An entropy-based approach for testing genetic epistasis underlying complex diseases

The genetic basis of complex diseases is expected to be highly heterogeneous, with complex interactions among multiple disease loci and environment factors. Due to the multi-dimensional property of interactions among large number of genetic loci, efficient statistical approach has not been well developed to handle the high-order epistatic complexity. In this article, we introduce a new approach for testing genetic epistasis in multiple loci using an entropy-based statistic for a case-only design. The entropy-based statistic asymptotically follows a χ² distribution. Computer simulations show that the entropy-based approach has better control of type I error and higher power compared to the standard χ² test. Motivated by a schizophrenia data set, we propose a method for measuring and testing the relative entropy of a clinical phenotype, through which one can test the contribution or interaction of multiple disease loci to a clinical phenotype. A sequential forward selection procedure is proposed to construct a genetic interaction network which is illustrated through a tree-based diagram. The network information clearly shows the relative importance of a set of genetic loci on a clinical phenotype. To show the utility of the new entropy-based approach, it is applied to analyze two real data sets, a schizophrenia data set and a published malaria data set. Our approach provides a fast and testable framework for genetic epistasis study in a case-only design.     

基于TCGA数据库分析甲状腺癌基因表达谱

为分析甲状腺癌基因表达谱,筛选疾病相关的基因标志物。基于肿瘤基因组图谱(TCGA)数据库中的甲状腺癌基因表达数据,运用R/Bioconductor统计平台进行数据处理与统计学分析。分别应用edgeR算法和limma算法选取肿瘤组织与对照组间倍数改变 > 2,P< 0.05的基因作为差异基因;进一步运用Medcalc统计软件进行受试者工作特征曲线(ROC)分析,鉴定出有诊断标志物潜在应用价值的基因标志物。通过两种运算方法筛选出甲状腺癌组织中存在着1 945个差异基因(上调基因1 033个,下调基因912个);根据差异倍数进一步鉴定出11个基因在肿瘤组织中表达上调,且对鉴别肿瘤组与对照组有较好的应用价值。本研究分析了TCGA中的甲状腺癌表达谱数据,鉴定出了与疾病诊断显著相关的差异表达基因,能够为探索疾病发生发展机制及寻找新型分子标志物提供依据。     

Advances in research into gamete and embryo-fetal origins of adult diseases

The fetal and infant origins of adult disease hypothesis proposed that the roots of adult chronic disease lie in the effects of adverse environments in fetal life and early infancy. In addition to the fetal period, fertilization and early embryonic stages, the critical time windows of epigenetic reprogramming, rapid cell differentiation and organogenesis, are the most sensitive stages to environmental disturbances. Compared with embryo and fetal development, gametogenesis and maturation take decades and are more vulnerable to potential damage for a longer exposure period. Therefore, we should shift the focus of adult disease occurrence and pathogenesis further back to gametogenesis and embryonic development events, which may result in intergenerational, even transgenerational, epigenetic re-programming with transmission of adverse traits and characteristics to offspring. Here, we focus on the research progress relating to diseases that originated from events in the gametes and early embryos and the potential epigenetic mechanisms involved.     

ERCC1 and ERCC2 Haplotype Modulates Induced BPDE-DNA Adducts in Primary Cultured Lymphocytes

Background

Benzo[a]pyrene(B[a]P), and its ultimate metabolite Benzo[a]pyrene 7,8-diol 9,10-epoxide (BPDE), are classic DNA damaging carcinogens. DNA damage caused by BPDE is normally repaired by Nucleotide Excision Repair (NER), of which ERCC1 and ERCC2/XPD exert an indispensable role. Genetic variations in ERCC1 and ERCC2 have been related to DNA repair efficiency. In this study we used lymphocytes from healthy individuals to show that polymorphisms in ERCC1 and ERCC2 are directly associated with decreased DNA repair efficiency.

Methods

ERCC1 (rs3212986 and rs11615) and ERCC2 (rs13181, rs1799793 and rs238406) were genotyped in 818 healthy Han individuals from the northeast of China. BPDE induced DNA adducts in lymphocytes were assessed by high performance liquid chromatography (HPLC) in 282 randomly selected participants. The effect of ERCC1 rs3212986 and ERCC2 rs238406 on DNA damage caused by B[a]P was assessed with a modified comet assay.

Results

We found that the variant genotypes of ERCC1 rs3212986 and ERCC2 rs238406 were associated with the high levels of BPDE-DNA adducts. Especially ERCC1 rs3212986 A-allele variant was significantly associated with the high BPDE-DNA adducts. Haplotype analysis showed that the ERCC1 haplotype AC (OR = 2.36, 95% CI = 1.84–2.97), ERCC2 haplotype AGA (OR = 1.51, 95% CI = 1.06–2.15) and haplotype block AGAAC (OR = 5.28, 95% CI = 2.95–9.43), AGCAC (OR = 1.35 95% CI = 1.13–1.60) were linked with high BPDE-DNA adducts. In addition, we found that the combined minor alleles of ERCC1 rs3212986 and ERCC2 rs238406 were associated with a reduced DNA repair capacity.

Conclusions

Our results suggest that the variant genotypes of ERCC1 rs3212986 and ERCC2 rs238406 are associated with decreased repair efficiency of BPDE induced DNA damage, and may be predictive for an individual’s DNA repair capacity in response to environmental carcinogens.     

Mechanism underlying the retarded nuclear translocation of androgen receptor splice variants

As shown in our previous study, two alternatively spliced androgen receptor(AR) variants, which are exclusively expressed in the granulosa cells of patients with polycystic ovary syndrome, exhibit retarded nuclear translocation compared with wild-type AR. However, researchers have not yet determined whether these abnormalities correlate with heat shock protein 90(HSP90)and importin α(the former is a generally accepted co-chaperone of AR, and the latter is a component of classical nuclear import complexes). Here, these two variants were mainly retained in cytoplasm with HSP90 and importin α in the presence of dihydrotestosterone(DHT), and their levels in nucleus were significantly reduced, according to the immunofluorescence staining. The binding affinity of two AR variants for importin α was consistently decreased, while it was increased in WT-AR following DHT stimulation, leading to reduced nuclear import, particularly for the insertion-AR(Ins-AR). However, the binding affinities of two AR variants for HSP90 were increased in the absence of DHT compared with WT-AR, which functioned to maintain spatial structural stability, particularly for the deletion-AR(Del-AR). Therefore, the retarded nuclear translocation of two AR variants is associated with HSP90 and importin α, and the abnormal binding affinities for them play critical roles in this process.     

Gene-centric genomewide association study via entropy

Genes are the functional units in most organisms. Compared to genetic variants located outside genes, genic variants are more likely to affect disease risk. The development of the human HapMap project provides an unprecedented opportunity for genetic association studies at the genomewide level for elucidating disease etiology. Currently, most association studies at the single-nucleotide polymorphism (SNP) or the haplotype level rely on the linkage information between SNP markers and disease variants, with which association findings are difficult to replicate. Moreover, variants in genes might not be sufficiently covered by currently available methods. In this article, we present a gene-centric approach via entropy statistics for a genomewide association study to identify disease genes. The new entropy-based approach considers genic variants within one gene simultaneously and is developed on the basis of a joint genotype distribution among genetic variants for an association test. A grouping algorithm based on a penalized entropy measure is proposed to reduce the dimension of the test statistic. Type I error rates and power of the entropy test are evaluated through extensive simulation studies. The results indicate that the entropy test has stable power under different disease models with a reasonable sample size. Compared to single SNP-based analysis, the gene-centric approach has greater power, especially when there is more than one disease variant in a gene. As the genomewide genic SNPs become available, our entropy-based gene-centric approach would provide a robust and computationally efficient way for gene-based genomewide association study.     

二氯喹啉酸降解菌MC-10的筛选、鉴定及其降解特性

【目的】为治理稻-烟轮作田块上茬土壤中二氯喹啉酸残留问题,筛选高效降解细菌菌株。【方法】通过富集培养和选择培养,从常年施用二氯喹啉酸的水稻田中筛选可以降解二氯喹啉酸的细菌;对其进行形态学观察、生理生化特征测定和16S r DNA序列系统发育鉴定。【结果】分离的降解菌株MC-10被鉴定为节杆属菌株(Arthrobacter sp.)。菌株MC-10在5%接种量p H 7、28℃时,对初始浓度为20 mg/L二氯喹啉酸7 d可降解90%以上。该降解菌的最佳降解条件为p H 7、30℃,二氯喹啉酸初始浓度在1-100mg/L间均有良好的降解效果;菌株MC-10在土壤中对二氯喹啉酸同样有良好的降解效果,温室内7 d对二氯喹啉酸污染土壤的修复率可达70%。【结论】菌株MC-10在二氯喹啉酸污染土壤和水质治理中具有潜在的应用前景。     

Glucocorticoids modulate amino acid-induced translation initiation in human skeletal muscle

Amino acids are unique anabolic agents in that they nutritively signal to mRNA translation initiation and serve as substrates for protein synthesis in skeletal muscle. Glucocorticoid excess antagonizes the anabolic action of amino acids on protein synthesis in laboratory animals. To examine whether excessive glucocorticoids modulate mixed amino acid-signaled translation initiation in human skeletal muscle, we infused an amino acid mixture (10% Travasol) systemically to 16 young healthy male volunteers for 6 h in the absence (n = 8) or presence (n = 8) of glucocorticoid excess (dexamethasone 2 mg orally every 6 h for 3 days). Vastus lateralis muscles were biopsied before and after amino acid infusion, and the phosphorylation of eukaryotic initiation factor (eIF) 4E-binding protein 1 (4E-BP1), ribosomal protein S6 kinase (p70(S6K)), and eIF2alpha and the guanine nucleotide exchange activity of eIF2B were measured. Systemic infusion of mixed amino acids significantly stimulated the phosphorylation of 4E-BP1 (P < 0.04) and p70(S6K) (P < 0.001) and the dephosphorylation of eIF2alpha (P < 0.003) in the control group. Dexamethasone treatment did not alter the basal phosphorylation state of 4E-BP1, p70(S6K), or eIF2alpha; however, it abrogated the stimulatory effect of amino acid infusion on the phosphorylation of 4E-BP1 (P = 0.31) without affecting amino acid-induced phosphorylation of p70(S6K) (P = 0.002) or dephosphorylation of eIF2alpha (P = 0.003). Neither amino acid nor dexamethasone treatment altered the guanine nucleotide exchange activity of eIF2B. We conclude that changes of amino acid concentrations within the physiological range stimulate mRNA translation by enhancing the binding of mRNA to the 43S preinitiation complex, and the activity of p70(S6K) and glucocorticoid excess blocks the former action in vivo in human skeletal muscle.     

Gene-based Genomewide Association Analysis: A Comparison Study

The study of gene-based genetic associations has gained conceptual popularity recently. Biologic insight into the etiology of a complex disease can be gained by focusing on genes as testing units. Several gene-based methods (e.g., minimum p-value (or maximum test statistic) or entropy-based method) have been developed and have more power than a single nucleotide polymorphism (SNP)-based analysis. The objective of this study is to compare the performance of the entropy-based method with the minimum p-value and single SNP–based analysis and to explore their strengths and weaknesses. Simulation studies show that: 1) all three methods can reasonably control the false-positive rate; 2) the minimum p-value method outperforms the entropy-based and the single SNP–based method when only one disease-related SNP occurs within the gene; 3) the entropy-based method outperforms the other methods when there are more than two disease-related SNPs in the gene; and 4) the entropy-based method is computationally more efficient than the minimum p-value method. Application to a real data set shows that more significant genes were identified by the entropy-based method than by the other two methods.