Untranslated Region Single Nucleotide Polymorphisms Research Articles

Sub-chronic nicotine exposure influences methamphetamine self-administration and dopamine overflow in a sex-and genotype-dependent manner in humanized CHRNA6 3'-UTR SNP (rs2304297) adolescent rats.

Introduction: The rewarding effects of drugs of abuse are associated with the dopaminergic system in the limbic circuitry. Nicotine exposure during adolescence is linked to increased use of drugs of abuse with nicotine and methamphetamine (METH) commonly used together. Nicotine acts on neuronal nicotinic acetylcholine receptor (nAChR) systems, critical for reward processing and drug reinforcement, while METH leads to a higher dopamine (DA) efflux in brain reward regions. A human single nucleotide polymorphism (SNP) in the 3'-untranslated region (UTR) of the α6 nicotinic receptor subunit gene (CHRNA6, rs2304297), has been linked with tobacco/nicotine and general substance use during adolescence. Using CRISPR-Cas9 genomic engineering, our lab recapitulated the CHRNA6 3'UTRC123G SNP, generating α6CC and α6GG allele carriers in Sprague Dawley rats. We hypothesized the CHRNA6 3'UTRC123G SNP would sex- and genotype-dependently enhance nicotine-induced METH self-administration as well as nicotine-induced DA overflow in the nucleus accumbens shell of adolescent α6GG and α6CC carriers. Methods: Adolescent male and female rats underwent a 4-day sub-chronic, low-dose (0.03mg/kg/0.1mL, x2) nicotine pretreatment paradigm to assess intravenous METH (0.02mg/kg/0.1mL) self-administration as well as nicotine- and METH (0.02mg/kg/0.1mL)-induced DA overflow in the nucleus accumbens shell (NAcS) using in vivo microdialysis coupled with high-performance liquid-chromatography-electrochemical detection (HPLC-ECD). Results: Nicotine pretreatment sex- and genotype-dependently enhanced subsequent METH self-administration in adolescent CHRNA6 3'UTRC123G SNP rats. Further nicotine and METH-induced DA overflow is observed in α6CC females as compared to α6GG females, with METH-induced DA overflow enhanced in α6GG males when compared to α6CC males. Conclusion: These findings demonstrate that the CHRNA6 3'-UTRC123G SNP can sex- and genotype-dependently impact adolescent nicotine-induced effects on METH self-administration and stimulant-induced DA overflow in reward regions of the brain.

The 5' untranslated region variant rs3811050 C/T of the interleukin-38 encoding gene is associated with susceptibility to rheumatoid arthritis in Iraqi women.

Interleukin (IL)-38, the latest member of the IL-1 cytokine family, is proposed to have a pathogenic role in rheumatoid arthritis (RA). It is encoded by the IL1F10 gene, which harbors single nucleotide polymorphisms (SNPs) that may predict the risk of autoimmune diseases. Among them are 5' untranslated region (UTR) SNPs, which play a key role in post-transcriptional control, but have not been studied in Iraqi RA patients. Two novel IL1F10 5'UTR SNPs (rs3811050 C/T and rs3811051 T/G) were explored in RA and control women (n = 120 and 110, respectively). SNPs were genotyped using TaqMan assay. An ELISA kit was used to measure serum IL-38 concentrations. A reduced risk of RA was associated with rs3811050 T allele and CT genotype (corrected probability [pc] = 0.01 and < 0.001, respectively), while there was no significant association with rs3811051. Haplotype analysis demonstrated that C-T haplotype was associated with a 1.65-fold greater risk of RA, whereas a reduced risk was linked to T-G haplotype. IL-38 concentrations were higher in patients than in controls (p < 0.001). In addition, IL-38 showed acceptable performance in distinguishing between RA and control women (p < 0.001). When IL-38 concentrations were stratified according to SNP genotypes, no significant differences were found. The rs3811050 variant was more likely to affect RA susceptibility in Iraqi women, and the T allele may play a role in reducing disease risk. IL-38 concentrations were elevated in RA patients, but were not affected by the rs3811050 and rs3811051 genotypes.

Dopamine and Norepinephrine Tissue Levels in the Developing Limbic Brain Are Impacted by the Human CHRNA6 3'-UTR Single-Nucleotide Polymorphism (rs2304297) in Rats.

We previously demonstrated that a genetic single-nucleotide polymorphism (SNP, rs2304297) in the 3' untranslated region (UTR) of the human CHRNA6 gene has sex- and genotype-dependent effects on nicotine-induced locomotion, anxiety, and nicotine + cue-induced reinstatement in adolescent rats. This study aims to investigate how the CHRNA6 3'-UTR SNP influences dopaminergic and noradrenergic tissue levels in brain reward regions during baseline and after the reinstatement of drug-seeking behavior. Naïve adolescent and adult rats, along with those undergoing nicotine + cue reinstatement and carrying the CHRNA6 3'-UTR SNP, were assessed for dopamine (DA), norepinephrine (NE), and metabolites in reward pathway regions. The results reveal age-, sex-, and genotype-dependent baseline DA, NE, and DA turnover levels. Post-reinstatement, male α6GG rats show suppressed DA levels in the Nucleus Accumbens (NAc) Shell compared to the baseline, while nicotine+ cue-induced reinstatement behavior correlates with neurotransmitter levels in specific brain regions. This study emphasizes the role of CHRNA6 3'-UTR SNP in the developmental maturation of the dopaminergic and noradrenergic system in the adolescent rat brain, with tissue levels acting as predictors of nicotine + cue-induced reinstatement.

Genetic polymorphisms of PKLR gene and their associations with milk production traits in Chinese Holstein cows.

Our previous work had confirmed that pyruvate kinase L/R (PKLR) gene was expressed differently in different lactation periods of dairy cattle, and participated in lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, suggesting that PKLR is a candidate gene to affect milk production traits in dairy cattle. Here, we verified whether this gene has significant genetic association with milk yield and composition traits in a Chinese Holstein cow population. In total, we identified 21 single nucleotide polymorphisms (SNPs) by resequencing the entire coding region and partial flanking region of PKLR gene, in which, two SNPs were located in 5′ promoter region, two in 5′ untranslated region (UTR), three in introns, five in exons, six in 3′ UTR and three in 3′ flanking region. The single marker association analysis displayed that all SNPs were significantly associated with milk yield, fat and protein yields or protein percentage (p ≤ 0.0497). The haplotype block containing all the SNPs, predicted by Haploview, had a significant association with fat yield and protein percentage (p ≤ 0.0145). Further, four SNPs in 5′ regulatory region and eight SNPs in UTR and exon regions were predicted to change the transcription factor binding sites (TFBSs) and mRNA secondary structure, respectively, thus affecting the expression of PKLR, leading to changes in milk production phenotypes, suggesting that these SNPs might be the potential functional mutations for milk production traits in dairy cattle. In conclusion, we demonstrated that PKLR had significant genetic effects on milk production traits, and the SNPs with significant genetic effects could be used as candidate genetic markers for genomic selection (GS) in dairy cattle.

Associations of Polymorphisms Localized in the 3'UTR Regions of the KRAS, NRAS, MAPK1 Genes with Laryngeal Squamous Cell Carcinoma.

Background: Genetic variations, localized in the 3′ untranslated region (UTR) in mitogen-activated protein kinase (MAPK) pathway-related genes, may alter the transcription and impact the pathogenesis of laryngeal squamous cell carcinoma (LSCC). The present study investigated the associations of single-nucleotide polymorphisms (SNP), localized in the 3′UTR) of the KRAS, NRAS, and MAPK1 genes with LSCC risk and clinicopathological features. Methods: Genomic DNA and clinical data were collected from 327 adult men with LSCC. The control group was formed from 333 healthy men. Genotyping of the SNPs was performed using TaqMan SNP genotyping assays. Five KRAS, NRAS, and MAPK1 polymorphisms were analyzed. All studied genotypes were in Hardy–Weinberg equilibrium and had the same allele distribution as the 1000 Genomes project Phase 3 dataset for the European population. Results: Significant associations of the studied SNPs with reduced LSCC risk were observed between NRAS rs14804 major genotype CC. Significant associations of the studied SNPs with clinicopathologic variables were also observed between NRAS rs14804 minor T allele and advanced tumor stage and positive lymph node status. SNP of MAPK1 rs9340 was associated with distant metastasis. Moreover, haplotype analysis of two KRAS SNPs rs712 and rs7973450 revealed that TG haplotype was associated with positive lymph node status in LSCC patients. Conclusions: According to the present study, 3′UTR SNP in the NRAS and MAPK1 genes may contribute to the identifications of patients at higher risk of LSCC lymph node and distant metastasis development.

Genetic variant in 3' untranslated region of the mouse pycard gene regulates inflammasome activity.

Quantitative trait locus mapping for interleukin-1β release after inflammasome priming and activation was performed on bone-marrow-derived macrophages (BMDM) from an AKRxDBA/2 mouse strain intercross. The strongest associated locus mapped very close to the Pycard gene on chromosome 7, which codes for the inflammasome adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC). The DBA/2 and AKR Pycard genes only differ at a single-nucleotide polymorphism (SNP) in their 3' untranslated region (UTR). DBA/2 vs. AKR BMDM had increased levels of Pycard mRNA expression and ASC protein, and increased inflammasome speck formation, which was associated with increased Pycard mRNA stability without an increased transcription rate. CRISPR/Cas9 gene editing was performed on DBA/2 embryonic stem cells to change the Pycard 3'UTR SNP from the DBA/2 to the AKR allele. This single base change significantly reduced Pycard expression and inflammasome activity after cells were differentiated into macrophages due to reduced Pycard mRNA stability.

APC gene 3'UTR SNPs and interactions with environmental factors are correlated with risk of colorectal cancer in Chinese Han population.

Objective: To study the correlation between adenomatous polyposis coli (APC) gene 3′ untranslated region (UTR) single nucleotide polymorphisms (SNPs) and their interactions with environmental factors and the risk of colorectal cancer (CRC) in a Chinese Han population.Methods: Genotypes of APC gene 3′UTR rs1804197, rs41116, rs448475, and rs397768 loci in 340 Chinese Han patients with CRC and 340 healthy controls were analyzed. All patients with CRC were analyzed for progression-free survival (PFS) during a 3-year follow-up.Results: The risk of CRC in subjects carrying the APC gene rs1804197 A allele was 2.95-times higher than for the C allele carriers. The interactions of the rs1804197 SNP with body mass index (BMI) and smoking were associated with the risk of CRC. The risk of CRC in the APC gene rs397768 G allele carriers was 1.68-times higher than in the A allele carriers. The interaction between the rs397768 locus SNP and gender was also associated with the risk of CRC. The 3-year PFS of patients with APC gene rs1804197 AA genotype, CA genotype, and CC genotype CRC decreased in this order, with significant difference. In addition, the 3-year PFS of rs397768 locus GG genotype, AG genotype, and AA genotype CRC patients decreased in this order, and the difference was significant.Conclusion: The rs1804197 locus in the 3′UTR region of the APC gene and its interactions with BMI and smoking are associated with the risk of CRC in a Chinese Han population. In addition, the interaction between rs397768 locus SNP and gender is related to the risk of CRC.

The CAV1 Gene 3' Untranslated Region Single Nucleotide Polymorphisms Are Associated with the Risk of Pulmonary Hypertension in Chinese Han Chronic Obstructive Pulmonary Patients.

Aims: Caveolin-1, which is encoded by the caveolin-1 (CAV1) gene, plays an important role in the development of pulmonary hypertension (PH). The purpose of this study was to determine the relationship between 3' untranslated region (UTR) single nucleotide polymorphisms (SNPs) of the CAV1 gene and the risk of PH in Chinese Han patients with chronic obstructive pulmonary disease (COPD). Methods: From March 2016 to October 2018, 235 patients with COPD combined with PH (COPD/PH+) and 240 patients with COPD and without PH (COPD/PH-) were recruited to the study. The CAV1 gene rs1049314, rs8713, rs1049334, rs6867, and rs1049337 loci were genotyped and the plasma hsa-miR-451 and caveolin-1 levels were measured in all subjects. Results: The risk of PH in patients with COPD carrying the C allele of the rs8713 locus was 2.82 times higher than that in A allele carriers (95% confidence interval [CI], 1.94-4.08; p < 0.001). The risk of PH in patients with COPD carrying the T allele of the rs1049337 locus was significantly lower than that in C allele carriers (odds ratio [OR], 0.48; 95% CI, 0.37-0.63; p < 0.001). The ACGAC haplotype was found to be a highly-significant risk factor for COPD combined with PH (OR, 2.24; 95% CI, 1.20-4.17; p = 0.01). Plasma levels of hsa-miR-451 and the caveolin1 protein in patients with the rs8713 C allele were significantly lower than in those with the wild type (WT) allele regardless of PH status. Conversely, the hsa-miRN-451 and caveolin-1 levels in patients with the rs1049337 mutant C allele were significantly higher than those in the WT T allele (p < 0.05). There was a positive correlation between plasma hsa-miR-451 and caveolin-1 levels in patients with COPD/PH+ and COPD/PH- (r = 0.72 and 0.63, respectively). Conclusion: SNPs of the CAV1 gene loci rs8713 and rs1049337 are associated with a risk of PH in COPD patients. The underlying mechanism is likely to be related to the effect of the SNPs on the regulation of caveolin-1 by hsa-miR-451.

Association of purinergic receptor P2RX7 gene polymorphisms with depression symptoms

IntroductionThe activation of the ATP-gated P2RX7 (purinergic receptor P2X, ligand-gated ion channel, 7) produces microglial activation, a process which has been demonstrated in depression, bipolar disorder, and schizophrenia. Emerging data over the last years highlighted the importance of P2X7 cation channel as a potential drug target for these central nervous system disorders. The Gln460Arg (rs2230912) polymorphism of the P2RX7 gene has been widely studied in mood disorders, however the results are still controversial. Therefore, we aimed to investigate the C-terminal region of this gene in major depressive and bipolar disorders (MDD and BD) by studying possibly functional, non-synonymous polymorphisms within a 7 kb long region around the Gln460Arg, including Ala348Thr (rs1718119), Thr357Ser (rs2230911), and Glu496Ala (rs3751143) variants. Since Gln460Arg is located at the 3′ end of the P2RX7 gene, we included additional, potentially functional single nucleotide polymorphisms (SNPs) from the 3′ untranslated region (UTR), which can be in linkage with Gln460Arg. Based on in silico search, we chose two SNPs in putative microRNA target sites which are located in consecutive positions: rs1653625 and rs1718106. MethodsP2RX7 SNPs from the C-terminal region were selected based on previous functional assays, 3′ UTR variants were chosen using PolymiRTS and Patrocles databases. The genotyping of the non-synonymous SNPs was carried out by pre-designed TaqMan® kits, while the 3′ UTR variants were analyzed by PCR-RFLP method. Case-control analyses were carried out between 315 inpatients with acute major depressive episode (195 MDD, 120 BD) and 406 healthy control subjects. The two subscales of the Hospital Anxiety and Depression Scale (HADS) self-report questionnaire were used for quantitative analyses, including an additional, “at-risk” population of 218 patients with diabetes mellitus. The in vitro reporter gene assays were carried out on HEK and SK-N-FI cells transiently transfected with pMIR vector constructs containing the P2RX7 3′ UTR downstream of the luciferase gene. ResultsHaplotype analysis indicated a relatively high linkage between the analyzed P2RX7 SNPs. Our case-control study did not yield any association between P2RX7 gene variants and depression. However, dimensional analyses showed significant associations of the HADS depression severity scores with Gln460Arg (rs2230912) and Ala348Thr (rs1718119) in the depressed and diabetic patient groups. In the in vitro experiments, the P2RX7 3′ UTR constructs with the lowest predicted binding efficiency to their miRNAs showed the highest expression of the gene. The combination of the depression-associated P2RX7 C-terminal and 3′ UTR SNPs contributed to the highest depression severity score in the haplotype analysis. ConclusionBased on our findings, we propose that a P2RX7 haplotype combination of the Gln460Arg and neighboring SNPs contribute to the observed genetic association with depressive symptoms.

Associations between variation in the ovine high glycine-tyrosine keratin-associated protein gene KRTAP20-1 and wool traits.

The keratin-associated proteins (KAPs) are important constituents of wool fibers. Of the many mammalian KAP genes (KRTAPs) identified, KRTAP20-1 has been described in humans, but it has not been described in any other species. A search of the sheep genome using the human KRTAP20-1 sequence revealed a homologous open reading frame on chromosome 1, which would encode a high glycine-tyrosine KAP. PCR-single-stranded conformational polymorphism (PCR-SSCP) analysis identified 8 different banding patterns representing 8 unique DNA sequences (named A to H). The sequences had highest similarity to the human KRTAP20-1 sequence, and this suggests that they are variants of ovine KRTAP20-1. Among these variants, a 12-bp insertion/deletion and 6 single nucleotide poly- morphisms (SNPs), including one 5' untranslated region (UTR) SNP, one 3' UTR SNP, and 2 nonsynonymous SNPs, were detected. Variant A was found to be associated with a decrease in mean fiber diameter, fiber diameter standard deviation, and prickle factor, whereas variant C was associated with increased greasy fleece weight and decreased wool yield. These associations persisted after adjusting for the effect of 2 nearby KRTAPs (KRTAP6-3 and KRTAP22-1) that have also been reported to associate with these wool traits. This suggests that variation in KRTAP20-1 affects wool yield and mean fiber diameter-associated traits, and that this effect is unlikely to be the result of the clustering of these KRTAPs on chromosome 1.

Relationship between single-nucleotide polymorphisms in un-translated region of human leukocyte antigen-G and preeclampsia

Purpose: The aim of this study was to unravel the link between human leukocyte antigen-G untranslated region (HLA-G 3-UTR) single-nucleotide polymorphism (SNP) and preeclampsia by examining polymorphisms in HLA-G 3-UTR in preeclampsia patients and their newborns, as well as those of women with normal pregnancy and their newborns.Methods: Single pregnant mothers and their newborns at the Third Affiliated Hospital of Zhengzhou University, China, were divided into preeclampsia group (144 cases), and normal pregnancy group (122 cases). Blood samples from the two groups were collected for DNA extraction, and the DNA samples were analyzed for HLA-G 3'-UTR SNP by polymerase chain reaction (RT-PCR) and direct sequencing method.Results: The frequency of CG genotype in HLA-G 3-UTR 3127 gene in the preeclampsia group was significantly lower, while the frequency of AA genotype in HLA-G 3-UTR 3172 gene in the preeclampsia group was significantly higher (p &lt; 0.05) when compared with the normal pregnancy group. Furthermore, frequencies of the compatible genotype AA/AA (mothers/newborns) in HLA-G 3-UTR 3172 gene in the preeclampsia group were significantly higher relative to the normal pregnancy group (p&lt; 0.05).Conclusion: These results suggest that when CC/GG is the compatible genotype in HLA-G 3-UTR 3127 gene of mothers/newborns, preeclampsia risk may decrease, but it may increase if the compatible genotype is AA/AA. Thus, SNP in HLA-G 3-UTR 3127 gene may be a protective factor against preeclampsia in Chinese Han pregnant women, while SNP in 3172 gene may be associated with susceptibility to preeclampsia.Keywords: Single-nucleotide polymorphisms, Human leukocyte antigen-G, Un-translated Region, Preeclampsia

Caries and Innate Immunity: DEFB1 Gene Polymorphisms and Caries Susceptibility in Genetic Isolates from North-Eastern Italy

Background: The DEFB1 gene, encoding for the constitutively expressed human β-defensin 1 (hBD1) antimicrobial peptide is a potential candidate when studying genetic susceptibility to caries. DEFB1 genetic variations have been reported as contributing to hBD1 production impairment, leading to a greater susceptibility to be infected by oral pathogens, also leading to periodontitis. Methods: We analysed 5 DEFB1 polymorphisms, namely 3 functional single-nucleotide polymorphisms (SNPs) at the 5′-untranslated region (UTR), -52G>A (rs1799946), -44C>G (rs1800972), and -20G>A (rs11362), 2 SNPs at the 3′-UTR, c*5G>A (rs1047031) and c*87A>G (rs1800971) SNP located in potential miRNA binding sites, looking for possible correlations with the risk to develop caries in 654 adult subjects from isolated populations of north-eastern Italy. Dental caries prevalence was evaluated with the DMFT (decayed, missing, filled teeth) index, calculated after an accurate oral examination. DEFB1 SNP genotyping was performed with an Illumina 370k high-density SNP array. Results: Two DEFB1 SNPs were significantly associated with the DMFT index: the strongest association emerged from rs11362 SNP (p = 0.008). In particular G/G homozygous individuals showed a higher DMFT index compared to both G/A heterozygous and A/A homozygous individuals; rs1799946 SNP was also significantly associated with DMFT (p = 0.030), and individuals homozygous for the T allele had a higher DMFT value compared to heterozygous C/T and homozygous C/C individuals. Conclusions: Our study replicated, on a larger number of individuals, previous findings showing the association between two 5′-UTR SNPs in the DEFB1 gene and DMFT, suggesting that these polymorphisms could be considered as potential markers for assessing the risk to develop caries.

Genetic Modifiers for the Long-QT Syndrome: How Important Is the Role of Variants in the 3' Untranslated Region of KCNQ1?

Long-QT syndrome is an inherited cardiac channelopathy characterized by delayed repolarization, risk of life-threatening arrhythmia, and significant clinical variability even within families. Three single-nucleotide polymorphisms (SNPs) in the 3' untranslated region of KCNQ1 were recently suggested to be associated with suppressed gene expression and hence decreased disease severity when located on the same haplotype with a disease-causing KCNQ1 mutation. We sought to replicate this finding in a larger and a genetically more homogeneous population of KCNQ1 mutation carriers. The 3 SNPs (rs2519184, rs8234, and rs10798) were genotyped in a total of 747 KCNQ1 mutation carriers with A341V, G589D, or IVS7-2A>G mutation. The SNP haplotypes were assigned based on family trees. The SNP allele frequencies and clinical severity differed between the 3 mutation groups. The different SNP haplotypes were neither associated with heart rate-corrected QT interval duration (QTc) nor cardiac events in any of the 3 mutation groups. When the mutation groups were combined, the derived SNP haplotype of rs8234 and rs10798 located on the same haplotype with the mutation was associated with a shorter QTc interval (P<0.05) and a reduced occurrence of cardiac events (P<0.01), consistent with the previous finding. However, when the population-specific mutation was controlled for, both associations were no longer evident. 3' Untranslated region SNPs are not acting as genetic modifiers in a large group of LQT1 patients. The confounding effect of merging a genetically and clinically heterogeneous group of patients needs to be taken into account when studying disease modifiers.

The genetic variation in monocarboxylic acid transporter 2 (MCT2) has functional and clinical relevance with male infertility.

Monocarboxylic acid transporter 2 (MCT2) transports pyruvate and lactate outside and inside of sperms, mainly as energy sources and plays roles in the regulation of spermatogenesis. We investigated the association among genetic variations in the MCT2 gene, male infertility and MCT2 expression levels in sperm. The functional and genetic significance of the intron 2 (+28201A > G, rs10506398) and 3’ untranslated region (UTR) single nucleotide polymorphism (SNP) (+2626G > A, rs10506399) of MCT2 variants were investigated. Two MCT2 polymorphisms were associated with male infertility (n = 471, P < 0.05). In particular, the MCT2-3’ UTR SNP (+2626 G > A) had a strong association with the oligoasthenoteratozoospermia (OAT) group. The +2626GG type had an almost 2.4-fold higher sperm count than that of the +2626AA type (+2626GG; 66 × 106 vs +2626AA; 27 × 106, P < 0.0001). The MCT2-3’ UTR SNP may be important for expression, as it is located at the MCT2 3’ UTR. The average MCT2 protein amount in sperm of the +2626GG type was about two times higher than that of the +2626AA type. The results suggest that genetic variation in MCT2 has functional and clinical relevance with male infertility.

Prenatal detection of TAR syndrome in a fetus with compound inheritance of an RBM8A SNP and a 334-kb deletion: A case report

Thrombocytopenia‑absent radius syndrome (TAR) is a rare genetic disorder that is characterized by the absence of the radius bone in each forearm and a markedly reduced platelet count that results in life‑threatening bleeding episodes (thrombocytopenia). Tar syndrome has been associated with a deletion of a segment of 1q21.1 cytoband. The 1q21.1 deletion syndrome phenotype includes Tar and other features such as mental retardation, autism and microcephaly. This study describes a case of a prenatally diagnosed fetus with compound inheritance of a small (334kb) deletion, as detected by array‑comparative genomic hybridization, and a 5' untranslated region (UTR) low‑frequency allele (rs139428292) in geneRBM8A as detected by Sanger sequencing. The study describes the first case of prenatal analysis of TAR syndrome in a fetus with compound inheritance of a 334‑kbdeletion in the 1q21.1region and a low‑frequency 5' UTRsingle nucleotide polymorphism, and provides confirmation of the causal nature of the RBM8Agene in the diagnosis of TAR syndrome.

Biological Effects of COMT Haplotypes and Psychosis Risk in 22q11.2 Deletion Syndrome

22q11.2 deletion syndrome (22q11.2DS) is the most common genetic syndrome associated with schizophrenia. The catechol-O-methyltransferase (COMT) gene is located in the obligatory deletion region, and possible associations between COMT variants and neuropsychiatric manifestations in 22q11.2DS have been reported. The purpose of the current study was to evaluate the effect of COMT hemizygosity and molecular haplotypes on gene expression and enzyme activity and its association with psychotic symptoms in 22q11.2DS. Lymphoblast samples were drawn from 53 individuals with 22q11.2DS and 16 typically developing control subjects. We measured COMT messenger (m)RNA and protein expression and enzyme activity using standard procedures. The presence of a psychotic disorder and cognitive deficits were also evaluated using structured testing. There was an approximately 50% reduction in COMT mRNA, protein, and enzyme activity levels in 22q11.2DS samples. Haplotype analysis revealed clear phenotypic differences between various Val-containing haplotypes on COMT-3' untranslated region extended mRNA, soluble COMT and membrane-bound proteins, and enzyme activity. The G variant of rs165599, a 3' untranslated region single nucleotide polymorphism, was associated with low levels of COMT expression and with the presence of psychosis and lower performance IQ scores in our 22q11.2DS sample. Finally, we demonstrate that the COMT rs74745580 "T" mutation is associated with absent soluble COMT expression and very low COMT activity in two 22q11.2DS individuals. Our findings confirm a robust effect of COMT hemizygosity on COMT activity and show complex interactions of variants within the COMT gene that influence COMT biology and confound conclusions based on associations with the Val158Met genotype alone.

Short communication: A mutation in the 3′ untranslated region diminishes microRNA binding and alters expression of the OLR1 gene

The oxidized low-density lipoprotein (lectin-like) receptor 1 (OLR1) gene plays an important role in the degradation of the oxidized low-density lipoprotein, which causes damage to the arterial endothelium. Previous studies have shown that a single nucleotide polymorphism (SNP) in the 3′ untranslated region (UTR) of OLR1 was associated with milk production and health traits in dairy cattle and with loin eye area and marbling depth in Qinchuan beef cattle. However, the mechanisms by which this SNP affects these traits are not well understood. MicroRNA (miRNA or mir) are small noncoding RNA that regulate gene expression by binding to target mRNA at their UTR to degrade or to repress translation of the target transcript. We hypothesized that miRNA bind to the 3′ UTR of OLR1 to cause expression changes of the gene. To test this hypothesis, the Bos taurus autosome (bta)-mir-370miRNA was selected for this study based on bioinformatics prediction analysis. Two vectors that included A or C nucleotides of the 3′ UTR SNP and 1 control vector were co-transfected with the vector of bta-miR-370 into human embryonic kidney 293 (HEK293) cells. Results of the dual-luciferase reporter assay showed that the activity of luciferase was significantly lower in cells transfected with the A nucleotide vector than that of the C nucleotide and control vectors. The assay also indicated that activity of miRNA bta-mir-370 was associated with a differential allelic regulation of OLR1 expression. These results imply that the 3′ UTR SNP of the OLR1 gene is a strong candidate marker for selection in cattle breeding programs.

Genetic variation in aldo-keto reductase 1D1 (AKR1D1) affects the expression and activity of multiple cytochrome P450s.

Human liver gene regulatory (Bayesian) network analysis was previously used to identify a cytochrome P450 (P450) gene subnetwork with Aldo-keto reductase 1D1 (AKR1D1) as a key regulatory driver of this subnetwork. This study assessed the biologic importance of AKR1D1 [a key enzyme in the synthesis of bile acids, ligand activators of farnesoid X receptor (FXR), pregnane X receptor (PXR), and constitutive androstane receptor (CAR), known transcriptional regulators of P450s] to hepatic P450 expression. Overexpression of AKR1D1 in primary human hepatocytes led to increased expression of CYP3A4, CYP2C8, CYP2C9, CYP2C19, and CYP2B6. Conversely, AKR1D1 knockdown decreased expression of these P450s. We resequenced AKR1D1 from 98 donor livers and identified a 3'-untranslated region (UTR) (rs1872930) single nucleotide polymorphism (SNP) significantly associated with higher AKR1D1 mRNA expression. AKR1D1 3'-UTR-luciferase reporter studies showed that the variant allele resulted in higher luciferase activity, suggesting that the SNP increases AKR1D1 mRNA stability and/or translation efficiency. Consistent with AKR1D1's putative role as a driver of the P450 subnetwork, the AKR1D1 3'-UTR SNP was significantly associated with increased hepatic mRNA expression of multiple P450s (CYP3A4, CYP2C8, CYP2C9, CYP2C19, and CYP2B6) and CYP3A4, CYP2C8, CYP2C19, and CYP2B6 activities. After adjusting for multiple testing, the association remained significant for AKR1D1, CYP2C9, and CYP2C8 mRNA expression and CYP2C8 activity. These results provide new insights into the variation in expression and activity of P450s that can account for interindividual differences in drug metabolism/efficacy and adverse drug events. In conclusion, we provide the first experimental evidence supporting a role for AKR1D1 as a key genetic regulator of the P450 network.

Are dopamine-related genotypes risk factors for excessive gestational weight gain?

BackgroundExcessive gestational weight gain is associated with postpartum weight retention and downstream child obesity. Dopamine plays a critical role in the regulation of energy intake and body weight. The purpose of this study was to examine the relationship between excessive gestational weight gain and dopamine pathway-related polymorphisms, namely the variable nucleotide tandem repeat in the 3′untranslated region (UTR) region of the SLC6A3 (DAT-1) dopamine transporter gene and the 30-base pair variable nucleotide tandem repeat polymorphism of the 5′UTR of the monoamine oxidase-A (MAO-A) gene.MethodsNinety-three women of mean age 31.7 ± 4.2 years were recruited from the Ottawa and Kingston birth cohort and assessed at 12–20 weeks’ gestation. Mean body mass index was 22.7 ± 2.5 kg/m2. Excessive gestational weight gain was defined according to the 2009 Institute of Medicine guidelines based on body mass index. Genotype analyses were performed using polymerase chain reaction and agarose gel electrophoresis.ResultsThere was no relationship between the prevalence or magnitude of excessive gestational weight gain among women with the 3′ UTR single nucleotide polymorphism of the DAT-1 gene. However, 70% (19 of 27) of women carrying the MAO-A 4/4 (high activity) allele exceeded recommendations for gestational weight gain compared with 48% (32 of 60) of those with the pooled 3/3, 3/4, and 3/3.5 (low activity) alleles (P < 0.05). Similarly, those with the MAO-A 4/4 allele had significantly greater gestational weight gain than those with the 3/3, 3/4, or 3/3.5 pooled genotypes (19.3 ± 4.1 versus 17.0 ± 5.0 kg, P = 0.03).ConclusionCarriers of the 4/4 variants of the MAO-A gene may be at increased risk for excessive gestational weight gain.

An individual coding polymorphism and the haplotype of the SPARC gene predict gastric cancer recurrence

The 5-year survival rate for gastric adenocarcinoma (GA) remains only 40% and biomarkers to identify patients at high risk of tumor recurrence are urgently needed. Secreted protein acidic and rich in cysteine (SPARC) is an extracellular matrix glycoprotein that mediates cell matrix interactions, and upregulation of SPARC can promote tumor progression and metastasis. This study investigated whether single-nucleotide polymorphisms (SNPs) in SPARC impact the prognosis of GA. Blood or formalin-fixed, paraffin-embedded tissues were obtained from 137 GA patients at the University of Southern California and Memorial Sloan-Kettering Cancer Center medical facilities. DNA was isolated and five SNPs in the SPARC 3'-untranslated region (UTR) were evaluated by DNA sequencing or PCR-restriction fragment length polymorphism. Associations between SNPs and time to tumor recurrence (TTR) were analyzed using Kaplan-Meier curves, log-rank tests, and likelihood-ratio test within logistic or Cox regression model as appropriate. Patients carrying at least one G allele of the SPARC rs1059829 polymorphism (GG, AG) showed a median TTR of 3.7 years compared with 2.1 years TTR for patients with AA (hazard ratio (HR) 0.57; P=0.033). In a multivariate analysis adjusted for T and N category as covariates and stratified by race, hospital and chemotherapy, patients with at least one SPARC rs1059829 G allele (GG, AG) remained significantly associated with superior TTR than patients with AA genotype (adjusted P=0.026). In addition, patients harboring the G-A-A haplotype had the highest risk of tumor recurrence (HR 1.892; adjusted P=0.016). Our findings suggest that SPARC 3'-UTR SNPs may be useful in predicting GA patients at increased risk of recurrence.