• Asian Pacific Journal of Cancer Prevention
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• v.15 no.5
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• pp.2345-2351
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• 2014

Lysyl oxidase-like 2 (LOXL2), a member of the lysyl oxidase (LOX) family, is a copper-dependent enzyme that catalyzes oxidative deamination of lysine residues on protein substrates. LOXL2 was found to be overexpressed in esophageal squamous cell carcinoma (ESCC) in our previous research. We later identified a LOXL2 splicing variant LOXL2-delta72 and we overexpressed LOXL2-delta72 and its wild type counterpart in ESCC cells following microarray analyses. First, the differentially expressed genes (DEGs) of LOXL2 and LOXL2-delta72 compared to empty plasmid were applied to generate protein-protein interaction (PPI) sub-networks. Comparison of these two sub-networks showed hundreds of different proteins. To reveal the potential specific roles of LOXL2- delta72 compared to its wild type, the DEGs of LOXL2-delta72 vs LOXL2 were also applied to construct a PPI sub-network which was annotated by Gene Ontology. The functional annotation map indicated the third PPI sub-network involved hundreds of GO terms, such as "cell cycle arrest", "G1/S transition of mitotic cell cycle", "interphase", "cell-matrix adhesion" and "cell-substrate adhesion", as well as significant "immunity" related terms, such as "innate immune response", "regulation of defense response" and "Toll signaling pathway". These results provide important clues for experimental identification of the specific biological roles and molecular mechanisms of LOXL2-delta72. This study also provided a work flow to test the different roles of a splicing variant with high-throughput data.

• Journal of Biomedical and Translational Research
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• v.19 no.4
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• pp.116-124
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• 2018

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP ${\times}$ Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (${\left|log2FC\right|}$ > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

• Reproductive and Developmental Biology
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• v.31 no.3
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• pp.207-213
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• 2007

This study was carried out to examine gene expression altered in endometrium of Korean cattle (Hanwoo) with endometritis using microarray. In this study, 4,560 diferentially expressed genes (DEGs) were identified in the endometrium of Hanwoo. Of 4,560 DEGs, 2,026 genes were up-regulated, while 2,536 genes were down-regulated in endometritis. Of them, top 10 regulated genes were listed. Filamin A, pancreatic anionic trypsinogen, Rho GDP dissociation inhibitor alpha, collagen type VI alpha 1, butyrate response factor 2, aggrecanses-2, annexin 14, aminopeptidease A, orphan transporter v7-3, and epithelial stromal interaction 1 were up-regulated, while MHC class II antigen, integrin-binding sialoprotein, uterine milk protein precursor, down-regulated in colon cancer 1, glycoprotein 330, dickkopf-1, cfh protein, $Ca^{2+}-dependent$ secretion activator, UL16 binding protein 3, and proenkephalin were down-regulated in the endometritis. Our results suggest that these genes could be useful biomarkers for diagnosis Hanwoo's endometritis.

• Development and Reproduction
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• v.8 no.1
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• pp.35-42
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• 2004

Oocyte maturation refers to the process that prophase I arrested germinal vesicle(GV) drives the progression of meiosis to metaphase II(MII) to have the capacity for fertilization and embryo development. To better understand the molecular mechanism(s) involved in oocyte maturation, we identified differentially expressed genes(DEGs) between GV and MII mouse oocytes using a new innovative annealing control primer (ACP) technology. Using 20 ACPs, we successfully cloned 32 DEGs between GV and Mll oocytes, and 26 out of these 32 DEGs were functionally known genes. Four genes including Pscd2 were GV-specific, 10 genes including PKD2 and CSN3 were highly expressed in GV oocytes(GV-selective), and 12 genes including Diva were highly expressed in MII oocytes (MII-selective). Ail of the genes identified in this study were first reported in the oocyte expression using ACP system and especially, we could characterize the existence of PKD-CSW signaling pathwayin the mouse oocytes. Results of the present study would provide insight for studying molecular mechanisms regulating oocyte maturation.

• Genomics & Informatics
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• v.11 no.4
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• pp.245-253
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• 2013

A radioresistant cell line was established by fractionated ionizing radiation (IR) and assessed by a clonogenic assay, flow cytometry, and Western blot analysis, as well as zymography and a wound healing assay. Microarray was performed to profile global expression and to search for differentially expressed genes (DEGs) in response to IR. H460R cells demonstrated increased cell scattering and acidic vesicular organelles compared with parental cells. Concomitantly, H460R cells showed characteristics of increased migration and matrix metalloproteinase activity. In addition, H460R cells were resistant to IR, exhibiting reduced expression levels of ionizing responsive proteins (p-p53 and ${\gamma}$-H2AX); apoptosis-related molecules, such as cleaved poly(ADP ribose) polymerase; and endoplasmic reticulum stress-related molecules, such as glucose-regulated protein (GRP78) and C/EBP-homologous protein compared with parental cells, whereas the expression of anti-apoptotic X-linked inhibitor of apoptosis protein was increased. Among DEGs, syntrophin beta 2 (SNTB2) significantly increased in H460R cells in response to IR. Knockdown of SNTB2 by siRNA was more sensitive than the control after IR exposure in H460, H460R, and H1299 cells. Our study suggests that H460R cells have differential properties, including cell morphology, potential for metastasis, and resistance to IR, compared with parental cells. In addition, SNTB2 may play an important role in radioresistance. H460R cells could be helpful in in vitro systems for elucidating the molecular mechanisms of and discovering drugs to overcome radioresistance in lung cancer therapy.

• Journal of The Korean Society of Grassland and Forage Science
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• v.34 no.2
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• pp.114-119
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• 2014

Salinity and drought stresses are probably the most significant abiotic factor limiting plant's growth, also negatively affect seed germination and early seedling development. To study on effect of NaCl and PEG stress on seed germination and gene expression pattern of tall fescue, the levels of NaCl and PEG-induced water stresses were determined in first experiment. Different concentration of NaCl (0 to 350 mM) and PEG (0 to 30%) were used for seed treatment. Seed Germination percentage reduced with increasing osmotic potential of growth medium either due to NaCl or PEG. Seeds were not germinate at 350 mM NaCl or 30% PEG treatment. On the basis of the results, Kentucky31(E-) had more resistant than Fawn in both stress conditions. Furthermore, we have used an annealing control primer-based differential display reverse transcription-polymerase chain reaction method to identify salt- and drought stress-induced differentially expressed genes (DEGs) in tall fescue leaves. Using 120 annealing control primers, a total of 4 genes were identified and sequenced. The possible roles of the identified DEGs are discussed in the context of their putative role during salinity and drought stresses.

• Genomics & Informatics
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• v.19 no.4
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• pp.42.1-42.17
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• 2021

Salivary gland carcinoma (SGC) is rare cancer, constituting 6% of neoplasms in the head and neck area. The most responsible genes and pathways involved in the pathology of this disorder have not been fully understood. We aimed to identify differentially expressed genes (DEGs), the most critical hub genes, transcription factors, signaling pathways, and biological processes (BPs) associated with the pathogenesis of primary SGC. The mRNA dataset GSE153283 in the Gene Expression Omnibus database was re-analyzed for determining DEGs in cancer tissue of patients with primary SGC compared to the adjacent normal tissue (adjusted p-value < 0.001; |Log2 fold change| > 1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. The hub genes of PIM were discovered, and their associated gene regulatory network was built to determine the master regulators involved in the pathogenesis of primary SGC. A total of 137 genes were found to be differentially expressed in primary SGC. The most significant pathways and BPs that were deregulated in the primary disease condition were associated with the cell cycle and fibroblast proliferation procedures. TP53, EGF, FN1, NOTCH1, EZH2, COL1A1, SPP1, CDKN2A, WNT5A, PDGFRB, CCNB1, and H2AFX were demonstrated to be the most critical genes linked with the primary SGC. SPIB, FOXM1, and POLR2A significantly regulate all the hub genes. This study illustrated several hub genes and their master regulators that might be appropriate targets for the therapeutic aims of primary SGC.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.66 no.1
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• pp.37-71
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• 2021

Rapeseed is a typical winter crop, and its freezing stress tolerance is a major feature for winter survival. Therefore, it is important to comprehend clearly the physical and molecular mechanisms of rapeseed under freezing stress conditions. This study investigates the physical and transcriptome changes of two rapeseed lines, 'J8634-B-30' and 'EMS26', under cold acclimation and freezing temperature treatments. The proline content of 'J8634-B-30' at 5 ℃ increased 8.7-fold compared to that before treatment, and there was no significant change in that of 'EMS26' RNA-sequencing analysis revealed 5,083 differentially expressed genes (DEGs) of 'J8634-B-30' under cold acclimation condition. Among the genes, 2,784 (54.8%) were up-regulated and 2,299 (45.2%) were down-regulated. The DEGs of 'EMS26' under cold acclimation condition were 5,831 genes, and contained 2,199 up-regulated genes (37.7%) and 3,632 down-regulated genes (62.3%). Among them, only DEGs annotated in the cold response-related signaling pathways were selected, and their expression in the two rapeseed lines was compared. Comparative DEGs analysis indicated that cold response related signaling pathways are proline metabolism and ABA (Abscisic acid) signaling. And ICE (Inducer of CBF expression) - CBF (C-repeat-binding factor) - COR (Cold-regulated) signaling were the significantly differentially expressed transcripts in the two rapeseed lines. The major induced transcripts of 'J8634-B-30' induced P5CS (Δ'-pyrroline-5-carboxylate synthetase), which is related to proline biosynthesis, PYL (pyrabactin resistance-like protein, ABA receptor) and COR413 (cold-regulated 413 plasma membrane 1). In conclusion, these result provide a foundation for understanding the mechanisms of freezing stress tolerance in rapeseeds. Further functional studies should be performed on the freezing stress-related genes identified in this study, which can contribute to the transgenic and molecular breeding for freezing stress tolerance in rapeseed.

• Journal of the korean academy of Pediatric Dentistry
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• v.32 no.1
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• pp.75-88
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• 2005

Ameloblastoma is the most commonly occurring odontogenic tumor in oral cavity. Although most are benign epithelial neoplasm, they are generally considered to be locally aggressive and destructive, exhibiting a high rate of recurrence. The biological behavior of this neoplasm is a slowly growing, locally invasive tumor without metastasis, therefore malignant neoplasm, changed its histological appearance to carcinoma or showed distant metastasis, is only defined clinically. In this study, we identified the differentially expressed genes(DEGs) in stages under benign or malignant ameloblastoma compared with normal patient using ordered differential display(ODD) reverse transcription(RT)-PCR and $GeneFishing^{TM}$ technology. ODD RT-PCR is rather effective when the investigation of samples containing very small amounts of total RNA must be accomplished. ODD RT-PCR used the means of amplification with anchored T-primer and adaptor specific primer. bearing definite two bases at their 3' ends and so this method could display differential 3'-expressed sequence taqs(ESTs) patterns without using full-length cDNAs. Compared with standard differential display, ODD RT-PCR is more simple and have enough sensitivity to search for molecular markers by comparing gene expression profiles, However, this method required much effort and skill to perform. $GeneFishing^{TM}$ modified from DD-PCR is an improved method for detecting differentially expressed genes in two or more related samples. This two step RT-PCR method uses a constant reverse primer(anchor ACP-T) to prime the RT reaction and arbitrary primer pairs(annealing control primers, ACPs) during PCR. Because of high annealing specificity of ACPs than ODD RT-PCR, the application of $GeneFishing^{TM}$ to DEG discovery generates reproducible, authentic, and long(100bp to 2kb) PCR products that are detectable on agarose gels. Consequently, various DEGs observed differential expression levels on agarose gels were isolated from normal, benign, and malignant tissues using these methods. The expression patterns of the some isolated DEGs through ODD RT-PCR and $GeneFishing^{TM}$ were confirmed by Northern blot analysis and RT-PCR. The results showed that these identified DEGs were implicated in ameloblastoma neoplasm processes. Therefore, the identified DEGs will be further studied in order to be applied in candidate selection for marker as an early diagnosis during ameloblastoma neoplasm processes.

• BMB Reports
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• v.40 no.5
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• pp.757-764
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• 2007

Marbling of cattle meat is dependent on the coordinated expression of multiple genes. Cattle dramatically increase their intramuscular fat content in the longissimus dorsi muscle between 12 and 27 months of age. We used the annealing control primer (ACP)-differential display RT-PCR method to identify differentially expressed genes (DEGs) that may participate in the development of intramuscular fat between early (12 months old) and late fattening stages (27 months old). Using 20 arbitrary ACP primers, we identified and sequenced 14 DEGs. BLAST searches revealed that expression of the MDH, PI4-K, ferritin, ICER, NID-2, WDNMI, telethonin, filamin, and desmin (DES) genes increased while that of GAPD, COP VII, ACTA1, CamK II, and nebulin decreased during the late fattening stage. The results of functional categorization using the Gene Ontology database for 14 known genes indicated that MDH, GAPD, and COP VII are involved in metabolic pathways such as glycolysis and the TCA cycle, whereas telethonin, filamin, nebulin, desmin, and ACTA1 contribute to the muscle contractile apparatus, and PI4-K, CamK II, and ICER have roles in signal transduction pathways regulated by growth factor or hormones. The final three genes, NID-2, WDNMI, and ferritin, are involved in iron transport and extracellular protein inhibition. The expression patterns were confirmed for seven genes (MDH, PI4-K, ferritin, ICER, nebulin, WDNMI, and telethonin) using real-time PCR. We found that the novel transcription repressor ICER gene was highly expressed in the late fattening stage and during bovine preadipocyte differentiation. This information may be helpful in selecting candidate genes that participate in intramuscular fat development in cattle.