Effects of Interleukin-1β on Long Noncoding RNA and mRNA Expression Profiles of Human Synovial Fluid-derived Mesenchymal Stem Cells

Synovial fluid-derived mesenchymal stem cells (SFMSCs) play important regulatory roles in the physiological balance of the temporomandibular joint. Interleukin (IL)-1β regulates the biological behavior of SFMSCs; however, the effects of IL-1β on long noncoding RNA (lncRNA) and mRNA expression in SFMSCs in the temporomandibular joint are unclear. Here, we evaluated the lncRNA and mRNA expression profiles of IL-1β-stimulated SFMSCs. Using microarrays, we identified 286 lncRNAs (222 upregulated, 64 downregulated) and 304 mRNAs (242 upregulated, 62 downregulated) that were differentially expressed after treatment with IL-1β (fold change ≥ 2, P < 0.05). Kyoto Encyclopedia of Genes and Genomes pathway analysis found that one of the most significantly enriched pathways was the NF-κB pathway. Five paired antisense lncRNAs and mRNAs, eight paired enhancer lncRNAs and mRNAs, and nine paired long intergenic noncoding RNAs and mRNAs were predicted to be co-expressed. A network constructed by the top 30 k-score genes was visualized and evaluated. We found a co-expression relationship between ENST00000427824 and ENST00000307407 and between LOC541472 and IL6, which are related to NF-κB pathway activation. Overall, our results provide important insights into changes in lncRNA and mRNA expression in IL-1β-stimulated SFMSCs, which can facilitate the identification of potential therapeutic targets.

Natural SINEUP RNAs in Autism Spectrum Disorders: RAB11B-AS1 Dysregulation in a Neuronal CHD8 Suppression Model Leads to RAB11B Protein Increase

CHD8 represents one of the highest confidence genetic risk factors implied in Autism Spectrum Disorders, with most mutations leading to CHD8 haploinsufficiency and the insurgence of specific phenotypes, such as macrocephaly, facial dysmorphisms, intellectual disability, and gastrointestinal complaints. While extensive studies have been conducted on the possible consequences of CHD8 suppression and protein coding RNAs dysregulation during neuronal development, the effects of transcriptional changes of long non-coding RNAs (lncRNAs) remain unclear. In this study, we focused on a peculiar class of natural antisense lncRNAs, SINEUPs, that enhance translation of a target mRNA through the activity of two RNA domains, an embedded transposable element sequence and an antisense region. By looking at dysregulated transcripts following CHD8 knock down (KD), we first identified RAB11B-AS1 as a potential SINEUP RNA for its domain configuration. Then we demonstrated that such lncRNA is able to increase endogenous RAB11B protein amounts without affecting its transcriptional levels. RAB11B has a pivotal role in vesicular trafficking, and mutations on this gene correlate with intellectual disability and microcephaly. Thus, our study discloses an additional layer of molecular regulation which is altered by CHD8 suppression. This represents the first experimental confirmation that naturally occurring SINEUP could be involved in ASD pathogenesis and underscores the importance of dysregulation of functional lncRNAs in neurodevelopment.

Potential Roles of Long Non-coding RNAs in Regulating Cell Proliferation, Invasion, and Metastasis in Ovarian Serous Cystadenocarcinoma

Background: Ovarian serous cystadenocarcinoma (OSC) is the most common gynecological malignancy. Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and involved in cell proliferation, apoptosis, angiogenesis, and invasion. Here, we investigated the functional roles of lncRNAs in OSC in detail.Methods: We analyzed a cohort of exon microarray datasets from The Cancer Genome Atlas and used differentially expressed lncRNAs and mRNAs to construct an lncRNA-mRNA co-expression network. Distinct lncRNAs were classified into lincRNA, enhancer-like lncRNAs, or antisense lncRNAs. Biological functions for lncRNAs were predicted according to the lncRNA-mRNA network and genomic adjacency by KEGG pathway analysis. A transcription factor (TF)-lncRNA regulatory network was constructed by integrating lncRNA molecular profiles and TF binding information. Results: We identified 2,939 lncRNAs and 2,766 mRNAs that were differentially expressed between OSC and normal ovary tissues. The 67 lncRNAs in the lncRNA-mRNA network, 23 lincRNAs, 19 antisense lncRNAs, and four enhancer-like lncRNAs were involved in cell proliferation, invasion, and metastasis. The TFs ING4, TTF-1, RUSH-l alpha, Kaiso, and STAT1 targeted regulation of lncRNAs in the pathological processes of OSC. Expression of 10 lncRNAs and mRNAs, as well as SOS1, ITGB1, and BIRC2 mRNAs with their identified lncRNAs were verified by qRT-PCR in OSC tissues. Conclusions: We predicted the biological functions of many lncRNAs, which may serve as diagnostic and prognostic biomarkers as well as therapeutic targets in OSC.

SINEUPs: a novel toolbox for RNA therapeutics

RNA molecules have emerged as a new class of promising therapeutics to expand the range of druggable targets in the genome. In addition to ‘canonical’ protein-coding mRNAs, the emerging richness of sense and antisense long non-coding RNAs (lncRNAs) provides a new reservoir of molecular tools for RNA-based drugs. LncRNAs are composed of modular structural domains with specific activities involving the recruitment of protein cofactors or directly interacting with nucleic acids. A single therapeutic RNA transcript can then be assembled combining domains with defined secondary structures and functions, and antisense sequences specific for the RNA/DNA target of interest. As the first representative molecules of this new pharmacology, we have identified SINEUPs, a new functional class of natural antisense lncRNAs that increase the translation of partially overlapping mRNAs. Their activity is based on the combination of two domains: an embedded mouse inverted SINEB2 element that enhances mRNA translation (effector domain) and an overlapping antisense region that provides specificity for the target sense transcript (binding domain). By genetic engineering, synthetic SINEUPs can potentially target any mRNA of interest increasing translation and therefore the endogenous level of the encoded protein. In this review, we describe the state-of-the-art knowledge of SINEUPs and discuss recent publications showing their potential application in diseases where a physiological increase of endogenous protein expression can be therapeutic.

Coexpression network analysis identified lncRNAs-mRNAs with potential relevance in African ancestry prostate cancer

Aim: This study aims to investigate similarities and differences using lncRNA and mRNA coexpression network analysis in African ancestry (AA) and European ancestry (EA) among prostate cancer (PCa) patients. Methods: We performed weighted gene coexpression network analysis of the expression from 49 of AA and 49 of EA to identify lncRNAs-mRNAs. Results: 27 lncRNAs and 36 mRNAs were highly expressed in patients of AA. Two mRNAs and their antisense lncRNAs were expressed. Additionally, seven mRNAs were DE or coexpressed and had an impact on survival. Conclusion: We present a list of lncRNAs and mRNAs that were DE and coexpressed when comparing patients of AA and EA, and these data are a resource for future studies to understand the role of lncRNAs.

Antisense lncRNA NNT-AS1 Promoted Esophageal Squamous Cell Carcinoma Progression by Regulating Its Sense Gene NNT Expression

BackgroundAntisense lncRNAs were endogenous productions from the antisense strand of coding genes and transcribed in the opposite direction of sense gene. This study aimed to systematically evaluate the roles and functions of antisense lncRNAs in esophageal squamous cell carcinoma (ESCC).MethodsDifferentially expressed antisense lncRNAs were initially screened using transcriptome data from 119 paired ESCC samples in GSE53624, and were further validated in 6 paired ESCC samples from our institution. Log-rank test was adopted to identify ESCC prognosis associated lncRNAs. Finally, functional assays were performed to reveal the functions of our identified antisense lncRNAs. ResultsIn total, 174 antisense lncRNAs were differentially expressed in both GSE53624 and JSPH samples. Five of them were significantly associated with ESCC prognosis (NNT-AS1, NKILA, CCDC18-AS1, SLCO4A1-AS1 and AC110619.1). The upregulation of NNT-AS1 was validated in ESCC cell lines. Knockdown of NNT-AS1 inhibited ESCC cell proliferation, migration, and promoted ESCC cells apoptosis and induced cell cycle arrest in G2/M stage. NNT-AS1 expression was significantly correlated with its sense gene NNT and NNT-AS1 knockdown could suppress NNT expression. Inhibition of NNT suppressed ESCC cell proliferation and migration. Mechanically, NNT-AS1 served as a competing endogenous RNA to sponge the miR-382-5p, which could repress NNT expression. Pathway enrichment analysis and western blot assay indicated that NNT-AS1 and NNT could regulate the cell cycle pathway. ConclusionAntisense lncRNA NNT-AS1 promoted ECSS progression by targeting NNT through sponging miR-382-5p. This study provided us a deeper insight into the roles of antisense lncRNAs in ESCC and identified potential therapeutic targets.

The regulatory role of antisense lncRNAs in cancer

Antisense long non-coding RNAs (antisense lncRNAs), transcribed from the opposite strand of genes with either protein coding or non-coding function, were reported recently to play a crucial role in the process of tumor onset and development. Functionally, antisense lncRNAs either promote or suppress cancer cell proliferation, migration, invasion, and chemoradiosensitivity. Mechanistically, they exert their regulatory functions through epigenetic, transcriptional, post-transcriptional, and translational modulations. Simultaneously, because of nucleotide sequence complementarity, antisense lncRNAs have a special role on its corresponding sense gene. We highlight the functions and molecular mechanisms of antisense lncRNAs in cancer tumorigenesis and progression. We also discuss the potential of antisense lncRNAs to become cancer diagnostic biomarkers and targets for tumor treatment.

Dysregulated long noncoding RNAs in the brainstem of the DBA/1 mouse model of SUDEP

Background Long noncoding RNAs (lncRNAs) play an important role in many neurological diseases. This study aimed to investigate differentially expressed lncRNAs and messenger RNAs (mRNAs) in the susceptibility gaining process of primed DBA/1 mice, a sudden unexpected death in epilepsy (SUDEP) model, to illustrate the potential role of lncRNAs in SUDEP. Methods The Arraystar mouse lncRNA Microarray V3.0 (Arraystar, Rockville, MD) was applied to identify the aberrantly expressed lncRNAs and mRNAs between primed DBA/1 mice and normal controls. The differences were verified by qRT-PCR. We conducted gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and coexpression analyses to explore the possible function of the dysregulated RNAs. Results A total of 502 lncRNAs (126 upregulated and 376 downregulated lncRNAs) and 263 mRNAs (141 upregulated and 122 downregulated mRNAs) were dysregulated with P < 0.05 and a fold change over 1.5, among which Adora3 and Gstt4 were possibly related to SUDEP. GO analysis revealed that chaperone cofactor-dependent protein refolding and misfolded protein binding were among the top ten downregulated terms, which pointed to Hspa1a, Hspa2a and their related lncRNAs. KEGG analysis identified 28 upregulated and 10 downregulated pathways. Coexpression analysis showed fifteen dysregulated long intergenic noncoding RNAs (lincRNAs) and three aberrantly expressed antisense lncRNAs, of which AK012034 and NR_040757 are potentially related to SUDEP by regulating LMNB2 and ITPR1, respectively. Conclusions LncRNAs and their coexpression mRNAs are dysregulated in the priming process of DBA/1 in the brainstem. Some of these mRNAs and lncRNAs may be related to SUDEP, including Adora3, Lmnb2, Hspa1a, Hspa1b, Itrp1, Gstt4 and their related lncRNAs. Further study on the mechanism of lncRNAs in SUDEP is needed.

Potential Roles of Long Non-Coding RNAs in Regulating Cell Proliferation, Invasion, and Metastasis in Ovarian Serous Cystadenocarcinoma

Background: Ovarian serous cystadenocarcinoma (OSC) is the most common gynecological malignancy. Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and involved in cell proliferation, apoptosis, angiogenesis, and invasion. Here, we investigated the functional roles of lncRNAs in OSC in detail.Methods: We analyzed a cohort of exon microarray datasets from The Cancer Genome Atlas and used differentially expressed lncRNAs and mRNAs to construct an lncRNA-mRNA co-expression network. Distinct lncRNAs were classified into lincRNA, enhancer-like lncRNAs, or antisense lncRNAs. Biological functions for lncRNAs were predicted according to the lncRNA-mRNA network and genomic adjacency by KEGG pathway analysis. A transcription factor (TF)-lncRNA regulatory network was constructed by integrating lncRNA molecular profiles and TF binding information. Results: We identified 2,939 lncRNAs and 2,766 mRNAs that were differentially expressed between OSC and normal ovary tissues. The 67 lncRNAs in the lncRNA-mRNA network, 23 lincRNAs, 19 antisense lncRNAs, and four enhancer-like lncRNAs were involved in cell proliferation, invasion, and metastasis. The TFs ING4, TTF-1, RUSH-l alpha, Kaiso, and STAT1 targeted regulation of lncRNAs in the pathological processes of OSC. Expression of 10 lncRNAs and mRNAs, as well as SOS1, ITGB1, and BIRC2 mRNAs with their identified lncRNAs were verified by qRT-PCR in OSC tissues. Conclusion: We predicted the biological functions of many lncRNAs, which may serve as diagnostic and prognostic biomarkers as well as therapeutic targets in OSC.

Upregulation of 15 Antisense Long Non-Coding RNAs in Osteosarcoma

The human genome encodes thousands of natural antisense long noncoding RNAs (lncRNAs); they play the essential role in regulation of gene expression at multiple levels, including replication, transcription and translation. Dysregulation of antisense lncRNAs plays indispensable roles in numerous biological progress, such as tumour progression, metastasis and resistance to therapeutic agents. To date, there have been several studies analysing antisense lncRNAs expression profiles in cancer, but not enough to highlight the complexity of the disease. In this study, we investigated the expression patterns of antisense lncRNAs from osteosarcoma and healthy bone samples (24 tumour-16 bone samples) using RNA sequencing. We identified 15 antisense lncRNAs (RUSC1-AS1, TBX2-AS1, PTOV1-AS1, UBE2D3-AS1, ERCC8-AS1, ZMIZ1-AS1, RNF144A-AS1, RDH10-AS1, TRG-AS1, GSN-AS1, HMGA2-AS1, ZNF528-AS1, OTUD6B-AS1, COX10-AS1 and SLC16A1-AS1) that were upregulated in tumour samples compared to bone sample controls. Further, we performed real-time polymerase chain reaction (RT-qPCR) to validate the expressions of the antisense lncRNAs in 8 different osteosarcoma cell lines (SaOS-2, G-292, HOS, U2-OS, 143B, SJSA-1, MG-63, and MNNG/HOS) compared to hFOB (human osteoblast cell line). These differentially expressed IncRNAs can be considered biomarkers and potential therapeutic targets for osteosarcoma.