• Korean Journal of Veterinary Service
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• v.42 no.2
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• pp.73-83
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• 2019

Foot-and-Mouth Disease (FMD) is a highly contagious trans-boundary viral disease caused by FMD virus, which causes huge economic losses. FMDV infects cloven hoofed (two-toed) mammals such as cattle, sheep, goats, pigs and various wildlife species. To control the FMDV, it is necessary to understand the life cycle and the pathogenesis of FMDV in host. Especially, the protein-protein interaction between FMDV and host will help to understand the survival cycle of viruses in host cell and establish new therapeutic strategies. However, the computational approach for protein-protein interaction between FMDV and pig hosts have not been applied to studies of the onset mechanism of FMDV. In the present work, we have performed the prediction of the pig's proteins which interact with FMDV based on RNA-Seq data, protein sequence, and structure information. After identifying the virus-host interaction, we looked for meaningful pathways and anticipated changes in the host caused by infection with FMDV. A total of 78 proteins of pig were predicted as interacting with FMDV. The 156 interactions include 94 interactions predicted by sequence-based method and the 62 interactions predicted by structure-based method using domain information. The protein interaction network contained integrin as well as STYK1, VTCN1, IDO1, CDH3, SLA-DQB1, FER, and FGFR2 which were related to the up-regulation of inflammation and the down-regulation of cell adhesion and host defense systems such as macrophage and leukocytes. These results provide clues to the knowledge and mechanism of how FMDV affects the host cell.

• Genomics & Informatics
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• v.21 no.2
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• pp.20.1-20.10
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• 2023

Aromatase inhibitors (AI) are drugs that are widely used in treating estrogen receptor (ER)-positive breast cancer patients. Drug resistance is a major obstacle to aromatase inhibition therapy. There are diverse reasons behind acquired AI resistance. This study aims at identifying the plausible cause of acquired AI resistance in patients administered with non-steroidal AIs (anastrozole and letrozole). We used genomic, transcriptomic, epigenetic, and mutation data of breast invasive carcinoma from The Cancer Genomic Atlas database. The data was then separated into sensitive and resistant sets based on patients' responsiveness to the non-steroidal AIs. A sensitive set of 150 patients and a resistant set of 172 patients were included for the study. These data were collectively analyzed to probe into the factors that might be responsible for AI resistance. We identified 17 differentially regulated genes (DEGs) among the two groups. Then, methylation, mutation, miRNA, copy number variation, and pathway analyses were performed for these DEGs. The top mutated genes (FGFR3, CDKN2A, RNF208, MAPK4, MAPK15, HSD3B1, CRYBB2, CDC20B, TP53TG5, and MAPK8IP3) were predicted. We also identified a key miRNA - hsa-mir-1264 regulating the expression of CDC20B. Pathway analysis revealed HSD3B1 to be involved in estrogen biosynthesis. This study reveals the involvement of key genes that might be associated with the development of AI resistance in ER-positive breast cancers and hence may act as a potential prognostic and diagnostic biomarker for these patients.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.23
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• pp.10355-10361
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• 2015

Background: MicroRNAs (miRNAs) are small non-coding RNA molecules found in multicellular eukaryotes which are implicated in development of cancer, including cutaneous squamous cell carcinoma (cSCC). Expression is controlled by transcription factors (TFs) that bind to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA. Interactions result in biological signal control networks. Materials and Methods: Molecular components involved in cSCC were here assembled at abnormally expressed, related and global levels. Networks at these three levels were constructed with corresponding biological factors in term of interactions between miRNAs and target genes, TFs and miRNAs, and host genes and miRNAs. Up/down regulation or mutation of the factors were considered in the context of the regulation and significant patterns were extracted. Results: Participants of the networks were evaluated based on their expression and regulation of other factors. Sub-networks with two core TFs, TP53 and EIF2C2, as the centers are identified. These share self-adapt feedback regulation in which a mutual restraint exists. Up or down regulation of certain genes and miRNAs are discussed. Some, for example the expression of MMP13, were in line with expectation while others, including FGFR3, need further investigation of their unexpected behavior. Conclusions: The present research suggests that dozens of components, miRNAs, TFs, target genes and host genes included, unite as networks through their regulation to function systematically in human cSCC. Networks built under the currently available sources provide critical signal controlling pathways and frequent patterns. Inappropriate controlling signal flow from abnormal expression of key TFs may push the system into an incontrollable situation and therefore contributes to cSCC development.

• Journal of the Korean Institute of Oriental Medical Informatics
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• v.15 no.1
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• pp.57-66
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• 2009

Objectives : The aim of the present study is to evaluate the wound healing-enhancing and anti-inflammatory effects of Pinus densiflora, Cornus officinalis, Zingiber officinale, Ganoderma japonicum and Scutellaria baikalensison human keratinocyte, HaCaT cells. Methods : We adopted in vitro wound healing assay to measure the proliferation-and migration-enhancing effects in HaCaT cells. The expressions of cytokine genes were measured in HaCaT cells using real-time PCR analysis. Results : The extracts of Pinus densiflora, Cornus officinalis, Zingiber officinale, Ganoderma japonicum and Scutellaria baikalensis enhanced the proliferation and migration of HaCaTcells. The expression of keratinocyte growth factor receptor(FGFR2-IIIb) gene was also induced. The extracts inhibited iNOS, IL-$1{\beta}$ and TNF-$\alpha$ gene expression. Conclusions : The extract of Pinus densiflora, Cornus officinalis, Zingiber officinale, Ganoderma japonicum and Scutellaria baikalensis has wound healing-enhancing effects and anti-inflammatory effects.

• Journal of Digestive Cancer Research
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• v.3 no.1
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• pp.30-34
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• 2015

We report a case of a 55-year-old man who diagnosed with advanced gastric cancer (AGC), with A review of the literature. A 55-year old man was transferred to our hospital for further evaluation and treatment after being diagnosed with adenocarcinoma through endoscopic biopsy during a regular health examination. An abdominal computed tomography (CT) showed AGC, stage IIA (T3N3M0), while an endoscopic examination showed AGC, Borrmann type 2. The patient is currently under observation after undergoing radical subtotal gastrectomy with gastroduodenostomy and subsequent administration of oral chemotherapeutic agents. As an abdominal CT response assessment performed after surgery revealed new metastasis to the liver, the patient received palliative chemotherapy as progressive disease was suspected. After receiving chemotherapy in the order of FOLFOX (5-fluorouracil (5-FU)) + Leucovorin + Oxaliplatin), FOLFIRI (5-FU + Leucovorin + Irinotecan), EAP-II (Etoposide + Doxorubicin + Cisplatin), ELF (Etoposide + Leucovorin + 5-FU), TS-1 (Tegafur + Gimeracil) + Cisplatin, an abdominal CT response assessment showed progressive disease for which the regimen was altered to PFL (Paclitaxel + 5-FU + Leucovorin). The patient has currently completed his second cycle of chemotherapy and after an abdominal CT response assessment, further course of therapy will be decided.