Dynamic and coordinated single-molecular interactions at TM4SF5-enriched microdomains guide invasive behaviors in 2- and 3-dimensional environments

Kim, Hye-Jin,Kwon, Sojung,Nam, Seo Hee,Jung, Jae Woo,Kang, Minkyung,Ryu, Jihye,Kim, Ji Eon,Cheong, Jin-Gyu,Cho, Chang Yun,Kim, Somi,Song, Dae-Geun,Kim, Yong-Nyun,Kim, Tai Young,Jung, Min-Kyo,Lee, Kyun The Federation of American Societies for Experimen 2017 The FASEB Journal Vol.31 No.4

<P>Membrane proteins sense extracellular cues and transduce intracellular signaling to coordinate directionality and speed during cellular migration. They are often localized to specific regions, as with lipid rafts or tetraspanin-enriched microdomains; however, the dynamic interactions of tetraspanins with diverse receptors within tetraspanin-enriched microdomains on cellular surfaces remain largely unexplored. Here, we investigated effects of tetraspan(in) TM4SF5 (transmembrane 4 L6 family member 5)-enriched microdomains (T5ERMs) on the directionality of cell migration. Physical association of TM4SF5 with epidermal growth factor receptor (EGFR) and integrin alpha 5 was visualized by live fluorescence cross-correlation spectroscopy and higher-resolution microscopy at the leading edge of migratory cells, presumably forming TM4SF5-enriched microdomains. Whereas TM4SF5 and EGFR colocalized at themigrating leading region more than at the rear, TM4SF5 and integrin a5 colocalized evenly throughout cells. Cholesterol depletion and disruption in TM4SF5 post-translational modifications, including N-glycosylation and palmitoylation, altered TM4SF5 interactions and cellular localization, which led to less cellular migration speed and directionality in 2-or 3-dimensional conditions. TM4SF5 controlled directional cell migration and invasion, and importantly, these TM4SF5 functions were dependent on cholesterol, TM4SF5 post-translational modifications, and EGFR and integrin alpha 5 activity. Altogether, we showed that TM4SF5 dynamically interacted with EGFR and integrin a5 in migratory cells to control directionality and invasion.-Kim, H.-J., Kwon, S., Nam, S. H., Jung, J. W., Kang, M., Ryu, J., Kim, J. E., Cheong, J.-G., Cho, C. Y., Kim, S., Song, D.-G., Kim, Y.-N., Kim, T. Y., Jung, M.-K., Lee, K.-M., Pack, C.-G., Lee, J. W. Dynamic and coordinated single-molecular interactions at TM4SF5-enriched microdomains guide invasive behaviors in 2-and 3-dimensional environments. FASEB J. 31, 1461-1481 (2017). www.fasebj.org</P>

A library of TAL effector nucleases spanning the human genome

Kim, Yongsub,Kweon, Jiyeon,Kim, Annie,Chon, Jae Kyung,Yoo, Ji Yeon,Kim, Hye Joo,Kim, Sojung,Lee, Choongil,Jeong, Euihwan,Chung, Eugene,Kim, Doyoung,Lee, Mi Seon,Go, Eun Mi,Song, Hye Jung,Kim, Hwangbeo Nature Publishing Group, a division of Macmillan P 2013 Nature biotechnology Vol.31 No.3

Transcription activator–like (TAL) effector nucleases (TALENs) can be readily engineered to bind specific genomic loci, enabling the introduction of precise genetic modifications such as gene knockouts and additions. Here we present a genome-scale collection of TALENs for efficient and scalable gene targeting in human cells. We chose target sites that did not have highly similar sequences elsewhere in the genome to avoid off-target mutations and assembled TALEN plasmids for 18,740 protein-coding genes using a high-throughput Golden-Gate cloning system. A pilot test involving 124 genes showed that all TALENs were active and disrupted their target genes at high frequencies, although two of these TALENs became active only after their target sites were partially demethylated using an inhibitor of DNA methyltransferase. We used our TALEN library to generate single- and double-gene-knockout cells in which NF-κB signaling pathways were disrupted. Compared with cells treated with short interfering RNAs, these cells showed unambiguous suppression of signal transduction.

Sorafenib for 9,923 Patients with Hepatocellular Carcinoma: An Analysis from National Health Insurance Claim Data in South Korea

Han Sojung,Kim Do Young,Lim Ho Yeong,Yoon Jung-Hwan,Ryoo Baek-Yeol,Kim Yujeong,Kim Kookhee,Kim Bo Yeon,Yi So Young,Kim Dong-Sook,Cho Do-Yeon,Yu Jina,Kim Suhyun,Park Joong-Won 거트앤리버 소화기연관학회협의회 2024 Gut and Liver Vol.18 No.1

Background/Aims: Sorafenib is the standard of care in the management of advanced hepatocellular carcinoma (HCC). The purpose of this study was to investigate the characteristics, treatment patterns and outcomes of sorafenib among HCC patients in South Korea. Methods: This population-based retrospective, single-arm, observational study used the Korean National Health Insurance database to identify patients with HCC who received sorafenib between July 1, 2008, and December 31, 2014. A total of 9,923 patients were recruited in this study. Results: Among 9,923 patients, 6,669 patients (68.2%) received loco-regional therapy prior to sorafenib, and 1,565 patients (15.8%) received combination therapy with concomitant sorafenib; 2,591 patients (26.1%) received rescue therapy after sorafenib, and transarterial chemoembolization was the most common modality applied in 1,498 patients (15.1%). A total of 3,591 patients underwent rescue therapy after sorafenib, and the median overall survival was 14.5 months compared to 4.6 months in 7,332 patients who received supportive care after sorafenib. The mean duration of sorafenib administration in all patients was 105.7 days; 7,023 patients (70.8%) received an initial dose of 600 to 800 mg. The longest survival was shown in patients who received the recommended dose of 800 mg, subsequently reduced to 400 mg (15.0 months). The second longest survival was demonstrated in patients with a starting dose of 800 mg, followed by a dose reduction to 400–600 mg (9.6 months). Conclusions: Real-life data show that the efficacy of sorafenib seems similar to that observed in clinical trials, suggesting that appropriate subsequent therapy after sorafenib might prolong patient survival.

Profiling of transcripts and proteins modulated by the E7 oncogene in the lung tissue of E7-Tg mice by the omics approach.

Kim, Eunjin,Kang, Jeongwoo,Cho, Minchul,Lee, Sojung,Seo, Eunhee,Choi, Heesook,Kim, Yumi,Kim, Junghee,Kang, Kum Yong,Kim, Kwang Pyo,Han, Jaeyong,Sheen, Yhunyhong,Yum, Young Na,Park, Sue-Nie,Yoon, Do-Yo D. A. Spandidos 2009 MOLECULAR MEDICINE REPORTS Vol.2 No.1

<P>The E6 and E7 oncoproteins of human papilloma virus (HPV) type 16 have been known to cooperatively induce the immortalization and transformation of primary keratinocytes. We established an E7 transgenic mouse model to screen HPV-related biomakers using the omics approach. The methods used to identify HPV-modulated factors were genomics analysis by microarray using the Affymetrix 430 2.0 array to screen E7-modulated genes, and proteomics analysis using nano-LC-ESI-MS/MS to screen E7-modulated proteins with the lung tissue of E7 transgenic mice. According to omics data, cyclin B1, cyclin E2, topoisomerase IIα, calnexin, activated leukocyte cell adhesion molecule CD166, actinin α1, diaphorase 1, gelsolin, platelet glycoprotein, and annexin A2 and A4 were up-regulated in the E7-Tg mice, while proteoglycan 4, sarcolipin, titin, vimentin, drep 1, troponin and cofilin-1 were down-regulated. We further confirmed the significance of differences between the expression levels of the selected factors in E7-Tg and non-Tg mice by real-time PCR. Genes related to cancer cell adhesion, cell cycle and migration, proliferation and apoptosis, as well as to the intermediate filament network and to endoplasmic reticulum proteins, were selected. Taken together, the results suggest that the E7 oncogene modulates the expression levels of cell cycle-related (cyclin B1, cyclin E2) and cell adhesion- and migration-related (actinin α1, CD166) factors, which may play important roles in cellular transformation in cancer. In addition, the solubilization of the rigid intermediate filament network by specific proteolysis mediated via up-regulating gelsolin and down-regulating cofilin-1, as well as increased levels of endoplasmic reticulum protein calnexin with chaperone functions, might also be involved in E7-lung epithelial cells.</P>

Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq

Kim, Daesik,Kim, Sojung,Kim, Sunghyun,Park, Jeongbin,Kim, Jin-Soo Cold Spring Harbor Laboratory Press 2016 Genome Research Vol.26 No.3

<P>We present multiplex Digenome-seq to profile genome-wide specificities of up to 11 CRISPR-Cas9 nucleases simultaneously, saving time and reducing cost. Cell-free human genomic DNA was digested using multiple sgRNAs combined with the Cas9 protein and then subjected to whole-genome sequencing. In vitro cleavage patterns, characteristic of on- and off-target sites, were computationally identified across the genome using a new DNA cleavage scoring system. We found that many false positive, bulge-type off-target sites were cleaved by sgRNAs transcribed from an oligonucleotide duplex but not by those transcribed from a plasmid template. Multiplex Digenome-seq captured many bona fide off-target sites, missed by other genome-wide methods, at which indels were induced at frequencies <0.1%. After analyzing 964 sites cleaved in vitro by these sgRNAs and measuring indel frequencies at hundreds of off-target sites in cells, we propose a guideline for the choice of target sites for minimizing CRISPR-Cas9 off-target effects in the human genome.</P>

Ctbp2 Modulates NuRD-Mediated Deacetylation of H3K27 and Facilitates PRC2-Mediated H3K27me3 in Active Embryonic Stem Cell Genes During Exit from Pluripotency : Ctbp2 Modulates H3K27-State in Active ESC Genes

Kim, Tae Wan,Kang, Byung-Hee,Jang, Hyonchol,Kwak, Sojung,Shin, Jihoon,Kim, Hyunsoo,Lee, Sang-Eun,Lee, Soon-Min,Lee, Jong-Hyuk,Kim, Jae-Hwan,Kim, Seon-Young,Cho, Eun-Jung,Kim, Ju Han,Park, Keun Soo,Che Wiley (John WileySons) 2015 Stem Cells Vol.33 No.8

<P>For cells to exit from pluripotency and commit to a lineage, the circuitry of a core transcription factor (CTF) network must be extinguished in an orderly manner through epigenetic modifications. However, how this choreographed epigenetic remodeling at active embryonic stem cell (ESC) genes occurs during differentiation is poorly understood. In this study, we demonstrate that C-terminal binding protein 2 (Ctbp2) regulates nucleosome remodeling and deacetylation (NuRD)-mediated deacetylation of H3K27 and facilitates recruitment of polycomb repressive complex 2 (PRC2)-mediated H3K27me3 in active ESC genes for exit from pluripotency during differentiation. By genomewide analysis, we found that Ctbp2 resides in active ESC genes and co-occupies regions with ESC CTFs in undifferentiated ESCs. Furthermore, ablation of Ctbp2 effects inappropriate gene silencing in ESCs by sustaining high levels of H3K27ac and impeding H3K27me3 in active ESC genes, thereby sustaining ESC maintenance during differentiation. Thus, Ctbp2 preoccupies regions in active genes with the NuRD complex in undifferentiated ESCs that are directed toward H3K27me3 by PRC2 to induce stable silencing, which is pivotal for natural lineage commitment.</P>

Telomerase Activity is Constitutively Expressed in the Murine CD8<SUP>+</SUP> T Cells and Controlled Transcriptionally and Post-Translationally

Sojung Kim,Mihyung Kim,Kilhyoun Kim 대한면역학회 2004 Immune Network Vol.4 No.3

The Relationship between Drinking habits, Health-related physical fitness, and Body Mass Index in college femalesSojung Kim

Sojung Kim(김소정),Jungho Cho(조정호),Heejung Kim(김희정),Malyun Sin(신말연),Jihyun Lee(이지현),Boin Choi(최보인),Heagin Choi(최혜진) 한국체육과학회 2005 한국체육과학회지 Vol.14 No.2

The purpose of this study was to investigate the effects of body mass index and health-related physical fitness on dinking habits in college females. 165subjects were participated in this study and their ages, college grade, academic major, height, weight, percent body fat, total body water, body mass index, waist hip ratio, back strength, sit-up, sit and reach, and physical efficiency index were measured. Their drinking habits were observed by Perceptions about Alcohol Use(Corbin, Welk, Lindsey, & Corbin, 2(04). Reliability Analysis, Factor Analysis(varimix), One-way Analysis of Variance(ANOVA), Multiple Range Test(Scheffe), Analysis of Multiple correlation, Analysis of Simple Linear Regression and Dubin Watson Test were used to examine the statistical significance using SPSS 11.0 windows. Drinking habits showed significant differences on health-related physical fitness (p<.05), but no significant differences on the body mass index. Also, drinking habits were significantly affected by lean body mass, total body water, back strength, sit-up, sit and reach, and physical efficiency index. In conclusion, this result indicated that college females comparatively consumed less alcohol, and appropriate alcohol drinking had better effects on health-related physical fitness than non-drinking or heavy drinking. Therefore, it is necessary to spread improved health-related physical fitness and the desirable alcohol drinking habits through the small amount of alcohol drinking and regular physical activity in their daily life to college females.

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

Kim, Sojung,Kim, Daesik,Cho, Seung Woo,Kim, Jungeun,Kim, Jin-Soo Cold Spring Harbor Laboratory Press 2014 Genome Research Vol.24 No.6

<P>RNA-guided engineered nucleases (RGENs) derived from the prokaryotic adaptive immune system known as CRISPR (clustered, regularly interspaced, short palindromic repeat)/Cas (CRISPR-associated) enable genome editing in human cell lines, animals, and plants, but are limited by off-target effects and unwanted integration of DNA segments derived from plasmids encoding Cas9 and guide RNA at both on-target and off-target sites in the genome. Here, we deliver purified recombinant Cas9 protein and guide RNA into cultured human cells including hard-to-transfect fibroblasts and pluripotent stem cells. RGEN ribonucleoproteins (RNPs) induce site-specific mutations at frequencies of up to 79%, while reducing off-target mutations associated with plasmid transfection at off-target sites that differ by one or two nucleotides from on-target sites. RGEN RNPs cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. Furthermore, RNP delivery is less stressful to human embryonic stem cells, producing at least twofold more colonies than does plasmid transfection.</P>

Telomerase Activity is Constitutively Expressed in the Murine $CD8^+$ T Cells and Controlled Transcriptionally and Post-Translationally

Kim, SoJung,Kim, MiHyung,Kim, KilHyoun The Korean Association of Immunobiologists 2004 Immune Network Vol.4 No.3

Background: Telomerase, a ribonucleoprotein enzyme capable of synthesizing telomeric repeats, attracts attention for its possible role in determining the replicative capacity of normal somatic cells, transformed cells, and cells of the germline lineage. Differently from normal somatic cells with no telomerase activity, normal lymphocytes has been reported to have telomerase activity comparable to that found in transformed cells during development and activation, which substantiate a role in supporting the capacity of lymphocytes for extensive clonal expansion. Methods: Here, in order to define the telomerase regulation in murine T lymphocytes, telomerase activity in cloned murine $CD8^+$ T cells and naive $CD8^+$ T cells isolated from C57BL/6 mice was examined. Next, the regulatory mechanism of telomerase activity at transcriptional and post- translational levels was investigated by determining the expression level of the TERT protein, a key component for telomerase activity. Results: It was demonstrated that telomerase activity was expressed in an inactivated state as well as in an activated state in the murine $CD8^+$ T lymphocytes by using TRAP assay. The increase of telomerase activity was partially dependent on the net increase of TERT expression. Also, telomerase activity was decreased after treatment with protein kinase inhibitors, indicating that telomerase activation was prevented by inhibition of phosphorylation. Conclusion: Therefore, these results suggest that telomerase activity is constitutively expressed in the murine resting T lymphocytes and controlled by both transcriptional regulation and post- ranslational modifications.