• Journal of Microbiology and Biotechnology
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• 제14권6호
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• pp.1239-1248
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• 2004

The methylotrophic yeast Hansenula polymorpha has been extensively studied as a model organism for methanol metabolism and peroxisome biogenesis. Recently, this yeast has also attracted attention as a promising host organism for recombinant protein production. Here, we describe the fabrication and evaluation of a DNA chip spotted with 382 open reading frames (ORFs) of H. polymorpha. Each ORF was PCR-amplified using gene-specific primer sets, of which the forward primers had 5'-aminolink. The PCR products were printed in duplicate onto the aldehyde-coated slide glasses to link only the coding strands to the surface of the slide via covalent coupling between amine and aldehyde groups. With the partial genome DNA chip, we compared efficiency of direct and indirect cDNA target labeling methods, and found that the indirect method, using fluorescent-labeled dendrimers, generated a higher hybridization signal-to-noise ratio than the direct method, using cDNA targets labeled by incorporation of fluorescence-labeled nucIeotides during reverse transcription. In addition, to assess the quality of this DNA chip, we analyzed the expression profiles of H. polymorpha cells grown on different carbon sources, such as glucose and methanol, and also those of cells treated with the superoxide­generating drug, menadione. The profiles obtained showed a high-level induction of a set of ORFs involved in methanol metabolism and oxidative stress response in the presence of methanol and menadione, respectively. The results demonstrate the sensitivity and reliability of our arrays to analyze global gene expression changes of H. polymorpha under defined environmental conditions.

• 한국미생물·생명공학회지
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• 제40권2호
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• pp.117-127
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• 2012

피부재생에 대한 지방줄기세포 배양상등액(ADSC-CM)의 효능에 대한 연구를 진행하였다. ADSC-CM이 피부재생에 기여하는 기작은 명확하지 못하지만, ADSC-CM은 다양한 분비물을 포함하고 있고 따라서 피부트러블 처리를 위한 훌륭한 재료이다. 저 산소 상태에서 생산된 ADSC-CM, 즉 advanced adipose-derived stem cell protein extract (AAPE)는 피부재생에 보다 좋은 재료이다. 본 연구는 피부 재생에 결정적 역할을 하는 인체 primary 세포인 섬유아세포(HDF)와 케라티노사이트(HK)를 이용하여 AAPE의 효능을 검증하였다. 0.32 ${\mu}g/ml$ AAPE에서 콜라겐 합성이 관찰 되었으며 AAPE는 stress fiber 형성을 강화하였다. DNA microarray 결과에서는 세포증식, 세포이동, 세포부착, 상처반응에 관여하는 133개의 유전자 발현이 조절되는 것을 알았다. Antibody array를 통해 CD54, FGF-2, GM-CSF, IL-4, IL-6, VEGF, TGF-${\beta}2$, TGF-${\beta}3$, MMP-1, MMP-10, 그리고 MMP-19와 같은 MMP, 성장인자, 사이토카인등 25개의 알려진 단백질이 포함되어 있다는 것을 알았다. 따라서, AAPE는 HK의 세포생물학적 기능을 활성화 할 수 있다고 사료되며 HDF에서는 콜라겐 합성을 유도하였다. 이러한 결과는 AAPE가 피부재생에 임상적 적용이 가능하리라는 것을 의미한다.

• Asian Pacific Journal of Cancer Prevention
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• 제15권23호
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• pp.10513-10524
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• 2015

Background: Metastasis is a major reason for poor prognosis in patients with cancer, including hepatocellular carcinoma (HCC). A salient feature is the ability of cancer cells to colonize different organs. Long non-coding RNAs (lncRNAs) play important roles in numerous cellular processes, including metastasis. Materials and Methods: In this study, the lncRNA expression profiles of two HCC cell lines, one with high potential for metastasis to the lung (HCCLM3) and the other to lymph nodes (HCCLYM-H2) were assessed using the Arraystar Human LncRNA Array v2.0, which contains 33,045 lncRNAs and 30,215 mRNAs. Coding-non-coding gene co-expression (CNC) networks were constructed and gene set enrichment analysis (GSEA) was performed to identify lncRNAs with potential functions in organ-specific metastasis. Levels of two representative lncRNAs and one representative mRNA, RP5-1014O16.1, lincRNA-TSPAN8 and TSPAN8, were further detected in HCC cell lines with differing metastasis potential by qRT-PCR. Results: Using microarray data, we identified 1,482 lncRNAs and 1,629 mRNAs that were differentially expressed (${\geq}1.5$ fold-change) between the two HCC cell lines. The most upregulated lncRNAs in H2 were RP11-672F9.1, RP5-1014O16.1, and RP11-501G6.1, while the most downregulated ones were lincRNA-TSPAN8, lincRNA-CALCA, C14orf132, NCRNA00173, and CR613944. The most upregulated mRNAs in H2 were C15orf48, PSG2, and PSG8, while the most downregulated ones were CALCB, CD81, CD24, TSPAN8, and SOST. Among them, lincRNA-TSPAN8 and TSPAN8 were found highly expressed in high lung metastatic potential HCC cells, while lowly expressed in no or low lung metastatic potential HCC cells. RP5-1014O16.1 was highly expressed in high lymphatic metastatic potential HCC cell lines, while lowly expressed in no lymphatic metastatic potential HCC cell lines. Conclusions: We provide the first detailed description of lncRNA expression profiles related to organ-specific metastasis in HCC. We demonstrated that a large number of lncRNAs may play important roles in driving HCC cells to metastasize to different sites; these lncRNAs may provide novel molecular biomarkers and offer a new basis for combating metastasis in HCC cases.

• Journal of Gastric Cancer
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• 제6권3호
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• pp.181-188
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• 2006

목적: Heregulin은 erbB3와 erbB4의 리간드로 작용한다. 그러나 위암에서 이들 단백의 역할에 대해서는 거의 알려져 있지 않다. 저자들은 위암에서 heregulin과 erbB family 단백 발현 빈도를 알아보고 이들 단백 발현과 임상 병리학적 예후인자와 비교하고자 한다. 대상 및 방법: Tissue microarray와 면역조직화학염색 방법을 이용하여 heregulin과 erbB 단백 발현을 검사하였다. 251 예의 위암을 조기위암, 진행성 위암, 림프절 전이 여부 등에 따라 구분하였다. 결과: Heregulin, erbB1, erbB2, erbB3, erbB4 단백은 각각 64%, 68%, 6%, 88%, 76%로 발현되었다. Heregulin, erbB2, erbB3, erbB4 단백은 장형에서 더 높은 발현을 보였다. Heregulin과 erbB4 단백은 진행성 위암에서 발현이 낮아졌다. ErbB2 단백은 진행성 위암에서 발현이 증가되었다. Heregvlin과 erbB family 단백은 생존율과는 상관관계가 없었다. Heregulin과 erbB3 혹은 heregulin과 erbB4 단백이 동시에 발현되는 군은 장형과 초기 병변에 더 많았다. 결론: Heregulin, erbB3, erbB4 단백들은 주로 위암 초기 병변에 관여하는 것으로 추정된다.

• Tuberculosis and Respiratory Diseases
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• 제60권4호
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• pp.412-418
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• 2006

연구배경 : 클라미디아 감염의 진단은 혈청검사로 이루어진다. 현재 표준 방법은 MIF(microimmunofluorescence)이나 이 방법은 주관적이고 시간이 많이 걸리는 단점이 있다. 최근을 SPR(surface plasmon resonance) 센서를 이용한 단백질 칩이 감염의 새로운 진단 방법으로 제시되고 있다. 클라미디아 감염의 진단을 위한 단백질 칩 개발을 위하여 금 칩 표면에 세균을 고정하고 클라미디아 균에 대한 항체와 표면 위 세균과의 반응을 SPR 센서를 이용하여 측정하고자 하였다. 방법 : 표면 항원으로 배양한 Chlamydophila pneumoniae LKK1의 EB를 정제하였다. 양전하를 띤 PDDA (polydiallyldimethylammonium chloride)를 이용하여 전하를 이용한 단백질 칩을 제작하였다. 클라미디아 균을 고정시킨 후에 atomic force microscopy를 이용하여 표면을 관찰하였다. 클라미디아 균에 대한 항체를 투여하고 나서 자체 제작한 SPR 센서를 이용하여 항원 항체 반응을 SPR 파장 변화로 측정하였다. 결과 : 양전하를 띤 PDDA 표면위에서 클라미디아 균이 고정되었음을 확인 하였다. 그리고, 항체를 투여한 후에 SPR 파장의 증가를 확인하였다. 파장 변화는 항원의 농도와 관련이 있었다. 결론 : 전하를 이용하여 클라미디아 폐렴균의 EB를 단백질 칩에 고정하였고, 단백질 칩 위에서의 항원 항체 반응을 확인하였다. 비정형 폐렴의 진단에 SPR 센서가 기여할 수 있을 것으로 사료되나, 실제 임상 시료에의 적용을 위해서는 좀더 연구가 필요할 것으로 사료된다.

• Molecules and Cells
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• 제37권12호
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• pp.873-880
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• 2014

In our previous study, miRNA-183, a miRNA in the miR-96-182-183 cluster, was significantly over-expressed in esophageal squamous cell carcinoma (ESCC). In the present study, we explored the oncogenic roles of miR-183 in ESCC by gain and loss of function analysis in an esophageal cancer cell line (EC9706). Genome-wide mRNA micro-array was applied to determine the genes that were regulated directly or indirectly by miR-183. 3'UTR luciferase reporter assay, RT-PCR, and Western blot were conducted to verify the target gene of miR-183. Cell culture results showed that miR-183 inhibited apoptosis (p < 0.05), enhanced cell proliferation (p < 0.05), and accelerated G1/S transition (p < 0.05). Moreover, the inhibitory effect of miR-183 on apoptosis was rescued when miR-183 was suppressed via miR-183 inhibitor (p < 0.05). Western blot analysis showed that the expression of programmed cell death 4 (PDCD4), which was predicted as the target gene of miR-183 by microarray profiling and bioinformatics predictions, decreased when miR-183 was over-expressed. The 3'UTR luciferase reporter assay confirmed that miR-183 directly regulated PDCD4 by binding to sequences in the 3'UTR of PDCD4. Pearson correlation analysis further confirmed the significant negative correlation between miR-183 and PDCD4 in both cell lines and in ESCC patients. Our data suggest that miR-183 might play an oncogenic role in ESCC by regulating PDCD4 expression.

• Molecules and Cells
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• 제24권2호
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• pp.200-209
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• 2007

We generated gene expression data from the tissues of 50 gastric cancer patients, and applied meta-analysis and gene set analysis to this data and three other stomach cancer gene expression data sets to define the gene expression changes in gastric tumors. By meta-analysis we identified genes consistently changed in gastric carcinomas, while gene set analysis revealed consistently changed biological themes. Genes and gene sets involved in digestion, fatty acid metabolism, and ion transport were consistently down-regulated in gastric carcinomas, while those involved in cellular proliferation, cell cycle, and DNA replication were consistently up-regulated. We also found significant differences between the genes and gene sets expressed in diffuse and intestinal type gastric carcinoma. By gene set analysis of cytogenetic bands, we identified many chromosomal regions with possible gross chromosomal changes (amplifications or deletions). Similar analysis of transcription factor binding sites (TFBSs), revealed transcription factors that may have caused the observed gene expression changes in gastric carcinomas, and we confirmed the overexpression of one of these, E2F1, in many gastric carcinomas by tissue array and immunohistochemistry. We have incorporated the results of our meta- and gene set analyses into a web accessible database (http://human-genome.kribb.re.kr/stomach/).