current understanding of genetic polymorphism studies in periodontitis, then summarizes the research status of Fcγ receptor polymorphisms and periodontitis and also of other genes involved in the regulatory network of Fcγ receptors, with special reference to their anticipated biological roles. Moreover, some possible future research directions in the related area are discussed.

Genetic variants at 1p11.2 and breast cancer risk: a two-stage study in Chinese women

Background

Genome-wide association studies (GWAS) have identified several breast cancer susceptibility loci, and one genetic variant, rs11249433, at 1p11.2 was reported to be associated with breast cancer in European populations. To explore the genetic variants in this region associated with breast cancer in Chinese women, we conducted a two-stage fine-mapping study with a total of 1792 breast cancer cases and 1867 controls.

Methodology/Principal Findings

Seven single nucleotide polymorphisms (SNPs) including rs11249433 in a 277 kb region at 1p11.2 were selected and genotyping was performed by using TaqMan® OpenArray™ Genotyping System for stage 1 samples (878 cases and 900 controls). In stage 2 (914 cases and 967 controls), three SNPs (rs2580520, rs4844616 and rs11249433) were further selected and genotyped for validation. The results showed that one SNP (rs2580520) located at a predicted enhancer region of SRGAP2 was consistently associated with a significantly increased risk of breast cancer in a recessive genetic model [Odds Ratio (OR)  =  1.66, 95% confidence interval (CI)  =  1.16–2.36 for stage 2 samples; OR  =  1.51, 95% CI  =  1.16–1.97 for combined samples, respectively]. However, no significant association was observed between rs11249433 and breast cancer risk in this Chinese population (dominant genetic model in combined samples: OR  =  1.20, 95% CI  =  0.92–1.57).

Conclusions/Significance

Genotypes of rs2580520 at 1p11.2 suggest that Chinese women may have different breast cancer susceptibility loci, which may contribute to the development of breast cancer in this population.