• 생명과학회지
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• 제26권10호
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• pp.1137-1152
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• 2016

세포는 다양한 인체 질환에 관련되어 있는 저산소 환경을 인지하고 반응하며 적응한다. 저산소 상태에 적응하기 위해서는 hypoxic 유전자의 발현을 증가시키고 aerobic 유전자의 발현을 감소시키는 유전자 발현 조절이 필요하다. 최근 연구에서 미토콘드리아 호흡계가 이러한 유전자 발현 조절에 관여됨이 밝혀지고 있다. 본 연구에서는 호흡이 가능한 곰팡이(Saccharomyces cerevisiae)와 호흡이 불가능한 돌연변이 곰팡이를 실험대상으로 하여 미토콘드리아 호흡계가 저산소 환경에서 유전자 발현 조절에 관여됨을 DNA microarray 기법을 이용하여 전체 유전자를 대상으로 조사하였다. 산소 농도가 감소함에 반응하여 많은 유전자의 발현에 변화가 있었으며, 이러한 차별적인 발현 양상을 보이는 유전자는 여러 그룹으로 분류할 수 있었다. 대부분의 hypoxic 그리고 aerobic 유전자는 저산소 상태에 적응하는 발현 양상을 위해서는 미토콘드리아 호흡계가 필요하였다. 그러나 일부 hypoxic 그리고 aerobic 유전자는 미토콘드리아 호흡계와 무관하게 저산소 상태에 적응하는 발현 양상을 보였다. 이러한 결과는 미토콘드리아 호흡계가 저산소 환경에 적응하는 유전자 발현 조절에 필요하며, 또한 여러 기전을 통하여 이러한 유전자 발현 조절에 관여함을 제시한다. 또한 microarray 실험 결과에서 도출된 산소 농도에 대해 차별적인 발현을 보이는 유전자에 대하여 gene ontology 및 promoter 분석을 수행하였고 이러한 추가 분석 결과는 산소에 의해 조절되는 유전자와 함께 세포가 저산소 환경에 적응하는 기작을 이해하는 데 유용한 자료가 될 것으로 기대된다.

• Asian Pacific Journal of Cancer Prevention
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• 제13권11호
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• pp.5433-5438
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• 2012

Background: Hepatocellular carcinoma (HCC) is a common and aggressive malignancy. Despite of the improvements in its treatment, HCC prognosis remains poor due to its recurrence after resection. This study provides complete genetic profile for Egyptian HCC. Genome-wide analyses were performed to identify the predictive signatures. Patients and Methods: Liver tissue was collected from 31 patients with diagnosis of HCC and gene expression levels in the tumours and their adjacent non-neoplastic tissues samples were studied by analyzing changes by microarray then correlate these with the clinico-pathological parameters. Genes were validated in an independent set by qPCR. The genomic profile was associated with genetic disorders and cancer focused on gene expression, cell cycle and cell death. Molecular profile analysis revealed cell cycle progression and arrest at G2/M, but progression to mitosis; unregulated DNA damage check-points, and apoptosis. Result: Nine hundred fifty eight transcripts out of the 25,000 studied cDNAs were differentially expressed; 503 were up-regulated and 455 were down-regulated. A total of 19 pathways were up-regulated through 27 genes and 13 pathways were down-regulated through 19 genes. Thirty-seven genes showed significant differences in their expression between HCC cases with high and low Alpha Feto Protein ($AFP{\geq}600$ IU/ml). The validation for the microarray was done by real time PCR assay in which PPP3CA, ATG-5, BACE genes showed down-regulation and ABCG2, RXRA, ELOVL2, CXR3 genes showed up-regulation. cDNA microarrays showed that among the major upregulated genes in HCC are sets. Conclusion: The identified genes could provide a panel of new diagnostic and prognostic aids for HCC.

• Genomics & Informatics
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• 제13권3호
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• pp.86-89
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• 2015

Because there are clear molecular differences entailing different treatment effectiveness between Korean and non-Korean cancer patients, identifying distinct molecular characteristics of Korean cancers is profoundly important. Here, we report a web-based data repository, namely Korean Cancer Genome Database (KCGD), for searching gene signatures associated with Korean cancer patients. Currently, a total of 1,403 cancer genomics data were collected, processed and stored in our repository, an ever-growing database. We incorporated most widely used statistical survival analysis methods including the Cox proportional hazard model, log-rank test and Kaplan-Meier plot to provide instant significance estimation for searched molecules. As an initial repository with the aim of Korean-specific marker detection, KCGD would be a promising web application for users without bioinformatics expertise to identify significant factors associated with cancer in Korean.

• Asian Pacific Journal of Cancer Prevention
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• 제15권22호
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• pp.9557-9565
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• 2014

MiRNAs are endogenous, single stranded ~22-nucleotide non-coding RNAs (ncRNAs) which are transcribed by RNA polymerase II and mediate negative post-transcriptional gene regulation through binding to 3'untranslated regions (UTR), possibly open reading frames (ORFs) or 5'UTRs of target mRNAs. MiRNAs are involved in the normal physiology of eukaryotic cells, so dysregulation may be associated with diseases like cancer, and neurodegenerative, heart and other disorders. Among all cancers, lung cancer, with high incidence and mortality worldwide, is classified into two main groups: non-small cell lung cancer and small cell lung cancer. Recent promising studies suggest that gene expression profiles and miRNA signatures could be a useful step in a noninvasive, low-cost and repeatable screening process of lung cancer. Similarly, every stage of lung development during fetal life is associated with specific miRNAs. Since lung development and lung cancer phenomena share the same physiological, biological and molecular processes like cell proliferation, development and shared mRNA or expression regulation pathways, and according to data adopted from various studies, they may have partially shared miRNA signature. Thus, focusing on lung cancer in relation to lung development in miRNA studies might provide clues for lung cancer diagnosis and prognosis.

• Journal of Microbiology
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• 제34권1호
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• pp.25-29
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• 1996

Since sequencing of randomly selected cDNA clones has been known to be a powerful approach to obtain information on gene expression pattern in specific cells or tissues, we have analyzed a 3'-directed cDNA library of vegetative mycelia of A. nidulans by single-pass sequencing of hundreds of randomly selected clones. Sequencing of 292 cDNA clones yielded 209 gene signatures (GSs) probably representing highly or lesser expressed genes in the vegetative mycelia. Among the 209 GSs, 25 (79 cDNA clones) appeared more than once and 184 only once. One GS appeared at a highest frequency of 6 times, 2 GSs5 times, 4 GSs 4 times, a GSs 3 times and 16 GSs twice. About 6.6% GSs comprizing of 13 GSs showed alternative polyadenylation. Among 23 redundant GSs, three were common in both mycelia and sexual organs, and 22 were probably mycelia-specific. Out of 209 GSs, 36 were identified in GenBank showing of 70% or greater similaritis. Only six GSs were for A. nidulans genes, and 13 GSs were of DNA or genes encoding cytoplasmic or organellar proteins. This pattern is similar to those in the human HepG2 cell line and in human colonic mucosa, although very few genes for nuclear proteins and for protein synthesis were in A. nidulans.

• Clinical and Experimental Pediatrics
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• 제64권7호
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• pp.355-363
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• 2021

Background: Nephrotic syndrome (NS) is a common renal disorder in children attributed to podocyte injury. However, children with the same diagnosis have markedly variable treatment responses, clinical courses, and outcomes, suggesting molecular heterogeneity. Purpose: This study aimed to explore the molecular responses of podocytes to nephrotic plasma to identify specific genes and signaling pathways differentiating various clinical NS groups as well as biological processes that drive injury in normal podocytes. Methods: Transcriptome profiles from immortalized human podocyte cell line exposed to the plasma of 8 subjects (steroid-sensitive nephrotic syndrome [SSNS], n=4; steroid-resistant nephrotic syndrome [SRNS], n=2; and healthy adult individuals [control], n=2) were generated using microarray analysis. Results: Unsupervised hierarchical clustering of global gene expression data was broadly correlated with the clinical classification of NS. Differential gene expression (DGE) analysis of diseased groups (SSNS or SRNS) versus healthy controls identified 105 genes (58 up-regulated, 47 down-regulated) in SSNS and 139 genes (78 up-regulated, 61 down-regulated) in SRNS with 55 common to SSNS and SRNS, while the rest were unique (50 in SSNS, 84 genes in SRNS). Pathway analysis of the significant (P≤0.05, -1≤ log2 FC ≥1) differentially expressed genes identified the transforming growth factor-β and Janus kinase-signal transducer and activator of transcription pathways to be involved in both SSNS and SRNS. DGE analysis of SSNS versus SRNS identified 2,350 genes with values of P≤0.05, and a heatmap of corresponding expression values of these genes in each subject showed clear differences in SSNS and SRNS. Conclusion: Our study observations indicate that, although podocyte injury follows similar pathways in different clinical subgroups, the pathways are modulated differently as evidenced by the heatmap. Such transcriptome profiling with a larger cohort can stratify patients into intrinsic subtypes and provide insight into the molecular mechanisms of podocyte injury.

• Asian-Australasian Journal of Animal Sciences
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• 제31권7호
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• pp.1062-1071
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• 2018

The misuse of anabolic hormones or illegal drugs is a ubiquitous problem in animal husbandry and in food safety. The ban on growth promotants in food producing animals in the European Union is well controlled. However, application regimens that are difficult to detect persist, including newly designed anabolic drugs and complex hormone cocktails. Therefore identification of molecular endogenous biomarkers which are based on the physiological response after the illicit treatment has become a focus of detection methods. The analysis of the 'transcriptome' has been shown to have promise to discover the misuse of anabolic drugs, by indirect detection of their pharmacological action in organs or selected tissues. Various studies have measured gene expression changes after illegal drug or hormone application. So-called transcriptomic biomarkers were quantified at the mRNA and/or microRNA level by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) technology or by more modern 'omics' and high throughput technologies including RNA-sequencing (RNA-Seq). With the addition of advanced bioinformatical approaches such as hierarchical clustering analysis or dynamic principal components analysis, a valid 'biomarker signature' can be established to discriminate between treated and untreated individuals. It has been shown in numerous animal and cell culture studies, that identification of treated animals is possible via our transcriptional biomarker approach. The high throughput sequencing approach is also capable of discovering new biomarker candidates and, in combination with quantitative RT-qPCR, validation and confirmation of biomarkers has been possible. These results from animal production and food safety studies demonstrate that analysis of the transcriptome has high potential as a new screening method using transcriptional 'biomarker signatures' based on the physiological response triggered by illegal substances.

• 한국지능시스템학회논문지
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• 제19권4호
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• pp.545-549
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• 2009

마이크로어레이 데이터는 수천가지 유전자의 발현정보를 포함할 수 있으며, 여기에서 의미있는 패턴을 추출하여 추가적인 분석을 위한 목적으로 활용되고 있다. 다수의 샘플 또는 실험에 대해서 마이크로어레이 데이터가 수집된 경우에 분석자가 관심을 갖는 유전자들이나 샘플들을 효과적으로 검색하는 것이 필요한 경우가 있다. 이 논문에서는 단순한 조건뿐만 아니라 복잡한 조건을 정의하여 원하는 특성을 만족하는 유전자나 샘플을 추출하는 방법으로 퍼지 시그너쳐 집합을 활용하는 방법을 제안한다. 퍼지 시그너쳐는 벡터값을 값을 갖는 퍼지 집합을 확장한 것으로, 벡터의 각 요소가 다시 벡터가 되는 것을 허용하는 재귀적인 구조이다. 퍼지 시그너쳐 집합은 단말 원소가 구간 [0,1] 사이에서 정의된 퍼지집합이라는 것을 제외하면 퍼지 시그너쳐와 같은 구조를 가진다. 이 논문에서는 각 내부 노드에 대해서 명시적으로 결합 연산자를 지정하도록 하고, 결합 연산을 위해 비교연산자를 사용할 수 있도록 확장한 퍼지 시그너쳐 집합을 소개한다. 또한 확장된 퍼지 시그너쳐 집합을 마이크로어레이 데이터 검색을 위해 사용하는 방법과 이를 사용한 예를 보인다.

• Bulletin of the Korean Chemical Society
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• 제31권6호
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• pp.1555-1560
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• 2010

Quantum dots (QDs) are extensively employed for biomedical research as a fluorescence reporter and their use for various labeling applications will continue to increase as they are preferred over conventional labeling methods for various reasons. However, concerns have been raised over the toxicity of these particles in the biological system. Till date no thorough investigation has been carried out to identify the molecular signatures of QD mediated toxicity. In this study we evaluated the toxicity of CdSe, $Cd_{1-x}Zn_xS$/ZnS and CdSe/ZnS quantum dots having different spectral properties (red, blue, green) using human embryonic kidney fibroblast cells (HEK293). Cell viability assay for both short and long duration exposure show concentration material dependent toxicity, in the order of CdSe > $Cd_{1-x}Zn_xS$/ZnS > CdSe/ZnS. Genome wide changes in the expression of genes upon QD exposure was also analyzed by wholegenome microarray. All the three QDs show increase in the expression of genes related to apoptosis, inflammation and response towards stress and wounding. Further comparison of coated versus uncoated CdSe QD-mediated cell death and molecular changes suggests that ZnS coating could reduce QD mediated cytotoxicity to some extent only.

• Genomics & Informatics
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• 제21권2호
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• pp.18.1-18.11
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• 2023

Immunologists have activated T cells in vitro using various stimulation methods, including phorbol myristate acetate (PMA)/ionomycin and αCD3/αCD28 agonistic antibodies. PMA stimulates protein kinase C, activating nuclear factor-κB, and ionomycin increases intracellular calcium levels, resulting in activation of nuclear factor of activated T cell. In contrast, αCD3/αCD28 agonistic antibodies activate T cells through ZAP-70, which phosphorylates linker for activation of T cell and SH2-domain-containing leukocyte protein of 76 kD. However, despite the use of these two different in vitro T cell activation methods for decades, the differential effects of chemical-based and antibody-based activation of primary human T cells have not yet been comprehensively described. Using single-cell RNA sequencing (scRNA-seq) technologies to analyze gene expression unbiasedly at the single-cell level, we compared the transcriptomic profiles of the non-physiological and physiological activation methods on human peripheral blood mononuclear cell-derived T cells from four independent donors. Remarkable transcriptomic differences in the expression of cytokines and their respective receptors were identified. We also identified activated CD4 T cell subsets (CD55⁺) enriched specifically by PMA/ionomycin activation. We believe this activated human T cell transcriptome atlas derived from two different activation methods will enhance our understanding, highlight the optimal use of these two in vitro T cell activation assays, and be applied as a reference standard when analyzing activated specific disease-originated T cells through scRNA-seq.