EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome

Background

Predicting the functional impact of amino acid substitutions (AAS) caused by nonsynonymous single nucleotide polymorphisms (nsSNPs) is becoming increasingly important as more and more novel variants are being discovered. Bioinformatics analysis is essential to predict potentially causal or contributing AAS to human diseases for further analysis, as for each genome, thousands of rare or private AAS exist and only a very small number of which are related to an underlying disease. Existing algorithms in this field still have high false prediction rate and novel development is needed to take full advantage of vast amount of genomic data.

Results

Here we report a novel algorithm that features two innovative changes: 1. making better use of sequence conservation information by grouping the homologous protein sequences into six blocks according to evolutionary distances to human and evaluating sequence conservation in each block independently, and 2. including as many such homologous sequences as possible in analyses. Random forests are used to evaluate sequence conservation in each block and to predict potential impact of an AAS on protein function. Testing of this algorithm on a comprehensive dataset showed significant improvement on prediction accuracy upon currently widely-used programs. The algorithm and a web-based application tool implementing it, EFIN (Evaluation of Functional Impact of Nonsynonymous SNPs) were made freely available (http://paed.hku.hk/efin/) to the public.

Conclusions

Grouping homologous sequences into different blocks according to the evolutionary distance of the species to human and evaluating sequence conservation in each group independently significantly improved prediction accuracy. This approach may help us better understand the roles of genetic variants in human disease and health.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-455) contains supplementary material, which is available to authorized users.     

Identification of novel single nucleotide polymorphisms in the DGAT1 gene of buffaloes by PCR-SSCP

Diacylglycerol O-acyltransferase 1 (DGAT1) is a microsomal enzyme that catalyzes the final step of triglyceride synthesis. The DGAT1 gene is a strong functional candidate for determining milk fat content in cattle. In this work, we used PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing to examine polymorphism in the region spanning exon 7 to exon 9 of the DGAT1 gene in Murrah and Pandharpuri buffaloes. Three alleles (A, B and C) and four novel single-nucleotide polymorphisms were identified in the buffalo DGAT1 gene. The frequencies of the alleles differed between the two buffalo breeds, with allele C being present in Murrah but not in Pandharpuri buffalo. The allele variation detected in this work may influence DGAT1 expression and function. The results described here could be useful in examining the association between the DGAT1 gene and milk traits in buffalo.     

The single nucleotide polymorphism A118G alters functional properties of the human mu opioid receptor

The most common single nucleotide polymorphism in the coding region of the human mu opioid receptor gene is the A118G variant, an adenine to guanine transition at nucleotide position 118 of the coding sequence of the gene. This polymorphism codes for an asparagine to aspartic acid substitution at amino acid 40 in the amino-terminus, thereby removing a potential extracellular glycosylation site. Using in vitro cellular expression assays, this variant has been reported to change binding of the endogenous agonist beta-endorphin and signaling of the receptor following binding of beta-endorphin. Three clinical studies report that A118G genotype affects opioid antagonist-mediated increases in cortisol levels. These studies demonstrate a functional role of this variant in responses to endogenous and exogenous opioids. To further characterize function, we expressed the prototype and variant receptors in two types of cells (human 293 embryonic kidney cells and Syrian hamster adenovirus-12-induced tumor cells). Stable expression of variant and prototype receptors was characterized by differences in levels of cell surface binding capacity (B(max)), forskolin-induced cAMP accumulation, as well as agonist-induced accumulation of cAMP (EC(50)) for several agonists, but not for beta-endorphin. In contrast, transiently expressed variant receptors showed only a minor difference in cell surface binding capacity compared to the prototype, and no differences in cAMP EC(50) values.     

Role of six single nucleotide polymorphisms,risk factors in coronary disease,in OLR1 alternative splicing

The OLR1 gene encodes the oxidized low-density lipoprotein receptor (LOX-1), which is responsible for the cellular uptake of oxidized LDL (Ox-LDL), foam cell formation in atheroma plaques and atherosclerotic plaque rupture. Alternative splicing (AS) of OLR1 exon 5 generates two protein isoforms with antagonistic functions in Ox-LDL uptake. Previous work identified six single nucleotide polymorphisms (SNPs) in linkage disequilibrium that influence the inclusion levels of OLR1 exon 5 and correlate with the risk of cardiovascular disease. Here we use minigenes to recapitulate the effects of two allelic series (Low- and High-Risk) on OLR1 AS and identify one SNP in intron 4 (rs3736234) as the main contributor to the differences in exon 5 inclusion, while the other SNPs in the allelic series attenuate the drastic effects of this key SNP. Bioinformatic, proteomic, mutational and functional high-throughput analyses allowed us to define regulatory sequence motifs and identify SR protein family members (SRSF1, SRSF2) and HMGA1 as factors involved in the regulation of OLR1 AS. Our results suggest that antagonism between SRSF1 and SRSF2/HMGA1, and differential recognition of their regulatory motifs depending on the identity of the rs3736234 polymorphism, influence OLR1 exon 5 inclusion and the efficiency of Ox-LDL uptake, with potential implications for atherosclerosis and coronary disease.     

人高迁移率族蛋白B1，高迁移率族蛋白B1Abox和Bbox的原核表达、纯化及高迁移率族蛋白B1多克隆抗血清的制备

目的：获取重组人高迁移率族蛋白B1（HMGB1）,HMGB1Abox和Bbox的纯化蛋白,制备HMGB1的多克隆抗血清。方法：采用PCR方法扩增人HMGB1,HMGB1的Abox和Bbox目的基因片段,构建原核表达载体,进行原核表达与蛋白纯化,然后用HMGB1免疫新西兰大白兔,制备多克隆抗血清。采用ELISA检测抗血清效价,用免疫组化检测HMGB1在小鼠肝损伤组织中的表达。结果：成功构建了人HMGB1,HMGB1的Abox和Bbox原核表达载体pET28-HMGB1、pET28一Abox、pET28-Bbox,在E．co1iBL21中表达,镍亲和层析柱提纯,获取纯净目的蛋白。HMGB1免疫新西兰大白兔后,抗血清效价为1：2,000,000,具有高度特异性。免疫组化显示小鼠坏死肝组织HMGB1表达增加。结论：本研究获得了人HMGB1以及HMGB1的Abox和Bbox的纯化蛋白,制备了人HMGB1的多克隆抗血清,为HMGB1的结构、组织表达谱及其功能的研究奠定了基础。     

人高迁移率族蛋白B1，高迁移率族蛋白B1 A box和B box的原核表达、 纯化及高迁移率族蛋白B1多克隆抗血清的制备

目的:获取重组人高迁移率族蛋白B1(HMGB1),HMGB1Abox和Bbox的纯化蛋白,制备HMGB1的多克隆抗血清。方法:采用PCR方法扩增人HMGB1,HMGB1的Abox和Bbox目的基因片段,构建原核表达载体,进行原核表达与蛋白纯化,然后用HMGB1免疫新西兰大白兔,制备多克隆抗血清。采用ELISA检测抗血清效价,用免疫组化检测HMGB1在小鼠肝损伤组织中的表达。结果:成功构建了人HMGB1,HMGB1的Abox和Bbox原核表达载体pET28-HMGB1、pET28-Abox、pET28-Bbox,在E.coli BL21中表达,镍亲和层析柱提纯,获取纯净目的蛋白。HMGB1免疫新西兰大白兔后,抗血清效价为1:2,000,000,具有高度特异性。免疫组化显示小鼠坏死肝组织HMGB1表达增加。结论:本研究获得了人HMGB1以及HMGB1的Abox和Bbox的纯化蛋白,制备了人HMGB1的多克隆抗血清,为HMGB1的结构、组织表达谱及其功能的研究奠定了基础。     

Interplay between in vitro acetylation and phosphorylation of tailless HMGB1 protein

The postsynthetic acetylation of HMGB1 protein and its truncated form affects significantly its properties as “architectural” factor - recognition of bent DNA and bending of short DNA fragments. We created mutants at the target sites (lysines 2 and 81) in the tailless HMGB1 modified by the histone acetyltransferase CBP. The results show that there is no preferential site for the enzymatic activity of CBP and both lysine moieties are modified independently. Our findings for the first time demonstrate the link between the acetylation and phosphorylation of HMGB1ΔC in vitro. The PKC phosphorylation prior to acetylation inhibits the CBP activity 40-60% for the truncated form and its mutants. The effect of the CBP acetylation on the phosphorylation level turns out to be much more prominent. In the case of HMGB1ΔC modified at Lys 2 and Lys 81 prior to PKC treatment background phosphorylation is detected. If only one of the lysines is modified the inhibitory effect decreases.     

HMGB1在卵巢癌中的表达及临床意义

目的：探讨高迁移率组蛋白B1（HMGB1）在卵巢癌患者血清及组织中的表达及临床意义。方法：采用ELISA技术检测96例女性血清中HMGB1水平,其中盆腔肿物住院患者66例按照术后病理结果分为卵巢良性肿瘤组40例和卵巢癌组26例,健康女性30例作为正常对照组,并通过免疫组织化学技术进一步检测卵巢癌、卵巢良性肿瘤组织中的表达情况。结果：卵巢癌组HMGB1水平明显高于其他两组,差异有统计学意义（P〈0.05）,正常对照组和卵巢良性肿瘤组比较差异无统计学意义（P〉0.05）。结论：HMGB1测定有助于鉴别卵巢良恶性肿瘤。     

HIV感染者/AIDS病人高迁移率族蛋白1的表达及其临床意义

通过检测74例处于不同病期的HIV感染者/AIDS患者和10例健康对照者PBMCs中HMGB1 mRNA的表达水平及其外周血浆HMGB1、TNF-a和IL-2水平,比较各组之间表达水平的差异及其与CD4＋T淋巴细胞的关系.发现HMGB1 mRNA的表达水平及血浆HMGB1含量在AIDS病人组明显高于感染者组和正常对照组（P〈0.05）;AIDS患者经HAART治疗后疗效差组HMGB1 mRNA的表达水平及血浆HMGB1含量也明显高于疗效好组（P〈0.05）;而经HAART治疗后效果好且免疫功能恢复的患者HMGB1 mRNA的表达及血浆HMGB1含量均较治疗前明显下降（P〈0.05）;当CD4＋T细胞数低于200/μL时,血浆HMGB1含量以及PBMCs中HMGB1 mRNA表达水平与CD4＋T细胞数呈负相关.显示HMGB1在HIV/AIDS发病及病情进展过程中可能起重要作用,HMGB1血浆含量及PBMCs中HMGB1 mRNA的表达水平高低与HIV/AIDS患者病情轻重密切相关.     

热休克转录因子1对高迁移率族蛋白B1的转录调控作用及机制

目的：探讨烧伤血清诱导下热休克转录因子1（HSF1）对高迁移率族蛋白B1（HMGB1）的转录调控作用及其机制.方法：构建热休克转录因子1真核表达载体pcDNA3.1-HSF1,HMGB1野生型启动子荧光素酶报告基因pGL3-HMGB1-Y,HMGB1突变型启动子荧光素酶报告基因pGL3-HMGB1-T.pcDNA3.1-HSF1转染巨噬细胞RAW264.7,烧伤血清诱导后,半定量RT-PCR检测HMGB1 mRNA的表达.pcDNA3.1-HSF1,HMGB1启动子荧光素酶报告基因共转染RAW264.7,烧伤血清诱导后,检测并比较pGL3-HMGB1-Y和 pGL3-HMGB1-T的相对萤光素酶活性.结果：烧伤血清诱导下,HSF1可以下调RAW264.7 HMGB1mRNA的表达.pGL3-HMGB1-T的相对荧光素酶值较pGL3-HMGB1-Y明显下降,P＜0.01,差异有显著统计学意义.结论：烧伤血清诱导下,HSF1可能通过与HMGB1启动子区HSE的结合下调小鼠巨噬细胞RAW264.7 HMGB1mRNA的表达.     

Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR,with an example from barley

Although the increasing number of expressed sequence tags (ESTs) from the public domain has facilitated the detection of single nucleotide polymorphisms (SNPs), further validation is needed before they can be used as markers. For SNP validation, we have compared 2 independent methods: (1) the primer extension method followed by capillary electrophoresis on an ABI PRISM 3100 Genetic Analyzer and (2) nested PCR followed by agarose-based visualization. We present an assessment of the efficiency and costs associated with these methods, based on a sample of barley cultivars.     

Association study of the single nucleotide polymorphisms in adiponectin-associated genes with type 2 diabetes in Han Chinese

Single-nucleotide polymorphisms （SNPs） of ADIPOQ, ADIPOR1, and ADIPOR2 have been associated with type 2 diabetes mellitus （T2DM）, but there are many conflicting results especially in Chinese populations. To investigate the contribution of the adiponectin genes and their receptors to T2DM, a case-control study was performed and 11 SNPs ofADIPOQ, ADIPOR1, and ADIPOR2 were genotyped in 985 T2DM and 1,050 control subjects, rs 16861194 （-11426 A〉G） in the putative promoter of ADIPOQ was associated with T2DM （P = 0.007; OR = 1.29, 95% CI 1.08-1.55）. None of the other 10 SNPs were associated with T2DM in this study, although rs2241766 and rs1501299 were reported to be associated with T2DM in previous Chinese studies. There was also no significant difference found from the ADIPOQ haplotype analysis, which contains rs 16861194. In addition, we also assessed potential gene-gene interactions in three genes and no interactions were found. In conclusion, our results supported the ADIPOQ gene as a possible risk factor for type 2 diabetes in Han Chinese population.     

HMGB1在卵巢癌中的表达及临床意义

目的:探讨高迁移率组蛋白B1(HMGB1)在卵巢癌患者血清及组织中的表达及临床意义。方法:采用ELISA技术检测96例女性血清中HMGB1水平,其中盆腔肿物住院患者66例按照术后病理结果分为卵巢良性肿瘤组40例和卵巢癌组26例,健康女性30例作为正常对照组,并通过免疫组织化学技术进一步检测卵巢癌、卵巢良性肿瘤组织中的表达情况。结果:卵巢癌组HMGB1水平明显高于其他两组,差异有统计学意义(P<0.05),正常对照组和卵巢良性肿瘤组比较差异无统计学意义(P>0.05)。结论:HMGB1测定有助于鉴别卵巢良恶性肿瘤。     

Patterns of nucleotide substitution in pseudogenes and functional genes

Summary The pattern of point mutations is inferred from nucleotide substitutions in pseudogenes. The pattern obtained suggests that transition mutations occur somewhat more frequently than transversion mutations and that mutations result more often in A or T than in G or C. Our results are discussed with respect to the predictions from Topal and Fresco's model for the molecular basis of point (substitution) mutations (Nature 263:285–289, 1976). The pattern of nucleotide substitution at the first and second positions of codons in functional genes is quite similar to that in pseudogenes, but the relative frequency of the transition CT in the sense strand is drastically reduced and those of the transversions CG and GC are doubled. The differences between the two patterns can be explained by the observation that in the protein evolution amino acid substitutions occur mainly between amino acids with similar biochemical properties (Grantham, Science 185:862–864, 1974). Our results for the patterns of nucleotide substitutions in pseudogenes and in functional genes lead to the prediction that both the coding and non-coding regions of protein coding genes should have high frequencies of A and T. Available data show that the non-coding regions are indeed high in A and T but the coding regions are low in T, though high in A.     

Cloning, sequencing and identification of single nucleotide polymorphisms of partial sequence on the porcine CACNA1S gene

CACNA1S gene encodes the α1 subunit of the calcium channel. The mutation of CACNA1S gene can cause hypokalemic periodic paralysis (HypoKPP) and maliglant hyperthermia synarome (MHS) in hu-man beings. Current research on CACNA1S was mainly in human being and model animal, but rarely in livestock and poultry. In this study, Yorkshire pigs (23), Pietrain pigs (30), Jinhua pigs (115) and the second generation (126) of crossbred of Jinhua and Pietrain were used. Primers were designed ac-cording to the sequence of human CACNA1S gene and PCR was carried out using pig genome DNA. PCR products were sequenced and compared with that of human, and then single nucleotide poly-morphisms (SNPs) were investigated by PCR-SSCP, while PCR-RFLP tests were performed to validate the mutations. Results indicated: (1) the 5211 bp DNA fragments of porcine CACNA1S gene were ac-quired (GenBank accession number: DQ767693 ) and the identity of the exon region was 82.6% be-tween human and pig; (2) fifty-seven mutations were found within the cloned sequences, among which 24 were in exon region; (3) the results of PCR-RFLP were in accordance with that of PCR-SSCP. Ac-cording to the EST of porcine CACNA1S gene published in GenBank (Bx914582, Bx666997), 8 of the 11 SNPs identified in the present study were consistent with the base difference between two EST frag-ments.     

The role of HMGB1 in liver inflammation in obese rats

ABSTRACT

Obesity is a chronic disease that is characterized by increased body fat owing to imbalance between consumed and expended energy. Inflammation generally is accompanied by accumulation of excess lipid in adipose tissue and liver. High mobility group box-1 (HMGB1) participates in the pathogenesis of inflammatory diseases. We investigated the relation of the number of HMGB1 positive cells to body mass index (BMI), liver inflammation and the number of Kupffer cells. We divided 18 female Wistar albino rats into two groups: group 1, untreated control fed normal commercial rat diet and group 2, obese rats fed a special diet containing 40% fat. The plasma concentrations of cholesterol, glucose, superoxide dismutase enzyme (SOD) and catalase activities were measured for all animals. The numbers of hepatocytes, Kupffer cells and HMGB1 positive cells were counted using stereological methods. The mean numbers of Kupffer cells and HMGB1 positive cells were higher for group 2 than for group 1. The concentrations of plasma cholesterol and glucose levels also were higher in group 2. Plasma levels of SOD and catalase were significantly lower in group 2 compared to group 1. The number of HMGB1 cells was related directly to BMI and inflammation. The role of HMGB1 was demonstrated for the liver of the obese group. We demonstrated the relations among HMGB1, BMI, obesity and inflammation.     

A program for annotating and predicting the effects of single nucleotide polymorphisms,SnpEff

We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted.

Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w¹¹¹⁸; iso-2; iso-3 strain and the reference y¹; cn¹ bw¹ sp¹ strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5′UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus.

As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.     

HMGB1, an alarmin promoting HIV dissemination and latency in dendritic cells

Dendritic cells (DCs) initiate immune responses by transporting antigens and migrating to lymphoid tissues to initiate T-cell responses. DCs are located in the mucosal surfaces that are involved in human immunodeficiency virus (HIV) transmission and they are probably among the earliest targets of HIV-1 infection. DCs have an important role in viral transmission and dissemination, and HIV-1 has evolved different strategies to evade DC antiviral activity. High mobility group box 1 (HMGB1) is a DNA-binding nuclear protein that can act as an alarmin, a danger signal to alert the innate immune system for the initiation of host defense. It is the prototypic damage-associated molecular pattern molecule, and it can be secreted by innate cells, including DCs and natural killer (NK) cells. The fate of DCs is dependent on a cognate interaction with NK cells, which involves HMGB1 expressed at NK–DC synapse. HMGB1 is essential for DC maturation, migration to lymphoid tissues and functional type-1 polarization of naïve T cells. This review highlights the latest advances in our understanding of the impact of HIV on the interactions between HMGB1 and DCs, focusing on the mechanisms of HMGB1-dependent viral dissemination and persistence in DCs, and discussing the consequences on antiviral innate immunity, immune activation and HIV pathogenesis.