Biomedical subjects

Hyunsoo Kim

Publications and source records attributed to Hyunsoo Kim.

7 recordsLinked to original sources

PubMed2005

Alpha-lipoic acid suppresses osteoclastogenesis despite increasing the receptor activator of nuclear factor kappaB ligand/osteoprotegerin ratio in human bone marrow stromal cells.

Growing evidence has shown a biochemical link between increased oxidative stress and reduced bone density. Although alpha-lipoic acid (alpha-LA) has been shown to act as a thiol antioxidant, its effect on bone cells has not been determined. Using proteomic analysis, we identified six differentially expressed proteins in the conditioned media of alpha-LA-treated human bone marrow stromal cell line (HS-5). One of these proteins, receptor activator of nuclear factor kappaB ligand (RANKL), was significantly up-regulated, as confirmed by immunoblotting with anti-RANKL antibody. ELISA showed that alpha-LA stimulated RANKL production in cellular extracts (membranous RANKL) about 5-fold and in conditioned medium (soluble RANKL) about 23-fold, but had no effect on osteoprotegerin (OPG) secretion. Despite increasing the RANKL/OPG ratio, alpha-LA showed a dose-dependent suppression of osteoclastogenesis, both in a coculture system of mouse bone marrow cells and osteoblasts and in a mouse bone marrow cell culture system, and reduced bone resorption in a dose-dependent manner. In addition, alpha-LA-induced soluble RANKL was not inhibited by matrix metalloprotease inhibitors, indicating that soluble RANKL is produced by alpha-LA without any posttranslational processing. In contrast, alpha-LA had no significant effect on the proliferation and differentiation of HS-5 cells. These results suggest that alpha-LA suppresses osteoclastogenesis by directly inhibiting RANKL-RANK mediated signals, not by mediating cellular RANKL production. In addition, our findings indicate that alpha-LA-induced soluble RANKL is not produced by shedding of membranous RANKL.

Animals↗

PubMed2004

Intracellular glutathione status regulates mouse bone marrow monocyte-derived macrophage differentiation and phagocytic activity.

Although a redox shift can regulate the development of cells, including proliferation, differentiation, and survival, the role of the glutathione (GSH) redox status in macrophage differentiation remains unclear. In order to elucidate the role of a redox shift, macrophage-like cells were differentiated from the bone marrow-derived monocytes that were treated with a macrophage colony stimulating factor (M-CSF or CSF-1) for 3 days. The macrophagic cells were characterized by a time-dependent increase in three major symptoms: the number of phagocytic cells, the number of adherent cells, and the mRNA expression of c-fms, a M-CSF receptor that is one of the macrophage-specific markers and mediates development signals. Upon M-CSF-driven macrophage differentiation, the GSH/GSSG ratio was significantly lower on day 1 than that observed on day 0 but was constant on days 1-3. To assess the effect of the GSH-depleted and -repleted status on the differentiation and phagocytosis of the macrophages, GSH depletion by BSO, a specific inhibitor of the de novo GSH synthesis, inhibited the formation of the adherent macrophagic cells by the down-regulation of c-fms, but did not affect the phagocytic activity of the macrophages. To the contrary, GSH repletion by the addition of NAC, which is a GSH precursor, or reduced GSH in media had no effect on macrophage differentiation, and led to a decrease in the phagocytic activity. Furthermore, we observed that there is checkpoint that is capable of releasing from the inhibition of the formation of the adherent macrophagic cells according to GSH depletion by BSO. Summarizing, these results indicate that the intracellular GSH status plays an important role in the differentiation and phagocytosis of macrophages.

Acetylcysteine↗

PubMed2004

Missing value estimation for DNA microarray gene expression data: local least squares imputation.

MOTIVATION: Gene expression data often contain missing expression values. Effective missing value estimation methods are needed since many algorithms for gene expression data analysis require a complete matrix of gene array values. In this paper, imputation methods based on the least squares formulation are proposed to estimate missing values in the gene expression data, which exploit local similarity structures in the data as well as least squares optimization process. RESULTS: The proposed local least squares imputation method (LLSimpute) represents a target gene that has missing values as a linear combination of similar genes. The similar genes are chosen by k-nearest neighbors or k coherent genes that have large absolute values of Pearson correlation coefficients. Non-parametric missing values estimation method of LLSimpute are designed by introducing an automatic k-value estimator. In our experiments, the proposed LLSimpute method shows competitive results when compared with other imputation methods for missing value estimation on various datasets and percentages of missing values in the data. AVAILABILITY: The software is available at http://www.cs.umn.edu/~hskim/tools.html CONTACT: hpark@cs.umn.edu

Algorithms↗

PubMed2004

Elucidation of CPX-1 involvement in RANKL-induced osteoclastogenesis by a proteomics approach.

To identify proteins potentially involved in osteoclast differentiation, we conducted a proteomics-based analysis using the osteoclastogenesis model cell line RAW264.7. Total proteins from undifferentiated cells, committed pre-osteoclasts, and differentiated osteoclasts were resolved by two-dimensional gel electrophoresis. Protein spots showing differential expression levels were processed for peptide mass fingerprinting. Among them, we identified the metallocarboxypeptidase CPX-1, which was prominently increased in pre-osteoclasts and then decreased in mature osteoclasts. Results of reverse transcription polymerase chain reaction, Western blot, and confocal microscopy were in agreement with the proteomics data. Notably, the forced overexpression of CPX-1 led to the inhibition of osteoclast formation, but not pre-osteoclast generation. Therefore, the transient up-regulation pattern of CPX-1 expression may be important for the successful progression from pre-osteoclasts to mature osteoclasts.

Animals↗

PubMed2004

Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor.

The prediction of protein relative solvent accessibility gives us helpful information for the prediction of tertiary structure of a protein. The SVMpsi method, which uses support vector machines (SVMs), and the position-specific scoring matrix (PSSM) generated from PSI-BLAST have been applied to achieve better prediction accuracy of the relative solvent accessibility. We have introduced a three-dimensional local descriptor that contains information about the expected remote contacts by both the long-range interaction matrix and neighbor sequences. Moreover, we applied feature weights to kernels in SVMs in order to consider the degree of significance that depends on the distance from the specific amino acid. Relative solvent accessibility based on a two state-model, for 25%, 16%, 5%, and 0% accessibility are predicted at 78.7%, 80.7%, 82.4%, and 87.4% accuracy, respectively. Three-state prediction results provide a 64.5% accuracy with 9%; 36% threshold. The support vector machine approach has successfully been applied for solvent accessibility prediction by considering long-range interaction and handling unbalanced data.

Computational Biology↗

PubMed2003

Protein secondary structure prediction based on an improved support vector machines approach.

The prediction of protein secondary structure is an important step in the prediction of protein tertiary structure. A new protein secondary structure prediction method, SVMpsi, was developed to improve the current level of prediction by incorporating new tertiary classifiers and their jury decision system, and the PSI-BLAST PSSM profiles. Additionally, efficient methods to handle unbalanced data and a new optimization strategy for maximizing the Q(3) measure were developed. The SVMpsi produces the highest published Q(3) and SOV94 scores on both the RS126 and CB513 data sets to date. For a new KP480 set, the prediction accuracy of SVMpsi was Q(3) = 78.5% and SOV94 = 82.8%. Moreover, the blind test results for 136 non-redundant protein sequences which do not contain homologues of training data sets were Q(3) = 77.2% and SOV94 = 81.8%. The SVMpsi results in CASP5 illustrate that it is another competitive method to predict protein secondary structure.

Artificial Intelligence↗

PubMed2002

Arrayed primer extension computing with variant mRNA splice forms. Multiple isoforms of CD44 in a human breast tumor.

The analysis of RNA splicing is important to understanding the diversity in protein sequences at specific disease loci, in the immune response, and across the proteome. The presence of each exon in a mature mRNA formed from a genomic sequence of n exons can be represented by a Boolean variable, enabling mRNA structure to be encoded by an n-bit binary number. The CD44 locus has been studied as an example of a variantly spliced RNA. Microarray methods can be used to address RNA splicing provided they exhibit high fidelity. Our previous work showed that the arrayed primer extension (APEX; single-nucleotide polymerase extension of microarrays of DNA primers) method gives high-fidelity, digital detection of nucleic acid sequences, and it has been used for the solution of Boolean computing problems. APEX was adapted to RNA analysis by the use of reverse transcriptase and arrays of primers specific to each exon in the CD44 locus. "Splicotypes" were readily assigned for a number of variant RNA templates. Because CD44 is known to be aberrantly spliced in a number of cancers, the RNA APEX method with a CD44 microarray was applied to samples from primary tumors of individual patients. Up to four different splicing forms of CD44 were detected, whereas there have been no previous reports of the presence of more than two CD44 isoforms within the same tissue.

Alternative Splicing↗