Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus-1 and simian immunodeficiency virus

The pathogenicity of the primate lentiviruses, human, and simian immunodeficiency viruses, is host-specific. Previous studies indicated that the highly pathogenic human lentivirus HIV-1 has markedly reduced pathogenicity compared to the pathogenic simian lentivirus SIV in pigtail macaques (Macaca nemestrina). We therefore hypothesized that the pigtail macaque peripheral blood mononuclear cells (mPBMCs) would respond differently to infections of HIV-1 and pathogenic SIV. To elucidate the cellular responses to the infections of HIV-1 and SIV, we infected mPBMC with these two viruses. Like infections in vivo, HIV-1 and SIV demonstrated distinct replication kinetics in mPBMCs, with HIV-1 replicating at significantly lower levels. Similarly, gene expression profiling facilitated by macaque-specific oligonucleotide microarrays also revealed distinct expression patterns of genes between the HIV-1- and SIV-infected mPBMCs; in particular, genes associated with the antigen presentation, T cell receptor, ERK/MAPK signaling, Wnt/beta-catenin signaling, and natural killer cell signaling pathways were differentially regulated between these two viruses. Most interestingly, despite the lower levels of replication, HIV-1 triggered a more robust regulation of immune response genes early after infection; the converse was true in SIV-infected mPBMCs. Our results therefore suggest that macaques may be controlling the infection of HIV-1 at an early stage through coordinated regulation of host defense pathways.     

Postauricular and eyeblink startle responses to facial expressions

Emotional facial expressions have affective significance. Smiles, for example, are perceived as positive and responded to with increased happiness, whereas angry expressions are perceived as negative and threatening. Yet, these perceptions are modulated in part by facial morphological cues related to the sex of the expresser. The present research assessed both eyeblink startle and the postauricular reflex during happy and angry expressions by men and women. For this 14 male and 16 female undergraduates saw happy, neutral, and angry facial expressions as well as positive and negative pictures. The postauricular reflex was potentiated during happy expressions and inhibited during anger expressions; however, as expected, this pattern was more clearly found for female expressers. Conversely, the expected pattern of eyeblink startle potentiation during angry faces and inhibition during happy faces was found only for male expressers.     

HLA-B*0749N: the first HLA-B*07 null allele

In the present article, we report the identification of the first HLA-B*07 null allele found in a Polish patient awaiting a kidney allograft. A discrepant result obtained between serological typing (HLA-B "blank") and high-resolution molecular typing using PCR-SSP method (HLA-B*070201 allele) suggested the presence of a null allele. Genomic DNA sequencing of the HLA-B*07 allele revealed a single nucleotide substitution at the 3' end of the exon 4 leading to a premature stop codon.     

A histological survey of green fluorescent protein expression in 'green' mice: implications for stem cell research

AIMS: The transgenic enhanced green fluorescent protein (EGFP) expressing 'green' mouse (C57BL/6-TgN(ACTbEGFP)1Osb) is a widely used tool in stem cell research, where the ubiquitous nature of EGFP expression is critical to track the fate of single or small groups of transplanted haematopoietic stem cells (HSC). Our aim was to investigate this assumed ubiquitous expression by performing a detailed histological survey of EGFP expression in these mice. METHODS: Fluorescent microscopy of frozen tissue sections was used to perform a detailed histological survey of the pattern of EGFP expression in these mice. Flow cytometry was also used to determine the expression pattern in blood and bone marrow. RESULTS: Three patterns of EGFP expression were noted. In most tissues there was an apparently stochastic variegation of the transgene, with individual cell types demonstrating highly variable rates of EGFP expression. Certain specific cell types such as pancreatic ductal epithelium, cerebral cortical neurones and glial cells and glomerular mesangial cells consistently lacked EGFP expression, while others, including pancreatic islet cells, expressed EGFP only at extremely low levels, barely distinguishable from background. Lastly, in the colon and stomach the pattern of EGFP expression was suggestive of clonal inactivation. Only cardiac and skeletal muscle showed near ubiquitous expression. CONCLUSIONS: These findings raise questions regarding the 'ubiquitous' expression of EGFP in these transgenic mice and suggest caution in relying overly on EGFP alone as an infallible marker of donor cell origin.     

Increased expression of Gab2, a scaffolding adaptor of the tyrosine kinase signalling, in gastric carcinomas

AIMS: Mounting evidence indicates that alterations of protein kinase signalling pathways play crucial roles in the pathogenesis of cancers. Gab2 (Grb2-associated binding protein 2), a member of the family of Gab scaffolding adaptors, transmits and amplifies the signals from receptor tyrosine kinases. A recent study demonstrated that Gab protein was over-expressed in breast cancers, and the over-expressed Gab2 increased proliferation and invasion of the cells, indicating that Gab2 is an oncogenic protein. However, the roles of Gab in other cancers are largely unknown. METHODS: In this study, to see whether Gab2 expression could be a characteristic of gastric cancers, we analysed the expression of Gab2 in 60 gastric adenocarcinomas by immunohistochemistry using a tissue microarray. RESULTS: In the normal gastric mucosal epithelial cells, Gab2 protein was expressed in parietal and zymogen cells, but not in other mucosal epithelial cells. In the cancer cells, Gab2 expression was detected in 40 (67%) of the 60 gastric adenocarcinomas. The Gab2 expression was observed in 12 (60%) of the 20 early gastric carcinomas and 28 (70%) of the 40 advanced gastric carcinomas. There was no significant association of Gab2 expression with clinocopathological characteristics, including invasion, metastasis and stage. CONCLUSION: Our data indicate that Gab2 over-expression is a feature not only of breast cancers, but also of gastric cancers. Increased expression of Gab2 in malignant gastric cells compared with normal epithelial cells suggests that Gab2 expression may play a role in gastric cancer development.     

Gene expression profile class prediction using linear Bayesian classifiers

Due to recent advances in DNA microarray technology, using gene expression profiles, diagnostic category of tissue samples can be predicted with high accuracy. In this study, we discuss shortcomings of some existing gene expression profile classification methods and propose a new approach based on linear Bayesian classifiers. In our approach, we first construct gene-level linear classifiers to identify genes that provide high class-prediction accuracies, i.e., low error rates. After this screening phase, starting with the gene that offers the lowest error rate, we construct a multi-dimensional linear classifier by incorporating next best-performing genes, until the prediction error becomes minimum or 0, if possible. When we compared classification performance of our approach against prediction analysis of microarrays (PAM) and support vector machines (SVM) based approaches, we found that our method outperforms PAM and produces comparable results with SVM. In addition, we observed that the gene selection scheme of PAM could be misleading. Albeit SVM achieves relatively higher prediction performance, it has two major disadvantages: Complexity and lack of insight about important genes. Our intuitive approach offers competing performance and also an efficient means for finding important genes.     

儿童肾上腺皮质癌表达谱时序分析用于筛选相关靶点的研究

目的 探讨肾上腺皮质癌（ACT）潜在致病机制,并筛选出可能作为相关生物靶标的基因。方法 从基因表达数据库Gene Expression Omnibus（GEO）中选取儿童ACT相关RNA芯片数据集（GSE75415）,利用R语言的相关函数包对其中的18个ACT组织样本（实验组）以及7个正常肾上腺皮质组织样本（对照组）中的mRNA表达数据进行预处理差异表达分析,对ACT各分级（stage1~4）的差异表达基因（DEGs）和重合差异基因（OLDEGs）,采用功能富集分析（GO功能富集和KEGG通路）,并筛选出中心基因。同时对TCGA数据库包括79个ACT样本的二代测序数据进 行分析,筛选出对ACT患者生存时间有影响的基因。结果 Stage1～4分别有248、334、315和561个基因发生了差异表达,各分级样本组间存在73个重合基因（OLDEGs）,中心基因HSPA13、GARS、STXBP1、AKIRIN1、TUBB3在各分级中均表达上调,中心基因ADH1B、DCN、RASSF2、PDGFRA、PLAT、C3、FOS在各分级中均表达下调,它们通过影响免疫反应、细胞周期、磷酸化、凝血及相应的信号通路,对ACT的发生与发展发挥作用。另外,OLDEGs在79个TCGA数据库ACT样本生存期分析发现,基因XPO1、RACGAP1、PDGFD、NR4A2、MXRA5、VPS51、TMED3、NDFIP1和CDKN1C与ACT的生存期密切相关。结论 在各级中均差异表达的基因和生存期相关基因可以作为ACT治疗的新靶点,这将有助于进一步理解肾上腺皮质癌的病因和预后治疗。     

rs294775 is a cis‐regulatory SNP for human UGT2B10

UGT2B10 is an important metabolism enzyme in human body and its substrates include multiple amine‐containing compounds, especially nicotine, tamoxifen and multiple antidepressants. Multiple common SNPs have been observed in its promoter region, but their role in expression regulation has never been investigated. In this preliminary study, we identified a novel cis‐regulatory SNP, rs294775, for UGT2B10 by plasmid construction, mutagenesis, and luciferase assay, whose mechanism was also investigated. Our work provides a basis for further pharmacogenetics study.