The Immunomodulatory Activity of Meningococcal Lipoprotein Ag473 Depends on the Conformation Made up of the Lipid and Protein Moieties

We have previously demonstrated that the meningococcal antigen Ag473 in the presence of Freund's adjuvant can elicit protective immune responses in mouse challenge model. In this study, we evaluated the structural requirement for the immunological activity and the possible signaling pathway of recombinant Ag473 antigen produced in E. coli. We found that lipidated Ag473 (L-Ag473) possesses an intrinsic adjuvant activity that could be attributed to its ability to activate dendritic cells and promote their maturation. In addition, we found that L-Ag473 can activate human monocytes and promote maturation of human monocyte-derived dendritic cells. These results provide an indirect support that L-Ag473 may also be immunogenic in human. Interestingly, the observed activity is dependent on the overall conformation of L-Ag473 because heating and proteinase K treatment can diminish and abolish the activity. Furthermore, our data suggest a species-differential TLR recognition of L-Ag473. Overall, these data suggest a new paradigm for the ligand-TLR interaction in addition to demonstrating the self-adjuvanting activity of the vaccine candidate L-Ag473.     

miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis

Glioblastoma (GBM) and other malignant gliomas are aggressive primary neoplasms of the brain that exhibit notable refractivity to standard treatment regimens. Recent large-scale molecular profiling has revealed distinct disease subclasses within malignant gliomas whose defining genomic features highlight dysregulated molecular networks as potential targets for therapeutic development. The "proneural" designation represents the largest and most heterogeneous of these subclasses, and includes both a large fraction of GBMs along with most of their lower-grade astrocytic and oligodendroglial counterparts. The pathogenesis of proneural gliomas has been repeatedly associated with dysregulated PDGF signaling. Nevertheless, genomic amplification or activating mutations involving the PDGF receptor (PDGFRA) characterize only a subset of proneural GBMs, while the mechanisms driving dysregulated PDGF signaling and downstream oncogenic networks in remaining tumors are unclear. MicroRNAs (miRNAs) are a class of small, noncoding RNAs that regulate gene expression by binding loosely complimentary sequences in target mRNAs. The role of miRNA biology in numerous cancer variants is well established. In an analysis of miRNA involvement in the phenotypic expression and regulation of oncogenic PDGF signaling, we found that miR-34a is downregulated by PDGF pathway activation in vitro. Similarly, analysis of data from the Cancer Genome Atlas (TCGA) revealed that miR-34a expression is significantly lower in proneural gliomas compared to other tumor subtypes. Using primary GBM cells maintained under neurosphere conditions, we then demonstrated that miR-34a specifically affects growth of proneural glioma cells in vitro and in vivo. Further bioinformatic analysis identified PDGFRA as a direct target of miR-34a and this interaction was experimentally validated. Finally, we found that PDGF-driven miR-34a repression is unlikely to operate solely through a p53-dependent mechanism. Taken together, our data support the existence of reciprocal negative feedback regulation involving miR-34 and PDGFRA expression in proneural gliomas and, as such, identify a subtype specific therapeutic potential for miR-34a.     

Multi-omic analyses of hepatocellular carcinoma to determine immunological characteristics and key nodes in gene-expression network

Hepatocellular carcinoma (HCC) is a common malignant tumor worldwide, but effective immunotherapy is still limited for those affected. Therefore, there is an urgent need to explore the specific mechanisms governing tumor immunity to improve the survival rate for those diagnosed with HCC. In the present study, we performed a new immune stratification of HCC samples into two subclasses (A and B) from The Cancer Genome Atlas and the International Cancer Genome Consortium databases, and comprehensive multi-omic analyses of major histocompatibility complex genes, gene copy-number variations, somatic mutations, DNA methylation, and non-coding RNAs. Subclass A was found to have a higher survival rate compared with subclass B, and there were significant immunological differences between the two clusters. Based on these differences, we identified DRD1 and MYCN as key hub genes in the immune-phenotype gene expression regulatory network. These results provide novel ideas and evidence for HCC regulatory mechanisms that may improve immunotherapy for this cancer.     

Genetic variation in ABCB5 associates with risk of hepatocellular carcinoma

Expression of ATP‐binding cassette B5 (ABCB5) has been demonstrated to confer chemoresistance, enhance cancer stem cell properties and associate with poor prognosis in hepatocellular carcinoma (HCC). The aim of this study was to evaluate the genetic variations of ABCB5 in HCC patients with reference to healthy individuals and the clinicopathological significance. A pilot study has examined 20 out of 300 pairs HCC and paralleled blood samples using conventional sequencing method to cover all exons and exon/intron regions to investigate whether there will be novel variant sequence and mutation event. A total of 300 HCC and 300 healthy blood DNA samples were then examined by Sequenom MassARRAY genotyping and pyrosequencing for 38 SNP and 1 INDEL in ABCB5. Five novel SNPs were identified in ABCB5. Comparison of DNA from blood samples of HCC and healthy demonstrated that ABCB5 SNPs rs75494098, rs4721940 and rs10254317 were associated with HCC risk. Specific ABCB5 variants were associated with aggressive HCC features. SNP rs17143212 was significantly associated with ABCB5 expression level. Nonetheless, the paralleled blood and tumour DNA sequences from HCC patients indicated that ABCB5 mutation in tumours was not common and corroborated the TCGA data sets. In conclusion, ABCB5 genetic variants had significant association with HCC risk and aggressive tumour properties.     

Integrative subtype discovery in glioblastoma using iCluster

Large-scale cancer genome projects, such as the Cancer Genome Atlas (TCGA) project, are comprehensive molecular characterization efforts to accelerate our understanding of cancer biology and the discovery of new therapeutic targets. The accumulating wealth of multidimensional data provides a new paradigm for important research problems including cancer subtype discovery. The current standard approach relies on separate clustering analyses followed by manual integration. Results can be highly data type dependent, restricting the ability to discover new insights from multidimensional data. In this study, we present an integrative subtype analysis of the TCGA glioblastoma (GBM) data set. Our analysis revealed new insights through integrated subtype characterization. We found three distinct integrated tumor subtypes. Subtype 1 lacks the classical GBM events of chr 7 gain and chr 10 loss. This subclass is enriched for the G-CIMP phenotype and shows hypermethylation of genes involved in brain development and neuronal differentiation. The tumors in this subclass display a Proneural expression profile. Subtype 2 is characterized by a near complete association with EGFR amplification, overrepresentation of promoter methylation of homeobox and G-protein signaling genes, and a Classical expression profile. Subtype 3 is characterized by NF1 and PTEN alterations and exhibits a Mesenchymal-like expression profile. The data analysis workflow we propose provides a unified and computationally scalable framework to harness the full potential of large-scale integrated cancer genomic data for integrative subtype discovery.     

多基因模型在肝细胞癌预后中的应用

利用较少分子信息预测肝细胞癌类型对患者的个性化治疗十分关键。探索已知的与肝细胞癌预后相关的信号通路,共发现41个关键基因。随后,运用机器学习的方法对其构建风险预测模型,并在4个肝细胞癌数据集上进行验证。结果显示,该模型能将肝细胞癌患者分成两个预后差异显著的类型:癌症基因图谱(The cancer genome atlas,TCGA)数据集交叉验证的平均log rank P值为0.03;其他测试数据集的log rank P 值分别为0.000 38、0.002 1和0.01。生物信息学分析显示肝细胞癌的预后与细胞周期等信号通路显著相关,并筛选出12个潜在的肝细胞癌分子标志物。研究结果表明,基于41个基因构建的肝细胞癌预后模型具有较好的稳健性和准确的风险预测能力。     

Identification of core genes and outcomes in hepatocellular carcinoma by bioinformatics analysis

Hepatocellular carcinoma (HCC) is the most common malignant liver disease in the world. However, the mechanistic relationships among various genes and signaling pathways are still largely unclear. In this study, we aimed to elucidate potential core candidate genes and pathways in HCC. The expression profiles GSE14520, GSE25097, GSE29721, and GSE62232, which cover 606 tumor and 550 nontumour samples, were downloaded from the Gene Expression Omnibus (GEO) database. Furthermore, HCC RNA-seq datasets were also downloaded from the Cancer Genome Atlas (TCGA) database. The differentially expressed genes (DEGs) were filtered using R software, and we performed gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using the online databases DAVID 6.8 and KOBAS 3.0. Furthermore, the protein-protein interaction (PPI) network complex of these DEGs was constructed by Cytoscape software, the molecular complex detection (MCODE) plug-in and the online database STRING. First, a total of 173 DEGs (41 upregulated and 132 downregulated) were identified that were aberrantly expressed in both the GEO and TCGA datasets. Second, GO analysis revealed that most of the DEGs were significantly enriched in extracellular exosomes, cytosol, extracellular region, and extracellular space. Signaling pathway analysis indicated that the DEGs had common pathways in metabolism-related pathways, cell cycle, and biological oxidations. Third, 146 nodes were identified from the DEG PPI network complex, and two important modules with a high degree were detected using the MCODE plug-in. In addition, 10 core genes were identified, TOP2A, NDC80, FOXM1, HMMR, KNTC1, PTTG1, FEN1, RFC4, SMC4, and PRC1. Finally, Kaplan-Meier analysis of overall survival and correlation analysis were applied to these genes. The abovementioned findings indicate that the identified core genes and pathways in this bioinformatics analysis could significantly enrich our understanding of the development and recurrence of HCC; furthermore, these candidate genes and pathways could be therapeutic targets for HCC treatment.     

Human antibodies to group A streptococcal carbohydrate. Ontogeny, subclass restriction, and clonal diversity

To investigate immuno-incompetence to polysaccharide Ag in young children, antibodies to the polysaccharide and protein Ag of Streptococcus pyogenes were studied. S. pyogenes was chosen because it commonly causes natural infections and has well-characterized polysaccharide and protein Ag. In children over the age of 2 yr it was found that the maturation of antibody responses to the polysaccharide Ag of S. pyogenes (A-CHO) appeared to occur in parallel with, or even earlier, than the responses to streptococcal protein Ag. When antibodies to group A carbohydrate (A-CHO) were studied in detail, qualitative differences between the antibodies of children and adults were demonstrated. Although anti-A-CHO antibodies of adults were strikingly restricted to the IgG2 subclass, those of children were found in both the IgG1 and IgG2 subclasses. In addition, the clonal diversity of IgG antibodies to A-CHO increased with age, and additional clonotypes were detectable in convalescent sera of some subjects of all ages after infection. Two cases with major additional clonotypes after group A streptococcal infection were studied in detail. In these two cases the additional clonotypes belonged to a different IgG subclass than the previously dominant clonotypes, and the expression of the additional major clonotypes occurred in both IgG1 and IgG2 subclasses.     

TL1A mediates fibroblast-like synoviocytes migration and Indian Hedgehog signaling pathway via TNFR2 in patients with rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joints inflammation. One of the aggressive characteristics of RA fibroblast-like synoviocytes (FLS) is the tendency for migration in the local environment, which plays a central role in the RA pathogenesis. Tumor Necrosis Factor (TNF)-like cytokine 1A (TL1A) is a member of TNF superfamily, which has a role in autoimmunity and influences the RA-FLS behavior through TNF receptor 2 (TNFR2).We investigated the effect of TNF-like cytokine 1A (TL1A) on RA-FLS migration using patients’ samples. Specifically, we examined the hedgehog signaling pathway which is a key regulator in chondrocyte growth and differentiation. We found that TL1A increased significantly the hedgehog homologue Indian hedgehog (IHH) and its receptor Patched 1, 2 (PTCH 1, 2) in RA-FLS. In addition, TL1A-stimulated RA-FLS promoted significantly IHH protein expression. However, both mRNA and protein levels decreased substantially after blocking TL1A with TNFR2 antagonist. The migratory property of RA-FLS was enhanced after stimulation of RA-FLS with TL1A, but was compromised following TL1A blockage. In conclusion, our study has revealed that TL1A modulated RA-FLS migration and Indian hedgehog signaling pathway using TNFR2.     

Ether phospholipid molecular species in human platelets

Molecular species of diacyl, alkenylacyl, and alkylacyl subclasses in human platelet phospholipids were quantitatively analyzed. Dinitrobenzoyldiradylglycerol derivatives prepared from phosphatidylcholine and phosphatidylethanolamine were separated into subclasses by TLC or normal-phase HPLC. Each subclass consisting of more than 20 molecular species was quantified by reverse-phase HPLC with the eluting solvent of acetonitrile-2-propanol (80 : 20). The retention times of molecular species in the alkenylacyl and alkylacyl subclasses were approximately 1.24 and 1.56 times as long as that of the diacyl type. Phosphatidylcholine contained mostly diacyl subclass (94.5%) and small amounts of alkenylacyl (0.8%) and alkylacyl (4.7%) subclasses, while phosphatidylethanolamine was comprised of 44.2% diacyl, 54.4% alkenylacyl, and 1.4% alkylacyl subclasses. The diacyl subclass of phosphatidylcholine mainly consisted of monoenoic and dienoic molecular species, whereas the other subclasses of phosphatidylcholine and all subclasses of phosphatidylethanolamine were mostly comprised of polyenoic molecular species. The distribution of arachidonic acid-containing molecular species in the diacyl, alkenylacyl, and alkylacyl subclasses were 18.7, 48.2, and 47.9%, respectively, in phosphatidylcholine, and 60.1, 63.0, and 46.9% in phosphatidylethanolamine. Hence, the alkylacyl and alkenylacyl subclasses of phosphatidylcholine seem to play physiological roles different from the diacyl subclass in human platelets.     

Identification and Validation of a Prognostic Model Based on Three MVI-Related Genes in Hepatocellular Carcinoma

MVI has significant clinical value for treatment selection and prognosis evaluation in hepatocellular carcinoma (HCC). We aimed to construct a model based on MVI-Related Genes (MVIRGs) for risk assessment and prognosis prediction in patients with HCC. This study utilized various statistical analysis methods for prognostic model construction and validation in the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) cohorts, respectively. In addition, immunohistochemistry and qRT-PCR were used to analyze and identify the value of the model in our cohort. After the analyses, 153 differentially expressed MVIRGs were identified, and three key genes were selected to construct a prognostic model. The high-risk group showed significantly lower overall survival (OS), and this trend was observed in all subgroups: different age groups, genders, stages, and grades. Risk score was a risk factor independent of age, gender, stage, and grade. Moreover, the ICGC cohort validated the prognostic value of the model corresponding to the TCGA. In our cohort, qRT-PCR and immunohistochemistry showed that all three genes had higher expression levels in HCC samples than in normal controls. High expression levels of genes and high-risk scores showed significantly lower recurrence-free survival (RFS) and OS, especially in MVI-positive HCC samples. Therefore, the prognostic model constructed by three MVIRGs can reliably predict the RFS and OS of patients with HCC and is valuable for guiding clinical treatment selection and prognostic assessment of HCC.