scholarly journals Hemophilia A Inhibitor Subjects Show Unique PBMC Gene Expression Profiles That Include up-Regulated Innate Immune Modulators

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 160-160
Author(s):  
Ahmad Faisal Karim ◽  
Anthony R. Soltis ◽  
Nadia P Ewing ◽  
Clifton L. Dalgard ◽  
Matthew D. Wilkerson ◽  
...  
Keyword(s):  
Differential Expression ◽  
Enrichment Analysis ◽  
Innate Immune ◽  
Rna Seq ◽  
Immune Modulators ◽  
Fviii Inhibitor ◽  
Go Enrichment ◽  
Group B ◽  
Go Enrichment Analysis ◽  
A Current

The formation of pathological anti-FVIII antibodies, referred to as "inhibitors", is the most serious complication of therapeutic FVIII infusions, affecting up to one third of severe Hemophilia A (HA) patients. Intensive FVIII therapy, i.e. "Immune Tolerance Induction" (ITI), enables ~2/3 of treated patients to achieve peripheral tolerance to FVIII. FVIII inhibitor formation is a classical T-cell dependent adaptive immune response. As such, it requires help from the innate immune system. However, the roles of innate immune cells and mechanisms of inhibitor development versus immune tolerance, achieved with or without ITI therapy, are not well understood. To address these questions, we carried out temporal transcriptomics profiling of FVIII-stimulated peripheral blood mononuclear cells (PBMCs) from HA subjects with and without a current or historic inhibitor using RNA-seq. PBMCs were isolated from 40 subjects in the following groups: (A) HA with an inhibitor that resolved either following ITI or spontaneously; (B) HA with a current inhibitor; (C) HA with no inhibitor history and (D) non-HA healthy controls. PBMCs were rested overnight and then stimulated with 5 nM FVIII, and total RNA was isolated 4, 16, 24 and 48 hours following stimulation. RNA from unstimulated cells at t = 4 hrs served as a negative control. Time-series differential expression analysis was performed with DESeq2 and genes with a log likelihood ratio test FDR <0.05 and an absolute fold change >1.25 at at least one stimulation time point compared to control were deemed significant. Subjects with a resolved past inhibitor (Group A) showed differential expression of only 15 genes. In contrast, subjects with a current inhibitor (Group B) showed differential expression of 56 genes. A clustering analysis divided the temporal trajectories of Group B genes into 3 distinct clusters. Twenty-three genes were up-regulated at 16 hr and 21 genes at 48 hr post-stimulation, respectively. Interestingly, gene ontology (GO) enrichment analysis of these genes revealed enrichments for innate immune modulators, including NLRP3, TLR8, IL32, CLEC10A and COLEC12.NLRP3 and TLR8 are associated with enhanced secretion of the pro-inflammatory cytokines IL-1beta and TNF-alpha, while IL32, which has several isoforms, has been associated with both inflammatory and regulatory immune processes. Expression levels of NLRP3, TLR8, CLEC10A and IL32 transcripts were validated by real time PCR, and changes in RNA transcript abundances correlated well with the RNA-seq results. IL-32 results were validated by both RT-qPCR on an aliquot of the original RNA sample and ELISA to measure the cytokine in supernatants at t=48 hrs. HA subjects with no inhibitor history (Group C) had 195 differentially expressed genes whose temporal profiles fell into 4 distinct clusters. GO enrichment analysis revealed biological processes related to epithelial cell proliferation, responses to toxic substances, and positive/negative regulation of cytokine secretion (TNF, NQO1, PMEPA1). The non-HA healthy control subjects (Group D) also showed cellular responses to ex vivo FVIII stimulation. A total of 63 differentially regulated genes fell into 4 distinct clusters. GO analysis identified expression patterns associated with leukocyte-mediated immunity, T-cell activation, and a hypoxia response. Overall, distinct transcriptional signatures were identified for each of the four groups, providing clues as to cellular mechanisms leading to or accompanying their disparate anti-FVIII antibody responses. We are currently characterizing PBMC immune cell subsets, e.g. macrophages and CD4+ T cells, to identify specific cell types responsible for the differentially regulated genes. Cellular responses of tolerized HA subjects and healthy non-HA controls were consistent with the known immunogenicity of FVIII, including persistence of FVIII-specific CD4+ T cells even in individuals with no measurable FVIII inhibitor. The inflammatory status of HA patients suffering from an ongoing inhibitor clearly includes up-regulation of innate immune modulators, some of which may act as ongoing danger signals that influence the responses to, and eventual outcome of, ITI therapy. Disclosures Pratt: Grifols, Inc: Research Funding; Bloodworks NW: Patents & Royalties: inventor on patents related to FVIII immunogenicity.

scholarly journals Analysis of small RNA changes in different Brassica napus synthetic allopolyploids

2019 ◽  
Author(s):  
Yunxiao Wei ◽  
Fei Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Differential Expression ◽  
Small Rna ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Small Rna Sequencing ◽  
Go Enrichment ◽  
Polyploid Formation ◽  
Differentially Expressed Mirnas ◽  
New Perspective ◽  
Go Enrichment Analysis

Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for solving the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective of small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.

scholarly journals Analysis of small RNA changes in different Brassica napus synthetic allopolyploids

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7621
Author(s):  
Yunxiao Wei ◽  
Fei Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Differential Expression ◽  
Small Rna ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Small Rna Sequencing ◽  
Go Enrichment ◽  
Polyploid Formation ◽  
Differentially Expressed Mirnas ◽  
New Perspective ◽  
Go Enrichment Analysis

Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for explaining the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective between small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.

scholarly journals The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Fu-Yu Hung ◽  
Chen Chen ◽  
Ming-Ren Yen ◽  
Jo-Wei Allison Hsieh ◽  
Chenlong Li ◽  
...  
Keyword(s):  
Histone Modification ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Rna Seq ◽  
Histone Deacetylase 6 ◽  
Lncrna Expression ◽  
Go Enrichment ◽  
Non Coding Rnas ◽  
Go Enrichment Analysis ◽  
Low Expression

Abstract In recent years, eukaryotic long non-coding RNAs (lncRNAs) have been identified as important factors involved in a wide variety of biological processes, including histone modification, alternative splicing and transcription enhancement. The expression of lncRNAs is highly tissue-specific and is regulated by environmental stresses. Recently, a large number of plant lncRNAs have been identified, but very few of them have been studied in detail. Furthermore, the mechanism of lncRNA expression regulation remains largely unknown. Arabidopsis HISTONE DEACETYLASE 6 (HDA6) and LSD1-LIKE 1/2 (LDL1/2) can repress gene expression synergistically by regulating H3Ac/H3K4me. In this research, we performed RNA-seq and ChIP-seq analyses to further clarify the function of HDA6-LDL1/2. Our results indicated that the global expression of lncRNAs is increased in hda6/ldl1/2 and that this increased lncRNA expression is particularly associated with H3Ac/H3K4me2 changes. In addition, we found that HDA6-LDL1/2 is important for repressing lncRNAs that are non-expressed or show low-expression, which may be strongly associated with plant development. GO-enrichment analysis also revealed that the neighboring genes of the lncRNAs that are upregulated in hda6/ldl1/2 are associated with various developmental processes. Collectively, our results revealed that the expression of lncRNAs is associated with H3Ac/H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex.

scholarly journals Analysis of small RNA changes in different Brassica napus synthetic allopolyploids

2019 ◽  
Author(s):  
Yunxiao Wei ◽  
Fei Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Differential Expression ◽  
Small Rna ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Small Rna Sequencing ◽  
Go Enrichment ◽  
Polyploid Formation ◽  
Differentially Expressed Mirnas ◽  
New Perspective ◽  
Go Enrichment Analysis

Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for solving the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective of small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.

scholarly journals Selenium Treatment Enhanced Clearance of Salmonella in Chicken Macrophages (HD11)

Antioxidants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 532 ◽  
Author(s):  
Zhexi Liu ◽  
Jianwei Huang ◽  
Yijuan Nie ◽  
Izhar Qazi ◽  
Yutao Cao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Glutathione Metabolism ◽  
Rna Seq ◽  
Apoptotic Signaling ◽  
Go Enrichment ◽  
Selenium Treatment ◽  
Underlying Mechanisms ◽  
Go Enrichment Analysis

As an important micronutrient, selenium (Se) plays many essential roles in immune response and protection against pathogens in humans and animals, but underlying mechanisms of Se-based control of salmonella growth within macrophages remain poorly elucidated. In this study, using RNA-seq analyses, we demonstrate that Se treatment (at an appropriate concentration) can modulate the global transcriptome of chicken macrophages HD11. The bioinformatic analyses (KEGG pathway analysis) revealed that the differentially expressed genes (DEGs) were mainly enriched in retinol and glutathione metabolism, revealing that Se may be associated with retinol and glutathione metabolism. Meanwhile, Se treatment increased the number of salmonella invading the HD11 cells, but reduced the number of salmonella within HD11 cells, suggesting that enhanced clearance of salmonella within HD11 cells was potentially modulated by Se treatment. Furthermore, RNA-seq analyses also revealed that nine genes including SIVA1, FAS, and HMOX1 were differentially expressed in HD11 cells infected with salmonella following Se treatment, and GO enrichment analysis showed that these DEGs were mainly enriched in an extrinsic apoptotic signaling pathway. In summary, these results indicate that Se treatment may not only affect retinol and glutathione metabolism in macrophages, but could also inhibit salmonella-induced macrophage apoptosis via an extrinsic apoptotic signaling pathway involving SIVA1.

scholarly journals A Comparative Transcriptome Analysis Reveals New Insights into Pre-Harvest Sprouting (PHS) in Wheat

2021 ◽  
Author(s):  
Xingyan Li ◽  
Hongyu Qiao ◽  
Zeng Wang ◽  
Bing Han ◽  
Yanping Xing ◽  
...  
Keyword(s):  
Differential Expression ◽  
Wheat Cultivar ◽  
Enrichment Analysis ◽  
Conclusive Evidence ◽  
Wild Type ◽  
Go Enrichment ◽  
Ethylmethane Sulfonate ◽  
Chitinase Genes ◽  
First Time ◽  
Go Enrichment Analysis

Abstract Background: pre-harvest sprouting (PHS) is a significant cause of yield loss in cereal crops, and is an important topic of study for the improvement of wheat quality. Many studies have focused on PHS in wheat during the last 10 years, especially on the involvement of abscisic acid (ABA) in PHS, however, a lot remained unknown about this topic.Results: In this study, a PHS resistant line was isolated from an ethylmethane sulfonate (EMS) mutant population derived from the wheat cultivar ‘Long 13-3778’, namely ‘LQ18’. The mutant line LQ18 showed highly significant resistance to PHS compared with the wild-type. Transcriptome sequencing was conducted to determine the differences between the LQ18 mutant and the wild-type at the level of gene expression. The results showed no conclusive evidence that the ABA biosynthesis and signaling pathways contribute to the differences in PHS between the mutant and the wild-type, and some genes and their alleles associated with PHS tolerance showed differential expression between the mutant and wild-type lines. The most interesting result of this study was that the expression levels of the chitinase family genes showed significant differences between the mutant and the wild-type as determined by GO enrichment analysis, and a subsequent analysis of differential expression profiling of the chitinase genes led to the same conclusion.Conclusions: Transcriptomic analysis in this study have revealed the global transcriptome profiles of the PHS sensitive wheat cultivar ‘Long 13-3778’ and its PHS resistant mutants. Furthermore, this study has proposed a possible explanation of the connection between PHS and the chitinase family for the first time, which added to our understanding of PHS and seed dormancy in common wheat.

scholarly journals Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Katerina Jureckova ◽  
Hana Raschmanova ◽  
Jan Kolek ◽  
Maryna Vasylkivska ◽  
Barbora Branska ◽  
...  
Keyword(s):  
Reference Genes ◽  
Enrichment Analysis ◽  
Clostridium Beijerinckii ◽  
Stable Expression ◽  
Rna Seq ◽  
Go Enrichment ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Go Enrichment Analysis ◽  
Selection Of

Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.

scholarly journals Comprehensive biological information analysis of PTEN gene in pan-cancer

2021 ◽  
Author(s):  
Hang Zhang ◽  
Wenhan Zhou ◽  
Xiaoyi Yang ◽  
Shuzhan Wen ◽  
Baicheng Zhao ◽  
...  
Keyword(s):  
3D Structure ◽  
Enrichment Analysis ◽  
Biological Information ◽  
Pten Gene ◽  
Clinical Prognosis ◽  
Regulatory Pathways ◽  
Go Enrichment ◽  
Go Enrichment Analysis ◽  
Pan Cancer ◽  
Low Expression

Abstract Background PTEN is a multifunctional tumor suppressor gene mutating at high frequency in a variety of cancers. However, its expression in pan-cancer, correlated genes, survival prognosis, and regulatory pathways are not completely described. Here, we aimed to conduct a comprehensive analysis from the above perspectives in order to provide reference for clinical application. Methods we studied the expression levels in cancers by using data from TCGA and GTEx database. Obtain expression box plot from UALCAN database. Perform mutation analysis on the cBioportal website. Obtain correlation genes on the GEPIA website. Construct protein network and perform KEGG and GO enrichment analysis on the STRING database. Perform prognostic analysis on the Kaplan-Meier Plotter website. We also performed transcription factor prediction on the PROMO database and performed RNA-RNA association and RNA-protein interaction on the RNAup Web server and RPISEq. The gene 3D structure, protein sequence and conserved domain were obtained in NCBI respectively. Results PTEN was underexpressed in all cancers we studied. It was closely related to the clinical stage of tumors, suggesting PTEN may involved in cancer development and progression. The mutations of PTEN were present in a variety of cancers, most of which were truncation mutations and missense mutations. Among cancers (KIRC, LUAD, THYM, UCEC, Gastric Cancer, Liver Cancer, Lung Cancer, Breast Cancer), patients with low expression of PTEN had a shorter OS time and poorer OS prognosis. The low expression of PTEN can cause the deterioration of RFS in certain cancers (TGCT, UCEC, LIHC, LUAD, THCA), suggesting that the expression of PTEN was related to the clinical prognosis. Our study identified genes correlated with PTEN and performed GO enrichment analysis on 100 PTEN-related genes obtained from the GEPIA website. Conclusions The understanding of PTEN gene and the in-depth exploration of its related regulatory pathways may provide insight for the discovery of tumor-specific biomarkers and clinical potential therapeutic targets.

Transcriptome Signatures Reveal Candidate Key Genes in the Peripheral Blood Mononuclear Cells of Patients With Coronary Artery Disease

2020 ◽  
Author(s):  
Vijayakrishna Kolur ◽  
Basavaraj Vastrad ◽  
Chanabasayya Vastrad ◽  
Iranna Kotturshetti ◽  
Anandkumar Tengli
Keyword(s):  
Coronary Artery Disease ◽  
Gene Ontology ◽  
Coronary Artery ◽  
Regulatory Network ◽  
Target Gene ◽  
Enrichment Analysis ◽  
Hub Genes ◽  
Go Enrichment ◽  
Artery Disease ◽  
Go Enrichment Analysis

Abstract BackgroundCoronary artery disease (CAD) is one of the most common disorders in the cardiovascular system. This study aims to explore potential signaling pathways and important biomarkers that drive CAD development. MethodsThe CAD GEO Dataset GSE113079 was featured to screen differentially expressed genes (DEGs). The pathway and Gene Ontology (GO) enrichment analysis of DEGs were analyzed using the ToppGene. We screened hub and target genes from protein-protein interaction (PPI) networks, target gene - miRNA regulatory network and target gene - TF regulatory network, and Cytoscape software. Validations of hub genes were performed to evaluate their potential prognostic and diagnostic value for CAD. Results1,036 DEGs were captured according to screening criteria (525upregulated genes and 511downregulated genes). Pathway and Gene Ontology (GO) enrichment analysis of DEGs revealed that these up and down regulated genes are mainly enriched in thyronamine and iodothyronamine metabolism, cytokine-cytokine receptor interaction, nervous system process, cell cycle and nuclear membrane. Hub genes were validated to find out potential prognostic biomarkers, diagnostic biomarkers and novel therapeutic target for CAD. ConclusionsIn summary, our findings discovered pivotal gene expression signatures and signaling pathways in the progression of CAD. CAPN13, ACTBL2, ERBB3, GATA4, GNB4, NOTCH2, EXOSC10, RNF2, PSMA1 and PRKAA1 might contribute to the progression of CAD, which could have potential as biomarkers or therapeutic targets for CAD.

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