Global correlation analysis for microRNA and gene expression profiles in human obesity

Li, Jiayu; Zhou, Chunyuan; Li, Jiarui; Su, Ziyuan; Sang, Haiyan; Jia, Erna; Si, Daoyuan

doi:10.1016/j.prp.2014.11.014

Cited by 20 publications

(10 citation statements)

References 34 publications

(34 reference statements)

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“…Regarding to the targeting interactions with miRNA, COL12A1 is reported as the target of miR-300-5p in adult rat cardiac fibroblasts 35 and the target of hsa-miR-16 in human obesity. 36 In the present study, COL12A1 was predicted as the target of hsa-miR-21, hsa-miR-30e, and hsa-miR-195. Reportedly, miR-21 is one of the miRNAs that induced by Angiotensin II.…”

Section: Discussionsupporting

confidence: 47%

Identification of crucial miRNAs and the targets in renal cortex of hypertensive patients by expression profiles

Wang

Chen

et al. 2016

Renal Failure

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Backgrounds: Defect in kidney is one major reason of hypertension. The study aimed ao uncovering the regulatory mechanisms of miRNAs and the targets in hypertensive kidney.Methods: Gene expression profile of GSE28345 and miRNA expression profile of GSE28283 were downloaded from GEO database. After data preprocessing, differently expressed genes (DEGs) and miRNAs (DE-miRs) were identified using limma package. Then targets of miRNAs were predicted according to information in relevant databases. Function and pathway enrichment analyses were performed for DEGs using DAVID software. Furthermore, protein–protein interaction (PPI) networks were constructed for up- and down-regulated genes, respectively, using the Cytoscape. Additionally, for down-regulated DEGs, the integrated regulatory network was established combining PPI network with the miRNA–mRNA interactions.Results: As a result, 285 DEGs were identified, including 177 up-regulated and 108 down-regulated genes. Combined with the predicted targets of miRNAs, 22 up-regulated DE-miRs were identified. In the integrated network for down-regulated DEGs, three crucial nodes were identified as ASPN, COL12A1, and SCN2A. ASPN was predicted as target of miR-21 and miR-374b, and COL12A1 was the target of miR-30e, miR-21, and miR-195, while SCN2A was the target of miR-30e, miR-374b, and miR-195. Notably, COL12A1 and ASPN were linked with each other in the network.Conclusion: Three crucial genes were identified in hypertensive kidney, such as COL12A1, ASPN, and SCN2A. ASPN might co-function with COL12A1, and they both might be the targets of miR-21. SCN2A might be a novel target of miR-30e and miR-374b. However, more experiments are needed to validate these results.

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Section: Discussionsupporting

confidence: 47%

Identification of crucial miRNAs and the targets in renal cortex of hypertensive patients by expression profiles

Wang

Chen

et al. 2016

Renal Failure

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“…MiR-27a and miR-27b abundance decreased PPARγ during adipogenesis of human pluripotent adipose-derived stem cells, thus counteracting PPARγ (Karbiener et al, 2009 ; Kim et al, 2010 ). MiR-122 decrease was described central in hepatic fatty-acid and cholesterol synthesis rate, by reducing hepatosteatosis (Esau et al, 2006 ), together with miR-223 in obesity (Kilic et al, 2015 ), also with miR-425, miR-126, miR-16, miR-634 (Li et al, 2015 ), miR-519d, miR-27 and miR-519d for target PPARγ (McGregor and Choi, 2011 ), miR-26 triglyceride accumulation (Song et al, 2014 ). MiR-370, miR-22, miR-758 also engaged in liver-adipocyte interaction (Flowers et al, 2013 ), furthermore miR-10b, miR-302a, miR-378, miR-613, miR-224 (Peng et al, 2013 , 2014 ).…”

Section: Findings On Epigenetic Modification and Gene Regulation In Mmentioning

confidence: 99%

Neuroendocrinological and Epigenetic Mechanisms Subserving Autonomic Imbalance and HPA Dysfunction in the Metabolic Syndrome

2016

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Impact of environmental stress upon pathophysiology of the metabolic syndrome (MetS) has been substantiated by epidemiological, psychophysiological, and endocrinological studies. This review discusses recent advances in the understanding of causative roles of nutritional factors, sympathomedullo-adrenal (SMA) and hypothalamic-pituitary adrenocortical (HPA) axes, and adipose tissue chronic low-grade inflammation processes in MetS. Disturbances in the neuroendocrine systems for leptin, melanocortin, and neuropeptide Y (NPY)/agouti-related protein systems have been found resulting directly in MetS-like conditions. The review identifies candidate risk genes from factors shown critical for the functioning of each of these neuroendocrine signaling cascades. In its meta-analytic part, recent studies in epigenetic modification (histone methylation, acetylation, phosphorylation, ubiquitination) and posttranscriptional gene regulation by microRNAs are evaluated. Several studies suggest modification mechanisms of early life stress (ELS) and diet-induced obesity (DIO) programming in the hypothalamic regions with populations of POMC-expressing neurons. Epigenetic modifications were found in cortisol (here HSD11B1 expression), melanocortin, leptin, NPY, and adiponectin genes. With respect to adiposity genes, epigenetic modifications were documented for fat mass gene cluster APOA1/C3/A4/A5, and the lipolysis gene LIPE. With regard to inflammatory, immune and subcellular metabolism, PPARG, NKBF1, TNFA, TCF7C2, and those genes expressing cytochrome P450 family enzymes involved in steroidogenesis and in hepatic lipoproteins were documented for epigenetic modifications.

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“…Adipogenesis is tightly controlled by a mixture regulatory signals including endocellular transcription factors and circulating hormones [ 12 ]. Additional regulators of adipogenesis also include microRNAs (miRNAs) [ 13 – 17 ]. These small non-coding RNAs, which have a length of only 20–24 nucleotides, are involved in the modulation of gene expression and, consequently, in the control of numerous cell functions [ 18 – 20 ].…”

Section: Introductionmentioning

confidence: 99%

Circulating microRNAs are deregulated in overweight/obese children: preliminary results of the I.Family study

et al. 2016

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BackgroundMicroRNAs (miRNAs) are small non-coding RNAs involved in the modulation of gene expression and in the control of numerous cell functions. Alterations of miRNA patterns frequently occur in cancer and metabolic disorders, including obesity. Recent studies showed remarkable stability of miRNAs in both plasma and serum making them suitable as potential circulating biomarkers for a variety of diseases and conditions.The aim of this study was to assess the profile of circulating miRNAs expressed in plasma samples of overweight or obese (OW/Ob) and normal weight (NW) prepubertal children from a European cohort (www.ifamilystudy.eu). The project, aimed to assess the determinants of eating behavior in children and adolescents of eight European countries, is built on the IDEFICS cohort (www.ideficsstudy.eu), established in 2006. Among the participants of the I.Family Italian Cohort, ten OW/Ob (age 10.7 ± 1.5 years, BMI 31.6 ± 4.3 kg/m2) and ten NW (age 10.5 ± 2.7 years, BMI 16.4 ± 1.7 kg/m2) children were selected for the study. Gene arrays were employed to differentially screen the expression of 372 miRNAs in pooled plasma samples. Deregulated miRNAs (p < 0.05) were further validated in the individual samples using a real-time PCR (RT-qPCR) approach.ResultsUsing a significance threshold of p < 0.05 and a fold-change threshold of ± 4.0, we preliminarily identified in the pooled samples eight miRNAs that differed between the OW/Ob and NW groups. The validation by RT-qPCR in the individual plasma samples showed a twofold upregulation of miR-31-5p, a threefold upregulation of miR-2355-5p, and a 0.5-fold downregulation of miR-206 in OW/Ob as compared with NW. The molecular functions of these differentially expressed plasma miRNAs as well as their expected mRNA targets were predicted by bioinformatics tools.ConclusionsThis pilot study shows that three circulating miRNAs are differentially regulated in OW/Ob as compared with NW children. Although causal pathways cannot be firmly inferred by these results, that deserve confirmation in larger samples, it is conceivable that circulating miRNAs may be novel biomarkers of obesity and related metabolic disturbances.Electronic supplementary materialThe online version of this article (doi:10.1186/s12263-016-0525-3) contains supplementary material, which is available to authorized users.

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Global correlation analysis for microRNA and gene expression profiles in human obesity

Cited by 20 publications

References 34 publications

Identification of crucial miRNAs and the targets in renal cortex of hypertensive patients by expression profiles

Identification of crucial miRNAs and the targets in renal cortex of hypertensive patients by expression profiles

Neuroendocrinological and Epigenetic Mechanisms Subserving Autonomic Imbalance and HPA Dysfunction in the Metabolic Syndrome

Circulating microRNAs are deregulated in overweight/obese children: preliminary results of the I.Family study

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