Hyoung-Sam Heo

Inhibitory Effect of mTOR Activator MHY1485 on Autophagy: Suppression of Lysosomal Fusion

Autophagy is a major degradative process responsible for the disposal of cytoplasmic proteins and dysfunctional organelles via the lysosomal pathway. During the autophagic process, cells form double-membraned vesicles called autophagosomes that sequester disposable materials in the cytoplasm and finally fuse with lysosomes. In the present study, we investigated the inhibition of autophagy by a synthesized compound, MHY1485, in a culture system by using Ac2F rat hepatocytes. Autophagic flux was measured to evaluate the autophagic activity. Autophagosomes were visualized in Ac2F cells transfected with AdGFP-LC3 by live-cell confocal microscopy. In addition, activity of mTOR, a major regulatory protein of autophagy, was assessed by western blot and docking simulation using AutoDock 4.2. In the result, treatment with MHY1485 suppressed the basal autophagic flux, and this inhibitory effect was clearly confirmed in cells under starvation, a strong physiological inducer of autophagy. The levels of p62 and beclin-1 did not show significant change after treatment with MHY1485. Decreased co-localization of autophagosomes and lysosomes in confocal microscopic images revealed the inhibitory effect of MHY1485 on lysosomal fusion during starvation-induced autophagy. These effects of MHY1485 led to the accumulation of LC3II and enlargement of the autophagosomes in a dose- and time- dependent manner. Furthermore, MHY1485 induced mTOR activation and correspondingly showed a higher docking score than PP242, a well-known ATP-competitive mTOR inhibitor, in docking simulation. In conclusion, MHY1485 has an inhibitory effect on the autophagic process by inhibition of fusion between autophagosomes and lysosomes leading to the accumulation of LC3II protein and enlarged autophagosomes. MHY1485 also induces mTOR activity, providing a possibility for another regulatory mechanism of autophagy by the MHY compound. The significance of this study is the finding of a novel inhibitor of autophagy with an mTOR activating effect.

The Anti-Inflammatory Effect of Kaempferol in Aged Kidney Tissues: The Involvement of Nuclear Factor-κB via Nuclear Factor-Inducing Kinase/IκB Kinase and Mitogen-Activated Protein Kinase Pathways

Kaempferol, one of the phytoestrogens, is found in berries and Brassica and Allium species and is known to have antioxidative and anti-inflammatory properties. In the present study, we examined the molecular mechanisms underlying the anti-inflammation effect of kaempferol in an aged animal model. To examine the effect of kaempferol in aged Sprague-Dawley rats, kaempferol was fed at 2 or 4 mg/kg/day for 10 days. The data show that kaempferol exhibited the ability to maintain redox balance. Kaempferol suppressed nuclear factor-kappaB (NF-kappaB) activation and expression of its target genes cyclooxygenase-2, inducible nitric oxide synthase, monocyte chemoattractant protein-1, and regulated upon activation, and normal T-cell expressed and secreted in aged rat kidney and in tert-butylhydroperoxide-induced YPEN-1 cells. Furthermore, kaempferol suppressed the increase of the pro-inflammatory NF-kappaB cascade through modulation of nuclear factor-inducing kinase (NIK)/IkappaB kinase (IKK) and mitogen-activated protein kinases (MAPKs) in aged rat kidney. Based on these results, we concluded that anti-oxidative kaempferol suppressed the activation of inflammatory NF-kappaB transcription factor through NIK/IKK and MAPKs in aged rat kidney.

Lysophosphatidylcholine Enhances Oxidative Stress Via the 5-Lipoxygenase Pathway in Rat Aorta During Aging

Lysophosphatidylcholine (LPC) is a lysolipid, acting as a potent cellular mediator of various biological processes. The purpose of this study was to define the role of LPC as a possible causative factor of disrupted redox balance in aged aorta from rats. In this study, we found elevated serum LPC levels in 24-month-old rats that were correlated with the age-related increase in cytosolic phospholipase A(2) (PLA(2)) activity. We also found that aortas from old rats showed increased 5-lipoxygenase (5-LO) activity. With the LPC-treated endothelial cells (YPEN-1 cells), we observed a rapid generation of reactive species, leading to enhanced oxidative stress. Our further investigations using specific 5-LO inhibitors led to the identification of a 5-LO pathway as the reactive species production source in the LPC-treated cells. Additional validation of this 5-LO pathway was made by the detection of increased leukotriene B4 generation in the LPC-treated cells. These in vitro data supported findings of increased expression and activation of aortic 5-LO in old rats by LPC. Together, our data strongly suggested that LPC caused the enhancement of oxidative stress in aged aorta through reactive species generation by an activated 5-LO pathway. LPC may well be an important contributor to age-related oxidative stress in aging aorta.

Inhibition of NF-κB-induced inflammatory responses by angiotensin II antagonists in aged rat kidney.

In this study, we explored the mechanisms by which the angiotensin converting enzyme inhibitor (ACEI), enalapril, and the Ang II receptor blocker (ARB), losartan suppress oxidative stress and NF-κB activation-induced inflammatory responses in aged rat kidney. The experimentations were carried out utilizing aged (24-month-old) Brown Norway×Fischer 344 (F1) male rats which were randomized into 3 groups and administered enalapril (40 mg/kg), losartan (30 mg/kg) or placebo for 6 months (daily p.o.). The level of reactive species (RS), peroxynitrite (ONOO(-)), GSH/GSSG and lipid peroxidation were measured. The activity of the pro-inflammatory transcription factor NF-κB, and gene expression of proteins in upstream signaling cascades were measured by electro-mobility shift assay (EMSA) and Western blotting. Enalapril and losartan differentially attenuated redox imbalance and the redox-sensitive transcription factor, the NF-κB pathway. Furthermore, stimulation of the NF-κB activation pathway by phosphorylation of p65 was attenuated by both compounds. Moreover, mediation of phosphorylation of p65 by phosphorylation of IκB kinase αβ (IKKαβ) and mitogen- and stress-activated protein kinase-1 (MSK-1), were also inhibited by enalapril and losartan. Finally, both compounds also lowered expression of NF-κB-dependent inflammatory genes, such as cyclooxygenase-2 (COX-2), and inducible NO synthase (iNOS). Only losartan lowered levels of 5-lipoxygenase (5-LOX). These findings indicate that enalapril and losartan differentially suppress inflammatory responses via inhibition of oxidative stress-induced NF-κB activation in aged rat kidney.

Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome

Although systems biology is a perfect framework for investigating system-level declines during aging, only a few reports have focused on a comprehensive understanding of system-level changes in the context of aging systems. The present study aimed to understand the most sensitive biological systems affected during aging and to reveal the systems underlying the crosstalk between aging and the ability of calorie restriction (CR) to effectively slow-down aging. We collected and analyzed 478 aging- and 586 CR-related mouse genes. For the given genes, the biological systems that are significantly related to aging and CR were examined according to three aspects. First, a global characterization by Gene Ontology (GO) was performed, where we found that the transcriptome (a set of genes) for both aging and CR were strongly related in the immune response, lipid metabolism, and cell adhesion functions. Second, the transcriptional modularity found in aging and CR was evaluated by identifying possible functional modules, sets of genes that show consistent expression patterns. Our analyses using the given functional modules, revealed systemic interactions among various biological processes, as exemplified by the negative relation shown between lipid metabolism and the immune response at the system level. Third, transcriptional regulatory systems were predicted for both the aging and CR transcriptomes. Here, we suggest a systems biology framework to further understand the most important systems as they age.

tsORFdb: theoretical small open reading frames (ORFs) database and massProphet: peptide mass fingerprinting (PMF) tool for unknown small functional ORFs.

Peptide mass fingerprinting (PMF) has become one of the most widely used methods for rapid identification of proteins in proteomics research. Many peaks, however, remain unassigned after PMF analysis, partly because of post-translational modification and the limited scope of protein sequences. Almost all PMF tools employ only known or predicted protein sequences and do not include open reading frames (ORFs) in the genome, which eliminates the chance of finding novel functional peptides. Unlike most tools that search protein sequences from known coding sequences, the tool we developed uses a database for theoretical small ORFs (tsORFs) and a PMF application using a tsORFs database (tsORFdb). The tsORFdb is a database for ORFeome that encompasses all potential tsORFs derived from whole genome sequences as well as the predicted ones. The massProphet system tries to extend the search scope to include the ORFeome using the tsORFdb. The tsORFdb and massProphet should be useful for proteomics research to give information about unknown small ORFs as well as predicted and registered proteins.

Protein function classification based on gene ontology

Most proteins interact with other proteins, cells, tissues or diseases. They have biological functions and can be classified according to their functions. With the functions and the functional relations of proteins, we can explain many biological phenomena and obtain answers in solving biological problems. Therefore, it is important to determine the functions of proteins. In this paper we present a protein function classification method for the function prediction of proteins. With human proteins assigned to GO molecular function terms, we measure the similarity of proteins to function classes using the functional distribution.

TREP_DB: Transcriptional regulatory elements pattern database

Predicting and assigning functions for putative genes and hypothetical proteins are important goals in the post-genomic era. Many methods have been developed for this challenge, among which the straightforward way is function prediction using sequence homology. Homology-based function prediction applies sequence-alignment tools to find homology relationships between functions of known genes and putative genes, and transfers the most similar functions of known genes to putative genes. This approach fails completely for about 30% of genes, and only 3% have any supporting experimental evidence. According to supporting evidence, genes are known to be regulated by a common transcriptional regulatory element if the expression profiles of the coregulated genes are highly correlated. We propose a new conceptual approach and method for nonhomology-based function-prediction methods for putative genes and hypothetical proteins. We have established patterns, also considered to be combinations, of common transcriptional regulatory elements for functional classes of mouse (Mus musculus) transcripts (the TREP_DB). Using these results, we have also established a function-prediction method for putative genes and hypothetical proteins.