Proliferator-activated Receptor Signaling Pathway Research Articles

To Explore the Mechanism of Hawthorn in the Intervention of Hyperlipidemia Based on the Gene Expression Omnibus and Network Pharmacology

A common clinical treatment for hyperlipidemia in China is hawthorn, a traditional Chinese herb. However, few researches have been done on its active ingredients and their possible mechanisms for treating hyperlipidemia. The active chemical constituents of hawthorn were obtained from the encyclopedia of traditional Chinese medicine, the bioavailability and druglikeness properties of each active ingredient of hawthorn were analyzed using SwissADME and their possible targets of action were predicted using SwissTargetPrediction and PharmMapper. Then, we used the Gene Expression Omnibus-related gene microarray data to mine the differentially expressed genes for hyperlipidemia. Meanwhile, we collected relevant targets of hyperlipidemia through the DrugBank, Online Mendelian Inheritance in Man, GeneCards, DisGeNET and Therapeutic Target Database. Based on this data, a component-target-disease pathway and a protein-protein interaction networks were constructed using search tool for the retrieval of interacting genes/proteins. Finally, Metascape was systematically used to analyze the targets of hawthorn intervention in hyperlipidemia. A total of 8 active components and 312 hawthorn targets were gathered and 343 prospective targets associated with hyperlipidemia were predicted, 25 of which shared targets with hawthorn-related targets. Gene ontology enrichment analysis revealed that the mechanism of action of hawthorn in intervention of hyperlipidemia lies in the regulation of lipid metabolism, nutrition level, hormone level and cholesterol transport process. The Kyoto encyclopedia of genes and genomes enrichment analysis revealed that the peroxisome proliferator activated receptor signaling pathway contained the majority of the core targets. Molecular docking verified that hawthorn could bind closely to the core targets. According to the findings of network pharmacology and enrichment analysis, we predicted that the main active components of hawthorn to intervene in hyperlipidemia are epicatechin, officinalic acid and quercetin, which mainly intervene in hyperlipidemia through the peroxisome proliferator activated receptor signaling pathway.

Abstract 3360: Identification of the pathway of BIA-ALCL by analyzing the difference in immune response according to the texture of the breast implant

Abstract Breast implant-associated ALCL (BIA-ALCL) is an extremely rare type of T-cell lymphoma. According to the American Society of Plastic Surgeons (ASPS), it was first reported in 1997 and 993 cases were reported worldwide by January 2021. Scar capsule is formed around the breast implant, and effusion exists surrounding the implant. BIA-ALCL arises either from the peri-implant capsule or seroma. We tried to understand the pathogenesis of BIA-ALCL by validating the difference in immune response according to implant texture with next generation sequencing (NGS) analysis and identifying the relevant genetic variables. Peri-implant capsule tissues were collected during the implant removal surgery and used for RNA-Seq. Breast implants were inserted for either breast reconstruction or aesthetic purposes. Implant types were grouped following the surface texturing; macrotextured, microtexturedm and smooth. Three macrotextured, four microtextured, and three smooth type samples were used in this study. After aligning the data to the GRCh38 genomic reference with a STAR aligner, the expression level was quantified using RSEM. Differentially expressed gene analysis was performed between groups using DESeq2 based on the obtained TPM values. Gene set enrichment analysis (GSEA) and enrichR were performed to obtain enriched pathways. In addition, the proportion of the cell type of the dataset was calculated using CIBERSORTx.DEG analysis identified a total of 185 up-regulated genes and 81 down-regulated genes between groups (Fold change > 2, fold change < 0.5, Q-value <= 0.05). As a result of pathway enrichment analysis using enrichR for up-regulated genes, the peroxisome proliferator-activated receptors (PPARs) signaling pathway was significantly enriched in microtextured type and smooth type compared to macrotextured type. There are three subtypes of PPAR, of which PPARγ inhibits the JAK-STAT pathway and is known to increase the suppressor of cytokine signaling. In this regard, it is expected that the macrotextured implant group, in which the PPAR signaling pathway is not enriched compared to other groups, may have affected the function of T helper cells due to dysregulation of the JAK-STAT pathway. It has been demonstrated at the whole exome level that mutations in JAK1 and STAT3 are associated with the pathogenesis of BIA-ALCL. As a result of CIBERSORTx analysis, the ratio of fibroblast in the Smooth type was small and the T cell distribution was relatively high. Identifying the various factors involved in these PPARγ related pathways and the correlation between them will lead to the development of the prognosis of breast reconstruction and the diagnosis and treatment of BIA-ALCL. Citation Format: Sanyeowool An, Jeong Hyun Ha, Youngil Koh, Ung Sik Jin, Sung-Soo Yoon. Identification of the pathway of BIA-ALCL by analyzing the difference in immune response according to the texture of the breast implant [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3360.

Network pharmacology-based study to identify the significant pathways of Lentinula edodes against cancer.

Lentinula edodes (LE) is known as a good food source with potent anticancer efficacy, but its active chemical compounds and pathways against cancer have not been revealed. This study was to uncover the active chemical constituents and pathways of LE against cancer through network pharmacology. The chemical compositions were recognized by gas chromatography-mass spectrometry (GC-MS) and filtered drug-like compounds (DLCs) by SwissADME. Targets related to filtered compounds were recognized by two public databases and the final overlapping targets were identified by Venn diagram. Then, protein-protein interaction (PPI) and pathway-target-compound (PTC) networks were built by RStudio. Ultimately, we recognized the key compounds and targets via molecular docking test (MDT). A total of 33 compounds from LE were accepted by Lipinski's rule were selected as DLCs. The 33 compounds were associated with 108 targets and a key target (cyclooxygenase2 [COX2]) was identified through PPI networks. Most significantly, inactivation of pathways in cancer and activation of peroxisome proliferator activated receptor signaling pathway were significant pathways of LE. On MDT, we identified a key compound (Indole, 2-methyl-3-phenyl) on COX2 related to inactivation of athways in cancer, additionally, the number of 6 ergostane steroids was associated with the two pathways might be dual efficacy to alleviate inflammation against cancer. Overall, 13 targets, 11 compounds, and 2 key pathways of LE were identified as the significant elements to treat cancer. Hence, this study shows therapeutic evidence to verify the promising clinical effect of LE on cancer, suggesting that LE might be an important mushroom against cancer. PRACTICAL APPLICATIONS: Lentinula edodes (LE) has been used widely in cuisine as well as alternative medicines, especially, for anticancer. The LE has rich nutritional compounds including proteins, vitamins, polyphenols, and glucans, however, most of which have a critical hurdle as poor bioavailability not to be applicable for pharmaceuticals. Its main cause is very hydrophilic property. Thus, we adopted GC-MS analysis to identify lipophilic compounds to enhance cell permeability involved in bioavailability. The compounds selected from LE were confirmed by Lipinski's rule for drug-like-compounds (DLCs). Then, we retrieved targets associated with DLCs, and multiple pathways, multiple targets, and multiple compounds against cancer on network-based analysis. In summary, our study reveals the medicinal value of LE on cancer based on the multicomponents. Overall, the aim of this work is to represent the pharmacological evidence to reveal the therapeutic efficacy of AC on cancer, suggesting that DLCs from AC might be alleviators to dampen cancer.

Transcriptome and iTRAQ-Based Proteome Reveal the Molecular Mechanism of Intestinal Injury Induced by Weaning Ewe's Milk in Lambs.

Early feeding regime has a substantial lifelong effect on lambs and weaning ewe's milk can lead to the intestinal injury of lambs. To explore the molecular regulatory mechanism of intestinal injury of lambs under weaning stress, the jejunum was conducted transcriptome and then integrated analyzed with our previous proteome data. A total of 255 upregulated genes and 285 downregulated genes were significantly identified. These genes showed low overlapping with differentially expressed proteins identified by isobaric tags for relative and absolute quantification (iTRAQ). However, according to their functions, the differentially expressed genes (DEGs) and proteins with the same expression trend were enriched for the similar Gene Ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as intestinal lipid absorption, urea cycle, peroxisome proliferator-activated receptor (PPAR) signaling pathway, and ferroptosis. Furthermore, the DEGs, including FABP2, ACSL3, APOA2, APOC3, and PCK1, might play essential roles in intestinal lipid absorption and immune response through the PPAR signaling pathway and ferroptosis. This study could provide new insights into early lamb breeding at the molecular level.

Transcriptomic profiling of pemphigus lesion infiltrating mononuclear cells reveals a distinct local immune microenvironment and novel lncRNA regulators

Pemphigus is an autoimmune skin disease. Ectopic lymphoid-like structures (ELSs) were found to be commonly present in the pemphigus lesions, presumably supporting in situ desmoglein (Dsg)-specific antibody production. Yet functional phenotypes and the regulators of Lymphoid aggregates in pemphigus lesions remain largely unknown. Herein, we used microarray technology to profile the gene expression in skin lesion infiltrating mononuclear cells (SIMC) from pemphigus patients. On top of that, we compared SIMC dataset to peripheral blood mononuclear cells (PBMC) dataset to characterize the unique role of SIMC. Functional enrichment results showed that mononuclear cells in skin lesions and peripheral blood both had over-represented IL-17 signaling pathways while neither was characterized by an activation of type I Interferon signaling pathways. Cell-type identification with relative subsets of known RNA transcripts (CIBERSORT) results showed that naïve natural killer cells (NK cells) were significantly more abundant in pemphigus lesions, and their relative abundance positively correlated with B cells abundance. Meanwhile, plasma cells population highly correlated with type 1 macrophages (M1) abundance. In addition, we also identified a lncRNA LINC01588 which might epigenetically regulate T helper 17 cells (Th17)/regulatory T cells (Treg) balance via the peroxisome proliferator-activated receptor (PPAR) signaling pathway. Here, we provide the first transcriptomic characterization of lesion infiltrating immune cells which illustrates a distinct interplay network between adaptive and innate immune cells. It helps discover new regulators of local immune response, which potentially will provide a novel path forward to further uncover pemphigus pathological mechanisms and develop targeted therapy.

Mechanism of Triclosan in the Treatment of Nonalcoholic Fatty Liver Disease Based on Network Pharmacology

Objective To explore the potential targets of triclosan in the treatment of nonalcoholic fatty liver disease(NAFLD) and to provide new clues for the future research on the application of triclosan. Methods The targets of triclosan and NAFLD were obtained via network pharmacology.The protein-protein interaction network was constructed with the common targets shared by triclosan and NAFLD.The affinity of triclosan to targets was verified through molecular docking.Gene ontology(GO) annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment were carried out to analyze the key targets and the potential mechanism of action.NAFLD model was established by feeding male C57BL/6J mice with high-fat diet for 12 weeks.The mice were randomly assigned into a model group and a triclosan group [400 mg/(kg·d),gavage once a day for 8 weeks].The hematoxylin-eosin(HE) staining was used for observation of the pathological changes and oil red O staining for observation of fat deposition in mouse liver.Western blotting was employed to detect the protein level of peroxisome proliferator-activated receptor alpha(PPARα) in the liver tissue. Results Triclosan and NAFLD had 34 common targets,19 of which may be the potential targets for the treatment,including albumin(ALB),PPARα,mitogen-activated protein kinase 8(MAPK8),and fatty acid synthase.Molecular docking predicted that ALB,PPARα,and MAPK8 had good binding ability to triclosan.KEGG pathway enrichment showcased that the targets were mainly enriched in peroxisome proliferator-activated receptor signaling pathway,in which ALB and MAPK8 were not involved.Triclosan alleviated the balloon-like change and lipid droplet vacuole,decreased the lipid droplet area,and up-regulated the expression level of PPARα in mouse liver tissue. Conclusion PPARα is a key target of triclosan in the treatment of NAFLD,which may be involved in fatty acid oxidation through the peroxisome proliferator activated receptor signaling pathway.

Potential Mechanism of Maslinic Acid against Hypolipidemia Based on Network Pharmacology and Molecular Docking Integration Strategy

Maslinic acid is a pentacyclic triterpenoid acid. Recent research has shown that it has various biological activities such as anti-tumor, hypoglycaemic and hypolipidemic. Among them, the hypolipidemic effect is prominent and this study aims to further explore its mechanism of action in the treatment of hyperlipidemia. The chemical structure of maslinic acid was obtained from PubChem. Based on its chemical structure, the bioavailability and drug-like properties of maslinic acid were analyzed using Swiss absorption, distribution, metabolism and excretion and its potential targets were obtained from SwissTargetPrediction and PharmMapper. Then, the differentially expressed genes between hyperlipidemia patients and the health group were analyzed through the gene expression omnibus data set, and the related targets of hyperlipidemia were complemented using DrugBank, online Mendelian inheritance in man, GeneCards, DisGeNET and therapeutic target databases. Then, the protein-protein interaction network was constructed, the CytoNCA plugin and VarElect were used to screen core targets and metascape was used to systematically analyze the core targets and explore the mechanism. Finally, molecular docking showcased the interaction model. A total of 288 maslinic acid targets and 289 hyperlipidemia-related targets were collected and 18 potential therapeutic targets were found. The enrichment analysis results further systematically explained the effect of maslinic acid on hyperlipidemia. Maslinic acid can treat hyperlipidemia through complex interactions in which the regulation of core genes including albumin, peroxisome proliferator activated receptor alpha and apolipoprotein, and the regulation of peroxisome proliferator activated receptor signaling pathway play a major role.

Exploring the Mechanism of Periplogenin in the treatment of Lung Cancer Based on Network Pharmacology and Molecular Biology

Lung cancer (the 5-year survival rate is only about 16%) has a low survival rate, and more-effective drugs are urgently needed. Our team discovered that cortex Periplocae Radicis has obvious toxic effects on various cancer cells, including lung cancer cells. However, the mechanism is not clear. Therefore, we used the PubChem database to obtain periplogenin as the target of therapeutic drugs and the TCGA database to obtain differential genes of lung cancer. The results showed that MMP9, PPARG, BMP2, and TGFB2 were the core proteins of periplogenin acting on lung adenocarcinoma (LUAD), and MMP9, angiotensin-converting enzyme (ACE), BMP2, PPARG, MMP13, MMP3, and TGFB2 were the core proteins of periplogenin acting on lung squamous cell carcinoma (LUCS). Through gene ontology (GO) enrichment analysis, it was found that periplogenin mainly acted on LUAD via fatty acid binding, metallopeptidase activity, and monocarboxylic acid binding, and mainly acted on lung squamous carcinoma (LUSC) via endopeptidase activity, metallopeptidase activity, and serine-type peptidase activity. Kyoto Encyclopedia of Genes, and Genomes (KEGG) analysis revealed that the IL-17 signaling pathway, fluid shear stress, atherosclerosis, hepatocellular carcinoma, and so on, were the main signaling pathways of periplogenin acting on LUSC, whereas glycolysis/gluconeogenesis, and the peroxisome proliferator-activated receptor (PPAR) signaling pathway were major signaling pathways of periplogenin acting on LUAD. This shows that treatment of lung cancer can be achieved through multi-targeted, and multi-channel periplogenin activity.

Proteomics reveals urine apolipoprotein A-I as a potential biomarker of acute kidney injury following percutaneous coronary intervention in elderly patients.

The aim of the present study was to investigate how changes in the lipid composition are involved in early stages of acute kidney injury (AKI) following percutaneous coronary intervention (PCI-AKI) in elderly patients. A prospective nested case-control study was performed. Alterations in the urine protein accumulation were investigated in patients with and without PCI-AKI using isobaric tags for relative and absolute quantitation (iTRAQ). In addition, differentially expressed proteins (DEPs) related to lipids were confirmed using parallel reaction monitoring (PRM)-based targeted proteomics. From the cohort of elderly patients (>60 years of age), 14 (12.28%) developed AKI within 48 h after PCI. No significant differences were detected between the AKI and control (CON) groups for serum creatinine at 24 h following treatment (P=0.27). Among the DEPs that overlapped in both the AKI-24 h/AKI-Pre (AKI group at 24 h post-PCI vs. pre-PCI) and AKI-24 h/CON-24 h groups (AKI group vs. CON group at 24 h post-PCI), only apolipoprotein A-I (apoA-I) was related to lipids, which displayed a significant upregulation in expression levels. The protein expression levels of apoA-I displayed a 5.98-fold increase at 24 h after PCI from the baseline and a 2.09-fold increase compared with the control group as determined using PRM, which exhibited a similar trend to the iTRAQ results. Using protein-protein interaction analyses, apoA-I was determined to be functionally linked to the complement and coagulation cascades, the renin-angiotensin system and the hypoxia-inducible factor-1 signaling pathway. Using the pathway analysis tool from the Kyoto Encyclopedia of Genes and Genomes, several pathways were identified to be associated with apoA-I, including fat digestion and absorption, vitamin digestion and absorption, as well as the peroxisome proliferator activated receptor signaling pathway. In conclusion, apoA-I may be a promising biomarker for the early diagnosis of PCI-AKI in elderly patients. The role of apoA-I in the pathobiology of PCI-AKI requires further exploration.

Deep Insight Into Long Non-coding RNA and mRNA Transcriptome Profiling in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3.

Swine hepatitis E (swine HE) is a new type of zoonotic infectious disease caused by the swine hepatitis E virus (swine HEV). Open reading frame 3 (ORF3) is an important virulent protein of swine HEV, but its function still is mainly unclear. In this study, we generated adenoviruses ADV4-ORF3 and ADV4 negative control (ADV4-NC), which successfully mediated overexpression of enhanced green fluorescent protein (EGFP)-ORF3 and EGFP, respectively, in HepG2 cells. High-throughput sequencing was used to screen for differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs). The cis-target genes of lncRNAs were predicted, functional enrichment (Gene Ontology [GO] and Kyoto Encyclopedia of Genes and Genomes [KEGG]) was performed, and 12 lncRNAs with statistically significant different expressions (p ≤ 0.05 and q ≤ 1) were selected for further quantitative real-time reverse transcription (qRT-PCR) validation. In HepG2 cells, we identified 62 significantly differentially expressed genes (DEGs) (6,564 transcripts) and 319 lncRNAs (124 known lncRNAs and 195 novel lncRNAs) that were affected by ORF3, which were involved in systemic lupus erythematosus, Staphylococcus aureus infection, signaling pathways pluripotency regulation of stem cells, the peroxisome proliferator-activated receptor (PPAR) signaling pathway, and platinum drug resistance pathways. Cis-target gene prediction identified 45 lncRNAs corresponding to candidate mRNAs, among which eight were validated by qRT-PCR: LINC02476 (two transcripts), RAP2C-AS1, AC016526, AL139099, and ZNF337-AS1 (3 transcripts). Our results revealed that the lncRNA profile in host cells affected by ORF3, swine HEV ORF3, might affect the pentose and glucuronate interconversions and mediate the formation of obstructive jaundice by influencing bile secretion, which will help to determine the function of ORF3 and the infection mechanism and treatment of swine HE.

Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs.

Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs' expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.

Identification of common signatures in idiopathic pulmonary fibrosis and lung cancer using gene expression modeling

BackgroundIdiopathic pulmonary fibrosis (IPF) is associated with an increased risk for lung cancer, but the underlying mechanisms driving malignant transformation remain largely unknown. This study aimed to identify differentially expressed genes (DEGs) distinguishing IPF and lung cancer from healthy individuals and common genes driving the transformation from healthy to IPF and lung cancer.MethodsThe gene expression data for IPF and non-small cell lung cancer (NSCLC) were retrieved from the Gene Expression Omnibus (GEO) database. The DEG signatures were identified via unsupervised two-way clustering (TWC) analysis, supervised support vector machine analysis, dimensional reduction, and mutual exclusivity analysis. Gene enrichment and pathway analyses were performed to identify common signaling pathways. The most significant signature genes in common among IPF and lung cancer were further verified by immunohistochemistry.ResultsThe gene expression data from GSE24206 and GSE18842 were merged into a super array dataset comprising 86 patients with lung disorders (17 IPF and 46 NSCLC) and 51 healthy controls and measuring 23,494 unique genes. Seventy-nine signature DEGs were found among IPF and NSCLC. The peroxisome proliferator-activated receptor (PPAR) signaling pathway was the most enriched pathway associated with lung disorders, and matrix metalloproteinase-1 (MMP-1) in this pathway was mutually exclusive with several genes in IPF and NSCLC. Subsequent immunohistochemical analysis verified enhanced MMP1 expression in NSCLC associated with IPF.ConclusionsFor the first time, we defined common signature genes for IPF and NSCLC. The mutually exclusive sets of genes were potential drivers for IPF and NSCLC.

Genome-Wide Regulation of Electroacupuncture and Treadmill Exercise on Diet-Induced Obese Rats.

Acupuncture has been widely used for obesity treatment, but its mechanism is still unclear. To investigate the molecular mechanisms, we applied electroacupuncture (EA) at the Zusanli (ST36) acupoint and treadmill exercise (TE) in a diet-induced obese (DIO) rat model and used RNA sequencing (RNA-seq) to identify molecular consequences. Forty Sprague-Dawley male rats were selected and randomly divided into five groups: control (C), DIO model (M), EA, TE, and EA + TE groups. According to the results, acupuncture reduced body weight and the ratio of retroperitoneal white adipose tissue (retro-WAT) to body weight. Total RNA was extracted from the retro-WAT from five groups for RNA-seq. Differentially expressed genes (DEG) analysis showed that there were obvious differences among the four comparisons of C vs. M, M vs. EA, M vs. TE, and M vs. EA + TE, followed by 1383, 913, 3324, and 2794 DE genes. Gene ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed to further classify the DEGs. Several GO terms were commonly significantly enriched in both M vs. TE and M vs. EA, such as myofibril and muscle contraction. In addition, some pathways were regulated by EA and TE, such as the peroxisome proliferator activated receptor signaling pathway and calcium signaling pathway. This study is the first to compare and analyze the differences in gene expression profiles in the retro-WAT of rats in different groups, which provide a clue for further investigation into the molecular mechanisms of obesity treatment by EA and TE.

P0011THE ROLE OF AQUAPORIN-11 (AQP11) IN THE THYMUS DEVELOPMENT

Abstract Background and Aims Some aquaporins transport not only water but also small non-ionic molecules such as glycerol. In fact, aquaporin-9 (AQP9) has been shown to transport glycerol which is critical to support memory T cell survival through metabolic fitness (Cui G et al. Cell. 161:750, 2015). As AQP11 is widely expressed and transport glycerol as well as water, AQP11 may also play a role in immunological system, which will expand the repertoire of the aquaporin research field. Method The AQP11 expression in the thymus was examined by RT-PCR, Western blot and immunohistochemistry in mice. Phenotypic analysis and microarray analysis of the thymus were conducted in wild and AQP11 null mice at 21 day old before the development of uremia due to polycystic kidneys. Results Both mRNA and protein expressions of AQP11 in the thymus were higher than those of the kidney by RT-PCR and Western blot. Interestingly, the size of the thymus from AQP11 null mice was smaller than that of the wild mice: 28mg vs. 56mg, even after the correction by the body weight: 0.59 % vs. 0.82 %, as the body size of AQP11 null mice was smaller. The vacuolated medullary epithelial cells were observed in the thymus of AQP11 null mice with narrowed cortex. The immunohistochemical analysis revealed the AQP11 expression at the stromal-epithelial cells in the thymus. The microarray analysis of the gene expression in the thymus was compared between the wild and AQP11 null thymus by the annotation analysis based on the David Bioinformatics Resources 6.8 (beta). The up-regulated 66 genes more than 1.5 folds in AQP11 null thymus are mainly related to the PI3K/Akt signaling pathway to promote metabolism, proliferation, cell survival, growth and angiogenesis. On the other hand, the down-regulated 55 genes less than half in AQP11 null thymus are related to energy production and the peroxisome proliferator-activated receptor (PPAR) signaling pathway. Further RT-qPCR analysis confirmed the enhanced expression of Egfr (Epidermal Growth Factor Receptor), Itgb4 (Integrin beta-4) and Il2ra (interleukin 2 receptor alpha) and the diminished expression of aquaglyceroporin AQP7, Pck1 (Phosphoenolpyruvate carboxy-kinase 1) and Ucp1 (Mitochondrial uncoupling protein 1). The up-regulated genes for growth signaling was unexpected with the smaller thymus but may support the survival of the hypoplastic thymus as a compensation. On the other hand, the down-regulated genes may compromise fat-glucose-energy metabolism in the thymus leading to the smaller thymus, which may be aggravated by the decreased expression of AQP7, another glycerol channel. Conclusion AQP11 may play an important role in the metabolic control of the developing thymus possibly through its glycerol transport. The smaller thymus with narrower cortex in AQP11 null mice may lead to immunological dysfunction, which is currently under study.

Long non-coding RNA expression profiling of macrophage line RAW264.7 infected by Mycobacterium tuberculosis

ABSTRACT Long non-coding RNAs (lncRNAs) have been implicated in regulation of biological processes. The role of lncRNAs in macrophages in response to Mycobacterium tuberculosis infection has not been explored. We used high throughput lncRNA microarray analysis to detect differentially expressed lncRNAs and mRNAs in RAW264.7 macrophages with or without M. tuberculosis infection. Quantitative real-time PCR (qRT-PCR) was used to verify the microarray results. Bioinformatics analysis (GO and KEGG) were used to explore the function of significantly dysregulated genes. Microarray results indicated that 1,487 lncRNAs (791 up and 696 down) and 910 mRNAs (536 up and 374 down) were expressed differentially in RAW264.7 macrophages with M. tuberculosis infection compared to controls. GO and pathway analysis revealed that up-regulated mRNAs were involved in immune response, immune system process, system development or TNF signaling pathway, and antigen processing and presentation. To the contrary, down-regulated mRNAs participated in system development, regulation of biological processes and peroxisome proliferator-activated receptor (PPAR) signaling pathway. qRT-PCR results of 10 lncRNAs and mRNAs were consistent with the microarray data. M. tuberculosis infection of macrophages caused enhanced expression of lncRNA AK151345 in a time- and dose-dependent manner. We determined comprehensive expression profiles of differentially expressed lncRNAs in RAW264.7 macrophages infected by M. tuberculosis.

Identification of circulating miRNAs as novel prognostic biomarkers for bladder cancer.

MicroRNAs (miRNAs) are a type of ncRNAs with 18-25 nucleotides in length and reported to play crucial roles in human cancers. Bladder cancer is one of the most common causes of cancer-related death. The discovery of new early biomarkers for BC may improve the patients' response to the treatment thus obtaining higher outcomes. The present study identified 7 miRNAs were up-regulated in bladder serum cancer samples compared to normal samples, including hsa-miR-185-5p, hsa-miR-663a, hsa-miR-30c-5p, hsa-miR-3648, hsa-miR-1270, hsa-miR-200c-3p, and hsa-miR-29c-5p. The dysregulation of these miRNAs were correlated to advanced stage and overall survival time in bladder cancer patients. Moreover, we identified a predictive model to predict the prognosis of bladder cancer. Kaplan-Meier survival curve analyses showed that bladder cancer patients with high-risk scores had significantly worse overall survival time than bladder patients with lower risk scores. Furthermore, we constructed a miRNA-mRNA regulating network. Bioinformatics analysis showed these miRNAs were involved in regulating sarcomere organization, positive regulation of multicellular organism growth, phosphorylation, phosphatidylinositol-mediated signaling, and peroxisome proliferator activated receptor signaling pathway. We thought this study could provide novel noninvasive early biomarkers for bladder cancer.

Hepatic transcriptome profile of sheep (Ovis aries) in response to overgrazing: novel genes and pathways revealed

BackgroundOvergrazing is a major factor that causes steppe degradation in Inner Mongolian, resulting in extensive ecosystem damage. Scarcity of grass means sheep are smaller and therefore mutton and cashmere production is greatly reduced, which has resulted in massive annual economic losses. Liver is the primary metabolic organ in mammals. It is also the key source of energy supply and detoxification of metabolites in animals, has a close relationship with animal growth. However, investigations on the responses of sheep induced by consequence of overgrazing, particularly those relating to liver-related molecular mechanisms and related metabolic pathways, remain elusive.ResultsThe body weight daily gain of sheep, immune organ indices (liver and spleen), and serum parameters related to immune response, protein synthesis and energy supply (IgG, albumin, glucose and non-esterified fatty acid) were significantly lower in the overgrazing group. Other serum parameters including alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, total bilirubin, blood urea nitrogen and interleukin-6 were significantly higher in the overgrazing group. For the RNA-Seq results, we identified approximately 50 differentially expressed genes, of which half of were up-regulated and the other half were down-regulated (overgrazing group versus light grazing group). Bioinformatics analysis identified two enriched KEGG pathways including peroxisome proliferator-activated receptor (PPAR) signaling pathway (related to lipolysis) and ECM-receptor interaction (related to liver injury and apoptosis). Additionally, several of the down-regulated genes were related to detoxification and immune response.ConclusionsOverall, based on the high-throughput RNA sequencing profile integrated with the results of serum biochemical analyses, consequences of lower forage availability and quality under overgrazing condition induced altered expression levels of genes participating in energy metabolism (particularly lipid metabolism) and detoxification and immune responses, causing lipolysis and impaired health status, which might be key reasons for the reduced growth performance of sheep. This investigation provides a novel foundation for the development of sheep hepatic gene interactive networks that are a response to the degraded forage availability under overgrazing condition.

Identification of regulatory role of DNA methylation in colon cancer gene expression via systematic bioinformatics analysis.

Colon cancer arises from the accumulations of genetic and epigenetic changes. Currently, profiles of DNA methylation and gene expression of colon cancer have not been elucidated clearly. This articles aims to characterize the profile of DNA methylation and gene expression of colon cancer systemically, and acquire candidate genes potentially regulated by altered methylation for this disease.Data were downloaded from The Cancer Genome Atlas database. Differentially methylated CpG sites (DMCs) and differentially methylated regions (DMRs) were calculated via COHCAP. Differentially expressed genes (DEGs) were identified by DESeq2. Weighted gene co-expression network analysis (WGCNA) package in R was applied for WGCNA.Data of 275 solid tumor tissues and 19 adjacent tumor tissues of colon cancer were obtained. A total of 1828 DMCs, including 1390 hypermethylated and 438 hypomethylated CpG sites, were identified between tumor and normal groups. A total of 789 DEGs, containing 435 upregulated genes and 354 downregulated genes were observed. It revealed that 8 DMRs-DEGs and 95 DMCs-DEGs pairs were significantly correlated. Furthermore, genes of yellow and brown modules from WGCNA were significantly correlated with tumor/normal status, and significantly enriched in peroxisome proliferator activated receptor signaling pathway, glutamatergic synapse, and neuroactive ligand-receptor interaction. Genes in the above 2 modules were also significantly enriched in DMCs or DMRs-associated genes. Specifically, ADHFE1, HAND2, and GNAO1 were hypermethylated and downregulated in colon cancer, suggesting that the low expression levels of these genes may be regulated by DNA hypermethylation. In addition, the 3 genes were involved in brown module of WGCNA, indicating their important roles in colon cancer.The investigation of the relationship between DNA methylation and gene expression may help to understand the effect of DNA methylation alteration on genes expression, especially gene co-expression network in the development of colon cancer. Genes such as ADHFE1, HAND2, and GNAO1 may be served as potential candidates for diagnosis and therapy targets in colon cancer.

Integrating genome and transcriptome profiling for elucidating the mechanism of muscle growth and lipid deposition in Pekin ducks

Muscle growth and lipid deposition are co-ordinately regulated processes. Cherry Valley Pekin duck is a lean-type duck breed with high growth rate, whereas the native Pekin duck of China has high lipid deposition. Phenotypic analysis showed that native Pekin ducks have smaller fibre diameter and larger density in the breast muscle at 3 weeks of age and higher intramuscular fat content at 6 weeks of age than those in Cherry Valley Pekin ducks. We detected 17 positively selected genes (PSGs) by comparing genes mainly involved with muscle organ development, muscle contraction, peroxisome proliferator activated receptor signalling pathway, and fatty acid metabolism. In all, 52 and 206 differentially expressed genes (DEGs) were identified in transcriptomic comparisons between the two breeds at 3 and 6 weeks of age, respectively, which could potentially affect muscle growth and lipid deposition. Based on the integration of PSGs and DEGs and their functional annotations, we found that 11 and 10 genes were correlated with muscle growth and lipid deposition, respectively. Identification of candidate genes controlling quantitative traits of duck muscle might aid in elucidating the mechanisms of muscle growth and lipid deposition and could help in improving duck breeding.

Effect of metformin on global gene expression in liver of KKAy mice.

Metformin is a first-line drug for treating type 2 diabetes mellitus, yet its mechanism remains only partially understood and controversial. In this study we assessed a global gene expression profiling in liver of KKAy mice affected by metformin. This study aimed to identify the novel anti-diabetic mechanisms of metformin. After KKAy mice were administered metformin for 5 weeks, the gene changes profile in the livers of KKAy mice were assessed by using the Agilent whole mice genome oligo microarray. Metformin altered the gene expression profiles in liver of KKAy mice. To our best knowledge, some genes have not been reported until now, such as Anxa2, Atf6, and so on. These genes were involved in many pathways, such as peroxisome proliferator activated receptor signaling pathway. Gene expression changes induced by metformin were in support of the improvement of glucolipid metabolism and insulin resistance in KKAy mice. These findings expanded our knowledge of pharmacological action of metformin, and provided the potential novel insights and interesting information about the molecules involved in the antidiabetic effects of metformin.