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Project description:Background & Aims: Gut microbiota dysbiosis is associated with the pathogenesis of Crohn's disease (CD), but the underlying mechanisms by which colon bacteria contribute to the development of CD remain largely unclear. Here, we investigated whether colon bacteria, particularly Bacteroides acidifaciens (B. acidifaciens), promote CD pathogenesis through their small RNAs (sRNAs). Methods: The composition of gut bacteria were analyzed in the fecal samples of IL-10 knockout (KO) mice and CD45RBhigh mice that spontaneously develop colitis via 16S amplification sequencing, and the expression pattern of B. acidifaciens in both experimental colitis mice and CD patients was confirmed by quantitative RT-PCR (qRT-PCR). The effects of B. acidifaciens and their total and small RNA contents on colitis development were evaluated in IL-10 KO mice. Furthermore, the expression profile of B. acidifaciens-derived sRNA (BA-sRNA) in IL-10 KO mice was established by RNA sequencing, and BA-sRNA-172 levels in experimental colitis mice and CD patients were determined. Lentivirus carrying BA-sRNA-172 and BA-sRNA-172-deficient B. acidifaciens were then constructed and used to investigate the role of BA-sRNA-172 in the development of colitis. The activities of BA-sRNA-172 in regulating mucin2 (MUC2) expression and gut mucosal barrier function was systematically studied by in situ hybridization, immunofluorescence staining, qRT-PCR, western blot, RNA pull-down and luciferase assays in vitro. Finally, the effects of anti-BA-sRNA-172 and anti-MUC2 shRNA on intestinal barrier function and colitis development were evaluated. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-08-13 | GSE155040 | GEO
Project description:Background & Aims: Gut microbiota dysbiosis is associated with the pathogenesis of Crohn's disease (CD), but the underlying mechanisms by which colon bacteria contribute to the development of CD remain largely unclear. Here, we investigated whether colon bacteria, particularly Bacteroides acidifaciens (B. acidifaciens), promote CD pathogenesis through their small RNAs (sRNAs). Methods: The composition of gut bacteria were analyzed in the fecal samples of IL-10 knockout (KO) mice and CD45RBhigh mice that spontaneously develop colitis via 16S amplification sequencing, and the expression pattern of B. acidifaciens in both experimental colitis mice and CD patients was confirmed by quantitative RT-PCR (qRT-PCR). The effects of B. acidifaciens and their total and small RNA contents on colitis development were evaluated in IL-10 KO mice. Furthermore, the expression profile of B. acidifaciens-derived sRNA (BA-sRNA) in IL-10 KO mice was established by RNA sequencing, and BA-sRNA-172 levels in experimental colitis mice and CD patients were determined. Lentivirus carrying BA-sRNA-172 and BA-sRNA-172-deficient B. acidifaciens were then constructed and used to investigate the role of BA-sRNA-172 in the development of colitis. The activities of BA-sRNA-172 in regulating mucin2 (MUC2) expression and gut mucosal barrier function was systematically studied by in situ hybridization, immunofluorescence staining, qRT-PCR, western blot, RNA pull-down and luciferase assays in vitro. Finally, the effects of anti-BA-sRNA-172 and anti-MUC2 shRNA on intestinal barrier function and colitis development were evaluated. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-08-13 | GSE155039 | GEO
Project description:Background & Aims: Gut microbiota dysbiosis is associated with the pathogenesis of Crohn's disease (CD), but the underlying mechanisms by which colon bacteria contribute to the development of CD remain largely unclear. Here, we investigated whether colon bacteria, particularly Bacteroides acidifaciens (B. acidifaciens), promote CD pathogenesis through their small RNAs (sRNAs). Methods: The composition of gut bacteria were analyzed in the fecal samples of IL-10 knockout (KO) mice and CD45RBhigh mice that spontaneously develop colitis via 16S amplification sequencing, and the expression pattern of B. acidifaciens in both experimental colitis mice and CD patients was confirmed by quantitative RT-PCR (qRT-PCR). The effects of B. acidifaciens and their total and small RNA contents on colitis development were evaluated in IL-10 KO mice. Furthermore, the expression profile of B. acidifaciens-derived sRNA (BA-sRNA) in IL-10 KO mice was established by RNA sequencing, and BA-sRNA-172 levels in experimental colitis mice and CD patients were determined. Lentivirus carrying BA-sRNA-172 and BA-sRNA-172-deficient B. acidifaciens were then constructed and used to investigate the role of BA-sRNA-172 in the development of colitis. The activities of BA-sRNA-172 in regulating mucin2 (MUC2) expression and gut mucosal barrier function was systematically studied by in situ hybridization, immunofluorescence staining, qRT-PCR, western blot, RNA pull-down and luciferase assays in vitro. Finally, the effects of anti-BA-sRNA-172 and anti-MUC2 shRNA on intestinal barrier function and colitis development were evaluated. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-08-13 | GSE155038 | GEO
Project description:Background & Aims: Gut microbiota dysbiosis is associated with the pathogenesis of Crohn's disease (CD), but the underlying mechanisms by which colon bacteria contribute to the development of CD remain largely unclear. Here, we investigated whether colon bacteria, particularly Bacteroides acidifaciens (B. acidifaciens), promote CD pathogenesis through their small RNAs (sRNAs). Methods: The composition of gut bacteria were analyzed in the fecal samples of IL-10 knockout (KO) mice and CD45RBhigh mice that spontaneously develop colitis via 16S amplification sequencing, and the expression pattern of B. acidifaciens in both experimental colitis mice and CD patients was confirmed by quantitative RT-PCR (qRT-PCR). The effects of B. acidifaciens and their total and small RNA contents on colitis development were evaluated in IL-10 KO mice. Furthermore, the expression profile of B. acidifaciens-derived sRNA (BA-sRNA) in IL-10 KO mice was established by RNA sequencing, and BA-sRNA-172 levels in experimental colitis mice and CD patients were determined. Lentivirus carrying BA-sRNA-172 and BA-sRNA-172-deficient B. acidifaciens were then constructed and used to investigate the role of BA-sRNA-172 in the development of colitis. The activities of BA-sRNA-172 in regulating mucin2 (MUC2) expression and gut mucosal barrier function was systematically studied by in situ hybridization, immunofluorescence staining, qRT-PCR, western blot, RNA pull-down and luciferase assays in vitro. Finally, the effects of anti-BA-sRNA-172 and anti-MUC2 shRNA on intestinal barrier function and colitis development were evaluated. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-08-13 | GSE155035 | GEO
Project description:B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function
| PRJNA648320 | ENA
Project description:B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [RNA-Seq]
| PRJNA648325 | ENA
Project description:B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [CD45RB high-16s-DNA-sequence]
| PRJNA648317 | ENA
Project description:B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [IL-10 KO-sRNA-sequence]
| PRJNA648319 | ENA
Project description:B. acidifaciens-derived small RNA promotes colitis development by targeting mucin 2 to impair the gut mucosal barrier function [IL-10 KO-16s-DNA-sequence]
| PRJNA648315 | ENA
Project description:Sites of inflammation are associated with profound changes in tissue metabolism. Studies in vitro and in vivo have shown that the activation of the hypoxia-inducible factor (HIF) serves as an adaptive pathway for the resolution of inflammation associated with various murine disease models. The resolution of disease occurs, at least in part, through transcriptional regulation of non-classical epithelial barrier genes. There is significant recent interest in harnessing hypoxia-inducible pathways, including targeting the HIF and the proyl-hydroxylase (PHD) enzymes that stabilize HIF, to promote mucosal healing. Here, we review the signaling pathways involved and define how hypoxia-associated signaling provides mechanistic insight into augmenting barrier function in mucosal inflammatory disease.
| S-EPMC5560425 | biostudies-other