MicroRNAs (miRNAs) are short, non-coding RNAs that target and silence protein coding genes through 3-UTR elements. Evidence increasingly assigns an immunosuppressive role for miRNAs in immunity, but relatively few miRNAs have been studied, and an overall understanding of the importance of these regulatory transcripts in complex in vivo systems is lacking.Here we have applied multiple technologies to globally analyze miRNA expression and function in allergic lung disease, an experimental model of asthma. Deep sequencing and microarray analyses of the mouse lung short RNAome revealed numerous extant and novel miRNAs and other transcript classes. Similar to mRNAs, lung miRNA expression changed dynamically during the transition from the naive to the allergic state, suggesting numerous functional relationships. A possible role for miRNA editing in altering the lung mRNA target repertoire was also identified. Multiple members of the highly conserved let-7 miRNA family were the most abundant lung miRNAs, and we confirmed in vitro that interleukin 13 (IL-13), a cytokine essential for expression for allergic lung disease, is regulated by mmulet-7a. However, inhibition of let-7 miRNAs in vivo using a locked nucleic acid profoundly inhibited production of allergic cytokines and the disease phenotype. Our findings thus reveal unexpected complexity in the miRNAome underlying allergic lung disease and demonstrate a proinflammatory role for let-7 miRNAs. MicroRNAs (miRNAs)3 are short regulatory RNAs with the potential to target and suppress multiple genes across diverse signaling pathways comprising biologically meaningful networks. Consequently, miRNAs that are inappropriately expressed in the context of specific diseases are of particular interest as therapeutic targets if they can be shown to coordinate such networks. Initially transcribed as relatively long primary transcripts, pri-miRNAs are subsequently modified by the nuclear RNAses Drosha and Pasha to yield precursor miRNAs (pre-miRNAs) that are further processed by the cytoplasmic RNase III Dicer to form short double-stranded miR-miR* duplexes, one strand of which (miR) is then integrated into the RNA-induced silencing complex that includes the enzymes Dicer and Argonaute (Ago). The mature miRNAs (ϳ17-24 nt) direct the RNA-induced silencing complex to specific target sites located within the 3Ј-UTR of target genes. Once bound to target sites, miRNAs repress translation through mRNA decay, translational inhibition, and/or sequestration into processing bodies (1-3).Recent estimates indicate that over 60% of protein-coding genes carry 3Ј-UTR miRNA target sites, suggesting a role for miRNAs in the control of gene expression in diverse processes (4). Indeed, miRNAs have now been firmly linked to the regulation of early development (5), cell proliferation, and cell death (6); apoptosis and fat metabolism (7); and cell differentiation (8). In addition, studies of miRNA expression in chronic lymphocytic leukemia (9), colonic adenocarcinoma (10), Burkitt lymphoma, and cardiac ...

The BCOR-CCNB3 fusion gene, resulting from a chromosome X paracentric inversion, was recently described in translocation-negative ‘Ewing-like’ sarcomas arising in bone and soft tissue. Genetic subclassification of undifferentiated unclassified sarcomas may potentially offer markers for reproducible diagnosis and substrates for therapy. Using whole transcriptome paired end RNA sequencing (RNA-seq) we unexpectedly identified BCOR-CCNB3 fusion transcripts in an undifferentiated spindle cell sarcoma. RNA-seq results were confirmed through direct RT-PCR of tumor RNA and cloning of the genomic breakpoints from tumor DNA. Five additional undifferentiated sarcomas with BCOR-CCNB3 fusions were identified in a series of 42 pediatric and adult unclassified sarcomas. Genomic breakpoint analysis demonstrated unique breakpoint locations in each case at the DNA level even though the resulting fusion mRNA was identical in all cases. All patients with BCOR-CCNB3 sarcoma were males diagnosed in mid-childhood (7-13 years of age). Tumors were equally distributed between axial and extra-axial locations. Five of the six tumors were soft tissue lesions with either predominant spindle cell morphology or spindle cell areas interspersed with ovoid to round cells. CCNB3 immunohistochemistry showed strong nuclear positivity in 5 tumors prior to oncologic therapy, but was patchy to negative in post-treatment tumor samples. An RT-PCR assay developed to detect the fusion transcript in archival formalin-fixed tissue was positive in all 6 cases, with high sensitivity and specificity in both pre- and post-treated samples. This study adds to recent reports on the clinicopathologic spectrum of BCOR-CCNB3 fusion-positive sarcomas, a newly-emerging entity within the undifferentiated unclassified sarcoma category, and describes a simple RT-PCR assay that in conjunction with CCNB3 immunohistochemistry can be useful in diagnosing these tumors.

Active fungal proteinases are powerful allergens that induce experimental allergic lung disease strongly resembling atopic asthma, but the precise relationship between proteinases and asthma remains unknown. Here, we analyzed dust collected from the homes of asthmatic children for the presence and sources of active proteinases to further explore the relationship between active proteinases, atopy, and asthma. Active proteinases were present in all houses and many were derived from fungi, especially Aspergillus niger. Proteinase-active dust extracts were alone insufficient to initiate asthma-like disease in mice, but conidia of A. niger readily established a contained airway mucosal infection, allergic lung disease, and atopy to an innocuous bystander antigen. Proteinase produced by A. niger enhanced fungal clearance from lung and was required for robust allergic disease. Interleukin 13 (IL-13) and IL-5 were required for optimal clearance of lung fungal infection and eosinophils showed potent anti-fungal activity in vitro. Thus, asthma and atopy may both represent a protective response against contained airway infection due to ubiquitous proteinase-producing fungi.

The innate immune response of airway epithelial cells to aeroallergen initiates the development of T cell responses that are central to allergic inflammation. Although proteinase allergens induce the expression of interleukin 25 we show that epithelial matrix metalloproteinase 7 (MMP7) was expressed in asthma and was required for maximal activity of IL-25 in promoting T helper type 2 cell differentiation. Allergen-challenged Mmp7−/− mice showed reduced airway hyperreactivity, allergic inflammatory cytokine production and increased expression of retinal dehydrogenase (RALDH)-1. Inhibition of RALDH-1 restored the asthma phenotype in Mmp7−/− mice and inhibited lung T regulatory cell responses while exogenous administration of retinoic acid attenuated the asthma phenotype. Thus, MMP7 coordinates allergic lung inflammation by activating IL-25 while simultaneously inhibiting retinoid-dependent T regulatory cell development.