Characterizing the Relation Between Expression QTLs and Complex Traits: Exploring the Role of Tissue Specificity

Measurement of gene expression levels and detection of eQTLs (expression quantitative trait loci) are difficult in tissues with limited sample availability, such as the brain. However, eQTL overlap between tissues might be high, which would allow for inference of eQTL functioning in the brain via eQTLs detected in readily accessible tissues, e.g. whole blood. Applying Stratified Linkage Disequilibrium Score Regression (SLDSR), we quantified the enrichment in polygenic signal of blood and brain eQTLs in genome-wide association studies (GWAS) of 11 complex traits. We looked at eQTLs discovered in 44 tissues by the Genotype-Tissue Expression (GTEx) consortium and two other large representative studies, and found no tissue-specific eQTL effects. Next, we integrated the GTEx eQTLs with regions associated with tissue-specific histone modifiers, and interrogated their effect on rheumatoid arthritis and schizophrenia. We observed substantially enriched effects of eQTLs located inside regions bearing modification H3K4me1 on schizophrenia, but not rheumatoid arthritis, and not tissue-specific. Finally, we extracted eQTLs associated with tissue-specific differentially expressed genes and determined their effects on rheumatoid arthritis and schizophrenia, these analysis revealed limited enrichment of eQTLs associated with gene specifically expressed in specific tissues. Our results pointed to strong enrichment of eQTLs in their effect on complex traits, without evidence for tissue-specific effects. Lack of tissue-specificity can be either due to a lack of statistical power or due to the true absence of tissue-specific effects. We conclude that eQTLs are strongly enriched in GWAS signal and that the enrichment is not specific to the eQTL discovery tissue. Until sample sizes for eQTL discovery grow sufficiently large, working with relatively accessible tissues as proxy for eQTL discovery is sensible and restricting lookups for GWAS hits to a specific tissue for which limited samples are available might not be advisable.     

Ontogeny of Expression of Pa and RT1.Aa Antigens on Rat Placenta and on Fetal Tissues

ABSTRACT: The unique pregnancy-associated (Pa) antigen, which is a class I antigen encoded by the major histocompatibility complex (MHC), elicits a nondestructive maternal antibody response. By contrast, the class I transplantation antigen RTI.A^a elicits a destructive antibody response in tissue transplantation but not during pregnancy. With the use of the avidin-biotin complex (ABC) immunohistochemical method, the Pa and RTl.A^a antigens were localized on the basophilic and giant cells of the basal zone trophoblast, the endovascular trophoblast and decidual interstitial trophoblast, and the chorioallantoic membrane but not on the labyrinthine zone trophoblast as early as the 12th day of gestation. These two antigens were also expressed on the epidermis, hair follicles, spleen, thymic medulla, bronchial epithelium, intestinal epithelium, the hepatic Kupffer cells, endocardium, endothelium of blood vessels, renal tubular cells and glomeruli, and renal pelvis and ureter of fetal and adult rat tissues. Absorption studies with placental tissue confirmed the presence of these two antigens in the rat placenta, and antibody-blocking studies confirmed their unique specificities.     

大鼠、小鼠各组织中的Lhx3同源盒基因的差异表达

目的分析新生及成年大鼠、小鼠各组织中Lhx3基因的表达情况。方法提取新生及成年大鼠、小鼠的骨骼肌、肝、肺、心脏、大脑皮层、脊髓等组织的总RNA,合成Lhx3基因特异性引物,用RT-PCR方法检测其表达情况。结果该基因在新生和成年大鼠和小鼠的大脑皮层和脊髓中有较高的表达,在肺中有中度表达。新生大小鼠的骨骼肌中有微量表达,而在成年大小鼠骨骼肌中未见表达。在新生大小鼠的心肌中未见表达,而在成年大小鼠心肌中有中度表达。结论Lhx3基因在不同年龄的大、小鼠的不同组织中的表达有明显的差异,说明该基因在不同组织发育和功能发挥中有不同的作用。     

小鼠Cpne5基因mRNA水平的表达分布及其在胚胎的表达定位

目的明确小鼠Cpne5基因在mRNA水平的组织表达分布及其在胚胎的表达定位。方法提取新生、成年小鼠主要脏器的总RNA,利用RT-PCR法检测Cpne5 mRNA的表达量;合成针对Cpne5 mRNA的杂交探针,取不同胎龄胎鼠进行整体原位杂交。结果 Cpne5 mRNA在成年小鼠10种脏器组织均有不同程度的表达,以大脑,小脑,睾丸和肺脏表达量较高;而肝脏和肌肉未表达。新生小鼠9种脏器中,Cpne5表达量最高的是脑组织,眼和肾次之,肺和肝脏表达量很少。制备并评估Cpne5原杂探针的产量,SP6转录的反义探针浓度为100ng/μL,T7转录的正义探针浓度为10ng/μL,原位杂交结果显示Cpne5 mRNA主要表达于胎鼠的端脑、间脑、中脑及菱脑原节。结论在新生和成年小鼠的脑组织中Cpne5基因mRNA高水平表达,并在胎鼠发育过程中定位于胎脑。     

Endothelial Gene Expression in Regions of Defined Shear Exposure in the Porcine Iliac Arteries

The effect of hemodynamic shear stress on endothelial gene expression was investigated in the porcine iliac arteries. A novel statistical approach was applied to computational fluid dynamics simulations of the iliac artery flow field to identify three anatomical regions likely to experience high, medium, and low levels of time average shear stress magnitude. Subsequently, endothelial cell mRNA was collected from these regions in the iliac arteries of six swine and analyzed by DNA microarray. Gene set enrichment analysis demonstrated a strong tendency for genes upregulated or downregulated in one of the extreme shear environments (low or high, relative to medium) to be regulated in the same direction in the other extreme shear environment. This tendency was confirmed for specific genes by real-time quantitative PCR. Specifically, β-catenin, c-jun, VCAM-1, and MCP-1 were all upregulated in low and high shear stress regions relative to the medium shear stress region. eNOS expression was not significantly different in any of the regions. These results are consistent with the notion that endothelial cells chronically exposed to abnormally low or high shear levels in vivo exhibit similar genetic responses. Alternative explanations of this outcome are proposed, and its implications for the role of shear stress in atherogenesis are examined.     

Lymphoid Tissue Ontogeny in the Mummichog,Fundulus heteroclitus

Most studies that examine the ontogeny of lymphoid organ development in teleostean fishes use species of interest to aquaculture or genetic research and, to date, have focused strictly on marine or freshwater species. The mummichog, Fundulus heteroclitus, also known as the estuarine killifish, is a unique model for studies on developmental immunobiology, because it is euryhaline, has a high degree of thermal tolerance, and has a unique reproductive strategy. Embryonic and larval mummichogs were examined for the ontogeny of lymphoid tissue development. The first lymphoid organ to appear was the head kidney at 1 dph, followed by the spleen at 1 wph, and then the thymus at 3 wph. Rag‐1 was partially cloned and sequenced and shown to be highly conserved among other vertebrate Rag‐1 genes. Using QT‐PCR to monitor the temporal expression of Rag‐1, it was shown to reach a maximum intensity at 3 and 4 wph and then to drop to pre‐2‐wph levels. Overall, this study suggests that juvenile mummichogs do not possess the ability to mount T‐ or B‐cell responses until some time after 5 wph. Even though the estuarine killifish tolerates a wide range of salinities, the developmental patterns of lymphoid tissues are similar to what has been reported for strictly marine (stenohaline) teleosts. Thus, the mummichog should be a convenient model for understanding the developmental immunobiology of most marine teleosts. Anat Rec, 2008. © 2008 Wiley‐Liss, Inc.     

Specificity of Fcγ Receptors in Human Malignant Tissue and Normal Lymphoreticular Tissue

The specificity of the Fcγ receptors in normal spleen and liver and in malignant tissues was studied using hemadsorption to cryostat sections. Indicator cells (EA) were sheep erythrocytes (E) sensitized with rabbit IgG antibody (A). The binding of EA to sections of normal and malignant tissues was inhibited by pooled IgG of human, rabbit, and guinea pig origin and by human IgG1, and IgG3, and IgG4 myeloma proteins. Heat-aggregated IgG inhibited the binding to sections of liver and some malignant tissues more effectively than monomeric IgG. The Fc fragments of IgG were also inhibitory, but not the F(ab')₂, Fab', and Facb fragments. The inhibition obtained increased with decreasing amounts of A used for sensitization of E. The inhibitory activity of IgG was abolished after partial reduction and alkylation. No inhibition was obtained with IgG2, IgM, IgA, or albumin. E sensitized with Facb or F(ab')₂ fragments of A did not bind to normal or malignant tissues. The specificity of the Fc receptors in normal spleen and liver and in malignant tissues is apparently very similar.     

喉癌组织中FEZ1／LZTS1基因的表达及其临床意义

目的：探讨FEZ1／LZTS1基因在喉鳞状细胞癌中的表达缺失及其与临床病理的关系。方法：采用逆转录聚合酶链反应（RT—PCR）法,分析50例原发性喉癌组织和癌旁组织中FEZ1／LZTS1基因的表达情况。结果：FEZ1／LZTS1基因在癌旁组织中表达率明显高于喉癌组织（P〈0．01）;在喉癌组织中FEZ1／LZTS1基因阳性表达率随其病理分级、临床分期升高而降低（P〈0．01）,而与患者年龄、性别和原发灶部位无关。结论：FEZ1／LZTS1基因的表达缺失可能对LSCC的发生发展起重要作用,是LSCC发展中的重要分子事件。     

脑胶质瘤中PTEN基因表达的实时定量PCR研究

目的:探讨PTEN基因在胶质瘤中的表达及意义,以及与预后的关系.方法:采用荧光实时定量PCR技术检测44例人脑胶质瘤组织及其19例邻近正常脑组织、7例良性脑肿瘤中的PTEN mRNA及内参GAPDH的表达水平.结果:高分化组(29例)PTEN基因的表达明显高于低分化组(15例)(P＜0.05)这两组分别与良性脑肿瘤组(7例)相比,均有显著差异(P＜0.05).19例胶质瘤与邻近正常脑组织有显著差异(P＜0.000).高分化组和底分化组之间在1年或3年存活率的比较中,存在明显差异(P＜0.05).结论:PTEN基因在胶质瘤的发生及发展中起重要作用,脑胶质瘤中PTEN基因的表达与胶质瘤的恶性程度及预后相关.     

DNA Microarray-Based Gene Expression Profiling in Porcine Keratocytes and Corneal Endothelial Cells and Comparative Analysis Associated with Xeno-related Rejection

Porcine to rat corneal xenotransplantation resulted in severe inflammation and rejection of the corneal stroma, whereas an allograft showed mainly endothelial cell-associated rejection. We, therefore, investigated and compared the gene expression between porcine keratocytes and corneal endothelial cells. RNA was isolated from primary cultured porcine or human keratocytes and porcine corneal endothelial cells. Gene expression was comparatively analyzed after normalization with microarray method using Platinum pig 13 K oligo chip (GenoCheck Co., Ltd., Ansan, Korea). Real-time polymerase chain reaction (PCR) was performed for C1R, CCL2, CXCL6, and HLA-A in porcine keratocytes and corneal endothelial cells. As a result, upregulated expression more than 2 folds was observed in 1,162 genes of porcine keratocytes versus porcine endothelial cells. Among the immune-regulatory genes, SEMA3C, CCL2, CXCL6, F3, HLA-A, CD97, IFI30, C1R, and G1P3 were highly expressed in porcine keratocytes, compared to porcine corneal endothelial cells or human keratocytes. When measured by real-time PCR, the expression of C1R, CCL2, and HLA-A was higher in porcine keratocytes compared to that in porcine corneal endothelial cells. In conclusion, the increased expression of C1R, CCL2, and HLA-A genes in porcine keratocytes might be responsible for the stromal rejection observed in a porcine to rat corneal xenotransplantation.