Functional Polymorphisms Research Articles

Vasotocin receptor gene genotypes moderate the relationship between cortical thickness and sensory processing

Sensory processing is the process by which the central nervous system gathers, interprets, and regulates sensory stimuli in response to environmental cues. However, our understanding of the genetic factors and neuroanatomical correlations that influence sensory processing is limited. The vasotocin system modulates sensory input responsiveness, making it a potential candidate for further investigation. Additionally, human neuroimaging studies have demonstrated that the ability to modulate sensory stimuli is related to neuroanatomical features such as cortical thickness. Therefore, this study aimed to examine the relationship between functional polymorphisms in vasotocin receptor (VTR) genes, sensory profiles, and neuroanatomical correlations. We used structural magnetic resonance imaging (MRI) and the Adolescent/Adult Sensory Profile (AASP) questionnaire in 98 healthy adult participants to assess sensory processing and identified seven single nucleotide polymorphisms. We found that A-allele carriers of rs1042615 in VTR had higher scores for “sensory sensitivity” and “sensation avoiding”. Moreover, higher scores for three AASP subscales were associated with decreased cortical thickness in various regions, including the right precentral, paracentral, and fusiform gyri, as well as bilateral inferior temporal gyri. This study sheds light on the potential role of genetic variations in the VTR in modulating sensory processing and correlation with cortical thickness which has future implications for better understanding sensory abnormalities in neurodevelopmental disorders.

Genotype AA of ACE2 G8790A (rs2285666) Has Protective Potential Against COVID-19 Disease Severity

Background: SARS-CoV-2 virus uses angiotensin converting enzyme 2 (ACE2), a key enzyme of the renin angiotensin system (RAS) as the functional receptor for cell fusion and induction of infections in the respiratory system. Functional ACE2 gene polymorphisms may lead to RAS imbalance and are associated with COVID-19 susceptibility and severity. ACE2 G8790A (rs2285666), a splice region variant, is well characterized in various populations across the world. In the present study, the role of ACE2 G8790A (rs2285666) variant as risk predictor for severity of COVID-19 infection was investigated.Materials and methods: One-hundred COVID-19 subjects were included in the study and divided into: subjects with a history of severe infection and ICU-admitted (Group 1) and subjects with mild to moderate COVID-19 infection (Group 2). Genotype analysis for rs2285666 of ACE2 was performed using polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) method.Results: The distribution of ACE2 G8790A (rs2285666) genotypes were GG 62%, GA 18%, and AA 20% in Group 1 and GG 34%, GA 14%, and AA 52% in Group 2, respectively. The A allele of rs2285666 (p≤0.001; OR=3.4; 95% CI=1.89–6.107) were less frequent in Group 1 as compared to Group 2. Also, a statistically significant difference was found between severity of COVID-19 infection with age and comorbidities such as diabetes, hypertension, chronic kidney disease, but not gender.Conclusion: Our findings suggest the possibility of a protective mechanism of the AA genotype of ACE2 G8790A (rs2285666) variant against COVID-19 disease severity.Keywords: COVID-19, ACE2 gene, renin-angiotensin system, genetic association, rs2285666, sanger sequencing

Cytochrome P450 2C19*2 Genetic Polymorphism in Patients with Acute Coronary Syndrome

Objectives: The study aimed to investigate the association between CP2C19*2 loss of function polymorphism and acute coronary syndrome (ACS) patients receiving Clopidogrel. It compared genotype frequencies of heterozygous GA, homozygous GG, and homozygous AA between ACS patients and healthy controls. The study assessed the statistical significance of the association in the Pakistani cohort. It contributed to understanding the role of genetic polymorphisms in response to Clopidogrel therapy in ACS patients and provided insights into the need for pharmacogenomics testing for patients with CAD, particularly in the Asian population, who are poor metabolizers and require long-term Clopidogrel therapy.
 Methodology: COHORT Study.
 Results: The study found no statistically significant association between the CYP2C19*2 loss of function polymorphism and acute coronary syndrome (ACS) in the Pakistani cohort. The frequency of the CP2C19*2 heterozygous GA genotype was 38.3% in ACS patients and 29.5% in control subjects, while the homozygous GG genotype was 58.7% in patients and 59.0% in controls. The homozygous AA genotype was 3.4% in patients and 11.4% in controls.
 The genotype frequency analysis showed that the wild type GG genotype was lower in patients (58.7%) compared to controls (59.0%), while the mutant AA genotype was also lower in patients (3.4%) compared to controls (11.4%). The heterozygous GA genotype was higher in patients (38.3%) compared to controls (29.5%).
 The population studied was in Hardy Weinberg equilibrium, with a frequency of mutant allele A at 0.26 and wild type allele G at 0.73.
 Conclusion: The study concludes that the CYP2C19*2 loss of function polymorphism is not associated with acute coronary syndrome (ACS) in the Pakistani cohort. The distribution of the CP2C19*2 genetic polymorphism was not statistically significant between ACS patients and healthy controls.
 The genotype frequency analysis showed no significant differences in the distribution of the heterozygous GA, homozygous GG, and homozygous AA genotypes between the patient and control groups.
 The population studied was in Hardy Weinberg equilibrium, with a frequency of mutant allele A at 0.26 and wild type allele G at 0.73.

Multilocus functional characterization of indigenous and exotic inbreds for dgat1-2, fatb, ge2 and wri1a genes affecting kernel oil and fatty acid profile in maize

Demand for maize oil is progressively increasing due to its diverse industrial applications, aside from its primary role in human nutrition and animal feed. Oil content and composition are two crucial determinants of maize oil in the international market. As kernel oil in maize is a complex quantitative trait, improving this trait presents a challenge for plant breeders and biotechnologists. Here, we characterized a set of 292 diverse maize inbreds of both indigenous and exotic origin by exploiting functional polymorphism of the dgat1-2, fatb, ge2, and wri1a genes governing kernel oil in maize. Genotyping using gene-based functional markers revealed a lower frequencies of dgat1-2 (0.15) and fatb (0.12) mutant alleles and a higher frequencies of wild-type alleles (Dgat1-2: 0.85; fatB: 0.88). The favorable wri1a allele was conserved across genotypes, while its wild-type allele (WRI1a) was not detected. In contrast, none of the genotypes possessed the ge2 favorable allele. The frequency of favorable alleles of both dgat1-2 and fatb decreased to 0.03 when considered together. Furthermore, pairwise protein-protein interactions among target gene products were conducted to understand the effect of one protein on another and their responses to kernel oil through functional enrichments. Thus, the identified maize genotypes with dgat1-2, fatb, and wri1a favourable alleles, along with insights gained through the protein-protein association network, serve as prominent and unique genetic resources for high-oil maize breeding programs. This is the first comprehensive report on the functional characterization of diverse genotypes at the molecular and protein levels.

Interleukin 10 (IL10) promoter region polymorphism is associated with IL10 serum concentrations and processing speed in healthy community-dwelling older adults

Inflammation is repressed by interleukin 10 (IL10), a potent anti-inflammatory cytokine, and unchecked inflammation can have detrimental effects on cognition. In healthy older adults enrolled in the Australian Research Council Longevity Intervention (ARCLI) cohort we explored whether a known functional single nucleotide polymorphism (SNP) in the promoter region of IL10, −1082 G/A (rs1800896), was associated with reaction times on computerized cognitive testing that included elements of processing speed (i.e., reaction time). Participants were aged 60–75 years (240 females, 158 males), free of dementia and psychiatric disorders, and provide a blood sample. Processing speed was measured using the Swinburne University Computerized Cognitive Assessment Battery (SUCCAB), which includes measures of reaction time (in milliseconds, ms) on six tasks. Blood-derived DNA was genotyped for the IL10 rs1800896 SNP and presence of the APOE E4 allele. General linear models for each SUCCAB subtest were fitted, with age, sex, education (years), APOE E4 carrier status, and IL10 genotype as independent variables. Carriers of the IL10 AA genotype had significantly slower reaction times on multiple tests compared to carriers of the minor allele (AG, GG) and lower IL10 serum levels. Although IL10 SNPs have not been detected in Alzheimer’s disease genome-wide associated studies, these results support further exploration of IL10 mechanisms as a possible resilience factor.

Impact of kidney function, ticagrelor and genetic polymorphism on high platelet reactivity

Abstract Background High platelet reactivity (HPR) is associated with worse clinical outcomes. Patients with chronic kidney disease (CKD) respond poorly to clopidogrel. The purpose was to investigate what is major determinant on HPR in CKD patients. Methods A total of 219 (139 normal kidney function, 80 CKD) patients who were treated with clopidogrel or ticagrlor were assessed platelet reactivity and genetic polymorphisms. Platelet function was evaluated by the VerifyNowTM P2Y12 assay. Genes tested were ABCB1, PON1, cytochrome P450 (CYP) 2C19, CYP2C9 and P2Y12. HPR was defined as P2Y12 reaction units ≥ 230. Results Platelet reactivity were significantly higher in patients with CKD compared to normal kidney function (288 ± 96 vs 223 ± 69, p < 0.01). But, there were no significant differences of genetic distribution between 2 groups. In patients with CKD and normal kidney function, CYP2C19 carriers had greater platelet reactivity during clopidogrel therapy but there were no differences during ticagrelor treatment regardless of CYP2C19 status (Figure). In multivariate analysis, CKD [hazard ratio (HR): 4.67 (2.27 – 9.78), p < 0.01], CYP2C19 carriers [HR: 2.81 (1.36 – 5.82), p < 0.01] and ticagrelor treatment [HR: 0.29 (0.18 – 0.48), p < 0.01] were significantly correlated with HPR. Conclusion Ticagrelor treatment achieved greater platelet inhibition in patients with CKD whereas CKD and CYP2C19 genotype were significantly correlated with HPR.

219 Identification of Functional Single Nucleotide Polymorphisms Responsible for Alternative Splicing Affecting Gastrointestinal Nematodes Resistance in Grazing Sheep

Abstract Sheep infected with gastrointestinal nematodes (GIN) can show weight loss, anemia, diarrhea, decrease appetite, and hypoproteinemia, which can sometimes lead to death. These signs of infection decrease productivity and cause economic losses. Economic losses can also be associated with treatment without efficacy due to GIN resistance to most anthelmintic classes. Combined approaches need to be used to reduce the reliance on anthelmintic as the only control method to GIN. The aim of this study is the identification of potential functional single nucleotide polymorphisms (SNPs) responsible for alternate splicing in Rideau X Dorset crossbred sheep with different immune profiles using RNA-Sequencing (RNA-Seq). Animals were exposed to GIN while grazing, after that those with the greatest and least gastrointestinal tract parasite burdens were selected for liver RNA extracting. These animals can be separated into groups of high (H; n = 5) and medium (M; n = 6) innate immune responses. In addition, liver RNA was extracted for GIN-unexposed control lambs (U; n = 4). RNA-Seq analysis was performed using the CLC genomics workbench software, version 20.0.4 (CLC Bio, Aarhus, Denmark). Quality control analyses, including guanine-cytosine (GC) content, ambiguous base content, Phred score, base coverage, nucleotide contributions, and over-represented sequences parameters, were performed on fastq files. Sequence reads were aligned to the annotated Oar_rambouillet_v.1 (release 109) ovine reference genome. After filtering steps, mRNA isoforms with multiple (³ 2) expressed mRNA isoforms with at least one mRNA isoform differently expressed (DE) between H- and M-innate immune response and GIN-unexposed control groups (FDR < 0.05 and |FC| > 2) were keep. A total of 1, 75, and 58 DE mRNA isoforms were identified for M versus H, U versus M, and U versus H comparisons, respectively. Gene ontology (GO) analysis including the biological process, molecular function, and cellular component GO categories and metabolic pathways analysis were performed using STRING-db software. Enriched biological processes and metabolic pathways related to the immune system, as well as cholesterol and other sterol metabolism (e.g., sterol biosynthesis, steroid metabolism, cholesterol biosynthesis, cholesterol metabolism, ascorbate and aldarate metabolism, drug metabolism, and terpenoid biosynthesis) were identified (FDR < 0.05). Next, the list of DE mRNA isoforms identified will be deeply studied by performing SNP discovery analysis to validate if specific functional SNPs are responsible for the alternative splicing affecting GIN resistance in grazing sheep. The complete results will help to better understand the biological mechanisms that may be regulating the immune response to GIN. Candidate functional SNPs have the potential to be included in a commercial SNP panel for selection of more resistant animals to improve GIN resistance in sheep flocks.

Genetic variations in a Sestrin2/Sestrin3/mTOR Axis and development of new-onset diabetes after kidney transplantation

BackgroundGenetic variations in Sestrin2/Sestrin3/ mTOR axis may cause obesity-associated metabolic syndrome, including lipid accumulation and insulin resistance thereby increasing individual's risk of diabetes. In this study, we explored the association between single nucleotide polymorphisms (SNPs) of these genes and new onset diabetes after transplantation in Hispanic renal transplant recipients (RTRs). MethodsNine potential functional polymorphisms in Sestrin2, Sestrin3 and mTOR genes were genotyped using the Taqman qPCR method in this study. We compared 160 Hispanic RTRs with no evidence of pre-existing diabetes, who developed new onset diabetes after transplantation (NODAT) with 152 controls with no history of diabetes. The logistic proportional hazard model was used to examine risks for NODAT. Nongenetic and genetic characteristics were included in the multivariate risk model. ResultsSignificant associations were observed between NODAT and mTOR TT (rs2295080 OR = 1.79, 95% CI =1.14–2.82, p = 0.01), Sestrin2 AA (rs580800, OR = 0.42, 95% CI =0.27–0.67, p = 0.002), and Sestrin3 AA (rs684856, OR = 0.45, 95% CI = 0.27–0.75, p = 0.001). Sestrin2 AA (rs580800), Sestrin3 AA (rs684856) and mTOR TT (rs2295080) remained significantly associated with NODAT after adjusting for acute rejection and sirolimus use. No interactions observed between the mTOR rs2295080 and Sestrin3 rs684856 and risk of NODAT (mTOR rs2295080 and Sestrin3 rs684856, p = 0.123 and mTOR rs2295080 and Sestrin2 rs580800, p = 0.167). Of the nongenetic factors, use of sirolimus and older age were associated with an increased risk for NODAT. ConclusionPolymorphisms in the Sestrin2/Sestrin3/ mTOR gene may confer certain protection/predisposition for NODAT.

Molecular basis of genetic improvement for key rice quality traits in Southern China

Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.

Massively parallel functional dissection of schizophrenia-associated noncoding genetic variants

Schizophrenia (SCZ) is a highly heritable mental disorder with thousands of associated genetic variants located mostly in the noncoding space of the genome. Translating these associations into insights regarding the underlying pathomechanisms has been challenging because the causal variants, their mechanisms of action, and their target genes remain largely unknown. We implemented a massively parallel variant annotation pipeline (MVAP) to perform SCZ variant-to-function mapping at scale in disease-relevant neural cell types. This approach identified 620 functional variants (1.7%) that operate in a highly developmental context and neuronal-activity-dependent manner. Multimodal integration of epigenomic and CRISPRi screening data enabled us to link these functional variants to target genes, biological processes, and ultimately alterations of neuronal physiology. These results provide a multistage prioritization strategy to map functional single-nucleotide polymorphism (SNP)-to-gene-to-endophenotype relations and offer biological insights into the context-dependent molecular processes modulated by SCZ-associated genetic variation.

A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants.

Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a large rice population with a total of 10 548 accessions to construct a rice super-population variation map (RSPVM), consisting of 54 378 986 single nucleotide polymorphisms, 11 119 947 insertion/deletion mutations and 184 736 presence/absence variations. Assessment of variation detection efficiency for different population sizes revealed a sharp increase of all types of variation as the population size increased and a gradual saturation of that after the population size reached 10 000. Variant frequency analysis indicated that ∼90% of the obtained variants were rare, and would therefore likely be difficult to detect in a relatively small population. Among the rare variants, only 2.7% were predicted to be deleterious. Population structure, genetic diversity and gene functional polymorphism of this large population were evaluated based on different subsets of RSPVM, demonstrating the great potential of RSPVM for use in downstream applications. Our study provides both a rich genetic basis for understanding natural rice variations and a powerful tool for exploiting great potential of rare variants in future rice research, including population genetics and functional genomics.

A Novel Mutation in the MAP7D3 Gene in Two Siblings with Severe Intellectual Disability and Autistic Traits: Concurrent Assessment of BDNF Functional Polymorphism, X-Inactivation and Oxidative Stress to Explain Disease Severity.

Intellectual disabilities (ID) and autism spectrum disorders (ASD) are characterized by extreme genetic and phenotypic heterogeneity. However, understanding this heterogeneity is difficult due to the intricate interplay among multiple interconnected genes, epigenetic factors, oxidative stress, and environmental factors. Employing next-generation sequencing (NGS), we revealed the genetic cause of ID and autistic traits in two patients from a consanguineous family followed by segregation analysis. Furthermore, in silico prediction methods and 3D modeling were conducted to predict the effect of the variants. To establish genotype-phenotype correlation, X-chromosome inactivation using Methylation-specific PCR and oxidative stress markers were also investigated. By analyzing the NGS data of the two patients, we identified a novel frameshift mutation c.2174_2177del (p.Thr725MetfsTer2) in the MAP7D3 gene inherited from their mother along with the functional BDNF Val66Met polymorphism inherited from their father. The 3D modeling demonstrated that the p.Thr725MetfsTer2 variant led to the loss of the C-terminal tail of the MAP7D3 protein. This change could destabilize its structure and impact kinesin-1's binding to microtubules via an allosteric effect. Moreover, the analysis of oxidative stress biomarkers revealed an elevated oxidative stress in the two patients compared to the controls. To the best of our knowledge, this is the first report describing severe ID and autistic traits in familial cases with novel frameshift mutation c.2174_2177del in the MAP7D3 gene co-occurring with the functional polymorphism Val66M in the BDNF gene. Besides, our study underlines the importance of investigating combined genetic variations, X-chromosome inactivation (XCI) patterns, and oxidative stress markers for a better understanding of ID and autism etiology.

The significant role of a functional polymorphism rs9637231 in long non-coding RNA, LINC02892 in colorectal cancer: Evidence from an Iranian cohort

BackgroundLong noncoding RNAs (lncRNAs) are known to be involved in cancer development and progression. Single nucleotide polymorphisms (SNPs) in lncRNAs may affect the structure, expression, and function of lncRNAs, influencing the cancer risk. In the present case-control study, we investigated the association of LINC02892 SNP rs963723l with colorectal cancer (CRC). MethodsA total of 1130 samples (530 cases and 600 controls), were collected to determine the association between rs9637231 C > T and CRC. Tetra Primer ARMS-PCR was used to determine the genotypes. Statistical analysis was performed employing logistic regression. ResultsThe analysis results indicated that individuals with TT genotype had 89% (95%CI = 1.40–2.57, P < 1.00E-3) and 53% (OR = 1.53, 95%CI = 1.12–2.1, P = 8.00E-3) higher risks of CRC compared to wild-type homozygotes and C allele carriers, respectively. Furthermore, T allele carriers demonstrated a 72% (OR = 1.72, 95%CI = 1.31–2.25, P < 0.001) increased risk of CRC in comparison with wild-type homozygotes. The outcomes were adjusted for factors such as age, gender, and smoking status. ConclusionsSNP rs9637231 might be a risk factor for CRC.

Association between Val158Met polymorphism in the COMT gene with anxiety and heart rate variability in children with irritable bowel syndrome

The aim of this study was to examine the peculiarities of trait anxiety and heart rate variability parameters as well as their relationship depending on the catechol O-methyltransferase (COMT) gene Val158Met polymorphism in children with irritable bowel syndrome. Materials and methods. A total of 26 children aged 6–12 years with a verified diagnosis of irritable bowel syndrome according to the Rome IV criteria were examined. Beforehand, all the patients underwent molecular genetic testing for the COMT Val158met single nucleotide polymorphism by using the polymerase chain reaction-restriction fragment length polymorphism method. Heart rate variability was analyzed via cardiointervalography (Neurosoft) based on short five-minute resting-state ECG recordings. The CMAS (Children’s Manifest Anxiety Scale) test was used to measure trait anxiety levels. The Pearson’s test was used to assess correlations between heart rate variability parameters and anxiety levels. Data were processed using Microsoft Excel 2016 and analyzed with GraphPad (Prism 5.0). Results. Depending on the functional COMT Val158met polymorphism, all the patients were allocated to 3 groups: 8 children with 472 GA (Val/Met) COMT genotype; 10 children with 472 AA (Met/Met) genotype; 8 children with 472 GG (Val/Val) genotype. Time and frequency domain parameters of heart rate variability were significantly different in each group. The highest level of anxiety and the largest percentage of LF component (mainly sympathetic activity) in the structure of heart rate variability was noted among Met/Met carriers. Val/Val carriers had a significantly lower anxiety level and an autonomic imbalance with a higher percentage of HF component (parasympathetic activity). Positive correlations between trait anxiety and heart rate variability parameters were found only in Val/Val and Val/Met groups. Conclusions. Our study has revealed the influence of the COMT Val158met polymorphism on the level of trait anxiety and heart rate variability parameters. It is important for a better understanding of the gut-brain axis dysregulation and impaired stress resilience in children with irritable bowel syndrome. Also, these data could be used to improve current schemes for the treatment of irritable bowel syndrome, supplementing them with activation therapy, psychotherapy, psychopharmacotherapy.

Analysis of Functional Single-Nucleotide Polymorphisms (SNPs) and Leaf Quality in Tea Collection under Nitrogen-Deficient Conditions.

This study discusses the genetic mutations that have a significant association with economically important traits that would benefit tea breeders. The purpose of this study was to analyze the leaf quality and SNPs in quality-related genes in the tea plant collection of 20 mutant genotypes growing without nitrogen fertilizers. Leaf N-content, catechins, L-theanine, and caffeine contents were analyzed in dry leaves via HPLC. Additionally, the photochemical yield, electron transport efficiency, and non-photochemical quenching were analyzed using PAM-fluorimetry. The next generation pooled amplicon-sequencing approach was used for SNPs-calling in 30 key genes related to N metabolism and leaf quality. The leaf N content varied significantly among genotypes (p ≤ 0.05) from 2.3 to 3.7% of dry mass. The caffeine content varied from 0.7 to 11.7 mg g-1, and the L-theanine content varied from 0.2 to 5.8 mg g-1 dry leaf mass. Significant positive correlations were detected between the nitrogen content and biochemical parameters such as theanine, caffeine, and most of the catechins. However, significant negative correlations were observed between the photosynthetic parameters (Y, ETR, Fv/Fm) and several biochemical compounds, including rutin, Quercetin-3-O-glucoside, Kaempferol-3-O-rutinoside, Kaempferol-3-O-glucoside, Theaflavin-3'-gallate, gallic acid. From our SNP-analysis, three SNPs in WRKY57 were detected in all genotypes with a low N content. Moreover, 29 SNPs with a high or moderate effect were specific for #316 (high N-content, high quality) or #507 (low N-content, low quality). The use of a linear regression model revealed 16 significant associations; theaflavin, L-theanine, and ECG were associated with several SNPs of the following genes: ANSa, DFRa, GDH2, 4CL, AlaAT1, MYB4, LHT1, F3'5'Hb, UFGTa. Among them, seven SNPs of moderate effect led to changes in the amino acid contents in the final proteins of the following genes: ANSa, GDH2, 4Cl, F3'5'Hb, UFGTa. These results will be useful for further evaluations of the important SNPs and will help to provide a better understanding of the mechanisms of nitrogen uptake efficiency in tree crops.

Functional Variation in the FAAH Gene Is Directly Associated with Subjective Well-Being and Indirectly Associated with Problematic Alcohol Use.

Fatty acid amide hydrolase (FAAH) is an enzyme that degrades anandamide, an endocannabinoid that modulates mesolimbic dopamine release and, consequently, influences states of well-being. Despite these known interactions, the specific role of FAAH in subjective well-being remains underexplored. Since well-being is a dynamic trait that can fluctuate over time, we hypothesized that we could provide deeper insights into the link between FAAH and well-being using longitudinal data. To this end, we analyzed well-being data collected three years apart using the WHO (Ten) Well-Being Index and genotyped a functional polymorphism in the FAAH gene (rs324420, Pro129Thr) in a sample of 2822 individuals. We found that the A-allele of rs324420, which results in reduced FAAH activity and elevated anandamide levels, was associated with lower well-being scores at both time points (Wave I, B: -0.52, p = 0.007; Wave II, B: -0.41, p = 0.03, adjusted for age and sex). A subsequent phenome-wide association study (PheWAS) affirmed our well-being findings in the UK Biobank (N = 126,132, alternative C-allele associated with elevated happiness, p = 0.008) and revealed an additional association with alcohol dependence. In our cohort, using lagged longitudinal mediation analyses, we uncovered evidence of an indirect association between rs324420 and problematic alcohol use (AUDIT-P) through the pathway of lower well-being (indirect effect Boot: 0.015, 95% CI [0.003, 0.030], adjusted for AUDIT in Wave I). We propose that chronically elevated anandamide levels might influence disruptions in the endocannabinoid system-a biological contributor to well-being-which could, in turn, contribute to increased alcohol intake, though multiple factors may be at play. Further genetic studies and mediation analyses are needed to validate and extend these findings.

Functional consequences of a rare human serotonergic 5-HT1A receptor variant.

Serotonin (5-HT) plays a central role in various brain functions via the activation of a family of receptors, most of them G protein coupled receptors (GPCRs). 5-HT1A receptor, the most abundant 5-HT receptors, was implicated in many brain dysfunctions and is a major target for drug discovery. Several genetic polymorphisms within the 5-HT1A receptor gene were identified and linked to different conditions, including anxiety and depression. Here, we used Xenopus oocytes to examine the effects of one of the functional polymorphism, Arg220Leu, on the function of the receptor. We found that the mutated receptor shows normal activation of G protein and normal 5-HT binding. On the other hand, the mutated receptor shows impaired desensitization, probably due to impairment in activation of β arrestin-dependent pathway. Furthermore, while the 5-HT1A receptor was shown to exhibit voltage dependent activation by serotonin and by buspirone, the mutated receptor was voltage-independent. Our results suggest a pronounced effect of the mutation on the function of the 5-HT1A receptor and add to our understanding of the molecular mechanism of its voltage dependence. Moreover, the findings of this study may suggest a functional explanation for the possible link between this variant and brain pathologies.

Mutations on a conserved distal enhancer in the porcine C-reactive protein gene impair its expression in liver.

C-reactive protein (CRP) is an evolutionary highly conserved protein. Like humans, CRP acts as a major acute phase protein in pigs. While CRP regulatory mechanisms have been extensively studied in humans, little is known about the molecular mechanisms that control pig CRP gene expression. The main goal of the present work was to study the regulatory mechanisms and identify functional genetic variants regulating CRP gene expression and CRP blood levels in pigs. The characterization of the porcine CRP proximal promoter region revealed a high level of conservation with both cow and human promoters, sharing binding sites for transcription factors required for CRP expression. Through genome-wide association studies and fine mapping, the most associated variants with both mRNA and protein CRP levels were localized in a genomic region 39.3 kb upstream of CRP. Further study of the region revealed a highly conserved putative enhancer that contains binding sites for several transcriptional regulators such as STAT3, NF-kB or C/EBP-β. Luciferase reporter assays showed the necessity of this enhancer-promoter interaction for the acute phase induction of CRP expression in liver, where differences in the enhancer sequences significantly modified CRP activity. The associated polymorphisms disrupted the putative binding sites for HNF4α and FOXA2 transcription factors. The high correlation between HNF4α and CRP expression levels suggest the participation of HNF4α in the regulatory mechanism of porcine CRP expression through the modification of its binding site in liver. Our findings determine, for the first time, the relevance of a distal regulatory element essential for the acute phase induction of porcine CRP in liver and identify functional polymorphisms that can be included in pig breeding programs to improve immunocompetence.

Association between polymorphisms of TLR2-1-6 and bipolar disorder in a tunisian population.

Bipolar disorder (BD) is a complex neuropsychiatric disease that has been strongly linked to immune dysregulation. In particular, an abnormal inflammatory response mediated by toll-like receptor 2 - 1/6 (TLR2-1/6) was described in BD. Nevertheless, genetic factors' contribution is still unknown. Thus, we suggested that functional polymorphisms of TLR2, 1 and 6 could be involved in BD predisposition. TLR2, 1 and 6 polymorphisms were genotyped by PCR-RFLP in 292 controls and 131 patients from a Tunisian population. Polymorphisms and haplotype associations were explored in BD and binary logistic regression analysis was performed for more powerful associations. In dominant model, we found a significantly higher genotype and minor allele frequencies in healthy females compared to patients for TLR2-196-174Ins/Del (p = 0.04; OR = 0.3, p = 0.04; OR = 0.3, respectively) and for TLR6-S249P only with minor allele (p = 0.03; OR = 0.2). In contrast, TLR2-R677W CT + TT and T allele frequencies were significantly higher in BD (padjusted<10- 4; ORadjusted =46.6, p < 10- 4; OR = 6.3, respectively), specifically in females (CT + TT: 100%). Similarly, TLR1-R80T showed significantly increased GC + CC and C allele frequencies in patients compared to controls (padjusted=0.04; ORadjusted=4, p = 0.009; OR = 4.3, respectively). Moreover, haplotype investigation demonstrated that InsGTCGT (p < 10- 4, OR = 275) and delGCCGT (p = 0.03, OR = 18.5) were significantly overrepresented in BD patients compared to controls. We suggest that TLR2-196-174Ins/Del and TLR6-S249P could be protective factors of females against BD. However, TLR2-R677W and TLR1-R80T could be strongly associated with higher risk of BD. Interestingly, TLR2-R677W could be a genetic marker for BD in females. However, further studies with larger groups are needed to confirm these findings.

A genetic variant in the immune-related gene ERAP1 affects colorectal cancer prognosis.

Findings on the association of genetic factors and colorectal cancer (CRC) survival are limited and inconsistent, and revealing the mechanism underlying their prognostic roles is of great importance. This study aimed to explore the relationship between functional genetic variations and the prognosis of CRC and further reveal the possible mechanism. We first systematically performed expression quantitative trait locus (eQTL) analysis using The Cancer Genome Atlas (TCGA) dataset. Then, the Kaplan-Meier analysis was used to filter out the survival-related eQTL target genes of CRC patients in two public datasets (TCGA and GSE39582 dataset from the Gene Expression Omnibus database). The seven most potentially functional eQTL single nucleotide polymorphisms (SNPs) associated with six survival-related eQTL target genes were genotyped in 907 Chinese CRC patients with clinical prognosis data. The regulatory mechanism of the survival-related SNP was further confirmed by functional experiments. The rs71630754 regulating the expression of endoplasmic reticulum aminopeptidase 1 ( ERAP1 ) was significantly associated with the prognosis of CRC (additive model, hazard ratio [HR]: 1.43, 95% confidence interval [CI]: 1.08-1.88, P = 0.012). The results of dual-luciferase reporter assay and electrophoretic mobility shift assay showed that the A allele of the rs71630754 could increase the binding of transcription factor 3 (TCF3) and subsequently reduce the expression of ERAP1 . The results of bioinformatic analysis showed that lower expression of ERAP1 could affect the tumor immune microenvironment and was significantly associated with severe survival outcomes. The rs71630754 could influence the prognosis of CRC patients by regulating the expression of the immune-related gene ERAP1 . No. NCT00454519 ( https://clinicaltrials.gov/ ).