Generalized multifactor dimensionality reduction approaches to identification of genetic interactions underlying ordinal traits

Gene‒environment interaction effect of hypothalamic‒pituitary‒adrenal axis gene polymorphisms and job stress on the risk of sleep disturbances

Background

Studies have shown that chronic exposure to job stress may increase the risk of sleep disturbances and that hypothalamic‒pituitary‒adrenal (HPA) axis gene polymorphisms may play an important role in the psychopathologic mechanisms of sleep disturbances. However, the interactions among job stress, gene polymorphisms and sleep disturbances have not been examined from the perspective of the HPA axis. This study aimed to know whether job stress is a risk factor for sleep disturbances and to further explore the effect of the HPA axis gene × job stress interaction on sleep disturbances among railway workers.

Methods

In this cross-sectional study, 671 participants (363 males and 308 females) from the China Railway Fuzhou Branch were included. Sleep disturbances were evaluated with the Pittsburgh Sleep Quality Index (PSQI), and job stress was measured with the Effort-Reward Imbalance scale (ERI). Generalized multivariate dimensionality reduction (GMDR) models were used to assess gene‒environment interactions.

Results

We found a significant positive correlation between job stress and sleep disturbances (P < 0.01). The FKBP5 rs1360780-T and rs4713916-A alleles and the CRHR1 rs110402-G allele were associated with increased sleep disturbance risk, with adjusted ORs (95% CIs) of 1.75 [1.38-2.22], 1.68 [1.30-2.18] and 1.43 [1.09-1.87], respectively. However, the FKBP5 rs9470080-T allele was a protective factor against sleep disturbances, with an OR (95% CI) of 0.65 [0.51-0.83]. GMDR analysis indicated that under job stress, individuals with the FKBP5 rs1368780-CT, rs4713916-GG, and rs9470080-CT genotypes and the CRHR1 rs110402-AA genotype had the greatest risk of sleep disturbances.

Conclusions

Individuals carrying risk alleles who experience job stress may be at increased risk of sleep disturbances. These findings may provide new insights into stress-related sleep disturbances in occupational populations.

Impact of tooth mineral tissues genes on dental caries: a birth-cohort study

OBJECTIVE

We aimed to investigate whether Single Nucleotide Polymorphisms present in the genes of tooth mineral tissues influence dental caries trajectory across the life course, and if there is an epistatic (gene-gene) interaction between these SNPs.

METHODS

A representative sample of all 5,914 births from the 1982 Pelotas birth cohort study was prospectively investigated. Dental caries trajectory across the life course was assessed at 15(n=888), 24(n=720), and 31 years old(n=539). Group-based trajectory modelling was used to identify distinct subgroups of individuals whose caries measurements followed a similar pattern over time. Genetic material was collected, and individuals were genotyped [rs4970957(TUFT1), rs1711437(MMP20), rs1784418(MMP20), rs2252070(MMP13), rs243847(MMP2), rs2303466(DLX3), rs11656951(DLX3), rs7501477(TIMP2), rs388286(BMP7), and rs5997096(TFIP11)]. Analyzes were performed for allele and genotype using logistic regression and generalized multifactor dimensionality reduction for epistatic interactions.

RESULTS

The analyses included 678 individuals, those with allele C (OR=0.74, CI95%[0.59-0.92]), genotype CC in the additive effect (OR=0.52, CI95%[0.31-0.89]), and the genotype TC/CC in dominant effect (OR=0.72, CI95%[0.53-0.98]) on the rs243847(MMP2) were associated with low caries trajectory. Individuals with the allele T (OR=0.79, CI95%[0.64-0.98]) and the genotype TC/CC in dominant effect (OR=0.66, CI95%[0.47-0.95]) on the rs5997096(TFIP11) were associated with low caries trajectory. Positive epistatic interactions were observed involving two (MMP2 and BMP7; p=0.006) and three (TUFT1, MMP2, and TFIP11; p<0.001) loci and high caries trajectory.

CONCLUSIONS

Some SNPs present in the genes of tooth mineral tissues were associated with caries trajectory and epistatic interactions increasing the network of SNPs involved in individual caries experience.

CLINICAL SIGNIFICANCE

Single nucleotide polymorphisms in the pathway of tooth mineral tissues genes may contribute significantly to the individual caries experience across the life course.

Association of COMT Polymorphisms with Multiple Physical Activity-Related Injuries among University Students in China

The catechol-O-methyltransferase (COMT) is a candidate gene to provide promising evidence of psychiatric disorders, but there is a knowledge gap between the genetic factor and multiple physical activity-related injuries (PARIs). The aim of this study was to explore the contribution of COMT to the risk of PARIs among university students in the Chinese Han population. We can further search for the intrinsic risk factors for the occurrence of multiple physical activity injuries and provide a scientific basis for early screening and precise intervention for the high-risk group of college students with multiple PARIs. A 1:1 matched case-control study of 61 PARIs cases and 61 healthy controls were carried out. DNA samples of the participants were isolated from saliva and genotyped on eight SNPs of the COMT gene (rs9265, rs4680, rs6269, rs4818, rs4633, rs165655, rs165656, and rs165722) using the MALDI-TOF MS method. We found that rs6269 and rs4818 were significantly associated with PARIs, and rs6269-GG and rs4818-GG contributed to the reduced risk of PARIs. Further haplotype analysis showed a four-marker C-G-C-G haplotype (rs165722-rs6269-rs4633-rs4818) acted with a protective role in the development of PARIs (p = 0.037; OR: 0.474, 95% CI: 0.269 to 0.834). However, the interactions between club membership and rs6269 or rs4818 would significantly increase the risk of PARIs (both p < 0.001, OR: 5.121 and 4.977, respectively). This is the first study to find the contribution of COMT to PARIs occurrence, suggesting that the COMT polymorphisms and the gene-environment interactions may alter the risk of PARIs.

Pro-inflammatory cytokine polymorphisms and interactions with dietary alcohol and estrogen, risk factors for invasive breast cancer using a post genome-wide analysis for gene-gene and gene-lifestyle interaction

Molecular and genetic immune-related pathways connected to breast cancer and lifestyles in postmenopausal women are not fully characterized. In this study, we explored the role of pro-inflammatory cytokines such as C-reactive protein (CRP) and interleukin-6 (IL-6) in those pathways at the genome-wide level. With single-nucleotide polymorphisms (SNPs) in the biomarkers and lifestyles together, we further constructed risk profiles to improve predictability for breast cancer. Our earlier genome-wide association gene-environment interaction study used large cohort data from the Women's Health Initiative Database for Genotypes and Phenotypes Study and identified 88 SNPs associated with CRP and IL-6. For this study, we added an additional 68 SNPs from previous GWA studies, and together with 48 selected lifestyles, evaluated for the association with breast cancer risk via a 2-stage multimodal random survival forest and generalized multifactor dimensionality reduction methods. Overall and in obesity strata (by body mass index, waist, waist-to-hip ratio, exercise, and dietary fat intake), we identified the most predictive genetic and lifestyle variables. Two SNPs (SALL1 rs10521222 and HLA-DQA1 rs9271608) and lifestyles, including alcohol intake, lifetime cumulative exposure to estrogen, and overall and visceral obesity, are the most common and strongest predictive markers for breast cancer across the analyses. The risk profile that combined those variables presented their synergistic effect on the increased breast cancer risk in a gene-lifestyle dose-dependent manner. Our study may contribute to improved predictability for breast cancer and suggest potential interventions for the women with the risk genotypes and lifestyles to reduce their breast cancer risk.

Association Mapping and Development of Marker-Assisted Selection Tools for the Resistance to White Pine Blister Rust in the Alberta Limber Pine Populations

Since its introduction to North America in the early 1900s, white pine blister rust (WPBR) caused by the fungal pathogen Cronartium ribicola has resulted in substantial economic losses and ecological damage to native North American five-needle pine species. The high susceptibility and mortality of these species, including limber pine (Pinus flexilis), creates an urgent need for the development and deployment of resistant germplasm to support recovery of impacted populations. Extensive screening for genetic resistance to WPBR has been underway for decades in some species but has only started recently in limber pine using seed families collected from wild parental trees in the USA and Canada. This study was conducted to characterize Alberta limber pine seed families for WPBR resistance and to develop reliable molecular tools for marker-assisted selection (MAS). Open-pollinated seed families were evaluated for host reaction following controlled infection using C. ribicola basidiospores. Phenotypic segregation for presence/absence of stem symptoms was observed in four seed families. The segregation ratios of these families were consistent with expression of major gene resistance (MGR) controlled by a dominant R locus. Based on linkage disequilibrium (LD)-based association mapping used to detect single nucleotide polymorphism (SNP) markers associated with MGR against C. ribicola, MGR in these seed families appears to be controlled by Cr4 or other R genes in very close proximity to Cr4. These associated SNPs were located in genes involved in multiple molecular mechanisms potentially underlying limber pine MGR to C. ribicola, including NBS-LRR genes for recognition of C. ribicola effectors, signaling components, and a large set of defense-responsive genes with potential functions in plant effector-triggered immunity (ETI). Interactions of associated loci were identified for MGR selection in trees with complex genetic backgrounds. SNPs with tight Cr4-linkage were further converted to TaqMan assays to confirm their effectiveness as MAS tools. This work demonstrates the successful translation and deployment of molecular genetic knowledge into specific MAS tools that can be easily applied in a selection or breeding program to efficiently screen MGR against WPBR in Alberta limber pine populations.

Pro-inflammatory cytokine polymorphisms in ONECUT2 and HNF4A and primary colorectal carcinoma: a post genome-wide gene-lifestyle interaction study

Immune-related molecular and genetic pathways that are connected to colorectal cancer (CRC) and lifestyles in postmenopausal women are incompletely characterized. In this study, we examined the role of pro-inflammatory biomarkers such as C-reactive protein (CRP) and interleukin-6 (IL-6) in those pathways. Through selection of the best predictive single-nucleotide polymorphisms (SNPs) and lifestyles, our goal was to improve the prediction accuracy and ability for CRC risk. Using large cohort data of postmenopausal women from the Women's Health Initiative Database for Genotypes and Phenotypes Study, we previously conducted a genome-wide association (GWA) for a CRP and IL-6 gene-behavioral interaction study. For the present study, we added GWA-SNPs from outside GWA studies, resulting in a total of 152 SNPs. Together with 41 selected lifestyles, we performed a 2-stage multimodal random survival forest analysis with generalized multifactor dimensionality reduction approach to construct CRC risk profiles. Overall and in obesity strata (by body mass index, waist circumference, waist-to-hip ratio, exercise, and dietary fat intake), we identified the best predictive genetic markers in inflammatory cytokines and lifestyles. Across the strata, 2 SNPs (ONECUT2 rs4092465 and HNF4A rs1800961) and 1 lifestyle factor (relatively short-term past use of oral contraceptives) were the most common and strongest predictive markers for CRC risk. The risk profile that combined those variables exhibited synergistically increased risk for CRC; this pattern appeared more strongly in obese and inactive subgroups. Our results may contribute to improved predictability for CRC and suggest genetically targeted lifestyle interventions for women carrying the inflammatory-risk genotypes, reducing CRC risk.

Effect of gene-gene and gene-environment interaction on the risk of first-ever stroke and poststroke death

BACKGROUND

Multiple genetic and environmental factors contribute to the individual-level heterogeneity in stroke. This study aimed to assess how the genetic interactions confer risk of stroke.

METHODS

In a Chinese case-control study including 1,405 strokes and 1,263 controls who were followed up (range, 0.1-6.0 years), eight genes, including apolipoprotein(a) (APOA1), methylenetetrahydrofolate reductase (MTHFR), vitamin K epoxide reductase complex subunit 1 (VKORC1), arachidonate 5-lipoxygenase-activating protein (ALOX5AP), NOTCH3, chromosome 9p21.3(Chr.9p21.3), vascular endothelial growth factor (VEGFA), and kinase insert domain-containing receptor (KDR), were analyzed for interactions by the generalized multifactor dimensionality reduction method and validated by the multivariate logistic regression models. The genetic associations with carotid artery intima-media thickness (IMT) were examined.

RESULTS

The interaction of VKORC1 and Chr.9p21.3 was identified for stroke and its worse prognosis, and subjects having the VKORC1 rs2359612C and Chr.9p21.3 rs10757274G alleles had higher risks for stroke (OR = 1.83, 95% CI = 1.32-2.52) as well as for stroke recurrence (HR = 1.84, 95% CI = 1.24-2.73), cardiovascular events (HR = 1.65, 95% CI = 1.15-2.38), and cardiovascular mortality (HR = 2.16, 95% CI = 1.24-3.79). Supporting, they were associated with higher IMT. Hypertension or physical inactivity increased the risk effect. The interaction of VEGFA rs833061C and KDR rs2305948T was identified for hemorrhagic stroke.

CONCLUSIONS

Our findings identified two novel genetic interactions of VKORC1 and Chr.9p21.3 and of VEGFA and KDR for risk of stroke and subtypes as well as future stroke prognosis.