Integrative methylome and transcriptome analysis of porcine abdominal fat indicates changes in fat metabolism and immune responses during different development.

Fat is involved in synthesizing fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. The samples were collected from the porcine abdominal fat of different developmental stages (10 and 26 weeks of age). Then, the samples were sequenced using MBD-seq and RNA-seq for profiling DNA methylation and RNA expression. In 26 weeks of age pigs, differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified as 2,251 and 5,768, compared with 10 weeks of age pigs, respectively. Gene functional analysis was performed using GO and KEGG databases. In functional analysis results of DMGs and DEGs, immune responses such as chemokine signaling pathways, B cell receptor signaling pathways, and lipid metabolism terms such as PPAR signaling pathways and fatty acid degradation were identified. It is thought that there is an influence between DNA methylation and gene expression through changes in genes with similar functions. The effects of DNA methylation on gene expression were investigated using cis-regulation and trans-regulation analysis to integrate and interpret different molecular layers. In the cis-regulation analysis using 629 overlapping genes between DEGs and DMGs, immune response functions were identified, while in trans-regulation analysis through the TF-target gene network, the co-expression network of lipid metabolism-related functions was distinguished. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.

Fat is involved in the synthesis of new fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. Modifications in DNA methylation and expression values were confirmed epigenetically with growth. Changed genes in each DNA and RNA showed identical trends in the function of immune response and lipid metabolism. The effects of DNA methylation on gene expression were investigated using cis-regulation (functional enrichment analysis of overlapping genes) and trans-regulation (transcription factor and target gene networking) analysis to integrate and interpret different molecular layers. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.

Estimation of Genetic Parameters by Single-Trait and Multi-Trait Models for Carcass Traits in Hanwoo Cattle.

Hanwoo breed is preferred in South Korea because of the high standards in marbling and the palatability of its meat. Numerous studies have been conducted and are ongoing to increase the meat production and quality in this beef population. The aim of this study was to estimate and compare genetic parameters for carcass traits using BLUPF90 software. Four models were constructed, single trait pedigree model (STPM), single-trait genomic model (STGM), multi-trait pedigree model (MTPM), and multi-trait genomic model (MTGM), using the pedigree, phenotype, and genomic information of 7991 Hanwoo cattle. Four carcass traits were evaluated: Back fat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Heritability estimates of 0.40 and 0.41 for BFT, 0.33 and 0.34 for CWT, 0.36 and 0.37 for EMA, and 0.35 and 0.38 for MS were obtained for the single-trait pedigree model and the multi-trait pedigree model, respectively, in Hanwoo. Further, the genomic model showed more improved results compared to the pedigree model, with heritability of 0.39 (CWT), 0.39 (EMA), and 0.46 (MS), except for 0.39 (BFT), which may be due to random events. Utilization of genomic information in the form of single nucleotide polymorphisms (SNPs) has allowed more capturing of the variance from the traits improving the variance components.

Reduced microRNA 375 in colorectal cancer upregulates metadherin-mediated signaling.

BACKGROUND: The human microRNA 375 (MIR375) is significantly downregulated in human colorectal cancer (CRC) and we have previously shown that MIR375 is a CRC-associated miRNA. The metadherin (MTDH) is a candidate target gene of MIR375. AIM: To investigate the interaction and function between MIR375 and MTDH in human CRC. METHODS: A luciferase reporter system was used to confirm the effect of MIR375 on MTDH expression. The expression levels of MIR375 and the target genes were evaluated by quantitative RT-PCR (qRT-PCR), western blotting, or immunohistochemistry. RESULTS: MTDH expression was found to be upregulated in human CRC tissues compared to that in healthy controls. We show that MIR375 regulates the expression of many genes involved in the MTDH-mediated signal transduction pathways [BRAF-MAPK and phosphatidylinositol-4,5-biphosphate-3-kinase catalytic subunit alpha (PIK3CA)-AKT] in CRC cells. Upregulated MTDH expression levels were found to inhibit NF-κB inhibitor alpha, which further upregulated NFKB1 and RELA expression in CRC cells. CONCLUSION: Our findings suggest that suppressing MIR375 expression in CRC regulates cell proliferation and angiogenesis by increasing MTDH expression. Thus, MIR375 may be of therapeutic value in treating human CRC.

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations.

The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and ß diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed Firmicutes to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, Bacteroidetes were present at 37.28% and 45.98% in L and LD, respectively. The genera Prevotella, Anaerovibrio, Succinivibrio, Megasphaera were differentially enriched in stage L, whereas Clostridium, Terrisporobacter, Rikenellaceae were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson's correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application.

Transcriptome analysis to identify long non coding RNA (lncRNA) and characterize their functional role in back fat tissue of pig.

Long non coding RNAs (lncRNA) have been previously found to be involved in important cellular activities like epigenetics, implantation, cell growth etc. in pigs. However, comprehensive analysis of lncRNA in back fat tissues at different developmental stages in pigs is still lacking. In this study we conducted transcriptome analysis in the back fat tissue of a F1 crossbred Korean Native Pig (KNP) × Yorkshire Pig to identify lncRNA. We investigated their role in 16 pigs at two different growth stages; stage 1 (10 weeks, n = 8) and stage 2 (26 weeks, n = 8). After quality assessment of sequencing reads, we got a total of 1,641,165 assembled transcripts out of eight paired end read from each stage. Among them, 6808 lncRNA transcripts were identified by filtering on the basis of multiple parameters like read length ≥ 200 nucleotides, exon numbers ≥2, FPKM ≥0.5, coding potential score < 0 etc. PFAM and RFAM were used to filter out all possible protein coding genes and housekeeping RNAs respectively. A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed (DE) between the two stages (|log2FC| > 2, q < 0.05). We also identified 306 genes located around 100 kb upstream and 234 genes downstream around these DE lncRNA transcripts. The expression of top eleven DE lncRNAs (COL4A6, LY7S, MYH2, OXCT1, SMPDL3A, TMEM182, TTC36, RFOOOO4, RFOOO15, RFOOO45, CADM2) had been validating by qRT-PCR. Pathway and GO terms analysis showed that, positive regulation of biosynthetic process, Wnt signaling pathway, cellular protein modification process, and positive regulation of nitrogen compound were differentially enriched. Our results suggested that, KEGG pathways such as protein digestion and absorption, Arrhythmogenic right ventricular cardiomyopathy (ARVC) to be significantly enriched in both DE lncRNAs as well as DE mRNAs and involved in back fat tissues development. It also suggests that, identified lncRNAs are involved in regulation of important adipose tissues development pathways.

MicroRNA 375 regulates proliferation and migration of colon cancer cells by suppressing the CTGF-EGFR signaling pathway.

MicroRNA 375 (MIR375) is significantly down regulated in human colorectal cancer (CRC) tissues; we have previously identified MIR375 as a colon cancer associated microRNA (miRNA). We identified putative MIR375 target genes by comparing the mRNA microarray analysis data of MIR375-overexpressing cells with the candidate MIR375 target genes predicted by public bioinformatic tools. We investigated that the connective tissue growth factor (CTGF) is a direct target gene of MIR375. Expression of CTGF, a ligand of epidermal growth factor receptor (EGFR), was markedly enhanced in human CRC tissues in comparison with the corresponding normal colon tissues. We demonstrated that the expression levels of molecules in EGFR signaling pathways were regulated by MIR375 in colorectal cells. Using immunohistochemistry and the xenograft of MIR375-overexpressing colorectal cells in mice, we showed that MIR375 regulates cell growth and proliferation, angiogenesis, cell migration, cell cycle arrest, apoptosis, and necrosis in colon cells. Furthermore, results of MIR375 overexpression and cetuximab treatment indicated that the apoptosis and necrosis in colon cells were synergistically enhanced. Our results suggest that the down-regulation of MIR375 modulates EGFR signaling pathways in human colorectal cells and tissues by increasing CTGF expression; therefore, MIR375 may have a therapeutic value in relation to human CRC.

Anti-melanogenic effects of resveratryl triglycolate, a novel hybrid compound derived by esterification of resveratrol with glycolic acid.

Resveratrol is known to inhibit cellular melanin synthesis by multiple mechanisms. Glycolic acid (GA) is used in skin care products for its excellent skin penetration. The purpose of this study was to examine the anti-melanogenic effects of resveratryl triglycolate (RTG), a novel hybrid compound of resveratrol and GA, in comparison with resveratrol, GA, resveratryl triacetate (RTA) and arbutin. Resveratrol, RTG, and RTA inhibited the catalytic activity human tyrosinase (TYR) more potently than arbutin or GA did. Their cytotoxic and anti-melanogenic effects were examined using murine melanoma B16/F10 cells and human epidermal melanocytes (HEMs). The cytotoxicity of RTG was similar to that of resveratrol and RTA. RTG at 3-10 µM decreased melanin levels and cellular TYR activities in α-melanocyte-stimulating hormone-stimulated B16/F10 cells, and L-tyrosine-stimulated HEMs. RTG also suppressed mRNA and protein expression of TYR, tyrosinase-related protein 1, L-3,4-dihydroxyphenylalanine chrome tautomerase, and microphthalmia-associated transcription factor (MITF) in HEMs stimulated with L-tyrosine. This study suggests that, like resveratrol and RTA, RTG can attenuate cellular melanin synthesis effectively through the suppression of MITF-dependent expression of melanogenic enzymes and the inhibition of catalytic activity of TYR enzyme. RTG therefore has potential for use as a cosmeceutical ingredient for skin whitening.

Clinical Implications of Methylenetetrahydrofolate Reductase Mutations and Plasma Homocysteine Levels in Patients with Thromboembolic Occlusion.

PURPOSE: Hyperhomocysteinemia has been identified as an independent risk factor in arterial and venous thrombosis. Mutations in genes encoding methylenetetrahydrofolate reductase (MTHFR), involved in the metabolism of homocysteine, may account for reduced enzyme activity and elevated plasma homocysteine levels. In this study, we investigated the interrelation of MTHFR C677T genotype and level of homocysteine in patients with arterial and venous thrombosis. MATERIALS AND METHODS: We retrospectively reviewed the medical records of 146 patients who were diagnosed as having arterial and venous thrombosis. We excluded patients diagnosed with atrial fibrillation. We examined routinely the plasma concentration of total homocysteine level and MTHFR C677T polymorphism for evaluation of thrombotic tendency in all patients. Screening processes of MTHFR C677T polymorphism were performed by real-time polymerase chain reaction. RESULTS: Investigated groups consisted of thrombotic arterial occlusion in 48 patients and venous occlusion in 63 patients. The distribution of the three genotypes was as follows: homozygous normal (CC) genotype in 29 (26.1%), heterozygous (CT) genotype in 57 (51.4%), and homozygous mutant (TT) genotype in 25 (22.5%) patients. There were no significant differences among individuals between each genotype group for baseline characteristics. Plasma concentration of homocysteine in patients with the TT genotype was significantly increased compared to the CC genotype (P<0.05). CONCLUSION: We observed a significant interaction between TT genotypes and homocysteine levels in our results. The results might reflect the complex interaction between candidate genes and external factors responsible for thrombosis.

Protective effects of the ethanolic extract of Melia toosendan fruit against colon cancer.

Colorectal cancer is one of the leading causes of death in the world. Plant-derived products have proven to be valuable sources for discovery and development of unique anticancer drugs. In this study, the inhibitory effects of ethanolic extract of Melia toosendan fruit (EMTF), a traditional medicine in the Chinese Pharmacopeia were evaluated in vitro and in vivo against colon cancer. Human colon cancer cells SW480 and murine colorectal adenocarcinoma cells CT26 were used to investigate cell proliferation. The results showed that EMTF inhibited cell proliferation of SW480 and CT26 by promoting apoptosis as indicated by nuclear chromatin condensation and DNA fragmentation. Through increasing mitochondrial membrane permeability and cytochrome c release from mitochondria, EMTF induced caspase-9 activity which further activated caspase-3 and poly(ADP-ribose) polymerase cleavage, leading the tumor cells to apoptosis. The in vivo results confirmed reduction of tumor volume and apoptotic effects and the side effects were not induced by EMTF. Therefore, EMTF may be an effective chemotherapeutic agent for colon cancer treatment.

The haplotypes of TNFRSF17 polymorphisms are associated with colon cancer in a Korean population.

PURPOSE: We previously found that the haplotypes of TNFRSF17 single nucleotide polymorphisms (SNPs) were associated with the susceptibility to inflammatory bowel disease on Korean population. The present study aimed to investigate whether the polymorphisms in the TNFRSF17 gene are associated with susceptibility to colorectal cancer (CRC). METHODS: Genotype analysis in the TNFRSF17 SNPs was performed by high-resolution melting and TaqMan probe analysis, and the genotype and allele frequencies of TNFRSF17 SNPs were compared between the CRC patients and the healthy controls. The haplotype frequencies of TNFRSF17 for multiple loci were estimated using the expectation maximization algorithm. RESULTS: Although, the genotype and allelic frequencies of these SNPs, in the colon cancer and rectal cancer patients, were not significantly different from those in the healthy controls, the genotype and allele frequency of g.2493G>A was significantly different between the healthy controls and the right colon cancer patients (P = 0.014 and 0.004, respectively). Moreover, the haplotypes frequencies in the healthy controls were significantly different from those in the colon cancer patients. CONCLUSION: Our results suggest that TNFRSF17 may be a candidate gene associated with the pathogenesis of colon cancer, and the haplotypes of the TNFRSF17 polymorphisms might be one of the markers for colon cancer susceptibility.

Asiatic acid induces colon cancer cell growth inhibition and apoptosis through mitochondrial death cascade.

Cancer is one of the leading causes of death in the world. The triterpenoid compound asiatic acid derived from the tropical medicinal plant Centella asiatica displays cytotoxic activity on fibroblast cells and several other kinds of cells. The present work studies asiatic acid-mediated growth inhibition of cancer cells and the underlying mechanism. Asiatic acid markedly inhibited cancer cell proliferation. Apoptosis of SW480 human colon cancer cells was induced by asiatic acid as shown by flow cytometry, DNA fragmentation and nuclear chromatin condensation experiments. Through increasing mitochondrial membrane permeability and cytochrome c release from mitochondria into cytosol, asiatic acid induced caspase-9 activity, which further activated caspase-3 and poly(ADP-ribose) polymerase cleavage resulting in irreversible apoptotic death in the tumor cells. Taken together, these results suggest that mitochondrial death apoptosis cascade plays very important roles in asiatic acid-induced cancer apoptosis.

Anti-toxoplasmosis effects of oleuropein isolated from Fraxinus rhychophylla.

Toxoplasmosis is a parasitic disease caused by Toxoplasma gondii, with very few therapeutic treatment options. Typically, the choices for treatment are pyrimethamine and sulfadiazine, however their utility is limited because of drug toxicity and serious side effects. For these reasons, new drugs with lower toxicity are urgently needed. In this study, the compound oleuropein isolated from Fraxinus rhynchophylla showed anti-T. gondii effects in vitro and in vivo. In Madin-Darby bovine kidney cells, the selectivity of oleuropein was 8.9, which was higher than sulfadiazine and pyrimethamine (3.8 and 2.5, respectively). In infected mice, the inhibition ratio of T. gondii in the peritoneal cavity was 55.4% compared to the negative control group after treatment with 300 mg/kg oleuropein. In addition, inhibitory effects on granuloma, apoptosis, necrosis and cyst-formation were shown in sections of spleen and liver. Oleuropein is therefore a potentially useful anti-T. gondii candidate for clinical application.