Polymorphic Dinucleotide Research Articles

High genetic diversity of Babesia canis (Piana & Galli‐Valerio, 1895) in a recent local outbreak in Berlin/ Brandenburg, Germany

Canine babesiosis caused by Babesia canis (Piana & Galli-Valerio, 1895) is emerging in new regions in Europe since its vector Dermacentor reticulatus (Fabricius, 1794) is expanding its geographic range. In the Berlin/Brandenburg area in northeast Germany, D. reticulatus is highly abundant but in the past only one autochthonous B. canis infection was reported. Since 2015, autochthonous cases were occasionally diagnosed but numbers increased since autumn 2019. The aim of the study was to genotype autochthonous canine Babesia spp. infections from Berlin/Brandenburg. Between 04/2015 and 01/2022, 46 dogs with acute babesiosis were presented to the small animal clinic (one dog was infected twice resulting in 47 samples). There were 32 dogs that had never left Berlin/Brandenburg and 14 others that had not left the region in the 6weeks prior to disease onset. PCRs targeting the 18S rRNA and the Bc28.1 merozoite surface antigen were positive in 47 and 42 samples, respectively. Sequencing of cloned PCR products identified all samples as B. canis with 17 18S rRNA and 12 Bc28.1 haplotypes. Based on network analysis for 18S rRNA sequences and a previously described polymorphic dinucleotide, samples were assigned to two distinct clusters. One contained 31 and the other 16 samples. Using network analysis, the Bc28.1 haplotypes could also be separated into two clusters differing by at least five polymorphisms. Analyses of sequences from multiple clones indicated the presence of up to five 18S rRNA and eight Bc28.1 haplotypes and thus high parasite variability in an individual host. The genetic diversity could suggest that the parasites in the region have multiple origins, but diversity in individual dogs and dog populations from endemic regions is unknown. The suitability of both markers for genotyping is questionable due to potential intragenomic diversity for the rRNA and high intergenomic variability for the Bc28.1 marker.

IFNL4 rs368234815 polymorphism does not predict risk of BK virus associated nephropathy after living‐donor kidney transplant: A case‐control study

BackgroundBK polyoma virus (BKPyV) associated nephropathy (BKPyVAN) is a major cause of kidney graft loss in renal transplant patients. Interferons (IFNs) are an important innate immune response against viral infections and genetic polymorphisms of the IFN‐pathways can affect susceptibility and mortality during viral infection. Here, we investigated whether the dinucleotide polymorphism rs368234815 (ΔG/TT) in the IFNL4 gene contributed to BKPyV reactivation or BKPyVAN after living‐donor kidney transplantation.MethodsThis retrospective case‐control study determines the prevalence of IFNL4 variants in a Caucasian population of living‐donor kidney transplant recipients and donors and explores its association with BKPyV infection and BKPyVAN development. We included 28 recipients with BKPyV reactivation, 10 of which developed BKPyVAN and 30 BKPyV negative controls. Targeted sequencing of the IFNL4 gene from both recipients and their respective donors was performed.ResultsWe found IFNL4 rs368234815 ΔG allele frequencies of 41.7% in BKPyV negative and 39.3% in BKPyV positive recipients (P = .85), and 41.7% and 40.4% (P>.99) in their respective donors. IFNL4 rs368234815 ΔG allele frequencies in BKPyVAN developing recipients and their respective donors were 50% and 43.7% (P = .60 and P>.99).ConclusionsOur results indicate that the IFNL4 rs368234815 ΔG allele is not associated with BKPyV reactivation, nor the manifestation of BKPyVAN.

Novel combined UGT1A1 mutations in Crigler Najjar Syndrome type I.

BackgroundUridine diphosphate‐glucuronosyl transferase 1A1 (UGT1A1), which is the major UGT1 gene product, is located on chromosome 2q37. The expression of UGT1A1 is relatively managed by a polymorphic dinucleotide repeat inside the promoter TATA box consisting of 5–8 copies of a TA repeat. A (TA) 6TAA is considered as the wild type. The A (TA) 7TAA allele has been identified as the most frequent allele in the Caucasian populations while A (TA) 8TAA allele remains the rarest allele worldwide in North Africa, including the Arab populations.MethodsThe spectrum of UGT1A1 genetic mutations in seventeen Tunisian children affected by persistent unconjugated hyperbilirubinemias is represented in addition to their relatives, notably parents, sisters, and brothers. Tunisian children, from 16 unrelated families as well as a 17th family without CN1 affected child, were originated from the West Center of Tunisia. The promoter region and coding exons of the UGT1A1 were PCR amplified, subsequently subjected to Sanger sequencing.ResultsThe frequencies of genotypes in CN1 patients were as follows (TA) (7/7) (12/17: 70.6%) and (TA) (8/8) (5/17: 29.4%). All patients harbored the c.1070A>G mutation of exon 3 (UGT1A1*16) in the homozygous state. Among relatives of our patients (n = 16), who were all heterozygotes for UGT1A1*16, 13/16 (81.25%) had a heterozygous state for UGT1A1∗1/UGT1A1∗28 or (TA) (6/7) and, 18.75% (3/16) were heterozygous for UGT1A1∗28/UGT1A1∗37 or (TA) (7/8) of the promoter polymorphisms.Conclusion UGT1A1*16 accompanied with UGT1A1*28 or UGT1A1*37 had a specific geographic and ethnic distribution for CN pathogenesis in this Tunisian cohort.

Endometriosis Is Associated with Functional Polymorphism in the Promoter of Heme Oxygenase 1 (HMOX1) Gene.

Endometriosis is a common gynecological disorder characterized by the ectopic growth of endometrial-like tissue outside the uterine cavity. Etiopathogenesis of endometriosis is poorly understood; it is plausible, however, that the disease may be associated with oxidative stress related to local heme and iron metabolism. Therefore, the aim of the study was to reveal a possible association of endometriosis with a stress-inducible heme oxygenase 1 (HMOX1). For this purpose, 228 patients with clinically confirmed endometriosis and 415 control parous women from general Polish population were examined for functional –413A>T (rs2071746) single-nucleotide polymorphism (SNP) and (GT)n dinucleotide repeat length polymorphism in the promoter of HMOX1 gene. In addition, –413A>T SNP was assessed by the specific TaqMan® SNP Genotyping Assay, and (GT)n polymorphism was determined by PCR product size analysis. We found that endometriosis is associated with an increased frequency of −413A(GT)31,32 haplotype (OR (95%CI) = 1.27 (1.01–1.60), p = 0.0381) and −413A(GT)31,32 homozygous genotype [OR (95%CI) = 1.51 (1.06–2.17), p = 0.0238]. These data suggest that endometriosis is associated with functional polymorphism of HMOX1 gene, and this gene may play a part in the pathogenesis of this disorder.

Diallelic self-incompatibility is the main determinant of fertilization patterns in olive orchards.

Self‐incompatibility (SI) in flowering plants potentially represents a major obstacle for sexual reproduction, especially when the number of S‐alleles is low. The situation is extreme in the commercially important olive tree, where in vitro pollination assays suggested the existence of a diallelic SI (DSI) system involving only two groups (G1 and G2). Varieties belonging to the same SI group cannot fertilize each other, such that successful fruit production is predicted to require pollination between varieties of different groups. To test this prediction, we explored the extent to which the DSI system determines fertilization patterns under field conditions. One hundred and seventeen olive cultivars were first genotyped using 10 highly polymorphic dinucleotide Simple Sequence Repeat (SSR) markers to ascertain varietal identity. Cultivars were then phenotyped through controlled pollination tests to assign each of them to one of the two SI groups. We then collected and genotyped 1440 open pollinated embryos from five different orchards constituted of seven local cultivars with known group of incompatibility groups. Embryos genotype information were used: (i) to assign embryos to the most likely pollen donor genotype in the neighbourhood using paternity analysis, and (ii) to compare the composition of the pollen cloud genetic among recipient trees in the five sites. The paternity analysis showed that the DSI system is the main determinant of fertilization success under field open pollination conditions: G1 cultivars sired seeds exclusively on G2 cultivars, and reciprocally. No self‐fertilization events were observed. Our results demonstrate that DSI is a potent force determining pollination success among varieties within olive orchards used for production. They have the potential to improve management practices by guiding the selection of compatible varieties to avoid planting orchards containing sets of varieties with strongly unbalanced SI groups, as these would lead to suboptimal olive production.

A Functional Variant rs3093023 in CCR6 Is Associated With IgA Nephropathy by Regulating Th17 Cells in a North Han Chinese Population.

C-C chemokine receptor 6 (CCR6) is a susceptibility gene of various immune-related diseases, which was suggested to be shared with immunoglobulin A nephropathy (IgAN). In this study, we aimed to identify the functional variants. First, we analyzed the associations of CCR6 common and rare variants detected by multi-platform chips with IgAN susceptibility using imputation and identified 68 significantly associated common variants located in the regulatory region. Among them, rs3093023 showed both statistical significance (rs3093023-A, odds ratio [OR] = 1.15, P = 2.00 × 10−2) and the expression quantitative trait loci (eQTL) effect (P = 1.45 × 10−3). It was independently replicated (rs3093023-A, OR = 1.18, P = 5.56 × 10−3) and the association was reinforced in the meta-analysis (rs3093023-A, OR = 1.17, P = 6.14 × 10−7). Although rs3093023 was in a strong linkage disequilibrium with the reported CCR6 functional variant dinucleotide polymorphism, CCR6DNP, the alleles of rs3093023 (G>A) rather than of CCR6DNP were shown differential nuclear protein binding effect by electrophoretic mobility shift assay. The RegulomeDB and JASPAR databases predicted Pou2f1 as the potential transcription factor, which was negatively associated with CCR6 mRNA (r = −0.60, P = 3.94 × 10−9). At the mRNA level, the eQTL effect of CCR6 was validated (P = 4.39 × 10−2), and CCR6 was positively associated with the expression of CCR4 and IL-17A rather than that of CXCR3 and IFNG. At the protein level, a higher CCR6+ cell ratio was observed in a risk allele dose-dependent manner in lymphocytes (P = 3.57 × 10−2), CD3+ T cells (P = 4.54 × 10−2), and CD4+ T cells (P = 1.32 × 10−2), but not in CD8+ T cells. Clinical-pathological analysis showed that rs3093023 risk allele was significantly associated with diastolic blood pressure, serum creatinine, and high ratio of tubular atrophy/interstitial fibrosis. Overall, the rs3093023 was prioritized as the function variant in CCR6, which may contribute to IgAN susceptibility by regulating Th17 cells.

PSX-30 Late-Breaking Abstract: Genotypes database of pedigree cattle population in Kazakhstan and the introduction of a calculating mechanism for livestock parentage verification

Abstract A significant increase in pedigree cattle in Kazakhstan has led to scientific work on the conservation of breed genotypes in Kazakhstan and the development of imported breeds. Aim of work: creation a national database and collection of genotyped DNA samples of cattle in Kazakhstan and the introduction of an automated statistical and mathematical calculation of the local pedigree cattle parentage verification. The methodology of work has been the selection of biological samples and registration of data on the animal. DNA and STR locus testing have been performed at the University of Queensland’s Animal Genetics Laboratory (Australia). DNA genotyping was carried out using 21 polymorphic dinucleotide microsatellite loci. The database of DNA genotypes of breeding animals has been written and introduced into the database of breeding livestock in Kazakhstan (www.plem.kz). The method of determining kinship and confirming the origin of the animal was implemented by calculating the probability of random coincidence of genetic markers, taking into account their distribution in the population according to the “product rule.” The frequency distribution of homozygous alleles for 12 microsatellite loci (table 1) recommended by ICAR and 21 DNA loci (table 2) in the context of breeds was calculated, which indicates an increase in reliability when calculating the origin of livestock, with an increase in the number of microsatellite loci studied to 21 markers. The lower probability threshold is established, with 95% statistical significance confirms the relationship between the compared animals (table 3). A database of genotyped DNA samples of beef and dairy cattle breeds in Kazakhstan has been created and is currently used in pedigree beef cattle breeding. Access to the DNA database is provided to Kazakhstan genetic laboratories, and an automated calculation of the mathematical probability of parentage verification for a breeding animal and the generation of a genetic certificate was introduced on the website www.plem.kz

Interferon-lambda (IFNL) germline variations and their significance for HCC and PDAC progression: an analysis of The Cancer Genome Atlas (TCGA) data

BackgroundHepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC) are malignancies with a leading lethality. With reference to interferons (IFNs) known to mediate antitumor activities, this study investigated the relationship between germline genetic variations in type III IFN genes and cancer disease progression from The Cancer Genome Atlas (TCGA) data. The genetic variations under study tag a gain-or-loss-of-function dinucleotide polymorphism within the IFNL4 gene, rs368234815 [TT/ΔG].MethodsThe entirety of the TCGA sequencing data was used to assess genotypes of 187 patients with HCC and of 162 patients with PDAC matched for ethnicity. Stratified for IFNL genotypes, both cohorts were subjected to time-to-event analyses according to Kaplan-Meier with regard to the length of the specific progression free interval (PFI) and the overall survival (OS) time as two clinical endpoints for disease progression.ResultsLogrank analysis revealed a significant relationship between IFNL genotypes and disease outcome for PDAC. This relationship was not found for HCC. A multiple Cox regression analysis employing patients’ age, tumor grade and tumor stage as further covariates proved IFNL genotypes to be independent predictors for PDAC disease outcome.ConclusionThis repository-based approach unveiled clinical evidence suggestive for an impact of IFNL germline variations for PDAC progression with an IFNL haplotype predisposing for IFNL4 expression being favorable.

Monocytes differentiated into macrophages and dendritic cells in the presence of human IFN-λ3 or IFN-λ4 show distinct phenotypes.

Human IFN‐λ4 is expressed by only a subset of individuals who possess the ΔG variant allele at the dinucleotide polymorphism rs368234815. Recent genetic studies have shown an association between rs368234815 and different infectious and inflammatory disorders. It is not known if IFN‐λ4 has immunomodulatory activity. The expression of another type III IFN, IFN‐λ3, is also controlled by genetic polymorphisms that are strongly linked to rs368234815. Therefore, it is of interest to compare these two IFNs for their effects on immune cells. Herein, using THP‐1 cells, it was confirmed that IFN‐λ4 could affect the differentiation status of macrophage‐like cells and dendritic cells (DCs). The global gene expression changes induced by IFN‐λ4 were also characterized in in vitro generated primary macrophages. Next, human PBMC‐derived CD14+ monocytes were used to obtain M1 and M2 macrophages and DCs in the presence of IFN‐λ3 or IFN‐λ4. These DCs were cocultured with CD4+ Th cells derived from allogenic donors and their in vitro cytokine responses were measured. The specific activity of recombinant IFN‐λ4 was much lower than that of IFN‐λ3, as shown by induction of IFN‐stimulated genes. M1 macrophages differentiated in the presence of IFN‐λ4 showed higher IL‐10 secretion than those differentiated in IFN‐λ3. Coculture experiments suggested that IFN‐λ4 could confer a Th2‐biased phenotype to allogenic Th cells, wherein IFN‐λ3, under similar circumstances, did not induce a significant bias toward either a Th1 or Th2 phenotype. This study shows for the first time that IFN‐λ4 may influence immune responses by immunomodulation.

Impact of IFNL4 Genetic Variants on Sustained Virologic Response and Viremia in Hepatitis C Virus Genotype 3 Patients

Hepatitis C virus (HCV) genotype 3 is very prevalent in Europe and Asia and is associated with worst outcomes than other genotypes. Genetic factors have been associated with HCV infection; however, no extensive genome-wide study has been performed among HCV genotype 3 patients. In this study, using a large cohort of 1,759 patients infected with HCV genotype 3, we explore the role of genetic variants on the response to interferon (IFN) and direct-acting antiviral (DAA) regimens and viremia in a combined candidate gene and genome-wide analysis. We show that genetic variants within the IFN lambda 4 (IFNL4) locus are the major factors associated with the studied traits, accordingly with observations in other HCV genotypes and with comparable effect sizes. In particular, the functional dinucleotide polymorphism rs368234815 was associated with IFN-based sustained virologic response (SVR) [odds ratio (OR) = 1.5, P = 2.3 × 10−7], viremia (beta = −0.23, P = 8.8 × 10−10), and also DAA-based SVR (OR = 1.7; P = 4.2 × 10−4). Our results provide evidence for a role of genetic variants on HCV viremia and SVR, notably DAA-based, in patients infected with HCV genotype 3.

Association between genetic polymorphism of heme oxygenase 1 promoter and neonatal hyperbilirubinemia: a meta-analysis

Objective: The association between a (GT)n dinucleotide length polymorphism in the promoter region of heme oxygenase 1 (HMOX1) and the risk of neonatal hyperbilirubinemia remains controversial. This meta-analysis was, therefore, performed with aims to examine the correlation between the HMOX1 (GT)n repeat length polymorphism and neonatal hyperbilirubinemia susceptibility.Materials and methods: We searched the databases including PubMed, Embase, Cochrane Library, China national knowledge infrastructure (CNKI), and Wanfang Data, with all reviewed studies published before 28 June 2018. After the evaluation of quality, we used RevMan to perform the meta-analyses. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the effect of HMOX1 gene promoter polymorphisms on the risk of neonatal hyperbilirubinemia.Results: Seven studies, involving 584 patients with neonatal hyperbilirubinemia and 1655 controls, were included. A statistically significant association was found between the HMOX1 (GT)n repeat length polymorphism and risk of neonatal hyperbilirubinemia under the allele (allele S vs. allele L: OR = 1.81, 95% CI = 1.22–2.67, p = .003), recessive (genotype SS vs. genotypes LS + LL: OR = 1.38, 95% CI = 1.02–1.86, p = .04), dominant (genotypes SS + LS vs. LL: OR = 1.37, 95% CI = 1.01–1.76, p = .01), and homozygous genetic models (genotype SS vs. genotype LL: OR = 1.47, 95% CI = 1.02–2.11, p = .003), but not under the heterozygous genetic model. Interestingly, subgroup analysis revealed that the cutoffs of the S allele < 25 showed significant associations in any of the five genetic models (allele S vs. allele L: OR = 2.26, 95% CI = 1.68–3.05, p < .00001; genotype SS vs. genotypes LS + LL: OR = 2.56, 95% CI = 1.41–4.65, p = .002; genotypes SS + LS vs. genotype LL: OR = 1.82, 95% CI = 1.28–2.59, p = .0009; genotype SS vs. genotype LL: OR = 3.09, 95% CI = 1.50–6.36, p = .002; genotype LS vs. genotype LL: OR = 1.64, 95% CI = 1.11–2.42, p = .01); however, this association was not observed in the cutoffs of the S allele ≥25.Conclusion: The results of this study indicate that there is a significant association between the HMOX1 (GT)n repeat length polymorphism and susceptibility to neonatal hyperbilirubinemia. Newborns carrying shorter (GT)n repeats in the HMOX1 gene promoter may have a higher risk of neonatal hyperbilirubinemia.

SU111 - EFFECT OF DINUCLEOTIDE POLYMORPHISM (RS67175440) OF DAT1 GENE: INCREASED RISK OF CLONINGER TYPE II ALCOHOLISM IN SEX-SPECIFIC MANNER

Background The role of dopamine in the addictions’ development, including alcoholism, is well shown. The Dopamine Transporter (DAT) regulates the dopamine levels in the synapse. In some studies, using autoradiography, a DAT density was higher in patients with Cloninger type II alcoholism, which may be due to genetic influence (Tupala E. et’al 2006, Karkkainen O. et’al 2013). The dinucleotide polymorphism RS67175440 (A allele - AG, B allele - GA) is located in intron 1 of the SLC6A3 gene and can be within the regulatory region of the gene, which is interesting for studying its effect on the alcoholism risk. This locus is presumably involved in cocaine dependence risk (Zhou Y. et’al 2014). We attempted to assess the influence of RS67175440 on the probability of development of alcoholism, including patients with the presence of Cloninger type II. Methods Our sample consisted of 1200 patients with alcoholism (mean age 42.94±11.001 years, 277 females) and 536 controls (mean age 43.65±4.318 years, 165 females), all ethnic Russians. The clinical variables (age at first alcohol use, age of onset and term of formation of alcohol abuse, age and term of alcohol withdrawal syndrome, age of first hospitalization, family history (FH) of alcoholism) were assessed by a clinical interview patient and close relative (more often mother). For each individual, RS67175440 was genotyped by PCR-RFLP method using BseRI. The observed genotype distributions didn’t deviate from Hardy-Weinberg equilibrium (Patients: 330AA, 596AB, 274BB, P=0.88, Control: 146AA, 253AB, 137BB, P=0.20). For comparison of groups the chi-squared test with Bonferroni correction for multiple comparisons, logistic regression and Mann-Whitney U-test were used. Results According to the logistic regression, the general group of patients has the influence of the combination GenderxGenotype in relation to the alcoholism risk, but this effect was provided by a group of patients with Cloninger type II alcoholism (age of onset of abuse ≤ 25 years) with the presence of FH (TypeII+FH) for other patients this effect is not revealed. In men, the AA genotype increases the risk of AD by 41.3% in the overall comparison (95%CI 1.07–1.866, P=0.015), and by 48.7% for the group Type II+FH (1.223–2.402; P=0.002); the AB genotype increases the risk by 47.6% in the overall comparison (1.173–1.857, P=0.001) and 71.4% for the group TypeII+FH (1.418–2.486; P=0.000). In women, the AA genotype reduces the risk by 71.3% for the group TypeII+FH (0.164–0.539; P=0.000); the AB genotype reduces the risk by 31.2% in the overall comparison (0.51–0.927, P=0.014), and by 52% for the group TypeII+FH (0.321–0.717; P=0.000). The independent effect of gender was identical: for men, the risk was 48.2% higher than for women in the overall comparison (1.181–1.86; P=0.001); and 48.7% higher for the group TypeII+FH (0.808–2.738; P=0.000). Discussion There were no differences in genotype or allele frequencies between patients and control using the dominant and recessive models. It can be assumed that the differences in the general group are provided by the influence of Cloninger type II, in particular, hereditary factors. Our results indicate that the locus RS67175440 in the DAT gene in men with the presence of Cloninger type II alcoholism with family history increases, while in women reduces alcoholism risk with an early onset, but doesn’t effect on the dynamics of alcoholism and clinical variables.

Study of cannabinoid receptor 2 Q63R gene polymorphism in Lebanese patients with rheumatoid arthritis.

The cannabinoid (CB) receptor 2, primarily expressed in immune cells, was shown to play important immune-regulatory functions. In particular, the CB2-R63 functional variant has been shown to alter the ability of the CB2 receptor to exert its inhibitory function on T lymphocytes. The aim of this study was to investigate the association between a common dinucleotide polymorphism, Q63R, in the cannabinoid receptor 2 gene (CNR2) and rheumatoid arthritis (RA) in the Lebanese population. One hundred five unrelated Lebanese RA patients and one hundred five controls from different Lebanese governorates were recruited in this study. Genomic DNA was extracted, polymerase chain reaction was performed, and CNR2 was genotyped in a blinded fashion. The χ2 test was used to determine the differences in genotypes and allele frequencies. CNR2 genotyping showed significantly higher frequencies of the CB2-R63 variant (allele frequencies, P < 0.00001; genotype distribution, P < 0.00001) in RA patients when compared with healthy controls. Moreover, RR carriers had more than 10-fold risk for developing RA (OR = 10.8444, 95% CI = 5.0950-23.0818; P < 0.0001), and QR carriers had more than 3-fold risk (OR = 3.8667, 95% CI = 1.7886-8.3591; P = 0.0006) as compared with QQ carriers. Our preliminary results suggest a role of CB2-Q63R gene polymorphism in the etiology of RA, thus supporting its potential use as a pharmacological target for selective agonists in clinical practice.

SNCA REP1 and Parkinson’s disease

REP1 is a polymorphic dinucleotide repeat sequence located in the promoter region of the SNCA gene (OMIM 163890). Opinions regarding the interaction between the various REP1 alleles and Parkinson’s disease (PD) or its phenotypes have been inconsistent and have thus far not been comprehensively analyzed. In this study, we searched Medline, Embase and Cochrane databases as well as the Chinese-language Wanfang and CNKI databases using strict inclusion and exclusion criteria and conducted our analysis using Revman 5.3 software. Our search produced 28 articles describing REP1 alleles and their associated PD risks and 8 articles which discussed the relationship between REP1 variation and PD phenotypes. We found that the 265-, 269-, and 271-bp alleles of REP1 (using the nomenclature established by Xia et al.) increased the risk of PD (OR: 1.81, 1.05, 1.17; p: 0.0002, 0.003, 0.002) while the 267-bp allele decreased PD risk (OR: 0.86, p: <0.00001) when taking all populations into account. By ethnicity, we observed an obvious population heterogeneity in the effects of various alleles, where the 269-, 271-, and 273-bp alleles increased PD risk (OR: 1.06, 1.22, 1.89; p: 0.001, 0.003, 0.001) and the 267-bp allele decreased PD risk (OR: 0.85; p: <0.00001) in Caucasian populations, and the 263- and 265-bp alleles increased the risk of PD (OR: 2.22, 2.03; p: 0.03, 0.0002) and the 267- and 273-bp alleles decreased PD risk (OR: 0.90, 0.78; p: 0.02, 0.03) in Asian populations. We also determined that the 267-, 269-, and 271-bp alleles occurred the most frequently, although the frequency distribution varied among different ethnicities. Phenotypic analysis demonstrated that PD patients carrying the 271-bp allele were prone to early onset PD (OR: 1.75, p: 0.02) while the 267-bp had the opposite effect (OR: 0.81; p: 0.01).

Interferon lambda4 polymorphism is not associated with human papillomavirus infection outcome.

Interferon (IFN) lambdas are important specific components of the mucosal innate immune response. The IFN lambda 4 (IFNL4) dinucleotide polymorphism (ΔG/TT) determines the IFN lambdas and related Interferon-stimulated genes activation, in HCV and other chronic infections. Our group first reported that IFN Lambda response was impaired in high-risk Human Papillomavirus (HPV) cervical infections and in precancerous lesions. Accordingly, we sought to evaluate the possible role of the IFNL4 polymorphism in determining HPV infection outcome. The ΔG/TT alleles were not differently distributed in 221 women with high- or low-risk HPV infection, with HPV infection clearance or persistence, and with abnormal cytology.

IFNL4 rs368234815 and rs117648444 variants predict off-treatment HBsAg seroclearance in IFN-treated HBeAg-negative chronic hepatitis B patients.

Robust baseline predictors of interferon (IFN) response in HBeAg-negative chronic hepatitis B (CHB) patients are not currently available. The recently described rs368234815 TT/ΔG dinucleotide and rs117648444 nonsynonymous P70S polymorphisms in IFN lambda 4 (IFNL4) gene, which are strongly associated with response to IFN in hepatitis C virus (HCV) infection, could be also useful in IFN-treated CHB patients. Here we assessed whether IFNL4 rs368234815 and rs117648444 polymorphisms predict IFN-induced HBsAg clearance in CHB patients. We sequenced the IFNL4 gene on genomic DNA collected from 126 HBeAg-negative CHB patients treated with IFN and followed up for a median of 11 (1-23)years. The 15-year cumulative probability of HBsAg loss in the 62 carriers of the rs368234815 TT/TT genotype, which abolishes the IFNλ4 protein production, was comparable to that of 19 patients carrying the rs117648444 T allele predicted to produce an impaired IFNλ4-S70 protein (39% vs 42%, P = .827). In contrast, these 81 patients, either not producing IFNλ4 or producing an impaired IFNλ4-S70 protein, had a significantly higher 15-year probability of HBsAg loss compared to the 45 subjects predicted to encode only the fully functional IFNλ4-P70 (42% vs 11% P = .003). At multivariate analysis, combination of the rs368234815 and rs117648444 genotypes strongly predicted HBsAg clearance (HR 5.90, 95% CI 1.70-20.9, P = .006) together with pretreatment serum HBV DNA levels (HR 0.57, 95% CI 0.39-0.83, P = .003). IFNL4 rs368234815 and rs117648444 functional variants are worth to be investigated as pretreatment combined predictors of IFN response in HBeAg-negative CHB patients.

Confounding by Single Nucleotide Polymorphism rs117648444 (P70S) Affects the Association of Interferon Lambda Locus Variants with Response to Interferon-α-Ribavirin Therapy in Patients with Chronic Genotype 3 Hepatitis C Virus Infection

Genome-wide association studies discovered interferon lambda (IFNL or IFN-λ) locus on chromosome 19 to be involved in clearance of chronic hepatitis C virus (HCV) infection in patients following interferon-α-ribavirin (IFN-RBV) therapy. Subsequent studies established a dinucleotide polymorphism rs368234815, as the prime causal variant behind this association. The ΔG allele of this variant gives rise to a new IFNL gene, IFNL4, coding for IFN-λ4 whose activity paradoxically associates with lesser viral clearance rates. A low-frequency, nonsynonymous single nucleotide polymorphism (SNP) rs117648444 within the 2nd exon of IFNL4 changes the 70th amino acid from proline to serine resulting in lower activity of the functional IFN-λ4 protein, thereby increasing HCV clearance rates. In the present study, we used a cohort of genotype 3 HCV-infected patients, drawn from different geographical regions of India who underwent IFN-RBV therapy, to examine the association of several important IFNL locus SNPs/variants with sustained virological response (SVR). Intriguingly, the causal variant rs368234815 did not show the best strength and significance of association with SVR, while further analysis revealed that a negative confounding effect of rs117648444 was responsible for this phenomenon. Our results indicate that IFNL locus SNPs are subject to either a positive or a negative confounding effect by rs117648444; the nature of confounding depends on the linkage of the IFNL SNPs with the low-activity IFN-λ4-generating minor allele of rs117648444. Thus, our work demonstrates that the linkage disequilibrium structure of the IFNL region may confound the results of association studies. These results have implications for the design and understanding of future case-control studies involving IFNL locus SNPs/variants.

Study on p73 gene polymorphism and genetic susceptibility to hepatocellular cancer

Objective To evaluate the potential role of the separately p73 gene polymorphism on hepatocellular carcinoma(HCC) susceptibility. Methods A hospital-based case-control study was conducted in 100 cases HCC patients and 100 cases age, sex-matched cancer-free controls in the same region.The matrix-assisted laser desorption ionization time-of-flight mass spectrometry and DNA sequencing methods were used to analyze polymorphisms of p73 genetic polymorphisms (G4C14-A4T14). Using χ2 test to exam the differences of genotype between the HCC group and control group, logistic regression was used to analysis odds ratio(Oddsratios, OR) and 95%CI(Confidence Intervals, CI), adjusted for age and sex, analysis the association between SNPs of P73 polymorphisms and HCC.All the results were analyzed by SPSS 18.0. Results (1)The differences of age(χ2=0.185, P=0.667), gender(χ2=0.026, P=0.873), drinking status(χ2=0.427, P=0.514), and family history (χ2=0.058, P=0.809)of cancer composition between HCC group and control group were not statistically significant.(2)There were CC, CT and TT three genotypes in p73 rs1801173 C/T.The frequencies of CC, CT and TT genotypes of P73 C/T in controls and HCC cases were 65.0%, 28.2%, 6.8 % and 62.2%, 31.1%, 6.7%, respectively, and there was no significant difference between the two groups(χ2=0.326, P=0.568). (3)When stratifying by age, gender, smoking status, alcohol consumption, HBV carrier status and family history of cancer we found that the variant genotypes of GC/AT + AT/AT in P73 was associated with a significantly increased risk of HCC among HbsAg-positive individuals(χ2=3.916, P=0.048) and female(χ2=6.545, P=0.01), and there were no significant correlation with age, smoking, alcohol consumption, family history of cancer. Conclusion (1)p73 G4C14-to-A4T14 dinucleotide polymorphism may play a role in the development of chronic HBV-infected HCC in the Chinese population.(2)p73 G4C14-to-A4T14 dinucleotide polymorphism may play a role in the development of chronic HCC in female of Chinese population. Key words: Gene polymorphism; p73; Hepatocellular carcinoma

Insulin-like Growth Factor 1 gene polymorphism and breast cancer risk.

Insulin-like Growth Factor-1 (IGF-1) gene polymorphism has been associated with an increased risk for breast cancer. IGF-1 is a key regulator of proliferation, cell differentiation and apoptosis. It has important mitogenic and anti-apoptotic activities in normal cells and in breast cancer cells, acting synergistically with estrogen to increase neoplastic cell proliferation. This review aims to present the recent finds of IGF-1 gene polymorphism and its relationship with the risk of breast cancer through following the polymorphic dinucleotide repeat cytosine-adenine (CA) and single nucleotide polymorphisms (SNPs) by searching in the PubMed database publications focused studies published from 2010 to 2015 related to IGF-1 gene polymorphism and breast cancer risk. A growing number of studies support an association between IGF-1 gene polymorphism and breast cancer risk with conflicting results, nevertheless elucidation of the patterns of IGF-1 gene expression may permit characterization of women at high-risk for breast cancer, as well as the development of strategies for early diagnosis and efficient treatment against the disease.

The DPYSL2 gene connects mTOR and schizophrenia.

We previously reported a schizophrenia-associated polymorphic CT di-nucleotide repeat (DNR) at the 5′-untranslated repeat (UTR) of DPYSL2, which responds to mammalian target of Rapamycin (mTOR) signaling with allelic differences in reporter assays. Now using microarray analysis, we show that the DNR alleles interact differentially with specific proteins, including the mTOR-related protein HuD/ELAVL4. We confirm the differential binding to HuD and other known mTOR effectors by electrophoretic mobility shift assays. We edit HEK293 cells by CRISPR/Cas9 to carry the schizophrenia risk variant (13DNR) and observe a significant reduction of the corresponding CRMP2 isoform. These edited cells confirm the response to mTOR inhibitors and show a twofold shortening of the cellular projections. Transcriptome analysis of these modified cells by RNA-seq shows changes in 12.7% of expressed transcripts at a false discovery rate of 0.05. These transcripts are enriched in immunity-related genes, overlap significantly with those modified by the schizophrenia-associated gene, ZNF804A, and have a reverse expression signature from that seen with antipsychotic drugs. Our results support the functional importance of the DPYSL2 DNR and a role for mTOR signaling in schizophrenia.