A5074546833- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Genomics and Chromatin Dynamics
- Helicobacter pylori-related gastroenterology studies
- Histone Deacetylase Inhibitors Research
- Cancer-related gene regulation
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Genetics, Bioinformatics, and Biomedical Research
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Acute Myeloid Leukemia Research
- RNA and protein synthesis mechanisms
- Protein Degradation and Inhibitors
- PI3K/AKT/mTOR signaling in cancer
- Inflammasome and immune disorders
- Nitrogen and Sulfur Effects on Brassica
- Cancer, Stress, Anesthesia, and Immune Response
- Peptidase Inhibition and Analysis
- Hedgehog Signaling Pathway Studies
- Cancer Mechanisms and Therapy
- Advanced Proteomics Techniques and Applications
- Enzyme function and inhibition
- Proteoglycans and glycosaminoglycans research
Korea Research Institute of Chemical Technology
2017-2024
Korea University of Science and Technology
2024
Korea Advanced Institute of Science and Technology
2009-2018
Korea Research Institute of Bioscience and Biotechnology
2010-2017
Genome Research Foundation
2015
We propose a novel, efficient and intuitive approach of estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data. Our method, NEUMA (Normalization by Expected Uniquely Mappable Area), is based on effective length normalization using uniquely mappable areas gene isoform models. Using known sequence model such as RefSeq, pre-computes numbers all possible gene-wise isoform-wise informative reads: former being sequences mapped to isoforms single exclusively...
Tumorigenesis is a consequence of failures multistep defense mechanisms against deleterious perturbations that occur at the genomic, epigenomic, transcriptomic and proteomic levels. To uncover previously unrecognized genes undergo multilevel in gastric cancer (GC), we integrated epigenomic approaches using two recently developed tools: MENT GENT. This integrative analysis revealed nine Hippo pathway-related genes, including components [FAT, JUB, LATS2, TEA domain family member 4 (TEAD4)...
// Byungho Lim 1 , Jihyeob Mun 1, 2 Jeong-Hwan Kim Chan Wook 3 Seon Ae Roh 3, 4 Dong-Hyung Cho 4, 5 Yong Sung 2, Seon-Young Jin Cheon Medical Genomics Research Center, Korea Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic Department Functional Genomics, University Science Technology, Surgery, Ulsan College Medicine, Seoul, Innovative Cancer Asan for Life Sciences, Graduate School East-West Science, Kyung Hee University, Gyeonggi-do, Correspondence to: Kim, e-mail:...
// Byungho Lim 1, * , Chan Kim 2, 3, Jeong-Hwan 4 Woo Sun Kwon 3 Won Seok Lee Jeong Min Jun Yong Park 5 Hyo Song 2 Kyu Hyun Tae Soo Jong-Lyul Cheol Chung 6 Young Rha Seon-Young 7 1 Genome Structure Research Center, Korea Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Division Medical Oncology, Department Internal Medicine, Yonsei Cancer University College Seoul, Song-Dang for Research, Epigenomics Medicine Gastroenterology, Brain 21 Project Science, Functional Genomics, Science...
Many studies have focused on global hypomethylation or hypermethylation of tumor suppressor genes, but less is known about the impact promoter oncogenes. We previously showed that methylation may gradually increase decrease during transition from gastric mucosa (GM) to intestinal metaplasia (IM) cancer (GC). In our study, we regional CpG promoter-proximal DNA transcription factor ONECUT2 (OC2) in IM and GC cells. validated OC2 160 primary GCs, which level correlated negatively with mRNA...
Recent evidence has shown that the level of 5-hydroxymethylcytosine (5 hmC) in chromosomal DNA is aberrantly decreased a variety cancers, but whether this decrease cause or consequence tumorigenesis unclear. Here we show that, gastric 5 hmC correlates with ten-eleven translocation 1 (TET1) expression, which strongly associated metastasis and poor survival patients cancer. In cancer cells, TET1-targeted siRNA induced hmC, whereas TET1 overexpression an increase reduced cell proliferation,...
Abstract BACKGROUND: A primary inhibitor of plasminogen activators, SERPINE1 (serpin peptidase 1, clade E, member also known as activator type 1), is an important regulator in tumorigenesis and highly expressed many cancers. METHODS: Five tag single nucleotide polymorphisms (SNPs) 1 insertion polymorphism within were genotyped 1101 unrelated Korean individuals (a case group 612 patients with gastric cancer a control 489 healthy individuals). Associations susceptibility to diffuse‐type (DGC)...
Abstract BACKGROUND: The runt‐related transcription factor RUNX3 plays essential roles in various types of tumors, including gastric cancer. Epigenetic changes the methylation proximal promoter, but not common genetic , have been associated with both gene expression and development METHODS: A case‐control association study was conducted by genotyping 865 unrelated Korean subjects. Subsequent functional studies were performed to reveal implication association. RESULTS: Several...
Epigenetic dysregulation is a major driver of tumorigenesis. To identify tumor-suppressive microRNAs repressed by DNA methylation in gastric cancer (GC), we analyzed the genome-wide and microRNA expression profiles EpCAM+/CD44+ GC cells. Among set screened, miR-1271 was identified as GC. Forced substantially suppressed growth, migration, invasion candidate target genes signaling pathways regulated miR-1271, performed RNA sequencing. down-regulated MAP2K1 (MEK1) significantly associated...
Human SERPINB5, commonly known as maspin, has diverse functions a tumor suppressor. In this study, we discovered that maspin novel role in cell cycle control, and common variants were to be associated with gastric cancer. The genotypes of 836 unrelated Korean participants (including 430 cancer) examined for 12 tag single-nucleotide polymorphisms (SNPs) imputed 178 SNPs the gene. Susceptibility diffuse-type cancer was strongly significantly several including rs3744941 ( C > T ) promoter TT...
PTPRCAP (CD45-AP) is a positive regulator of protein tyrosine phosphatase PTPRC (CD45), which activates Src family kinases implicated in tumorigenesis. Single-nucleotide polymorphism (SNP) rs869736 located at position -309 the promoter was associated with susceptibility to diffuse-type gastric cancer current case-control study. The minor-allele homozygote significantly 2.5-fold increased (P = .0021, n 252), but not intestinal-type .30, 178), versus major-allele homozygote, when comparing...
Abstract Dynamic chromatin structures result in differential chemical reactivity to mutational processes throughout the genome. To identify features responsible for mutagenesis, we compared architecture around single-nucleotide variants (SNV), insertion/deletions (indels), and their context-matched, nonmutated positions. We found epigenetic differences between genomic regions containing missense SNVs those frameshift indels across multiple cancer types. Levels of active histone marks were...
Abstract Variations in protein coding sequence may sometimes play important roles cancer development. However, since variants not express into proteins due to various cellular quality control systems, it is get protein-level evidence of the genomic variations. We present a proteogenomic strategy getting variants, which we call sequential targeted LC-MS/MS based on prediction peptide pI and Retention time (STaLPIR). Our approach shows improved identification, has potential for unbiased...
Epigenetic dysregulation characterized by aberrant DNA hypermethylation is a hallmark of cancer, and it can be targeted hypomethylating agents (HMAs). Recently, we described the superior therapeutic efficacy novel HMA, namely, NTX-301, when used as monotherapy in combination with venetoclax treatment acute myeloid leukemia. Following previous study, further explored properties NTX-301 based on experimental investigations integrative data analyses. Comprehensive sensitivity profiling revealed...