• Title/Summary/Keyword: RNA microarray

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Integrative analysis of microRNA-mediated mitochondrial dysfunction in hippocampal neural progenitor cell death in relation with Alzheimer's disease

  • A Reum Han;Tae Kwon Moon;Im Kyeung Kang;Dae Bong Yu;Yechan Kim;Cheolhwan Byon;Sujeong Park;Hae Lin Kim;Kyoung Jin Lee;Heuiran Lee;Ha-Na Woo;Seong Who Kim
    • BMB Reports
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    • v.57 no.6
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    • pp.281-286
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    • 2024
  • Adult hippocampal neurogenesis plays a pivotal role in maintaining cognitive brain function. However, this process diminishes with age, particularly in patients with neurodegenerative disorders. While small, non-coding microRNAs (miRNAs) are crucial for hippocampal neural stem (HCN) cell maintenance, their involvement in neurodegenerative disorders remains unclear. This study aimed to elucidate the mechanisms through which miRNAs regulate HCN cell death and their potential involvement in neurodegenerative disorders. We performed a comprehensive microarray-based analysis to investigate changes in miRNA expression in insulin-deprived HCN cells as an in vitro model for cognitive impairment. miR-150-3p, miR-323-5p, and miR-370-3p, which increased significantly over time following insulin withdrawal, induced pronounced mitochondrial fission and dysfunction, ultimately leading to HCN cell death. These miRNAs collectively targeted the mitochondrial fusion protein OPA1, with miR-150-3p also targeting MFN2. Data-driven analyses of the hippocampi and brains of human subjects revealed significant reductions in OPA1 and MFN2 in patients with Alzheimer's disease (AD). Our results indicate that miR-150-3p, miR-323-5p, and miR-370-3p contribute to deficits in hippocampal neurogenesis by modulating mitochondrial dynamics. Our findings provide novel insight into the intricate connections between miRNA and mitochondrial dynamics, shedding light on their potential involvement in conditions characterized by deficits in hippocampal neurogenesis, such as AD.

Gene Expression Profiles in Cervical Cancer with Radiation Therapy Alone and Chemo-radiation Therapy (자궁경부암의 방사선치료 및 방사선항암화학 병용치료에 따른 유전자발현 조절양상)

  • Lee Kyu Chan;Kim Meyoung-kon;Kim Jooyoung;Hwang You Jin;Choi Myung Sun;Kim Chul Yong
    • Radiation Oncology Journal
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    • v.21 no.1
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    • pp.54-65
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    • 2003
  • Purpose : To analyze the gene expression Profiles of uterine ceulcal cancer, and its variation after radiation therapy, with or without concurrent chemotherapy, using a CDNA microarray. Materials and Methods :Sixteen patients, 8 with squamous ceil carcinomas of the uterine cervix, who were treated with radiation alone, and the other 8 treated w14h concurrent chemo-radiation, were Included in the study. Before the starling of the treatment, tumor biopsies were carried out, and the second time biopsies were peformed after a radiation dose of 16.2$\~$27 Gy. Three normal cervix tissues were used as a control group. The microarray experiments were peformed with 5 groups of the total RNAs extracted individually and then admixed as control, pre-radiation therapy alone, during-radiation therapy alone, pre-chemoradiation therapy, and during-chemoradlation therapy. The 33P-iabeled CDNAS were synthesized from the total RNAs of each group, by reverse transcription, and then they were hybridized to the CDNA microarray membrane. The gene expression of each microarrays was captured by the intensity of each spot produced by the radioactive isotopes. The pixels per spot were counted with an Arrayguage, and were exported to Microsoft Excel The data were normalized by the Z transformation, and the comparisons were peformed on the Z-ratio values calculated. Results : The expressions of 15 genes, including integrin linked kinase (ILK), CDC28 protein kinase 2, Spry 2, and ERK 3, were increased with the Z-ratio values of over 2.0 for the cervix cancer tissues compared to those for the normal controls. Those genes were involved In cell growth and proliferation, cell cycle control, or signal transduction. The expressions of the other 6 genes, Including G protein coupled receptor kinase 5, were decreased with the Z-ratio values of below -2.0. After the radiation thorapy, most of the genes, with a previously Increase expressions, represented the decreased expression profiles, and the genes, with the Z-ratio values of over 2.0, were cyclic nucleotlde gated channel and 3 Expressed sequence tags (EST). In the concurrent chemo-radiation group, the genes involved in cell growth and proliferation, cell cycle control, and signal transduction were shown to have increased expressions compared to the radiation therapy alone group. The expressions of genes involved in anglogenesis (angiopoietln-2), immune reactions (formyl peptide receptor-iike 1), and DNA repair (CAMP phosphodiesterase) were increased, however, the expression of gene involved In apoptosls (death associated protein kinase) was decreased. Conclusion : The different kinds of genes involved in the development and progression of cervical cancer were identified with the CDNA microarray, and the proposed theory is that the proliferation signal stalls with ILK, and is amplified with Spry 2 and MAPK signaling, and the cellular mitoses are Increased with the increased expression oi Cdc 2 and cell division kinases. After the radiation therapy, the expression profiles demonstrated 4he evidence of the decreased cancer cell proliferation. There was no sigificant difference in the morphological findings of cell death between the radiation therapy aione and the chemo-radiation groups In the second time biopsy specimen, however, the gene expression profiles were markedly different, and the mechanism at the molecular level needs further study.

A gene filtering method based on fuzzy pattern matching for whole genome microarray data analysis (마이크로어레이 데이터의 게놈수준 분석을 위한 퍼지 패턴 매칭에 의한 유전자 필터링 방법)

  • Lee, Seon-A;Lee, Geon-Myeong;Lee, Seung-Ju;Kim, Won-Jae;Kim, Yong-Jun;Bae, Seok-Cheol
    • Proceedings of the Korean Institute of Intelligent Systems Conference
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    • 2007.11a
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    • pp.145-148
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    • 2007
  • 생명과학분야에서 마이크로어레이 기술은 세포에서의 RNA 발현 프로파일을 관찰할 수 있도록 함으로써 생명현상의 규명 및 약물개발 둥에서 분자수준의 생명현상에 대한 관찰과 분석이 가능 해지고 있다. 마이크로어레이 데이터분석에서는 특정한 처리나 과정에서 현저한 특성을 보이는 유전자를 식별하기 위한 분석뿐만 아니라 유전자 전체인 게놈수준에서의 분석도 이루어진다. 최근 유전자의 발현이 다양한 조절, 신호전달 및 대사경로에 의해서 영향을 받고 있다는 관점에서 게놈수준의 분석에 관심이 증가하고 있다. 약물반응 실험에서는 약물에 대한 게놈수준의 발현 프로파일을 관찰하는 것도 많은 정보를 제공할 수 있다. 약물실험에서는 대조군과 실험군들간에 관심 있는 상대적인 발현특성을 갖는 유전자군을 전체적으로 추출하는 것이 필요한 경우가 있다. 예를 들면 정상군은 두개의 실험군에 대해서 중간청도의 발현정도를 갖는 유전자군을 식별하는 분석을 하는 경우, 생물학적인 데이터의 특성상 절대값을 비교하는 방법으로는 유용한 유전자들을 효과적으로 식별해 낼 수 없다. 이 논문에서는 정상군과 실험군들의 발현정도값의 경향을 판단하기 위해서 각 유전자에 대해서 집단별 대표값을 선정하여 퍼지집합으로 집단의 값의 범위를 결정하고, 이를 이용하여 특정 패턴을 갖는 유전자들을 식별해내는 방법을 제안하고, 실제 데이터를 통해서 실험한 결과를 보인다.

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Genome-wide analysis on the effects of Salviae miltiorrhizae Radix in hyperlipidemic mice (단삼(丹蔘)이 고지혈증 생쥐의 혈중 지질 및 간조직 유전자 변화에 미치는 영향)

  • Kim, Hyung Cheul;Kim, Young Kyun
    • Journal of Haehwa Medicine
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    • v.21 no.2
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    • pp.73-84
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    • 2013
  • 단삼(丹蔘) (Salvia miltiorrhiza Bunge)은 꿀풀과 배암차즈기속에 속하며 중국(中國)이 원산지(原産地)인 여러해살이풀로, 동의보감(東醫寶鑑)에는 "성질(性質)은 약간 차고 맛이 쓰며 독(毒)이 없다. 다리가 약하면서 저리고 아픈것과 팔다리를 쓰지 못하는 것을 치료한다. 또는 고름을 빨아내고 아픈 것을 멎게 하며 살찌게 하고 오래된 어혈(瘀血)을 헤치며${\ldots}$" 등으로 기술되어 있으며 이전부터 부인과(婦人科)에 많이 응용하는 약재 중 하나로 그 효능이 어혈(瘀血)을 없애는데 있기 때문이다. 임상(臨床)에서는 부인과(婦人科) 질환(疾患)뿐만 아니라 심혈관(心血管) 질환(疾患)에도 사용되고 있다. 본 연구에서는 이러한 효능의 객관적 근거를 마련하고 약재의 작용 기전 중 일부를 확인하기 위해 고지혈증이 유발된 생쥐에 단삼(丹蔘) 추출물을 투여하여 혈중 콜레스테롤 및 트리글리세라이드 수치를 낮추는 작용을 확인했으며 동시에 간조직 내 지방의 축적도 억제하는 것으로 나타났다. 이러한 변화가 간조직 내 유전자의 변화와 어떠한 관련이 있는지 확인하기 위해 RNA를 분리하여 Microarray 분석을 수행한 결과 고지혈증으로 인해 변화된 유전자들이 단삼(丹蔘) 추출물의 투여로 인해 정상에 가까운 정도로 조절됨을 확인하였으며 향후 본 연구를 통해 확인된 핵심 유전자를 고지혈증 치료의 지표 등으로 활용할 수 있을 것으로 기대된다.

Nuclear Akt promotes neurite outgrowth in the early stage of neuritogenesis

  • Park, Ji-Hye;Lee, Sang-Bae;Lee, Kyung-Hoon;Ahn, Jee-Yin
    • BMB Reports
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    • v.45 no.9
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    • pp.521-525
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    • 2012
  • In addition to its pivotal role in neuronal survival, PI3K/Akt signaling is integral to neuronal differentiation and neurite outgrowth. However, the exact role of Akt in neuronal differentiation is still controversial. Here, we found that nuclear expression of CA-Akt resulted in unusual rapid neurite outgrowth and overexpression of KD-Akt caused multiple dendrite growth without specific axon elongation. Moreover, microarray data revealed that the expression of FOXQ1 expression was about 10-fold higher in cells with nuclear, active Akt than in control cells. Quantitative real-time PCR analysis showed that mRNA levels were upregulated in NLS-CA-Akt cells as compared to KD or EV cells. Furthermore, our FACS analysis demonstrated that overexpression of NLS-CA-Akt accumulate cells in the G1 phase within 24 h, fitting with the rapid sprouting of neuritis. Thus, our data implied that at least in this early time frame, the overexpression of nuclear, active Akt forced cells into neurite development through probably FOXQ1regulation.

Construction of the Full-length cDNA Library and Selection of Diapause-Associated cDNA Clones from Bombyx mori Diapausing Eggs and Diapause-Activated Eggs

  • Hwnag, Jae-Sam;Go, Hyun-Jeong;Goo, Tae-Won;Yun, Eun-Young;Choi, Kwang-Ho;Seong, Su-Il;Kim, Sung-Kuk;Lee, Sang-Mong;Kim, Iksoo;Kim, Nam-Soon;Kang, Seok-Woo
    • International Journal of Industrial Entomology and Biomaterials
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    • v.9 no.1
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    • pp.145-148
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    • 2004
  • As an initial step to define the molecular mechanism of diapause during embryogenesis of the silkworm, Bombyx mori, mRNA transcripts from diapausing eggs and diapause-activated eggs were compared by differential expression using cDNA microarray. Twenty-four individual cDNA clones were identified. Amomg them, ten genes including alcohol dehydrogenase, dead box-l, cytochrome oxidase subunit I and 18 wheeler showed increased expression in the diapause-activated eggs. The rest of fourteen genes showed increased expression in diapausing eggs.

Current Trends in Nutrigenomics (영양유전체학(Nutrigenomics)의 최근 경향)

  • Choi, Bong-Hyuk;Kim, Jong-Bae;Do, Myoung-Sool
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.34 no.10
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    • pp.1642-1654
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    • 2005
  • With the decoding of human genome in 2004 and the recent development in nutritional science there has been an integration of molecular biology and nutrition. As a consequenc a now word ' molecular nutrition ' has been formed and recently the word 'nutrigenomics' is coined and widely being used. The field of science that showed the most positive result from grafting the science of nutrition and nutrigenomics is obesity. In 1994, Jeffrey Friedman from Rockeffeler University announced that ob gene and obesity has a close relationship and since then there's been a huge research done on genes related to obesity from the molecular nutrition's Point of view. Even now there are many genes presented which are supposed to be related to obesity and big efforts are put into finding what exactly those genes do. Moreover studying only in the context of genes was not enough so functional genomics, which is the study of the functions of cells and the functions and effects between genes and Protein Products, is being studied. This review article discusses the relationship between nutrition and genes and the general idea of nutrigenomics. The article also discusses about the current research status on these subjects.

Transcriptional Responses of Human Respiratory Epithelial Cells to Nontypeable Haemophilus influenzae Infection Analyzed by High Density cDNA Microarrays

  • Lee, Ji-Yeon;Lee, Na-Gyong
    • Journal of Microbiology and Biotechnology
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    • v.14 no.4
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    • pp.836-843
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    • 2004
  • Nontypeable H. influenzae (NTHi), a Gram-negative obligate human pathogen, causes pneumonia, chronic bronchitis, and otitis media, and the respiratory epithelium is the first line of defense that copes with the pathogen. In an effort to identify transcriptional responses of human respiratory epithelial cells to infection with NTHi, we examined its differential gene expression using high density cDNA microarrays. BEAS-2B human bronchial epithelial cells were exposed to NTHi for 3 hand 24 h, and the alteration of mRNA expression was analyzed using microarrays consisting of 8,170 human cDNA clones. The results indicated that approximately 2.6% of the genes present on the microarrays increased in expression over 2-fold and 3.8% of the genes decreased during the 24-h infection period. Upregulated genes included cytokines (granulocyte-macrophage colony stimulating factor 2, granulocyte chemotactic protein 2, IL-6, IL-10, IL-8), transcription factors (Kruppel-like factor 7, CCAAT/enhancer binding protein $\beta$, E2F-1, NF-$\kappa$B, cell surface molecules (CD74, ICAM-1, ICAM-2, HLA class I), as well as those involved in signal transduction and cellular transport. Selected genes were further confirmed by reverse-transcription-PCR. These data expand our knowledge of host cellular responses during NTHi infection and should provide a molecular basis for the study of host-NTHi interaction.

Inactivation of SMAD$_4$ Tumor Suppressor gene during Gastric Cancer Progression

  • Shin, Young-Kee
    • Proceedings of the Korean Society of Toxicology Conference
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    • 2006.11a
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    • pp.19-24
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    • 2006
  • Mothers against decapentaplegic homolog 4 (SMAD4) is a tumor suppressor gene associated with gastrointestinal carcinogenesis. The aim of the present study was to characterize more precisely its role in the development and progression of human gastric carcinoma. In this study, using tissue microarray analysis of 283 gastric cancers and related lesions, we found loss of SMAD4 protein expression in the cytoplasm (36/114, 32%) and in the nucleus (46/114, 40%) of gastric cancer cells. The loss of nuclear SMAD4 expression in primary tumors correlated significantly with poor survival, and was an independent prognostic marker in multivariate analysis. We also found a substantial decrease in SMAD4 expression at both the RNA and protein level in several human gastric carcinoma cell lines. To identify the genetic and/or epigenetic mechanisms of altered SMAD4 expression in gastric carcinoma, loss of heterozygosity (LOH), promoter hypermethylation, and exon mutations were examined. We found that LOH (20/70, 29%) and promoter hypermethylation (4/73, 5%) were associated with the loss of SMAD4 expression. SMAD4 protein levels wore also affected in certain gastric carcinoma cell lines following incubation with Mc132, a proteasome inhibitor. Taken together, our results indicate that the loss of SMAD4, especially loss of nuclear SMAD4 expression, is involved in gastric cancer progression. The loss of SMAD4 in gastric carcinomas is due to several mechanisms, including LOH, hypermethylation, and proteasome degradation.

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Inhibition of Cell Proliferation and Migration by miR-509-3p That Targets CDK2, Rac1, and PIK3C2A

  • Yoon, Sena;Han, Eunji;Choi, Young-Chul;Kee, Honghwan;Jeong, Yongsu;Yoon, Jaeseung;Baek, Kwanghee
    • Molecules and Cells
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    • v.37 no.4
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    • pp.314-321
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    • 2014
  • CDK2 is a key regulator of cell cycle progression. In this study, we screened for miRNAs targeting CDK2 using a luciferase-3'-untranslated region reporter assay. Among 11 hit miRNAs, miR-509-3p reduced CDK2 protein levels and significantly inhibited cancer cell growth. Microarray, Western blotting, and luciferase reporter analyses revealed additional targets of miR-509-3p, including Rac1 and PIK3C2A. Overexpression of miR-509-3p induced G1 cell-cycle arrest and inhibited colony formation and migration. RNAi experiments indicated that the growth-inhibitory effects of miR-509-3p may occur through down-regulation of CDK2, Rac1, and PIK3C2A. Targeting of multiple growth regulatory genes by miR-509-3p may contribute to effective anti-cancer therapy.