5 results on '"Je-Keun Rhee"'
Search Results
2. Complement proteins C7 and CFH control the stemness of liver cancer cells via LSF-1
- Author
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Shree Ram Singh, Joon Seon Song, Sang Eun Lee, Se Jin Jang, Hyang Sook Seol, Je-Keun Rhee, and Suhwan Chang
- Subjects
Adult ,Male ,0301 basic medicine ,Cancer Research ,Time Factors ,Cellular differentiation ,Mice, SCID ,Biology ,Transfection ,Article ,03 medical and health sciences ,0302 clinical medicine ,Mice, Inbred NOD ,Cell Line, Tumor ,Spheroids, Cellular ,Tumor Cells, Cultured ,Animals ,Humans ,Transcription factor ,Aged ,Cell Proliferation ,Gene knockdown ,Cluster of differentiation ,Liver Neoplasms ,Cell Differentiation ,Middle Aged ,Molecular biology ,Complement C7 ,Immunity, Innate ,Tumor Burden ,Complement system ,Cell biology ,DNA-Binding Proteins ,Gene Expression Regulation, Neoplastic ,Phenotype ,030104 developmental biology ,Oncology ,Complement Factor H ,030220 oncology & carcinogenesis ,Factor H ,Neoplastic Stem Cells ,Heterografts ,Female ,RNA Interference ,Signal transduction ,Signal Transduction ,Transcription Factors - Abstract
Tumor-initiating cells are important for the formation and maintenance of tumor bulks in various tumors. To identify surface markers of liver tumor-initiating cells, we performed primary tumorsphere culture and analyzed the expression of cluster of differentiation (CD) antigen genes using NanoString. Interestingly, we found significant upregulation of the complement proteins (p = 1.60 × 10(-18)), including C7 and CFH. Further studies revealed that C7 and CFH are required to maintain stemness in liver cancer cells. Knockdown of C7 and CFH expression abrogated tumorsphere formation and induced differentiation, whereas overexpression stimulated stemness factor expression as well as in vivo cell growth. Mechanistically, by studying C7 and CFH-dependent LSF-1 expression and its direct role on stemness factor transcription, we found that LSF-1 is involved in this regulation. Taken together, our data demonstrate the unprecedented role of complement proteins on the maintenance of stemness in liver tumor-initiating cells.
- Published
- 2016
3. Bioinformatic and metabolomic analysis reveals miR-155 regulates thiamine level in breast cancer
- Author
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Shree Ram Singh, Jong Han Yu, Sung-Bae Kim, Suhwan Chang, Byung Ho Son, Gyungyup Gong, Hee Jin Lee, Hyun Ju Yoo, Sinae Kim, Eun Ji Lee, Jong Won Lee, Je-Keun Rhee, and Sei Hyun Ahn
- Subjects
Cancer Research ,Blotting, Western ,Breast Neoplasms ,Triple Negative Breast Neoplasms ,Transketolase ,Mitochondrial Membrane Transport Proteins ,Article ,Cofactor ,Tandem Mass Spectrometry ,Cell Line, Tumor ,Thiamine transporter ,Homeostasis ,Humans ,Metabolomics ,Thiamine ,Oligonucleotide Array Sequence Analysis ,Gene knockdown ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,Thiamin Pyrophosphokinase ,Gene Expression Profiling ,Computational Biology ,Membrane Transport Proteins ,food and beverages ,Pyruvate dehydrogenase complex ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,HEK293 Cells ,Oncology ,Biochemistry ,Cancer cell ,MCF-7 Cells ,biology.protein ,SLC19A2 ,Cancer research ,human activities ,Chromatography, Liquid ,HeLa Cells - Abstract
microRNA-155 (miR-155) is one of the well-known oncogenic miRNA implicated in various types of tumors. Thiamine, commonly known as vitamin B1, is one of critical cofactors for energy metabolic enzymes including pyruvate dehydrogenase, alpha ketoglutarate dehydrogenase, and transketolase. Here we report a novel role of miR-155 in cancer metabolism through the up-regulation of thiamine in breast cancer cells. A bioinformatic analysis of miRNA array and metabolite-profiling data from NCI-60 cancer cell panel revealed thiamine as a metabolite positively correlated with the miR-155 expression level. We confirmed it in MCF7, MDA-MB-436 and two human primary breast cancer cells by showing reduced thiamine levels upon a knock-down of miR-155. To understand how the miR-155 controls thiamine level, a set of key molecules for thiamine homeostasis were further analyzed after the knockdown of miR-155. The results showed the expression of two thiamine transporter genes (SLC19A2, SLC25A19) as well as thiamine pyrophosphokinase-1 (TPK1) were decreased in both RNA and protein level in miR-155 dependent manner. Finally, we confirm the finding by showing a positive correlation between miR-155 and thiamine level in 71 triple negative breast tumors. Taken altogether, our study demonstrates a role of miR-155 in thiamine homeostasis and suggests a function of this oncogenic miRNA on breast cancer metabolism.
- Published
- 2015
4. Fast single individual haplotyping method using GPGPU
- Author
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Joong Chae Na, Je-Keun Rhee, Soo-Yong Shin, and In-Bok Lee
- Subjects
0301 basic medicine ,Heuristic (computer science) ,Computer science ,Computation ,Probabilistic logic ,Evolutionary algorithm ,High-Throughput Nucleotide Sequencing ,Health Informatics ,Sequence Analysis, DNA ,Parallel computing ,Software_PROGRAMMINGTECHNIQUES ,Computer Science Applications ,Running time ,03 medical and health sciences ,CUDA ,030104 developmental biology ,0302 clinical medicine ,Haplotypes ,Estimation of distribution algorithm ,General-purpose computing on graphics processing units ,Databases, Nucleic Acid ,Algorithms ,030217 neurology & neurosurgery - Abstract
Background Most bioinformatic tools for next generation sequencing (NGS) data are computationally intensive, requiring a large amount of computational power for processing and analysis. Here the utility of graphic processing units (GPUs) for NGS data computation is assessed. Method In a previous study, we developed a probabilistic evolutionary algorithm with toggling for haplotyping (PEATH) method based on the estimation of distribution algorithm and toggling heuristic. Here, we parallelized the PEATH method (PEATH/G) using general-purpose computing on GPU (GPGPU). Results The PEATH/G runs approximately 46.8 times and 25.4 times faster than PEATH on the NA12878 fosmid-sequencing dataset and the HuRef dataset, respectively, with an NVIDIA GeForce GTX 1660Ti. Moreover, the PEATH/G is approximately 13.3 times faster on the fosmid-sequencing dataset, even with an inexpensive conventional GPGPU (NVIDIA GeForce GTX 950). Conclusions PEATH/G can be a practical single individual haplotyping tool in terms of both its accuracy and speed. GPGPU can help reduce the running time of NGS analysis tools.
- Published
- 2019
5. Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex
- Author
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Yoontae Lee, Jinju Han, Sun Young Sohn, Je-Keun Rhee, Kyu-Hyeon Yeom, Jin Wu Nam, V. Narry Kim, Byoung-Tak Zhang, Yunje Cho, and Inha Heo
- Subjects
Models, Molecular ,Ribonuclease III ,Lin-4 microRNA precursor ,DGCR8 ,RNA Stability ,Oligonucleotides ,Computational biology ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,Terminal loop ,Microprocessor complex ,Mirtron ,RNA interference ,RNA Precursors ,Animals ,Humans ,RNA Processing, Post-Transcriptional ,Drosha ,RNA, Double-Stranded ,Genetics ,Base Sequence ,biology ,Biochemistry, Genetics and Molecular Biology(all) ,Proteins ,RNA-Binding Proteins ,RNA ,MicroRNAs ,biology.protein ,RNA Interference - Abstract
The Drosha-DGCR8 complex initiates microRNA maturation by precise cleavage of the stem loops that are embedded in primary transcripts (pri-miRNAs). Here we propose a model for this process that is based upon evidence from both computational and biochemical analyses. A typical metazoan pri-miRNA consists of a stem of approximately 33 bp, with a terminal loop and flanking segments. The terminal loop is unessential, whereas the flanking ssRNA segments are critical for processing. The cleavage site is determined mainly by the distance (approximately 11 bp) from the stem-ssRNA junction. Purified DGCR8, but not Drosha, interacts with pri-miRNAs both directly and specifically, and the flanking ssRNA segments are vital for this binding to occur. Thus, DGCR8 may function as the molecular anchor that measures the distance from the dsRNA-ssRNA junction. Our current study thus facilitates the prediction of novel microRNAs and will assist in the rational design of small hairpin RNAs for RNA interference.
- Published
- 2006
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