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Ryu, Daeun,Cho, SeongBeom,Kim, Hun,Lee, Sanghyuk,Kim, Wankyu Oxford University Press 2014 Bioinformatics Vol.30 No.17
<P><B>Summary:</B> GEPdb integrates both genome-wide association studies and expression quantitative trait loci information, the two primary sources of genome-wide mapping for genotype–phenotype and genotype–expression associations together with phenotype-associated gene lists. The GEPdb provides simultaneous interpretation of both genetic risks and potential gene regulatory pathways toward phenotypic outcome by establishing the ternary relationship of genotype–expression–phenotype (GEP). The analytic scope is further extended by linkage disequilibrium from five different populations of the international HapMap Project.</P><P><B>Availability and implementation:</B> http://ercsbweb.ewha.ac.kr/gepdb.</P><P><B>Contact:</B> wkim@ewha.ac.kr</P>
Ryu, Daeun,Kim, Seok Jin,Hong, Yourae,Jo, Areum,Kim, Nayoung,Kim, Hee-Jin,Lee, Hae-Ock,Kim, Kihyun,Park, Woong-Yang American Association for Cancer Research 2020 Clinical Cancer Research Vol.26 No.4
<P><B>Purpose:</B></P><P>In multiple myeloma, extramedullary progression is associated with treatment resistance and a high mortality rate. To understand the molecular mechanisms controlling the devastating progression of myeloma, we applied single-cell RNA-sequencing (RNA-seq) to myeloma in the bone marrow and myelomatous pleural effusions or ascites.</P><P><B>Experimental Design:</B></P><P>Bone marrow or extramedullary myeloma samples were collected from 15 patients and subjected to single-cell RNA-seq. The single-cell transcriptome data of malignant plasma cells and the surrounding immune microenvironment were analyzed.</P><P><B>Results:</B></P><P>Comparisons of single-cell transcriptomes revealed the systematic activation of proliferation, antigen presentation, proteasomes, glycolysis, and oxidative phosphorylation pathways in extramedullary myeloma cells. The myeloma cells expressed multiple combinations of growth factors and receptors, suggesting autonomous and pleiotropic growth potential at the single-cell level. Comparisons of the tumor microenvironment revealed the presence of cytotoxic T lymphocytes and natural killer (NK) cells in both the bone marrow and extramedullary ascites, demonstrating a gene-expression phenotype indicative of functional compromise. In parallel, isolated myeloma cells persistently expressed class I MHC molecules and upregulated inhibitory molecules for cytotoxic T and NK cells.</P><P><B>Conclusions:</B></P><P>These data suggest that myeloma cells are equipped with specialized immune evasion mechanisms in cytotoxic microenvironments. Taken together, single-cell transcriptome analysis revealed transcriptional programs associated with aggressive myeloma progression that support autonomous cell proliferation and immune evasion.</P>
A Case of Idiopathic Infratentorial Superficial Siderosis
Shin, Daeun,Yang, Seok-Yul,Kim, Youngwook,Ryu, Ho-Sung,Lee, Hoseok Korean Society of Magnetic Resonance in Medicine 2020 Investigative Magnetic Resonance Imaging Vol.24 No.1
Superficial siderosis is attributed to hemosiderin deposition in the subpial layers of the nervous system. The clinical features of infratentorial superficial siderosis (ISS) are hearing loss, cerebellar ataxia, and corticospinal tract signs and the most common cause of idiopathic ISS is a dural defect. As magnetic resonance imaging (MRI) has advanced, the diagnosis of infratentorial superficial siderosis can be confirmed by unique radiological findings in MRI. Here, we report on a female patient diagnosed with idiopathic ISS by means of clinical symptoms and radiological findings.
메가이벤트를 통한 도시재생 사례분석 - 부산 국제영화제를 중심으로 -
손다은(Son, Daeun),유지원(Ryu, Jiwon),주범(Chu, Beom) 대한건축학회 2022 대한건축학회 학술발표대회 논문집 Vol.42 No.2
Events or festivals are the means that can bring out economic effects in the shortest time among local revitalizations. Therefore, at the national level, attempts to hold events on an international or large scale with cities, provinces, and regions for balanced regional development are increasing. These large-scale events are being used as a means of urban regeneration in underdeveloped areas. Therefore, this study aims to examine the theory of urban marketing through events and to suggest the development direction of the city centering on cases.
Tumor-promoting macrophages prevail in malignant ascites of advanced gastric cancer
Hye Hyeon Eum,권민석,Ryu Daeun,Jo Areum,Chung Woosung,Kim Nayoung,홍유래,손대순,Kim Seung Tae,Lee Jeeyun,이혜옥,박웅양 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-
Gastric cancer (GC) patients develop malignant ascites as the disease progresses owing to peritoneal metastasis. GC patients with malignant ascites have a rapidly deteriorating clinical course with short survival following the onset of malignant ascites. Better optimized treatment strategies for this subset of patients are needed. To define the cellular characteristics of malignant ascites of GC, we used single-cell RNA sequencing to characterize tumor cells and tumor-associated macrophages (TAMs) from four samples of malignant ascites and one sample of cerebrospinal fluid. Reference transcriptomes for M1 and M2 macrophages were generated by in vitro differentiation of healthy blood-derived monocytes and applied to assess the inflammatory properties of TAMs. We analyzed 180 cells, including tumor cells, macrophages, and mesothelial cells. Dynamic exchange of tumor-promoting signals, including the CCL3–CCR1 or IL1B–IL1R2 interactions, suggests macrophage recruitment and anti-inflammatory tuning by tumor cells. By comparing these data with reference transcriptomes for M1-type and M2-type macrophages, we found noninflammatory characteristics in macrophages recovered from the malignant ascites of GC. Using public datasets, we demonstrated that the single-cell transcriptome-driven M2-specific signature was associated with poor prognosis in GC. Our data indicate that the anti-inflammatory characteristics of TAMs are controlled by tumor cells and present implications for treatment strategies for GC patients in which combination treatment targeting cancer cells and macrophages may have a reciprocal synergistic effect.
Park, Jimin,Lee, Daeun,Seo, Eun Kyoung,Ryu, Jae-Sang,Shin, Dong Hae Springer International 2017 Applied microbiology and biotechnology Vol.101 No.11
<P>The ADP-l-glycero-beta-d-manno-heptose and the GDP-6-deoxy-alpha-d-manno-heptose biosynthesis pathways play important roles in constructing lipopolysaccharide of Gram-negative bacteria. Blocking the pathways is lethal or increases antibiotic susceptibility to pathogens. Therefore, the enzymes involved in the pathways are novel antibiotic drug targets. Here, we designed an efficient method to assay the whole enzymes in the pathways using mass spectrometry and screened 148 compounds. One promising lead is (-)-nyasol targeting d-glycero-alpha-d-manno-heptose-1-phosphate guanylyltransferase (HddC) included in the GDP-6-deoxy-alpha-d-manno-heptose biosynthesis pathway from Burkholderia pseudomallei. The inhibitory activity of the lead compound against HddC has been confirmed by blocking the system transferring the guanosine monophosphate (GMP) moiety to alpha-d-glucose-1-phosphate. (-)-Nyasol exhibits the half maximal inhibitory concentration (IC50) value of 17.6 mu M. A further study is going on using (-)-nyasol derivatives to find better leads with high affinity.</P>
gsGator: an integrated web platform for cross-species gene set analysis
Kang, Hyunjung,Choi, Ikjung,Cho, Sooyoung,Ryu, Daeun,Lee, Sanghyuk,Kim, Wankyu BioMed Central 2014 BMC bioinformatics Vol.15 No.-
<P><B>Background</B></P><P>Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways. Phenotypic annotation is sparse for human genes, but is far more abundant for other model organisms such as mouse, fly, and worm. Often, GSA needs to be done highly interactively by combining or modifying gene lists or inspecting gene-gene interactions in a molecular network.</P><P><B>Description</B></P><P>We developed <I>gsGator</I>, a web-based platform for functional interpretation of gene sets with useful features such as cross-species GSA, simultaneous analysis of multiple gene sets, and a fully integrated network viewer for visualizing both GSA results and molecular networks. An extensive set of gene annotation information is amassed including GO & pathways, genomic annotations, protein-protein interaction, transcription factor-target (TF-target), miRNA targeting, and phenotype information for various model organisms. By combining the functionalities of <I>Set Creator, Set Operator and Network Navigator</I>, user can perform highly flexible and interactive GSA by creating a new gene list by any combination of existing gene sets (intersection, union and difference) or expanding genes interactively along the molecular networks such as protein-protein interaction and TF-target. We also demonstrate the utility of our interactive and cross-species GSA implemented in gsGator by several usage examples for interpreting genome-wide association study (GWAS) results. gsGator is freely available at http://gsGator.ewha.ac.kr.</P><P><B>Conclusions</B></P><P>Interactive and cross-species GSA in gsGator greatly extends the scope and utility of GSA, leading to novel insights via conserved functional gene modules across different species.</P>