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δ-Tocotrienol feeding modulates gene expression of EIF2, mTOR, protein ubiquitination through multiple-signaling pathways in chronic hepatitis C patients.
Qureshi, AA, Khan, DA, Mushtaq, S, Ye, SQ, Xiong, M, Qureshi, N
Lipids in health and disease. 2018;(1):167
Abstract
BACKGROUND δ-Tocotrienol is a naturally occurring proteasome inhibitor, which has the capacity to inhibit proliferation and induce apoptosis in several cancer cells obtained from several organs of humans, and other cancer cell lines. Moreover, results of plasma total mRNAs after δ-tocotrienol feeding to hepatitis C patients revealed significant inhibition in the expression of pro-inflammatory cytokines (TNF-α, VCAM1, proteasome subunits) and induction in the expression of ICAM1 and IFN-γ after post-treatment. This down-regulation of proteasome subunits leads to autophagy, apoptosis of immune cells and several genes. The present study describes RNA-sequence analysis of plasma total mRNAs obtained from δ-tocotrienol treatment of hepatitis C patients on gene expression regulated by proteasome. METHODS Pooled specimens of plasma total mRNAs of pre-dose versus post-dose of δ-tocotrienol treatment of hepatitis C patients were submitted to RNA-sequence analyses. The data based on > 1 and 8-fold expression changes of 2136 genes were uploaded into "Ingenuity Pathway Analyses (IPA)" for core analysis, which describes possible canonical pathways, upstream regulators, diseases and functional metabolic networks. RESULTS The IPA of "molecules" indicated fold change in gene expression of 953 molecules, which covered several categories of biological biomarkers. Out of these, gene expression of 220 related to present study, 12 were up-regulated, and 208 down-regulated after δ-tocotrienol treatment. The gene expression of transcription regulators (ceramide synthase 3 and Mohawk homeobox) were up-regulated, and gene expression of 208 molecules were down-regulated, involved in several biological functions (HSP90AB1, PSMC3, CYB5R4, NDUFB1, CYP2R1, TNFRF1B, VEGFA, GPR65, PIAS1, SFPQ, GPS2, EIF3F, GTPBP8, EIF4A1, HSPA14, TLR8, TUSSC2). IPA of "causal network" indicated gene regulators (676), in which 76 down-regulated (26 s proteasomes, interleukin cytokines, and PPAR-ligand-PPA-Retinoic acid-RXRα, PPARγ-ligand-PPARγ-Retinoic acid-RARα, IL-21, IL-23) with significant P-values. The IPA of "diseases and functions" regulators (85) were involved with cAMP, STAT2, 26S proteasome, CSF1, IFNγ, LDL, TGFA, and microRNA-155-5p, miR-223, miR-21-5p. The IPA of "upstream analysis" (934) showed 57 up-regulated (mainly 38 microRNAs) and 64 gene regulators were down-regulated (IL-2, IL-5, IL-6, IL-12, IL-13, IL-15, IL-17, IL-18, IL-21, IL-24, IL-27, IL-32), interferon β-1a, interferon γ, TNF-α, STAT2, NOX1, prostaglandin J2, NF-κB, 1κB, TCF3, and also miRNA-15, miRNA-124, miRNA-218-5P with significant activation of Z-Score (P < 0.05). CONCLUSIONS This is first report describing RNA-sequence analysis of δ-tocotrienol treated plasma total mRNAs obtained from chronic hepatitis C patients, that acts via multiple-signaling pathways without any side-effects. These studies may lead to development of novel classes of drugs for treatment of chronic hepatitis C patients.
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2.
The Combined Effects of ω -3 Fatty Acids and Nano-Curcumin Supplementation on Intercellular Adhesion Molecule-1 (ICAM-1) Gene Expression and Serum Levels in Migraine Patients.
Soveyd, N, Abdolahi, M, Djalali, M, Hatami, M, Tafakhori, A, Sarraf, P, Honarvar, NM
CNS & neurological disorders drug targets. 2018;(10):1120-1126
Abstract
BACKGROUND Migraine is an episodic headache, which is an endothelial disorder with neurological inflammation. Intercellular Adhesion Molecule-1 (ICAM-1), as an endothelial factor, leads to the adhesion of leukocytes to the walls of the cerebral blood vessels, which is an important step in the inflammation process. Curcumin and omega-3 fatty acids, by affecting transcription factors, can regulate the gene expression and serum levels of ICAM-1. Thus, this study aimed to evaluate the synergistic effects of ω-3 fatty acids and nano-curcumin on ICAM-1 gene expression and serum levels in migraine patients. METHOD This clinical trial study was conducted on 72 episodic migraine patients in 4 groups for 2 months, with patients receiving ω-3 fatty acids, nano-curcumin, a combination of them, or a placebo during the study. At the beginning and end of the study, the gene expression and serum level of ICAM-1 were measured by real-time PCR and ELISA. RESULT The results showed no significant change in ICAM-1 gene expression in any of the 4 groups. The ICAM-1 serum concentration in the combination group, and omega-3 alone, showed a significant reduction at the end of the study compared to the beginning. In addition, a significant reduction in attack frequency was observed in the combination group. CONCLUSION Considering the results of supplementation with omega-3 fatty acids plus curcumin led to reductions of both attack frequency and ICAM-1 serum level in patients, it seems that supplementation with these two nutrients not only can lead to improvements in the function of metabolic pathways, but can also be used effectively as a treatment or prevention of migraine complications.
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Separation of circadian- and behavior-driven metabolite rhythms in humans provides a window on peripheral oscillators and metabolism.
Skene, DJ, Skornyakov, E, Chowdhury, NR, Gajula, RP, Middleton, B, Satterfield, BC, Porter, KI, Van Dongen, HPA, Gaddameedhi, S
Proceedings of the National Academy of Sciences of the United States of America. 2018;(30):7825-7830
Abstract
Misalignment between internal circadian rhythmicity and externally imposed behavioral schedules, such as occurs in shift workers, has been implicated in elevated risk of metabolic disorders. To determine underlying mechanisms, it is essential to assess whether and how peripheral clocks are disturbed during shift work and to what extent this is linked to the central suprachiasmatic nuclei (SCN) pacemaker and/or misaligned behavioral time cues. Investigating rhythms in circulating metabolites as biomarkers of peripheral clock disturbances may offer new insights. We evaluated the impact of misaligned sleep/wake and feeding/fasting cycles on circulating metabolites using a targeted metabolomics approach. Sequential plasma samples obtained during a 24-h constant routine that followed a 3-d simulated night-shift schedule, compared with a simulated day-shift schedule, were analyzed for 132 circulating metabolites. Nearly half of these metabolites showed a 24-h rhythmicity under constant routine following either or both simulated shift schedules. However, while traditional markers of the circadian clock in the SCN-melatonin, cortisol, and PER3 expression-maintained a stable phase alignment after both schedules, only a few metabolites did the same. Many showed reversed rhythms, lost their rhythms, or showed rhythmicity only under constant routine following the night-shift schedule. Here, 95% of the metabolites with a 24-h rhythmicity showed rhythms that were driven by behavioral time cues externally imposed during the preceding simulated shift schedule rather than being driven by the central SCN circadian clock. Characterization of these metabolite rhythms will provide insight into the underlying mechanisms linking shift work and metabolic disorders.
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Using YFP as a Reporter of Gene Expression in the Green Alga Chlamydomonas reinhardtii.
Blaby-Haas, CE, Page, MD, Merchant, SS
Methods in molecular biology (Clifton, N.J.). 2018;:135-148
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Abstract
The unicellular green alga Chlamydomonas reinhardtii is a valuable experimental system in plant biology for studying metal homeostasis. Analyzing transcriptional regulation with promoter-fusion constructs in C. reinhardtii is a powerful method for connecting metal-responsive regulation with cis-regulatory elements, but overcoming expression-level variability between transformants and optimizing experimental conditions can be laborious. Here, we provide detailed protocols for the high-throughput cultivation of C. reinhardtii and assaying Venus fluorescence as a reporter for promoter activity. We also describe procedural considerations for relating metal supply to transcriptional activity.
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Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes.
Xue, A, Wu, Y, Zhu, Z, Zhang, F, Kemper, KE, Zheng, Z, Yengo, L, Lloyd-Jones, LR, Sidorenko, J, Wu, Y, et al
Nature communications. 2018;(1):2941
Abstract
Type 2 diabetes (T2D) is a very common disease in humans. Here we conduct a meta-analysis of genome-wide association studies (GWAS) with ~16 million genetic variants in 62,892 T2D cases and 596,424 controls of European ancestry. We identify 139 common and 4 rare variants associated with T2D, 42 of which (39 common and 3 rare variants) are independent of the known variants. Integration of the gene expression data from blood (n = 14,115 and 2765) with the GWAS results identifies 33 putative functional genes for T2D, 3 of which were targeted by approved drugs. A further integration of DNA methylation (n = 1980) and epigenomic annotation data highlight 3 genes (CAMK1D, TP53INP1, and ATP5G1) with plausible regulatory mechanisms, whereby a genetic variant exerts an effect on T2D through epigenetic regulation of gene expression. Our study uncovers additional loci, proposes putative genetic regulatory mechanisms for T2D, and provides evidence of purifying selection for T2D-associated variants.
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The effects of magnesium supplementation on gene expression related to inflammatory markers, vascular endothelial growth factor, and pregnancy outcomes in patients with gestational diabetes.
Ahmadi, S, Naderifar, M, Samimi, M, Mirhosseini, N, Amirani, E, Aghadavod, E, Asemi, Z
Magnesium research. 2018;(4):131-142
Abstract
Magnesium has been introduced as one of the micronutrients with several metabolic benefits, mainly anti-inflammatory properties. The aim of this study was to evaluate the effects of magnesium supplementation on gene expression of inflammatory markers, vascular endothelial growth factor (VEGF), and pregnancy outcomes in women diagnosed with gestational diabetes mellitus (GDM). This randomized, double-blinded, placebo-controlled trial was conducted among 36 women, aged 18-40 years old, diagnosed with GDM. Study participants were randomly allocated into two groups to receive either 250 mg/day magnesium oxide (n = 18) or placebo (n = 18) for six weeks. Gene expression related to inflammatory markers and VEGF was assessed using peripheral blood mononuclear cells (PBMCs) of women with GDM, via RT-PCR method. Quantitative results of RT-PCR demonstrated that magnesium supplementation downregulated gene expression levels of interleukin-8 (IL-8) (P = 0.03) and tumor necrosis factor-α (TNF-α) (P = 0.006) and upregulated gene expression levels of transforming growth factor beta (TGF-β) (P = 0.03) in PBMCs of women with GDM, compared with placebo. Magnesium supplementation did not significantly affect gene expression of IL-1 and vascular endothelial growth factor. Additionally, magnesium administration resulted in a lower incidence of newborn hyperbilirubinemia (11.1% versus 44.4%, P = 0.02) and newborn hospitalization (11.1% versus 44.4%, P = 0.02) compared with placebo. Overall, magnesium supplementation for six weeks significantly decreased gene expression levels of IL-8 and TNF-α, and increased TGF-β in women with GDM. Therefore, magnesium supplementation might be recommended to decrease metabolic complications in women with GDM, due to its beneficial effects on gene expression of inflammatory markers.
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The role of zinc plus octenidine in the regulation of gene expression: an in vitro study.
Lauritano, D, Candotto, V, Bignozzi, CA, Pazzi, D, Carinci, F, Cura, F, Tagliabue, A, Tettamanti, L
Journal of biological regulators and homeostatic agents. 2018;(2 Suppl. 1):237-244
Abstract
Zinc was known in ancient times, and is diffused in the environment. The potential benefits offered by zinc supplementary therapy have been demonstrated in numerous clinical trials using oral or topical zinc products. The benefit of zinc can be in principle increased through association with other actives. The aim of this study is to evaluate the effect on primary human gingival fibroblast cell of a new formulation containing zinc and octenidine cations. Human gingival fibroblast cells were obtained from three healthy patients (14-year-old man, 15-year-old woman and 20-year-old man) during extraction of teeth. The gene expression of 14 genes (ELANE, FN1, FBN, ITGA1, HAS1, ELN, DSP, ITGB1, HYAL1,TGFB1, TGFB2, TGFB3, TGFBR1 and TGFBR2) was investigated in HGF cell culture treated with 80μm of Octenidine, 1000μm of Zinc, 80μm Octenidine + Zinc solution and the medium alone at 30 min. Prestoblue data showed that as the active concentration increases (Octenidine, Zinc and Octenidine + Zinc) the percentage of cell vitality compared to that of untreated cells decrease. In this study, no statistically significant gene expression was observed between cells, treated with difference substances, and control cells. Our results points out that zinc plus octenidine shows a positive potential in periodontal disease treatment.
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The Footprints of Poly-Autoimmunity: Evidence for Common Biological Factors Involved in Multiple Sclerosis and Hashimoto's Thyroiditis.
Perga, S, Martire, S, Montarolo, F, Giordani, I, Spadaro, M, Bono, G, Corvisieri, S, Messuti, I, Panzica, G, Orlandi, F, et al
Frontiers in immunology. 2018;:311
Abstract
Autoimmune diseases are a diverse group of chronic disorders and affect a multitude of organs and systems. However, the existence of common pathophysiological mechanisms is hypothesized and reports of shared risk are emerging as well. In this regard, patients with multiple sclerosis (MS) have been shown to have an increased susceptibility to develop chronic autoimmune thyroid diseases, in particular Hashimoto's thyroiditis (HT), suggesting an autoimmune predisposition. However, studies comparing such different pathologies of autoimmune origin are still missing till date. In the present study, we sought to investigate mechanisms which may lead to the frequent coexistence of MS and HT by analyzing several factors related to the pathogenesis of MS and HT in patients affected by one or both diseases, as well as in healthy donors. In particular, we analyzed peripheral blood mononuclear cell gene-expression levels of common candidate genes such as TNFAIP3, NR4A family, BACH2, FOXP3, and PDCD5, in addition to the regulatory T cell (Treg) percentage and the 25-hydroxy vitamin D serum levels. Our findings support the plausibility of the existence of common deregulated mechanisms shared by MS and HT, such as BACH2/PDCD5-FOXP3 pathways and Tregs. Although the biological implications of these data need to be further investigated, we have highlighted the relevance of studies comparing different autoimmune pathologies for the understanding of the core concepts of autoimmunity.
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Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response.
Loughran, G, Jungreis, I, Tzani, I, Power, M, Dmitriev, RI, Ivanov, IP, Kellis, M, Atkins, JF
The Journal of biological chemistry. 2018;(12):4434-4444
Abstract
Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian readthrough have only recently been uncovered by systems biology and comparative genomics approaches. Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. Four mRNAs display highly efficient stop codon readthrough, and these mRNAs have a UGA stop codon immediately followed by CUAG (UGA_CUAG) that is conserved throughout vertebrates. Extending on the identification of this readthrough motif, we here investigated stop codon readthrough, using tissue culture reporter assays, for all previously untested human genes containing UGA_CUAG. The readthrough efficiency of the annotated stop codon for the sequence encoding vitamin D receptor (VDR) was 6.7%. It was the highest of those tested but all showed notable levels of readthrough. The VDR is a member of the nuclear receptor superfamily of ligand-inducible transcription factors, and it binds its major ligand, calcitriol, via its C-terminal ligand-binding domain. Readthrough of the annotated VDR mRNA results in a 67 amino acid-long C-terminal extension that generates a VDR proteoform named VDRx. VDRx may form homodimers and heterodimers with VDR but, compared with VDR, VDRx displayed a reduced transcriptional response to calcitriol even in the presence of its partner retinoid X receptor.
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Gene-gene interactions among coding genes of iron-homeostasis proteins and APOE-alleles in cognitive impairment diseases.
Tisato, V, Zuliani, G, Vigliano, M, Longo, G, Franchini, E, Secchiero, P, Zauli, G, Paraboschi, EM, Vikram Singh, A, Serino, ML, et al
PloS one. 2018;(3):e0193867
Abstract
Cognitive impairments of different aetiology share alterations in iron and lipid homeostasis with mutual relationships. Since iron and cholesterol accumulation impact on neurodegenerative disease, the associated gene variants are appealing candidate targets for risk and disease progression assessment. In this light, we explored the role of common single nucleotide polymorphisms (SNPs) in the main iron homeostasis genes and in the main lipoprotein transporter gene (APOE) in a cohort of 765 patients with dementia of different origin: Alzheimer's disease (AD) n = 276; vascular dementia (VaD), n = 255; mild cognitive impairment (MCI), n = 234; and in normal controls (n = 1086). In details, four genes of iron homeostasis (Hemochromatosis (HFE: C282Y, H63D), Ferroportin (FPN1: -8CG), Hepcidin (HAMP: -582AG), Transferrin (TF: P570S)), and the three major alleles of APOE (APOE2, APOE3, APOE4) were analyzed to explore causative interactions and synergies. In single analysis, HFE 282Y allele yielded a 3-fold risk reduction in the whole cohort of patients (P<0.0001), confirmed in AD and VaD, reaching a 5-fold risk reduction in MCI (P = 0.0019). The other iron SNPs slightly associated with risk reduction whereas APOE4 allele resulted in increased risk, reaching more than 7-fold increased risk in AD homozygotes (P = 0.001), confirmed to a lower extent in VaD and MCI (P = 0.038 and P = 0.013 respectively) as well as in the whole group (P<0.0001). Comparisons of Mini Mental State Examination (MMSE) among AD showed appreciable lowering in APOE4 carriers (P = 0.038), confirmed in the whole cohort of patients (P = 0.018). In interaction analysis, the HFE 282Y allele completely extinguished the APOE4 allele associated risk. Conversely, the coexistence in patients of a substantial number of iron SNPs accrued the APOE4 detrimental effect on MMSE. Overall, the analysis highlighted how a specific iron-allele burden, defined as different combinations of iron gene variants, might have different effects on cognitive impairment and might modulate the effects of established genetic risk factors such as APOE4. Our results suggest that established genetic risk factors might be affected by specific genetic backgrounds, making patients differently suited to manage iron accumulation adding new genetic insights in neurodegeneration. The recently recognized interconnections between iron and lipids, suggest that these pathways might share more than expected. We therefore extended to additional iron gene variants the newly proposed influencing mechanisms that HFE gene has on cholesterol metabolism. Our results have a strong translational potential promoting new pharmacogenetics studies on therapeutic target identification aimed at optimally tuning brain iron levels.