Yoojin Kwon, Ji Wook Kim, Jo Ae Jeoung, Mi-Sung Kim, and Chanhee KangMol. Cells 2017; 40(9): 607-612 https://doi.org/10.14348/molcells.2017.0151
Abstract : When mammalian cells and animals face a variety of internal or external stresses, they need to make homeostatic changes so as to cope with various stresses. To this end, mammalian cells are equipped with two critical stress responses, autophagy and cellular senescence. Autophagy and cellular senescence share a number of stimuli including telomere shortening, DNA damage, oncogenic stress and oxidative stress, suggesting their intimate relationship. Autophagy is originally thought to suppress cellular senescence by removing damaged macromolecules or organelles, yet recent studies also indicated that autophagy promotes cellular senescence by facilitating the synthesis of senescence-associated secretory proteins. These seemingly opposite roles of autophagy may reflect a complex picture of autophagic regulation on cellular senescence, including different types of autophagy or a unique spatiotemporal activation of autophagy. Thus, a better understanding of autophagy process will lead us to not only elucidate the conundrum how autophagy plays dual roles in the regulation of cellular senescence but also helps the development of new therapeutic strategies for many human diseases associated with cellular senescence. We address the pro-senescence and anti-senescence roles of autophagy while focusing on the potential mechanistic aspects of this complex relationship between autophagy and cellular senescence.
Sangyun JeongMol. Cells 2017; 40(9): 613-620 https://doi.org/10.14348/molcells.2017.0096
Abstract : The most common form of senile dementia is Alzheimer’s disease (AD), which is characterized by the extracellular deposition of amyloid β-peptide (Aβ) plaques and the intracellular formation of neurofibrillary tangles (NFTs) in the cerebral cortex. Tau abnormalities are commonly observed in many neurodegenerative diseases including AD, Parkinson’s disease, and Pick’s disease. Interestingly, tau-mediated formation of NFTs in AD brains shows better correlation with cognitive impairment than Aβ plaque accumulation; pathological tau alone is sufficient to elicit frontotemporal dementia, but it does not cause AD. A growing amount of evidence suggests that soluble Aβ oligomers in concert with hyperphosphorylated tau (pTau) serve as the major pathogenic drivers of neurodegeneration in AD. Increased Aβ oligomers trigger neuronal dysfunction and network alternations in learning and memory circuitry prior to clinical onset of AD, leading to cognitive decline. Furthermore, accumulated damage to mitochondria in the course of aging, which is the best-known nongenetic risk factor for AD, may collaborate with soluble Aβ and pTau to induce synapse loss and cognitive impairment in AD. In this review, I summarize and discuss the current knowledge of the molecular and cellular biology of AD and also the mechanisms that underlie Aβ-mediated neurodegeneration.
Namgyu Lee, Dae-Kyum Kim, Seung Hyun Han, Hye Guk Ryu, Sung Jin Park, Kyong-Tai Kim, and Kwan Yong ChoiMol. Cells 2017; 40(9): 621-631 https://doi.org/10.14348/molcells.2017.0108
Abstract : Vaccinia-related kinase 1 (VRK1) and VRK3 are members of the VRK family of serine/threonine kinases and are principally localized in the nucleus. Despite the crucial roles of VRK1/VRK3 in physiology and disease, the molecular and functional interactions of VRK1/VRK3 are poorly understood. Here, we identified over 200 unreported VRK1/VRK3-interacting candidate proteins by affinity purification and LC-MS/MS. The networks of VRK1 and VRK3 interactomes were found to be associated with important biological processes such as the cell cycle, DNA repair, chromatin assembly, and RNA processing. Interactions of interacting proteins with VRK1/VRK3 were confirmed by biochemical assays. We also found that phosphorylations of XRCC5 were regulated by both VRK1/VRK3, and that of CCNB1 was regulated by VRK3. In liver cancer cells and tissues, VRK1/VRK3 were highly upregulated and its depletion affected cell cycle progression in the different phases. VRK3 seemed to affect S phase progression and G2 or M phase entry and exit, whereas VRK1 affects G1/S transition in the liver cancer, which could be explained by different interacting candidate proteins. Thus, this study not only provides a resource for investigating the unidentified functions of VRK1/VRK3, but also an insight into the regulatory roles of VRK1/VRK3 in biological processes.
Hyun-Jung Bae, Ha-Na Lee, Mi-Na Baek, Eun-Jin Park, Chi-Yong Eom, In-Jeong Ko, Ho-Young Kang, and Jeong-Il OhMol. Cells 2017; 40(9): 632-642 https://doi.org/10.14348/molcells.2017.0076
Abstract : The DevSR (DosSR) two-component system, which is a major regulatory system involved in oxygen sensing in mycobacteria, plays an important role in hypoxic induction of many genes in mycobacteria. We demonstrated that overexpression of the kinase domain of
Shenshen Zou, Dan Sun, and Yongheng LiangMol. Cells 2017; 40(9): 643-654 https://doi.org/10.14348/molcells.2017.0030
Abstract : Autophagy is a degradation pathway in eukaryotic cells in which aging proteins and organelles are sequestered into double-membrane vesicles, termed autophagosomes, which fuse with vacuoles to hydrolyze cargo. The key step in autophagy is the formation of autophagosomes, which requires different kinds of vesicles, including COPII vesicles and Atg9-containing vesicles, to transport lipid double-membranes to the phagophore assembly site (PAS). In yeast, the
Sangkyu Kim, Insoo Park, Seung Gu Park, Seulki Cho, Jin Hong Kim, Nagesh S. Ipper, Sun Shim Choi, Eung Suk Lee, and Hyo Jeong HongMol. Cells 2017; 40(9): 655-666 https://doi.org/10.14348/molcells.2017.0106
Abstract : We constructed a large na?ve human Fab library (3 × 1010 colonies) from the lymphocytes of 809 human donors, assessed available diversities of the heavy-chain variable (VH) and κ light-chain variable (VK) domain repertoires, and validated the library by selecting Fabs against 10 therapeutically relevant antigens by phage display. We obtained a database of unique 7,373 VH and 41,804 VK sequences by 454 pyrosequencing, and analyzed the repertoires. The distribution of VH and VK subfamilies and germline genes in our antibody repertoires slightly differed from those in earlier published natural antibody libraries. The frequency of somatic hypermutations (SHMs) in heavy-chain complementarity determining region (HCDR)1 and HCDR2 are higher compared with the natural IgM repertoire. Analysis of position-specific SHMs in CDRs indicates that asparagine, threonine, arginine, aspartate and phenylalanine are the most frequent non-germline residues on the antibody-antigen interface and are converted mostly from the germline residues, which are highly represented in germline SHM hotspots. The amino acid composition and length-dependent changes in amino acid frequencies of HCDR3 are similar to those in previous reports, except that frequencies of aspartate and phenylalanine are a little higher in our repertoire. Taken together, the results show that this antibody library shares common features of natural antibody repertoires and also has unique features. The antibody library will be useful in the generation of human antibodies against diverse antigens, and the information about the diversity of natural antibody repertoires will be valuable in the future design of synthetic human antibody libraries with high functional diversity.
Sang Kyung Byun, Tae Hyeon An, Min Jeong Son, Da Som Lee, Hyun Sup Kang, Eun-Woo Lee, Baek Soo Han, Won Kon Kim, Kwang-Hee Bae, Kyoung-Jin Oh, and Sang Chul LeeMol. Cells 2017; 40(9): 667-676 https://doi.org/10.14348/molcells.2017.0116
Abstract : Abnormal differentiation of muscle is closely associated with aging (sarcopenia) and diseases such as cancer and type II diabetes. Thus, understanding the mechanisms that regulate muscle differentiation will be useful in the treatment and prevention of these conditions. Protein lysine acetylation and methylation are major post-translational modification mechanisms that regulate key cellular processes. In this study, to elucidate the relationship between myogenic differentiation and protein lysine acetylation/methylation, we performed a PCR array of enzymes related to protein lysine acetylation/methylation during C2C12 myoblast differentiation. Our results indicated that the expression pattern of HDAC11 was substantially increased during myoblast differentiation. Furthermore, ectopic expression of HDAC11 completely inhibited myoblast differentiation, concomitant with reduced expression of key myogenic transcription factors. However, the catalytically inactive mutant of HDAC11 (H142/143A) did not impede myoblast differentiation. In addition, wild-type HDAC11, but not the inactive HDAC11 mutant, suppressed MyoD-induced promoter activities of
Arum Lee, Man Ryul Lee, Hae-Hyeog Lee, Yeon-Suk Kim, Jun-Mo Kim, Temuulee Enkhbold, and Tae-Hee KimMol. Cells 2017; 40(9): 677-684 https://doi.org/10.14348/molcells.2017.0026
Abstract : Postmenopausal atrophic vagina (PAV) is the thinning of the walls of the vagina and decreased lugae of the vagina. PAV is caused by decreased estrogen levels in postmenopausal women. However, the harmful effects of hormone replacement therapy (HRT) have resulted in considerable caution in its use. Various estrogen agonist treatment options are available. Vitamin D is influences the regulation of differentiation and proliferation of various cells, especially tissues lining stratified squamous epithelium, such as the vaginal epithelium. In this study, we hypothesized that vitamin D could provide an alternative and a safe treatment option for PAV by promoting the proliferation and differentiation of the vaginal epithelium. Thirty six patients were enrolled in this case-control study. Vitamin D associated proteins in a vitamin D and sex hormone treated vaginal epithelial cell line as well as normal and PAV tissues were measured. To confirm of cell-to-cell junction protein expression, cell line and tissue studies included RT-PCR, immunohistochemistry staining, and immunoblot analyses. The expression of cell-to-cell junction proteins was higher in women with symptoms of atrophic vagina tissue compared to women without the symptoms. Vitamin D stimulated the proliferation of the vaginal epithelium by activating p-RhoA and Erzin through the vitamin D receptor (VDR). The results suggest that vitamin D positively regulates cell-to-cell junction by increasing the VDR/p-RhoA/p-Ezrin pathway. This is the first study to verify the relationship of the expression of RhoA and Ezrin proteins in vaginal tissue of PAV.
Assim A. Alfadda, Afshan Masood, Mohammed Y. Al-Naami, Pierre Chaurand, and Hicham BenabdelkamelMol. Cells 2017; 40(9): 685-695 https://doi.org/10.14348/molcells.2017.0073
Abstract : Obesity and the metabolic disorders that constitute metabolic syndrome are a primary cause of morbidity and mortality in the world. Nonetheless, the changes in the proteins and the underlying molecular pathways involved in the relevant pathogenesis are poorly understood.In this study a proteomic analysis of the visceral adipose tissue isolated from metabolically healthy and unhealthy obese patients was used to identify presence of altered pathway(s) leading to metabolic dysfunction. Samples were obtained from 18 obese patients undergoing bariatric surgery and were subdivided into two groups based on the presence or absence of comorbidities as defined by the International Diabetes Federation. Two dimensional difference in-gel electrophoresis coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was carried out. A total of 28 proteins were identified with a statistically significant difference in abundance and a 1.5-fold change (ANOVA, p ≤ 0.05) between the groups. 11 proteins showed increased abundance while 17 proteins were decreased in the metabolically unhealthy obese compared to the healthy obese. The differentially expressed proteins belonged broadly to three functional categories: (i) protein and lipid metabolism (ii) cytoskeleton and (iii) regulation of other metabolic processes. Network analysis by Ingenuity pathway analysis identified the NFκB, IRK/MAPK and PKC as the nodes with the highest connections within the connectivity map. The top network pathway identified in our protein data set related to cellular movement, hematological system development and function, and immune cell trafficking. The VAT proteome between the two groups differed substantially between the groups which could potentially be the reason for metabolic dysfunction.
MHO and MUHO samples were labeled with Cy3 and Cy5, respectively, while the protein reference pool (internal standard) was labeled with Cy2. VAT proteins were focused on linear pH 3–11, IPG strips (24 cm), and were then separated by 12.5% polyacrylamide gels. (A) Cy3 and Cy5 channel overlap image. Differentially expressed protein spots identified by MALDI-TOF are marked on the gels by arrows. (B) An example of protein spot (# 960, Peptidylprolyl Isomerase A) analysis showing differential expression of proteins in 2D and 3D. Individual 2D-DIGE gel image of VAT samples labeled with Cy3 (C), Cy5 (D), and Cy2 (E).|@|~(^,^)~|@|Confirmation of the proteomic data using immunoblot analysis of selected proteins, identified by 2D-DIGE analysis.
(A) The results obtained by immunoblotting were similar to the results obtained by 2D-DIGE. (B) Graphical representation of the relative intensity values of normalized protein bands for MHO and MUHO. The data are presented as histograms of mean ± SD.|@|~(^,^)~|@|Schematic representation of the most significant IPA network from differentially regulated proteins in the MHO compared to those from the MUHO group.
IPA analysis indicated a functional interaction of networks with the highest score of 40 related to the cellular movement, hematological system development and function, and immune cell trafficking, revealing NFκB, ERK1/2, IL-13 and P38 MAPK as central nodes that are deregulated in MUHO. Nodes in green and red correspond to the up and down-regulated proteins in MUHO vs. MHO, respectively. Uncoloured nodes are proposed by IPA and indicate potential targets functionally coordinated with the differentially expressed proteins. Solid lines indicate direct molecular interactions, and dashed lines represent indirect relations.|@|~(^,^)~|@|Comparative depiction of the differentially abundant identified proteins categorized into groups according to their function based on the GO terms using UniprotKB.
The representative pie diagram shows the (%) of involvement for different functional categories of the proteins between MHO and MUHO group.