Polymorphisms of the DNA repair gene EXO1 modulate cognitive aging in old adults in a Taiwanese population

Analysis of complement system and its related factors in Alzheimer's disease

Alzheimer's disease (AD) is a primary cause of dementia. The complement system is closely related to AD pathology and may be a potential target for the prevention and treatment of AD. In our study, we conducted a bioinformatics analysis to analyze the role of the complement system and its related factors in AD using Gene Expression Omnibus (GEO) data. We also conducted a functional analysis. Our study verified that 23 genes were closely related to differentially expressed complement system genes in diseases after intersecting the disease-related complement system module genes and differentially expressed genes. The STRING database was used to predict the interactions between the modular gene proteins of the differential complement system. A total of 21 gene proteins and 44 interaction pairs showed close interactions. We screened key genes and created a diagnostic model. The predictive effect of the model was constructed using GSE5281 and our study indicated that the predictive effect of the model was good. Our study also showed enriched negative regulation of Notch signaling, cytokine secretion involved in the immune response pathway, and cytokine secretion involved in immune response hormone-mediated apoptotic signaling pathway. We hope that our study provides a promising target to prevent and delay the onset, diagnosis, and treatment of AD.

DNA damage in dementia: Evidence from patients affected by severe Chronic Obstructive Pulmonary Disease (COPD) and meta-analysis of most recent literature

Oxidative stress that leads to oxidatively damaged DNA, plays a crucial role in chronic obstructive pulmonary disease (COPD) as well as in the onset of neurodegenerative diseases. The consequent genomic instability is the first neuropathological event found in the preclinical phase of cognitive impairment (CI), and the level of DNA damage is closely related to the degree of dementia. Since CI has been associated with COPD, we investigated the extent of DNA damage in isolated lymphocytes with the Comet assay, in a group of severe COPD patients with cognitive function measured by the Mini-Mental State Examination (MMSE). An increase in DNA damage was observed in COPD patients with dementia (MMSE≤24), although the difference was only borderline (22.4 ± 6.9 vs. 18.5 ± 7.1; p = 0.055). Meta-analysis, including the results of the current study, confirmed that patients with MMSE≤ 24 showed higher level of DNA damage than patients with MMSE> 24. We observed a significant reduction (p < 0.001) in the MMSE score in patients with cognitive decline in areas I (Orientation), III (Attention and Calculus) and V (Language). Only the temporal orientation category in area I was also associated with the level of oxidative damage, with higher levels of MDA (p < 0.01) and DNA damage (p < 0.03). Patients with the lowest temporal orientation score had a 12% higher mean DNA damage (Odds Ratio=1.12; 95% confidence interval (95%CI) 1.01-1.25; p < 0.036). Temporal orientation is a component of most screening tests for the diagnosis of cognitive impairment, on the bases that disorientation is a common factor in dementia. Present results show that each component of cognitive decline can have a different etiopathogenesis and clinical relevance. A more thorough assessment of the cognitive functions of patients starting COPD rehabilitation, together with the assessment of DNA and the level of oxidative stress, can provide essential information to adapt and customize the rehabilitation project.

An association study in the Taiwan Biobank elicits the GABAA receptor genes GABRB3, GABRA5, and GABRG3 as candidate loci for sleep duration in the Taiwanese population

BACKGROUND

Gamma-aminobutyric acid type A (GABAA) receptors mainly mediate the effects of gamma-aminobutyric acid, which is the primary inhibitory neurotransmitter in the central nervous system. Abundant evidence suggests that GABAA receptors play a key role in sleep-regulating processes. No genetic association study has explored the relationships between GABAA receptor genes and sleep duration, sleep quality, and sleep timing in humans.

METHODS

We determined the association between single-nucleotide polymorphisms (SNPs) in the GABAA receptor genes GABRA1, GABRA2, GABRB3, GABRA5, and GABRG3 and sleep duration, sleep quality, and sleep timing in the Taiwan Biobank with a sample of 10,127 Taiwanese subjects. There were 10,142 subjects in the original study cohort. We excluded 15 subjects with a medication history of sedative-hypnotics.

RESULTS

Our data revealed an association of the GABRB3-GABRA5-GABRG3 gene cluster with sleep duration, which has not been previously identified: rs79333046 (beta = - 0.07; P = 1.21 × 10-3) in GABRB3, rs189790076 (beta = 0.92; P = 1.04 × 10-3) in GABRA5, and rs147619342 (beta = - 0.72; P = 3.97 × 10-3) in GABRG3. The association between rs189790076 in GABRA5 and sleep duration remained significant after Bonferroni correction. A variant (rs12438141) in GABRB3 was also found to act as a potential expression quantitative trait locus. Additionally, we discovered interactions between variants in the GABRB3-GABRA5-GABRG3 gene cluster and lifestyle factors, such as tea and coffee consumption, smoking, and physical activity, that influenced sleep duration, although some interactions became nonsignificant after Bonferroni correction. We also found interactions among GABRB3, GABRA5, and GABRG3 that affected sleep duration. Furthermore, we identified an association of rs7165524 (beta = - 0.06; P = 2.20 × 10-3) in GABRA5 with sleep quality and an association of rs79465949 (beta = - 0.12; P = 3.95 × 10-3) in GABRB3 with sleep timing, although these associations became nonsignificant after Bonferroni correction. However, we detected no evidence of an association of individual SNPs in GABRA1 and GABRA2.

CONCLUSIONS

Our results indicate that rs189790076 in GABRA5 and gene-gene interactions among GABRB3, GABRA5, and GABRG3 may contribute to sleep duration in the Taiwanese population.

Integrated Analysis of Weighted Gene Coexpression Network Analysis Identifying Six Genes as Novel Biomarkers for Alzheimer's Disease

BACKGROUND

Alzheimer's disease (AD) is a chronic progressive neurodegenerative disease; however, there are no comprehensive therapeutic interventions. Therefore, this study is aimed at identifying novel molecular targets that may improve the diagnosis and treatment of patients with AD.

METHODS

In our study, GSE5281 microarray dataset from the GEO database was collected and screened for differential expression analysis. Genes with a P value of <0.05 and ∣log2FoldChange | >0.5 were considered differentially expressed genes (DEGs). We further profiled and identified AD-related coexpression genes using weighted gene coexpression network analysis (WGCNA). Functional enrichment analysis was performed to determine the characteristics and pathways of the key modules. We constructed an AD-related model based on hub genes by logistic regression and least absolute shrinkage and selection operator (LASSO) analyses, which was also verified by the receiver operating characteristic (ROC) curve.

RESULTS

In total, 4674 DEGs were identified. Nine distinct coexpression modules were identified via WGCNA; among these modules, the blue module showed the highest positive correlation with AD (r = 0.64, P = 3e - 20), and it was visualized by establishing a protein-protein interaction network. Moreover, this module was particularly enriched in "pathways of neurodegeneration-multiple diseases," "Alzheimer disease," "oxidative phosphorylation," and "proteasome." Sixteen genes were identified as hub genes and further submitted to a LASSO regression model, and six genes (EIF3H, RAD51C, FAM162A, BLVRA, ATP6V1H, and BRAF) were identified based on the model index. Additionally, we assessed the accuracy of the LASSO model by plotting an ROC curve (AUC = 0.940).

CONCLUSIONS

Using the WGCNA and LASSO models, our findings provide a better understanding of the role of biomarkers EIF3H, RAD51C, FAM162A, BLVRA, ATP6V1H, and BRAF and provide a basis for further studies on AD progression.

An association study in the Taiwan Biobank elicits three novel candidates for cognitive aging in old adults: NCAM1, TTC12 and ZBTB20

The dopamine receptor-related loci have been suggested to be associated with cognitive functions and neurodegenerative diseases. It is unknown whether genetic variants such as single nucleotide polymorphisms (SNPs) in the dopamine receptor-related loci could contribute to cognitive aging independently as well as by virtue of complicated interplays in the elder population. To assess whether SNPs in the dopamine receptor-related loci are associated with cognitive aging in the elder population, we evaluated SNPs in the DRD1, NCAM1-TTC12-ANKK1-DRD2, DRD3-LOC107986115-ZNF80-TIGIT-MIR568-ZBTB20, DRD4, and DRD5-SLC2A9 loci from 25,195 older Taiwanese individuals from the Taiwan Biobank. Mini-Mental State Examination (MMSE) was scrutinized for all participants, where MMSE scores were employed to evaluate cognitive functions. From our analysis, we identified three novel genes for cognitive aging that have not previously been reported: ZBTB20 on chromosome 3 and NCAM1 and TTC12 on chromosome 11. NCAM1 and ZBTB20 are strong candidates for having a role in cognitive aging with mutations in ZBTB20 resulting in intellectual disability, and NCAM1 previously found to be associated with associative memory in humans. Additionally, we found the effects of interplays between physical activity and these three novel genes. Our study suggests that genetic variants in the dopamine receptor-related loci may influence cognitive aging individually and by means of gene-physical activity interactions.

Genome-wide association study in the Taiwan biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5

Numerous genome-wide association studies (GWASs) have been conducted for the identification of genetic variants involved with human height. The vast majority of these studies, however, have been conducted in populations of European ancestry. Here, we report the first GWAS of adult height in the Taiwan Biobank using a discovery sample of 14 571 individuals and an independent replication sample of 20 506 individuals. From our analysis we generalize to the Taiwanese population genome-wide significant associations with height and 18 previously identified genes in European and non-Taiwanese East Asian populations. We also identify and replicate, at the genome-wide significance level, associated variants for height in four novel genes at two loci that have not previously been reported: RASA2 on chromosome 3 and NABP2, RNF41, and SLC39A5 at 12q13.3 on chromosome 12. RASA2 and RNF41 are strong candidates for having a role in height with copy number and loss of function variants in RASA2 previously found to be associated with short stature disorders, and decreased expression of the RNF41 gene resulting in insulin resistance in skeletal muscle. The results from our analysis of the Taiwan Biobank underscore the potential for the identification of novel genetic discoveries in underrepresented worldwide populations, even for traits, such as height, that have been extensively investigated in large-scale studies of European ancestry populations.

Early onset senescence and cognitive impairment in a murine model of repeated mTBI

Mild traumatic brain injury (mTBI) results in broad neurological symptoms and an increased risk of being diagnosed with a neurodegenerative disease later in life. While the immediate oxidative stress response and post-mortem pathology of the injured brain has been well studied, it remains unclear how early pathogenic changes may drive persistent symptoms and confer susceptibility to neurodegeneration. In this study we have used a mouse model of repeated mTBI (rmTBI) to identify early gene expression changes at 24 h or 7 days post-injury (7 dpi). At 24 h post-injury, gene expression of rmTBI mice shows activation of the DNA damage response (DDR) towards double strand DNA breaks, altered calcium and cell–cell signalling, and inhibition of cell death pathways. By 7 dpi, rmTBI mice had a gene expression signature consistent with induction of cellular senescence, activation of neurodegenerative processes, and inhibition of the DDR. At both timepoints gliosis, microgliosis, and axonal damage were evident in the absence of any gross lesion, and by 7 dpi rmTBI also mice had elevated levels of IL1β, p21, 53BP1, DNA2, and p53, supportive of DNA damage-induced cellular senescence. These gene expression changes reflect establishment of processes usually linked to brain aging and suggests that cellular senescence occurs early and most likely prior to the accumulation of toxic proteins. These molecular changes were accompanied by spatial learning and memory deficits in the Morris water maze. To conclude, we have identified DNA damage-induced cellular senescence as a repercussion of repeated mild traumatic brain injury which correlates with cognitive impairment. Pathways involved in senescence may represent viable treatment targets of post-concussive syndrome. Senescence has been proposed to promote neurodegeneration and appears as an effective target to prevent long-term complications of mTBI, such as chronic traumatic encephalopathy and other related neurodegenerative pathologies.

Peripheral Vascular Disease Susceptibility Based on Diabetes Mellitus and rs17367504 Polymorphism of the MTHFR Gene

PURPOSE

Peripheral vascular disease (PVD) is a life-threatening condition affecting the lower extremities. Common risk factors include type 2 diabetes (T2D), hypertension, dyslipidemia, smoking, and older age. There is a little-documented research on the genetic basis of the disease in Taiwan. We examined the impact of T2D and the blood pressure-associated rs17367504 variant of the Methylenetetrahydrofolate reductase (MTHFR) gene on PVD risk.

MATERIALS AND METHODS

In this population-based association study, we linked data from 8992 participants in Taiwan Biobank (TWB) to their medical records in the National Health Insurance Research Database (NHIRD). Participants were 30 to 70 years old at recruitment and included those assessed between 2008 and 2015. We tested for association of PVD with rs17367504 and T2D using multiple logistic regression models. The rs17367504 variant was assessed using the Axiom-Taiwan Biobank Array Plate (TWB chip: Affymetrix, Inc., Santa Clara, CA, USA).

RESULTS

Among cases with T2D (n = 1294), 158 (12.21%) were identified with PVD. T2D was associated with PVD (odds ratio [OR], 1.52; 95% confidence interval [CI], 1.21-1.91; p<0.001) whereas rs17367504 variant was not (OR, 0.96; CI, 0.76-1.21; p = 0.728 in AG/GG compared to AA homozygotes). However, T2D and rs17367504 had an interactive effect on PVD (p for interaction = 0.0076). Results from our stratified analyses displayed OR of 1.75 (CI, 1.35-2.26; p<0.001) in AA individuals with DM and 0.94 (CI, 0.56-1.58; p = 0.811) in AG+GG individuals with T2D. Using the AA genotype and no T2D as the reference group, the respective OR of PVD was 1.77 (CI, 1.38-2.28; p<0.001) in AA individuals with T2D; 1.18 (CI, 0.91-1.55; p = 0.215) in AG+GG individuals with no T2D, and 1.03 (CI, 0.66-1.60; p = 0.892) in AG+GG individuals with T2D .

CONCLUSION

We found that type 2 diabetes was associated with increased risk of peripheral vascular disease, particularly in AA genotype carriers of the rs17367504 variant in Taiwan.

Precision Psychiatry Applications with Pharmacogenomics: Artificial Intelligence and Machine Learning Approaches

A growing body of evidence now suggests that precision psychiatry, an interdisciplinary field of psychiatry, precision medicine, and pharmacogenomics, serves as an indispensable foundation of medical practices by offering the accurate medication with the accurate dose at the accurate time to patients with psychiatric disorders. In light of the latest advancements in artificial intelligence and machine learning techniques, numerous biomarkers and genetic loci associated with psychiatric diseases and relevant treatments are being discovered in precision psychiatry research by employing neuroimaging and multi-omics. In this review, we focus on the latest developments for precision psychiatry research using artificial intelligence and machine learning approaches, such as deep learning and neural network algorithms, together with multi-omics and neuroimaging data. Firstly, we review precision psychiatry and pharmacogenomics studies that leverage various artificial intelligence and machine learning techniques to assess treatment prediction, prognosis prediction, diagnosis prediction, and the detection of potential biomarkers. In addition, we describe potential biomarkers and genetic loci that have been discovered to be associated with psychiatric diseases and relevant treatments. Moreover, we outline the limitations in regard to the previous precision psychiatry and pharmacogenomics studies. Finally, we present a discussion of directions and challenges for future research.

Association and Interaction Effects of Interleukin-12 Related Genes and Physical Activity on Cognitive Aging in Old Adults in the Taiwanese Population

Evidence suggests that the neuro-inflammation mechanisms associated with interleukin-12 (IL-12) may be linked to Alzheimer's diseases and cognitive aging. In this study, we speculate that single nucleotide polymorphisms (SNPs) in IL-12-associated genes, such as IL12A, IL12B, IL12RB1, and IL12RB2 genes, could be associated with cognitive aging individually and/or via complicated interactions in the elder Taiwanese population. There were totally 3,730 Taiwanese individuals with age ≥60 years from the Taiwan Biobank. Mini-Mental State Examination (MMSE) was analyzed for all participants. We employed MMSE scores to assess cognitive functions. Our analysis revealed that the IL12A gene (including rs116910715, rs78902931, and rs78569420), the IL12B gene (including rs730691), and the IL12RB2 gene (including rs3790558, rs4655538, rs75699623, and rs1874396) were associated with cognitive aging. Among these SNPs, the association with the IL12RB2 rs3790558 SNP remained significant after performing Bonferroni correction (P = 6.87 × 10⁻⁴). Additionally, we found that interactions between the IL12A and IL12RB2 genes influenced cognitive aging (P = 0.022). Finally, we pinpointed the effects of interactions between IL12A, IL12B, and IL12RB2 with physical activity (P < 0.001, = 0.002, and < 0.001, respectively). Our study suggests that the IL-12-associated genes may contribute to susceptibility to cognitive aging independently as well as through gene-gene and gene-physical activity interactions.