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1.
Disassociation of Vitamin D's Calcemic Activity and Non-calcemic Genomic Activity and Individual Responsiveness: A Randomized Controlled Double-Blind Clinical Trial.
Shirvani, A, Kalajian, TA, Song, A, Holick, MF
Scientific reports. 2019;(1):17685
Abstract
The aims of this randomized controlled double-blind clinical trial were to assess the impact of vitamin D supplementation on calcium metabolism and non-calcemic broad gene expression by relating them to the individual's responsiveness to varying doses of vitamin D3. Thirty healthy adults were randomized to receive 600, 4,000 or 10,000 IU/d of vitamin D3 for 6 months. Circulating parathyroid hormone (PTH), 25(OH)D, calcium and peripheral white blood cells broad gene expression were evaluated. We observed a dose-dependent increase in 25(OH)D concentrations, decreased PTH and no change in serum calcium. A plateau in PTH levels was achieved at 16 weeks in the 4000 and 10,000 IU/d groups. There was a dose-dependent 25(OH)D alteration in broad gene expression with 162, 320 and 1289 genes up- or down-regulated in their white blood cells, respectively. Our results clearly indicated that there is an individual's responsiveness on broad gene expression to varying doses of vitamin D3. Vitamin D3 supplementation at 10,000 IU/d produced genomic alterations several fold higher than 4,000 IU/d even without further changes in PTH levels. Our findings may help explain why there are some inconsistency in the results of different vitamin D's clinical trials.
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2.
The Fibrillin-1 RGD Integrin Binding Site Regulates Gene Expression and Cell Function through microRNAs.
Zeyer, KA, Zhang, RM, Kumra, H, Hassan, A, Reinhardt, DP
Journal of molecular biology. 2019;(2):401-421
Abstract
Fibrillins are the major components of microfibrils in the extracellular matrix of elastic and non-elastic tissues. Fibrillin-1 contains one evolutionarily conserved RGD sequence that mediates cell-matrix interactions through cell-surface integrins. Here, we present a novel paradigm how extracellular fibrillin-1 controls cellular function through integrin-mediated microRNA regulation. Comparative mRNA studies by global microarray analysis identified growth factor activity, actin binding and integrin binding as the most important functional groups that are regulated upon fibrillin-1 binding to dermal fibroblasts. Many of these mRNAs are targets of miRNAs that were identified when RNA from the fibrillin-1-ligated fibroblasts was analyzed by a miRNA microarray. The expression profile was specific to fibrillin-1 since interaction with fibronectin displayed a partially distinct profile. The importance of selected miRNAs for the regulation of the identified mRNAs was suggested by bioinformatics prediction and the interactions between miRNAs and mRNAs were experimentally validated. Functionally, we show that miR-503 controls p-Smad2-dependent TGF-β signaling, and that miR-612 and miR-3185 are involved in the focal adhesion formation regulated by fibrillin-1. In conclusion, we demonstrate that fibrillin-1 interaction with fibroblasts regulates miRNA expression profiles which in turn control critical cell functions.
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3.
Immunoblotting for Calpastatin Expression.
Averna, M, De Tullio, R
Methods in molecular biology (Clifton, N.J.). 2019;:195-206
Abstract
Immunoblotting is a procedure routinely used to analyze calpastatin expression. However, immunoblotting alone may not be adequate for this task, since calpastatin isoforms can vary by tissue, can be modified by partial digestion, and can undergo posttranslational modifications. Here we describe a method for more precise evaluation of calpastatin expression by combining immunoblot analysis with an assay for the inhibitory activity of a single calpastatin species isolated by SDS-PAGE and protein elution from the gel.
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4.
A Hazelnut-Enriched Diet Modulates Oxidative Stress and Inflammation Gene Expression without Weight Gain.
Di Renzo, L, Cioccoloni, G, Bernardini, S, Abenavoli, L, Aiello, V, Marchetti, M, Cammarano, A, Alipourfard, I, Ceravolo, I, Gratteri, S
Oxidative medicine and cellular longevity. 2019;:4683723
Abstract
INTRODUCTION Inflammation is associated with obesity condition and plays a pivotal role in the onset and progression of many chronic diseases. Among several nutraceutical foods, hazelnuts (Corylus avellana L.) are considered an excellent anti-inflammatory and hypolipidemic food being the second richest source of monounsaturated fatty acids among nuts and because they are rich in vitamins, minerals, and phenolic compounds. MATERIALS AND METHODS A prospective pilot clinical trial on 24 healthy volunteers who consumed daily, as a snack, 40 g of hazelnuts (261.99 kcal/1096.17 kJ) for six weeks was conducted. Anthropometric measurements, body composition analysis, and nutrigenomic analysis on 12 anti-inflammatory and antioxidant genes were evaluated at baseline (T0) and after hazelnut intervention (T1). RESULTS No significant changes were detected on body composition analysis after hazelnut consumption. Conversely, significant upregulation was detected for SOD1 (2-ΔΔCt = 2.42), CAT (2-ΔΔCt = 2.41), MIF (2-ΔΔCt = 4.12), PPARγ (2-ΔΔCt = 5.89), VDR (2-ΔΔCt = 3.61), MTHFR (2-ΔΔCt = 2.40), and ACE (2-ΔΔCt = 2.16) at the end of the study. CONCLUSIONS According to emerging evidences, hazelnut consumption does not lead to weight gain probably due to the improvement of the body's antioxidant capacity by the upregulation of genes implied in oxidant reactions and inflammation.
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5.
The effects of omega-3 fatty acids and vitamin E co-supplementation on gene expression related to inflammation, insulin and lipid in patients with Parkinson's disease: A randomized, double-blind, placebo-controlled trial.
Tamtaji, OR, Taghizadeh, M, Aghadavod, E, Mafi, A, Dadgostar, E, Daneshvar Kakhaki, R, Abolhassani, J, Asemi, Z
Clinical neurology and neurosurgery. 2019;:116-121
Abstract
OBJECTIVE This study was conducted to evaluate the effects of omega-3 fatty acids and vitamin E co-supplementation on gene expression related to inflammation, insulin and lipid in subjects with Parkinson's disease (PD). PATIENTS AND METHODS This randomized, double-blind, placebo-controlled clinical trial was performed in 40 subjects with PD. Participants were randomly allocated into two groups to take either 1000 mg/day of omega-3 fatty acids from flaxseed oil plus 400 IU/day of vitamin E supplements or placebo (n = 20 each group) for 12 weeks. Gene expression related to inflammation, insulin and lipid were quantified in peripheral blood mononuclear cells (PBMC) of PD patients with RT-PCR method. RESULTS After the 12-week intervention, compared with the placebo, omega-3 fatty acids and vitamin E co-supplementation downregulated gene expression of tumor necrosis factor alpha (TNF-α) (P = 0.002) in PBMC of subjects with PD. In addition, omega-3 fatty acids and vitamin E co-supplementation upregulated peroxisome proliferator-activated receptor gamma (PPAR-γ) (P = 0.03), and downregulated oxidized low-density lipoprotein receptor (LDLR) (P = 0.002) in PBMC of subjects with PD compared with the placebo. We did not observe any significant effect of omega-3 fatty acids and vitamin E co-supplementation on gene expression of interleukin-1 (IL-1) and IL-8 in PBMC of patients with PD. CONCLUSIONS Overall, omega-3 fatty acids and vitamin E co-supplementation for 12 weeks in PD patients significantly improved gene expression of TNF-α, PPAR-γ and LDLR, but did not affect IL-1 and IL-8.
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6.
Insights Into a "Negative" ICU Trial Derived From Gene Expression Profiling.
Hoekstra, M, Maslove, DM, Veldhoen, RA, Marshall, JC, Muscedere, J
Critical care medicine. 2019;(12):e941-e947
Abstract
OBJECTIVES Randomized controlled trials in the ICU often fail to show differences in endpoints between groups. We sought to explore reasons for this at a molecular level by analyzing transcriptomic data from a recent negative trial. Our objectives were to determine if randomization successfully balanced transcriptomic features between groups, to assess transcriptomic heterogeneity among the study subjects included, and to determine if the study drug had any effect at the gene expression level. DESIGN Bioinformatics analysis of transcriptomic and clinical data collected in the course of a randomized controlled trial. SETTING Tertiary academic mixed medical-surgical ICU. PATIENTS Adult, critically ill patients expected to require invasive mechanical ventilation more than 48 hours. INTERVENTIONS Lactoferrin or placebo delivered enterally and via an oral swab for up to 28 days. MEASUREMENTS AND MAIN RESULTS We found no major imbalances in transcriptomic features between groups. Unsupervised analysis did not reveal distinct clusters among patients at the time of enrollment. There were marked differences in gene expression between early and later time points. Patients in the lactoferrin group showed changes in the expression of genes associated with immune pathways known to be associated with lactoferrin. CONCLUSIONS In this clinical trial, transcriptomic data provided a useful complement to clinical data, suggesting that the reasons for the negative result were less likely related to the biological efficacy of the study drug, and may instead have been related to poor sensitivity of the clinical outcomes. In larger studies, transcriptomics may also prove useful in predicting response to treatment.
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7.
Comparing the effects of vitamin E tocotrienol-rich fraction supplementation and α-tocopherol supplementation on gene expression in healthy older adults.
Ghani, SMA, Goon, JA, Azman, NHEN, Zakaria, SNA, Hamid, Z, Ngah, WZW
Clinics (Sao Paulo, Brazil). 2019;:e688
Abstract
OBJECTIVES This study aims to compare the differential gene expression resulting from tocotrienol-rich fraction and α-tocopherol supplementation in healthy older adults. METHODS A total of 71 eligible subjects aged 50 to 55 years from Gombak and Kuala Lumpur, Malaysia, were divided into three groups and supplemented with placebo (n=23), α-tocopherol (n=24) or tocotrienol-rich fraction (n=24). Blood samples were collected at baseline and at 3 and 6 months of supplementation for microarray analysis. RESULTS The number of genes altered by α-tocopherol was higher after 6 months (1,410) than after 3 months (273) of supplementation. α-Tocopherol altered the expression of more genes in males (952) than in females (731). Similarly, tocotrienol-rich fraction modulated the expression of more genes after 6 months (1,084) than after 3 months (596) and affected more genes in males (899) than in females (781). α-Tocopherol supplementation modulated pathways involving the response to stress and stimuli, the immune response, the response to hypoxia and bacteria, the metabolism of toxins and xenobiotics, mitosis, and synaptic transmission as well as activated the mitogen-activated protein kinase and complement pathways after 6 months. However, tocotrienol-rich fraction supplementation affected pathways such as the signal transduction, apoptosis, nuclear factor kappa B kinase, cascade extracellular signal-regulated kinase-1 and extracellular signal-regulated kinase-2, immune response, response to drug, cell adhesion, multicellular organismal development and G protein signaling pathways. CONCLUSION Supplementation with either α-tocopherol or tocotrienol-rich fraction affected the immune and drug response and the cell adhesion and signal transduction pathways but modulated other pathways differently after 6 months of supplementation, with sex-specific responses.
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8.
The Diagnostic Performance of Afirma Gene Expression Classifier for the Indeterminate Thyroid Nodules: A Meta-Analysis.
Liu, Y, Pan, B, Xu, L, Fang, D, Ma, X, Lu, H
BioMed research international. 2019;:7150527
Abstract
BACKGROUND Approximately 15 to 30% of thyroid nodules evaluated by fine-needle aspiration (FNA) were classified as indeterminate; the accurate diagnostic molecular tests of these nodules remain a challenge. We aimed to evaluate the diagnostic performance of Afirma gene expression classifier (GEC) for the indeterminate thyroid nodules (ITNs). METHODS Studies published from January 2005 to December 2018 were systematically reviewed. The gold reference standard relied on the histopathologic results diagnosis from thyroidectomy surgical specimens. MetaDisc software was used to investigate the pooled sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV), diagnostic odds ratio (DOR), and summary receiver operating characteristic (SROC) curves. RESULTS A total of 18 studies involving 5290 patients with 3290 cases of ITNs were included. Collected data revealed that the pooled sensitivity of GEC was 95.5% (95% CI 93.3%-97.0%, p < 0.001), the specificity was 22.1% (95% CI 19.4%-24.9%, p < 0.001), the NPV was 88.2% (95% CI 0.833-0.921, p < 0.001), the PPV was 44.3% (95% CI 0.416-0.471, p < 0.001), and the DOR was 5.25 (95% CI 3.42-8.04, p= 0.855). CONCLUSION The GEC has quite high sensitivity of 95.5% but low specificity of 22.1%. The high sensitivity makes it probable to rule out malignant nodules. Thus, over half of nodules with GEC-suspicious results still require further validation like molecular markers, diagnostic surgery, or long follow-up, which limits its use in future clinical practice.
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9.
Genome-wide DNA methylomic differences between dorsolateral prefrontal and temporal pole cortices of bipolar disorder.
Ho, AM, Winham, SJ, Armasu, SM, Blacker, CJ, Millischer, V, Lavebratt, C, Overholser, JC, Jurjus, GJ, Dieter, L, Mahajan, G, et al
Journal of psychiatric research. 2019;:45-54
Abstract
Dorsolateral prefrontal cortex (DLPFC) and temporal pole (TP) are brain regions that display abnormalities in bipolar disorder (BD) patients. DNA methylation - an epigenetic mechanism both heritable and sensitive to the environment - may be involved in the pathophysiology of BD. To study BD-associated DNA methylomic differences in these brain regions, we extracted genomic DNA from the postmortem tissues of Brodmann Area (BA) 9 (DLPFC) and BA38 (TP) gray matter from 20 BD, ten major depression (MDD), and ten control age-and-sex-matched subjects. Genome-wide methylation levels were measured using the 850 K Illumina MethylationEPIC BeadChip. We detected striking differences between cortical regions, with greater numbers of between-brain-region differentially methylated positions (DMPs; i.e., CpG sites) in all groups, most pronounced in the BD group, and with substantial overlap across groups. The genes of DMPs common to both BD and MDD (hypothetically associated with their common features such as depression) and those distinct to BD (hypothetically associated with BD-specific features such as mania) were enriched in pathways involved in neurodevelopment including axon guidance. Pathways enriched only in the BD-MDD shared list pointed to GABAergic dysregulation, while those enriched in the BD-only list suggested glutamatergic dysregulation and greater impact on synaptogenesis and synaptic plasticity. We further detected group-specific between-brain-region gene expression differences in ODC1, CALY, GALNT2, and GABRD, which contained significant between-brain-region DMPs. In each brain region, no significant DMPs or differentially methylated regions (DMRs) were found between diagnostic groups. In summary, the methylation differences between DLPFC and TP may provide molecular targets for further investigations of genetic and environmental vulnerabilities associated with both unique and common features of various mood disorders and suggest directions of future development of individualized treatment strategies.
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10.
Exercise training impacts skeletal muscle gene expression related to the kynurenine pathway.
Allison, DJ, Nederveen, JP, Snijders, T, Bell, KE, Kumbhare, D, Phillips, SM, Parise, G, Heisz, JJ
American journal of physiology. Cell physiology. 2019;(3):C444-C448
Abstract
Exercise positively impacts mood and symptoms of depression; however, the mechanisms underlying these effects are not fully understood. Recent evidence highlights a potential role for skeletal muscle-derived transcription factors to influence tryptophan metabolism, along the kynurenine pathway, which has important implications in depression. This has important consequences for older adults, whose age-related muscle deterioration may influence this pathway and may increase their risk for depression. Although exercise training has been shown to improve skeletal muscle mass in older adults, whether this also translates into improvements in transcription factors and metabolites related to the kynurenine pathway has yet to be examined. The aim of the present study was to examine the influence of a 12-wk exercise program on skeletal muscle gene expression of transcription factors, kynurenine aminotransferase (KAT) gene expression, and plasma concentrations of tryptophan metabolites (kynurenines) in healthy older men over 65 yr of age. Exercise training significantly increased skeletal muscle gene expression of transcription factors (peroxisome proliferator-activated receptor-γ coactivator 1α, peroxisome proliferator-activated receptor-α, and peroxisome proliferator-activated receptor-δ: 1.77, 1.99, 2.18-fold increases, respectively, P < 0.01] and KAT isoforms 1-4 (6.5, 2.1, 2.2, and 2.6-fold increases, respectively, P ≤ 0.01). Concentrations of plasma kynurenines were not altered. These results demonstrate that 12 wk of exercise training significantly altered skeletal muscle gene expression of transcription factors and gene expression related to the kynurenine pathway, but not circulating kynurenine metabolites in older men. These findings warrant future research to determine whether distinct exercise modalities or varying intensities could induce a shift in the kynurenine pathway in depressed older adults.