Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection

Background

Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. However, the precise mechanism of H5N1 infection eliciting the unique host response are still not well understood.

Methods

To obtain a better understanding of the molecular events at the earliest time points, we used RNA-Seq to quantify and compare the host mRNA and miRNA transcriptomes induced by the highly pathogenic influenza A H5N1 (A/Vietnam/3212/04) or low virulent H1N1 (A/Hong Kong/54/98) viruses in human monocyte-derived macrophages at 1-, 3-, and 6-h post infection.

Results

Our data reveals that two macrophage populations corresponding to M1 (classically activated) and M2 (alternatively activated) macrophage subtypes respond distinctly to H5N1 virus infection when compared to H1N1 virus or mock infection, a distinction that could not be made from previous microarray studies. When this confounding variable is considered in our statistical model, a clear set of dysregulated genes and pathways emerges specifically in H5N1 virus-infected macrophages at 6-h post infection, whilst was not found with H1N1 virus infection. Furthermore, altered expression of genes in these pathways, which have been previously implicated in viral host response, occurs specifically in the M1 subtype. We observe a significant up-regulation of genes in the RIG-I-like receptor signaling pathway. In particular, interferons, and interferon-stimulated genes are broadly affected. The negative regulators of interferon signaling, the suppressors of cytokine signaling, SOCS-1 and SOCS-3, were found to be markedly up-regulated in the initial round of H5N1 virus replication. Elevated levels of these suppressors could lead to the eventual suppression of cellular antiviral genes, contributing to pathophysiology of H5N1 virus infection.

Conclusions

Our study provides important mechanistic insights into the understanding of H5N1 viral pathogenesis and the multi-faceted host immune responses. The dysregulated genes could be potential candidates as therapeutic targets for treating H5N1 disease.

Electronic supplementary material

The online version of this article (10.1186/s12920-018-0335-0) contains supplementary material, which is available to authorized users.

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and group 4 subgroup medulloblastomas account for most paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1 or GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate 'enhancer hijacking' as an efficient mechanism driving oncogene activation in a childhood cancer.

Abstract 1428: A CpG island methylator phenotype defines a clinically aggressive subgroup of posterior fossa ependymoma

Ependymoma is the third most common pediatric brain tumor and remains incurable in 45% of patients. It arises in the spinal cord, supratentorial brain, and most commonly in children, the posterior fossa (PF). We recently reported the identification of two molecularly and clinically distinct subgroups of PF ependymoma, which we named Group A and B. While patients with Group B tumors harbor a large number of gross chromosomal gains and losses (approx. 17 arm events per tumor) and have favorable prognoses (5 year PFS = 92%), patients with Group A tumors have balanced genomic profiles (approx. 1 arm event per tumor) with poor clinical outcomes (5 year PFS = 24%). We hypothesized that aberrant DNA methylation could be a mechanism driving the tumorigenesis of Group A PF ependymoma. To this end, we isolated methylated DNA in 92 ependymomas by Methyl Binding Domain 2 protein assisted recovery, and hybridized enriched DNA to promoter tiling arrays (Nimblegen). Using unsupervised hierarchical clustering we determined that the DNA methylation profiles of ependymoma were regionally specified, dividing tumors into subgroups according to their anatomical origin. Using both gene expression and DNA methylation platforms, we identified a subset of PF ependymoma, which clustered with spinal tumors, supporting the vast molecular differences between Group A and B PF ependymoma. We next compared the number of methylated genes identified in Group A versus B, and observed that Group A tumors exhibited a greater number of methylated genes at specific CpG islands, a feature described as a CpG island methylator phenotype (CIMP) in glioma, colon cancer, and breast cancer. We validated these findings in a non-overlapping cohort of 48 PF ependymomas, analyzed using a different array technology (Illumina Infinium 450K). Using various unsupervised clustering methods (HCL, K-MEANS, NMF, and SOM), we verified that Group A and B exhibited highly distinct DNA methylation profiles. Further, we confirmed that Group A tumours were defined by a greater overall number of methylated genes (A: 855, B: 233; Wilcoxon-Rank Sum Test), and a greater number of methylated genes per tumour (A: 511, B: 425; Wilcoxon-Rank Sum Test). We performed Gene Set Enrichment analysis and observed that many genes methylated in Group A exhibited a significant overlap with genes marked by the polycomb repressor (PRC2) complex in embryonic stem cells (p<0.0001, FDR<0.1%), a phenomenon seen in other cancer CIMPs. We propose two diverse mechanisms leading to tumourigenesis in Group A and B ependymoma. The greater number of chromosomal alterations in Group B suggests a Chromosomal Instability (CIN) phenotype, while the greater number of methylated CpG islands in Group A suggests a CpG island Methylator (CIMP) phenotype. Understanding these underlying mechanisms driving Group A and B pathogenesis may yield new leads for subgroup-specific treatments of PF ependymoma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1428. doi:1538-7445.AM2012-1428

Treating asthma means treating airway smooth muscle cells

Asthma is characterised by airway hyperresponsiveness, airway inflammation and airway remodelling. Airway smooth muscle cells are known to be the main effector cells of airway narrowing. In the present paper, studies will be discussed that have led to a novel view of the role of airway smooth muscle in the pathogenesis of asthma in which airway hyperresponsiveness, remodelling and inflammation are, at least in part, attributable to airway smooth muscle. Furthermore, how this new view may lead to a change in the phenotyping and treatment of patients with asthma will be discussed.

Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines

We describe the details of a serial analysis of gene expression (SAGE) library construction and analysis platform that has enabled the generation of >298 high-quality SAGE libraries and >30 million SAGE tags primarily from sub-microgram amounts of total RNA purified from samples acquired by microdissection. Several RNA isolation methods were used to handle the diversity of samples processed, and various measures were applied to minimize ditag PCR carryover contamination. Modifications in the SAGE protocol resulted in improved cloning and DNA sequencing efficiencies. Bioinformatic measures to automatically assess DNA sequencing results were implemented to analyze the integrity of ditag structure, linker or cross-species ditag contamination, and yield of high-quality tags per sequence read. Our analysis of singleton tag errors resulted in a method for correcting such errors to statistically determine tag accuracy. From the libraries generated, we produced an essentially complete mapping of reliable 21-base-pair tags to the mouse reference genome sequence for a meta-library of approximately 5 million tags. Our analyses led us to reject the commonly held notion that duplicate ditags are artifacts. Rather than the usual practice of discarding such tags, we conclude that they should be retained to avoid introducing bias into the results and thereby maintain the quantitative nature of the data, which is a major theoretical advantage of SAGE as a tool for global transcriptional profiling.

Cryptococcus neoformans gene expression during experimental cryptococcal meningitis

Cryptococcus neoformans, an encapsulated basidiomycete fungus of medical importance, is capable of crossing the blood-brain barrier and causing meningitis in both immunocompetent and immunocompromised individuals. To gain insight into the adaptation of the fungus to the host central nervous system (CNS), serial analysis of gene expression (SAGE) was used to characterize the gene expression profile of C. neoformans cells recovered from the CNS of infected rabbits. A SAGE library was constructed, and 49,048 tags were sequenced; 16,207 of these tags were found to represent unique sequences or tag families. Of the 304 most-abundant tags, 164 were assigned to a putative gene for subsequent functional grouping. The results (as determined according to the number of tags that identified genes encoding proteins required for these functions) indicated that the C. neoformans cells were actively engaged in protein synthesis, protein degradation, stress response, small-molecule transport, and signaling. In addition, a high level of energy requirement of the fungal cells was suggested by a large number of tags that matched putative genes for energy production. Taken together, these findings provide the first insight into the transcriptional adaptation of C. neoformans to the host environment and identify the set of fungal genes most highly expressed during cerebrospinal fluid infection.

Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans

The basidiomycete fungus Cryptococcus neoformans is an opportunistic pathogen of worldwide importance that causes meningitis, leading to death in immunocompromised individuals. Unlike many basidiomycete fungi, C. neoformans is thermotolerant, and its ability to grow at 37 degrees C is considered to be a virulence factor. We used serial analysis of gene expression (SAGE) to characterize the transcriptomes of C. neoformans strains that represent two varieties with different polysaccharide capsule serotypes. These include a serotype D strain of the C. neoformans variety neoformans and a serotype A strain of variety grubii. In this report, we describe the construction and characterization of SAGE libraries from each strain grown at 25 degrees C and 37 degrees C. The SAGE data reveal transcriptome differences between the two strains, even at this early stage of analysis, and identify sets of genes with higher transcript levels at 25 degrees C or 37 degrees C. Notably, growth at the lower temperature increased transcript levels for histone genes, indicating a general influence of temperature on chromatin structure. At 37 degrees C, we noted elevated transcript levels for several genes encoding heat shock proteins and translation machinery. Some of these genes may play a role in temperature-regulated phenotypes in C. neoformans, such as the adaptation of the fungus to growth in the host and the dimorphic transition between budding and filamentous growth. Overall, this work provides the most comprehensive gene expression data available for C. neoformans; this information will be a critical resource both for gene discovery and genome annotation in this pathogen.