Flanking Region Of Promoter Research Articles

A Network‐based Deep Learning Framework Translates GWAS and Multi‐Omics Findings to Pathobiology and Drug Repurposing for Alzheimer’s Disease

AbstractBackgroundHuman genome sequencing studies have identified numerous loci associated with complex diseases, including Alzheimer’s disease (AD). However, translating human genetic and genomic findings (i.e., genome‐wide association studies [GWAS]) to pathobiology and therapeutic discovery remains a major challenge. Today, artificial intelligence and deep learning approaches that identify new risk genes and drug targets from human genome sequencing findings are enabling a more complete mechanistic understanding of disease biology. This is facilitating more rapid development of targeted therapeutic interventions for AD.MethodWe presented a network topology‐based deep learning framework to identify disease‐associated genes (NETTAG). NETTAG integrates multi‐genomics data and the human protein‐protein interactome to infer putative risk genes and drug targets impacted by GWAS loci. Specifically, we leveraged non‐coding GWAS loci effects on expression quantitative trait loci (eQTLs), histone‐QTLs, transcription factor binding‐QTLs, enhancers and CpG islands, promoter regions, open chromatin, and promoter flanking regions. The fundamental premise of NETTAG is that disease risk genes exhibit distinct functional characteristics compared to non‐risk genes, and can therefore be distinguished by their aggregated genomic features under the human protein interactome.ResultApplying NETTAG to the latest AD GWAS data, we identified 156 putative AD‐risk genes (i.e., APOE, BIN1, GSK3B, MARK4, and PICALM). We showed that predicted risk genes are: 1) significantly enriched in AD‐related pathobiological pathways, 2) more likely to be differentially expressed in transcriptomes and proteomes of AD brains, and 3) enriched in druggable targets with approved medicines. Specifically, we showed that NETTAG‐predicted genes (e.g., MEF2D, CPLX2, KLF4, ACTL6B, P2RX7 and etc.) are differentially expressed in AD‐associated microglia and astrocytes from single‐nuclei RNA‐sequencing data of human postmortem brains with varying degrees of AD neurobiology. Via network‐based prediction, we identified multiple repurposable drug candidates (i.e., choline, deferoxamine and ibudilast) for potential treatment of AD.ConclusionOur findings suggest that understanding human pathobiology and therapeutic development could benefit from network‐based deep learning methodology that utilizes GWAS findings with multimodal genomic analyses.

Interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer's disease.

Translating human genetic findings (genome-wide association studies [GWAS]) to pathobiology and therapeutic discovery remains a major challenge for Alzheimer's disease (AD). We present a network topology-based deep learning framework to identify disease-associated genes (NETTAG). We leverage non-coding GWAS loci effects on quantitative trait loci, enhancers and CpG islands, promoter regions, open chromatin, and promoter flanking regions under the protein-protein interactome. Via NETTAG, we identified 156 AD-risk genes enriched in druggable targets. Combining network-based prediction and retrospective case-control observations with 10 million individuals, we identified that usage of four drugs (ibuprofen, gemfibrozil, cholecalciferol, and ceftriaxone) is associated with reduced likelihood of AD incidence. Gemfibrozil (an approved lipid regulator) is significantly associated with 43% reduced risk of AD compared with simvastatin using an active-comparator design (95% confidence interval 0.51-0.63, p<0.0001). In summary, NETTAG offers a deep learning methodology that utilizes GWAS and multi-genomic findings to identify pathobiology and drug repurposing in AD.

Genome-wide association study of primary dysmenorrhea in the Taiwan Biobank validates associations near the NGF and IL1 gene loci.

Using the Taiwan Biobank, we aimed to identify traits and genetic variations that could predispose Han Chinese women to primary dysmenorrhea. Cases of primary dysmenorrhea included those who self-reported "frequent dysmenorrhea" in a dysmenorrhea-related Taiwan Biobank questionnaire, and those who have been diagnosed with severe dysmenorrhea by a physician. Controls were those without self-reported dysmenorrhea. Customized Axiom-Taiwan Biobank Array Plates were used to perform whole-genome genotyping, PLINK was used to perform association tests, and HaploReg was used to conduct functional annotations of SNPs and bioinformatic analyses. The GWAS analysis included 1186 cases and 24,020 controls. We identified 53 SNPs that achieved genome-wide significance (P < 5 × 10-8, which clustered in 2 regions. The first SNP cluster was on chromosome 1, and included 24 high LD (R2 > 0.88) variants around the NGF gene (lowest P value of 3.83 × 10-13 for rs2982742). Most SNPs occurred within NGF introns, and were predicted to alter regulatory binding motifs. The second SNP cluster was on chromosome 2, including 7 high LD (R2 > 0.94) variants around the IL1A and IL1B loci (lowest P value of 7.43 × 10-10 for rs11676014) and 22 SNPs that did not reach significance after conditional analysis. Most of these SNPs resided within IL1A and IL1B introns, while 2 SNPs may be in the promoter histone marks or promoter flanking regions of IL1B. To conclude, data from this study suggest that NGF, IL1A, and IL1B may be involved in the pathogenesis of primary dysmenorrhea in the Han Chinese in Taiwan.

Abstract 10651: Identification of Allele-Specific Gene Expression in Association with Blood Pressure

Introduction: Risk of hypertension is explained by both behavioral and genetic factors that may act on transcriptomic mechanisms to affect blood pressure variability. Methods: Whole genome sequencing and RNA sequencing data were obtained on 1,671 Framingham Heart Study (FHS) participants (mean age 54±13 years). Allelic expression of heterozygous SNPs was measured and allelic imbalance was identified using a binomial test. SNPs with significant allelic imbalance were evaluated in linear regression to test the association between the reference/total allele count ratio and 1) systolic blood pressure (SBP), and 2) diastolic blood pressure (DBP). Models were adjusted for age, sex, BMI, and family structure. Results: At a Bonferroni-corrected p-value&lt;6.4E-8, we identified 20,890 SNPs with significant allelic imbalance at MAF&gt;0.01. Prior GWAS have identified &gt;2,000 SNPs associated with SBP, DBP, or hypertension; we identified allelic expression imbalance of 60 SNPs (in 44 genes) that were reported in GWAS to be associated with SBP, and of eight SNPs (in two genes) that are associated with DBP. These genes were significantly enriched for the immune effector process pathway (p=1.4E-7). Fifteen SNPs were located in promoter or promoter-flanking regions, while the remaining SNPs were located in protein-coding regions. Seventeen SNPs were also cis -eQTLs, of which four transcripts also were associated with SBP or DBP in the FHS cohort. Conclusion: We identified ASE linked to blood pressure. Our results suggested that novel transcriptomic regulatory mechanisms involving allelic imbalance at specific SNPs may play a role in blood pressure regulation.

The effect of single-nucleotide polymorphism in the promoter region of bovinealpha-lactalbumin(LALBA) gene onLALBAexpression in milk cells and milk traits of cows

Polymorphisms of milk protein genes have been proposed as candidate markers for dairy production traits in cattle. In the present study, a polymorphism was detected in the 5'-flanking (promoter) region of the bovine alpha-lactalbumin (LALBA) gene, a T/C transition located at nucleotide -1,001 relative to the transcription start site g.-1001T > C (NC_037332.1:g.31183170T > C), which is recognizable with PstI restriction endonuclease. In silico analyses showed that this mutation created novel retinoid X receptor alpha and vitamin D receptor transcription factor binding sites. Real-time PCR found that cows with different genetic variants of the promoter demonstrated different levels of expression of LALBA mRNA in milk somatic cells (MSCs). The TT genotype cows demonstrated low expression, whereas those with CT demonstrated much higher expression (P < 0.05). ELISA analysis found milk LALBA protein levels also differed between the TT and CT cows (P < 0.05) and that these levels were not correlated with the mRNA abundance in MSC. Association analysis found that the g.-1001T > C polymorphism in the promoter region of the LALBA gene influenced milk production traits in Polish Holstein-Friesian cows. High daily milk yield and dry matter yield, and high lactose yield and concentration were associated with the TT genotype. The TT genotype cows also had a lower number of somatic cells in the milk, considered as an indicator of udder health status. Therefore, the TT genotype could be more desirable from the breeder's perspective.

Transcription Factor TonEBP Stimulates Hyperosmolality-Dependent Arginine Vasopressin Gene Expression in the Mouse Hypothalamus.

The hypothalamic neuroendocrine system is strongly implicated in body energy homeostasis. In particular, the degree of production and release of arginine vasopressin (AVP) in the hypothalamus is affected by plasma osmolality, and that hypothalamic AVP is responsible for thirst and osmolality-dependent water and metabolic balance. However, the osmolality-responsive intracellular mechanism within AVP cells that regulates AVP synthesis is not clearly understood. Here, we report a role for tonicity-responsive enhancer binding protein (TonEBP), a transcription factor sensitive to cellular tonicity, in regulating osmosensitive hypothalamic AVP gene transcription. Our immunohistochemical work shows that hypothalamic AVP cellular activity, as recognized by c-fos, was enhanced in parallel with an elevation in TonEBP expression within AVP cells following water deprivation. Interestingly, our in vitro investigations found a synchronized pattern of TonEBP and AVP gene expression in response to osmotic stress. Those results indicate a positive correlation between hypothalamic TonEBP and AVP production during dehydration. Promoter and chromatin immunoprecipitation assays confirmed that TonEBP can bind directly to conserved binding motifs in the 5’-flanking promoter regions of the AVP gene. Furthermore, dehydration- and TonEBP-mediated hypothalamic AVP gene activation was reduced in TonEBP haploinsufficiency mice, compared with wild TonEBP homozygote animals. Therefore, our result support the idea that TonEBP is directly necessary, at least in part, for the elevation of AVP transcription in dehydration conditions. Additionally, dehydration-induced reductions in body weight were rescued in TonEBP haploinsufficiency mice. Altogether, our results demonstrate an intracellular machinery within hypothalamic AVP cells that is responsible for dehydration-induced AVP synthesis.

S100P Expression via DNA Hypomethylation Promotes Cell Growth in the Sessile Serrated Adenoma/Polyp-Cancer Sequence

Background/Aims: Sessile serrated adenomas/polyps (SSA/Ps) are a putative precursor lesion of colon cancer. Although the relevance of DNA hypermethylation in the SSA/P-cancer sequence is well documented, the role of DNA hypomethylation is unknown. We investigated the biological relevance of DNA hypomethylation in the SSA/P-cancer sequence by using 3-dimensional organoids of SSA/P. Methods: We first analyzed hypomethylated genes using datasets from our previous DNA methylation array analysis on 7 SSA/P and 2 cancer in SSA/P specimens. Expression levels of hypomethylated genes in SSA/P specimens were determined by RT-PCR and immunohistochemistry. We established 3-dimensional SSA/P organoids and performed knockdown experiments using a lentiviral shRNA vector. DNA hypomethylation at CpG sites of the gene was quantitated by MassARRAY analysis. Results: The mean number of hypomethylated genes in SSA/P and cancer in SSA/P was 41.6 ± 27.5 and 214 ± 19.8, respectively, showing a stepwise increment in hypomethylation during the SSA/P-cancer sequence. S100P, S100α2, PKP3, and MUC2 were most commonly hypomethylated in SSA/P specimens. The mRNA and protein expression levels of S100P, S100α2, and MUC2 were significantly elevated in SSA/P compared with normal colon tissues, as revealed by RT-PCR and immunohistochemistry, respectively. Among these, mRNA and protein levels were highest for S100P. Knockdown of the S100P gene using a lentiviral shRNA vector in 3-dimensional SSA/P organoids inhibited cell growth by >50% (p < 0.01). The mean diameter of SSA/P organoids with S100P gene knockdown was significantly smaller compared with control organoids. MassARRAY analysis of DNA hypomethylation in the S100P gene revealed significant hypomethylation at specific CpG sites in intron 1, exon 1, and the 5′-flanking promoter region. Conclusion: These results suggest that DNA hypomethylation, including S100P hypomethylation, is supposedly associated with the SSA/P-cancer sequence. S100P overexpression via DNA hypomethylation plays an important role in promoting cell growth in the SSA/P-cancer sequence.

Regulatory mechanism of chicken lysozyme gene expression in oviducts examined using transgenic technology

The use of promoters that strongly express target genes in the chicken oviduct is beneficial for the production of proteinaceous materials into egg white by transgenic chickens. To examine the regulatory mechanisms of chicken lysozyme gene expression invivo, genetically manipulated chickens that express human erythropoietin under the control of a lysozyme promoter-enhancer were established. By using several deletion mutants of the promoter-flanking region, we found that a-1.9kb DNase I hypersensitive site (DHS) was essential for oviduct-specific expression in genetically manipulated chickens. The concentration of human erythropoietin in egg white was 14-75μg/ml, suggesting that the chicken lysozyme promoter containing-1.9kb DHS is sufficient for the production of pharmaceuticals using transgenic chickens.

Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts.

5-Hydroxymethylcytosine (5hmC) is a functionally active epigenetic modification. We analyzed whether changes in DNA 5-hydroxymethylation are an element of age-related epigenetic drift. We tested primary fibroblast cultures originating from individuals aged 22–35 years and 74–94 years. Global quantities of methylation-related DNA modifications were estimated by the dot blot and colorimetric methods. Regions of the genome differentially hydroxymethylated with age (DHMRs) were identified by hMeDIP-seq and the MEDIPS and DiffBind algorithms. Global levels of DNA modifications were not associated with age. We identified numerous DHMRs that were enriched within introns and intergenic regions and most commonly associated with the H3K4me1 histone mark, promoter-flanking regions, and CCCTC-binding factor (CTCF) binding sites. However, only seven DHMRs were identified by both algorithms and all of their settings. Among them, hypo-hydroxymethylated DHMR in the intron of Rab Escort Protein 1 (CHM) coexisted with increased expression in old cells, while increased 5-hydroxymethylation in the bodies of Arginine and Serine Rich Protein 1 (RSRP1) and Mitochondrial Poly(A) Polymerase (MTPAP) did not change their expression. These age-related differences were not associated with changes in the expression of any of the ten-eleven translocation (TET) enzymes or their activity. In conclusion, the distribution of 5hmC in DNA of in vivo aged human fibroblasts underwent age-associated modifications. The identified DHMRs are, likely, marker changes.

Hypoxic activation of glucose-6-phosphate dehydrogenase controls the expression of genes involved in the pathogenesis of pulmonary hypertension through the regulation of DNA methylation.

Metabolic reprogramming is considered important in the pathogenesis of the occlusive vasculopathy observed in pulmonary hypertension (PH). However, the mechanisms that link reprogrammed metabolism to aberrant expression of genes, which modulate functional phenotypes of cells in PH, remain enigmatic. Herein, we demonstrate that, in mice, hypoxia-induced PH was prevented by glucose-6-phosphate dehydrogenase deficiency (G6PDDef), and further show that established severe PH in Cyp2c44-/- mice was attenuated by knockdown with G6PD shRNA or by G6PD inhibition with an inhibitor (N-ethyl-N'-[(3β,5α)-17-oxoandrostan-3-yl]urea, NEOU). Mechanistically, G6PDDef, knockdown and inhibition in lungs: 1) reduced hypoxia-induced changes in cytoplasmic and mitochondrial metabolism, 2) increased expression of Tet methylcytosine dioxygenase 2 (Tet2) gene, and 3) upregulated expression of the coding genes and long noncoding (lnc) RNA Pint, which inhibits cell growth, by hypomethylating the promoter flanking region downstream of the transcription start site. These results suggest functional TET2 is required for G6PD inhibition to increase gene expression and to reverse hypoxia-induced PH in mice. Furthermore, the inhibitor of G6PD activity (NEOU) decreased metabolic reprogramming, upregulated TET2 and lncPINT, and inhibited growth of control and diseased smooth muscle cells isolated from pulmonary arteries of normal individuals and idiopathic-PAH patients, respectively. Collectively, these findings demonstrate a previously unrecognized function for G6PD as a regulator of DNA methylation. These findings further suggest that G6PD acts as a link between reprogrammed metabolism and aberrant gene regulation and plays a crucial role in regulating the phenotype of cells implicated in the pathogenesis of PH, a debilitating disorder with a high mortality rate.

Mendelian Randomization Identifies CpG Methylation Sites With Mediation Effects for Genetic Influences on BMD in Peripheral Blood Monocytes.

Osteoporosis is mainly characterized by low bone mineral density (BMD) and is an increasingly serious public health concern. DNA methylation is a major epigenetic mechanism that may contribute to the variation in BMD and may mediate the effects of genetic and environmental factors of osteoporosis. In this study, we performed an epigenome-wide DNA methylation analysis in peripheral blood monocytes of 118 Caucasian women with extreme BMD values. Further, we developed and implemented a novel analytical framework that integrates Mendelian randomization with genetic fine mapping and colocalization to evaluate the causal relationships between DNA methylation and BMD phenotype. We identified 2,188 differentially methylated CpGs (DMCs) between the low and high BMD groups and distinguished 30 DMCs that may mediate the genetic effects on BMD. The causal relationship was further confirmed by eliminating the possibility of horizontal pleiotropy, linkage effect and reverse causality. The fine-mapping analysis determined 25 causal variants that are most likely to affect the methylation levels at these mediator DMCs. The majority of the causal methylation quantitative loci and DMCs reside within cell type-specific histone mark peaks, enhancers, promoters, promoter flanking regions and CTCF binding sites, supporting the regulatory potentials of these loci. The established causal pathways from genetic variant to BMD phenotype mediated by DNA methylation provide a gene list to aid in designing future functional studies and lead to a better understanding of the genetic and epigenetic mechanisms underlying the variation of BMD.

Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates

BackgroundHuman chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression.ResultsWe examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential.ConclusionsThe pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.

The Molecular Characteristics of the FAM13A Gene and the Role of Transcription Factors ACSL1 and ASCL2 in Its Core Promoter Region.

The gene family with sequence similarity 13 member A (FAM13A) has recently been identified as a marker gene in insulin sensitivity and lipolysis. In this study, we first analyzed the expression patterns of this gene in different tissues of adult cattle and then constructed a phylogenetic tree based on the FAM13A amino acid sequence. This showed that subcutaneous adipose tissue had the highest expression in all tissues except lung tissue. Then we summarized the gene structure. The promoter region sequence of the gene was successfully amplified, and the −241/+54 region has been identified as the core promoter region. The core promoter region was determined by the unidirectional deletion of the 5’ flanking promoter region of the FAM13A gene. Based on the bioinformatics analysis, we examined the dual luciferase activity of the vector constructed by the mutation site, and the transcription factors ACSL1 and ASCL2 were found as transcriptional regulators of FAM13A. Moreover, electrophoretic mobility shift assay (EMSA) further validated the regulatory role of ACSL1 and ASCL2 in the regulation of FAM13A. ACSL1 and ASCL2 were finally identified as activating transcription factors. Our results provide a basis for the function of the FAM13A gene in bovine adipocytes in order to improve the deposition of fat deposition in beef cattle muscle.

A GH3-like gene, LaGH3, isolated from hybrid larch (Larix leptolepis × Larix olgensis) is regulated by auxin and abscisic acid during somatic embryogenesis

A Gretchen Hagen 3-like gene, LaGH3 from hybrid larch (Larix leptolepis × Larix olgensis), was identified, and the effects of abscisic acid (ABA) and indole-3-acetic acid (IAA) on its transcriptional levels and expression patterns during somatic embryogenesis were analyzed. A full-length cDNA sequence of a Gretchen Hagen 3 (GH3) gene was isolated from hybrid larch (Larix leptolepis × Larix olgensis) and designated LaGH3. The cDNA was 2053 bp in length and contained an 1848-bp open-reading frame encoding a predicted protein of 615 amino acids, characterized by four conserved motifs of the GH3 protein family: P-loop, α5, α6, and β8–β9. The 5′-flanking promoter region of LaGH3 was cloned using an improved TAIL-PCR technique. In this region, we identified several auxin- and abscisic acid (ABA)-inducible elements. Expression analysis showed that LaGH3 was induced by indole-3-acetic acid and that its transcript accumulation was inhibited by ABA. Further experiments demonstrated that ABA was the main factor in LaGH3 downregulation during the early stage of somatic embryogenesis, although the absence of auxin decreased LaGH3 expression slightly. LaGH3 transcripts gradually increased and peaked at 28 days with the rapid development of somatic embryos and then declined as the somatic embryos matured. We suggest that the level of LaGH3 transcripts partly represents the dynamics of endogenous auxin during somatic embryo development in larch. Taken together, our results provide evidence that GH3 genes play important roles in the crosstalk between auxin and ABA by maintaining auxin homeostasis during somatic embryo development.

Differential effects on neurodevelopment of FTO variants in obesity and bipolar disorder suggested by in silico prediction of functional impact: An analysis in Mexican population.

IntroductionSeveral studies indicate that polygenic obesity is linked to fat‐mass and obesity‐associated (FTO) genetic variants. Nevertheless, the link between variants in FTO and mental disorders has been barely explored. The present work aims to determine whether FTO genetic variants are associated with bipolar disorder and obesity, and to perform an in silico prediction of variant‐dependent functional impact on the developing brain transcriptome.MethodsFour hundred and forty‐six Mexican mestizos were included in a genetic association analysis. SNP‐sequence kernel association test and linear mixed models were implemented for genetic association assessment. For functional impact prediction, we analyzed the mapping of regulatory elements, the modification of binding sites of transcription factors and the expression of transcription factors in the brain developing transcriptome, searching on different databases.ResultsIn the set‐based analysis, we found different associated regions to BD (bipolar disorder) and obesity. The promoter flanking region of FTO intron 1 was associated with differential effects on BMI, while intron 2 of RPGRIP1L and FTO upstream regions were associated with BD. The prediction analysis showed that FTO BD‐associated variants disturb binding sites of SP1 and SP2; obesity‐associated variants, on the other hand, disturb binding sites of FOXP1, which are transcription factors highly expressed during prenatal development stages of the brain.ConclusionOur results suggest a possible effect of FTO variants on neurodevelopment in obesity and bipolar disorder, which gives new insights into the molecular mechanism underlying this association.

Tandem repeats of the 5′ flanking region of human MUC5AC have a role as a novel enhancer in MUC5AC gene expression

MUC5AC is a well-known gastric differentiation marker, which has been frequently used for the classification of stomach cancer. However, the molecular mechanism of regulation of MUC5AC expression remains to be elucidated. In previous studies, we have shown that Gli regulated MUC5AC transcription through the Gli-binding motif in the 5′ region of MUC5AC. Gli played important roles, but independently was not sufficient for MUC5AC expression. In this study, we analyzed a 4010 bp fragment of the 5′-flanking promoter region of the human MUC5AC gene by luciferase assay, and found a novel distal enhancer region located between −1434 bp to −3000 bp upstream from the first ATG initiation codon. This region is composed of repetitive DNA sequences 5′-TCACTCAC-3′. The strength of enhancer activities depended on the length of the repetitive region. The tandem repeats are conserved among primates, but not in other mammals. The tandem repeat regions enhanced promoter activities not only of MUC5AC but also of other genes. The enhancer effect of the tandem repeat regions was maintained even when inverted. ChIP analysis revealed that H3K9me3 binds to the tandem repeat regions. Together, our results suggest that the tandem repeat region in the MUC5AC promoter has the potential to act as a strong enhancer, and H3K9me3 may contribute to histone modifications of this region.

Serotonin transporter gene linked polymorphism (5-HTTLPR) determines progredience of alcohol dependence in Belarusian young males

PurposeAllelic duality and functional impact of degenerate repeat at 5′- flanking promoter region in SLC6A4 gene of the serotonin transporter (5-HTTLPR), have been in the focus of investigations over the years. Various outcomes regarding an association of its polymorphism with risks of alcohol dependence syndrome (ADS) were presented. Such studies have not been conducted in the Eastern European population e.g. Belarus. We therefore checked: the association of 5-HTTLPR polymorphism with ADS, and functional impact of the polymorphism on progredience of ADS in Belarusian population. Material and methodsThe study involved 499 Belarusian males: 377 subjects with ADS (AG), and a control group (CG) with 122 subjects without alcohol-related problems. The ADS group was further divided into two groups of individuals with rapid (AG (R)) and delayed (AG (D)) progression of ADS. Clinical diagnosis was carried-out using ICD-10 criteria, Belarusian Addiction Severity Index, “B-ASI” and Alcohol-Use-Disorders-Identification-Test (AUDIT). PCR-RFLP analysis was performed. ResultsThere were no significant differences in the distribution of frequencies of either the 5-HTTLPR genotype or the short and long allele among AG and CG. However, the ADS 5-HTTLPR genotype and allele distribution frequencies differ significantly by the variation in progression of ADS. ConclusionsThere is no significant association between polymorphism of serotonin transporter gene and risk of ADS. However, the polymorphism significantly determines progredience of ASD in subjects with pathological patterns of alcohol consumption. Findings from this study carry preliminary significance as a facility to effective alcohol addiction treatment, rehabilitation and preventive services in the Eastern Europe.

Efficient region-based test strategy uncovers genetic risk factors for functional outcome in bipolar disorder

Genome-wide association studies of case-control status have advanced the understanding of the genetic basis of psychiatric disorders. Further progress may be gained by increasing sample size but also by new analysis strategies that advance the exploitation of existing data, especially for clinically important quantitative phenotypes. The functionally-informed efficient region-based test strategy (FIERS) introduced herein uses prior knowledge on biological function and dependence of genotypes within a powerful statistical framework with improved sensitivity and specificity for detecting consistent genetic effects across studies. As proof of concept, FIERS was used for the first genome-wide single nucleotide polymorphism (SNP)-based investigation on bipolar disorder (BD) that focuses on an important aspect of disease course, the functional outcome. FIERS identified a significantly associated locus on chromosome 15 (hg38: chr15:48965004 – 49464789 bp) with consistent effect strength between two independent studies (GAIN/TGen: European Americans, BOMA: Germans; n = 1592 BD patients in total). Protective and risk haplotypes were found on the most strongly associated SNPs. They contain a CTCF binding site (rs586758); CTCF sites are known to regulate sets of genes within a chromatin domain. The rs586758 – rs2086256 – rs1904317 haplotype is located in the promoter flanking region of the COPS2 gene, close to microRNA4716, and the EID1, SHC4, DTWD1 genes as plausible biological candidates. While implication with BD is novel, COPS2, EID1, and SHC4 are known to be relevant for neuronal differentiation and function and DTWD1 for psychopharmacological side effects. The test strategy FIERS that enabled this discovery is equally applicable for tag SNPs and sequence data.

Involvement of JNK signaling pathway in lipopolysaccharide-induced complement C3 transcriptional activation from amphioxus Branchiostoma belcheri

Complement C3 is a pivotal component of three cascades of complement activation. C3 in circulation is mainly provided by the hepatic cecum. The expression and secretion of C3 by hepatocytes is increased during acute inflammation. The detailed information on the regulationary mechanism underlying C3 transcriptional activation is limited. Here, we characterized the 5′-flanking region of the amphioxus C3 gene. To functionally analyze the upstream regulatory region of the C3 gene, a series of luciferase reporter gene constructs containing deleted or mutant regulatory elements were prepared. Using luciferase assay, we revealed that a potential C-JUN-1 binding sites within the proximal promoter region were necessary for full activation of the C3 promoter, whereas NF-κB, AP-1, C-JUN-2 and NFAT transcription factor binding sites played roles in governing the promoter activity at a homeostatic level. Our data also indicated that sp600125, a c-Jun N-terminal kinase (JNK) inhibitor, decreased lipopolysaccharide (LPS)-stimulated C3 promoter activity, mRNA expression and protein secretion using western blotting and quantitative real-time PCR analysis. These findings demonstrated that JNK signaling pathway is involved in the regulation of C3 gene transcription by targeting C-JUN transcription factor binding sites in the 5′-flanking promoter region, leading to LPS-induced C3 activation and therefore providing a potential target for regulating C3 expression.

A meta-analysis on association of CYP2E1 rs2031920 and rs3813867 polymorphisms with breast cancer risk

Breast cancer remains a challenging disease globally due to its heterogeneity and complexity, with an annual increase rate of 3.1%. Cytochrome P450 2E1 (CYP2E1) rs2031920 and rs3813867 polymorphisms that reside in the 5’-flanking promoter region of the gene are in a complete linkage disequilibrium and have been associated with breast cancer risk, but the findings are inconsistent and inconclusive. Therefore, we investigated the association of the CYP2E1 rs2031920 and rs3813867 polymorphisms with the risk of breast cancer through a meta-analysis. After literature search, eight eligible studies were included in this meta-analysis with a total of 3650 breast cancer cases and 3607 controls. Our meta-analysis revealed no significant association of the CYP2E1 rs2031920 and rs3813867 polymorphisms with breast cancer risk in all comparison models including the allelic (OR = 0.968, 95% CI = 0.855-1.097; p = 0.612), heterozygous (OR = 1.003, 95% CI = 0.869-1.159; p = 0.963), homozygous (OR = 0.792, 95% CI = 0.519-1.207; p = 0.278), dominant (OR = 0.987, 95% CI = 0.858-1.134; p = 0.851), and recessive (OR = 1.265, 95% CI = 0.831-1.924; p = 0.273). In conclusion, this meta-analysis suggests that the CYP2E1 rs2031920 and rs3813867 polymorphisms are not associated with the risk of breast cancer.