Genomic and Functional Analysis of the Toxic Effect of Tachyplesin I on the Embryonic Development of Zebrafish

Computational and Mathematical Methods in Medicine ◽

10.1155/2014/454310 ◽

2014 ◽

Vol 2014 ◽

pp. 1-6 ◽

Cited By ~ 2

Author(s):

Hongya Zhao ◽

Jianguo Dai ◽

Gang Jin

Keyword(s):

Toxic Effect ◽

Antigen Processing ◽

Horseshoe Crab ◽

Statistical Data ◽

Biological Processes ◽

Embryonic Cells ◽

Gene Expressions ◽

Coexpressed Genes ◽

Different Doses ◽

Tachyplesin I

Tachyplesin I (TP I) is an antimicrobial peptide isolated from the hemocytes of the horseshoe crab. With the developments of DNA microarray technology, the genetic analysis of the toxic effect of TP I on embryo was originally considered in our recent study. Based on our microarray data of the embryonic samples of zebrafish treated with the different doses of TP I, we performed a series of statistical data analyses to explore the toxic effect of TP I at the genomic level. In this paper, we first employed the hexaMplot to illustrate the continuous variation of the gene expressions of the embryonic cells treated with the different doses of TP I. The probabilistic model-based Hough transform was used to classify these differentially coexpressed genes of TP I on the zebrafish embryos. As a result, three line rays supported with the corresponding 174 genes were detected in our analysis. Some biological processes of the featured genes, such as antigen processing, nuclear chromatin, and structural constituent of eye lens, were significantly filtered with the smallerPvalues.

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NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

Scientific Reports ◽

10.1038/s41598-021-92632-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Pep Amengual-Rigo ◽

Victor Guallar

Keyword(s):

Open Source ◽

Antigen Processing ◽

High Accuracy ◽

Biological Processes ◽

Mhc I ◽

Mhc Ii ◽

Prediction Tools ◽

Immunogenic Peptides ◽

Physicochemical Descriptors ◽

Peptide Presentation

AbstractAntigens presented on the cell surface have been subjected to multiple biological processes. Among them, C-terminal antigen processing constitutes one of the main bottlenecks of the peptide presentation pathways, as it delimits the peptidome that will be subjected downstream. Here, we present NetCleave, an open-source and retrainable algorithm for the prediction of the C-terminal antigen processing for both MHC-I and MHC-II pathways. NetCleave architecture consists of a neural network trained on 46 different physicochemical descriptors of the cleavage site amino acids. Our results demonstrate that prediction of C-terminal antigen processing achieves high accuracy on MHC-I (AUC of 0.91), while it remains challenging for MHC-II (AUC of 0.66). Moreover, we evaluated the performance of NetCleave and other prediction tools for the evaluation of four independent immunogenicity datasets (H2-Db, H2-Kb, HLA-A*02:01 and HLA-B:07:02). Overall, we demonstrate that NetCleave stands out as one of the best algorithms for the prediction of C-terminal processing, and we provide one of the first evidence that C-terminal processing predictions may help in the discovery of immunogenic peptides.

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Discovering Distinct Patterns in Gene Expression Profiles

Journal of Integrative Bioinformatics ◽

10.1515/jib-2008-105 ◽

2008 ◽

Vol 5 (2) ◽

Cited By ~ 1

Author(s):

Li Teng ◽

Laiwan Chan

Keyword(s):

Gene Expression ◽

Large Scale ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Clustering Methods ◽

Gene Expressions ◽

Real Gene ◽

Large Scale Dataset ◽

Coexpressed Genes

SummaryTraditional analysis of gene expression profiles use clustering to find groups of coexpressed genes which have similar expression patterns. However clustering is time consuming and could be diffcult for very large scale dataset. We proposed the idea of Discovering Distinct Patterns (DDP) in gene expression profiles. Since patterns showing by the gene expressions reveal their regulate mechanisms. It is significant to find all different patterns existing in the dataset when there is little prior knowledge. It is also a helpful start before taking on further analysis. We propose an algorithm for DDP by iteratively picking out pairs of gene expression patterns which have the largest dissimilarities. This method can also be used as preprocessing to initialize centers for clustering methods, like K-means. Experiments on both synthetic dataset and real gene expression datasets show our method is very effective in finding distinct patterns which have gene functional significance and is also effcient.

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Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment

Cancers ◽

10.3390/cancers10110461 ◽

2018 ◽

Vol 10 (11) ◽

pp. 461 ◽

Cited By ~ 31

Author(s):

Jiahui Zheng ◽

Min Wu ◽

Haiyan Wang ◽

Shasha Li ◽

Xin Wang ◽

...

Keyword(s):

Cancer Treatment ◽

Tumor Cells ◽

High Throughput ◽

Antigen Processing ◽

Killer Cell ◽

Network Pharmacology ◽

Gene Expressions ◽

Antitumor Effects ◽

Biological Basis ◽

Radix Paeoniae Alba

Health-strengthening (Fu-Zheng) herbs is a representative type of traditional Chinese medicine (TCM) widely used for cancer treatment in China, which is in contrast to pathogen eliminating (Qu-Xie) herbs. However, the commonness in the biological basis of health-strengthening herbs remains to be holistically elucidated. In this study, an innovative high-throughput research strategy integrating computational and experimental methods of network pharmacology was proposed, and 22 health-strengthening herbs were selected for the investigation. Additionally, 25 pathogen-eliminating herbs were included for comparison. First, based on network-based, large-scale target prediction, we analyzed the target profiles of 1446 TCM compounds. Next, the actions of 166 compounds on 420 antitumor or immune-related genes were measured using a unique high-throughput screening strategy by high-throughput sequencing, referred to as HTS2. Furthermore, the structural information and the antitumor activity of the compounds in health-strengthening and pathogen-eliminating herbs were compared. Using network pharmacology analysis, we discovered that: (1) Functionally, the predicted targets of compounds from health strengthening herbs were enriched in both immune-related and antitumor pathways, similar to those of pathogen eliminating herbs. As a case study, galloylpaeoniflorin, a compound in a health strengthening herb Radix Paeoniae Alba (Bai Shao), was found to exert antitumor effects both in vivo and in vitro. Yet the inhibitory effects of the compounds from pathogen eliminating herbs on tumor cells proliferation as a whole were significantly stronger than those in health-strengthening herbs (p < 0.001). Moreover, the percentage of assay compounds in health-strengthening herbs with the predicted targets enriched in the immune-related pathways (e.g., natural killer cell mediated cytotoxicity and antigen processing and presentation) were significantly higher than that in pathogen-eliminating herbs (p < 0.05). This finding was supported by the immune-enhancing effects of a group of compounds from health-strengthening herbs indicated by differentially expressed genes in the HTS2 results. (2) Compounds in the same herb may exhibit the same or distinguished mechanisms in cancer treatment, which was demonstrated as the compounds influence pathway gene expressions in the same or opposite directions. For example, acetyl ursolic acid and specnuezhenide in a health-strengthening herb Fructus Ligustri lucidi (Nv Zhen Zi) both upregulated gene expressions in T cell receptor signaling pathway. Together, this study suggested greater potentials in tumor immune microenvironment regulation and tumor prevention than in direct killing tumor cells of health-strengthening herbs generally, and provided a systematic strategy for unveiling the commonness in the biological basis of health-strengthening herbs in cancer treatment.

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Studies on peptides. CLXVIII. Syntheses of three peptides isolated from horseshoe crab hemocytes, tachyplesin I, tachyplesin II, and polyphemusin I.

Chemical and Pharmaceutical Bulletin ◽

10.1248/cpb.37.2661 ◽

1989 ◽

Vol 37 (10) ◽

pp. 2661-2664 ◽

Cited By ~ 23

Author(s):

Kenichi AKAJI ◽

Nobutaka FUJII ◽

Fuminori TOKUNAGA ◽

Toshiyuki MIYATA ◽

Sadaaki IWANAGA ◽

...

Keyword(s):

Horseshoe Crab ◽

Tachyplesin I

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Increased IGFBP7 Expression Correlates with Poor Prognosis and Immune Infiltration in Gastric Cancer: An Integrated Bioinformatics Analysis

10.21203/rs.3.rs-33369/v1 ◽

2020 ◽

Author(s):

Qiaoyun Zhao ◽

Rulin Zhao ◽

Conghua Song ◽

Huan Wang ◽

Jianfang Rong ◽

...

Keyword(s):

Gene Expression ◽

Gastric Cancer ◽

Poor Prognosis ◽

Bioinformatics Analysis ◽

Immune Cell ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Biological Processes ◽

Coexpressed Genes

Abstract Background Insulin-like growth factor binding protein-7 (IGFBP7) contributes to multiple biological processes in various tumors. However, the role of IGFBP7 in gastric cancer (GC) is still undetermined. The study aims to explore the role of IGFBP7 in GC via an integrated bioinformatics analysis.Methods IGFBP7 expression levels in GC and its normal gastric tissues were analyzed using multiple databases, including the Tumor Immune Estimation Resource (TIMER), Oncomine, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The methylation analysis was conducted with MEXPRESS, UALCAN and Xena online tools. The survival analysis was conducted using the Kaplan-Meier Plotter and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Coexpressed genes of IGFBP7 were selected with the cBioPortal tool and enrichment analysis was conducted with the clusterProfiler package in R software. Gene set enrichment analysis (GSEA) was performed to explore the IGFBP7-related biological processes involved in GC. Correlations between IGFBP7 and immune cell infiltrates were analyzed using the TIMER database.Results IGFBP7 expression was significantly upregulated in GC and correlated with stage, grade, tumor status and Helicobacter pylori infection. High IGFBP7 expression and low IGFBP7 methylation levels were significantly associated with short survival of patients with GC. Univariate and multivariate analyses revealed that IGFBP7 was an independent risk factor for GC. The coexpressed genes LHFPL6, SEPTIN4, HSPB2, LAYN and GGT5 predicted unfavorable outcomes of GC. Enrichment analysis showed that the coexpressed genes were involved in extracellular matrix (ECM)-related processes. GSEA indicated that IGFBP7 was positively related to ECM and inflammation-related pathways. TIMER analysis indicated that the IGFBP7 expression level was strongly correlated with genes related to various infiltrating immune cells in GC, especially with gene markers of tumor associated macrophages (TAMs).Conclusions We demonstrate that increased IGFBP7 expression correlates with poor prognosis and immune cell infiltration in GC. IGFBP7 might be a potential biomarker for the diagnosis and targeted therapy for GC.

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Seven-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-chromen-4- one reduces atherogenic index and Nrf2 and GPx gene expressions in hyperlipidemic rats

Tropical Journal of Pharmaceutical Research ◽

10.4314/tjpr.v18i6.4 ◽

2021 ◽

Vol 18 (6) ◽

pp. 1173-1177

Author(s):

Prasetyastuti ◽

Rahmah Dara Ayunda ◽

Sunarti

Keyword(s):

Density Lipoprotein ◽

Atherogenic Index ◽

Related Factor ◽

Nuclear Factor ◽

Chain Reaction ◽

Gene Expressions ◽

Expression Levels ◽

Qrt Pcr ◽

Polymerase Chain ◽

Different Doses

Purpose: To investigate the effect of 7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-chromen-4-one isolated from mahogany (Swietenia macrophylla King) seeds on atherogenic index, expressions of nuclear factor erythroid 2-related factor 2 (Nrf2) and expression of the glutathione peroxidase (GPx) genes in hyperlipidemic rats. Methods: A total of 25 rats male aged 8 weeks and weighing an average of 200 g were used. They were divided into five groups as follows: (I) normal (N), (II) hyperlipidemic (HL), (III) hyperlipidemic rats treated with simvastatin (HL+SV), (IV and V) hyperlipidemic rats treated with 30 or 90mg, respectively, of 7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-chromen-4-one per 200 g body weight per day for 4 weeks. Atherogenic index (AI) was calculated from the levels of triglyceride (TG) and high-density lipoprotein (HDL) while Nrf2 and GPx gene expressions were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Results: Two different doses of 7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-chromen-4-one in hyperlipidemic rats significantly reduced their atherogenic index (p < 0.05). Nrf2 and GPx expression levels were lower than (p > 0.05) those of hyperlipidemic group. Conclusion: Seven-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-chromen-4-one reduces the atherogenic index and expression levels of Nrf2 and GPx genes in hyperlipidemic rats. Thus, this compound has potential as an antihyperlipidemic agent

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Genetic analysis of the toxic effect of Tachyplesin I on the embryonic development of zebrafish

2013 6th International Conference on Biomedical Engineering and Informatics ◽

10.1109/bmei.2013.6747014 ◽

2013 ◽

Author(s):

Hongya Zhao ◽

Jianguo Dai ◽

Gang Jin

Keyword(s):

Genetic Analysis ◽

Embryonic Development ◽

Toxic Effect ◽

Tachyplesin I

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3P024 Analysis of chitin binding ability of an antimicrobial peptide tachyplesin I derived from horseshoe crab(01A. Protein: Structure,Poster)

Seibutsu Butsuri ◽

10.2142/biophys.53.s215_6 ◽

2013 ◽

Vol 53 (supplement1-2) ◽

pp. S215

Author(s):

Takahiro Kushibiki ◽

Masakatsu Kamiya ◽

Tomoyasu Aizawa ◽

Yasuhiro Kumiki ◽

Takashi Kikukawa ◽

...

Keyword(s):

Protein Structure ◽

Antimicrobial Peptide ◽

Horseshoe Crab ◽

Binding Ability ◽

Tachyplesin I

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Extracellular Vesicles Mediated Early Embryo–Maternal Interactions

International Journal of Molecular Sciences ◽

10.3390/ijms21031163 ◽

2020 ◽

Vol 21 (3) ◽

pp. 1163 ◽

Cited By ~ 8

Author(s):

Alessandra Bridi ◽

Felipe Perecin ◽

Juliano Coelho da Silveira

Keyword(s):

Embryonic Development ◽

Extracellular Vesicles ◽

Early Pregnancy ◽

Early Embryo ◽

Bioactive Molecules ◽

Biological Processes ◽

Embryonic Cells ◽

Uterine Fluid ◽

Zygote Stage

Embryo–maternal crosstalk is an important event that involves many biological processes, which must occur perfectly for pregnancy success. This complex communication starts from the zygote stage within the oviduct and continues in the uterus up to the end of pregnancy. Small extracellular vesicles (EVs) are part of this communication and carry bioactive molecules such as proteins, lipids, mRNA, and miRNA. Small EVs are present in the oviductal and uterine fluid and have important functions during fertilization and early embryonic development. Embryonic cells are able to uptake oviductal and endometrium-derived small EVs. Conversely, embryo-derived EVs might modulate oviductal and uterine function. In this review, our aim is to demonstrate the role of extracellular vesicles modulating embryo–maternal interactions during early pregnancy.

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