scholarly journals Identification of targets of JS-K against HBV-positive human hepatocellular carcinoma HepG2.2.15 cells with iTRAQ proteomics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhengyun Liu ◽  
Yan Xu ◽  
Wanling Zhang ◽  
Xinghong Gao ◽  
Guo Luo ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Rt Pcr ◽  
Expression Levels ◽  
Liver Cancer Cells ◽  
Important Target ◽  
B Virus ◽  
Itraq Proteomics ◽  
Nitric Oxide Releasing

AbstractJS-K, a nitric oxide-releasing diazeniumdiolates, is effective against various tumors. We have discovered that JS-K was effective against Hepatitis B virus (HBV)-positive HepG2.2.15 cells. This study used iTRAQ to identify differentially expressed proteins following JS-K treatment of HepG2.2.15 cells. Silenced Transgelin (shTAGLN-2.15) cells were constructed, and the cell viability was analyzed by the CCK8 assay after treatment with JS-K. There were 182 differentially expressed proteins in JS-K treated-HepG2.2.15 cells; 73 proteins were up-regulated and 109 proteins were down-regulated. These proteins were categorized according to GO classification. KEGG enrichment analysis showed that Endocytosis, Phagosome and Proteoglycans were the most significant pathways. RT-PCR confirmed that the expression levels of TAGLN, IGFBP1, SMTN, SERPINE1, ANXA3, TMSB10, LGALS1 and KRT19 were significantly up-regulated, and the expression levels of C5, RBP4, CHKA, SIRT5 and TRIM14 were significantly down-regulated in JS-K treated-HepG2.2.15 cells. Western blotting confirmed the increased levels of USP13 and TAGLN proteins in JS-K treated-HepG2.2.15 cells. Molecular docking revealed the binding of JS-K to TAGLN and shTAGLN-2.15 cells were resistant to JS-K cytotoxicity, suggesting that TAGLN could be an important target in JS-K anti-HBV-positive liver cancer cells. These proteomic findings could shed new insights into mechanisms underlying the effect of JS-K against HBV-related HCC.

scholarly journals Influence of estradiol on bovine trophectoderm and uterine gene transcripts around maternal recognition of pregnancy

2021 ◽  
Author(s):  
Emmalee J Northrop-Albrecht ◽  
Jerica J J Rich ◽  
Robert A Cushman ◽  
Runan Yao ◽  
Xijin Ge ◽  
...  
Keyword(s):  
Artificial Insemination ◽  
Mrna Level ◽  
Fixed Time ◽  
Beef Cows ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Rt Pcr ◽  
Embryo Survival ◽  
Uterine Fluid ◽  
Gene Transcripts

Abstract Embryo survival and pregnancy success is increased among animals that exhibit estrus prior to fixed time artificial insemination (AI), but there are no differences in conceptus survival to d16. The objective of this study was to determine effects of preovulatory estradiol on uterine transcriptomes, select trophectoderm transcripts, and uterine luminal fluid (ULF) proteins. Beef cows/heifers were synchronized, artificially inseminated (d0), and grouped into either high (highE2) or low (lowE2) preovulatory estradiol. Uteri were flushed (d16); conceptuses and endometrial biopsies (n = 29) were collected. RNA sequencing was performed on endometrium. Real-Time PCR (RT-PCR) was performed on trophectoderm (TE; n = 21) RNA to measure relative abundance of IFNT, PTGS2, TM4SF1, C3, FGFR2, and GAPDH. Uterine fluid was analyzed using 2D LC–MS/MS based iTRAQ method. RT-PCR data were analyzed using the MIXED procedure in SAS. There were no differences in mRNA abundances in TE, but there were 432 differentially expressed genes (DEGs) (253 downregulated, 179 upregulated) in highE2/conceptus versus lowE2/conceptus groups. There were also 48 differentially expressed proteins (DEPs; 19 upregulated, 29 downregulated), 6 of these were differentially expressed (FDR < 0.10) at the mRNA level. Similar pathways for mRNA and proteins included: calcium signaling, protein kinase A signaling, and corticotropin releasing hormone (CRH) signaling. These differences in uterine function, may be preparing the conceptus for improved likelihood of survival after d16 among highE2 animals.

scholarly journals Analysis of Differentially Expressed Proteins Involved in Autoimmune Cirrhosis and Normal Serum by iTRAQ Proteomics

2018 ◽  
Vol 13 (3) ◽  
pp. 1700153 ◽  
Author(s):  
Zheng Minghui ◽  
Hu Kunhua ◽  
Bao Yunwen ◽  
Lu Hongmei ◽  
Li Jing ◽  
...  
Keyword(s):  
Normal Serum ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Itraq Proteomics

Proteomic analysis of tears and serum for dry eye disease using ovariectomized cynomolgus monkey

2020 ◽  
Author(s):  
xiaolong yang ◽  
Yue Xu ◽  
Yun Wang ◽  
Chang Li ◽  
Xiaofeng Zhang
Keyword(s):  
Gene Ontology ◽  
Growth Factor ◽  
Dry Eye ◽  
Cynomolgus Monkey ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Differentially Expressed Proteins ◽  
Dry Eyes ◽  
Experimental Group

Abstract Background Ovariectomized cynomolgus monkey 30 months after surgery was selected as the research object to identify protein changes in tears and serum to provide a reference for the diagnosis and pathogenesis of dry eye in menopausal women. Methods Six cynomolgus monkey were randomly divided into an experimental group and a control group (3 in each group). The experimental group underwent bilateral ovariectomy, while the control group underwent sham surgery with their ovaries reserved. Proteomic analysis was performed by LC-MS/MS on tears and serum collected from two groups. Differentially expressed proteins were identified and were performed cluster analysis, which included gene ontology, the Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein interaction. Results 33 differentially expressed proteins have been identified in tears and17 differentially expressed proteins have been identified in serum. Kyoto Encyclopedia of Genes and Genomes enrichment analysis in tears has discovered Glucagon signaling pathway and neurotrophin signaling pathway may play an important role in the pathogenesis of dry eye. Gene ontology enrichment analysis in serum has discovered insulin-like growth factor binding and growth factor binding in molecular function probably make effort in pathogenesis of dry eye. KEGG analysis in serum has discovered salivary secretion may be the key pathway in pathogenesis of dry eye. Conclusions Protein G7PCH4, Q2PG17 and G7PT55 in tears may be the key protein in pathogenesis of dry eyes. Protein G7P1T1, G7PUN9 and G8F302 in serum may play an important role in pathogenesis of dry eyes.

Quantitative proteomics analysis of FFPE tumor samples reveals the influences of novel targeting nanobubbles conjugated with NET-1 siRNA on tetraspanin protein involved in HCC

2020 ◽  
Author(s):  
Bolin Wu ◽  
Haitao Shang ◽  
Xitian Liang ◽  
Huajing Yang Huajing Yang ◽  
Hui Jing ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Interaction Analysis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Protein Protein Interaction ◽  
Study Results ◽  
Ffpe Tumor

Abstract Background: Hepatocellular carcinoma (HCC) poses a severe threat to human health. The NET-1 protein has been proved to be strongly associated with HCC proliferation and metastasis in our previous study. Methods: Here, we developed a label-free proteome mass spectrometry workflow to analyze formalin-fixed and paraffin-embedded HCC xenograft samples collected in our previous study. Results: The result showed that 78 proteins were differentially expressed after NET-1 protein inhibited. Among them, the expression of 61 proteins up-regulated and the expression of 17 proteins were significantly down-regulated. Of the differentially expressed proteins, the vast majority of Gene Ontology enrichment terms belong to the biological process. The KEGG pathway enrichment analysis showed that the 78 differentially expressed proteins significantly enriched in 45 pathways. We concluded that the function of the NET-1 gene is not only to regulate HCC but also to participate in a variety of biochemical metabolic pathways in the human body. Furthermore, the protein-protein interaction analysis indicated that the interactions of differentially expressed proteins are incredibly sophisticated. All the protein-protein interactions happened after the NET-1 gene has been silenced. Conclusions: Finally, our study also provides a useful proposal for targeted therapy based on tetraspanin proteins to treat HCC, and further mechanism investigations are needed to reveal a more detailed mechanism of action for NET-1 protein regulation of HCC.

scholarly journals Notch1 down-regulation in lineage-restricted niches of mouse eccrine sweat glands

2021 ◽  
Author(s):  
Yuzhen Wang ◽  
Bin Yao ◽  
Xianlan Duan ◽  
Jianjun Li ◽  
Wei Song ◽  
...  
Keyword(s):  
Stem Cells ◽  
Gene Ontology ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Sweat Glands ◽  
Sequencing Analysis ◽  
Differentially Expressed Proteins ◽  
Epidermal Stem Cells ◽  
Eccrine Sweat Glands

Abstract BackgroundEccrine sweat gland (SG) restrictedly exists in mouse foot pads indicating that mouse plantar dermis (PD) contains the SG lineage-restricted niches. However, it is still unclear how niches can affect stem cell fates.MethodsIn this study, we tried to find the key cues by which stem cells sense and interact with the SG lineage-specific niches. Briefly, we used transcriptomics RNA sequencing analysis to screen differentially expressed genes between SG cells and epidermal stem cells (ES), and then we used proteomic analysis to screen differentially expressed proteins between PD and dorsal dermis (DD).ResultsWe found that Notch1 is not only closely related to embryonic SG morphogenesis based on Gene Ontology enrichment analysis but also differentially down-regulated during SG formation in the levels of genes and proteins. Furthermore, immunochemistry and immunofluorescence staining verified that Notch1 was continuously down-regulated along with the process of SG morphogenesis. Especially, Notch1 positive cells almost disappeared neither in the emerging SG buds or in the newly-formed glandular structures.ConclusionHence, we speculated that Notch1 possibly acts as the role of “gatekeeper” during embryonic SG development and is the promising key cue that regulates the interactions between stem cells and the SG lineage-specific niches. Our attempts highlighted the role of Notch1 during embryonic SG organogenesis.Trial registration Not applicable.

Analysis of Differentially Expressed Proteins Involved in miR-449a for Hepatocellular Carcinoma by iTRAQ Proteomics

2021 ◽  
Vol 67 (03/2021) ◽  
Author(s):  
Xuesong Deng ◽  
Jun Cheng ◽  
Naiyang Zhan ◽  
Jianwei Chen ◽  
Yongqiang Zhan ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Itraq Proteomics

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 Screening for proteins related to the biosynthesis of hispidin and its derivatives in Phellinus igniarius using iTRAQ proteomic analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jinjing Guo ◽  
Xiaoxi Liu ◽  
Yuanjie Li ◽  
Hongyan Ji ◽  
Cheng Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Biosynthetic Pathway ◽  
Multiple Reaction Monitoring ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Common Source ◽  
Differentially Expressed Proteins ◽  
Phellinus Igniarius ◽  
Chemical Structures

Abstract Background Hispidin (HIP) and its derivatives, a class of natural fungal metabolites, possess complex chemical structures with extensive pharmacological activities. Phellinus igniarius, the most common source of HIP, can be used as both medicine and food. However, the biosynthetic pathway of HIP in P. igniarius remains unclear and we have a limited understanding of the regulatory mechanisms related to HIP. In this work, we sought to illustrate a biosynthesis system for hispidin and its derivatives at the protein level. Results We found that tricetolatone (TL) is a key biosynthetic precursor in the biosynthetic pathway of hispidin and that its addition led to increased production of hispidin and various hispidin derivatives. Based on the changes in the concentrations of precursors and intermediates, key timepoints in the biosynthetic process were identified. We used isobaric tags for relative and absolute quantification (iTRAQ) to study dynamic changes of related proteins in vitro. The 270 differentially expressed proteins were determined by GO enrichment analysis to be primarily related to energy metabolism, oxidative phosphorylation, and environmental stress responses after TL supplementation. The differentially expressed proteins were related to ATP synthase, NAD binding protein, oxidoreductase, and other elements associated with electron transfer and dehydrogenation reactions during the biosynthesis of hispidin and its derivatives. Multiple reaction monitoring (MRM) technology was used to selectively verify the iTRAQ results, leading us to screen 11 proteins that were predicted to be related to the biosynthesis pathways. Conclution These findings help to clarify the molecular mechanism of biosynthesis of hispidin and its derivatives and may serve as a foundation for future strategies to identify new hispidin derivatives.

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