Microarray Analysis of lncRNA and mRNA Expression Profiles in Patients with Neuromyelitis Optica

Significant up-regulation of lncRNAs in neuromyelitis optica spectrum disorder

Neuromyelitis optica spectrum disorder (NMOSD) is an immune-related demyelinating defect. Long non-coding RNAs (lncRNAs) might influence the pathobiology and progression of NMOSD. The current study assessed expression level of NEAT1, PANDAR, MEG3 and TUG1 lncRNAs in the peripheral blood of NMOSD patients compared with healthy individuals. All mentioned lncRNAs were shown to be over-expressed in total NMOSD cases, male NMOSD cases and female NMOSD cases compared with the matching control subgroups. MEG3 had the most robust over-expression in patients subgroups compared with normal subjects. There was no noteworthy difference in the expression of any of lncRNAs between female and male patients. MEG3 had an ideal performance in the differentiation of NMOSD cases from healthy persons (Sensitivity and specificity values = 100%). Other lncRNAs could also efficiently separate NMOSD cases from control subjects (AUC values = 0.97, 0.89 and 0.88 for PANDAR, NEAT1 and TUG1, respectively). Cumulatively, NEAT1, PANDAR, MEG3 and TUG1 lncRNAs can be considered as appropriate disease markers for NMOSD.

Excessive MALAT1 promotes the immunologic process of neuromyelitis optica spectrum disorder by upregulating BAFF expression

Increased B cell activating factor (BAFF) expression in patients with neuromyelitis optica spectrum disorder (NMOSD) is associated with B cell overstimulation, but the underlying mechanism remains unclear. This study aimed to reveal the emerging mechanisms that regulate BAFF expression in the inflammatory process of NMOSD. The results showed that the expression of miR-30b-5p was significantly decreased in NMOSD CD14+ monocytes compared with the normal control. Furthermore, we confirmed that metastasis-associated lung adenocarcinoma transcription 1 (MALAT1) is an upstream target of miR-30b-5p, and it could act as a ceRNA and absorb miR-30b-5p with reduced expression of miR-30b-5p. The low expression of miR-30b-5p could not bind to BAFF messenger RNA (mRNA), which resulted in the overexpression of both BAFF mRNA and protein expression. Overexpression of BAFF could bind to the corresponding receptors on B cells, which may initiate activation and proliferation of B cells and increase their production of autoantibodies. Therefore, these findings interpreted that excessive MALAT1 expression in NMOSD mononuclear macrophages led to increased BAFF expression by targeting miR-30b-5p, which caused B cell autoimmune reaction and autoantibodies production, aggravated the disease progression of NMOSD.

Altered non-coding RNA profiles and potential disease marker identification in peripheral blood mononuclear cells of patients with NMOSD

Neuromyelitis optica spectrum disorder (NMOSD) is an inflammatory demyelination disorder, and dysregulation of RNAs contributes to its pathogenesis. We aimed to reveal the expression profiles of RNAs, including messenger RNA (mRNA), circular RNA (circRNA) and long non-coding RNA (lncRNA), in the peripheral blood mononuclear cells (PBMCs) of patients with NMOSD. Seven NMOSD patients and seven healthy controls (HCs) were enrolled in the competitive endogenous RNA (ceRNA) microarray analysis. Bioinformatics analysis was then performed on the microarray data. Selected RNAs were validated by RT-qPCR. Differentially expressed (DE) RNA profiles of patients and HCs were related to NK cell mediated cytotoxicity, the IL-17 signaling pathway, and the B cell receptor signaling pathway. Moreover, DE non-coding RNAs (DE ncRNAs) including DE circRNAs and DE lncRNAs, may participate in the transforming growth factor beta (TGF-β) signaling pathway, leukocyte migration and neutrophil chemotaxis. Immune cell infiltration analysis showed that the abundance of M1 macrophages and plasma cells significantly increased, while that of M2 macrophages significantly decreased in the NMOSD group. Finally, through RT-qPCR validation, lnc-HELZ-7:1 (95% confidential interval of area under curve [95%CI of AUC] = 0.6633-1.0000), ring finger protein-LIM domain interacting (RLIM; 95%CI of AUC = 0.6980-1.0000), and hsa_circ_0026993 (95%CI of AUC = 0.7550-1.0000) could discriminate NMOSD from HCs by receiver operating characteristic curve analysis. To our knowledge, this is the first study to preliminarily investigate the RNA profiles, especially circRNA profiles in PBMCs of NMOSD patients from North China. We identified lnc-HELZ-7:1, RLIM, and hsa_circ_0026993 as the potential disease markers for NMOSD.

Expression profiles of long noncoding RNAs in human corneal epithelial cells exposed to fine particulate matter

PURPOSE

The aim of this study was to investigate the expression profiles of long noncoding RNAs (lncRNAs) in human corneal epithelial cells (HCECs) exposed to fine particulate matter (PM_2.5) and to identify potential biological pathways involved in PM_2.5-induced toxicity in HCECs.

METHODS

Using RNA sequencing (RNA-seq) and hierarchy clustering analysis, lncRNA expression profiles in PM_2.5-treated and untreated HCECs were examined. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to predict the role of altered lncRNAs in biological processes and pathways. A quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) assay was conducted to verify the RNA-seq results in HCECs and human corneal epithelial cell sheets.

RESULTS

In total, 65 lncRNAs were altered in the PM_2.5-treated HCECs, including 41 upregulated and 24 downregulated lncRNAs. The results of the qRT-PCR assay were consistent with those of the RNA-seq analysis. The expression of two significantly upregulated lncRNAs was confirmed in human corneal epithelial cell sheets. The GO analysis demonstrated that altered lncRNAs in the PM_2.5-treated HCECs were significantly enriched in three domains: cellular component, molecular function, and biological process. The KEGG pathway analysis revealed enriched pathways of lncRNA co-expressed mRNAs, including cancer, RNA transport, and Rap1 signaling.

CONCLUSIONS

Our results suggest that lncRNAs are involved in the pathogenesis of PM_2.5-induced ocular diseases, exerting their effects through biological processes and pathogenic pathways. Among the altered lncRNAs, RP3-406P24.3 and RP11-285E9.5 may play significant roles in PM_2.5-induced ocular surface injury.

A Comprehensive Review on the Role of Genetic Factors in Neuromyelitis Optica Spectrum Disorder

Neuromyelitis optica spectrum disorders (NMOSD) comprise a variety of disorders being described by optic neuritis and myelitis. This disorder is mostly observed in sporadic form, yet 3% of cases are familial NMO. Different series of familial NMO cases have been reported up to now, with some of them being associated with certain HLA haplotypes. Assessment of HLA allele and haplotypes has also revealed association between some alleles within HLA-DRB1 or other loci and sporadic NMO. More recently, genome-wide SNP arrays have shown some susceptibility loci for NMO. In the current manuscript, we review available information about the role of genetic factors in NMO.

Metabolic Adjustments by LncRNAs in Peripheral Neutrophils Partly Account for the Complete Compensation of Asymptomatic MMD Patients

BACKGROUND

Due to the recent development of non-invasive examinations, more asymptomatic patients with Moyamoya Disease (MMD) have been diagnosed than ever. However, its underlying molecular mechanisms and clinical intervention guidelines are all still obscure.

METHODS

Microarray was used to explore those differentially expressed mRNAs and lncRNAs in peripheral neutrophils of asymptomatic MMD patients. Then enrichment analyses based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for those differentially expressed mRNAs and lncRNA associated mRNAs were performed for underlying molecular mechanisms.

RESULTS

Here, we identified a total of 2824 differentially expressed lncRNAs and 522 differentially expressed mRNAs (fold change > 2 and P<0.05) in peripheral neutrophils of asymptomatic MMD patients, compared with healthy controls. Then enrichment analyses based on GO and KEGG showed that the neighboring protein-coding mRNAs of those up-regulated and down-regulated lncRNAs were mainly involved in distinct metabolic processes respectively, which may act as a complementary response to insufficient blood supplies in MMD. Further enrichment analyses of those differentially expressed mRNAs preferentially listed essential physiological processes such as peptide cross-linking, chromatin assembly among others. Moreover, altered mRNAs also revealed to be enriched in renin secretion, platelet activation, inflammation and others.

CONCLUSION

We demonstrated for the first time that metabolic adjustments by dysregulated lncRNAs in peripheral neutrophils might partially account for the complete compensation of asymptomatic MMD patients. In addition, more attention should be paid on renin secretion and platelet activation in order to better understand the pathogenesis and guide clinical intervention for asymptomatic MMDs.

The role and mechanisms of Microglia in Neuromyelitis Optica Spectrum Disorders

Neuromyelitis optica spectrum disorder (NMOSD) is an autoimmune neurological disease that can cause blindness and disability. As the major mediators in the central nervous system, microglia plays key roles in immunological regulation in neuroinflammatory diseases, including NMOSD. Microglia can be activated by interleukin (IL)-6 and type I interferons (IFN-Is) during NMOSD, leading to signal transducer and activator of transcription (STAT) activation. Moreover, complement C3a secreted from activated astrocytes may induce the secretion of complement C1q, inflammatory cytokines and progranulin (PGRN) by microglia, facilitating injury to microglia, neurons, astrocytes and oligodendrocytes in an autocrine or paracrine manner. These processes involving activated microglia ultimately promote the pathological course of NMOSD. In this review, recent research progress on the roles of microglia in NMOSD pathogenesis is summarized, and the mechanisms of microglial activation and microglial-mediated inflammation, and the potential research prospects associated with microglial activation are also discussed.

Transcriptomic Analysis of circRNAs in the Peripheral Blood of Nonarteritic Anterior Ischemic Optic Neuropathy

The aim of the study is to explore the expression profile variation of circular RNAs (circRNAs) in the peripheral blood of subjects with nonarteritic anterior ischemic optic neuropathy (NAION) and without NAION, to analyze the differential expression results, and to predict the role of circRNAs in disease development, providing novel ideas and methods for treatment and diagnosis. High-throughput sequencing to explore the expression profiles of RNAs in the peripheral blood of 6 NAION patients and 5 healthy controls was applied. Quality control obtained the advanced data from the original data by ticking out the unqualified data. Then, cluster analysis, volcano plot, coexpression network, and protein-protein interaction network (PPI) were performed. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to analyze the whole expressed genes. Lastly, the quantitative real-time Polymerase Chain Reaction (qRT-PCR) was used to verify those significantly differentially expressed circRNAs and do some bioinformatics analysis and prediction in 12 NAION patients and 12 controls. There were significant differences in the expression of 49 circRNAs in the peripheral blood of NAION patients, in which there were 24 upregulations and 25 downregulations (variation folds > 2 and P < 0.05), and it was confirmed that hsa_circ_0005583, hsa_circ_0003922, hsa_circ_0002021, and hsa_circ_0000462 were significantly downregulated (variation folds > 2 and P < 0.05), especially hsa_circ_0005583 which was the most significantly changed one (P < 0.001), and are related to processes such as neurodegeneration, oxidative stress, immunity, and metabolism. The expression profile of circRNAs in the peripheral blood of NAION patients is significantly changed, enriching our understanding of the disease.

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

BACKGROUND

Drought stress is a major abiotic factor that affects rapeseed (Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs' response to drought stress is still lacking, especially in the case of B. napus. In order to further understand the molecular mechanism of the response of B. napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) responding drought stress and rehydration treatment at the seedling stage.

RESULTS

A total of 5546 down-regulated and 6997 up-regulated mRNAs were detected in Q2 compared with 7824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up- regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA-mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 transcription factors (TFs) corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes. Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response.

CONCLUSIONS

The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

Tissue Expression Difference between mRNAs and lncRNAs

Messenger RNA (mRNA) and long noncoding RNA (lncRNA) are two main subgroups of RNAs participating in transcription regulation. With the development of next generation sequencing, increasing lncRNAs are identified. Many hidden functions of lncRNAs are also revealed. However, the differences in lncRNAs and mRNAs are still unclear. For example, we need to determine whether lncRNAs have stronger tissue specificity than mRNAs and which tissues have more lncRNAs expressed. To investigate such tissue expression difference between mRNAs and lncRNAs, we encoded 9339 lncRNAs and 14,294 mRNAs with 71 expression features, including 69 maximum expression features for 69 types of cells, one feature for the maximum expression in all cells, and one expression specificity feature that was measured as Chao-Shen-corrected Shannon's entropy. With advanced feature selection methods, such as maximum relevance minimum redundancy, incremental feature selection methods, and random forest algorithm, 13 features presented the dissimilarity of lncRNAs and mRNAs. The 11 cell subtype features indicated which cell types of the lncRNAs and mRNAs had the largest expression difference. Such cell subtypes may be the potential cell models for lncRNA identification and function investigation. The expression specificity feature suggested that the cell types to express mRNAs and lncRNAs were different. The maximum expression feature suggested that the maximum expression levels of mRNAs and lncRNAs were different. In addition, the rule learning algorithm, repeated incremental pruning to produce error reduction algorithm, was also employed to produce effective classification rules for classifying lncRNAs and mRNAs, which gave competitive results compared with random forest and could give a clearer picture of different expression patterns between lncRNAs and mRNAs. Results not only revealed the heterogeneous expression pattern of lncRNA and mRNA, but also gave rise to the development of a new tool to identify the potential biological functions of such RNA subgroups.

Aberrant expression of lncRNAs and mRNAs in patients with intracranial aneurysm

Intracranial aneurysm (IA) is pathological dilatations of the cerebral artery and rupture of IAs can cause subarachnoid hemorrhage, which has a high ratio of fatality and morbidity. However, the pathogenesis of IAs remains unknown. We performed long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in IA tissues and superficial temporal arteries (STAs). A total of 4129 differentially expressed lncRNAs and 2926 differentially expressed mRNAs were obtained from the microarrays (P < 0.05). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that up-regulated mRNAs were enriched in immune response, inflammatory response, regulation of immune response and lysosome, et al; while the down-regulated mRNAs were enriched in muscle contraction, smooth muscle contraction, cGMP-PKG signaling pathway and vascular smooth muscle contraction, et al. The lncRNA-mRNA co-expression networks were represented in immune response, inflammatory response, muscle contraction and vascular smooth muscle contraction. These findings may gain insight in the pathogenesis of IAs and provide clues to find key roles for IA patients.

An immune-related lncRNA signature for patients with anaplastic gliomas

We investigated immune-related long non-coding RNAs (lncRNAs) that may be exploited as potential therapeutic targets in anaplastic gliomas. We obtained 572 lncRNAs and 317 immune genes from the Chinese Glioma Genome Atlas microarray and constructed immune-related lncRNAs co-expression networks to identify immune-related lncRNAs. Two additional datasets (GSE16011, REMBRANDT) were used for validation. Gene set enrichment analysis and principal component analysis were used for functional annotation. Immune-lncRNAs co-expression networks were constructed. Nine immune-related lncRNAs (SNHG8, PGM5-AS1, ST20-AS1, LINC00937, AGAP2-AS1, MIR155HG, TUG1, MAPKAPK5-AS1, and HCG18) signature was identified in patients with anaplastic gliomas. Patients in the low-risk group showed longer overall survival (OS) and progression-free survival than those in the high-risk group (P < 0.0001; P < 0.0001). Additionally, patients in the high-risk group displayed no-deletion of chromosomal arms 1p and/or 19q, isocitrate dehydrogenase wild-type, classical and mesenchymal TCGA subtype, G3 CGGA subtype, and lower Karnofsky performance score (KPS). Moreover, the signature was an independent factor and was significantly associated with the OS (P = 0.000, hazard ratio (HR) = 1.434). These findings were further validated in two additional datasets (GSE16011, REMBRANDT). Low-risk and high-risk groups displayed different immune status based on principal components analysis. Our results showed that the nine immune-related lncRNAs signature has prognostic value for anaplastic gliomas.

Distinct Hippocampal Expression Profiles of Long Non-coding RNAs in an Alzheimer's Disease Model

Alzheimer's disease (AD), the most prevalent form of dementia worldwide, is a complex neurodegenerative disease characterized by the progressive loss of memory and other cognitive functions. The pathogenesis of AD is not yet completely understood. Although long non-coding RNAs (lncRNAs) have recently been shown to play a role in AD pathogenesis, the specific influences of lncRNAs in AD remain largely unknown; in particular, hippocampal lncRNA expression profiles in AD rats are lacking. In this study, microarray analysis was performed to investigate the hippocampal expression patterns of dysregulated lncRNAs in a rat model of AD. A total of 315 lncRNAs and 311 mRNAs were found to be significantly dysregulated in the AD model (≥2.0 fold, p < 0.05). Then, quantitative real-time PCR was used to validate the expression of selected lncRNAs and mRNAs. Bioinformatics tools and databases were employed to explore the potential lncRNA functions. This is the first study to comprehensively identify dysregulated hippocampal lncRNAs in AD and to demonstrate the involvement of different lncRNA expression patterns in the hippocampal pathogenesis of AD. This information will enable further research on the pathogenesis of AD and facilitate the development of novel AD therapeutics targeting lncRNAs.

Integrated Analysis of LncRNA-mRNA Co-Expression Profiles in Patients with Moyamoya Disease

Moyamoya disease (MMD) is an idiopathic disease associated with recurrent stroke. However, the pathogenesis of MMD remains unknown. Therefore, we performed long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in blood samples from MMD patients (N = 15) and healthy controls (N = 10). A total of 880 differentially expressed lncRNAs (3649 probes) and 2624 differentially expressed mRNAs (2880 probes) were obtained from the microarrays of MMD patients and healthy controls (P < 0.05; Fold Change >2.0). Gene ontology (GO) and pathway analyses showed that upregulated mRNAs were enriched for inflammatory response, Toll-like receptor signaling pathway, chemokine signaling pathway and mitogen-activated protein kinase (MAPK) signaling pathway among others, while the downregulated mRNAs were enriched for neurological system process, digestion, drug metabolism, retinol metabolism and others. Our results showed that the integrated analysis of lncRNA-mRNA co-expression networks were linked to inflammatory response, Toll-like signaling pathway, cytokine-cytokine receptor interaction and MAPK signaling pathway. These findings may elucidate the pathogenesis of MMD, and the differentially expressed genes could provide clues to find key components in the MMD pathway.

Expression profile of long noncoding RNAs and mRNAs in peripheral blood mononuclear cells from myasthenia gravis patients

For the epigenetic characterization of myasthenia gravis (MG), we determined whether long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) are expressed differentially in subjects with and without MG. Compared with healthy control subjects, the MG patients had 1561 upregulated lncRNAs, 1034 downregulated lncRNAs, 921 upregulated mRNAs, and 806 downregulated mRNAs (fold change>2.0). Several GO terms including nucleic acid transcription factor activity, inflammatory response, regulation of leukocyte activation, lymphocyte proliferation and regulation of B cell proliferation were enriched in gene lists, suggesting a potential correlation with MG. Pathway analysis then demonstrated that cytokine-cytokine receptor interaction, intestinal immune network for lgA production, NOD-like receptor signaling pathway, NF-kappaB signaling pathway, cell adhesion molecules and TNF signaling pathway play important roles in MG. Co-expression network analysis indicated that 33 lncRNAs were predicted to have 31 cis-regulated target genes, and 65 lncRNAs appeared to regulate the patients' 45 trans target genes among differentially expressed lncRNAs. Our present study identified a subset of dysregulated lncRNAs and mRNAs in patients with MG, which may impact this disease process.