scholarly journals Identification of long noncoding RNAs reveals the effects of dinotefuran on the brain in Apis mellifera (Hymenopptera: Apidae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Minjie Huang ◽  
Jie Dong ◽  
Haikun Guo ◽  
Minghui Xiao ◽  
Deqian Wang
Keyword(s):  
Immune Response ◽  
Honey Bee ◽  
Honey Bees ◽  
Transforming Growth Factor ◽  
Sublethal Effects ◽  
Inflammatory Responses ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Long Noncoding Rnas ◽  
Gene Set Enrichment Analysis

Abstract Background Dinotefuran (CAS No. 165252–70-0), a neonicotinoid insecticide, has been used to protect various crops against invertebrate pests and has been associated with numerous negative sublethal effects on honey bees. Long noncoding RNAs (lncRNAs) play important roles in mediating various biological and pathological processes, involving transcriptional and gene regulation. The effects of dinotefuran on lncRNA expression and lncRNA function in the honey bee brain are still obscure. Results Through RNA sequencing, a comprehensive analysis of lncRNAs and mRNAs was performed following exposure to 0.01 mg/L dinotefuran for 1, 5, and 10 d. In total, 312 lncRNAs and 1341 mRNAs, 347 lncRNAs and 1458 mRNAs, and 345 lncRNAs and 1155 mRNAs were found to be differentially expressed (DE) on days 1, 5 and 10, respectively. Gene set enrichment analysis (GSEA) indicated that the dinotefuran-treated group showed enrichment in carbohydrate and protein metabolism and immune-inflammatory responses such as glycine, serine and threonine metabolism, pentose and glucuronate interconversion, and Hippo and transforming growth factor-β (TGF-β) signaling pathways. Moreover, the DE lncRNA TCONS_00086519 was shown by fluorescence in situ hybridization (FISH) to be distributed mainly in the cytoplasm, suggesting that it may serve as a competing endogenous RNA and a regulatory factor in the immune response to dinotefuran. Conclusion This study characterized the expression profile of lncRNAs upon exposure to neonicotinoid insecticides in young adult honey bees and provided a framework for further study of the role of lncRNAs in honey bee growth and the immune response.

scholarly journals Identification and Validation of Three Autophagy-Related Long Noncoding RNAs as Prognostic Signature in Cholangiocarcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Ya Jun Liu ◽  
Alphonse Houssou Hounye ◽  
Zheng Wang ◽  
Xiaowei Liu ◽  
Jun Yi ◽  
...  
Keyword(s):  
Risk Score ◽  
Immune Cell ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Long Noncoding Rnas ◽  
Gene Set Enrichment Analysis ◽  
Risk Scores ◽  
Roc Curve Analysis ◽  
Good Reliability ◽  
Normal Tissues

Cholangiocarcinoma (CCA) is featured by common occurrence and poor prognosis. Autophagy is a biological process that has been extensively involved in the progression of tumors. Long noncoding RNAs (lncRNAs) have been discovered to be critical in diagnosing and predicting various tumors. It may be valuable to elaborate autophagy-related lncRNAs (ARlncRNAs) in CCA, and indeed, there are still few studies concerning the role of ARlncRNAs in CCA. Here, a prognostic ARlncRNA signature was constructed to predict the survival outcome of CCA patients. Through identification, three differentially expressed ARlncRNAs (DEARlncRNAs), including CHRM3.AS2, MIR205HG, and LINC00661, were screened and were considered predictive signatures. Furthermore, the overall survival (OS) of patients with high-risk scores was significantly lower than that of patients with low scores. Interestingly, the risk score was an independent factor for the OS of patients with CCA. Moreover, receiver operating characteristic (ROC) curve analysis showed that the screened and constructed prognosis signature for 1 year (AUC = 0.884), 3 years (AUC =0.759), and 5 years (AUC = 0.788) presented a high score of accuracy in predicting OS of CCA patients. Gene set enrichment analysis (GSEA) revealed that the three DEARlncRNAs were significantly enriched in CCA-related signaling pathways, including “pathways of basal cell carcinoma”, “glycerolipid metabolism”, etc. Quantitative real-time PCR (qRT-PCR) showed that expressions of CHRM3.AS2, MIR205HG, and LINC00661 were higher in CCA tissues than those in normal tissues, similar to the trends detected in the CCA dataset. Furthermore, Pearson’s analysis reported an intimate correlation of the risk score with immune cell infiltration, indicating a predictive value of the signature for the efficacy of immunotherapy. In addition, the screened lncRNAs were found to have the ability to modulate the expression of mRNAs by interacting with miRNAs based on the established lncRNA-miRNA-mRNA network. In conclusion, our study develops a novel nomogram with good reliability and accuracy to predict the OS of CCA patients, providing a significant guiding value for developing tailored therapy for CCA patients.

scholarly journals Expression Signatures of Long Noncoding RNAs in Left Ventricular Noncompaction

2021 ◽  
Vol 8 ◽  
Author(s):  
Qingshan Tian ◽  
Hanxiao Niu ◽  
Dingyang Liu ◽  
Na Ta ◽  
Qing Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Left Ventricular ◽  
Long Noncoding Rnas ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Left Ventricular Noncompaction ◽  
Ventricular Noncompaction

Long noncoding RNAs have gained widespread attention in recent years for their crucial role in biological regulation. They have been implicated in a range of developmental processes and diseases including cancer, cardiovascular, and neuronal diseases. However, the role of long noncoding RNAs (lncRNAs) in left ventricular noncompaction (LVNC) has not been explored. In this study, we investigated the expression levels of lncRNAs in the blood of LVNC patients and healthy subjects to identify differentially expressed lncRNA that develop LVNC specific biomarkers and targets for developing therapies using biological pathways. We used Agilent Human lncRNA array that contains both updated lncRNAs and mRNAs probes. We identified 1,568 upregulated and 1,141 downregulated (log fold-change > 2.0) lncRNAs that are differentially expressed between LVNC and the control group. Among them, RP11-1100L3.7 and XLOC_002730 are the most upregulated and downregulated lncRNAs. Using quantitative real-time reverse transcription polymerase chain reaction (RT-QPCR), we confirmed the differential expression of three top upregulated and downregulated lncRNAs along with two other randomly picked lncRNAs. Gene Ontology (GO) and KEGG pathways analysis with these differentially expressed lncRNAs provide insight into the cellular pathway leading to LVNC pathogenesis. We also identified 1,066 upregulated and 1,017 downregulated mRNAs. Gene set enrichment analysis (GSEA) showed that G2M, Estrogen, and inflammatory pathways are enriched in differentially expressed genes (DEG). We also identified miRNA targets for these differentially expressed genes. In this study, we first report the use of LncRNA microarray to understand the pathogenesis of LVNC and to identify several lncRNA and genes and their targets as potential biomarkers.

scholarly journals Increased VEGF-A in solid type of lung adenocarcinoma reduces the patients’ survival

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Woon Yong Jung ◽  
Kyueng-Whan Min ◽  
Young Ha Oh
Keyword(s):  
Immune Response ◽  
Survival Analysis ◽  
Lung Adenocarcinoma ◽  
Survival Rates ◽  
Treatment Strategies ◽  
Enrichment Analysis ◽  
Genetic Alterations ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Solid Type

AbstractThe histological classification of lung adenocarcinoma includes 5 types: lepidic, acinar, papillary, micropapillary and solid. The complex gene interactions and anticancer immune response of these types are not well known. The aim of this study was to reveal the survival rates, genetic alterations and immune activities of the five histological types and provide treatment strategies. This study reviewed the histological findings of 517 patients with lung adenocarcinoma from The Cancer Genome Atlas (TCGA) database and classified them into five types. We performed gene set enrichment analysis (GSEA) and survival analysis according to the different types. We found six oncogenic gene sets that were higher in lung adenocarcinoma than in normal tissues. In the survival analysis of each type, the acinar type had a favorable prognosis, and the solid subtype had an unfavorable prognosis; however, the survival differences between the other types were not significant. Our study focused on the solid type, which had the poorest prognosis. The solid type was related to adaptive immune resistance associated with elevated CD8 T cells and high CD274 (encoding PD-L1) expression. In the pathway analyses, the solid type was significantly related to high vascular endothelial growth factor (VEGF)-A expression, reflecting tumor angiogenesis. Non-necrosis/low immune response affected by high VEGF-A was associated with worse prognosis. The solid type associated with high VEGF-A expression may contribute to the development of therapeutic strategies for lung adenocarcinoma.

scholarly journals Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide

2020 ◽  
Vol 21 (12) ◽  
pp. 4217
Author(s):  
Lukasz Paukszto ◽  
Anita Mikolajczyk ◽  
Jan P. Jastrzebski ◽  
Marta Majewska ◽  
Kamil Dobrzyn ◽  
...  
Keyword(s):  
Immune Response ◽  
Rna Editing ◽  
Salmonella Enteritidis ◽  
Clinical Symptoms ◽  
Expression Patterns ◽  
Noncoding Rnas ◽  
Variant Calling ◽  
Long Noncoding Rnas ◽  
Specific Expression

Endometrial infections at a young age can lead to fertility issues in adulthood. Bacterial endotoxins, such as lipopolysaccharide (LPS), can participate in long-term molecular changes even at low concentrations. Lipopolysaccharide plays a crucial role in the progression of septic shock, inflammation and auto-immune diseases. The aim of this study was to describe transcriptomic modulations in the porcine endometrium, induced in vivo by a single subclinical dose of LPS from Salmonella Enteritidis. which did not produce clinical symptoms of toxicity. The RNA-seq methodology was applied to reveal 456 differentially expressed regions, including 375 genes, four long noncoding RNAs, and 77 other unclassified transcripts. Two independent methods confirmed 118 alternatively spliced genes that participate i.a., in the formation of the MHC-I complex and the adaptive immune response. Single nucleotide variant-calling algorithms supported the identification of 3730 allele-specific expression variants and 57 canonical A-to-I RNA editing sites. The results demonstrated that the differential expression of genes involved in inflammation, immune response, angiogenesis and endometrial development may be maintained for up to 7 days after exposure to LPS. RNA editing sites and long noncoding RNAs (lncRNAs) play an important role in transcriptional regulatory machinery in the porcine endometrium in response to LPS administration.

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years

2019 ◽  
Vol 10 (3) ◽  
pp. 245-252 ◽  
Author(s):  
P.D. Kusumo ◽  
B. Bela ◽  
H. Wibowo ◽  
Z. Munasir ◽  
I.S. Surono
Keyword(s):  
Immune Response ◽  
Young Children ◽  
Lactobacillus Plantarum ◽  
Transforming Growth Factor ◽  
Inflammatory Responses ◽  
Enzyme Linked Immunosorbent Assay ◽  
Treatment Groups ◽  
Tnf Α ◽  
Intestinal Immune System ◽  
Tgf Β1

The immature intestinal immune system in young children develops as it comes into contact with dietary and microbial antigens in the gut. Intestinal microbiota plays a significant role in host defence mechanisms as shown by inflammatory responses towards potential pathogens. We investigated the probiotic function of Lactobacillus plantarum IS-10506 of ‘dadih’ origin in modulating immune response in young children. We aimed to assess its effect on their immune response by assessing transforming growth factor-β1 (TGF-β1) and tumour necrosis factor-α (TNF-α) responses and faecal secretory immunoglobulin A (sIgA) titre in a randomised, double-blinded placebo-controlled trial in 12-24-month-old children (n=38). We used four treatment groups for a 90-day supplementation period: placebo (n=11), probiotic (n=9), zinc (n=8) and probiotic and zinc (n=10). Faecal sIgA, plasma TGF-β1 and TNF-α titre were evaluated using the enzyme-linked immunosorbent assay standard technique. Statistical analysis divided the results (pre/post treatment) into high (>1) and low (<1) ratios. The results showed that faecal sIgA titre increased in all treatment groups compared with the control (placebo) and significantly increased in the probiotic group (P=0.05). In addition, the TGF-β1 ratio in the zinc group was significantly higher (P=0.05) than that in the placebo group. We observed a significant positive correlation between TGF-β1/TNF-α and faecal sIgA (r=0.27, P=0.04). Post hoc test results revealed that zinc supplementation has a significant effect on body-weight gain. Taken together, probiotic L. plantarum IS-10506 supplementation stimulates TGF-β1, which in turn increases the production of sIgA, in line with the significant correlation between TGF-β1/TNF-α and faecal sIgA.

scholarly journals Towards Precision Nutrition: A Novel Concept Linking Phytochemicals, Immune Response and Honey Bee Health

Insects ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 401 ◽  
Author(s):  
Pedro Negri ◽  
Ethel Villalobos ◽  
Nicolás Szawarski ◽  
Natalia Damiani ◽  
Liesel Gende ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Cold Stress ◽  
Honey Bee ◽  
Honey Bees ◽  
Bee Health ◽  
Honey Bee Health ◽  
Pesticides Exposure ◽  
Novel Concept ◽  
The Relationship

The high annual losses of managed honey bees (Apis mellifera) has attracted intensive attention, and scientists have dedicated much effort trying to identify the stresses affecting bees. There are, however, no simple answers; rather, research suggests multifactorial effects. Several works have been reported highlighting the relationship between bees’ immunosuppression and the effects of malnutrition, parasites, pathogens, agrochemical and beekeeping pesticides exposure, forage dearth and cold stress. Here we analyze a possible connection between immunity-related signaling pathways that could be involved in the response to the stress resulted from Varroa-virus association and cold stress during winter. The analysis was made understanding the honey bee as a superorganism, where individuals are integrated and interacting within the colony, going from social to individual immune responses. We propose the term “Precision Nutrition” as a way to think and study bees’ nutrition in the search for key molecules which would be able to strengthen colonies’ responses to any or all of those stresses combined.

scholarly journals Low expression of CHRDL1 and SPARCL1 predicts poor prognosis of lung adenocarcinoma based on comprehensive analysis and immunohistochemical validation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huan Deng ◽  
Qingqing Hang ◽  
Dijian Shen ◽  
Yibi Zhang ◽  
Ming Chen
Keyword(s):  
Lung Adenocarcinoma ◽  
Molecular Mechanisms ◽  
Transforming Growth Factor ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Prognostic Indicators ◽  
Hub Genes ◽  
Coexpressed Genes

Abstract Purpose Exploring the molecular mechanisms of lung adenocarcinoma (LUAD) is beneficial for developing new therapeutic strategies and predicting prognosis. This study was performed to select core genes related to LUAD and to analyze their prognostic value. Methods Microarray datasets from the GEO (GSE75037) and TCGA-LUAD datasets were analyzed to identify differentially coexpressed genes in LUAD using weighted gene coexpression network analysis (WGCNA) and differential gene expression analysis. Functional enrichment analysis was conducted, and a protein–protein interaction (PPI) network was established. Subsequently, hub genes were identified using the CytoHubba plug-in. Overall survival (OS) analyses of hub genes were performed. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Human Protein Atlas (THPA) databases were used to validate our findings. Gene set enrichment analysis (GSEA) of survival-related hub genes were conducted. Immunohistochemistry (IHC) was carried out to validate our findings. Results We identified 486 differentially coexpressed genes. Functional enrichment analysis suggested these genes were primarily enriched in the regulation of epithelial cell proliferation, collagen-containing extracellular matrix, transforming growth factor beta binding, and signaling pathways regulating the pluripotency of stem cells. Ten hub genes were detected using the maximal clique centrality (MCC) algorithm, and four genes were closely associated with OS. The CPTAC and THPA databases revealed that CHRDL1 and SPARCL1 were downregulated at the mRNA and protein expression levels in LUAD, whereas SPP1 was upregulated. GSEA demonstrated that DNA-dependent DNA replication and catalytic activity acting on RNA were correlated with CHRDL1 and SPARCL1 expression, respectively. The IHC results suggested that CHRDL1 and SPARCL1 were significantly downregulated in LUAD. Conclusions Our study revealed that survival-related hub genes closely correlated with the initiation and progression of LUAD. Furthermore, CHRDL1 and SPARCL1 are potential therapeutic and prognostic indicators of LUAD.

scholarly journals Organoids Are Limited in Modeling the Colon Adenoma–Carcinoma Sequence

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 488
Author(s):  
Yoshihisa Tokumaru ◽  
Masanori Oshi ◽  
Ankit Patel ◽  
Wanqing Tian ◽  
Li Yan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Immune Response ◽  
Immune Cells ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Related Gene ◽  
Gene Set Enrichment ◽  
Colon Adenoma ◽  
Tissue Samples ◽  
Gene Sets

The colon adenoma–carcinoma sequence is a multistep genomic-altering process that occurs during colorectal cancer (CRC) carcinogenesis. Organoids are now commonly used to model both non-cancerous and cancerous tissue. This study aims to investigate how well organoids mimic tissues in the adenoma–carcinoma sequence by comparing their transcriptomes. A total of 234 tissue samples (48 adenomas and 186 CRC) and 60 organoid samples (15 adenomas and 45 CRC) were analyzed. We found that cell-proliferation-related gene sets were consistently enriched in both CRC tissues and organoids compared to adenoma tissues and organoids by gene set enrichment analysis (GSEA). None of the known pathways in the colon adenoma–carcinoma sequence were consistently enriched in CRC organoids. There was no enrichment of the tumor microenvironment-related gene sets in CRC organoids. CRC tissues enriched immune-response-related gene sets, whereas CRC organoids did not. The proportions of infiltrating immune cells were different between tissues and organoids, whereas there was no difference between cancer and adenoma organoids. The amounts of cancer stem cells and progenitor cells were not different between CRC and adenoma organoids, whereas a difference was noted between CRC and adenoma tissues. In conclusion, we demonstrated that organoids model only part of the adenoma–carcinoma sequence and should be used with caution after considering their limitations.

Sign in / Sign up

Export Citation Format

Share Document