• 제목/요약/키워드: gene expression profiling

검색결과 303건 처리시간 0.034초

Gene Expression Profiling of the Habenula in Rats Exposed to Chronic Restraint Stress

  • Yoo, Hyeijung;Kim, Hyun Jung;Yang, Soo Hyun;Son, Gi Hoon;Gim, Jeong-An;Lee, Hyun Woo;Kim, Hyun
    • Molecules and Cells
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    • 제45권5호
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    • pp.306-316
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    • 2022
  • Chronic stress contributes to the risk of developing depression; the habenula, a nucleus in epithalamus, is associated with many neuropsychiatric disorders. Using genome-wide gene expression analysis, we analyzed the transcriptome of the habenula in rats exposed to chronic restraint stress for 14 days. We identified 379 differentially expressed genes (DEGs) that were affected by chronic stress. These genes were enriched in neuroactive ligand-receptor interaction, the cAMP (cyclic adenosine monophosphate) signaling pathway, circadian entrainment, and synaptic signaling from the Kyoto Encyclopedia of Genes and Genomes pathway analysis and responded to corticosteroids, positive regulation of lipid transport, anterograde trans-synaptic signaling, and chemical synapse transmission from the Gene Ontology analysis. Based on protein-protein interaction network analysis of the DEGs, we identified neuroactive ligand-receptor interactions, circadian entrainment, and cholinergic synapse-related subclusters. Additionally, cell type and habenular regional expression of DEGs, evaluated using a recently published single-cell RNA sequencing study (GSE137478), strongly suggest that DEGs related to neuroactive ligand-receptor interaction and trans-synaptic signaling are highly enriched in medial habenular neurons. Taken together, our findings provide a valuable set of molecular targets that may play important roles in mediating the habenular response to stress and the onset of chronic stress-induced depressive behaviors.

페닐부타존에 의해 간손상이 유발된 생쥐의 유전자 발현 분석 (Gene Expression Analysis of Phenylbutazone-induced Liver Damage in Mice)

  • 이은주;정인해;김한나;정희경;공구;강경선;윤병일;이병훈;이미옥;김주한;김형래
    • Toxicological Research
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    • 제22권2호
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    • pp.87-93
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    • 2006
  • The KFDA (Korea Food & Drug Administration) has performed a collaborative toxico-genomics project since 2003. Its aim is to construct a toxicologenomic database of 12 hepatotoxic compounds from mice livers. Phenylbutazone which is non-steroidal anti-inflammatory drug was assigned. It was administered at low (0.0238 mg/kg) and at high (0.238 mg/kg) dose (5 mice per group) orally to the postnatal 6 weeks ICR mice, then the serum and liver were collected at the indicated time (6, 24 and 72 h) after administration. Serum biochemical markers for liver toxicity were measured and histopathologic studies also were carried out. The gene expression profiling was carried out by using Applied Biosystems 1700 Full Genome Expression Mouse. The 2-way ANOVA was used to find genes that reflected phenylbutazone-induced acute toxicity or dose-dependant changes. By self-organization maps (SOM), we identified groups with unique gene expression patterns, some of them are supposed to be related to phenylbutazone induced toxicity, including lipid metabolism abnormality, oxidative stress, cell death and cytoskeleton destruction.

Gene Expression Analysis of Methotrexate-induced Hepatotoxicity between in vitro and in vivo

  • Jung, Jin-Wook;Kim, Seung-Jun;Kim, Jun-Sup;Park, Joon-Suk;Yeom, Hye-Jung;Kim, Ji-Hoon;Her, Young-Sun;Lee, Yong-Soon;Kang, Jong-Soo;Lee, Gyoung-Jae;Kim, Yang-Seok;Kang, Kyung-Sun;Hwang, Seung-Yong
    • Molecular & Cellular Toxicology
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    • 제1권4호
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    • pp.256-261
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    • 2005
  • The recent DNA microarray technology enables us to understand gene expression profiling in cell line and animal models. The technology has potential possibility to comprehend mechanism of multiple genes were related to compounds which have toxicity in biological system. So, microarray system has been used for the prediction of toxicity through gene expression induced by toxicants. It has been shown that compounds with similar toxic mechanisms produce similar changes in gene expression in vivo system. Here we focus on the use of toxicogenomics for the determination of gene expression analysis associated with hepatotoxicity in rat liver and cell line (WB-F344). Methotrexate (MTX) is a chemotherapy agent that has been used for many years in the treatment of cancer because it affects cells that are rapidly dividing. Also it has been known the toxicity of MTX, in a MTX abortion, it stops embryonic cells from dividing and multiplying and is a non-surgical method of ending pregnancy in its early stages. We have shown DNA microarray analyses to assess MTX-specific expression profiles in vivo and in vitro. Male Sprague-Dawely VAF+ albino rats of 5-6 weeks old and WB-F344 cell line have been treated with MTX. Total RNA was isolated from Rat liver and cell line that has treated with MTX. 4.8 K cDNA microarray in house has been used for gene expression profiling of MTX treatment. We have found quite distinct gene expression patterns induced by MTX in a cell line and in vivo system.

Expressional Profiling of Telomerase and Telomere-Associated Molecules in the Rat Testis and Seminal Vesicle during Postnatal Developmental Period

  • Seo, Hee-Jung;Lee, Seong-Kyu;Baik, Haing-Woon;Cheon, Yong-Pil;Chun, Tae-Hoon;Choi, In-Ho;Lee, Ki-Ho
    • Journal of Animal Science and Technology
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    • 제53권3호
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    • pp.195-202
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    • 2011
  • Maintenance of adequate telomere length in developing cells is the most important concern to preserve the integrity of the genome. The length of telomere is strictly regulated by numerous telomere-binding proteins and/or interacting factors. Even though the expression of telomerase in the male reproductive tract has been characterized, developmental expressional profiling of telomerase and other telomere-associated proteins has not been determined in detail. The present study was attempted to examine expression patterns of catalytic subunit (Tert) and RNA component (Terc) of telomerase and two telomerase associated factors, telomerase associated protein 1 (Tep1) and TERF1 (TRF1) interacting nuclear factor 2 (Tinf2) in the testis and seminal vesicle of male rat during postnatal development. The real-time PCR analysis was utilized to quantify mRNA expression of molecules. The abundance of Tep1 mRNA in the testis and seminal vesicle was the highest at 5 months of age. Expressional fluctuation of Tinf2 during postnatal development was found in the testis, while expression of Tinf2 in the seminal vesicle was gradually increased until 5 months of age and then significantly decreased later. mRNA level of Tert gene in the testis was significantly increased at the adult and the elder, while the highest expression of Tert gene in the seminal vesicle was found at 5 months of age. Expression of Terc transcript in the testis and seminal vesicle was the highest at 5 months of age, followed by significant reduction at 1 and 2 years of ages. Such differential gene expression of telomere-associated factors and telomerase components in different male reproductive tissues during postnatal development indicates that maintenance of telomere length would be regulated in tissue- and/or age-specific manners.

SLA Genetic Polymorphism and Large Scale Gene Expression Profiling of Cloned SNU Miniature Pigs Derived from Same Cell Line

  • Yeom, Su-Cheong;Koo, Ok Jae;Park, Chung-Gyu;Lee, Byeong-Chun;Lee, Wang-Jae
    • Reproductive and Developmental Biology
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    • 제37권1호
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    • pp.1-8
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    • 2013
  • In order to investigate genetic stability and gene expression profile after cloning procedure, two groups of cloned pigs were used for swine leukocyte antigen (SLA) gene nucleotide alteration and microarray analyses. Each group was consist of cloned pigs derived from same cell line (n=3 and 4, respectively). Six SLA loci were analyzed for cDNA sequences and protein translations. In total, 16 SLA alleles were identified and there were no evidence of SLA nucleotide alteration. All SLA sequences and protein translations were identical among the each pig in the same group. On the other hand, microarray assay was performed for profiling gene expression of the cloned pigs. In total, 43,603 genes were analyzed and 2,150~4,300 reliably hybridized spots on the each chip were selected for further analysis. Even though the cloned pigs in the same group had identical genetic background, 18.6~47.3% of analyzed genes were differentially expressed in between each cloned pigs. Furthermore, on gene clustering analysis, some cloned pigs showed abnormal physiological phenotypes such as inflammation, cancer or cardiomyopathy. We assumed that individual environmental adaption, sociality and rank in the pen might have induced these different phenotypes. In conclusion, the results of the present study indicate that SLA locus genes appear to be stable following SCNT. However, gene expressions and phenotypes between cloned pigs derived from the same cell line were not identical even under the same rearing conditions.

Hypoxia suffocates histone demethylases to change gene expression: a metabolic control of histone methylation

  • Park, Hyunsung
    • BMB Reports
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    • 제50권11호
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    • pp.537-538
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    • 2017
  • Hypoxia affects various physiological and pathophyological processes. Hypoxia changes the expression of hypoxia-responsive genes through two main pathways. First, hypoxia activates transcription factors (TF) such as Hypoxia-inducible Factor (HIF). Second, hypoxia decreases the activity of Jumonji C domain-containing histone demethylases (JMJDs) that require $O_2$ and ${\alpha}$-Ketoglutarate (${\alpha}$-KG) as substrates. The JMJDs affect gene expression through their regulation of active or repressive histone methylations. Profiling of H3K4me3, H3K9me3, and H3K27me3 under both normoxia and hypoxia identified 75 TFs whose binding motifs were significantly enriched in the methylated regions of the genes. TFs showing similar binding strengths to their target genes might be under the 'metabolic control' which changes histone methylation and gene expression by instant changing catalytic activities of resident histone demethylases.

폐 편평세포암종 내 Leucine-Rich Repeat Kinase 2 암촉진 효과와 Interleukin-10 발현과의 연관성 (Correlation of Protumor Effects of Leucine-Rich Repeat Kinase 2 with Interleukin-10 Expression in Lung Squamous Cell Carcinoma)

  • 이성원;박상욱
    • 대한임상검사과학회지
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    • 제55권2호
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    • pp.105-112
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    • 2023
  • Leucine-rich repeat kinase 2 (LRRK2)는 파킨슨병과 같은 신경퇴행성 질환의 병태생리학적인 측면에서 중요한 역할을 하는 것으로 알려져 있고 주로 뇌뿐만 아니라 폐에서도 발현된다. 그러나 LRRK2 발현이 폐 편평세포암(lung squamous cell carcinoma, LUSC)과 같은 일반적인 폐암의 아형과 병인성이 있는지는 불분명하다. 본 연구에서는 Kaplan Meier 플로터 생물정보학 온라인 도구를 사용하여 폐 편평세포암종 내에서 LRRK2와의 예후 진단가치를 분석하였다. 폐 편평세포암종 환자는 LRRK2의 발현이 높아지면 더 나쁜 예후를 나타낸다고 알려져 왔다. LRRK2 발현이 높은 환자의 경우 종양 돌연변이 부담, 높은 신항원부하, 더 나쁜 생존율, 성별과 상관관계를 보였다. 더욱이, gene expression profiling interactive analysis 데이터분석에서 높은 LRRK2 발현을 가진 환자에서의 심각한 증상은 항염증성 사이토카인(예, IL-4, IL-10)의 높은 발현에 양의 상관관계를 보였지만 염증성 사이토카인은 상관성이 없었다. 이러한 결과에서 IL-10관련 유전자의 높은 발현은 더 나쁜 예후를 보이는 LRRK2-high 환자들에서 유의미하게 연관성을 보였다. 또한, tumor immunity estimation resource 데이터는 큰포식세포가 LRRK2-high LUSC환자에서 IL-10의 기원세포 중 하나임을 보여주었다. 본 연구를 통해 결과적으로 LRRK2-IL10 축의 가설이 LUSC 환자의 잠재적이 치료 표적과 예후 바이오 마커일 수 있음을 보여주었다.

Differential Gene Expression Profiling in Human Promyelocytic Leukemia Cells Treated with Benzene and Ethylbenzene

  • Sarma, Sailendra Nath;Kim, Youn-Jung;Ryu, Jae-Chun
    • Molecular & Cellular Toxicology
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    • 제4권4호
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    • pp.267-277
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    • 2008
  • Benzene and ethylbenzene (BE), the volatile organic compounds (VOCs) are common constituents of cleaning and degreasing agents, paints, pesticides, personal care products, gasoline and solvents. VOCs are evaporated at room temperature and most of them exhibit acute and chronic toxicity to human. Chronic exposure of benzene is responsible for myeloid leukemia and also ethylbenzene is also recognized as a possible carcinogen. To evaluate the BE effect on human, whole human genome 35 K oligonucleotide microarray were screened for the identification of the differential expression profiling. We identified 280 up-regulated and 201 down-regulated genes changed by more than 1.5 fold by BE exposure. Functional analysis was carried out by using DAVID bioinformatics software. Clustering of these differentially expressed genes were associated with immune response, cytokine-cytokine receptor interaction, toll-like signaling pathway, small cell lung cancer, immune response, apoptosis, p53 signaling pathway and MAPKKK cascade possibly constituting alternative or subordinate pathways of hematotoxicity and immune toxicity. Gene ontology analysis methods including biological process, cellular components, molecular function and KEGG pathway thus provide a fundamental basis of the molecular pathways through BEs exposure in human lymphoma cells. This may provides a valuable information to do further analysis to explore the mechanism of BE induced hematotoxicity.

Expression of dehydration responsive element-binding protein-3 (DREB3) under different abiotic stresses in tomato

  • Islam, Mohammad Saiful;Wang, Myeong-Hyeon
    • BMB Reports
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    • 제42권9호
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    • pp.611-616
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    • 2009
  • We investigated the expression pattern of dehydration responsive element-binding protein-3 in tomato under different abiotic stresses. Full length LeDREB3 cDNA was isolated from tomato plant, followed by phylogenetic analysis based on deduced amino acid sequences that revealed significant sequence similarity to DREB proteins belonging to diverse families of plant species. Southern blot analysis showed duplicate copies of LeDREB3 in the tomato genome while organ-specific expression profiling indicated constitutive expression of LeDREB3 in all tested organs, which was particularly strong in flower. LeDREB3 expression was significantly induced by Nacl, drought, low temperature and $H_2O_2$. Moreover, LeDREB3 was slightly regulated by treatment with ABA and MV. These observations suggest that the LeDREB3 gene may be involved in the response of the tomato plant to stress.