Integrated analysis of microRNA and mRNA expression profiles in rats with selenium deficiency and identification of associated miRNA-mRNA network

Selenium intake and multiple health-related outcomes: an umbrella review of meta-analyses

Selenium is an essential trace metalloid element that is associated with fundamental importance to human health. Our umbrella review aimed to evaluate the quality of evidence, validity, and biases in the relationship between selenium intake and health-related outcomes according to published systematic reviews with pooled data and meta-analyses. Selenium intake is associated with a decreased risk of digestive system cancers, all-cause mortality, depression, and Keshan disease, when in children reduce the risk of Kashin-Beck disease. Additionally, selenium supplementation can improve sperm quality, polycystic ovary syndrome, autoimmune thyroid disease, cardiovascular disease, and infective outcomes. Selenium supplementation also has relationship with a decreased concentration of serum lipids including total cholesterol and very low-density lipoprotein cholesterol. However, no evidence has shown that selenium is associated with better outcomes among patients in intensive care units. Furthermore, selenium intake may be related with a higher risk of type 2 diabetes and non-melanoma skin cancers. Moreover, most of included studies are evaluated as low quality according to our evidence assessment. Based on our study findings and the limited advantages of selenium intake, it is not recommended to receive extra supplementary selenium for general populations, and selenium supplementation should not be continued in patients whose selenium-deficient status has been corrected.

miRModuleNet: Detecting miRNA-mRNA Regulatory Modules

Increasing evidence that microRNAs (miRNAs) play a key role in carcinogenesis has revealed the need for elucidating the mechanisms of miRNA regulation and the roles of miRNAs in gene-regulatory networks. A better understanding of the interactions between miRNAs and their mRNA targets will provide a better understanding of the complex biological processes that occur during carcinogenesis. Increased efforts to reveal these interactions have led to the development of a variety of tools to detect and understand these interactions. We have recently described a machine learning approach miRcorrNet, based on grouping and scoring (ranking) groups of genes, where each group is associated with a miRNA and the group members are genes with expression patterns that are correlated with this specific miRNA. The miRcorrNet tool requires two types of -omics data, miRNA and mRNA expression profiles, as an input file. In this study we describe miRModuleNet, which groups mRNA (genes) that are correlated with each miRNA to form a star shape, which we identify as a miRNA-mRNA regulatory module. A scoring procedure is then applied to each module to further assess their contribution in terms of classification. An important output of miRModuleNet is that it provides a hierarchical list of significant miRNA-mRNA regulatory modules. miRModuleNet was further validated on external datasets for their disease associations, and functional enrichment analysis was also performed. The application of miRModuleNet aids the identification of functional relationships between significant biomarkers and reveals essential pathways involved in cancer pathogenesis. The miRModuleNet tool and all other supplementary files are available at https://github.com/malikyousef/miRModuleNet/

MiR-135b-5p is an oncogene in pancreatic cancer to regulate GPRC5A expression by targeting transcription factor KLF4

KLF4 is implicated in tumor progression of pancreatic cancer, but the molecular regulatory mechanism of KLF4 needs to be further specified. We aimed to probe molecular regulatory mechanism of KLF4 in malignant progression of pancreatic cancer. qRT-PCR or western blot was completed to test levels of predicted genes. Dual-luciferase and chromatin immunoprecipitation (ChIP) assays were designed to validate binding between genes. Cell viability and oncogenicity detection were used for in vitro and vivo functional assessment. KLF4 was a downstream target of miR-135b-5p. KLF4 could regulate GPRC5A level. MiR-135b-5p was notably increased in cancer cells, and overexpressing KLF4 functioned a tumor repressive role, which could be restored by miR-135b-5p. Besides, cell malignant phenotypes could be inhibited through reducing miR-135b-5p level, but they were restored by GPRC5A. Our results stressed that KLF4, as a vital target of miR-135b-5p, could influence promoter region of GPRC5A, thus affecting the malignant progression of pancreatic cancer.

Selenium Deficiency Induces Pathological Cardiac Lipid Metabolic Remodeling and Inflammation

SCOPE

Selenium (Se) disequilibrium is closely involved in many cardiac diseases, although its in vivo mechanism remains uncertain. Therefore, a pig model was created in order to generate a comprehensive picture of cardiac response to dietary Se deficiency.

METHODS AND RESULTS

A total of 24 pigs were divided into two equal groups, which were fed a diet with either 0.007 mg/kg Se or 0.3 mg/kg Se for 16 weeks. Se deficiency caused cardiac oxidative stress by blocking glutathione and thioredoxin systems and increased thioredoxin domain-containing protein S-nitrosylation. Energy production was disordered as free fatty acids were overloaded, the tricarboxylic acid cycle was strengthened, and three respiratory chain proteins enhanced S-nitrosylation. Excess free fatty acids led to increased synthesis of diacylglycerol, phosphatidylcholine, and phosphatidylethanolamine, where the latter two are vulnerable to oxidation and caused an increase in malondialdehyde. Moreover, increased palmitic acid enhanced de novo ceramide synthesis and accumulation. Additionally, Se deficiency initiated inflammation via cytosolic DNA-sensing pathways, which activated downstream interferon regulatory factor 7 and nuclear factor kappa B.

CONCLUSIONS

The present study identified a lipid metabolic vulnerability and inflammation initiation pathways via Se deficiency, which may provide targets for human redox imbalance-induced cardiac disease treatment. This article is protected by copyright. All rights reserved.

circ_0038718 promotes colon cancer cell malignant progression via the miR-195-5p/Axin2 signaling axis and also effect Wnt/β-catenin signal pathway

OBJECTIVE

Colon cancer (CC) is one of the most common cancers whose progression is regulated by a number of factors, including circular RNAs (circRNAs). Nonetheless, circ_0038718 is a novel circRNA, and its regulatory mechanism in CC remains unclear.

METHODS

Real-time quantitative PCR (qRT-PCR) was performed to detect the expression of circ_0038718, miR-195-5p and Axin2. Western blot was conducted to determine the protein expression of Axin2 and the key proteins on Wnt/β-catenin signaling pathway. Oligo (dT) ₁₈ primers and RNase R were employed to identify the circular features of circ_0038718, and the location of circ_0038718 in cells was detected via nucleocytoplasmic separation. Dual-luciferase reporter assay and RNA binding protein immunoprecipitation experiment were carried out to investigate the molecular mechanism of circ_0038718/miR-195-5p/Axin2. Additionally, MTT assay was conducted to assess cell proliferation; Transwell assay was performed to evaluate cell migration and invasion, respectively. The effect of circ_0038718 on CC tumor growth was tested through tumor formation in nude mice.

RESULTS

circ_0038718 was highly expressed in CC and could sponge miR-195-5p in cytoplasm. Silencing circ_0038718 suppressed the proliferative, migratory and invasive abilities of CC cells, while the promoting effect of high circ_0038718 expression on CC cells was reversed upon miR-195-5p over-expression. Axin2 was a downstream target of miR-195-5p and could regulate the Wnt/β-catenin signaling pathway. Axin2 expression was modulated by circ_0038718/miR-195-5p. Knockdown of Axin2 could also attenuate the promoting effect of high circ_0038718 expression on CC cell malignant progression, thus inhibiting tumor growth.

CONCLUSION

circ_0038718 is able to facilitate CC cell malignant progression via the miR-195-5p/Axin2 axis, which will provide a new idea for finding a novel targeted treatment of CC.

Selenium-mediated gga-miR-29a-3p regulates LMH cell proliferation, invasion, and migration by targeting COL4A2

Selenium (Se) is an essential trace element that has several functions in cellular processes related to cancer prevention. While the cancericidal effect of Se has been reported in liver cancer, the mechanism has not been clarified. MiR-29a has widely been reported as a tumor suppressor; however, it also acts as a carcinogenic agent by increasing cell invasion in human epithelial cancer cells and hepatoma cells. In a previous study, we found that miR-29a-3p is a Se-sensitive miRNA. However, its effect in the chicken hepatocellular carcinoma cell line (LMH) is still unknown. In the present study, we found that the expression of miR-29a-3p in LMH cells was decreased by Se supplementation and increased under Se-deficient conditions. Flow cytometry and CCK-8 results suggested that Se decreased LMH cell proliferation induced by miR-29a-3p overexpression. Transwell and gap-closure assays implied that Se mediated LMH cell invasion and migration by downregulating miR-29a-3p. Quantitative real-time polymerase chain reaction and Western blotting results suggested that Se mitigated miR-29a-3p overexpression-induced LMH cell proliferation by downregulating CDK2, cyclin-D1, CDK6, and cyclin-E1. We further demonstrated that collagen type IV alpha 2 (COL4A2) is a target gene of miR-29a-3p. COL4A2 activates the RhoA/ROCK pathway to promote LMH cell invasion and migration. In conclusion, Se mediated miR-29a-3p overexpression induced LMH cell invasion and migration by targeting COL4A2 to inactivate the RhoA/ROCK pathway.

miR-152-3p Affects the Progression of Colon Cancer via the KLF4/IFITM3 Axis

OBJECTIVE

The purpose of this study was to investigate the relationship between miR-152-3p and the KLF4/IFITM3 axis, thereby revealing the mechanism underlying colon cancer occurrence and development, consequently providing a promising target for colon cancer treatment.

METHODS

Bioinformatics methods were implemented to analyze the differential expression of miRNAs and mRNAs in colon cancer, confirm the target miRNA, and predict the downstream targeted mRNAs. qRT-PCR and Western blot were performed to detect the expression of miR-152-3p, KLF4, and IFITM3. CCK-8 and colony formation assays were conducted for the assessment of cell proliferation, and flow cytometry was carried out for the detection of cell apoptosis. Finally, dual-luciferase reporter gene assay was employed to verify the targeting relationship between miR-152-3p and KLF4.

RESULTS

miR-152-3p was highly expressed in colon cancer cells, whereas KLF4 was poorly expressed. Dual-luciferase assay verified that miR-152-3p targeted to bind to KLF4 and suppressed its expression. Moreover, silencing miR-152-3p or overexpressing KLF4 was found to downregulate IFITM3, thereby inhibiting cell proliferation and potentiating cell apoptosis. In rescue experiments, we found that miR-152-3p deficiency decreased the expression of IFITM3 and weakened cancer cell proliferation, and such effects were restored when miR-152-3p and KLF4 were silenced simultaneously.

CONCLUSION

In sum, we discovered that miR-152-3p can affect the pathogenesis of colon cancer via the KLF4/IFITM3 axis.

Interplay among miR-29 family, mineral metabolism, and gene regulation in Bos indicus muscle

An interplay between gene expression, mineral concentration, and beef quality traits in Bos indicus muscle has been reported previously under a network approach. However, growing evidence suggested that miRNAs not only modulate gene expression but are also involved with mineral homeostasis. To our knowledge, understanding of the miRNA-gene expression-mineral concentration relationship in mammals is still minimal. Therefore, we carried out a miRNA co-expression and multi-level miRNA-mRNA integration analyses to predict the putative drivers (miRNAs and genes) associated with muscle mineral concentration in Nelore steers. In this study, we identified calcium and iron to be the pivotal minerals associated with miRNAs and gene targets. Furthermore, we identified the miR-29 family (miR-29a, -29b, -29c, -29d-3p, and -29e) as the putative key regulators modulating mineral homeostasis. The miR-29 family targets genes involved with AMPK, insulin, mTOR, and thyroid hormone signaling pathways. Finally, we reported an interplay between miRNAs and minerals acting cooperatively to modulate co-expressed genes and signaling pathways both involved with mineral and energy homeostasis in Nelore muscle. Although we provided some evidence to understand this complex relationship, future work should determine the functional implications of minerals for miRNA levels and their feedback regulation system.\\An interplay between gene expression, mineral concentration, and beef quality traits in Bos indicus muscle has been reported previously under a network approach. However, growing evidence suggested that miRNAs not only modulate gene expression but are also involved with mineral homeostasis. To our knowledge, understanding of the miRNA-gene expression-mineral concentration relationship in mammals is still minimal. Therefore, we carried out a miRNA co-expression and multi-level miRNA-mRNA integration analyses to predict the putative drivers (miRNAs and genes) associated with muscle mineral concentration in Nelore steers. In this study, we identified calcium and iron to be the pivotal minerals associated with miRNAs and gene targets. Furthermore, we identified the miR-29 family (miR-29a, -29b, -29c, -29d-3p, and -29e) as the putative key regulators modulating mineral homeostasis. The miR-29 family targets genes involved with AMPK, insulin, mTOR, and thyroid hormone signaling pathways. Finally, we reported an interplay between miRNAs and minerals acting cooperatively to modulate co-expressed genes and signaling pathways both involved with mineral and energy homeostasis in Nelore muscle. Although we provided some evidence to understand this complex relationship, future work should determine the functional implications of minerals for miRNA levels and their feedback regulation system.

The hepatic transcriptome of the turkey poult (Meleagris gallopavo) is minimally altered by high inorganic dietary selenium

There is interest in supplementing animals and humans with selenium (Se) above Se-adequate levels, but the only good biomarker for toxicity is tissue Se. We targeted liver because turkeys fed 5 μg Se/g have hepatic Se concentrations 6-fold above Se-adequate (0.4 μg Se/g) levels without effects on growth or health. Our objectives were (i) to identify transcript biomarkers for high Se status, which in turn would (ii) suggest proteins and pathways used by animals to adapt to high Se. Turkey poults were fed 0, 0.025, 0.4, 0.75 and 1.0 μg Se/g diet in experiment 1, and fed 0.4, 2.0 and 5.0 μg Se/g in experiment 2, as selenite, and the full liver transcriptome determined by RNA-Seq. The major effect of Se-deficiency was to down-regulate expression of a subset of selenoprotein transcripts, with little significant effect on general transcript expression. In response to high Se intake (2 and 5 μg Se/g) relative to Se-adequate turkeys, there were only a limited number of significant differentially expressed transcripts, all with only relatively small fold-changes. No transcript showed a consistent pattern of altered expression in response to high Se intakes across the 1, 2 and 5 μg Se/g treatments, and there were no associated metabolic pathways and biological functions that were significant and consistently found with high Se supplementation. Gene set enrichment analysis also found no gene sets that were consistently altered by high-Se and supernutritional-Se. A comparison of differentially expressed transcript sets with high Se transcript sets identified in mice provided high Se (~3 μg Se/g) also failed to identify common differentially expressed transcript sets between these two species. Collectively, this study indicates that turkeys do not alter gene expression in the liver as a homeostatic mechanism to adapt to high Se.

Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model

Background

The established role miRNA-mRNA regulation of gene expression has in oncogenesis highlights the importance of integrating miRNA with downstream mRNA targets. These findings call for investigations aimed at identifying disease-associated miRNA-mRNA pairs. Hierarchical integrative models (HIM) offer the opportunity to uncover the relationships between disease and the levels of different molecules measured in multiple omic studies.

Methods

The HIM model we formulated for analysis of mRNA-seq and miRNA-seq data can be specified with two levels: (1) a mechanistic submodel relating mRNAs to miRNAs, and (2) a clinical submodel relating disease status to mRNA and miRNA, while accounting for the mechanistic relationships in the first level.

Results

mRNA-seq and miRNA-seq data were acquired by analysis of tumor and normal liver tissues from 30 patients with hepatocellular carcinoma (HCC). We analyzed the data using HIM and identified 157 significant miRNA-mRNA pairs in HCC. The majority of these molecules have already been independently identified as being either diagnostic, prognostic, or therapeutic biomarker candidates for HCC. These pairs appear to be involved in processes contributing to the pathogenesis of HCC involving inflammation, regulation of cell cycle, apoptosis, and metabolism. For further evaluation of our method, we analyzed miRNA-seq and mRNA-seq data from TCGA network. While some of the miRNA-mRNA pairs we identified by analyzing both our and TCGA data are previously reported in the literature and overlap in regulation and function, new pairs have been identified that may contribute to the discovery of novel targets.

Conclusion

The results strongly support the hypothesis that miRNAs are important regulators of mRNAs in HCC. Furthermore, these results emphasize the biological relevance of studying miRNA-mRNA pairs.

Cross talk between mineral metabolism and meat quality: a systems biology overview

Meat quality has an inherent complexity because of the multiple interrelated causative factors and layers of feedback regulation. Understanding the key factors and their interactions has been challenging, despite the availability of remarkable high-throughput tools and techniques that have provided insights on muscle metabolism and the genetic basis of meat quality. Likewise, we have deepened our knowledge about mineral metabolism and its role in cell functioning. Regardless of these facts, complex traits like mineral content and meat quality have been studied under reductionist approaches. However, as these phenotypes arise from complex interactions among different biological layers (genome, transcriptome, proteome, epigenome, etc.), along with environmental effects, a holistic view and systemic-level understanding of the genetic basis of complex phenotypes are in demand. Based on the state of the art, we addressed some of the questions regarding the interdependence of meat quality traits and mineral content. Furthermore, we sought to highlight potential regulatory mechanisms arising from the genes, miRNAs, and mineral interactions, as well as the pathways modulated by this interplay affecting muscle, mineral metabolism, and meat quality. By answering these questions, we did not intend to give an exhaustive review but to identify the key biological points, the challenges, and benefits of integrative genomic approaches.