Biomedical subjects

Minjung Kim

Publications and source records attributed to Minjung Kim.

17 recordsLinked to original sources

PubMed2025

Identification of MMP14 and MKLN1 as colorectal cancer susceptibility genes and drug-repositioning candidates from a genome-wide association study.

BACKGROUND: Genome-wide association studies (GWAS) and subsequent functional interpretation have been used to identify susceptible genes and potential drug-repositioning candidates. This study aimed to identify genes associated with colorectal cancer (CRC) and potential drug-repositioning candidates. METHODS: Patients with CRC at Seoul National University Hospital (SNUH, discovery study) and Chonnam National University Hospital (CNUH, replication study) were included as case groups. The Korean Genome and Epidemiology Study (KoGES) participants were included as a control group. Single-nucleotide polymorphisms (SNPs) were extracted from blood-derived DNA (N = 409,063). A SNP-based logistic regression model was applied. Furthermore, post-GWAS analysis was conducted. Drug-repositioning candidates were identified using a pre-trained deep neural network and the druggability assessment tool. RESULTS: In the discovery study, we conducted a 1:3 age- and sex-matched case-control study that included 500 CRC cases (mean age 63.0 ± 7.15 years) and 1,500 healthy controls (mean age 62.9 ± 7.07 years), each group comprising 50% males and 50% females. The replication study enrolled 4,860 patients with CRC and 46,384 healthy controls. The two-stage GWAS revealed statistically significant associations among MKLN1 (rs75170436, 7q32.3, beta (log odds ratio) = - 0.90, Pmeta = 5.90 × 10-13), MMP14 (rs3751489, 14q11.2, beta (log odds ratio) = - 1.91, Pmeta = 2.31 × 10-12). Post-GWAS functional analysis revealed strong associations on two genes highlighting deleterious effects and increased gene expression. Drug-repositioning analysis identified GW0742 (PPARβ/δ agonist) with the highest binding score and druggability score for MMP14 with a reference allele (12.06, 0.85). CONCLUSIONS: Using GWAS, MKLN1 and MMP14 were found to be associated with CRC development and we identified GW0742 (PPARβ/δ agonist) as a potential drug-repositioning candidate for CRC based on MKLN1 and MMP14. These findings improve the understanding of CRC development and provide insights into novel therapeutic targets and candidates for CRC treatment.

Humans↗

PubMed2006

Fluorescent protein expression driven by her4 regulatory elements reveals the spatiotemporal pattern of Notch signaling in the nervous system of zebrafish embryos.

Notch activation inhibits neuronal differentiation during development of the nervous system; however, the dynamic role of Notch signaling in individual cell lineages remains poorly understood. We have characterized 3.4 kb 5'-regulatory sequence of a Notch target gene, her4, and used it to drive fluorescent gene expression in transgenic lines where the spatiotemporal pattern of Notch activation can be examined in vivo. The 3.4 kb her4 promoter contains five predicted Su(H) binding sites of which two proximal sites were confirmed to be required for Notch-mediated transcriptional activation. Without Notch, Su(H) effectively represses transcription regulated by the promoter. Analyses of transgenic zebrafish showed that while the expression of proneural genes and Notch activation were both critical for endogenous her4 expression, reporter gene expression was primarily regulated by Notch activity. This study also showed that her4 may be differently regulated in sensory cranial ganglia, where Notch activity is not essential for her4 expression and where Su(H) may repress her4 expression. The establishment of a reporter line with Notch-Su(H)-dependent fluorescent gene expression provides a tool to explore the complex role of Notch signaling in the development of vertebrate nervous system.

Animals↗

PubMed2006

Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene.

Genomes of human cancer cells are characterized by numerous chromosomal aberrations of uncertain pathogenetic significance. Here, in an inducible mouse model of melanoma, we characterized metastatic variants with an acquired focal chromosomal amplification that corresponds to a much larger amplification in human metastatic melanomas. Further analyses identified Nedd9, an adaptor protein related to p130CAS, as the only gene within the minimal common region that exhibited amplification-associated overexpression. A series of functional, biochemical, and clinical studies established NEDD9 as a bona fide melanoma metastasis gene. NEDD9 enhanced invasion in vitro and metastasis in vivo of both normal and transformed melanocytes, functionally interacted with focal adhesion kinase and modulated focal contact formation, and exhibited frequent robust overexpression in human metastatic melanoma relative to primary melanoma. Thus, comparative oncogenomics has enabled the identification and facilitated the validation of a highly relevant cancer gene governing metastatic potential in human melanoma.

Adaptor Proteins, Signal Transducing↗

PubMed2006

Assembly of metal nanoparticle-carbon nanotube composite materials at the liquid/liquid interface.

Carbon nanotubes (CNTs)-mediated self-assembly of metal (Au and Ag) nanoparticles at the liquid/liquid interface in the form of a stable nanocomposite film is reported. The metallic luster results from the electronic coupling of nanoparticles, suggesting the formation of closely packed nanoparticle thin films. The interfacial film could be transferred to mica substrates and carbon-coated transmission electron microscopy (TEM) grids. The transferred films were very stable for a prolonged time. The samples were characterized by UV-vis spectroscopy, scanning electron microscopy (SEM), TEM, and X-ray photoelectron spectroscopy (XPS). SEM and TEM results show that the films formed at the liquid/liquid interface are indeed composite materials consisting of CNTs and nanoparticles. XPS measurements further indicate the presence of the interaction between nanoparticles and CNTs.

Journal Article↗

PubMed2005

In vivo assessment of RAS-dependent maintenance of tumor angiogenesis by real-time magnetic resonance imaging.

New blood vessel formation is a prominent feature of human cancers and tumor progression and is frequently accompanied by the acquisition of an angiogenic phenotype associated with a switch in the balance of proangiogenic and antiangiogenic molecules. This study was designed to investigate the role of activated H-RAS on the angiogenic phenotype of melanoma that arises in the inducible Tyr/Tet-RAS Ink4a/Arf(-/-) model using in vivo imaging with histopathologic correlation. We show that loss of RAS activity in fully established melanomas led to a reduction in tumor volume, which was preceded by impairment of vascular function as determined by in vivo magnetic resonance imaging. This correlated with activation of apoptosis in host-derived endothelial cells as well as in tumor cells. Thus, real-time in vivo imaging provided evidence that maintenance of tumor angiogenesis requires activated RAS in this model system, and that loss of vascular integrity upon inactivation of RAS is an active process rather than a consequence of loss of tumor cell viability.

Animals↗

PubMed2005

Coxsackie and adenovirus receptor binding ablation reduces adenovirus liver tropism and toxicity.

Human adenovirus-based vectors have emerged as a new promising vehicle for in vivo gene transfer-mediated therapy. However, the full potential of this methodology has not been fully realized because of the nonspecific tissue distribution of adenoviral vectors. Adenovirus infection is initiated by forming a complex between the fiber protein and a ubiquitously expressed host cell membrane protein, coxsackie B virus and adenovirus receptor (CAR). Therefore, ablating the adenovirus vector's ability to bind to the CAR is the first step in redirecting adenoviral tropism. To ablate CAR binding, we mutated the Bbeta sheet of the fiber knob, generating CAR-binding ablated replication-incompetent (dl-K420A-Z) and replication-competent (YKLK420A) adenoviral vectors. The in vitro transduction efficiency of dl-K420A-Z was significantly reduced in comparison to dl-LacZ carrying the wild-type fiber in CAR-positive cells but not in CAR-negative cells, suggesting that the mutation introduced in the Bbeta sheet of the fiber knob could disable the CAR-dependent transduction pathway. The in vivo transduction was also dramatically reduced in the liver and other organs for mice treated with dl-K420A-Z, compared with a cognate control vector, dl-LacZ. Concomitant with this attenuated gene transfer efficiency in vivo was a substantial reduction in the amount of general toxicity observed in the YKL-K420A-treated mice. Diminished toxicity was surmised from quantitative measurement of serum level of enzymes for liver and kidney function, hematologic chemistries, histopathology, and differences in lethality. Significant decrease in serum transaminases (alanine transferase [ALT] and aspartate transferase [AST]) was observed in mice treated with YKL-K420A. In addition, the lethality was lower in the YKLK420A- treated groups compared to the YKL-1-treated groups at all doses examined. Furthermore, the hepatopathologic analysis revealed that YKL-1 induced focal zonal necrosis and hepatocyte degeneration, while YKL-K420A induced mild spotty necrosis. In summary, this decreased vector tropism of CAR-binding ablated adenoviruses in normal tissues may increase the amount of virus available for infecting tumor cells and thus increase the antitumor efficacy with fewer unwanted side effects.

Adenoviridae↗

PubMed2005

Role of epidermal growth factor receptor signaling in RAS-driven melanoma.

The identification of essential genetic elements in pathways governing the maintenance of fully established tumors is critical to the development of effective antioncologic agents. Previous studies revealed an essential role for H-RAS(V12G) in melanoma maintenance in an inducible transgenic model. Here, we sought to define the molecular basis for RAS-dependent tumor maintenance through determination of the H-RAS(V12G)-directed transcriptional program and subsequent functional validation of potential signaling surrogates. The extinction of H-RAS(V12G) expression in established tumors was associated with alterations in the expression of proliferative, antiapoptotic, and angiogenic genes, a profile consistent with the observed phenotype of tumor cell proliferative arrest and death and endothelial cell apoptosis during tumor regression. In particular, these melanomas displayed a prominent RAS-dependent regulation of the epidermal growth factor (EGF) family, leading to establishment of an EGF receptor signaling loop. Genetic complementation and interference studies demonstrated that this signaling loop is essential to H-RAS(V12G)-directed tumorigenesis. Thus, this inducible tumor model system permits the identification and validation of alternative points of therapeutic intervention without neutralization of the primary genetic lesion.

Animals↗

PubMed2004

A critical role for p27kip1 gene dosage in a mouse model of prostate carcinogenesis.

In human prostate cancer, the frequent down-regulation of p27(kip1) protein expression is correlated with poor clinical outcome, yet p27(kip1) rarely undergoes mutational inactivation. Here, we investigate the consequences of reducing or eliminating p27(kip1) function for prostate carcinogenesis in the context of a mouse modeling lacking the Nkx3.1 homeobox gene and the Pten tumor suppressor. Unexpectedly, we find that triple mutant mice heterozygous for a p27(kip1) null allele (Nkx3.1(+/- or -/-); Pten(+/-); p27(+/-)) display enhanced prostate carcinogenesis, whereas mice that are homozygous null for p27(kip1) (Nkx3.1(+/- or -/-); Pten(+/-); p27(-/-)) show inhibition of cancer progression. Expression profiling reveals that Cyclin D1 is highly up-regulated in compound p27(kip1) heterozygotes, but is down-regulated in the compound p27(kip1) homozygous mutants. Using RNA interference in prostate cancer cell lines with distinct p27(kip1) gene doses, we show that prostate tumorigenicity depends on levels of p27(kip1) and that the consequences of p27(kip1) gene dosage can be attributed, in part, to altered levels of Cyclin D1. Our findings suggest that p27(kip1) possesses dosage-sensitive positive as well as negative modulatory roles in prostate cancer progression.

Animals↗

PubMed2004

Nuclear cloning of embryonal carcinoma cells.

Embryonal carcinoma (EC) cells have served as a model to study the relationship between cancer and cellular differentiation given their potential to produce tumors and, to varying degrees, participate in embryonic development. Here, nuclear transplantation was used to assess the extent to which the tumorigenic and developmental potential of EC cells is governed by epigenetic as opposed to genetic alterations. Nuclei from three independent mouse EC cell lines (F9, P19, and METT-1) with differing developmental and tumorigenic potentials all were able to direct early embryo development, producing morphologically normal blastocysts that gave rise to nuclear transfer (NT)-derived embryonic stem (ES) cell lines at a high efficiency. However, when tested for tumor or chimera formation, the resulting NT ES cells displayed an identical potential as their respective donor EC cells, in stark contrast to previously reported NT ES cells derived from transfer of untransformed cells. Consistent with this finding, comparative genomic hybridization identified previously undescribed genetic lesions in the EC cell lines. Therefore, nonreprogrammable genetic modifications within EC nuclei define the developmental and tumorigenic potential of resulting NT ES cells. Our findings support the notion that cancer results from the deregulation of stem cells and further suggest that the genetics of ECs will reveal genes involved in stem cell self-renewal and pluripotency.

Animals↗

PubMed2004

Reprogramming of a melanoma genome by nuclear transplantation.

We have used nuclear transplantation to test whether the reprogramming activity of oocytes can reestablish developmental pluripotency of malignant cancer cells. We show here that the nuclei of leukemia, lymphoma, and breast cancer cells could support normal preimplantation development to the blastocyst stage but failed to produce embryonic stem (ES) cells. However, a blastocyst cloned from a RAS-inducible melanoma nucleus gave rise to ES cells with the potential to differentiate into multiple cell types in vivo including melanocytes, lymphocytes, and fibroblasts. Chimeras produced from these ES cells developed cancer with higher penetrance, shorter latency, and an expanded tumor spectrum when compared with the donor mouse model. These results demonstrate that the secondary changes of a melanoma nucleus are compatible with a broad developmental potential but predispose mice to melanomas and other malignant tumors on reactivation of RAS. Our findings serve as a paradigm for studying the tumorigenic effect of a given cancer genome in the context of a whole animal.

Animals↗

PubMed2004

High-resolution global profiling of genomic alterations with long oligonucleotide microarray.

Cancer represents the phenotypic end point of multiple genetic lesions that endow cells with a full range of biological properties required for tumorigenesis. Among the hallmark features of the cancer genome are recurrent regional gains and losses that, upon detailed characterization, have provided highly productive discovery paths for new oncogenes and tumor suppressor genes. In this study, we describe the use of an oligonucleotide-based microarray platform and development of requisite assay conditions and bioinformatic mining tools that permits high-resolution genome-wide array-comparative genome hybridization profiling of human and mouse tumors. Using a commercially available 60-mer oligonucleotide microarray, we demonstrate that this platform provides sufficient sensitivity to detect single-copy difference in gene dosage of full complexity genomic DNA while offering high resolution. The commercial availability of the microarrays and associated reagents, along with the technical protocols and analytical tools described in this report, should provide investigators with the immediate capacity to perform DNA analysis of normal and diseased genomes in a global and detailed manner.

Animals↗

PubMed2003

Anti-parasitic activity of depudecin on Neospora caninum via the inhibition of histone deacetylase.

Neospora caninum is an apicomplexan parasite associated with abortion in cattle worldwide. Apicidin, histone deacetylase (HDAC) inhibitor, has shown a broad spectrum of anti-protozoal activity against apicomplexan parasites. Cultured vero cells infected with N. caninum tachyzoites were treated with 0.5 microg/ml of depudecin, another known natural product isolated from Altermaria brassiciicola with anti-histone deacetylase activity, to examine the efficacy of depudecin against intracellular multiplication of N. caninum tachyzoite, using 15 ng/ml of apicidin as the control. Depudecin significantly inhibited the intracellular multiplication of N. caninum at a level similar to that of apicidin without exerting any cytotoxicity on the host vero cells. Acid/urea/Triton gel electrophoresis analysis show anti-parasitic activity of depudecin appears to be due to the inhibition of protozoal histone deacetylase, which induces hyperacetylation of histones in N. caninum.

Alkadienes↗

PubMed2003

Histone deacetylase in carcinogenesis and its inhibitors as anti-cancer agents.

The acetylation state of histone is reversibly regulated by histone acetyltransferase (HAT) and deacetylase (HDAC). An imbalance of this reaction leads to an aberrant behavior of the cells in morphology, cell cycle, differentiation, and carcinogenesis. Recently, these key enzymes in the gene expression were cloned. They revealed a broad use of this modification, not only in histone, but also other proteins that involved transcription, nuclear transport, and cytoskeleton. These results suggest that HAT/HDAC takes charge of multiple-functions in the cell, not just the gene expression. HDAC is especially known to play an important role in carcinogenesis. The enzyme has been considered a target molecule for cancer therapy. The inhibition of HDAC activity by a specific inhibitor induces growth arrest, differentiation, and apoptosis of transformed or several cancer cells. Some of these inhibitors are in a clinical trial at phase I or phase II. The discovery and development of specific HDAC inhibitors are helpful for cancer therapy, and decipher the molecular mode of action for HDAC.

Acetyltransferases↗

PubMed2002

RACK-1, a receptor for activated C kinase, interacts with the transcription factor NFAT and represses its transactivation.

To isolate and characterize a novel protein that interacts with nuclear factor of activated T cells (NFAT) and potentially regulates its activity, we screened a Jurkat cDNA library by using the NFAT regulatory domain as bait in the yeast two-hybrid system. RACK-1, a receptor for activated protein kinase C and a homologue of the G-protein beta subunit, was identified as a NFAT-binding protein. Mammalian two hybrid tests in CV-1 cells and a coimmunoprecipitation assay confirmed protein-protein interaction between NFAT and RACK-1. In addition, overexpression of RACK-1 specifically suppressed transcriptional activation derived by NFAT, but not by NF-kappaB. These results demonstrate RACK-1 as a potent negative modulator of NFAT activation and suggest a novel mechanism in NFAT regulation.

Animals↗

PubMed2002

Transcription of Schizosaccharomyces pombe thioltransferase-1 in response to stress conditions.

Thioltransferase, also known as glutaredoxin, is an enzyme that catalyzes the reduction of a variety of disulfide compounds. In Schizosaccharomyces pombe, two thioltransferases were reported and the cDNA of one of the thioltransferases (thioltransferase-1) was cloned. Using a Northern blot assay, we investigated the thioltransferase transcription in response to various stress conditions. When the culture was shifted to a high temperature, the thioltransferase transcription was not significantly changed compared to the unshifted 30 degrees culture. Treatment of zinc chloride to exponentially-growing cells remarkably increased the thioltransferase transcription, whereas the treatment of mercury chloride greatly reduced the transcription. Treatment of hydrogen peroxide and cadmium chloride caused no significant effects on the transcription of the thioltransferase. These results suggest that the transcription of thioltransferase-1 in S. pombe is induced in response to metal stress that is caused by zinc chloride, but not in response to heat stress or oxidative stress that is caused by hydrogen peroxide.

Chlorides↗

PubMed2002

A potential membrane protein involved in pre-tRNA splicing of Schizosaccharomyces pombe.

We had previously isolated six pre-tRNA splicing mutants of Schizosaccharomyces pombe named ptp1 to ptp6. To investigate the molecular mechanism of tRNA splicing, we cloned the ptp4(+) gene by complementation of the temperature-sensitive growth defect. The ptp4(+) gene consists of three exons and encodes a putative protein of 218 amino acids with a molecular mass of 24.4 kDa. Analysis of the amino acid sequence reveals that the protein is a potential membrane protein with four membrane-spanning regions. The ptp4(+) shows significant similarity to the Saccharomyces cerevisiae putative protein YOR311C. Expression of the ptp4(+) gene in the ptp4(-) mutant restores the ability to splice tRNA. Northern blot analysis showed that the ptp4(+) gene is expressed in both mating-type cells of S. pombe. These results suggest that the Ptp4(+) could be a component involved in tRNA splicing.

Amino Acid Sequence↗

PubMed2002

Prostatic intraepithelial neoplasia in genetically engineered mice.

Several mouse models of human prostate cancer were studied to identify and characterize potential precursor lesions containing foci of atypical epithelial cells. These lesions exhibit a sequence of changes suggesting progressive evolution toward malignancy. Based on these observations, a grading system is proposed to classify prostatic intraepithelial neoplasia (PIN) in genetically engineered mice (GEM). Four grades of GEM PIN are proposed based on their architecture, differentiation pattern, and degree of cytological atypia. PIN I lesions have one or two layers of atypical cells. PIN II has two or more layers of atypical cells. PIN III has large, pleomorphic nuclei with prominent nucleoli and the cells tend to involve the entire lumen with expansion of the duct outlines. PIN IV lesions contain atypical cells that fill the lumen and bulge focally into, and frequently compromise, the fibromuscular sheath. Within the same cohorts, the lower grade PINs first appear earlier than the higher grades. Morphometric and immunohistochemical analyses confirm progressive change. Although the malignant potential of PIN IV in mice has not been proven, GEM PIN is similar to human PIN. This PIN classification system is a first step toward a systematic evaluation of the biological potential of these lesions in GEM.

Animals↗