An Exploration of Non-Coding RNAs in Extracellular Vesicles Delivered by Swine Anterior Pituitary

Extracellular vesicles are lipid bilayer-delimited particles carrying proteins, lipids, and small RNAs. Previous studies have demonstrated that they had regulatory functions both physiologically and pathologically. However, information remains inadequate on extracellular vesicles from the anterior pituitary, a key endocrine organ in animals and humans. In this study, we separated and identified extracellular vesicles from the anterior pituitary of the Duroc swine model. Total RNA was extracted and RNA-seq was performed, followed by a comprehensive analysis of miRNAs, lncRNAs, and circRNAs. Resultantly, we obtained 416 miRNAs, 16,232 lncRNAs, and 495 circRNAs. Furthermore, GO and KEGG enrichment analysis showed that the ncRNAs in extracellular vesicles may participate in regulating intracellular signal transduction, cellular component organization or biogenesis, small molecule binding, and transferase activity. The cross-talk between them also suggested that they may play an important role in the signaling process and biological regulation. This is the first report of ncRNA data in the anterior pituitary extracellular vesicles from the duroc swine breed, which is a fundamental resource for exploring detailed functions of extracellular vesicles from the anterior pituitary.

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An exploration of non-coding RNA in exosomes delivered by swine anterior pituitary

10.21203/rs.3.rs-36112/v1 ◽

2020 ◽

Author(s):

Jiali Xiong ◽

Haojie Zhang ◽

Bin Zeng ◽

Jie Liu ◽

Junyi Luo ◽

...

Keyword(s):

Anterior Pituitary ◽

Enrichment Analysis ◽

Regulatory Function ◽

Swine Model ◽

Transferase Activity ◽

Rna Seq ◽

Biological Regulation ◽

Endocrine Organ ◽

Non Coding Rna ◽

First Time

Abstract Background: The anterior pituitary is a key endocrine organ both in animal and human being drawing much concern. Exosomes are extracellular secretory vesicles carrying proteins, lipids and small RNAs. Previous studies have demonstrated that they had regulatory function both physiologically and pathologically. However, information on exosomes from anterior pituitary remains unknown.Results: In this study, we separated and identified exosomes from anterior pituitary of Duroc swine model for the first time. Total RNA was extracted and RNA-seq was performed, followed by a comprehensive analysis of miRNAs, lncRNAs and circRNAs. Resultantly, we obtained 343 known miRNAs and 73 novel miRNAs, 15545 lncRNAs and 494 circRNAs. Furthermore, GO and KEGG enrichment analysis showed that the ncRNAs in exosomes may participate in regulating intracellular signal transduction, cellular component organization or biogenesis, small molecule binding, transferase activity. The cross-talk between them also suggested that they may play an important role in signaling process and the biological regulation.Conclusions: This work firstly provides ncRNAs data in anterior pituitary exosomes from duroc swine breed. These results may serve as a fundamental resource for exploring the detailed functions of exosomes from anterior pituitary.

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Comprehensive Expression Profiling Analysis of Pituitary Indicates that circRNA Participates in the Regulation of Sheep Estrus

Genes ◽

10.3390/genes10020090 ◽

2019 ◽

Vol 10 (2) ◽

pp. 90 ◽

Cited By ~ 3

Author(s):

Xiaoyue Li ◽

Cunyuan Li ◽

Junchang Wei ◽

Wei Ni ◽

Yueren Xu ◽

...

Keyword(s):

Expression Profiles ◽

Interaction Network ◽

Enrichment Analysis ◽

Circular Rna ◽

Differentially Expressed ◽

Rna Seq ◽

Endocrine Organ ◽

Reverse Transcription Quantitative Pcr ◽

Significant Difference ◽

Profiling Analysis

The pituitary gland is the most important endocrine organ that mainly regulates animal estrus by controlling the hormones synthesis. There is a significant difference between the estrus state and anestrus state of sheep pituitary system. Here, we studied the circular RNA (circRNA) expression profiles of the anterior pituitary of estrus and anestrus sheep using RNA-seq technology. Through this study, we identified a total of 12,468 circRNAs and 9,231 differentially expressed circRNAs in the estrus and anestrus pituitary system of sheep. We analyzed some differentially expressed circRNAs by reverse transcription quantitative-PCR (RT-qPCR), and some circRNAs were demonstrated using RNase-R+ resistance experiments. CircRNAs involving the regulation of estrus-related terms and pathways are enriched by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In addition, we also predicted partial microRNA-circRNA interaction network for circRNAs that regulate sheep estrus. Overall, this study explored a potential substantial role played by circRNAs involved in pituitary regulation on sheep estrus and proposed new questions for further study.

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Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-001610 ◽

2021 ◽

Vol 9 (3) ◽

pp. e001610

Author(s):

Incheol Seo ◽

Hye Won Lee ◽

Sang Jun Byun ◽

Jee Young Park ◽

Hyeonji Min ◽

...

Keyword(s):

Rectal Cancer ◽

Locally Advanced ◽

Enrichment Analysis ◽

Advanced Rectal Cancer ◽

Locally Advanced Rectal Cancer ◽

Neoadjuvant Chemoradiation ◽

Cytolytic Activity ◽

Gene Set Enrichment Analysis ◽

Preoperative Treatment ◽

Rna Seq

BackgroundNeoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC.MethodsWe analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets.ResultsGene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature.ConclusionsTaken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.

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Increased Tenascin C, Osteopontin and HSP90 Levels in Plasmatic Small Extracellular Vesicles of Pediatric ALK-Positive Anaplastic Large Cell Lymphoma: New Prognostic Biomarkers?

Diagnostics ◽

10.3390/diagnostics11020253 ◽

2021 ◽

Vol 11 (2) ◽

pp. 253

Author(s):

Federica Lovisa ◽

Anna Garbin ◽

Sara Crotti ◽

Piero Di Battista ◽

Ilaria Gallingani ◽

...

Keyword(s):

Extracellular Vesicles ◽

Anaplastic Large Cell Lymphoma ◽

Cell Lymphoma ◽

Enrichment Analysis ◽

Heat Shock Protein 90 ◽

Large Cell ◽

Tenascin C ◽

Anaplastic Lymphoma ◽

Large Cell Lymphoma ◽

Alk Positive

Over the past 15 years, several biological and pathological characteristics proved their significance in pediatric anaplastic lymphoma kinase (ALK)-positive anaplastic large-cell lymphoma (ALCL) prognostic stratification. However, the identification of new non-invasive disease biomarkers, relying on the most important disease mechanisms, is still necessary. In recent years, plasmatic circulating small extracellular vesicles (S-EVs) gathered great importance both as stable biomarker carriers and active players in tumorigenesis. In the present work, we performed a comprehensive study on the proteomic composition of plasmatic S-EVs of pediatric ALCL patients compared to healthy donors (HDs). By using a mass spectrometry-based proteomics approach, we identified 50 proteins significantly overrepresented in S-EVs of ALCL patients. Gene Ontology enrichment analysis disclosed cellular components and molecular functions connected with S-EV origin and vesicular trafficking, whereas cell adhesion, glycosaminoglycan metabolic process, extracellular matrix organization, collagen fibril organization and acute phase response were the most enriched biological processes. Of importance, consistently with the presence of nucleophosmin (NPM)-ALK fusion protein in ALCL cells, a topological enrichment analysis based on Reactome- and Kyoto Encyclopedia of Genes and Genomes (KEGG)-derived networks highlighted a dramatic increase in proteins of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway in ALCL S-EVs, which included heat shock protein 90-kDa isoform alpha 1 (HSP90AA1), osteopontin (SPP1/OPN) and tenascin C (TNC). These results were validated by Western blotting analysis on a panel of ALCL and HD cases. Further research is warranted to better define the role of these S-EV proteins as diagnostic and, possibly, prognostic parameters at diagnosis and for ALCL disease monitoring.

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Meta-Analysis of Oxidative Transcriptomes in Insects

Antioxidants ◽

10.3390/antiox10030345 ◽

2021 ◽

Vol 10 (3) ◽

pp. 345

Author(s):

Hidemasa Bono

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Meta Analysis ◽

Adherens Junction ◽

Enrichment Analysis ◽

Oxidative Stress Response ◽

Insect Species ◽

Rna Seq ◽

Manual Curation ◽

Analysis Workflow

Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.

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Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

BMC Genomic Data ◽

10.1186/s12863-020-00957-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Chunyan Li ◽

Xiaoyun He ◽

Zijun Zhang ◽

Chunhuan Ren ◽

Mingxing Chu

Keyword(s):

Pineal Gland ◽

Expression Pattern ◽

Noncoding Rna ◽

Target Genes ◽

Expression Profiles ◽

Enrichment Analysis ◽

Rna Seq ◽

Important Regulator ◽

Gsh Metabolism ◽

Transcriptome Expression

Abstract Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

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Transcriptomic and ChIP-seq Integrative Analysis Reveals Important Roles of Epigenetically Regulated lncRNAs in Placental Development in Meishan Pigs

Genes ◽

10.3390/genes11040397 ◽

2020 ◽

Vol 11 (4) ◽

pp. 397

Author(s):

Dadong Deng ◽

Xihong Tan ◽

Kun Han ◽

Ruimin Ren ◽

Jianhua Cao ◽

...

Keyword(s):

Differentially Expressed ◽

Rna Seq ◽

Sequencing Data ◽

Placental Development ◽

Cytoskeleton Organization ◽

New Class ◽

Chromatin Immunoprecipitation Sequencing ◽

Non Coding Rnas ◽

Two Stages ◽

Regulatory Functions

The development of the placental fold, which increases the maternal–fetal interacting surface area, is of primary importance for the growth of the fetus throughout the whole pregnancy. However, the mechanisms involved remain to be fully elucidated. Increasing evidence has revealed that long non-coding RNAs (lncRNAs) are a new class of RNAs with regulatory functions and could be epigenetically regulated by histone modifications. In this study, 141 lncRNAs (including 73 up-regulated and 68 down-regulated lncRNAs) were identified to be differentially expressed in the placentas of pigs during the establishment and expanding stages of placental fold development. The differentially expressed lncRNAs and genes (DElncRNA-DEgene) co-expression network analysis revealed that these differentially expressed lncRNAs (DElncRNAs) were mainly enriched in pathways of cell adhesion, cytoskeleton organization, epithelial cell differentiation and angiogenesis, indicating that the DElncRNAs are related to the major events that occur during placental fold development. In addition, we integrated the RNA-seq (RNA sequencing) data with the ChIP-seq (chromatin immunoprecipitation sequencing) data of H3K4me3/H3K27ac produced from the placental samples of pigs from the two stages (gestational days 50 and 95). The analysis revealed that the changes in H3K4me3 and/or H3K27ac levels were significantly associated with the changes in the expression levels of 37 DElncRNAs. Furthermore, several H3K4me3/H3K27ac-lncRNAs were characterized to be significantly correlated with genes functionally related to placental development. Thus, this study provides new insights into understanding the mechanisms for the placental development of pigs.

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Circulating or tissue microRNAs and extracellular vesicles as potential lung cancer biomarkers: a systematic review

The International Journal of Biological Markers ◽

10.5301/ijbm.5000307 ◽

2017 ◽

Vol 33 (1) ◽

pp. 3-9 ◽

Cited By ~ 7

Author(s):

Yan Song ◽

Xiuli Yu ◽

Zongmei Zang ◽

Guijuan Zhao

Keyword(s):

Lung Cancer ◽

Systematic Review ◽

Cancer Patients ◽

Extracellular Vesicles ◽

Target Genes ◽

Enrichment Analysis ◽

Cancer Biomarkers ◽

Biological Processes ◽

Lung Cancer Patients ◽

Prediction Of Prognosis

For both lung cancer patients and clinical physicians, tumor biomarkers for more efficient early diagnosis and prediction of prognosis are always wanted. Biomarkers in circulating serum, including microRNAs (miRNAs) and extracellular vesicles, hold the greatest possibilities to partially substitute for tissue biopsy. In this systematic review, studies on circulating or tissue miRNAs and extracellular vesicles as potential biomarkers for lung cancer patients were reviewed and are discussed. Furthermore, the target genes of the miRNAs indicated were identified through the miRTarBase, while the relevant biological processes and pathways of miRNAs in lung cancer were analyzed through MiRNA Enrichment Analysis and Annotation (MiEAA). In conclusion, circulating or tissue miRNAs and extracellular vesicles provide us with a window to explore strategies for diagnosing and assessing prognosis and treatment in lung cancer patients.

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RNA Sequencing (RNA-Seq) Based Transcriptome Analysis in Immune Response of Holstein Cattle to Killed Vaccine against Bovine Viral Diarrhea Virus Type I

Animals ◽

10.3390/ani10020344 ◽

2020 ◽

Vol 10 (2) ◽

pp. 344 ◽

Cited By ~ 3

Author(s):

Bryan Irvine Lopez ◽

Kier Gumangan Santiago ◽

Donghui Lee ◽

Seungmin Ha ◽

Kangseok Seo

Keyword(s):

Immune Response ◽

Enrichment Analysis ◽

Receptor Interaction ◽

Type I ◽

Rna Seq ◽

Diarrhea Virus ◽

Viral Diarrhea ◽

Kegg Pathways ◽

Viral Diarrhea Virus

Immune response of 107 vaccinated Holstein cattle was initially obtained prior to the ELISA test. Five cattle with high and low bovine viral diarrhea virus (BVDV) type I antibody were identified as the final experimental animals. Blood samples from these animals were then utilized to determine significant differentially expressed genes (DEGs) using the RNA-seq transcriptome analysis and enrichment analysis. Our analysis identified 261 DEGs in cattle identified as experimental animals. Functional enrichment analysis in gene ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed the DEGs potentially induced by the inactivated BVDV type I vaccine, and might be responsible for the host immune responses. Our findings suggested that inactivated vaccine induced upregulation of genes involved in different GO annotations, including antigen processing and presentation of peptide antigen (via MHC class I), immune response, and positive regulation of interferon-gamma production. The observed downregulation of other genes involved in immune response might be due to inhibition of toll-like receptors (TLRs) by the upregulation of the Bcl-3 gene. Meanwhile, the result of KEGG pathways revealed that the majority of DEGs were upregulated and enriched to different pathways, including cytokine-cytokine receptor interaction, platelet activation, extracellular matrix (ECM) receptor interaction, hematopoietic cell lineage, and ATP-binding cassette (ABC) transporters. These significant pathways supported our initial findings and are known to play a vital role in shaping adaptive immunity against BVDV type 1. In addition, type 1 diabetes mellitus pathways tended to be significantly enriched. Thus, further studies are needed to investigate the prevalence of type 1 diabetes mellitus in cattle vaccinated with inactivated and live BVDV vaccine.

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Bioinformatics-based Screening of Key Genes for Saponin Metabolism in Quinoa

10.21203/rs.3.rs-139481/v1 ◽

2021 ◽

Author(s):

Chengang Guo ◽

Zhimin wei ◽

Wei Lyu ◽

Yanlou Geng

Keyword(s):

Differentially Expressed Genes ◽

Principal Component ◽

Enrichment Analysis ◽

Hierarchical Cluster ◽

Gene Set Enrichment Analysis ◽

Differentially Expressed ◽

Differential Analysis ◽

Rna Seq ◽

Protein Coding ◽

Key Genes

Abstract Quinoa saponins have complex, diverse and evident physiologic activities. However, the key regulatory genes for quinoa saponin metabolism are not yet well studied. The purpose of this study was to explore genes closely related to quinoa saponin metabolism. In this study, the significantly differentially expressed genes in yellow quinoa were firstly screened based on RNA-seq technology. Then, the key genes for saponin metabolism were selected by gene set enrichment analysis (GSEA) and principal component analysis (PCA) statistical methods. Finally, the specificity of the key genes was verified by hierarchical clustering. The results of differential analysis showed that 1654 differentially expressed genes were achieved after pseudogenes deletion. Therein, there were 142 long non-coding genes and 1512 protein-coding genes. Based on GSEA analysis, 116 key candidate genes were found to be significantly correlated with quinoa saponin metabolism. Through PCA dimension reduction analysis, 57 key genes were finally obtained. Hierarchical cluster analysis further demonstrated that these key genes can clearly separate the four groups of samples. The present results could provide references for the breeding of sweet quinoa and would be helpful for the rational utilization of quinoa saponins.

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