Guo Lp

The neural correlates of reward-related processing in major depressive disorder: A meta-analysis of functional magnetic resonance imaging studies

BACKGROUND A growing number of functional magnetic resonance imaging (fMRI) studies have been conducted in major depressive disorder (MDD) to elucidate reward-related brain functions. The aim of this meta-analysis was to examine the common reward network in the MDD brain and to further distinguish the brain activation patterns between positive stimuli and monetary rewards as well as reward anticipation and outcome. METHODS A series of activation likelihood estimation (ALE) meta-analyses were performed across 22 fMRI studies that examined reward-related processing, with a total of 341 MDD patients and 367 healthy controls. RESULTS We observed several frontostriatal regions that participated in reward processing in MDD. The common reward network in MDD was characterized by decreased subcortical and limbic areas activity and an increased cortical response. In addition, the cerebellum, lingual gyrus, parahippocampal gyrus and fusiform gyrus preferentially responded to positive stimuli in MDD, while the insula, precuneus, cuneus, PFC and inferior parietal lobule selectively responded to monetary rewards. Our results indicated a reduced caudate response during both monetary anticipation and outcome stages as well as increased activation in the middle frontal gyrus and dorsal anterior cingulate during reward anticipation in MDD. LIMITATIONS The reward-related tasks and mood states of patients included in our analysis were heterogeneous. CONCLUSIONS Our current findings suggest that there exist emotional or motivational pathway dysfunctions in MDD during reward-related processing. Future studies may be strengthened by paying careful attention to the types of reward used as well as the different components of reward processing examined.

rSNPBase: a database for curated regulatory SNPs

In recent years, human regulatory SNPs (rSNPs) have been widely studied. Here, we present database rSNPBase, freely available at http://rsnp.psych.ac.cn/, to provide curated rSNPs that analyses the regulatory features of all SNPs in the human genome with reference to experimentally supported regulatory elements. In contrast with previous SNP functional annotation databases, rSNPBase is characterized by several unique features. (i) To improve reliability, all SNPs in rSNPBase are annotated with reference to experimentally supported regulatory elements. (ii) rSNPBase focuses on rSNPs involved in a wide range of regulation types, including proximal and distal transcriptional regulation and post-transcriptional regulation, and identifies their potentially regulated genes. (iii) Linkage disequilibrium (LD) correlations between SNPs were analysed so that the regulatory feature is annotated to SNP-set rather than a single SNP. (iv) rSNPBase provides the spatio-temporal labels and experimental eQTL labels for SNPs. In summary, rSNPBase provides more reliable, comprehensive and user-friendly regulatory annotations on rSNPs and will assist researchers in selecting candidate SNPs for further genetic studies and in exploring causal SNPs for in-depth molecular mechanisms of complex phenotypes.

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

Genome-wide association study (GWAS) is widely utilized to identify genes involved in human complex disease or some other trait. One key challenge for GWAS data interpretation is to identify causal SNPs and provide profound evidence on how they affect the trait. Currently, researches are focusing on identification of candidate causal variants from the most significant SNPs of GWAS, while there is lack of support on biological mechanisms as represented by pathways. Although pathway-based analysis (PBA) has been designed to identify disease-related pathways by analyzing the full list of SNPs from GWAS, it does not emphasize on interpreting causal SNPs. To our knowledge, so far there is no web server available to solve the challenge for GWAS data interpretation within one analytical framework. ICSNPathway is developed to identify candidate causal SNPs and their corresponding candidate causal pathways from GWAS by integrating linkage disequilibrium (LD) analysis, functional SNP annotation and PBA. ICSNPathway provides a feasible solution to bridge the gap between GWAS and disease mechanism study by generating hypothesis of SNP → gene → pathway(s). The ICSNPathway server is freely available at http://icsnpathway.psych.ac.cn/.

Alpha fetoprotein is a novel protein-binding partner for caspase-3 and blocks the apoptotic signaling pathway in human hepatoma cells

Although there is increasing evidence that alpha fetoprotein (AFP) may function as regulatory factor in the growth of tumor cells, the precise mechanism is still unclear. In the current study, we investigated the role of the cytoplasmic AFP in caspase‐3‐mediated signaling of apoptosis. Our results showed that low doses of TNF‐related apoptosis‐inducing ligand (TRAIL) elevated the activity of caspase‐8, but not caspase‐3. Caspase‐3 colocalized and interacted with AFP in the cytoplasm of Bel 7402 cells, and translocated into nuclei in association with the occurrence of apoptosis while cells were under cotreatment with all‐trans retinoic acid (ATRA) or TRAIL. AFP was able to form complexes with caspase‐3 and block onward transmission of signaling from caspase‐8. Knockdown of AFP increased the sensitivity of Bel 7402 cells to TRAIL, and thereby, triggered caspase‐3 signaling. No intermolecule interaction occurred between AFP and caspase‐8, nor was caspase‐8 activity altered after AFP knockdown, demonstrating the selectivity of AFP in interfering with the apoptotic signaling pathway. The effect of AFP on caspase‐3 was further confirmed by transfection of the AFP gene into HLE cells (AFP negative). We conclude that ATRA or TRAIL resistance in AFP producing hepatoma is at least, in part, attributable to the high level of the cytoplasmic AFP. Therefore, it is possible that the combination of AFP gene silencing together with ATRA/TRAIL cotreatment will benefit the enhancement of the chemotherapeutic efficiency of these agents on tumors.

Cytoplasmic alpha-fetoprotein functions as a co-repressor in RA-RAR signaling to promote the growth of human hepatoma Bel 7402 cells

The role of AFP in the retinoic acid-RAR signaling pathway was investigated in human hepatoma Bel 7402 cells. The results showed that AFP and RAR-beta were co-localized and interacted in cytoplasm. AFP may inhibit translocation of RAR-beta into the nucleus via competitive binding to RAR-beta with ATRA, which was reversed by AFP-siRNA transfection. Our data suggest that the ATRA resistance of Bel 7402 cells is at least in part attributable to their high level of cytoplasmic AFP. Thus, by counteracting the effect of AFP, it may be possible to increase the sensitivity of tumor cells to ATRA.

The role of transcription factors Sp1 and YY1 in proximal promoter region in initiation of transcription of the mu opioid receptor gene in human lymphocytes.

Although previous studies have shown that the mechanism of the lymphocyte mu opioid receptor (MOR) gene expression was distinctly different from that in the central nervous system, and is involved in several disparate aspects of the immune response, its precise molecular mechanism is still undefined. In this study, we analyzed the proximal promoter region of the MOR gene in lymphocytes to identify the influences of potential trans‐acting factors in activating the initiation of the expression of the MOR gene in lymphocytes. The electrophoretic mobility shift assay showed that two transcription factors, Sp1 and YY1, were able to bind the promoter region. Using sequence overlapping probes and mutation assays, we determined that the CCC sequence of Sp1 and the GGC sequence of YY1 binding elements were core sequences, and replacement of these sequences lead to substantial loss of promoter activity. Stimulation with morphine was capable of up‐regulating the intracellular level of Sp1 and YY1 proteins. Chromatin immunoprecipitation assays showed that the blockage of naloxone is achieved through down‐regulation of transcription factor YY1. Furthermore, coimmunoprecipitation and transfection assays confirmed that the functional interaction of Sp1 and YY1 transcription factors was a crucial step in the initiation of expression of the MOR in lymphocytes. Thus, we conclude that the cooperative interaction of Sp1 and YY1 transcription factors is the critical event triggering the initiation of transcription of the MOR gene in lymphocytes, and this finding will be helpful to understand the pharmacological effect of morphine on lymphocytes. J. Cell. Biochem. 104: 237–250, 2008.

Mechanisms involved in phosphatidylinositol 3-kinase pathway mediated up-regulation of the mu opioid receptor in lymphocytes.

Despite the substantial progress made in understanding initiation expression of the MOR gene in lymphocytes, the signal pathway associated with MOR gene transcription remains to be better defined. As the phosphatidylinositol 3-kinase (PI3K)/AKT pathway can mediate diverse biological responses and is crucial for optimal immune responses and lymphocyte development, this study was undertaken to delineate the role of PI3K/AKT signaling in expression of the MOR gene in CEM x174 cells. The data show that morphine treatment enhanced the level of phosphorylated, rather than un-phosphorylated, PI3K and AKT, which were synchronously recruited to membrane. The levels of PTEN and p53 which are negative regulators of these signal molecules were reduced, and as a result, the interaction between PTEN and p53 was completely interrupted. With morphine treatment, the levels of both cytoplasmic and nuclear E2F1 which is the downstream effecter of AKT were elevated and the interaction of E2F1 with YY1, rather than Sp1, was also increased. Subsequently, E2F1 triggered the transcription of the MOR gene through its enhanced ability to bind the element in promoter region of the MOR gene. All responses to morphine were abolished by naloxone, which is an antagonist of MOR, or by LY294002, an inhibitor of PI3K, implying specific involvement of PI3K/AKT. These results strongly suggest that the PI3K/AKT pathway plays a critical role in the transfer of signal from morphine stimuli to the machinery by which MOR gene transcription is initiated.

rVarBase: an updated database for regulatory features of human variants

We present here the rVarBase database (http://rv.psych.ac.cn), an updated version of the rSNPBase database, to provide reliable and detailed regulatory annotations for known and novel human variants. This update expands the database to include additional types of human variants, such as copy number variations (CNVs) and novel variants, and include additional types of regulatory features. Now rVarBase annotates variants in three dimensions: chromatin states of the surrounding regions, overlapped regulatory elements and variants’ potential target genes. Two new types of regulatory elements (lncRNAs and miRNA target sites) have been introduced to provide additional annotation. Detailed information about variants’ overlapping transcription factor binding sites (TFBSs) (often less than 15 bp) within experimentally supported TF-binding regions (∼150 bp) is provided, along with the binding motifs of matched TF families. Additional types of extended variants and variant-associated phenotypes were also added. In addition to the enrichment in data content, an element-centric search module was added, and the web interface was refined. In summary, rVarBase hosts more types of human variants and includes more types of up-to-date regulatory information to facilitate in-depth functional research and to provide practical clues for experimental design.

The mechanism involved in the repression of the μ opioid receptor gene expression in CEM ×174 cells infected by simian immunodeficiency virus

Morphine can promote the pathogenesis of human acquired immunodeficiency syndrome through binding to the μ opioid receptor (MOR) in immune cells. Previous investigation has suggested that expression of the MOR gene in lymphocytes is triggered by cooperative interaction between transcription factors, specificity protein 1 (Sp1) and Ying Yang 1 (YY1), in the promoter region. However, the specific molecular mechanism by which immunodeficiency virus infection impacts regulation of the MOR gene expression in lymphocytes is still unclear. In this study, it was demonstrated that SIV (SIVmac239) infection may result in gradual reduction of the MOR gene expression and Sp1 during a period of 48 h postinfection by analysis of quantitative real‐time RT‐PCR and Western blotting. The results of methylation‐specific PCR showed that two of 14 CpG islands adjacent to the Sp1 and YY1 elements in the promoter region were methylated, which together with reduced Sp1, contributed to the failure of interaction of Sp1 with YY1 and their binding to the elements, as determined by coimmunoprecipitation, chromatin immunoprecipitation‐real‐time PCR, and EMSAs. The repression of the MOR gene secondary to SIVmac239 infection could be abolished by the demethylating agent 5‐aza‐2′‐deoxycytidine. Transfection with Sp1‐expressing vector (PN3‐Sp1) was also able to enhance the activity of the promoter in SIVmac239‐infected cells. We therefore concluded that aberrant methylation of the promoter and reduction of Sp1 resulting from SIVmac239 infection led to the silencing of the MOR gene. This finding will be helpful in understanding the synergistic mechanism of HIV infection and morphine addiction in the pathogenesis of AIDS.

I -GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study

The standard data analysis of genome-wide association study (GWAS) is based on single SNP (single nucleotide polymorphism), thus it ignores combined effect of modest SNPs/genes. To solve this problem, pathway-based analysis (PBA) has been introduced to GWAS data analysis. PBA aims to identify biological functions and mechanisms associated with complex trait (Wang et al., 2007; Wang et al., 2010). By now it has been one of the key ways to interpret GWAS data (Wang et al., 2010). The results of PBA are trait-associated pathways, which represent combined effect of modest genes. Further validation study needs to explore candidate causative SNPs from the PBA-identified pathways, by annotating the SNPs of the genes involved in pathways based on genomic features including protein coding features and non-coding features. For coding features, the SNPs impacting protein functions (such as deleterious non-synonymous sites) have been widely investigated, and the information has been well collected in some databases like Ensembl (Flicek et al., 2014). Meanwhile, to assign the biochemical function of the noncoding part of human genome (particular functional elements for gene expression regulation), the Encyclopedia of DNA Elements (ENCODE) project (Bernstein et al., 2012) has identified plenty of regulatory regions, like DNase I hypersensitive sites (DHSs) and transcription factor binding sites (TFBSs) in human genome. Particularly, the result of ENCODE indicates that most of the SNPs identified by GWASs are enriched within non-coding functional elements, with a majority residing in or near ENCODE-defined regions, including DHSs and TFBSs across several cell types (Bernstein et al., 2012). By now there have been several tools, such as GenomeRunner (Dozmorov et al., 2012) and GREAT (McLean et al., 2010), which can annotate and analyze the non-coding genomic features for input genomic regions. However, these tools are general tools and not specific for trait-associated pathways identified from GWAS. Furthermore, coding region annotation and linkage disequilibrium (LD), which is the basic concept of GWAS, need to be considered. On the other hand, except for genomic features, expression quantitative trait loci (eQTLs) analysis is widely utilized to interpret biological mechanisms of GWAS-identified variants (Cookson et al., 2009). Taken together, a PBA tool combined with solutions for functional analysis (considering all above issues) of SNPs in PBA-identified pathways associated with trait will provide an objective and comprehensive way to interpret GWAS data. In our previous work, we have developed a PBA web server, i-GSEA4GWAS (improved gene set enrichment analysis for GWAS), which detects pathways associated with traits by applying an improved gene set enrichment analysis (i-GSEA) (Zhang et al., 2010). Here, we report a new version, i-GSEA4GWAS v2, which is featured by implementing both i-GSEA and follow-up functional analysis for SNPs in trait-associated pathways identified by i-GSEA as well as their linkage disequilibrium (LD) proxies. The functional analysis of i-GSEA4GWAS v2 is based on putative functional SNP annotation data from Ensembl, regulatory regions from ENCODE and eQTLs data. Both annotation analysis and enrichment analysis were conducted for each type of functional elements. Data sources used for functional analysis were shown in Tables S1–3. Details about the annotation and enrichment analysis methods are in Materials and Methods section in Supplementary Materials. Fig. 1 shows the analytical framework of i-GSEA4GWAS v2. I-GSEA4GWAS v2 is freely available at http://gsea4gwasv2.psych.ac.cn/. It supports all major browsers. The main options of it are in Table 1. There is no any restriction to use it by academics and non-academics. It is written in Java and JSP and distributed using Apache and Tomcat web servers. I-GSEA4GWAS v2 was run in an upgraded web server (DELL R910 with 256G memory, 40 core CPUs and almost 10T storage) than i-GSEA4GWAS to improve the computing speed and work load. It is platform independent and easy to use by genetic and biological researchers; web browser is the only requirement to use it. We applied i-GSEA4GWAS v2 to analyze 312,565 SNP P-values of a schizophrenia GWAS with 871 schizophrenia cases and 863 healthy controls (all of European origin) at