• Asian Pacific Journal of Cancer Prevention
• /
• 제14권9호
• /
• pp.5495-5501
• /
• 2013

Background: Alu elements are one of the most common repetitive sequences that now constitute more than 10% of the human genome and potential targets for epigenetic alterations. Correspondingly, methylation of these elements can result in a genome-wide event that may have an impact in cancer. However, studies investigating the genome-wide status of Alu methylation in cancer remain limited. Objectives: Oral squamous cell carcinoma (OSCC) presents with high incidence in South-East Asia and thus the aim of this study was to evaluate the Alu methylation status in OSCCs and explore with the possibility of using this information for diagnostic screening. We evaluated Alu methylation status in a) normal oral mucosa compared to OSCC; b) peripheral blood mononuclear cells (PBMCs) of normal controls comparing to oral cancer patients; c) among oral epithelium of normal controls, smokers and oral cancer patients. Materials and Methods: Alu methylation was detected by combined bisulfite restriction analysis (COBRA) at 2 CpG sites. The amplified products were classified into three patterns; hypermethylation ($^mC^mC$), partial methylation ($^uC^mC+^mC^uC$), and hypomethylation ($^uC^uC$). Results: The results demonstrate that the $%^mC^mC$ value is suitable for differentiating normal and cancer in oral tissues (p=0.0002), but is not significantly observe in PBMCs. In addition, a stepwise decrease in this value was observed in the oral epithelium from normal, light smoker, heavy smoker, low stage and high stage OSCC (p=0.0003). Furthermore, receiver operating characteristic (ROC) curve analyses demonstrated the potential of combined $%^mC$ or $%^mC^mC$ values as markers for oral cancer detection with sensitivity and specificity of 86.7% and 56.7%, respectively. Conclusions: Alu hypomethylation is likely to be associated with multistep oral carcinogenesis, and might be developed as a screening tool for oral cancer detection.

• Asian Pacific Journal of Cancer Prevention
• /
• 제13권9호
• /
• pp.4469-4475
• /
• 2012

Background: The potential use of hypomethylation of Long INterspersed Element 1 (LINE-1) and Alu elements (Alu) as a biomarker has been comprehensively assessed in several cancers, including head and neck squamous cell carcinoma (HNSCC). Failure to detect occult metastatic head and neck tumors on radical neck lymph node dissection can affect the therapeutic measures taken. Objective: The aim of this study was to investigate the LINE-1 and Alu methylation status and determine whether it can be applied for detection of occult metastatic tumors in HNSCC cases. Methods: We used the Combine Bisulfite Restriction Analysis (COBRA) technique to analyse LINE-1 and Alu methylation status. In addition to the methylation level, LINE-1 and Alu loci were classified based on the methylation statuses of two CpG dinucleotides in each allele as follows: hypermethylation ($^mC^mC$), hypomethylation ($^uC^uC$), and 2 forms of partial methylation ($^mC^uC$ and $^uC^mC$). Sixty-one lymph nodes were divided into 3 groups: 1) non-metastatic head and neck cancer (NM), 2) histologically negative for tumor cells of cases with metastatic head and neck cancer (LN), and 3) histologically positive for tumor cells (LP). Results: Alu methylation change was not significant. However, LINE-1 methylation of both LN and LP was altered, as demonstrated by the lower LINE-1 methylation levels (p<0.001), higher percentage of $^mC^uC$ (p<0.01), lower percentage of $^uC^mC$ (p<0.001) and higher percentage of $^uC^uC$ (p<0.001). Using receiver operating characteristic (ROC) curve analysis, $%^uC^mC$ and $%^mC^uC$ values revealed a high level of AUC at 0.806 and 0.716, respectively, in distinguishing LN from NM. Conclusion: The LINE-1 methylation changes in LN have the same pattern as that in LP. This epigenomic change may be due to the presence of occult metastatic tumor in LN cases.

• 한국동물학회:뉴스레터
• /
• 제12권2호
• /
• pp.128.2-128
• /
• 1995

• 한국동물학회:학술대회논문집
• /
• 한국동물학회 1995년도 한국생물과학협회 학술발표대회
• /
• pp.304.2-304
• /
• 1995

• Molecules and Cells
• /
• 제40권2호
• /
• pp.100-108
• /
• 2017

Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element-AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crabeating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues. Results demonstrated that AluYRa1 was only integrated into the genome of Macaca species and this lineage-specific integration led to exonization events by producing a conserved 3' splice site. Six transcript variants (V1-V6) were generated by alternative splicing (AS) events, including intron retention and alternative 5' splice sites in the 5' and 3' flanking regions of CTSF_AluYRa1. Among them, V3-V5 transcripts were ubiquitously expressed in all tissues of rhesus monkey and crab-eating monkey, whereas AluYRa1-exonized V1 was dominantly expressed in the testis of the crab-eating monkey, and V2 was only expressed in the testis of the two monkeys. These five transcript variants also had different amino acid sequences in the C-terminal region of CTSF, as compared to reference sequences. Thus, species-specific Alu-derived exonization by lineage-specific integration of Alu elements and AS events seems to have played an important role during primate evolution by producing transcript variants and gene diversification.

• Genomics & Informatics
• /
• 제10권4호
• /
• pp.226-233
• /
• 2012

Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.

• Progress in Superconductivity
• /
• 제8권2호
• /
• pp.181-185
• /
• 2007

For more than two decades Nb trilayer ($Nb/Al_2O_3/Nb$) process has been serving as the most stable fabrication process of the Josephson junction integrated circuits. Fast development of semiconductor fabrication technology has been possible with the recent advancement of the fabrication equipments. In this work, we took an advantage of advanced fabrication equipments in developing a superconducting Arithmetic Logic Unit (ALU) by using Nb trilayers. The ALU is a core element of a computer processor that performs arithmetic and logic operations on the operands in computer instruction words. We used DC magnetron sputtering technique for metal depositions and RF sputtering technique for $SiO_2$ depositions. Various dry etching techniques were used to define the Josephson junction areas and film pattering processes. Our Nb films were stress free and showed the $T{_c}'s$ of about 9 K. To enhance the step coverage of Nb films we used reverse bias powered DC magnetron sputtering technique. The fabricated 1-bit, 2-bit, and 4-bit ALU circuits were tested at a few kilo-hertz clock frequency as well as a few tens giga-hertz clock frequency, respectively. Our 1-bit ALU operated correctly at up to 40 GHz clock frequency, and the 4-bit ALU operated at up to 5 GHz clock frequency.

• Molecules and Cells
• /
• 제37권6호
• /
• pp.467-472
• /
• 2014

Obesity is known to be strongly associated with cardiovascular disease and cancer, the leading causes of mortality worldwide, and develops owing to interactions between genes and the environment. DNA methylation can act as a downstream effector of environmental signals, and analysis of this process therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk. Global DNA methylation of peripheral blood cells has recently been proposed as a potential biomarker for disease risk. Repetitive element DNA methylation has been shown to be associated with prominent obesity-related chronic diseases, but little is known about its relationship with weight status. In this study, we quantified the methylation of Alu elements in the peripheral blood DNA of 244 healthy women with a range of body mass indexes (BMIs) using pyrosequencing technology. Among the study participants, certain clinical laboratory parameters, including hemoglobin, serum glutamic oxaloacetic transaminase, serum glutamic- pyruvic transaminase, total cholesterol, and triglyceride levels were found to be strongly associated with BMI. Moreover, a U-shaped association between BMI and Alu methylation was observed, with the lowest methylation levels occurring at BMIs of between 23 and $30kg/m^2$. However, there was no significant association between Alu methylation and age, smoking status, or alcohol consumption. Overall, we identified a differential influence of BMI on global DNA methylation in healthy Korean women, indicating that BMI-related changes in Alu methylation might play a complex role in the etiology and pathogenesis of obesity. Further studies are required to elucidate the mechanisms underlying this relationship.

• 생명과학회지
• /
• 제27권10호
• /
• pp.1215-1224
• /
• 2017

현재까지 다양한 암의 발병 원인이 밝혀졌는데, 그 중 하나로써 DNA에 돌연변이가 축적되어 유전체가 불안정 해짐에 따라 암이 발생될 수 있는 기작들이 주목받고 있다. 생물정보학과 유전체학의 발달에 따라 질병 연구에 있어서 보다 더 정확하고 신뢰성 있는 바이오마커를 찾는 것이 가능해졌다. 따라서, 생물정보학과 유전체학의 연구 기반을 바탕으로 한 암의 바이오마커는 암의 조기진단뿐만 아니라, 더 나아가 암 발생 예측과 암환자의 예후 진단에 적용될 수 있다. 최근 들어 인간 유전체에서 약 45%를 차지하는 이동성 유전인자(transposable elements, TEs)가 유전자의 발현 조절과 DNA의 돌연변이를 유도함으로써 다양한 질병에 영향을 미친다는 사실이 밝혀짐에 따라, 이러한 이동성 유전인자들이 암의 발생과 어떤 연관이 있는지에 대한 연구 또한 활발히 진행되고 있다. 따라서 우리는 이동성 유전인자가 대장암과 어떤 연관성이 있는지에 대해 조사를 하였으며, 이를 어떻게 바이오마커로 활용할 수 있는지 알아보았다. 우선, 이동성 유전인자 중 인간 유전체에 많이 존재하면서 유전체에 많은 영향을 미치는 LINE-1 (long interspersed nuclear element-1, L1)과 Alu, LTR (long terminal repeat) 위주로 확인하였다. 흥미롭게도, 대장암 세포에서 LINE-1의 저메틸화, APC 유전자 내에 LINE-1 삽입, Alu의 저메틸화와 과메틸화, LTR 삽입에 따른 isoform 발생 등이 특징적으로 나타나는 것을 알 수 있었다. 또한 원발암유전자에서의 L1 저메틸화가 대장암 전이의 바이오마커로 쓰일 수 있다는 것과 Alu에 의한 MLH1 돌연변이가 가족성 및 유전성 대장암에서 흔히 발견된다는 것을 알 수 있었다. 이 때 이동성 유전인자에 의하여 영향 받는 유전자들의 발현을 in silico 발현 분석을 통하여 분석하였으며, 조직별, 성별 특이적 발현 양상을 제시하였다. 이들을 토대로 대장암 바이오마커를 개발하여 유전성 대장암의 예측 및 대장암 진단 또는 대장암 예후 예측을 통한 개인 맞춤형 치료에 활용할 수 있을 것으로 예상된다.

• 한국동물학회:학술대회논문집
• /
• 한국동물학회 1996년도 한국생물과학협회 국제학술대회
• /
• pp.242.2-242
• /
• 1996

No Abstract, See Full Text