scholarly journals Comparative analysis of the exosomal contents of DF-1 cells infected by ALV-J

2021 ◽  
Author(s):  
J Yang ◽  
P Zhuang ◽  
Z Cheng ◽  
G Wang
Keyword(s):  
Target Genes ◽  
Viral Pathogenesis ◽  
Signal Pathway ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Signal Pathways ◽  
Differentially Expressed Proteins ◽  
Detection Technology ◽  
Subgroup J ◽  
Avian Leukosis Virus Subgroup

Exploration of the abnormal expression of exosomal molecules during the infection of avian leukosis virus subgroup J (ALV-J) is essential to provide a deeper understanding of the exosome’s role in the viral pathogenesis involved. The study aimed to investigate the differentially expressed proteins and miRNAs of the exosomes derived from DF-1 cells infected by ALV-J, their gene function and involved signal pathways. We isolated exosomes from DF-1 cells infected by ALV-J. The differentially expressed proteins and miRNAs of the exosomes were determined by proteomics and transcription detection technology. A Gene Ontology (GO) analysis and a Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway analysis identified the miRNAs target genes and the signal pathways regulated by the different proteins or/and miRNAs. A total of 116 proteins (58 upregulated and 58 downregulated) and 3 miRNAs (all upregulated) were determined. These proteins were involved in 155 signal pathways, in which the highest number of proteins involved in the cancer pathway was (up to) seven. The target genes of the miRNAs were involved in 3 signal pathways. Both the proteins and target genes of the miRNAs were involved in the Ribosome pathway and ECM-receptor interaction pathway. The results suggested that the ALV-J infection changed the proteins and miRNAs of the exosomes significantly.

scholarly journals MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 468 ◽  
Author(s):  
Xiangfei Ma ◽  
Junwei Sun ◽  
Shuaipeng Zhu ◽  
Zhenwei Du ◽  
Donghua Li ◽  
...  
Keyword(s):  
Production Efficiency ◽  
Target Genes ◽  
Strong Association ◽  
Abdominal Fat ◽  
Signal Pathway ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Signal Pathways ◽  
Abdominal Fat Deposition

The excessive deposition of abdominal fat has become an important factor in restricting the production efficiency of chickens, so reducing abdominal fat deposition is important for improving growth rate. It has been proven that miRNAs play an important role in regulating many physiological processes of organisms. In this study, we constructed a model of adipogenesis by isolating preadipocytes (Ab-Pre) derived from abdominal adipose tissue and differentiated adipocytes (Ab-Ad) in vitro. Deep sequencing of miRNAs and mRNAs expressed in Ab-Pre and Ab-Ad groups was conducted to explore the effect of miRNAs and mRNAs on fat deposition. We identified 80 differentially expressed miRNAs (DEMs) candidates, 58 of which were up-regulated and 22 down-regulated. Furthermore, six miRNAs and six mRNAs were verified by qRT-PCR, and the results showed that the expression of the DEMs and differentially expressed genes (DEGs) in the two groups was consistent with our sequencing results. When target genes of miRNA were combined with mRNA transcriptome data, a total of 891 intersection genes were obtained, we predicted the signal pathways of cross genes enrichment to the MAPK signal pathway, insulin signal pathway, fatty acid metabolism, and ECM–receptor interaction. Meanwhile, we constructed miRNA and negatively correlated mRNA target networks, including 12 miRNA–mRNAs pairs, which showed a strong association with the abdominal adipocyte differentiation (miR-214−ACSBG2, NFKB2, CAMK2A, ACLY, CCND3, PLK3, ITGB2; miR-148a-5p−ROCK2; miR-10a-5p−ELOVL5; miR-146b-5p−LAMA4; miR-6615-5p−FLNB; miR-1774−COL6A1). Overall, these findings provide a background for further research on lipid metabolism. Thus, we can better understand the molecular genetic mechanism of chicken abdominal fat deposition.

scholarly journals Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Suxiang Lu ◽  
Qian Xiong ◽  
Kang Du ◽  
Xiaoni Gan ◽  
Xuzhen Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Multiple Reaction Monitoring ◽  
Limb Regeneration ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Differentially Expressed Proteins ◽  
Absolute Quantitation ◽  
Bioinformatics Analyses ◽  
Fin Regeneration ◽  
Early Stages

Abstract Background Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown. Methods To identify the differentially expressed proteins (DEPs) during the early stages of lobed fin regeneration in P. senegalus, we performed a differential proteomic analysis using isobaric tag for relative and absolute quantitation (iTRAQ) approach based quantitative proteome from the pectoral lobed fins at 3 time points. Furthermore, we validated the changes in protein expression with multiple-reaction monitoring (MRM) analysis. Results The experiment yielded a total of 3177 proteins and 15,091 unique peptides including 1006 non-redundant (nr) DEPs. Of these, 592 were upregulated while 349 were downregulated after lobed fin amputation when compared to the original tissue. Bioinformatics analyses showed that the DEPs were mainly associated with Ribosome and RNA transport, metabolic, ECM-receptor interaction, Golgi and endoplasmic reticulum, DNA replication, and Regulation of actin cytoskeleton. Conclusions To our knowledge, this is the first proteomic research to investigate alterations in protein levels and affected pathways in bichirs’ lobe-fin/limb regeneration. In addition, our study demonstrated a highly dynamic regulation during lobed fin regeneration in P. senegalus. These results not only provide a comprehensive dataset on differentially expressed proteins during the early stages of lobe-fin/limb regeneration but also advance our understanding of the molecular mechanisms underlying lobe-fin/limb regeneration.

Differentially expressed circRNA and mRNA profiles of neural stem cells with radiation irradiation

2020 ◽  
Author(s):  
Zhaopeng Cai ◽  
Shan Wang ◽  
Zhongyu Xie ◽  
Peng Wang ◽  
Huiyong Shen ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Circular Rna ◽  
Signal Pathway ◽  
Differentially Expressed ◽  
Signal Pathways ◽  
Spine Metastasis ◽  
Radiation Induced ◽  
Differentially Expressed Mrna ◽  
Oncology Practice ◽  
Mapk Signal Pathway

Abstract Background Spine metastasis is common but highly problematic in clinical oncology practice. Radiotherapy plays an important role in the treatment of spine metastasis, but it at the same time damages the nervous tissue, especially the neural stem cell (NSC), and leads to radiation induced myelopathy. Circular RNA (circRNA) is a kind of non-coding RNA which responses to external stimulus and regulates cellular functions. However, the mechanism of radiotherapy affecting NSC and the role of circRNA in this process are still unclear. Methods The circRNA and mRNA of NSC treated with radiation or not were detect using next-generation sequencing. RT-PCR assays were preformed to confirm the sequencing results and the feature of differentially expressed circRNA. Bioinformation analyses were conducted to identified the critical circRNA and mRNA, as well as the enriched functions and pathways. Moreover, a circRNA-miRNA-mRNA network was constructed to investigate the possible regulatory mechanism. Results A total of 421 differentially expressed circRNA and 1602 differentially expressed mRNA of NSC were identified after radiotherapy. The GO and KEGG analysis of the differentially expressed mRNA as well as the host genes of the differentially expressed circRNA were performed and several key signal pathways such as MAPK signal pathway were identified. Moreover, a circRNA-miRNA-mRNA network focusing on MAPK signal pathway was shown and predicted that chr5:127160496|127165240 could be the critical circRNA in the regulatory mechanism of radiation treated NSCs. Conclusion Our finding showed the differentially expressed circRNA and mRNA profiles of NSC after radiotherapy, suggesting that circRNA may contribute to the pathogenesis of radiation induced myelopathy.

scholarly journals Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress inBrassica rapaL. (Inbred Line “Chiifu”)

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Soon-Wook Kwon ◽  
Mijeong Kim ◽  
Hijin Kim ◽  
Joohyun Lee
Keyword(s):  
Drought Stress ◽  
Inbred Line ◽  
Stress Responses ◽  
Target Genes ◽  
Antioxidant Activities ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Family Protein

Through a comparative shotgun quantitative proteomics analysis inBrassica rapa(inbred line Chiifu), total of 3,009 nonredundant proteins were identified with a false discovery rate of 0.01 in 3-week-old plants subjected to dehydration treatment for 0, 24, and 48 h, plants subjected to drought stress. Ribulose-bisphosphate carboxylases, chlorophyll a/b-binding protein, and light harvesting complex in photosystem II were highly abundant proteins in the leaves and accounted for 9%, 2%, and 4%, respectively, of the total identified proteins. Comparative analysis of the treatments enabled detection of 440 differentially expressed proteins during dehydration. The results of clustering analysis, gene ontology (GO) enrichment analysis, and analysis of composite expression profiles of functional categories for the differentially expressed proteins indicated that drought stress reduced the levels of proteins associated with photosynthesis and increased the levels of proteins involved in catabolic processes and stress responses. We observed enhanced expression of many proteins involved in osmotic stress responses and proteins with antioxidant activities. Based on previously reported molecular functions, we propose that the following five differentially expressed proteins could provide target genes for engineering drought resistance in plants: annexin, phospholipase D delta, sDNA-binding transcriptional regulator, auxin-responsive GH3 family protein, and TRAF-like family protein.

scholarly journals Genome-wide profiling of miRNA expression patterns in tubal endometriosis

Reproduction ◽  
2019 ◽  
Vol 157 (6) ◽  
pp. 525-534 ◽  
Author(s):  
Hang Qi ◽  
Guiling Liang ◽  
Jin Yu ◽  
Xiaofeng Wang ◽  
Yan Liang ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Mirna Expression ◽  
Gene Networks ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Signal Pathways ◽  
Differentially Expressed Mirnas

MicroRNA (miRNA) expression profiles in tubal endometriosis (EM) are still poorly understood. In this study, we analyzed the differential expression of miRNAs and the related gene networks and signaling pathways in tubal EM. Four tubal epithelium samples from tubal EM patients and five normal tubal epithelium samples from uterine leiomyoma patients were collected for miRNA microarray. Bioinformatics analyses, including Ingenuity Pathway Analysis (IPA), Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were performed. Quantitative real-time polymerase chain reaction (qRT-PCR) validation of five miRNAs was performed in six tubal epithelium samples from tubal EM and six from control. A total of 17 significantly differentially expressed miRNAs and 4343 potential miRNA-target genes involved in tubal EM were identified (fold change >1.5 and FDR-adjustedPvalue <0.05). IPA indicated connections between miRNAs, target genes and other gynecological diseases like endometrial carcinoma. GO and KEGG analysis revealed that most of the identified genes were involved in the mTOR signaling pathway, SNARE interactions in vesicular transport and endocytosis. We constructed an miRNA-gene-disease network using target gene prediction. Functional analysis showed that the mTOR pathway was connected closely to tubal EM. Our results demonstrate for the first time the differentially expressed miRNAs and the related signal pathways involved in the pathogenesis of tubal EM which contribute to elucidating the pathogenic mechanism of tubal EM-related infertility.

scholarly journals Identification of Differentially Expressed Non-coding RNA Networks With Potential Immunoregulatory Roles During Salmonella Enteritidis Infection in Ducks

2021 ◽  
Vol 8 ◽  
Author(s):  
Yu Zhang ◽  
Xiaoqian Dong ◽  
Lie Hou ◽  
Zhengfeng Cao ◽  
Guoqiang Zhu ◽  
...  
Keyword(s):  
Granulosa Cells ◽  
Regulatory Networks ◽  
Egg Production ◽  
Salmonella Enteritidis ◽  
Time Course ◽  
Target Genes ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Circular Rnas ◽  
Preovulatory Follicles

Salmonella enterica serovar Enteritidis (S. Enteritidis) is a pathogen that can colonize the preovulatory follicles of poultry, thereby causing both reduced egg production and an elevated risk of foodborne salmonellosis in humans. Although a few studies have revealed S. Enteritidis preferentially invades the granulosa cell layer within these follicles, it can readily persist and proliferate through mechanisms that are not well-understood. In this study, we characterized competing endogenous RNA (ceRNA) regulatory networks within duck granulosa cells following time-course of S. Enteritidis challenge. The 8108 long non-coding RNAs (lncRNAs), 1545 circular RNAs (circRNAs), 542 microRNAs (miRNAs), and 4137 mRNAs (fold change ≥2; P &lt; 0.01) were differentially expressed during S. Enteritidis challenge. Also, eight mRNAs, eight lncRNAs and five circRNAs were selected and the consistent expression trend was found between qRT-PCR detection and RNA-seq. Moreover, the target genes of these differentially expressed ncRNAs (including lncRNAs, circRNAs and miRNAs) were predicted, and significantly enriched in the innate immune response and steroidogenesis pathways. Then, the colocalization and coexpression analyses were conducted to investigate relationships between ncRNAs and mRNAs. The 16 differentially expressed miRNAs targeting 60 differentially expressed mRNAs were identified in granulosa cells at 3 and 6 h post-infection (hpi) and enriched in the MAPK, GnRH, cytokine-cytokine receptor interaction, Toll-like receptor, endocytosis, and oxidative phosphorylation signaling pathways. Additionally, underlying lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks were then constructed to further understand their interaction during S. Enteritidis infection. Lnc_012227 and novel_circ_0004892 were identified as ceRNAs, which could compete with miR-let-7g-5p and thereby indirectly modulating map3k8 expression to control S. Enteritidis infection. Together, our data thus identified promising candidate ncRNAs responsible for regulating S. Enteritidis infection in the preovulatory follicles of ducks, offering new insights regarding the ovarian transmission of this pathogen.

The study of the significance and prognosis of the differential expressed miRNAs and their target genes associated with biological in colorectal cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15088-e15088
Author(s):  
Mingyun Wang ◽  
Mi Yang
Keyword(s):  
Colorectal Cancer ◽  
Target Genes ◽  
Biological Significance ◽  
Differentially Expressed ◽  
Prognostic Indicators ◽  
Receptor Interaction ◽  
Ppi Network ◽  
Prognostic Information ◽  
Chemokine Signaling ◽  
Chemokine Signaling Pathway

e15088 Background: MicroRNAs (miRNAs) have been related to prognostic indicators (such as stage and survival) in colorectal cancer. This study aimed to identify differentially expressed miRNAs and their target genes associated with biological significance and prognosis in colorectal cancer. Methods: The colorectal cancer, colorectal adenoma, and normal samples were obtained from the gene expression profile of GSE71187. A union of differentially expressed genes (DEGs) in the three groups was identified. The significantly different modules with highly interconnected DEGs were identified using weighted correlation network analysis (WGCNA) and were enriched to the KEGG pathway and GO function. Subsequently, the protein-protein interaction (PPI) network for DEGs in the module and the integrated regulatory network of miRNA-DEGs were constructed. In addition, the relationship of target DEGs and prognostic information was analyzed. Results: Three significantly different modules were identified, such as the brown, turquoise, and grey modules. The turquoise module including LTC4S, KLRK1, UNC5C, etc., which was mainly enriched to cell adhesion, cytokine−cytokine receptor interaction, and chemokine signaling pathway, inhibited the development of colorectal cancer. Subsequently, PPI network was constructed with the 678 DEGs in the three modules. Moreover, the miRNA-DEGs network was constructed with the 17 target DEGs (CXCR1, LTC4S, BTK, IGF1, etc.) and 14 miRNA (hsa-miR-335-5p, etc.). Finally, the overexpressed LTC4S was a good prognostic biomarker for colorectal cancer. Conclusions: The hsa-miR-335-5p might have potential prognosis value by targeting LTC4S and CXCR1 in colorectal cancer.

scholarly journals An RNA-seq-Based Expression Profiling of Radiation-Induced Esophageal Injury in a Rat Model

Dose-Response ◽  
2019 ◽  
Vol 17 (2) ◽  
pp. 155932581984337 ◽  
Author(s):  
Zhiqiang Sun ◽  
Jinhui Li ◽  
Min Lin ◽  
Shuyu Zhang ◽  
Judong Luo ◽  
...  
Keyword(s):  
Immune Responses ◽  
Target Genes ◽  
Cell Damage ◽  
Differentially Expressed ◽  
Acute Injury ◽  
Esophageal Injury ◽  
Receptor Interaction ◽  
Rna Seq ◽  
Unsuccessful Treatment ◽  
Radiation Induced

Radiation-induced acute injury is the main reason for the suspension of radiotherapy and unsuccessful treatment of cancer. It is of great importance to understand the molecular mechanism of radiation-induced esophageal injury. We used RNA-seq data from normal esophageal tissue and irradiated esophageal tissues and applied computational approaches to identify and characterize differentially expressed genes and detected 40 059 messenger RNAs (mRNAs) previously annotated and 717 novel long noncoding RNAs (lncRNAs). There were 14 upregulated and 32 downregulated lncRNAs among the differentially expressed lncRNA group. Their target genes were involved in the mRNA surveillance pathway, pathological immune responses, and cellular homeostasis. Additionally, we found 853 differentially expressed mRNAs, and there were 384 upregulated and 469 downregulated mRNAs. Notably, we found that the differentially expressed mRNAs were enriched for steroid biosynthesis, the tumor necrosis factor signaling pathway, focal adhesion, pathways in cancer, extracellular matrix–receptor interaction, and so on. The response of normal esophageal tissues to ionizing radiation is multifarious. The radiation-induced cell damage response by multiple pathways followed by pathological immune responses activated. Studies on the dynamic network of molecules involved in radiation-induced esophageal injury are under way to clarify the regulatory mechanisms and identify the candidate targets.

scholarly journals Quantitative iTRAQ-based proteomic analysis of differentially expressed proteins in aging in human and monkey

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hao Wang ◽  
Xiaoqi Zhu ◽  
Junyan Shen ◽  
En-Feng Zhao ◽  
Dajun He ◽  
...  
Keyword(s):  
Western Blotting ◽  
Inflammatory Responses ◽  
Circulatory System ◽  
Absolute Quantification ◽  
Fold Change ◽  
Differentially Expressed ◽  
Behavioral Experiment ◽  
Receptor Interaction ◽  
Differentially Expressed Proteins ◽  
Itraq Analysis

Abstract Background The underlying physiological mechanisms associated with aging are still complex and unclear. As a very important tissue of human body, the circulatory system also plays a very important role in the process of aging. In this study, we use the isobaric tags for relative and absolute quantification (iTRAQ) method to identify differentially expressed proteins in plasma for humans and monkeys between young and aged. Western blotting and behavioral experiment in mice were performed to validate the expression of the candidate protein. Results Between the young / the old humans and the young / the old monkeys 74 and 69 proteins were found to be differently expressed, respectively. For the human samples, these included 38 up-regulated proteins and 36 down-regulated proteins (a fold change ≥1.3 or ≤ 0.667, p value ≤0.05).For the monkey samples, 51 up-regulated proteins and 18 down-regulated proteins (a fold change ≥1.3 or ≤ 0.667, p value ≤0.05). KEGG pathway analysis revealed that phagosome, focal adhesion, ECM-receptor interaction and PI3K/AKT signaling pathway were the most common pathways involved in aging. We found only IGFBP4 protein that existed in up-regulated proteins in aged both for human and monkey. In addition, the differential expression of IGFBP4 was validated by western blot analysis and IGFBP4 treatment mimicked aging-related cognitive dysfunction in mice. Conclusions This first, the integrated proteomics for the plasma protein of human and monkey reveal one protein-IGFBP4, which was validated by western blotting and behavioral analysis can promote the process of aging. And, iTRAQ analysis showed that proteolytic systems, and inflammatory responses plays an important role in the process of aging. These findings provide a basis for better understanding of the underlying mechanisms involved in aging.

An integrated analysis of mRNA and miRNA in skeletal muscle from myostatin-edited Meishan pigs

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 305-315 ◽  
Author(s):  
Shanshan Xie ◽  
Xiang Li ◽  
Lili Qian ◽  
Chunbo Cai ◽  
Gaojun Xiao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Growth And Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Genetically Engineered ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Signal Pathways ◽  
Skeletal Muscle Growth ◽  
Differentially Expressed Mirnas

Myostatin (MSTN) is a key muscle factor that negatively regulates skeletal muscle growth and development. Our laboratory recently produced genetically engineered Meishan pigs containing a ZFN-edited MSTN loss-of-function mutation (MSTN−/−, MKO) that led to the hypertrophy of skeletal muscles. In this study, we performed transcriptome sequencing and miRNA sequencing in skeletal muscle samples from MKO and wildtype Meishan (MWT) pigs to investigate the effect of MSTN−/− on expression of mRNA and miRNA. Our results indicated that, compared to MWT pigs, there were 200 genes and 4 miRNAs being significantly up-regulated, and 238 genes and 5 miRNAs being significantly down-regulated in MKO pigs. Analysis by GO and KEGG pathways revealed that differentially expressed miRNAs and their target genes of those differentially expressed miRNAs were involved in the signal pathways of skeletal muscle growth and development such as AMPK, mTOR, and TGF-beta. An integrated analysis of the correlation between miRNA-mRNA and transcriptome predicated that XK and METTL8 were target genes for miR-499-5p, while LRP4 was a target gene for miR-490-3p. Our results provide important clues to help us further investigate MSTN′s regulatory mechanisms during skeletal muscle growth and development.

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