Diagnostic and Therapeutic Value of Hsa_circ_0002594 for T Helper 2-Mediated Allergic Asthma.

INTRODUCTION: Circular RNAs (circRNAs) are an endogenous mircoRNA sponge that could act as potential biomarkers for the diagnosis and treatment of diseases. However, the role of circRNAs in asthma is far from clear. OBJECTIVE: The aim of this study is to assess the diagnostic and therapeutic value of hsa_circ_0002594 for T helper (Th) 2-mediated allergic asthma. METHODS: The expression profiles of hsa_circ_0002594 in CD4+ T cells were revealed by circRNA microarray. Hsa_circ_0002594 expression was confirmed via quantitative real-time PCR (qRT-PCR) in asthmatic patients and healthy subjects. Hsa_circ_0002594 levels were compared between subgroups. The clinical diagnostic abilities and therapeutic response of hsa_circ_0002594 were evaluated. The analyses utilized included a student's t test, nonparametric tests, Spearman's rank-order correlation, Fisher's exact test, and the generation of receiver operating characteristic (ROC) curves. RESULTS: Hsa_circ_0002594 was upregulated and positively correlated with fraction of exhaled nitric oxide while negatively correlated with methacholine dose producing a decrease of 20% from baseline in forced expiratory volume in the first second (PD20) in CD4+ T cells of asthma. Furthermore, hsa_circ_0002594 expression was higher in subgroups with a family history, skin pricking test (SPT)-positive, or Th2-high. The hsa_circ_0002594-high subgroup was more frequently associated with Th2-high biomarker profiles and positive SPT. Hsa_circ_0002594 was decreased after inhaled corticosteroids (ICS) treatment. ROC curve analyses of hsa_circ_0002594 showed high area under the curve values in the presence of ICS or not. CONCLUSIONS: Our data suggested that hsa_circ_0002594 was upregulated in CD4+ T cells and might have potential value in the diagnosis and treatment of Th2-mediated allergic asthma.

Hsa_circ_0005519 increases IL-13/IL-6 by regulating hsa-let-7a-5p in CD4+ T cells to affect asthma.

BACKGROUND: Circular RNAs (circRNAs) are a class of non-coding RNAs that could serve as novel biomarkers for the diagnosis and treatment of diseases. We hypothesized that circRNAs of CD4+ T cells are involved in asthma. OBJECTIVE: In this study, we investigated the circRNA expression profile and the possible mechanism by which hsa_circ_0005519 participates in asthma. METHODS: The expression profiles of circRNAs in CD4+ T cells were revealed by circRNA microarray. Hsa_circ_0005519 expression in CD4+ T cells was confirmed in asthmatic patients (n = 65) and healthy subjects (n = 30). Hsa-let-7a-5p, the target of hsa_circ_0005519, was predicted by online algorithms and verified by a dual-luciferase reporter assay. Correlation assays between the expression of hsa_circ_0005519 and hsa-let-7a-5p, the mRNA levels of interleukin (IL)-13 and IL-6 in CD4+ T cells, and the clinical characteristics of asthmatic patients were performed. The role of hsa_circ_0005519 in proinflammatory cytokine expression was investigated in CD4+ T cells from asthmatic patients in vitro. Hsa_circ_0005519 expression in PBMCs was determined in another cohort including 30 asthmatic patients and 24 controls. Correlation assays of hsa_circ_0005519 expressions between CD4+ T cells and PBMCs were performed. RESULTS: Hsa_circ_0005519 was up-regulated and negatively correlated with hsa-let-7a-5p expression in CD4+ T cells of asthmatic patients. Both the fraction of exhaled nitric oxide (FeNO) and the peripheral blood eosinophil ratio were positively correlated with hsa_circ_0005519 expression in CD4+ T cells. These outcomes were also different in asthmatic patients with low vs high hsa_circ_0005519 levels. Hsa_circ_0005519 expressions between CD4+ T cells and PBMCs were concordant in asthmatic patients. Mechanistically, hsa_circ_0005519 might bind to hsa-let-7a-5p and relieve suppression for IL-13/IL-6 in CD4+ T cells. CONCLUSIONS AND CLINICAL RELEVANCE: Our data suggest that hsa_circ_0005519 may induce IL-13 and IL-6 expression by regulating hsa-let-7a-5p in CD4+ T cells to affect asthma. And hsa_circ_0005519 may be a potential biomarker of asthma.

Targeted resequencing reveals genetic risks in patients with sporadic idiopathic pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a genetic heterogeneous disease with high mortality and poor prognosis. However, a large fraction of genetic cause remains unexplained, especially in sporadic IPF (∼80% IPF). By systemically reviewing related literature and potential pathogenic pathways, 92 potentially IPF-related genes were selected and sequenced in genomic DNAs from 253 sporadic IPF patients and 125 matched health controls using targeted massively parallel next-generation sequencing. The identified risk variants were confirmed by Sanger sequencing. We identified two pathogenic and 10 loss-of-function (LOF) candidate variants, accounting for 4.74% (12 out of 253) of all the IPF cases. In burden tests, rare missense variants in three genes (CSF3R, DSP, and LAMA3) were identified that have a statistically significant relationship with IPF. Four common SNPs (rs3737002, rs2296160, rs1800470, and rs35705950) were observed to be statistically associated with increased risk of IPF. In the cumulative risk model, high risk subjects had 3.47-fold (95%CI: 2.07-5.81, P = 2.34 × 10-6 ) risk of developing IPF compared with low risk subjects. We drafted a comprehensive map of genetic risks (including both rare and common candidate variants) in patients with IPF, which could provide insights to help in understanding mechanisms, providing genetic diagnosis, and predicting risk for IPF.

Aberrantly expressed lncRNAs identified by microarray analysis in CD4+T cells in asthmatic patients.

The aim of the study was to determine the expression profiles of message RNAs and long non-coding RNAs in CD4+T cells of asthmatic patients and to explore the clinical value and biological function. Expression profiles in CD4+T cells of asthmatic patients and healthy controls were analyzed by microarray. We found 2725 lncRNAs and 3167 mRNAs differentially expressed. The data were validated by quantitative real time polymerase chain reaction, with 3 up-regulated (ENST00000444682, ENST00000566098, ENST00000583179) and 1 down-regulated (ENST00000579468) lncRNAs found. Receiver operating characteristic curve analysis showed the area under the curve was 0.7058, 0.9026, 0.8361, 0.8316, respectively. Spearman correlation analysis showed that ENST00000566098 was positively related with IL-13 and ENST00000579468 was positively related with peak expiratory flow. Bioinformatics analyses were performed to explore the function of lncRNAs. Specific lncRNAs aberrantly expressed in CD4+T cells may take part in the development of asthma and may be used as biomarkers for diagnosis.

Circular RNA hsa_circ_0000326 acts as a miR-338-3p sponge to facilitate lung adenocarcinoma progression.

BACKGROUND: Circular RNAs (circRNAs) are a novel class of noncoding RNAs that regulate gene expression at the transcriptional or posttranscriptional level. According to recent studies, circRNAs are involved in the pathogenesis of cancer, but the roles of circRNAs in lung adenocarcinoma are largely unknown. METHODS: In this study, we identified a novel upregulated circRNA, hsa_circ_0000326, in human lung adenocarcinoma tissues using microarray analysis and qRT-PCR. We then explored the biological role of hsa_circ_0000326 using gain- and loss-of-function assays in adenocarcinoma cells. Bioinformatics databases were used to screen for potential target miRNAs and the luciferase reporter assays and RNA-FISH further validated the interaction. Downstream protein was detected by western blot. Finally, we established xenografts in nude mice to assess the function of hsa_circ_0000326 in vivo. RESULTS: We found that high expression of hsa_circ_0000326 was correlated with tumor size, regional lymph node status and differentiation in human lung adenocarcinoma. Additionally, we conducted gain- and loss-of-function assays and found that hsa_circ_0000326 acted as a positive regulator of cell proliferation and migration and a negative regulator of apoptosis. Mechanistic studies showed that hsa_circ_0000326 acted as a miR-338-3p sponge and altered the function of miR-338-3p, which in turn upregulated the expression of the downstream target RAB14 and affected the proliferation, migration and apoptosis of lung adenocarcinoma cells. CONCLUSIONS: Collectively, our study results reveal crucial roles for hsa_circ_0000326 in the proliferation, migration and apoptosis of lung adenocarcinoma cells and suggest that hsa_circ_0000326 may represent a potential therapeutic target in patients with lung adenocarcinoma.

LncRNAs NR-026690 and ENST00000447867 are upregulated in CD4+ T cells in patients with acute exacerbation of COPD.

Objective: The aim of the study was to determine the expression profile of long noncoding RNAs (lncRNAs) in CD4+ T cells from COPD patients and explore the clinical value of the lncRNAs. Methods: First, microarray analysis was performed. Differentially expressed lncRNAs were validated by quantitative real-time reverse transcription-PCR (qRT-PCR) in samples from 56 patients with acute exacerbations of COPD (AECOPD), 56 patients with stable COPD, and 35 healthy controls. Meanwhile, the clinical value was tested by receiver operating characteristic curve analysis. The functions of lncRNAs were analyzed by the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database. The potential target genes that might be regulated by NR-026690 and ENST00000447867 were identified by the lncRNA-mRNA network and competing endogenous RNA network. The transcriptional expression level of rap guanine nucleotide exchange factor 3 (RAPGEF3) was tested by qRT-PCR. The correlation of the expression between NR-026690, ENST00000447867, and RAPGEF3 was analyzed by Spearman's correlation test. Results: We found that the relative expression levels of ENST00000447867 and NR-026690 in the CD4+ T cells of AECOPD patients were significantly higher than in the stable COPD patients and control subjects by microarray and qRT-PCR validation. The transcriptional expression level of RAPGEF3 in the CD4+ T cells was significantly higher in the AECOPD group compared to the control group (P<0.01) and the stable COPD group (P<0.05). RAPGEF3 expression was positively associated with NR-026690 (r=0.4925, P<0.01) and ENST00000447867 (r=0.4065, P<0.01). Conclusion: NR-026690 and ENST00000447867 might be potential biomarkers for COPD. They might affect RAPGEF3 as miRNA sponges to regulate COPD development.

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest.

The tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect's natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India-South China-Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.

PC, a Novel Oral Insecticidal Toxin from Bacillus bombysepticus Involved in Host Lethality via APN and BtR-175.

Insect pests have developed resistance to chemical insecticides, insecticidal toxins as bioinsecticides or genetic protection built into crops. Consequently, novel, orally active insecticidal toxins would be valuable biological alternatives for pest control. Here, we identified a novel insecticidal toxin, parasporal crystal toxin (PC), from Bacillus bombysepticus (Bb). PC shows oral pathogenic activity and lethality towards silkworms and Cry1Ac-resistant Helicoverpa armigera strains. In vitro assays, PC after activated by trypsin binds to BmAPN4 and BtR-175 by interacting with CR7 and CR12 fragments. Additionally, trypsin-activated PC demonstrates cytotoxicity against Sf9 cells expressing BmAPN4, revealing that BmAPN4 serves as a functional receptor that participates in Bb and PC pathogenicity. In vivo assay, knocking out BtR-175 increased the resistance of silkworms to PC. These data suggest that PC is the first protein with insecticidal activity identified in Bb that is capable of causing silkworm death via receptor interactions, representing an important advance in our understanding of the toxicity of Bb and the contributions of interactions between microbial pathogens and insects to disease pathology. Furthermore, the potency of PC as an insecticidal protein makes it a good candidate for inclusion in integrated agricultural pest management systems.

Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG) and posterior silk gland (PSG). Three sericin genes (sericin 1, sericin 2, and sericin 3) were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25) were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs) and 361 insertion-deletions (INDELs) were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research.

Production of transgenic silver sea bream (Sparus sarba) by different gene transfer methods.

We have been interested in developing convenient mass gene transfer methods for producing strains of silver sea bream (Sparus sarba) with superior genetic traits for aquaculture. A transgene construct carrying rainbow trout growth hormone (rtGH) complementary DNA driven by a common carp b-actin promoter was introduced into silver sea bream by electroporating the sperm with the rtGH transgene and using the treated sperm to fertilize eggs stripped from mature females. The presence of the GH transgene in presumptive transgenic individuals was detected by polymerase chain reaction (PCR) analysis. Between 56% and 70% of the animals carried the GH transgene. We refer to this method as sperm-mediated gene transfer (SMGT). Since the handling stress of stripping gametes from female sliver sea bream brood fish could cause severe mortality, an alternative gene transfer method would be highly desirable. We developed a liposome-based method to transfer the GH transgene into the fish. This method, referred as testis-mediated gene transfer (TMGT), involves injecting the liposome-transgene mixture into the gonads of male sea bream at least 48 hours before spawning. The males were mated to reproductively active females, and fertilized eggs were collected for further incubation. Between 59% and 76% of the hatched fry were found by PCR analysis to carry the rtGH transgene. The efficiency of gene transfer was improved more than 80% by injecting multiple doses of the liposome-transgene mixture into the gonads of treated males. Results of Southern blot analysis of DNA isolated from PCR-positive animals showed that the transgene was integrated into the host genome and could be transmitted to its offspring. The rtGH transgene was expressed in many of the rtGH-transgenic fish. Several P1 GH-transgenic silver sea bream exhibited significant growth enhancement compared with nontransgenic controls. Our studies showed that faster-growing silver sea bream could be produced by a variety of mass gene transfer technologies. These gene transfer technologies would be of great value to aquaculture.

Complete Genome Sequence of Bacillus bombysepticus, a Pathogen Leading to Bombyx mori Black Chest Septicemia.

Bacillus bombysepticus is a Gram-positive spore-forming bacterium. Here, we announce the first complete genome sequence of this organism isolated from the cadavers of silkworm larvae that had been sick. The genome contains a single circular chromosome and a circular plasmid. Analyses of the B. bombysepticus genome will provide insights into its pathomechanisms and biology.