Genetic Variation In Susceptibility Research Articles

Genetic variation in susceptibility of Phytophthora cinnamomi-infected holm oak in the absence or presence of severe drought

Abstract The evergreen oaks Quercus ilex and Quercus suber are exposed to widespread Phytophthora infestation in natural forests. To restore diseased forests, deploying trees less susceptible to combined stress is the most promising approach. We aimed to determine whether drought affects the susceptibility of Q. ilex and Q. suber seedlings to Phytophthora cinnamomi (Pc) differently. Additionally, to provide scientific support for a genetic improvement program to reduce the susceptibility of holm oak to decline, genetic variation and heritability in susceptibility to Pc in Q. ilex in the absence or presence of drought were estimated. About 7000 seedlings of 66 Q. ilex and 9 Q. suber trees from the Extremadura region (Spain) were inoculated with Pc at age 1. The following year, half the experimental blocks were regularly watered and half were exposed to severe drought, and inoculated again with Pc. In the absence of drought, Q. ilex was more susceptible than Q. suber to Pc (mortality 97% and 59%, respectively), but in the presence of drought after Pc infection the species were equally susceptible (~97% plant mortality). It could therefore be expected that under the climate change scenarios predicted for the south of the Iberian Peninsula, offspring of Q. suber will be as compromised as offspring of Q. ilex to soil infestation by Pc. Significant additive genetic variation and heritability in the susceptibility of Q. ilex to combined Pc infection and drought were observed (hi2 = 0.46 for time to death of plants), indicating that breeding for tolerance to combined stress is possible. Family variance component estimates of time to death in Q. ilex were highest in the presence of drought, and genetic control of susceptibility in Q. ilex decreased over time as plant stress increased. This is the first study to define a production population against combined stress in oak.

Exploring Genetic Link of Residual Ridge Resorption in Completely Edentulous Individuals: A Prospective Case-Control Clinical Study.

Residual ridge resorption presents obstacles in prosthodontic treatment, affecting denture stability and the success of dental implants. Genetic elements, specifically the single nucleotide polymorphism (SNP) 1772C>T variant within the hypoxia-inducible factor 1 subunit alpha (HIF-1α) gene, are hypothesized to contribute to residual ridge resorption progression. Nevertheless, its impact remains insufficiently investigated, especially within the context of South Indian populations. We sought to investigate the connection between SNP 1772C>T and residual ridge resorption (RRR) among fully edentulous individuals, considering demographic factors, genotyping methodologies, and statistical evaluations. In a prospective case-control study, we recruited 100 completely edentulous participants from South India. Participants were categorized based on alveolar ridge height. Saliva samples were non-invasively collected for DNA extraction, and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was employed to determine genotype distribution using the HphI restriction enzyme. The statistical evaluations comprised the utilization of chi-square and Fisher's exact tests. We observed no significant variations in genotype distributions between the case and control cohorts (CT: p=0.24; CC: p=0.65; TT: p=0.30). The heterozygous genotype CT was prevalent in both groups. Although we did not observe significant associations between SNP 1772C>T and RRR, our findings imply a genetic predisposition to residual ridge resorption that warrants further exploration. Variations in genetic susceptibility across ethnicities and the influence of other genetic variants on residual ridge resorption require additional investigation. This study lays the groundwork for personalized prosthodontic care by highlighting the potential of genetic analysis in routine dental practice to improve treatment strategies.

Genetic Variations in Susceptibility to Traumatic Muscle Injuries and Muscle Pain among Brazilian High-Performance Athletes.

Traumatic muscle injuries (TMIs) and muscle pain (MP) negatively impact athletes' performance and quality of life. Both conditions have a complex pathophysiology involving the interplay between genetic and environmental factors. Yet, the existing data are scarce and controversial. To provide more insights, this study aimed to investigate the association of single-nucleotide polymorphisms (SNPs) previously linked to athletic status with TMI and MP after exercise among Brazilian high-performance athletes from different sports modalities (N = 345). The impact of important environmental determinants was also assessed. From the six evaluated SNPs (ACTN3 rs1815739, FAAH rs324420, PPARGC1A rs8192678, ADRB2 rs1042713, NOS3 rs1799983, and VDR rs731236), none was significantly associated with TMI. Regarding MP after exercise, ACTN3 rs1815739 (CC/CT vs. TT; adjusted odds ratio (aOR) = 1.90; 95% confidence interval (95%Cl), 1.01-3.57) and FAAH rs324420 (AA vs. AC/CC; aOR = 2.30; 95%Cl, 1.08-4.91) were independent predictors according to multivariate binomial analyses adjusted for age (≥23 vs. <23 years), sex (male vs. female), and tobacco consumption (yes vs. no). External validation is warranted to assess the predictive value of ACTN3 rs1815739 and FAAH rs324420. This could have implications for prophylactic interventions to improve athletes' quality of life.

Exercise-mediated macrophage polarization modulates the targeted therapeutic effect of NAFLD: a review.

This review aims to explore the exercise-mediated hepatic macrophage polarization mechanism and its effect on improving and regulating non-alcoholic fatty liver disease (NAFLD) by analyzing the pathogenesis of NAFLD and the cause of the influence of hepatic macrophage polarization. In addition to exploring the varied effects of different exercise types on macrophage polarization regulation in NAFLD, to provide a direction and basis for the treatment of NAFLD. The research methodology involved a comprehensive search of the PubMed database using specific keywords such as "NAFLD", "macrophage polarization", and "exercise", to retrieve relevant literature published. (1) The main factors inducing NAFLD were high-fat diet, obesity, insulin resistance (IR), changes in gut microbiota, and genetic variation in susceptibility. (2) Drug treatment, nutrient induction, microfactor induction, physiological environment induction, and other factors can induce the polarization of hepatic macrophages and affect NAFLD. (3) Different intensities, types, and frequencies of exercise have different effects on polarization macrophages, and may also differently effects improving liver inflammation, fibrosis, and NAFLD. Curently, regular moderate-intensity aerobic exercise is the most effective therapy for treating NAFLD. Approaches to ameliorate NAFLD with exercise involve strategies to alter macrophage polarization by inhibiting M1 or driving M2 activation. However, research on the different types of exercise-mediated macrophage polarization mechanisms and differences in therapeutic effects is not yet sufficient. Future research is necessary to explore the exact mechanisms and differences in the effects of different exercises on the treatment of NAFLD.

Investigating the outcomes of virus coinfection within and across host species.

Interactions between coinfecting pathogens have the potential to alter the course of infection and can act as a source of phenotypic variation in susceptibility between hosts. This phenotypic variation may influence the evolution of host-pathogen interactions within host species and interfere with patterns in the outcomes of infection across host species. Here, we examine experimental coinfections of two Cripaviruses-Cricket Paralysis Virus (CrPV), and Drosophila C Virus (DCV)-across a panel of 25 Drosophila melanogaster inbred lines and 47 Drosophilidae host species. We find that interactions between these viruses alter viral loads across D. melanogaster genotypes, with a ~3 fold increase in the viral load of DCV and a ~2.5 fold decrease in CrPV in coinfection compared to single infection, but we find little evidence of a host genetic basis for these effects. Across host species, we find no evidence of systematic changes in susceptibility during coinfection, with no interaction between DCV and CrPV detected in the majority of host species. These results suggest that phenotypic variation in coinfection interactions within host species can occur independently of natural host genetic variation in susceptibility, and that patterns of susceptibility across host species to single infections can be robust to the added complexity of coinfection.

MicroRNAs as a therapeutic target in IgA nephropathy in Indian population.

Immunoglobulin A nephropathy (IgAN) is the most frequent glomerular disease with rapid development to end stage renal disease, requiring renal replacement therapy. Genome-wide studies suggest geographical variations in genetic susceptibility to IgAN and disease progression. Specific 'candidate genes' were indicated to correlate with different functions that are involved in the pathogenesis of renal conditions. MicroRNAs (miRNAs/miRs) have a major role in mRNA degradation or translation repression, thereby regulating the expression of their target proteins. Previously, a small number of miRNAs were reported to have direct associations with IgAN. In the present study, new miRNAs linked to IgAN were identified in the Indian population. The miRNA was isolated from kidney biopsies of patients with IgAN (n=6) and healthy control tissue from patients with renal cell carcinoma (n=6). The sequencing results indicated that the miRNA percentage acquired from controls and patients with IgAN was 5.61 and 4.35%, respectively. From the results, 10 upregulated and 15 downregulated miRNAs were identified. Of the 25 differentially expressed miRNAs (DEMs), miR-181a-5p, miR-28-3p, let-7g-5p, miR-92a-3p and miR-30c-5p were not reported previously. Furthermore, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses suggested that the target genes of the DEMs were mainly enriched in pathways such as cancer, ErbB signalling, proteoglycans in cancer, Hippo signalling and MAPK pathways. The newly identified miRNAs may impact the behaviour of tissues or IgA deposition by regulating signalling pathways, which forms a basis for future studies aimed at improving the diagnosis and care of patients with IgAN in the Indian community.

Natural variation in host feeding behaviors impacts host disease and pathogen transmission potential.

Animals ranging from mosquitoes to humans often vary their feeding behavior when infected or merely exposed to pathogens. These so-called "sickness behaviors" are part of the innate immune response with many consequences, including avoiding orally transmitted pathogens. Fully understanding the role of this ubiquitous behavior in host defense and pathogen evolution requires a quantitative account of its impact on host and pathogen fitness across environmentally relevant contexts. Here, we use a zooplankton host and fungal pathogen as a case study to ask if infection-mediated feeding behaviors vary across pathogen exposure levels and natural genetic variation in susceptibility to infection. Then, we connect these changes in behavior to pathogen transmission potential (spore yield) and fitness and growth costs to the host. Our results validate a protective effect of altered feeding behavior during pathogen exposure while also revealing significant variation in the magnitude of this response across host susceptibility and pathogen exposure levels. Across all four host genotypes, feeding rates were negatively correlated with susceptibility to infection and transmission potential. The most susceptible genotypes exhibited either strong anorexia, reducing food intake by 26%-42%, ("Standard") or pronounced hyperphagia, increasing food intake by 20%-54% ("A45"). Together, these results suggest that infection-mediated changes in host feeding behavior-which are traditionally interpreted as immunopathology-may in fact serve as crucial components of host defense strategiesandwarrantfurtherinvestigation.

Parametric mapping of QTL for resistance to European canker in apple in ‘Aroma’ × ‘Discovery’

Resistance to European canker (Neonectria ditissima) in apple is currently one of the most important breeding targets for commercial production in Sweden. Previous research has identified significant genetic variation in susceptibility to the disease, with the local Swedish cultivar ‘Aroma’ considered as one of the most resistant cultivars. Identification of genetic regions underlying the resistance of this cultivar would be a valuable tool for future breeding. Thus, we performed Bayesian quantitative trait loci (QTL) mapping for resistance to European canker in a full-sib family of ‘Aroma’ × ‘Discovery’. Mapping was performed with the area under the disease progression curves (AUDPCs) from all seven (AUDPC_All7) and the first four assessments (AUDPC_First4), and three parameters of a sigmoid growth model for lesion length. As a scale for the effect of the different parameters, historic phenotypic data from screenings of a genetically diverse germplasm was compiled and re-analyzed. The parametrization of the data on lesion growth increased the number of QTL that could be identified with high statistical power, and provided some insight into their roles during different stages of disease development in the current experimental setup. Five QTL regions with strong or decisive evidence were identified on linkage groups 1, 8, 15, and 16. The QTL regions could be assigned to either of the parameters lesion length at the first assessment (‘LL_A1’), the maximal lesion growth rate (lesion length doubling time, ‘t_gen’), and the lesion length at girdling (‘LL_G’). Three of these QTL were traced along the pedigrees of some known relatives of the FS family, and discussed in relation to future crosses for breeding and genetic research.

Racial and Ethnic Variation in Genetic Susceptibility: Are Disparities in Infertility Prevalence and Outcomes more than Black and White?

Race, as a social construct without a clear genetic underpinning, is frequently referenced in medicine as predictor of multiple diseases including that of infertility. The authors will discuss how systematic racism can have downstream consequences ranging from overt physician bias to use of medical algorithms that may potentiate the same disparities they attempt to narrow. Then, the authors explore the utility and pragmatic use of genetic ancestry to estimate disease prevalence, instead of racial categories. Finally, the authors explore how health inequities, rooted in systematic racism, can influence disease heritability effectively advocating for research to disentangle the contributions of racism to genetic susceptibility in infertility.

Assessing Genetic Variation in Resistance to Pinewood Nematode (Bursaphelenchus xylophilus) in Pinus radiata D. Don Half-Sib Families

Full understanding and control of pine wilt disease (PWD) is a work in progress and breeding for disease resistance constitutes an essential management strategy for reducing its impact, as evidenced by advanced breeding programs in countries such as Japan. Since Pinus radiata is one of the most commercially relevant species in northern Spain, we designed a study to assess genetic variation in susceptibility to this pathogen using 44 P. radiata half-sib families from the Galician breeding program. Three Bursaphelenchus xylophilus (pinewood nematode, PWN) inoculation experiments were performed to evaluate disease-related variables, estimate genetic parameters, and study sources of genotype by environment interaction (G × E). We also looked at differences in the constitutive chemical compounds of susceptible and non-susceptible individuals. The results showed great variation in PWN susceptibility, with survival rates for P. radiata families ranging from 0% to 90%. In addition, heritability estimates (hi2 = 0.43, hf2 = 0.72) and genetic gain (&gt;26% selecting 50% of the families) were both moderately high for survival. Significant differences in several constitutive chemical compounds were found between susceptible and non-susceptible seedlings in the two susceptibility groups considered. These results confirm the potential of breeding to obtain P. radiata genotypes that are resistant to pine wilt disease and open possibilities for mitigating its future impact on P. radiata stands.

Extensive bidirectional genetic overlap between bipolar disorder and cardiovascular disease phenotypes

Patients with bipolar disorder (BIP) have a high risk of cardiovascular disease (CVD), despite considerable individual variation. The mechanisms underlying comorbid CVD in BIP remain largely unknown. We investigated polygenic overlap between BIP and CVD phenotypes, including CVD risk factors and coronary artery disease (CAD). We analyzed large genome-wide association studies of BIP (n = 51,710) and CVD phenotypes (n = 159,208–795,640), using bivariate causal mixture model (MiXeR), which estimates the total amount of shared genetic variants, and conjunctional false discovery rate (FDR), which identifies specific overlapping loci. MiXeR revealed polygenic overlap between BIP and body mass index (BMI) (82%), diastolic and systolic blood pressure (20–22%) and CAD (11%) despite insignificant genetic correlations. Using conjunctional FDR < 0.05, we identified 129 shared loci between BIP and CVD phenotypes, mainly BMI (n = 69), systolic (n = 53), and diastolic (n = 53) blood pressure, of which 22 are novel BIP loci. There was a pattern of mixed effect directions of the shared loci between BIP and CVD phenotypes. Functional analyses indicated that the shared loci are linked to brain-expressed genes and involved in neurodevelopment, lipid metabolism, chromatin assembly/disassembly and intracellular processes. Altogether, the study revealed extensive polygenic overlap between BIP and comorbid CVD, implicating shared molecular genetic mechanisms. The mixed effect directions of the shared loci suggest variation in genetic susceptibility to CVD across BIP subgroups, which may underlie the heterogeneity of CVD comorbidity in BIP patients. The findings suggest more focus on targeted lifestyle interventions and personalized pharmacological treatment to reduce CVD comorbidity in BIP.

Genome-Wide Association Analyses Identify Variants in IRF4 Associated With Acute Myeloid Leukemia and Myelodysplastic Syndrome Susceptibility.

The role of common genetic variation in susceptibility to acute myeloid leukemia (AML), and myelodysplastic syndrome (MDS), a group of rare clonal hematologic disorders characterized by dysplastic hematopoiesis and high mortality, remains unclear. We performed AML and MDS genome-wide association studies (GWAS) in the DISCOVeRY-BMT cohorts (2,309 cases and 2,814 controls). Association analysis based on subsets (ASSET) was used to conduct a summary statistics SNP-based analysis of MDS and AML subtypes. For each AML and MDS case and control we used PrediXcan to estimate the component of gene expression determined by their genetic profile and correlate this imputed gene expression level with risk of developing disease in a transcriptome-wide association study (TWAS). ASSET identified an increased risk for de novo AML and MDS (OR = 1.38, 95% CI, 1.26-1.51, Pmeta = 2.8 × 10–12) in patients carrying the T allele at s12203592 in Interferon Regulatory Factor 4 (IRF4), a transcription factor which regulates myeloid and lymphoid hematopoietic differentiation. Our TWAS analyses showed increased IRF4 gene expression is associated with increased risk of de novo AML and MDS (OR = 3.90, 95% CI, 2.36-6.44, Pmeta = 1.0 × 10–7). The identification of IRF4 by both GWAS and TWAS contributes valuable insight on the role of genetic variation in AML and MDS susceptibility.

On the origin of the genetic variation in infectious disease prevalence: Genetic analysis of disease status versus infections for Digital Dermatitis in Dutch dairy cattle.

The purpose of this study was to investigate the origin of the genetic variation in the prevalence of bovine digital dermatitis (DD) by comparing a genetic analysis of infection events to a genetic analysis of disease status. DD is an important endemic infectious disease affecting the claws of cattle. For disease status, we analysed binary data on individual disease status (0,1; indicating being free versus infected), whereas for infections, we analysed binary data on disease transmission events (1,0; indicating becoming infected or not). The analyses of the two traits were compared using cross‐validation. The analysis of disease status captures a combination of genetic variation in disease susceptibility and the ability of individuals to recover, whereas the analysis of infections captures genetic variation in susceptibility only. Estimated genetic variances for both traits indicated substantial genetic variation. The GEBV for disease status and infections correlated with only 0.60, indicating that both models indeed capture distinct information. Together, these results suggest the presence of genetic variation not only in disease susceptibility, but also in the ability of individuals to recover from DD. We argue that the presence of genetic variation in recovery implies that breeders should distinguish between infected individuals versus infectious individuals. This is because epidemiological theory shows that selection for recovery is effective only when it targets recovery from being infectious.

Inflammatory bowel disease and psoriasis: modernizing the multidisciplinary approach

Psoriasis and inflammatory bowel disease (IBD) are immune-mediated diseases occurring in barrier organs whose main task is to protect the organism from attack. These disorders are highly prevalent especially in northern Europe where psoriasis has a prevalence of around 3-4% and IBD around 0.3%. The prevalence of IBD in North America has been estimated at around 0.4%. The total incidence rates in northern Europe have been estimated at around 6 for Crohn's disease and 11 for ulcerative colitis per 100000 person-years, compared with an incidence rate of around 280 per 100000 person-years for psoriasis. Both diseases are less common in countries with a lower index of development. The rise in IBD appears to occur as populations adopt a westernized lifestyle, whereas psoriasis seems more stable and prevalence differences may derive more from variation in genetic susceptibility. The gut microbiota is clearly an important driver of IBD pathogenesis; in psoriasis, changes in gut and skin microbiota have been reported, but it is less clear whether and how these changes contribute to the pathogenesis. Large studies show that most identified genes are involved in the immune system. However, psoriasis and IBD are highly heterogeneous diseases and there is a need for more precise and deeper phenotyping to identify specific subgroups and their genetic, epigenetic and molecular signatures. Epigenetic modifications of DNA such as histone modifications, noncoding RNA effects on transcription and translation and DNA methylation are increasingly recognized as the mechanism underpinning much of the gene-environment interaction in the pathogenesis of both IBD and psoriasis. Our understanding of underlying pathogenetic mechanisms has deepened fundamentally over the past decades developing hand in hand with novel therapies targeting pathways and proinflammatory cytokines incriminated in disease. There is not only substantial overlap between psoriasis and IBD, but also there are differences with implication for therapy. In psoriasis, drugs targeting interleukin-23 and interleukin-17 have shown superior efficacy compared with anti-TNFs, whilst in IBD, drugs targeting interleukin-17 may be less beneficial. The therapeutic toolbox for psoriasis is impressive and is enlarging also for IBD. Still, there are unmet needs reflecting the heterogeneity of both diseases and there is a need for closer molecular diagnostics to allow for the development of precise therapeutics.

Association of the host genetic factors, hypercholesterolemia and diabetes with mild influenza in an Iranian population

BackgroundVariation in host genetic factors may result in variation in the host immune response to the infection. Some chronic diseases may also affect individuals’ susceptibility to infectious diseases. The aim of this study was to evaluate the association of the host genetic factors mostly involved in inflammation, as well as hypercholesterolemia and diabetes with mild flu in an Iranian population.MethodsIn this cross-sectional study, nasopharyngeal swab samples were collected from 93 patients referred to primary care centers of Markazi, Semnan, and Zanjan provinces (central Iran) due to flu-like symptoms between March 2015 and December 2018. Of these, PCR test identified 49 influenza A/H1N1 and 44 flu-negative individuals. Twelve single-nucleotide polymorphisms (SNPs) in RPAIN, FCGR2A, MBL-2, CD55, C1QBP, IL-10, TNF-α and an unknown gene were genotyped using iPLEX GOLD SNP genotyping analysis. Hypercholesterolemia and diabetes status was determined based on the physician diagnosis. Association of the host genetic variants, hypercholesterolemia and diabetes with mild A/H1N1 flu was assessed with univariable and multivariable logistic regression analysis as implemented in Stata software (v.14). Statistical tests were considered as significant at 0.05 levels.ResultsFrequency of diabetes and hypercholesterolemia, as well as participants mean age was significantly higher in the flu-negative rather than the flu-positive group. Of 12 SNPs, nine did not show any significant association with mild flu in our study (rs1801274, rs1800451, rs2564978, rs361525, rs1800450, rs1800871, rs1800872, rs1800896, rs1800629). Possessing G vs. A allele in two SNPs (rs3786054 and rs8070740) was associated with a threefold increase in the chance of mild flu when compared to flu-negative patients (95% CI: 1.1, 22.0). Possessing C allele (vs. A) in the rs9856661 locus also increased the chance of mild flu up to 2 folds (95% CI: 1.0, 10.0).ConclusionThe results showed that possessing the G allele in either rs3786054 or rs8070740 loci in C1QBP and RPAIN genes, respectively, increased the risk of H1N1 infection up to 3.3 folds, regardless of the patient’s age, BMI, diabetes, and hypercholesterolemia. Complementary functional genomic studies would shed more light on the underlying mechanism of human immunity associated with these genetic markers. The identified genetic factors may have the same role in susceptibility to similar respiratory infections with RNA viruses, like SARS, MERS and COVID-19. Future genetic association studies targeting these RNA viruses, especially COVID-19 is recommended. Studies on other ethnic groups would also shed light on possible ethnic variations in genetic susceptibility to respiratory RNA viruses.Trial registry IR.PII.REC.1399.063

Burden of Disease of Guillain-Barré Syndrome in Brazil before and during the Zika virus epidemic 2014-2016.

To estimate the burden of disease of Guillain-Barré syndrome (GBS) in Brazil in 2014, 1year before the Zika virus epidemic, and in 2015 and 2016 during the epidemic. The burden of disease of GBS was estimated using the summary measure of population health: Disability Adjusted Life Years (DALY), that combines both mortality (Years of Life Lost YLLs) and morbidity (Years Lived with Disability) components. The study population was composed of GBS hospitalised cases and deaths from the information systems of the Brazilian Unified Health System. The GBS incidence rate in 2014, 2015 and 2016 was 0.74, 0.96, 1.02/100000 respectively, and the mortality rate in the same period was 0.08, 0.009 and 0.11/100000 habitants. The DALYs calculated using the point estimate of GBS disability weight and its values of the confidence interval (0.198 and 0.414) were 5725.90 (5711.79-5742.89) in 2014, 6054.61 (6035.57-6077.54) in 2015 and 7588.49 (7570.20-7610.51) in 2016. The DALYs were high among the male population and in age groups between 20 and 50years. The increase in DALYs in the years 2015 and 2016 compared to 2014 probably resulted from the introduction of ZIKV in Brazil, reinforcing the importance of investments in the prevention of ZIKV infection and in the care of GBS patients.

CACNA1S haploinsufficiency confers resistance to New World arenavirus infection

Understanding the genetics of susceptibility to infectious agents is of great importance to our ability to combat disease. Here, we show that voltage-gated calcium channels (VGCCs) are critical for cellular binding and entry of the New World arenaviruses Junín and Tacaribe virus, suggesting that zoonosis via these receptors could occur. Moreover, we demonstrate that α1s haploinsufficiency renders cells and mice more resistant to infection by these viruses. In addition to being more resistant to infection, haploinsufficient cells and mice required a lower dosage of VGCC antagonists to block infection. These studies underscore the importance of genetic variation in susceptibility to both viruses and pharmaceutics.

A Systematic Analysis of Interactions between Environmental Risk Factors and Genetic Variation in Susceptibility to Colorectal Cancer.

The underlying etiology of colorectal cancer includes both genetic variation and environmental exposures. The main aim of this study was to search for interaction effects between well-established environmental risk factors and published common genetic variants exerting main effects on colorectal cancer risk. We used a two-phase approach: (i) discovery phase (2,652 incident colorectal cancer cases and 10,608 controls from UK Biobank) and (ii) validation phase (1,656 cases and 2,497 controls from the Study of Colorectal Cancer in Scotland). Interactions with nominal P < 0.05 in phase I were taken forward for validation in phase II. Furthermore, we constructed a weighted genetic risk score (GRS) of colorectal cancer risk for each individual and studied interactions between the GRS and the environmental risk factors. Seventy of the 1,500 tested interactions were nominally significant in phase I. After testing these 70 interactions in phase II, an interaction between rs11903757 (2q32.3) and body mass index (BMI) was nominally significant (P = 0.02) with the same direction of effect. The rs11903757*BMI interaction was also significant (ratio of ORs = 1.26; 95% confidence interval, 1.10-1.44; P interaction = 6.03 × 10-4; P heterogeneity = 0.63) in a meta-analysis combining results from both phases. No interactions were significant in phase II after accounting for multiple testing. No interactions involving the GRS were found with statistical significance. Limited evidence of gene-environment interactions in colorectal cancer risk was observed. There are potential modifications of the rs11903757 effect by BMI on colorectal cancer risk. Our findings might contribute to identifying subpopulations with different susceptibility to the effect of BMI on colorectal cancer risk.

Transethnic Genome-Wide Association Study Provides Insights in the Genetic Architecture and Heritability of Long QT Syndrome.

Long QT syndrome (LQTS) is a rare genetic disorder and a major preventable cause of sudden cardiac death in the young. A causal rare genetic variant with large effect size is identified in up to 80% of probands (genotype positive) and cascade family screening shows incomplete penetrance of genetic variants. Furthermore, a proportion of cases meeting diagnostic criteria for LQTS remain genetically elusive despite genetic testing of established genes (genotype negative). These observations raise the possibility that common genetic variants with small effect size contribute to the clinical picture of LQTS. This study aimed to characterize and quantify the contribution of common genetic variation to LQTS disease susceptibility. We conducted genome-wide association studies followed by transethnic meta-analysis in 1656 unrelated patients with LQTS of European or Japanese ancestry and 9890 controls to identify susceptibility single nucleotide polymorphisms. We estimated the common variant heritability of LQTS and tested the genetic correlation between LQTS susceptibility and other cardiac traits. Furthermore, we tested the aggregate effect of the 68 single nucleotide polymorphisms previously associated with the QT-interval in the general population using a polygenic risk score. Genome-wide association analysis identified 3 loci associated with LQTS at genome-wide statistical significance (P<5×10-8) near NOS1AP, KCNQ1, and KLF12, and 1 missense variant in KCNE1(p.Asp85Asn) at the suggestive threshold (P<10-6). Heritability analyses showed that ≈15% of variance in overall LQTS susceptibility was attributable to common genetic variation (h2SNP 0.148; standard error 0.019). LQTS susceptibility showed a strong genome-wide genetic correlation with the QT-interval in the general population (rg=0.40; P=3.2×10-3). The polygenic risk score comprising common variants previously associated with the QT-interval in the general population was greater in LQTS cases compared with controls (P<10-13), and it is notable that, among patients with LQTS, this polygenic risk score was greater in patients who were genotype negative compared with those who were genotype positive (P<0.005). This work establishes an important role for common genetic variation in susceptibility to LQTS. We demonstrate overlap between genetic control of the QT-interval in the general population and genetic factors contributing to LQTS susceptibility. Using polygenic risk score analyses aggregating common genetic variants that modulate the QT-interval in the general population, we provide evidence for a polygenic architecture in genotype negative LQTS.

Geographic and genetic variation in susceptibility of Butomus umbellatus to foliar fungal pathogens

Large-scale patterns of plant invasions may reflect regional heterogeneity in biotic and abiotic factors and genetic variation within and between invading populations. Having information on how effects of biotic resistance vary spatially can be especially important when implementing biological control because introduced agents may have different impacts through interactions with host-plant genotype, local environment, or other novel enemies. We conducted a series of field surveys and laboratory studies to determine whether there was evidence of biotic resistance, as foliar fungal pathogens, in two introduced genotypes (triploid G1, diploid G4) of the Eurasian wetland weed, Butomus umbellatus L. in the USA. We tested whether genotypes differed in disease attack and whether spatial patterns in disease incidence were related to geographic location or climate for either genotype. We surveyed 27 B. umbellatus populations (17 G1, 10 G4) to determine disease incidence and associated fungal pathogens. For a subset of plant populations, we isolated foliar fungi and tested pathogenicity of three isolates in laboratory assays. After accounting for location (latitude, climate), G1 plants had lower disease incidence than G4 plants in the field (38% vs. 70%) but similar pathogen richness. In contrast, bioassays revealed G1 plants consistently received a higher damage score and had larger leaf lesions regardless of pathogen. The seemingly contradictory results between the field and laboratory may be due to climatic differences between areas that limit the regional pool of pathogens or their effect on plant genotype. These results demonstrate that two widespread B. umbellatus genotypes exhibit different susceptibility to pathogens and effectiveness of pathogen biological controls may depend on local conditions.