Long noncoding RNA LINC00305 promotes inflammation by activating the AHRR-NF-κB pathway in human monocytes

The aryl hydrocarbon receptor: a rehabilitated target for therapeutic immune modulation

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor originally identified as the target mediating the toxic effects of environmental pollutants including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and dioxins. For years, AHR activation was actively avoided during drug development. However, the AHR was later identified as an important physiological regulator of the immune response. These findings triggered a paradigm shift that resulted in identification of the AHR as a regulator of both innate and adaptive immunity and outlined a pathway for its modulation by the diet, commensal flora and metabolism in the context of autoimmunity, cancer and infection. Moreover, the AHR was revealed as a candidate target for the therapeutic modulation of the immune response. Indeed, the first AHR-activating drug (tapinarof) was recently approved for the treatment of psoriasis. Clinical trials are underway to evaluate the effects of tapinarof and other AHR-targeting therapeutics in inflammatory diseases, cancer and infections. This Review outlines the molecular mechanism of AHR action, and describes how it regulates the immune response. We also discuss links to disease and AHR-targeting therapeutics that have been tested in past and ongoing clinical trials.

Targeting noncoding RNAs to treat atherosclerosis

Noncoding RNAs (ncRNAs) are pivotal for various pathological processes, impacting disease progression. The potential for leveraging ncRNAs to prevent or treat atherosclerosis and associated cardiovascular diseases is of great significance, especially given the increasing prevalence of atherosclerosis in an ageing and sedentary population. Together, these diseases impose a substantial socio-economic burden, demanding innovative therapeutic solutions. This review explores the potential of ncRNAs in atherosclerosis treatment. We commence by examining approaches for identifying and characterizing atherosclerosis-associated ncRNAs. We then delve into the functional aspects of ncRNAs in atherosclerosis development and progression. Additionally, we review current RNA and RNA-targeting molecules in development or under approval for clinical use, offering insights into their pharmacological potential. The importance of improved ncRNA delivery strategies is highlighted. Finally, we suggest avenues for advanced research to accelerate the use of ncRNAs in treating atherosclerosis and mitigating its societal impact. LINKED ARTICLES: This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.

Aryl hydrocarbon receptor repressor ( AHRR ) methylation predicts risk of vascular disease: A cohort study of the general population

AIMS

Smoking is a risk factor for cardiovascular disease, but there is currently no clinically established biomarker for its cardiovascular damage. We aimed to investigate the hypothesis that aryl hydrocarbon receptor repressor ( AHRR ) methylation at CpG site cg05575921, a biomarker of smoking behavior, is associated with the risk of peripheral artery disease (PAD) and aortic aneurysm (AA) in the general population.

METHODS AND RESULTS

In this prospective cohort study of the general population, we measured AHRR methylation in individuals from three visits to the Copenhagen City Heart Study. Information on risk factors was collected at visits with 10 years intervals; visit 1 (1991-1994), visit 2 (2001-2003), and visit 3 (2011-2015). Individuals were followed up in the Danish National Patient Register for PAD and AA until December 2018. Subhazard ratios were calculated using Fine and Gray competing risk regression. In 11 332 individuals from visit 1 ( n =9234), visit 2 ( n =5384), and visit 3 ( n =4387), there were 613 and 219 events of PAD and AA during up to 26.5 years of follow-up. AHRR hypomethylation was associated with a higher risk of PAD and AA with multivariable-adjusted subhazard ratios of 2.82 (1.91; 4.15) for PAD and 2.88 (1.42; 5.88) for AA in individuals within the lowest versus highest methylation quintile.

CONCLUSIONS

We found that AHRR methylation, a strong biomarker for smoking, was associated with the risk of PAD and AA. AHRR methylation could be a useful tool in more personalized risk prediction of PAD and AA.

Current insights into genome-based personalized nutrition technology: a patent review

Unlike general nutritional ranges that meet the nutritional needs essential for maintaining the life of an entire population, personalized nutrition is characterised by maintaining health through providing customized nutrition according to individuals' lifestyles or genetic characteristics. The development of technology and services for personalized nutrition is increasing, owing to the acquisition of knowledge about the differences in nutritional requirements according to the diversity of individuals and an increase in health interest. Regarding genetics, technology is being developed to distinguish the various characteristics of individuals and provide customized nutrition. Therefore, to understand the current state of personalized nutrition technology, understanding genomics is necessary to acquire information on nutrition research based on genomics. We reviewed patents related to personalized nutrition-targeting genomics and examined their mechanisms of action. Using the patent database, we searched 694 patents on nutritional genomics and extracted 561 highly relevant valid data points. Furthermore, an in-depth review was conducted by selecting core patents related to genome-based personalized nutrition technology. A marked increase was observed in personalized nutrition technologies using methods such as genetic scoring and disease-specific dietary recommendations.

Dysregulation of LncRNAs ANRIL, MALAT1, and LINC00305 in Coronary Slow Flow Patients: Implications for Inflammation and Endothelial Dysfunction

Coronary Slow Flow (CSF) is observed in individuals who experience delayed blood supply in the coronary arteries. Inflammation and endothelial dysfunction may play a role in the etiology and development of CSF. The current investigation aimed to compare the expression of specific long noncoding RNAs (lncRNAs) associated with endothelial dysfunction and inflammation in CSF patients. This case‒control study enrolled 72 CSF patients and 71 healthy individuals. Blood samples were collected, and serum marker levels were measured. The expression levels of lncRNAs ANRIL, MALAT1, and LINC00305 in peripheral blood mononuclear cells (PBMCs) were assessed using real-time Polymerase Chain Reaction (PCR). All statistical analyses were performed using SPSS 22, with the significance level set at P < 0.05. The study revealed that the relative expression of MALAT1 and LINC00305 was significantly lower in the CSF group (p < 0.01), whereas ANRIL was expressed at higher levels (p < 0.0001). The areas under the ROC curves (AUCs) for MALAT1, LINC00305, and ANRIL were 0.64, 0.66, and 0.75, respectively. Notably, the expression level of LINC00305 exhibited an inverse correlation with CSF incidence (OR: 0.83, p: 0.008) in contrast to that of ANRIL (OR: 1.43, p < 0.0001). Additionally, compared to those in the control group, the average BMI, WBC, RBC, Hb, LDH, LDL, FBS, and percentage of neutrophils in the CSF group were significantly greater (p< 0.05). lncRNA ANRIL is upregulated in CSF patients, whereas MALAT1 and LINC00305 are downregulated. Dysregulation of ANRIL, MALAT1, and LINC00305 may serve as diagnostic and predictive factors for CSF leakage.

The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici

Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling future molecular genetics and functional analyses in an important pathogen.

The HDAC2-MTA3 interaction induces nonsmall cell lung cancer cell migration and invasion by targeting c-Myc and cyclin D1

Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs) associated with lung cancer; however, the functions of histone deacetylase 2 (HDAC2) rs13213007 and HDAC2 in nonsmall cell lung cancer (NSCLC) remain unclear. Here we identified HDAC2 rs13213007 as a risk SNP and showed that HDAC2 was upregulated in both peripheral blood mononuclear cells (PBMCs) and NSCLC tissues with the rs13213007 A/A genotype compared with those with the rs13213007 G/G or G/A genotype. Patient clinical data indicated strong associations between rs13213007 genotype and N classification. Immunohistochemical staining confirmed that higher expression of HDAC2 was associated with NSCLC progression. Furthermore, we generated 293T cells with the rs13213007 A/A genotype using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 gene editing. Chromatin immunoprecipitation sequencing followed by motif analysis showed that HDAC2 can bind to c-Myc in rs13213007 A/A 293T cells. Cell Counting Kit-8, colony formation, wound-healing, and Transwell assays revealed that HDAC2 upregulates c-Myc and cyclin D1 expression and promotes NSCLC cell proliferation, migration, and invasion. Co-immunoprecipitation, quantitative reverse transcription-polymerase chain reaction, and western blot analysis assays showed that MTA3 interacts with HDAC2, decreases HDAC2 expression, and rescues the migration and invasion abilities of NSCLC cells. Taken together, these findings identify HDAC2 as a potential therapeutic biomarker in NSCLC.

Dynamic relationship between the aryl hydrocarbon receptor and long noncoding RNA balances cellular and toxicological responses

The aryl hydrocarbon receptor (AhR) is a cytosolic transcription factor activated by endogenous ligands and xenobiotic chemicals. Once the AhR is activated, it translocates to the nucleus, dimerizes with the AhR nuclear translator (ARNT) and binds to xenobiotic response elements (XRE) to promote gene transcription, notably the cytochrome P450 CYP1A1. The AhR not only mediates the toxic effects of environmental chemicals, but also has numerous putative physiological functions. This dichotomy in AhR biology may be related to reciprocal regulation of long non-coding RNA (lncRNA). lncRNA are defined as transcripts more than 200 nucleotides in length that do not encode a protein but are implicated in many physiological processes such as cell differentiation, cell proliferation, and apoptosis. lncRNA are also linked to disease pathogenesis, particularly the development of cancer. Recent studies have revealed that AhR activation by environmental chemicals affects the expression and function of lncRNA. In this article, we provide an overview of AhR signaling pathways activated by diverse ligands and highlight key differences in the putative biological versus toxicological response of AhR activation. We also detail the functions of lncRNA and provide current data on their regulation by the AhR. Finally, we outline how overlap in function between AhR and lncRNA may be one way in which AhR can be both a regulator of endogenous functions but also a mediator of toxicological responses to environmental chemicals. Overall, more research is still needed to fully understand the dynamic interplay between the AhR and lncRNA.

AhRR methylation contributes to disease progression in urothelial bladder cancer

BACKGROUND

Bladder Cancer (BCa) is the tenth most incidental malignancy worldwide. BCa is mostly attributed to environmental exposure and lifestyle, particularly tobacco smoking. The Aryl Hydrocarbon Receptor Repressor (AhRR) participates in the induction of many enzymes involved in metabolizing carcinogens, including tobacco smoke components. Additionally, studies have shown that smoking demethylates the (AhRR) gene in blood, suggesting AhRR demethylation as a specific serum smoking biomarker.

OBJECTIVE

This study aimed to validate AhRR demethylation as a smoking biomarker in the target tissue and investigate its contribution to bladder carcinogenesis.

METHODS

AhRR percent methylation was tested for its association with patient smoking status and oncogenic outcome indicators, particularly p53, RB1, and FGFR3 activating mutations, muscle-invasiveness, and tumor grade, in 180 BCa tissue-based DNA.

RESULTS

Results showed significantly higher AhRR percent methylation in muscle-invasive compared to non-muscle invasive tumors (42.86% vs. 33.98%; p= 0.011), while lower AhRR methylation was significantly associated with FGFR3 Codon 248 mutant genotype compared to wild-type (28.11% ± 9.44 vs. 37.87% ± 22.53; p= 0.036). All other tested associations were non-statistically significant.

CONCLUSIONS

Although AhRR methylation did not predict smoking status in BCa tumors, it seems to play a role in carcinogenesis and disease progression. Our findings make a basis for further research.

The human long noncoding RNAs CoroMarker, MALAT1, CDR1as, and LINC00460 in whole blood of individuals after controlled short-term exposure with ultrafine metal fume particles at workplace conditions, and in human macrophages in vitro

BACKGROUND

Short-term inhalation of occupationally relevant ultrafine zinc/copper (Zn/Cu) containing welding fumes has been shown to induce subclinical systemic inflammation, associated with an elevated risk for cardiovascular diseases. The involvement of noncoding RNAs (lncRNAs) in this setting is currently unknown. However, lncRNAs have been reported to fulfill essential roles in, e.g., cardiovascular diseases, inflammation, infectious diseases, and pollution-related lung disorders.

METHODS

In this study, the specific lncRNAs levels of the 4 lncRNAs CoroMarker, MALAT1, CDR1as and LINC00460 were determined by RT-qPCR in THP-1 macrophages exposed to Zn/Cu metal fume suspensions for 1, 2, and 4 hours in vitro. Furthermore, 14 subjects were exposed to Zn/Cu containing welding fumes (at 2.5 mg/m3) for 6 hours. Before, 6, 10, and 29 hours after exposure start, whole blood cell lncRNAs levels were determined by RT-qPCR.

RESULTS

In THP-1 macrophages, we observed a 2.3-fold increase of CDR1as at 1 h (Wilcoxon p = 0.03), a non-significant increase of CoroMarker at 1 h, and an increase of LINC00460 at 2 h (p = 0.03) and at 4 h (p = 0.06). In whole blood cells, we determined a non-significant upregulation of CDR1as at 6 h (p = 0.2), a significant downregulation of CoroMarker at 6 h (p = 0.04), and a significant upregulation of LINC00460 levels at 10 h (p = 0.04) and 29 h (p = 0.04). MALAT-1 remained unchanged in both settings.

CONCLUSION

The orientation of regulation of the lncRNAs is (except for CoroMarker) similar in the in vitro and in vivo experiments and in line with their described functions. Therefore, these results, e.g. the upregulation of the potential risk marker for cardiovascular diseases, CDR1as, contribute to understanding the underlying mechanisms of Zn/Cu-induced subclinical inflammation in metal workers.

Tocotrienols: Exciting Biological and Pharmacological Properties of Tocotrienols and Naturally Occurring Compounds, Part II

δ-Tocotrienol plus AHA Step-1 diet in hypercholesterolemic subjects caused reductions in lipid parameters (14% to 18%) with 250 mg/d dose, and 500 mg/d resulted induction in these parameters. Although, α-tocopherol is the most bioavailable form of vitamin E. There are few reports on bioavailability of tocotrienols in humans. Pharmacokinetics and bioavailability of δ-tocotrienol was quantified on plasma levels of tocol isomers, cytokines, and microRNAs. Subjects were fed doses of 125 mg/d to 500 mg/d. Plasma samples collected between 0 h to 10 h, levels of tocols estimated by HPLC, which resulted dose-dependent increases in AUC0-10, Cmax0-∞, Tmaxh, t1/2h, Cl-T 1/h, Vd/f, keh-1. Maximum plasma levels of δ-tocotrienol were at 3 h (125 mg/d to 250 mg/d), 6 h (500 mg/d). Effects of 32 compounds were evaluated on TNF-α secretion, nitric oxide production, and gene expression (TNF-α, IL-1β, IL-6, iNOS activity) in PPAR-α knockout mice. Anticancer activities of thiostrepton, dexamethasone, 2-methoxyestradiol, δ-tocotrienol, quercetin, amiloride, quinine sulfate showed significant anti-proliferative properties in Hela cells, pancreatic, prostate, breast, lungs, melanoma, B-lymphocytes, T-cells (40% to 95%). Results of plasma total mRNAs after δ-tocotrienol feeding to hepatitis C patients revealed significant down-regulated gene expression of pro-inflammatory cytokines. A mixture of δ-tocotrienol, resveratrol, vitamin D3 (NS-3) were given two capsules/d or cellulose/olive oil as placebo to individuals with T2DM (24-weeks). Significant down-regulation (15% to 74%) of gene expression in diabetes biomarkers and decreases i n serum levels of fasting-glucose, HbA1c, hs-CRP, fasting-insulin, HOMA-IR, MDA (9% to 23%) were observed with NS-3 treated T2DM. Pure plasma mRNAs and miRNAs of pre-dose vs. post-dose of NS-3 treated samples were analyzed by Next Generation Sequencing (NGS). Venn diagrams have established genetic regulatory network images and canonical signaling pathways for mRNA, miRNA, and paired mRNA-miRNA.

Abnormal expression of long non-coding RNA rhabdomyosarcoma 2-associated transcript (RMST) participates in the pathological mechanism of atherosclerosis by regulating miR-224-3p

Study shows that long non-coding RNA (lncRNA) plays a regulatory role in cardiovascular diseases, and the mechanism of rhabdomyosarcoma 2-associated transcript (RMST) in atherosclerosis (AS) is still unclear. This study aimed to evaluate the expression of RMST and its possible role in the occurrence of AS. RMST and miR-224-3p level in serum and human umbilical vein endothelial cells (HUVECs) were determined by real-time quantitative PCR (RT-qPCR). In vitro atherosclerotic cell model was achieved by treating HUVECs with ox-LDL. Receiver operating characteristic (ROC) curve assessed the diagnostic value of RMST in AS, and Pearson correlation coefficient estimated the correlation of RMST with carotid intima-media thickness (CIMT) and carotid-femoral pulse wave velocity (cfPWV). Cell counting kit-8 (CCK-8) assay and Enzyme-linked immunosorbent assay (ELISA) were performed to evaluate the effect of RMST on cell viability and inflammatory response. The luciferase analysis was used to validate the relationship between RMST and miR-224-3p. The results showed that in serum and HUVECs, RMST levels were increased, while miR-224-3p level was decreased. ROC curve suggested that RMST had clinical diagnostic value for AS. Besides, CIMT and cfPWV were positively correlated with RMST levels, respectively. In HUVECs, RMST-knockdown notably improved the cell viability and inhibited the production of inflammatory factors. Moreover, miR-224-3p was the target of RMST. In conclusion, RMST has the potential to be a diagnostic marker for AS. RMST-knockdown contributes to the enhancement of cell viability and the inhibition of inflammatory response, which may provide new insights into the conquest of AS.

Aryl Hydrocarbon Receptor Repressor Is Hypomethylated in Psoriasis and Promotes Psoriasis-like Inflammation in HaCaT Cells

It is known that DNA hypomethylation of aryl hydrocarbon receptor repressor (AhRR), one of the epigenetic markers of environmental pollutants, causes skin diseases. However, the function and mechanisms are still unknown. We aimed to determine whether AhRR is hypomethylated in PBMC of psoriasis patients, as well as to examine the expression of psoriasis-related inflammatory cytokines and antimicrobial peptides after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treatment in HaCaT cells overexpressing or silencing AhRR. AhRR was determined by qPCR, Western blot, immunohistochemistry, and immunocytochemistry in skin tissue and HaCaT cells. DNA methylation of AhRR was performed by Infinium Human Methylation450 BeadChip in PBMC of psoriasis patients and methylation-specific PCR (MSP) in HaCaT cells. NF-κB pp50 translocation and activity were performed by immunocytochemistry and luciferase reporter assay, respectively. We verified AhRR gene expression in the epidermis from psoriasis patients and healthy controls. AhRR hypomethylation in PBMC of psoriasis patients and pAhRR-HaCaT cells was confirmed. The expression level of AhRR was increased in both TCDD-treated HaCaT cells and pAhRR-HaCaT cells. NF-κB pp50 translocation and activity increased with TCDD. Our results showed that AhRR was hypomethylated and overexpressed in the lesional skin of patients with psoriasis, thereby increasing AhRR gene expression and regulating pro-inflammatory cytokines through the NF-κB signaling pathway in TCDD-treated HaCaT cells.

The Combined Regulation of Long Non-coding RNA and RNA-Binding Proteins in Atherosclerosis

Atherosclerosis is a complex disease closely related to the function of endothelial cells (ECs), monocytes/macrophages, and vascular smooth muscle cells (VSMCs). Despite a good understanding of the pathogenesis of atherosclerosis, the underlying molecular mechanisms are still only poorly understood. Therefore, atherosclerosis continues to be an important clinical issue worthy of further research. Recent evidence has shown that long non-coding RNAs (lncRNAs) and RNA-binding proteins (RBPs) can serve as important regulators of cellular function in atherosclerosis. Besides, several studies have shown that lncRNAs are partly dependent on the specific interaction with RBPs to exert their function. This review summarizes the important contributions of lncRNAs and RBPs in atherosclerosis and provides novel and comprehensible interaction models of lncRNAs and RBPs.

The diversity of lipocalin receptors

Lipocalins are important carriers of preferentially hydrophobic molecules, but they can also bind other ligands, like highly polar siderophores or intact proteins. Consequently, they are involved in a variety of physiological processes in many species. Since lipocalins are mainly extracellular proteins, they have to interact with cell receptors to exert their biological effects. In contrast to the large number of lipocalins identified in the last years, the number of receptors known is still limited. Nevertheless, some novel findings concerning the molecules involved in cellular uptake or signaling effects of lipocalins have been made recently. This review presents a detailed overview of the receptors identified so far. The methods used for isolation or identification are described and structural as well as functional information on these proteins is presented essentially in chronological order of their initial discovery.

Non-coding RNAs in cardiac inflammation: key drivers in the pathophysiology of heart failure

Heart failure is among the most progressive diseases and a leading cause of morbidity. Despite several advances in cardiovascular therapies, pharmacological treatments are limited to relieve symptoms without curing cardiac injury. Multiple observations point to the involvement of immune cells as key drivers in the pathophysiology of heart failure. In particular, there is a growing recognition that heart failure is related to a prolonged and insufficiently repressed inflammatory response leading to molecular, cellular, and functional cardiac alterations. Over the last decades, non-coding RNAs are recognized as prominent mediators of the cardiac inflammation, affecting the function of several immune cells. In the current review, we explore the contribution of the diverse immune cells in the progression of heart failure, revealing mechanistic functions for non-coding RNAs in cardiac immune cells as a new and exciting field of investigation.

Up-regulated long noncoding RNA AC007128.1 and its genetic polymorphisms associated with Tuberculosis susceptibility

Background

Tuberculosis (TB) remains a major public health problem. Long non-coding RNAs (lncRNAs) are important regulators of gene expression. In this study, we explored the association between the expression of lncRNA AC007128.1 and TB susceptibility.

Methods

Three single-nucleotide polymorphisms (SNPs) (rs12333784, rs6463794, and rs720964) of lncRNA AC007128.1 were selected using the 1000 Genomes Project database and offline software Haploview V4.2, and were genotyped by a customized 2×48-Plex SNPscan™ Kit.

Results

We identified two differentially expressed lncRNA including AC007128.1 and AP001065.3 in comparisons of expression profiles between ATB vs. LTBI, LTBI vs. HCs, and AC700128.1 expression was specifically and significantly up-regulated in TB patients by verification of external data. Gene Ontology functional enrichment analysis and co-expression network showed up-regulated mRNA was mainly involved in negative regulation of the G protein-coupled receptor (GPCR) signaling pathway, and FPR1 and CYP27B1 were involved in the co-expression of AC007128.1. Using the 1000 Genomes Project, software Haploview V4.2, and SNP genotype, we screened out SNP rs12333784 which locus at 7p21.3 in AC007128.1 associated with TB susceptibility. The G carrier of rs12333784 was then finally verified to be significantly associated with pulmonary TB (PTB) and extrapulmonary tuberculosis (EPTB) susceptibility (pBonferroni =0.03878), and a similar but more significant effect was observed under the dominant model analysis (pBonferroni =0.013, OR =1.349, 95% CI, 1.065–1.709). In addition, the GG + GA genotype of SNP rs12333784 was significantly correlated with higher glucose (GLU) (P=0.03), higher gamma-glutamyl transferase (GGT) (P=0.05), and higher erythrocyte sedimentation rate (ESR) (P=0.05).

Conclusions

Our findings show lncRNA AC007128.1 can be regarded as biomarkers discriminating between ATB and LTBI and may also be a diagnostic biomarker for LBTI. These findings may aid clinical decision making in the management of TB.

Screening of Potential Key Genes Related to Tubal Factor Infertility Based on Competitive Endogenous RNA Network

Background: The molecular biological mechanism of tubal factor infertility (TFI) is still unclear. Long noncoding RNAs (lncRNAs) are considered a major part of the competitive endogenous RNA (ceRNA) network and have attracted growing attention. Our study aimed to explore the regulatory mechanisms of lncRNAs associated with TFI and screen potential key genes related to TFI. Materials and Methods: Differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) were identified by comparing normal and TFI expression patterns of lncRNAs and mRNAs in eutopic endometrial tissues obtained from 3 normal and 3 TFI patients during implantation. These data were used to develop a protein-protein interaction (PPI) network of DEGs using the STRING online software. The identified DELs and DEGs were then used to construct a ceRNA network, and the Network Analyzer Tool Kit in Cytoscape was used to analyze the ceRNA network topology and stability. Finally, the overlapping genes present in both the ceRNA and PPI networks were selected as the potential key genes related to TFI. Results: Ninety-six DEGs (59 up and 37 down) and 45 DELs (28 up and 17 down) were identified. Thirty-four DEGs were mapped in a PPI network. A ceRNA network, including two lncRNAs (LINC00305 and DLX6-AS1), four microRNAs (hsa-miR-20b-5p, hsa-miR-17-5p, hsa-miR-107, and hsa-miR-24-3p), and four mRNAs (MAP3K3, HMGB3, FAM103A1, and TMEM209), was successfully constructed. Importantly, a potential key gene (TMEM209) related to TFI was identified. Conclusion: The construction of a ceRNA network related to TFI may help elucidate the regulatory mechanism by which genes and lncRNAs function as ceRNA networks. Importantly, TMEM209 may be further evaluated as potential therapeutic targets for TFI.

Long Non-Coding RNAs (lncRNAs) in Cardiovascular Disease Complication of Type 2 Diabetes

The discovery of non-coding RNAs (ncRNAs) has opened a new paradigm to use ncRNAs as biomarkers to detect disease progression. Long non-coding RNAs (lncRNA) have garnered the most attention due to their specific cell-origin and their existence in biological fluids. Type 2 diabetes patients will develop cardiovascular disease (CVD) complications, and CVD remains the top risk factor for mortality. Understanding the lncRNA roles in T2D and CVD conditions will allow the future use of lncRNAs to detect CVD complications before the symptoms appear. This review aimed to discuss the roles of lncRNAs in T2D and CVD conditions and their diagnostic potential as molecular biomarkers for CVD complications in T2D.

Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci

The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.

Functioning of Long Noncoding RNAs Expressed in Macrophage in the Development of Atherosclerosis

Chronic inflammation is part of the pathological process during atherosclerosis (AS). Due to the abundance of monocytes/macrophages within the arterial plaque, monocytes/macrophages have become a critical cellular target in AS studies. In recent decades, a number of long noncoding RNAs (lncRNAs) have been found to exert regulatory roles on the macrophage metabolism and macrophage plasticity, consequently promoting or suppressing atherosclerotic inflammation. In this review, we provide a comprehensive overview of lncRNAs in macrophage biology, highlighting the potential role of lncRNAs in AS based on recent findings, with the aim to identify disease biomarkers and future therapeutic interventions for AS.

A SNP-mediated lncRNA (LOC146880) and microRNA (miR-539-5p) interaction and its potential impact on the NSCLC risk

BACKGROUND

Many cancer-associated single nucleotide polymorphisms (SNPs) are located in the genomic regions of long non-coding RNAs (lncRNAs). Mechanisms of these SNPs in connection to cancer risk are not fully understood.

METHODS

Association of SNP (rs140618127) in lncRNA LOC146880 with non-small cell lung cancer (NSCLC) was evaluated in a case-control study of 2707 individuals. The mechanism of the SNP's biologic influence was explored with in vitro and in vivo experiments, including plasmid transfection, siRNA knockdown, flow cytometry assessment, and assays of cell proliferation, migration, invasion, and colony formation.

RESULTS

Association analysis showed that A allele of SNP rs140618127 was associated with low risk of NSCLC in the Chinese population. Lab experiments indicated that SNP rs140618127 contained a binding site for miR-539-5p and the binding between miR-539-5p and LOC146880 resulted in declined phosphorylation of an oncogene, ENO1. The reduced phosphorylation of ENO1 led to decreased phosphorylation of PI3K and Akt, which is further linked to the decline in cell proliferation and tumor progression.

CONCLUSION

The study demonstrates that SNP rs140618127 in lncRNA loc146880 provides an alternate binding site for microRNA miR-539-5p which affects the phosphorylation of ENO1 and activation of the PI3K and Akt pathway.

A comprehensive analysis of AHRR gene as a candidate for cleft lip with or without cleft palate

Cleft lip and palate (CL/P) is among the most common congenital malformations and affects 1 in 700 newborns. CL/P is caused by genetic and environmental factors (maternal smoking, alcohol or drug use and others). Many genes and loci were associated with cleft lip/palate but the amount of heterogeneity justifies identifying new causal genes and variants. AHRR (Aryl-Hydrocarbon Receptor Repressor) gene has recently been related to CL/P however, few functional studies analyze the genotypephenotype interaction of AHRR with CL/P. Several studies associate the molecular pathway of AHRR to CL/P which indicates this gene as a functional candidate in CL/P etiology.

METHODS

Systematic Literature Review was performed using PUBMED database with the keywords cleft lip, cleft palate, orofacial cleft, AHRR and synonyms. SLR resulted in 37 included articles.

RESULTS

AHRR is a positional and functional candidate gene for CL/P. In silico analysis detected interactions with other genes previously associated to CL/P like ARNT and CYP1A1. AHRR protein regulates cellular toxicity through TCDD mediated AHR pathway. Exposure to TCDD in animal embryos is AHR mediated and lead to cleft palate due to palate fusion failure and post fusion rupture. AHRR regulates cellular growth and differentiation, fundamental to lip and palatogenesis. AHRR decreases carcinogenesis and recently a higher tumor risk has been described in CL/P patients and families. AHRR is also a smoking biomarker due to changed methylation sites found in smokers DNA although folate intake may partially revert these methylation alterations. This corroborates the role of maternal smoking and lack of folate supplementation as risk factors for CL/P.

CONCLUSION

This research identified the importance of AHRR in dioxin response and demonstrated an example of genetic and environmental interaction, indispensable in the development of many complex diseases.

The Long Non-Coding RNA Landscape of Atherosclerotic Plaques

Currently, cardiovascular diseases continue to be the leading cause of death worldwide; therefore, atherosclerosis remains one of the most crucial public health problems. This chronic and complex disease is considered to be a result of aberrant lipid homeostasis and inflammation of the inner wall of arteries that leads to plaque development. In recent years, a specific class of non-coding RNAs that are characterised by transcript lengths longer than 200 nucleotides, called long non-coding RNAs (lncRNAs), has emerged. Moreover, a growing body of evidence indicates that deregulation of lncRNA expression may contribute to the development of many diseases. Despite continuous efforts in deciphering the molecular basis of atherosclerotic plaque (AP) formation, many aspects of this process remain elusive. Therefore, continuing efforts in this area should remain the highest priority in the coming years. Establishment of a standardised experimental pipeline and validation of lncRNAs as possible relevant biomarkers for cardiovascular disease would enable the translation of gathered findings into clinical practice.

Serum LINC00305 expression and its genetic variant rs2850711 are associated with clinical and laboratory features of rheumatoid arthritis

BACKGROUND

Long intergenic non-protein coding (lnc) RNA 00305 (LINC00305) is a pro-inflammatory atherosclerosis-associated lncRNA. We hypothesised that LINC00305 expression and its variant rs2850711 (A/T) are implicated in rheumatoid arthritis (RA) and linked with clinical and routine laboratory markers.

METHODS

100 RA patients and 100 healthy controls were recruited. LINC00305 genotyping and expression were performed using allelic-discrimination PCR and quantitative real-time PCR. LINC00305 diagnostic power was evaluated using area under the receiver operating characteristic curve (AUC). Serum nuclear factor- κB (NF-κB) and matrix metalloproteinase-3 (MMP-3) levels were determined by ELISA, standard laboratory markers by routine methods.

RESULTS

LINC00305 expression was significantly increased in RA patients and positively correlated with DAS28, C-reactive protein, erythrocyte sedimentation rate, rheumatoid factor and anti-cyclic citrullinated peptide antibody. In multivariate analysis, NF-κB, MMP-3 and LINC00305 were significant predictors of RA (P< 0.0001). Individuals carrying AT and TT genotypes of rs2850711 polymorphism had significantly more likely to have RA than AA genotype carriers (P< 0.05). LINC00305 expression, DAS28 score and serum levels of NF-κB and MMP-3 were significantly increased in the patients carrying LINC00305 AT and TT genotypes as compared with AA genotype patients (P< 0.01).

CONCLUSION

Increased expression level of LINC00305 and its rs2850711 genetic variant may play a role in the diagnosis and management of RA, and its severity and activity.

The how and why of lncRNA function: An innate immune perspective

Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.

Long non-coding RNAs in immune regulation and their potential as therapeutic targets

Long non-coding RNAs (lncRNAs) are potent regulators of immune cell development and function. Their implication in multiple immune-mediated disorders highlights lncRNAs as exciting biomarkers and potential drug targets. Recent technological innovations in oligo-based therapeutics, development of RNA-targeting small molecules, and CRISPR-based approaches, position RNA as the next therapeutic frontier. Here, we review the latest advances made toward understanding the role of lncRNAs in human immunological disorders and further discuss RNA-targeting approaches that could be potentially exploited to manipulate lncRNA function as a clinical intervention.

Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression

Background

Peroxisome proliferator-activated receptor gamma (PPARγ) is a major regulator in sepsis. Our previous study identified the enhancer polymorphism rs10865710C/G to be associated with susceptibility to sepsis in trauma patients. We performed two-stage cohort studies integrating biological experiments of potential functional variants that modify susceptibility to traumatic sepsis.

Methods

Improved multiplex ligation detection reaction (iMLDR) was used to genotype rs10865710 in 797 Han Chinese trauma patients in Chongqing. Clinical relevance was validated in 334 patients in Guizhou. The potential function of rs10865710 in transcriptional regulation was explored through a dual luciferase reporter assay and electrophoretic mobility shift assay (EMSA). Expression of PPARγ was assessed by expression quantitative trait locus (e-QTL) and western blot analyses.

Results

The association results confirmed rs10865710 to be significantly strongly associated with sepsis risk in trauma patients of the Chongqing and Guizhou cohorts (OR = 1.41 (1.11–1.79), P = 0.004 and OR = 1.45 (1.01–2.09), P = 0.046, both for allele-dose effect, respectively). A meta-analysis of both cohorts and a previous study indicated strong evidence for this association (OR = 1.41 (1.17–1.71), P = 0.0004 for the dominant model, OR = 1.78 (1.34–2.36), P < 0.0001 for the recessive model and OR = 1.38 (1.20–1.58), P < 0.0001 for the allelic model). Functional experiments verified that rs10865710 was a causative variant influencing enhancer activity (G vs. C, 0.068 ± 0.004 vs. 0.096 ± 0.002, P = 0.0005) and CREB2 binding. Expression analysis also indicatevd rs10865710 genotypes to be associated with levels of PPARγ expression (P = 9.2 × 10⁻⁵ for dominant effect and P = 0.005 for recessive effect).

Conclusions

Our study provides evidence that the enhancer-region polymorphism rs10865710 might influence transcription factor binding and regulate PPARγ expression, thus conferring susceptibility to traumatic sepsis.

Trial registration

ClinicalTrials.gov, NCT01713205. Registered 18 October 2012, retrospectively registered.

Differential DNA methylation in blood as a mediator of the association between cigarette smoking and bladder cancer risk among postmenopausal women

Smoking accounts for approximately 52% of bladder cancer incidence among postmenopausal women, but the underlying mechanism is poorly understood. Our study investigates whether changes in DNA methylation, as measured in blood, mediate the impact of smoking on bladder cancer risk among postmenopausal women. We conducted analyses among 206 cases and 251 controls that were current or never smokers at baseline from a previous case-control study of bladder cancer and genome-wide DNA methylation nested within the Women's Health Initiative. Separate mediation analyses were conducted for three CpG sites demonstrating robust associations with smoking in prior methylome-wide association studies: cg05575921 (AhRR), cg03636183 (F2RL3), and cg19859270 (GPR15). We estimated causal effects using the regression-based, four-way decomposition approach, which addresses the interaction between smoking and each CpG site. The overall proportion of the excess relative risk mediated by cg05575921 was 92% (p-value = 0.004) and by cg19859270 was 79% (p-value = 0.02). The largest component of the excess relative risk of bladder cancer due to 30 pack-years of smoking history in current smokers was the mediated interaction for both cg05575921 (72%, p = 0.02) and cg19859270 (72%, p-value = 0.04), where the mediated interaction is the effect of smoking on bladder cancer that both acts through differential methylation and depends on smoking history. There was little evidence that smoking was mediated through cg03636183. Our results suggest that differential methylation of cg05575921 and cg19859270 mediate the effects of smoking on bladder cancer, potentially revealing downstream effects of smoking relevant for carcinogenesis.

Disease-Associated SNPs in Inflammation-Related lncRNAs

Immune-mediated diseases, such as celiac disease, type 1 diabetes or multiple sclerosis, are a clinically heterogeneous group of diseases that share many key genetic triggers. Although the pathogenic mechanisms responsible for the development of immune mediated disorders is not totally understood, high-throughput genomic studies, such as GWAS and Immunochip, performed in the past few years have provided intriguing hints about underlying mechanisms and pathways that lead to disease. More than a hundred gene variants associated with disease susceptibility have been identified through such studies, but the progress toward understanding the underlying mechanisms has been slow. The majority of the identified risk variants are located in non-coding regions of the genome making it difficult to assign a molecular function to the SNPs. However, recent studies have revealed that many of the non-coding regions bearing disease-associated SNPs generate long non-coding RNAs (lncRNAs). LncRNAs have been implicated in several inflammatory diseases, and many of them have been shown to function as regulators of gene expression. Many of the disease associated SNPs located in lncRNAs modify their secondary structure, or influence expression levels, thereby affecting their regulatory function, hence contributing to the development of disease.

CRISPR links to long noncoding RNA function in mice: A practical approach

Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.

Inflammatory cells and their non-coding RNAs as targets for treating myocardial infarction

Myocardial infarction triggers infiltration of several types of immune cells that coordinate both innate and adaptive immune responses. These play a dual role in post-infarction cardiac remodeling by initiating and resolving inflammatory processes, which needs to occur in a timely and well-orchestrated way to ensure a reestablishment of normalized cardiac functions. Thus, therapeutic modulation of immune responses might have benefits for infarct patients. While such strategies have shown great potential in treating cancer, applications in the post-infarction context have been disappointing. One challenge has been the complexity and plasticity of immune cells and their functions in cardiac regulation and healing. The types appear in patterns that are temporally and spatially distinct, while influencing each other and the surrounding tissue. A comprehensive understanding of the immune cell repertoire and their regulatory functions following infarction is sorely needed. Processes of cardiac remodeling trigger additional genetic changes that may also play critical roles in the aftermath of cardiovascular disease. Some of these changes involve non-coding RNAs that play crucial roles in the regulation of immune cells and may, therefore, be of therapeutic interest. This review summarizes what is currently known about the functions of immune cells and non-coding RNAs during post-infarction wound healing. We address some of the challenges that remain and describe novel therapeutic approaches under development that are based on regulating immune responses through non-coding RNAs in the aftermath of the disease.

Combined bead-based multiplex detection of RNA and protein biomarkers: Implications for understanding the time course of skeletal muscle injury and repair

Biological response to skeletal muscle injury time course is generally classified as initial (elevated within first 4-h), delayed (elevated at 24-h), and/or prolonged (elevated at 4-h and sustained to 24-h). Accurate description of this process requires the ability to measure a robust set of RNA and protein biomarkers, yet such an approach is not common and not always feasible. This method proposes a novel experimental approach that focuses on the use of bead-based multiplex detection to measure mRNA, lncRNA, cytokines, soluble cytokine receptors, and myokines at 4-h and 24-h post muscle injury. We used an extreme aerobic exercise session (half-marathon race) to create a consistent muscle injury stimulus via oxidative stress and eccentric contractions. Venous blood samples were analyzed to determine the change in 90 targets. Specifically, we identified 14 mRNA, 2 lncRNA, 4 cytokines, and 5 myokines that had only an initial response (change at 4-h). We identified 2 mRNA, 2 cytokines, 13 soluble cytokine receptors, and 1 myokine that had only a delayed response (change at 24-h). Finally, we identified 18 mRNA, 4 lncRNA, 6 myokines and 15 cytokines that had a prolonged response (change at 4-h and sustained at 24-h). We found 4 targets to be undetectable or having no response relative to muscle injury recovery. These findings demonstrate the interplay between RNA and protein biomarkers in response to skeletal muscle injury. This novel experimental application of bead-based multiplexing is applicable to a variety of clinical models that involve muscle injury and/or wasting.

Genome-wide analysis of long non-coding RNAs in Catalpa bungei and their potential function in floral transition using high-throughput sequencing

BACKGROUND

Long non-coding RNAs (lncRNAs) have crucial roles in various biological regulatory processes. However, the study of lncRNAs is limited in woody plants. Catalpa bungei is a valuable ornamental tree with a long cultivation history in China, and a deeper understanding of the floral transition mechanism in C. bungei would be interesting from both economic and scientific perspectives.

RESULTS

In this study, we categorized C. bungei buds from early flowering (EF) and normal flowering (NF) varieties into three consecutive developmental stages. These buds were used to systematically study lncRNAs during floral transition using high-throughput sequencing to identify molecular regulatory networks. Quantitative real-time PCR was performed to study RNA expression changes in different stages. In total, 12,532 lncRNAs and 26,936 messenger RNAs (mRNAs) were detected. Moreover, 680 differentially expressed genes and 817 differentially expressed lncRNAs were detected during the initiation of floral transition. The results highlight the mRNAs and lncRNAs that may be involved in floral transition, as well as the many lncRNAs serving as microRNA precursors. We predicted the functions of lncRNAs by analysing the relationships between lncRNAs and mRNAs. Seven lncRNA-mRNA interaction pairs may participate in floral transition.

CONCLUSIONS

This study is the first to identify lncRNAs and their potential functions in floral transition, providing a starting point for detailed determination of the functions of lncRNAs in C. bungei.

Role of lncRNAs in aging and age-related diseases

Aging is progressive physiological degeneration and consequently declined function, which is linked to senescence on both cellular and organ levels. Accumulating studies indicate that long noncoding RNAs (lncRNAs) play important roles in cellular senescence at all levels-transcriptional, post-transcriptional, translational, and post-translational. Understanding the molecular mechanism of lncRNAs underlying senescence could facilitate interpretation and intervention of aging and age-related diseases. In this review, we describe categories of known and novel lncRNAs that have been involved in the progression of senescence. We also identify the lncRNAs implicated in diseases arising from age-driven degeneration or dysfunction in some representative organs and systems (brains, liver, muscle, cardiovascular system, bone pancreatic islets, and immune system). Improved comprehension of lncRNAs in the aging process on all levels, from cell to organismal, may provide new insights into the amelioration of age-related pathologies and prolonged healthspan.

δ-Tocotrienol feeding modulates gene expression of EIF2, mTOR, protein ubiquitination through multiple-signaling pathways in chronic hepatitis C patients

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.

Electronic supplementary material

The online version of this article (10.1186/s12944-018-0804-7) contains supplementary material, which is available to authorized users.

Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression

BACKGROUND

Cigarette smoke is a causal factor in cancers and cardiovascular disease. Smoking-associated differentially methylated regions (SM-DMRs) have been observed in disease studies, but the causal link between altered DNA methylation and transcriptional change is obscure.

OBJECTIVE

Our objectives were to finely resolve SM-DMRs and to interrogate the mechanistic link between SM-DMRs and altered transcription of enhancer noncoding RNA (eRNA) and mRNA in human circulating monocytes.

METHOD

We integrated SM-DMRs identified by reduced representation bisulfite sequencing (RRBS) of circulating CD14+ monocyte DNA collected from two independent human studies [n=38 from Clinical Research Unit (CRU) and n=55 from the Multi-Ethnic Study of Atherosclerosis (MESA), about half of whom were active smokers] with gene expression for protein-coding genes and noncoding RNAs measured by RT-PCR or RNA sequencing. Candidate SM-DMRs were compared with RRBS of purified CD4+ T cells, CD8+ T cells, CD15+ granulocytes, CD19+ B cells, and CD56+ NK cells (n=19 females, CRU). DMRs were validated using pyrosequencing or bisulfite amplicon sequencing in up to 85 CRU volunteers, who also provided saliva DNA.

RESULTS

RRBS identified monocyte SM-DMRs frequently located in putative gene regulatory regions. The most significant monocyte DMR occurred at a poised enhancer in the aryl-hydrocarbon receptor repressor gene (AHRR) and it was also detected in both granulocytes and saliva DNA. To our knowledge, we identify for the first time that SM-DMRs in or near AHRR, C5orf55-EXOC-AS, and SASH1 were associated with increased noncoding eRNA as well as mRNA in monocytes. Functionally, the AHRR SM-DMR appeared to up-regulate AHRR mRNA through activating the AHRR enhancer, as suggested by increased eRNA in the monocytes, but not granulocytes, from smokers compared with nonsmokers.

CONCLUSIONS

Our findings suggest that AHRR SM-DMR up-regulates AHRR mRNA in a monocyte-specific manner by activating the AHRR enhancer. Cell type-specific activation of enhancers at SM-DMRs may represent a mechanism driving smoking-related disease. https://doi.org/10.1289/EHP2395.

Suppressive effects of aryl-hydrocarbon receptor repressor on adipocyte differentiation in 3T3-L1 cells

The aryl-hydrocarbon receptor repressor (AhRR) negatively regulates aryl-hydrocarbon receptor (AhR) signaling via its inhibitory transactivation. AhR is well known to suppress adipocyte differentiation, but the function of AhRR during adipogenesis is unclear. The purpose of this study was to investigate the role of AhRR in adipocyte differentiation using 3T3-L1 cells. During the early phase of differentiation, AhRR expression was transiently induced, but throughout the entire differentiation process, low levels of AhR expression were maintained. AhRR knockdown significantly increased not only glycerol-3-phosphate dehydrogenase (GPDH) activity but also lipid accumulation inside the cells. AhRR overexpression clearly reduced GPDH activity and lipid accumulation, indicating that AhRR upregulation during the early stage of adipogenesis suppresses adipocyte differentiation. Since AhRR knockdown increases the expression and activity of peroxisome proliferator-activated receptor γ (PPARγ), AhRR negatively regulates PPARγ during adipogenesis. In summary, similar to AhR, AhRR acts as an inhibitor of adipocyte differentiation. In addition to controlling the negative feedback loop of AhR, AhRR might be involved in other functions, especially in adipocyte differentiation processes.

LncRNAs in vascular biology and disease

Accumulating studies indicate that long non-coding RNAs (lncRNAs) play important roles in the regulation of diverse biological processes involved in homeostatic control of the vessel wall in health and disease. However, our knowledge of the mechanisms by which lncRNAs control gene expression and cell signaling pathways is still nascent. Furthermore, only a handful of lncRNAs has been functionally evaluated in response to pathophysiological stimuli or in vascular disease states. For example, lncRNAs may regulate endothelial dysfunction by modulating endothelial cell proliferation (e.g. MALAT1, H19) or angiogenesis (e.g. MEG3, MANTIS). LncRNAs have also been implicated in modulating vascular smooth muscle cell (VSMC) phenotypes or vascular remodeling (e.g. ANRIL, SMILR, SENCR, MYOSLID). Finally, emerging studies have implicated lncRNAs in leukocytes activation (e.g. lincRNA-Cox2, linc00305, THRIL), macrophage polarization (e.g. GAS5), and cholesterol metabolism (e.g. LeXis). This review summarizes recent findings on the expression, mechanism, and function of lncRNAs implicated in a range of vascular disease states from mice to human subjects. An improved understanding of lncRNAs in vascular disease may provide new pathophysiological insights and opportunities for the generation of a new class of RNA-based biomarkers and therapeutic targets.

The emerging role of long non-coding RNA in spinal cord injury

Spinal cord injury (SCI) is a significant health burden worldwide which causes permanent neurological deficits, and there are approximately 17,000 new cases each year. However, there are no effective and current treatments that lead to functional recovery because of the limited understanding of the pathogenic mechanism of SCI. In recent years, the biological roles of long non-coding RNAs (lncRNAs) in SCI have attracted great attention from the researchers all over the world, and an increasing number of studies have investigated the regulatory roles of lncRNAs in SCI. In this review, we summarized the biogenesis, classification and function of lncRNAs and focused on the investigations on the roles of lncRNAs involved in the pathogenic processes of SCI, including neuronal loss, astrocyte proliferation and activation, demyelination, microglia activation, inflammatory reaction and angiogenesis. This review will help understand the molecular mechanisms of SCI and facilitate the potential use of lncRNAs as diagnostic markers and therapeutic targets for SCI treatment.

Emerging Roles for Epigenetic Programming in the Control of Inflammatory Signaling Integration in Heath and Disease

Macrophages and dendritic cells initiate the innate immune response to infection and injury and contribute to inflammatory signaling to maintain the homeostasis of various tissues, which includes resident macrophages for the elimination of invading microorganisms and tissue damage. Inappropriate inflammatory signaling can lead to persistent inflammation and further develop into autoimmune and inflammation-associated diseases. Inflammatory signaling pathways have been well characterized, but how these signaling pathways are converted into sustained and diverse patterns of expression of cytokines, chemokines, and other genes in response to environmental challenges is unclear. Emerging evidence suggests the important role of epigenetic mechanisms in finely tuning the outcome of the host innate immune response. An understanding of epigenetic regulation of innate immune cell identity and function will enable the identification of the mechanism between gene-specific host defenses and inflammatory disease and will also allow for exploration of the program of innate immune memory in health and disease. This information could be used to develop therapeutic agents to enhance the host response, preventing chronic inflammation through preserving tissues and signaling integrity.