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Early detection is critical for minimizing mortality from cancer. Plasma cell-free DNA (cfDNA) contains the signatures of tumor DNA, allowing us to quantify the signature and diagnose early-stage tumors. Here, we report a novel tumor fragment quantification method, TOF (Tumor Originated Fragment) for the diagnosis of lung cancer by quantifying and analyzing both the plasma cfDNA methylation patterns and fragmentomic signatures. TOF utilizes the amount of ctDNA predicted from the methylation density information of each cfDNA read mapped on 6243 lung-tumor-specific CpG markers. The 6243 tumor-specific markers were derived from lung tumor tissues by comparing them with corresponding normal tissues and healthy blood from public methylation data. TOF also utilizes two cfDNA fragmentomic signatures: 1) the short fragment ratio, and 2) the 5' end-motif profile. We used 298 plasma samples to analyze cfDNA signatures using enzymatic methyl-sequencing data from 201 lung cancer patients and 97 healthy controls. The TOF score showed 0.98 of the area under the curve in correctly classifying lung cancer from normal samples. The TOF score resolution was high enough to clearly differentiate even the early-stage non-small cell lung cancer patients from the healthy controls. The same was true for small cell lung cancer patients.

// Joo Mi Yi 1 , Eun-Jin Kang 1 , Hyun-Mi Kwon 1 , Jin-Han Bae 1 , Keunsoo Kang 2 , Nita Ahuja 3 , Kwangmo Yang 1 1 Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, Republic of Korea 2 Department of Microbiology, Dankook University, Cheonan, Korea, Republic of Korea 3 Department of Surgery, Oncology, and Urology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA Correspondence to: Joo Mi Yi, email: jmyi@dirams.re.kr Kwangmo Yang, email: kmyang@dirams.re.kr Keywords: microRNA, miR-1247, hypermethylation, tumor suppressor, pancreatic cancer Received: October 25, 2016 Accepted: February 13, 2017 Published: February 24, 2017 ABSTRACT Altered expression of microRNAs has been strongly implicated in human cancers, and growing evidence is emerging that a number of miRNAs are downregulated in cancer associated with CpG island hypermethylation. Although pancreatic cancer is one of the most malignant human cancers, the roles of miRNAs underlying the tumorigenesis of pancreatic cancer are still poorly understood. In the present study, we explored the molecular functional role of microRNA-1247 as tumor suppressor associated with epigenetic alteration in pancreatic cancer. CpG islands methylation of miR-1247 is frequently observed in various pancreatic cancer cell lines and in primary pancreatic tumors, but not in normal pancreatic tissue. Ectopic expression of miR-1247 in five pancreatic cancer cell lines results in suppressing of cell growth, proliferation, migration, and invasion in vitro and tumorigenicity of pancreatic cancer cells in vivo . Interestingly, we found one putative target gene of miR-1247, regulator of chromosome condensation 2 ( RCC2 ), harbored miR-1247 target sequences in the 3′ UTR of its mRNA. In functional studies in vitro to understand the interaction between miR-1247 and RCC2 , decreasing of RCC2 gene expression by miR-1247 was observed by immunoblotting and immunohistochemistry at both mRNA and protein levels. Moreover, luciferase reporter assay confirmed that RCC2 was a direct target of miR-1247. Taken together, our data suggest that CpG island hypermethylation of miR-1247 is responsible for its downregulation in pancreatic cancer, and ectopic expression of miR-1247 functions as a potential tumor suppressor targeting RCC2 in pancreatic cancer cells.

microRNAs (miRNAs), which are small non‑coding RNA molecules, can participate in diverse biological functions and act as oncogenes or tumor suppressors by inhibiting target gene expression. The alteration of miRNA expression is observed in many types of human cancers and has been implicated in carcinogenesis. Since miRNAs have been known to be downregulated in most cancer types, there is growing evidence that several miRNAs are downregulated by DNA hypermethylation. Here, we determined that MIR219.2, MIR663b and MIR1237 were transcriptionally silenced by DNA hypermethylation in human gastric cancer cell lines. Moreover, we demonstrated the functional roles of these epigenetically silenced miRNAs by ectopically expressing them in gastric cancer cells, which caused the suppression of growth and proliferation. In addition, wound closure, cell migration, and invasion were significantly reduced in AGS cells following transfection with MIR219.2, MIR663b or MIR1237 mimics. Notably, epithelial-to-mesenchymal transition (EMT)-associated proteins were decreased in response to ectopic expression of these miRNAs, supporting the notion that these miRNAs have a tumor-suppressive effect in gastric cancer. We finally predicted the targets of these miRNAs and identified several candidate genes, the expression levels of which were significantly downregulated by ectopic expression of MIR219.2, MIR663b or MIR1237 mimics in the gastric cancer cell lines. Our study provides strong evidence that these miRNAs are transcriptionally regulated by DNA methylation in gastric cancer and have tumor-suppressive roles by decreasing the mesenchymal traits in cancer as well as by targeting cancer-associated genes.

With the advent of next-generation sequencing technology, genome-wide maps of DNA methylation are now available. The Thoroughbred horse is bred for racing, while the Jeju horse is a traditional Korean horse bred for racing or food. The methylation profiles of equine organs may provide genomic clues underlying their athletic traits. We have developed a database to elucidate genome-wide DNA methylation patterns of the cerebrum, lung, heart, and skeletal muscle from Thoroughbred and Jeju horses. Using MeDIP-Seq, our database provides information regarding significantly enriched methylated regions beyond a threshold, methylation density of a specific region, and differentially methylated regions (DMRs) for tissues from two equine breeds. It provided methylation patterns at 784 gene regions in the equine genome. This database can potentially help researchers identify DMRs in the tissues of these horse species and investigate the differences between the Thoroughbred and Jeju horse breeds.

Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethylated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.

Background The polarization of macrophages was the expressed to M1/M2 phenotype by various stimuli or environment signals. The M1 macrophage was pro-inflammatory phenotype and was key effector cells in the immune response of rheumatoid arthritis (RA). So, M1 macrophage influenced the inflammation of RA synovial membrane and joint destruction in RA, whereas M2 macrophage was anti-inflammatory phenotype and could down-regulate the production of proinflammatory cytokines in RA. The SIRT1 attenuated the RA inflammation via down-regulation of NF-κB signaling. However, the effect of SIRT1 on macrophages polarization remained uncler. Objectives We aimed to check out that activated SIRT1 modulated macrophages polarization into M1 phenotype and controlled the inflammation of RA. Methods Monocytes from synovial fluid of RA patients, bone marrow–derived monocytes (BMDCs) from mice were studied. monocytes were cultured with M-CSF for 7days to differentiate into M0 macrophages (monocyte-derived mature macrophages M0 phenotype). M0 macrophages were incubated with LPS and IFN-gamma in order to obtain M1 macrophages. M1 macrophage markers were detected by real-time PCR. Results Activation of SIRT1 was achieved by Resveratrol, activated SIRT1 attenuated M1 macrophage phenotypes and pro-inflammatory cytokine expression. macrophages obtained from SIRT1-tg mice, which were overexpression of SIRT1, exhibited decreased M1 markers in association with enhanced activation of AMPK/ACC compared with macrophage from control C57BL/6 mice. In addition to SIRT1 activation, M1 polarizing signal, acetylation of NF-κB p65, was suppressed. In SIRT1-deficient macrophages, resveratrol fail to increase AMPK activity and to decrease the expression M1 markers owing to enhanced acetylation of NF-κB p65. Conclusions SIRT1 maybe an important modulator of M1 macrophages polarization and increased AMPK activity, which suppressed acetylation of NF-κB p65 during inflammation of RA. so, modulation of SIRT1 maybe a new target in RA treatment. References SIRT1 inhibits differentiation of monocytes to macrophages: amelioration of synovial inflammation in rheumatoid arthritis. J Mol Med (Berl). 2016 Aug;94(8):921–31. Disclosure of Interest None declared

Mobile genetic elements within genomes have been known to drive genome evolution in diverse ways. Since developing high-technology for whole-genome sequencing, many researchers have focused on not only how mobile genetic elements have affected the evolution of genes and their function, particularly of human and mammals, but also how these elements involve in gene activation or inactivation associated with a number of human diseases. Here we describe what kind of biological changes by mobile genetic elements contribute to disease, especially cancer and present an overview of what is known about this large, and largely unexplored, segment of the genome. Finally, we discuss understanding the genomic changes or cellular responses to genotoxic stress such as radiation may permit to implicate for potential clinical application.

DNA methylation is an essential biochemical modification that regulates gene expression. Exercise induces changes in gene expression that adapt as metabolic changes in the blood. We provide a database for the epigenetic changes after horse exercise ( http://www.primate.or.kr/hexdb ). Horse Exercise Epigenetic Database (HExDB) explicates the change in genome-wide DNA methylation patterns after exercise. Exercise changes the genome-wide epigenetic patterns, and understanding the regions that change is important for confirming exercise physiological mechanisms. For this purpose, our database provides information on differentially methylated regions after exercise that pass a set threshold. A total of 784 genes based on NCBI RefSeq were identified as differentially methylated in equines after exercise. Our database provides clues for the study of exercise-related epigenetic pathways in the thoroughbred horse.

Altered expression of microRNA (miRNA) can significantly contribute to cancer development and recent studies have shown that a number of miRNAs may be regulated by DNA methylation. Through a candidate gene approach, we identified MIR941 and MIR1247 to be transcriptionally silenced by DNA hypermethylation in several gastric cancer cell lines. We confirmed that these miRNAs are also densely methylated in primary gastric cancers but not in normal gastric tissues. In addition, we demonstrated that ectopic expression of these two miRNAs in AGS gastric cancer cells resulted in suppression of growth and migration. Furthermore, we tested genes predicted to be the targets of MIR941 and MIR1247 and identified 7 and 6 genes, whose expressions were significantly downregulated by transfection of MIR941 and MIR1247 mimics, respectively, in gastric cancer cell lines. Some of these genes are known to promote proliferation and invasion, phenotypes we observed upon ectopic expression of the two miRNAs. Thus, we examined these candidates more closely and found that downregulation of mRNA corresponded to a decrease in protein levels (observed by western blot). Our study provides unequivocal evidence that MIR941 and MIR1247 are transcriptionally regulated by DNA methylation in gastric cancer and that they have tumor suppressor properties through their inhibition of key cancer promoting genes in this context.

Mounting evidence suggests that inflammatory bowel disease (IBD) is caused by genetic predisposition of various genes as well as an abnormal interaction with environmental factors, resulting in epigenetic alterations. It has become evident that epigenetic factors play a significant contributory role during disease development. Additionally, DNA methylation has been reported to be correlated with the development of IBD. In the present study, we examined the role of DNA hypermethylation in Crohn's disease (CD) patients. The transcription elongation regulator 1-like (TCERG1L) gene, which has been previously reported to be highly frequently methylated in colon tumors was selected as a candidate for the early detection of biomarkers for colon cancer patients. DNA methylation of TCERG1L in 101 serum samples of CD patients was examined. Results of conventional MSP analysis revealed high methylation [57% (58/101)] of serum samples in CD patients. The DNA methylation pattern of TCEEG1L was confirmed using bisulfate sequencing analysis. The results of the present study suggest that using regular colonoscopic surveillance sensitive DNA methylation markers may detect serum samples of CD patients, leading to reduced risk or prevention of the progression of advanced stages of disease.

Transposable elements (TEs) are repetitive sequences dispersed throughout mammalian genomes, and they occupy important genetic positions. TEs have been shown to have both harmful and beneficial effects such as exonization, polyadenylation, and/or altering transcription rates in various vertebrate genomes. However, to the best of our knowledge, no study has yet considered the relationship between TEs and horse genes. In this study, we examined the contribution of TEs to the horse genome by collecting TEs inserted within mRNA genes. By screening the abundance, distribution, and orientation of TEs, we found that the majority of TE insertions belong to retroelements and DNA elements, most of which exist in the coding sequences of horse genes. In addition, the MIR, L1, L2, ERVL, and ERVL-MaLR subfamilies were found to be the most abundant in both non-LTR and LTR elements. Retroelements (LTRs, LINEs, and SINEs) among the TEs inserted in the coding sequences showed a preference for antisense orientation. The most pronounced imbalance in insertional orientation was observed in LINEs, which represent 40 % of all TEs in antisense orientation. Through these analyses, we identified that a total of 1310 TEs have been integrated into horse mRNA genes and small fractions of them have been exonized into coding sequences.

Eukaryotic genomes comprise numerous retroelements that have a major impact on the structure and regulation of gene function. Retroelements are regulated by epigenetic controls, and they generate multiple miRNAs that are involved in the induction and progression of genomic instability. Elucidation of the biological roles of retroelements deserves continuous investigation to better understand their evolutionary features and implications for disease.

The cause of inflammatory bowel disease (IBD) is still unknown, but there is growing evidence that environmental factors such as epigenetic changes can contribute to the disease etiology. The aim of this study was to identify newly hypermethylated genes in ulcerative colitis (UC) using a genome-wide DNA methylation approach. Using an Infinium HumanMethylation450 BeadChip array, we screened the DNA methylation changes in three normal colon controls and eight UC patients. Using these methylation profiles, 48 probes associated with CpG promoter methylation showed differential hypermethylation between UC patients and normal controls. Technical validations for methylation analyses in a larger series of UC patients (n = 79) were performed by methylation-specific PCR (MSP) and bisulfite sequencing analysis. We finally found that three genes (FAM217B, KIAA1614 and RIBC2) that were significantly elevating the promoter methylation levels in UC compared to normal controls. Interestingly, we confirmed that three genes were transcriptionally silenced in UC patient samples by qRT-PCR, suggesting that their silencing is correlated with the promoter hypermethylation. Pathway analyses were performed using GO and KEGG databases with differentially hypermethylated genes in UC. Our results highlight that aberrant hypermethylation was identified in UC patients which can be a potential biomarker for detecting UC. Moreover, pathway-enriched hypermethylated genes are possibly implicating important cellular function in the pathogenesis of UC. Overall, this study describes a newly hypermethylated gene panel in UC patients and provides new clinical information that can be used for the diagnosis and therapeutic treatment of IBD.

Current evidence indicates that there is a relationship between microRNA (miRNA)-mediated gene silencing and low-dose irradiation (LDIR) responses. Here, alterations of miRNA expression in response to LDIR exposure in male BALB/c mice and three different types of hepatocytes were investigated. The miRNome of the LDIR-exposed mouse spleens (0.01 Gy, 6.5 mGy/h) was analyzed, and the expression of miRNA and mRNA was validated by qRT-PCR. Western blotting, chromatin immunoprecipitation (ChIP), and luciferase assays were also performed to evaluate the interaction between miRNAs and their target genes and to gain insight into the regulation of miRNA expression. The expression of miRNA-193b-3p was down-regulated in the mouse spleen and liver and in various hepatocytes (NCTC, Hepa, and HepG2 cell lines) in response to LDIR. The down-regulation of miR-193b-3p expression was caused by histone deacetylation on the miR-193b-3p promoter in the HepG2 cells irradiated with 0.01 Gy. However, the alteration of histone deacetylation and miR-193b-3p and Rad51 expression in response to LDIR was restored by pretreatment with N-acetyl-cyctein. In conclusion, we provide evidence that miRNA responses to LDIR include the modulation of cellular stress responses and repair mechanisms.

Cartilage increases flexibility of motion and helps protect the body from physical shock. Strong physical shock or some biological factor could cause joint disease. ADAMTS4 (a disintegrin and metalloproteinase with thrombospondin motifs 4) has been related to degradation of aggrecans in cartilage. It has been associated with joint disease, which could influence the ability of horses to exercise. Here, we performed sequence analysis and expression profiling of the ADAMTS4 gene in thoroughbred horses. Quantitative real-time RT-PCR data indicated that higher expression of the ADAMTS4 gene appeared in the cartilage tissues compared to those of pancreas, stomach, lung and colon. The expression pattern was also higher in the muscle tissues after exercise than before exercise. These data could be of great use for further studies in relation to both horse racing and joint disease.

Retroelements play important roles in primate evolution. Specifically, human endogenous retroviruses (HERVs) and Alu elements are primate-specific retroelements. In addition, SVA elements belong to the youngest family of hominid non-long terminal repeat (LTR) retrotransposons. Retroelements can affect adjacent gene expression, supplying cis-regulatory elements, splice sites, and poly-A signals. We developed a database, GEnome-wide Browser for RETroelement (GEBRET, http://neobio.cs.pusan.ac.kr/~gebre/), for comparing the distribution of primate-specific retroelements and adjacent genes. GEBRET database components include 47,381 HERVs, 53,924 Alus and 4639 SVAs in five primate genomes of human, chimpanzee, orangutan, rhesus macaque, and marmoset. Host genes located upstream of a retroelement were also visualized and classified as five categories (0.0, 0.5, 1.0, 2.0, and 3.0Kb). Our results suggest that retroelements preferentially integrate into the distal promoter region relative to the core promoter region. GEBRET database is designed to investigate the distribution of retroelements (HERVs, Alus and SVAs) in the primate genomes that have been sequenced. Our software will be useful in the field to study the impact of retroelements on primate genome evolution.

The heavy metal contents and chemical compositions among mackerel species were investigated. Atlantic and chub mackerel had higher mercury, but lower lead than blue mackerel. Chub mackerel had the highest crude fat (18.62%) and the lowest moisture (58.29%), whereas blue mackerel had the highest moisture (70.10%) and the lowest crude fat (2.89%). Atlantic and blue mackerel had total saturated fatty acids (SFA)>polyunsaturated fatty acids (PUFA)>monounsaturated fatty acids (MUFA), whereas chub mackerel had PUFA>SFA>MUFA. The main SFA of the 3 mackerels were 16:0 and the main PUFAs were 22:6n-3 and 20:5n-3. The total amino acid contents in Atlantic, blue, and chub mackerel were 190.63, 169.49, and 172.97 mg/g, respectively. The major amino acids of the 3 mackerels were glutamic acid, aspartic acid, lysine, and leucine.

Heavy metal contents and biochemical characteristics of Japanese (J-abalone) and Korean abalone (K-abalone) were compared. Heavy metal contents of Jand K-abalone were less than the maximum levels in the Korea Food Code. There were significant differences in contents of crude protein and ash between J- and K-abalone (p

A simple, rapid method for determining amoxicillin (AMO) and ampicillin (AMP) in aquatic products (flatfish, salmon, shrimp, tilapia, and yellow croaker) was evaluated. For quantification, the AMO and AMP ions at m/z 348.9 and 105.9, respectively, were selected. The limit of detection (LOD) and limit of quantification (LOQ) for detecting AMO were 0.09 and , respectively. The respective values for AMP were 0.02 and . After AMO treatment, the level decreased 10% after 7 days at , while it decreased 20% at . After 7 days, 94.9.100% of AMP remained after storage at , while 62.3.100% remained after storage at . Using the food code method, the recovery of AMO ranged from 64.1.92.0% and that of AMP from 44.8.86.2%. With a protein centrifugation method, the recovery of AMO ranged from 39.8.87.9% and that of AMP from 78.0.98.1%. With liquid-liquid extraction, the recovery of AMO ranged from 36.5.88.3% and that of AMP from 31.8.75.1%.

Chub and blue mackerels are popular fish resources in Korea, but little is known about each biochemical characters of different anatomical regions. To investigate biochemical characters of chub and blue mackerels, three ordinary muscle regions were identified by their fin position; namely anterior, median, posterior. In addition, red muscle, as a dark muscle, was obtained from beneath the lateral line to compare with ordinary muscles. Proximate and lipid-class compositions did not show any discernible trends in the different anatomical ordinary muscles from mackerel of the same kind, while significant differences between ordinary and red muscles in the same mackerel, or between chub and blue mackerels, were observed. Red muscles from both mackerels had higher levels in lipids with higher neutral lipid class compared with ordinary muscles. The major difference between chub and blue mackerels was the levels of lipids and neural lipid class, indicating that all muscles from chub mackerel showed higher levels of neural lipids compared with those of blue mackerel (P

Genetic mutations by gene fusion result from chromosomal rearrangement, trans-splicing, and intergenic splicing. Trans-splicing is a phenomenon in which two pre-mRNAs grow together into one. We analyzed the trans-splicing products in embryonic stem cells. By using bioinformatic tools, 70 trans-splicing transcripts were identified. They are classified into 6 types according to fusion pattern: 5'UTR-5'UTR, 5'UTR-3'UTR, 3'UTR-3'UTR, 5'UTR-CDS, 3'UTR-CDS, CDS-CDS. The fusion products are more abundant in CDS regions than in UTR regions, which contain multiple intron numbers. Chromosome analysis showing gene fusion via trans-splicing indicated that chromosomes 17 and 19 were activated. These data are of great use for further studies in relation to fusion genes and human diseases.

Malachite green (MG), a triphenylmethane dye, is carcinogenic, mutagenic, teratogenic, a respiratory toxin, and causes chromosomal fractures. It is not permitted for use as an aquaculture veterinary drug in a number of countries. Sensitive extraction methods for MG and leucomalachite green (LMG), which have long residence times in fish tissues, were developed. For LMG, the average recovery of liquid extraction (LE) ranged from 41.71 (yellowtail) to 71.60% (snakehead); the recovery of liquid-liquid extraction (LLE) was between 67.68 (yellowtail) and 83.68% (snakehead); and the average recovery of solid-phase extraction (SPE) ranged from 84.16 (yellowtail) to 92.92% (shrimp). The recovery of MG was less than 30% with SPE. However, the dye is found primarily as the colorless reduced leuco form in fish tissues.

Recent studies have reported that embryonic stem (ES) cell-associated gene expression signatures have been identified in poorly differentiated tumors, revealing a link between ES cell identity and cancer cells. Cancer cells originate from cancer stem cells (CSCs). Both types of cells share common properties such as self-renewal and heterogeneity. CSCs are also resistant to conventional chemotherapy and radiotherapy. Here, we show similar gene expression patterns between ES cells and ionizing radiation (IR)-treated cancer cells. Using genome-wide transcriptome analysis, we compared the gene expression profiles among ES cells, cancer cells, and irradiated cancer cells, and identified a subset of similar gene expression patterns between ES cells and irradiated cancer cells, indicated by hierarchical clustering. These gene expression patterns were then confirmed by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) analyses. Using bioinformatic analyses, these candidate genes are also associated with various biological pathways related to stemness in cancer. Taken together, our data suggest that identification of common molecular characteristics between ES cells and irradiated cancer cells is important to understand the properties of cancer stem cells and their resistance to radiotherapy.

Background Exposure to ionizing radiation (IR) results in the simultaneous activation or downregulation of multiple signaling pathways that play critical roles in cell type-specific control of survival or death. IR is a well-known genotoxic agent and human carcinogen that induces cellular damage through direct and indirect mechanisms. However, its impact on epigenetic mechanisms has not been elucidated, and more specifically, little information is available regarding genome-wide DNA methylation changes in cancer cells after IR exposure. Recently, genome-wide DNA methylation profiling technology using the Illumina HumanMethylation450K platform has emerged that allows us to query >450,000 loci within the genome. This improved technology is capable of identifying genome-wide DNA methylation changes in CpG islands and other CpG island-associated regions. Results In this study, we employed this technology to test the hypothesis that exposure to IR not only induces differential DNA methylation patterns at a genome-wide level, but also results in locus- and gene-specific DNA methylation changes. We screened for differential DNA methylation changes in colorectal cancer cells after IR exposure with 2 and 5 Gy. Twenty-nine genes showed radiation-induced hypomethylation in colon cancer cells, and of those, seven genes showed a corresponding increase in gene expression by reverse transcriptase polymerase chain reaction (RT-PCR). In addition, we performed chromatin immunoprecipitation (ChIP) to confirm that the DNA-methyltransferase 1 (DNMT1) level associated with the promoter regions of these genes correlated with their methylation level and gene expression changes. Finally, we used a gene ontology (GO) database to show that a handful of hypomethylated genes induced by IR are associated with a variety of biological pathways related to cancer. Conclusion We identified alterations in global DNA methylation patterns and hypomethylation at specific cancer-related genes following IR exposure, which suggests that radiation exposure plays a critical role in conferring epigenetic alterations in cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1229-6) contains supplementary material, which is available to authorized users.

Quaternary marine terrace deposits consisting of gravels interbedded with thin sandy gravel layers have been subjected to subaerial weathering. Restricted to the sandy gravel layers, allophane gel either replaced bytownite sands to form a pseudomorph or coated the pebbles. The allophane has an average Al/Si atomic ratio of 1.5 with 45% H2O. The sandy gravels were originally rich in bytownite (av. An86) sands derived from underlying Tertiary basaltic lapilli tuff. The highly soluble and aluminous bytownite favored the formation of allophane. In the sandy gravel layers, pebbles coated with allophane gel were almost fresh whereas those in the gravel layers were highly weathered to form halloysite-rich clays. Allophane gels acted as a somewhat impermeable geochemical barrier impeding a mineral-water reaction in the bytownite-rich sandy gravel layers and thus significantly retarding pebble weathering, while prolonged weathering in the gravel layers resulted in the severe decomposition of pebbles. Bytownite protected the pebbles against weathering, implying that minor soluble minerals might be one of the factors in the natural variation of the weathering rates of rocks and sediments.

Exposure of cells to ionizing radiation (IR) induces, not only, activation of multiple signaling pathways that play critical roles in cell fate determination, but also alteration of molecular pathways involved in cell death or survival. Recently, DNA methylation has been established as a critical epigenetic process involved in the regulation of gene expression in cancer cells, suggesting that DNA methylation inhibition may be an effective cancer treatment strategy. Because alterations of gene expression by DNA methylation have been considered to influence radioresponsiveness, we investigated the effect of a DNA methyltransferase inhibitor, 5-aza-2′-deoxycytidine (5-aza-dC), on radiosensitivity. In addition, we investigated the underlying cellular mechanisms of combination treatments of ionizing irradiation (IR) and 5-aza-dC in human colon cancer cells. Colon cancer cell lines were initially tested for radiation sensitivity by IR in vitro and were treated with two different doses of 5-aza-dC. Survival of these cell lines was measured using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and clonogenic assays. The effects of 5-aza-dC along with irradiation on cell growth, cell cycle distribution, apoptosis, and apoptosis-related gene expression were examined. Combination irradiation treatment with 5-aza-dC significantly decreased growth activity compared with irradiation treatment alone or with 5-aza-dC treatment alone. The percentage of HCT116 cells in the sub-G1 phase and their apoptotic rate was increased when cells were treated with irradiation in combination with 5-aza-dC compared with either treatment alone. These observations were strongly supported by increased caspase activity, increased comet tails using comet assays, and increased protein levels of apoptosis-associated molecules (caspase 3/9, cleaved PARP). Our data demonstrated that 5-aza-dC enhanced radiosensitivity in colon cancer cells, and the combination effects of 5-aza-dC with radiation showed greater cellular effects than that of single treatment, suggesting that the combination of 5-aza-dC and radiation has the potential to become a clinical strategy for the treatment of cancer.

Background DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known. Results We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density. Conclusions We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.

This study investigated to compare lipid profiles in ordinary and dark muscles from chub mackerel and to examine antiproliferative and antioxidative properties of lipid classes. The average levels of neutral lipids (NL), glycolipids (GL), and phospholipids (PL) in ordinary muscle were 92.32±0.19%, 5.10±0.48%, and 2.58±0.46%; in dark muscle were 96.88±0.15%, 2.59±0.36%, and 0.54±0.29%, respectively. The fatty acid composition indicated that PL had a higher percentage of PUFA (especially 22:6n-3) with lower percentages of SFA and MUFA compared to NL and GL (p0.05). The main ion peaks of GL in ordinary and dark muscles showed that monocharged and bischarged molecular ion were presented at m/z 876.9 and 438.8, respectively. In MTT assay, inhibition of AGS and HT-29 cell proliferation was greatest with the 0.5 and 1.0 mg mL(-1) GL treatments. The GL of ordinary muscle with 0.05 mg mL(-1) concentrations markedly decreased the levels of reactive oxygen species (ROS) induced by H2O2 compared to the control (p0.05). From our results, GL might have antiproliferative and antioxidant properties based on protective effect against the production of intracellular ROS.

The horse BMAL1 gene encodes the brain and muscle Arnt-like protein 1, which is a key regulator of circadian rhythmic systems in most organs and cells. The first exon of the horse-specific BMAL1 gene is produced by an exonization event of LINE3 (CR1) and SINE (MIR) was detected by bioinformatic analysis. Alternative variants generated by cassette exon event in various horse tissues were also detected by RT-PCR amplification and sequencing. The cDNA sequences of the horse transcripts (BMAL1a, BMAL1b) contain additional 21 bp and 71 bp fragments relative to horse BMAL1. Quantitative real-time RT-PCR was performed to compare the expression patterns between transcript variants in various horse tissues. The results of these experiments showed splice variants that were widely expressed in most tissues. Furthermore, they were highly expressed in cerebellum, heart, and kidney.

In the mitochondrial matrix, the OXCT1 gene catalyzes the reversible transfer of coenzyme A from succinyl-CoA to acetoacetate in a reaction related to energy production from ketone bodies. Here, horse OXCT1 gene containing coenzyme A transferase domain was identified in the transcriptome analysis of cDNAs derived from skeletal muscles. Horse OXCT1 gene consisted of 1761 [corrected] nucleotide sequences with an open reading frame of 1560 nucleotides encoding a protein of 520 putative amino acid residues.The number of non-synonymous substitutions was lower than the number of synonymous substitutions in the OXCT1 genes of other species, indicating that purifying selection occurred in the OXCT1 genes during evolutionary radiation. Quantitative real-time RT-RCR analysis showed a dominant expression pattern of horse OXCT1 gene in the cerebrum, heart, and skeletal muscle. Different expression levels of horse OXCT1 transcripts between before- and after-exercise samples were also measured in the skeletal muscles of six horses. These data could be of great use for further investigation of the relationship between energy products and horse OXCT1 gene.

We aimed to evaluate whether methotrexate (MTX) in vitro induces apoptosis in synoviocytes obtained from rheumatoid arthritis patients and whether the apoptosis inducing effect of MTX to synoviocytes is correlated with the clinical responsiveness to MTX in patients with rheumatoid arthritis (RA). We evaluated 18 patients with RA taking MTX 15–20 mg/week as the subject group (nine responders and nine non-responders) and ten patients with osteoarthritis (OA) and nine patients with ankylosing spondylitis (AS) as the control group. Synoviocytes, cultured from the synovial fluid of the knee joint of each subject, were used for experiments between passages 4 and 6, and were treated with MTX. The induction of apoptosis was determined by the quantification of DNA hypoploidy by flow cytometry, nuclear morphology, caspases activation, DNA electrophoresis, and mitochondrial membrane potential measurements. The viability of synoviocytes treated with MTX was different between the MTX responders and nonresponders. MTX induced apoptosis in cultured synoviocytes by mitochondria- and caspase-dependent manners in the MTX responders but did not in the MTX non-responder, OA, and AS patients. The apoptotic responsiveness of the synoviocytes to MTX predicts the sensitivity to MTX treatment and provides a method determine the early application of an anti-tumor necrosis factor-α agent in RA treatment.

Background Methotrexate (MTX) was the corner stone treatment of rheumatoid arhtirits. So for long time, MTX was used in rheumatoid arhtirits treatment with other Immunosuppressive drug. There were many hypothesis in mechanism of MTX on RA treatments, but accurate mechanism of MTX was not known Objectives To investigate the apoptotic mechanism of MTX in synoviocyte of rhuematoid arhtirits Methods Synovial cells were cultured from synovial fluid of Rhuematoid arhtirits (RA) patients and Osteoarhtirtis (OA) patients. In each group, the subculture was conducted for 5-6 passages and synovioctes was treated with 300μM 500μM MTX directly. In 400μM The cell viability was observed and apoptosis of synoviocyte was measured by flow cytometry Results MTX treated synovial cell death was higher RA than OA in 300μM 500μM MTX, In 400μM MTX, high Sub-G1 pick was observed and continued to 24 hours in RA synoviocytes Conclusions Apoptosis was the one of MTX mechasnism in RA treatment and RA synoviocytes apoptosis may be one of tool for RA treatment in the future References Determinants of Red Blood Cell Methotrexate Polyglutamate Concentrations in Rheumatoid Arthritis Patients Receiving Long-Term Methotrexate Treatment Lisa K. Stamp, John L. O’Donnell, Peter T. Chapman, Mei Zhang, Christopher Frampton, Jill James, Murray L. Barclay. Arthritis & Rheumatism Vol. 60, No. 8, August 2009, pp 2248–2256. Disclosure of Interest None Declared

Background NK cellare approximately 10–15% of circulating lymphocytes and 5% of lymphocytes in lymphoid tissue and a subset of NK cells has been detected in the synovial fluid (SF) from rheumatoid arthritis (RA) patients recently. The best characterised NK cell activating receptor is NKG2D, is expressed on all human NK cells and the ligands for NKG2D are not expressed on normal, healthy tissue, but are in induced under conditions of cellular stress such as inflammation and malignant transformation Objectives To investigated expression of NKG2D ligands in synovial cell of rhuematoid arhtirits Methods Synovial cell was cultured from SF of RA patients. The subculture was conducted for 5-6 passages and the PCR was done for detection of NKG2D ligands. To evaluated NKG2D ligands in inflammatory RA synoviocytes, TNF-α were treated Results Five NKG2D ligands (MICA, MICB, ULPB1, ULBP2, ULBP3) were expressed in both RA synoviocytes and inflammatory RA synoviocytes Conclusions RA synoviocytes had NKG2D ligands, so NKG2D receptors in NK cell were associated with pathogenesis of RA. The blocking of NKG2D ligands was the one of method in RA treatment References Emerging role for NK cells in the pathogenesis of inflammatory arthropathies, Paola Conigliaro, Rossana Scrivo, Guido Valesini, Roberto Perricone. Autoimmunity Reviews 10 (2011) 577–581 Disclosure of Interest None Declared

Muscle glycogen Phosphorylase (PYGM) has been shown to catalyze the degradation of glycogen to glucose-1-phosphate. The PYGM gene can contribute to providing energy to the body by disassembling the glycogen in muscle. Here, we analyzed the genomic structure and expression of the PYGM gene in the thoroughbred horse. The PYGM gene, containing several transposable elements (MIRs, LINEs, and MERs), was highly conserved in mammalian genomes. In order to understand the expression of the horse PYGM gene, we performed quantitative RT-PCR using 11 thoroughbred horse tissue samples. The horse PYGM gene was broadly expressed in all tissues tested. In particular, the highest expression of the horse PYGM gene was observed in skeletal muscle tissue relative to the other tissues. Interestingly, the horse PYGM gene contains fewer mobile elements than its human ortholog, resulting in an increase in the structural stability of the PYGM gene sequence. This study provides insights into the genomic structure of the horse PYGM gene that may be useful in future studies of its association with exercise capability.