scholarly journals Upregulation of 15 Antisense Long Non-Coding RNAs in Osteosarcoma

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1132
Author(s):  
Emel Rothzerg ◽  
Xuan Dung Ho ◽  
Jiake Xu ◽  
David Wood ◽  
Aare Märtson ◽  
...  
Keyword(s):  
Tumour Progression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Osteosarcoma Cell ◽  
Osteoblast Cell Line ◽  
Antisense Lncrnas ◽  
Non Coding Rnas ◽  
Polymerase Chain ◽  
Multiple Levels

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.

scholarly journals Systematic and integrated analysis of tRNA-derived small RNAs reveals novel potential pathogenesis targets of sarcoidosis

2022 ◽  
Author(s):  
Min Zhao ◽  
Chang Tian ◽  
Xin Di ◽  
Xin Jin ◽  
Shan Cong ◽  
...  
Keyword(s):  
Visual Analysis ◽  
Expression Profiles ◽  
Target Prediction ◽  
Integrated Analysis ◽  
Hub Genes ◽  
Bioinformatics Analyses ◽  
Deep Sequencing Technology ◽  
Non Coding Rnas ◽  
Polymerase Chain ◽  
Regulatory Functions

Abstract The pathogenesis of sarcoidosis, which involves several systems, is unclear, and its pathological type is non-caseating epithelioid granulomas. tRNA-derived small RNA (tsRNA) is a novel class of short non-coding RNAs with potential regulatory functions. However, whether tsRNA contributes to sarcoidosis pathogenesis remains unclear. Deep sequencing technology was used to identify alterations in tsRNA expression profiles between patients with sarcoidosis and healthy controls. A total of 360 tsRNAs were identified for exact matches. Among them, the expression of three tRNAs (tiRNA-Glu-TTC-001, tiRNA-Lys-CTT-003, and tRF-Ser-TGA-007) was markedly regulated in sarcoidosis and validated by quantitative real-time polymerase chain reaction. The expression of various tsRNAs was significantly correlated with age, the number of affected systems, and calcium levels in the blood. Additionally, target prediction and bioinformatics analyses revealed that these tsRNAs may play roles in chemokine, cAMP, cGMP-PKG, retrograde endorphin, and FoxO signalling pathways. The Cytoscape software was used for visual analysis to obtain 10 hub genes of each target tsRNA. Among the hub genes, APP, PRKACB, ARRB2, and NR5A1 finding may participate in the occurrence and development of sarcoidosis through immune inflammation. This study provides novel insights to explore tsRNA as a novel and efficacious pathogenic target of sarcoidosis.

scholarly journals Characterisation and functional predictions of canine long non-coding RNAs

2018 ◽  
Author(s):  
Céline Le Béguec ◽  
Valentin Wucher ◽  
Lætitia Lagoutte ◽  
Edouard Cadieu ◽  
Nadine Botherel ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Domestic Dog ◽  
Tissue Type ◽  
Protein Coding ◽  
Functional Roles ◽  
Integrative Study ◽  
Non Coding Rnas ◽  
Biological Functionality

AbstractLong non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and humans through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.

Long Non-Coding RNAs Involved in Gynecological Cancer

2014 ◽  
Vol 24 (7) ◽  
pp. 1140-1145 ◽  
Author(s):  
Manyin Zhao ◽  
Yiran Qiu ◽  
Baicai Yang ◽  
Li Sun ◽  
Kaiwen Hei ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Malignant Tumors ◽  
Expression Profiles ◽  
Gynecological Cancer ◽  
Expression Patterns ◽  
Research Progress ◽  
Benign Tumors ◽  
Biological Functions ◽  
Gynecological Cancers ◽  
Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) are defined as transcripts longer than 200 nucleotides with little or no protein-coding capacity. Previously, they were considered transcription byproducts without biological functions. Further studies have shown that lncRNAs are involved in multiple biological and pathological processes, including regulation of epigenetic, transcriptional, and posttranscriptional events. Long non-coding RNA expression patterns in various malignant tumors differ from those of benign tumors and normal tissue, and such alterations may promote or suppress tumorigenesis and cancer progression. The expression profiles of lncRNAs are abnormal in gynecological cancers, such as ovarian cancer, cervical cancer, and endometrial cancer, suggesting an important role for lncRNAs in tumorigenesis/progression of these cancers. Here, we summarized the research progress on identifying the biological functions of lncRNAs in tumorigenesis, progression, and metastasis in gynecological cancers. We provide references for exploring the clinical applications of lncRNAs as early diagnostic biomarkers or ideal therapeutic targets in gynecological cancers.

scholarly journals Identification and Characterization of Osmoregulation Related MicroRNAs in Gills of Hybrid Tilapia Under Three Types of Osmotic Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Huanhuan Su ◽  
Jiajia Fan ◽  
Dongmei Ma ◽  
Huaping Zhu
Keyword(s):  
Polymerase Chain Reaction ◽  
Osmotic Stress ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Protein Translation ◽  
Control Group ◽  
Alkali Stress ◽  
Chain Reaction ◽  
Polymerase Chain

Researchers have increasingly suggested that microRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression and protein translation in organs and respond to abiotic and biotic stressors. To understand the function of miRNAs in osmotic stress regulation of the gills of hybrid tilapia (Oreochromis mossambicus ♀ × Oreochromis urolepis hornorum ♂), high-throughput Illumina deep sequencing technology was used to investigate the expression profiles of miRNAs under salinity stress (S, 25‰), alkalinity stress (A, 4‰) and salinity–alkalinity stress (SA, S: 15‰, A: 4‰) challenges. The results showed that 31, 41, and 27 upregulated and 33, 42, and 40 downregulated miRNAs (P < 0.05) were identified in the salt stress, alkali stress, and saline–alkali stress group, respectively, which were compared with those in the control group (C). Fourteen significantly differently expressed miRNAs were selected randomly and then validated by a quantitative polymerase chain reaction. On the basis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, genes related to osmoregulation and biosynthesis were enriched in the three types of osmotic stress. In addition, three miRNAs and three predicted target genes were chosen to conduct a quantitative polymerase chain reaction in the hybrid tilapia and its parents during 96-h osmotic stress. Differential expression patterns of miRNAs provided the basis for research data to further investigate the miRNA-modulating networks in osmoregulation of teleost.

scholarly journals Data Mining Identifies Differentially Expressed Circular RNAs in Skeletal Muscle of Thermally Challenged Turkey Poults

2021 ◽  
Vol 12 ◽  
Author(s):  
Kent M. Reed ◽  
Kristelle M. Mendoza ◽  
Juan E. Abrahante ◽  
Sandra G. Velleman ◽  
Gale M. Strasburg
Keyword(s):  
Gene Expression ◽  
Data Mining ◽  
Growth And Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Muscle Growth ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Turkey Poults

Precise regulation of gene expression is critical for normal muscle growth and development. Changes in gene expression patterns caused by external stressors such as temperature can have dramatic effects including altered cellular structure and function. Understanding the cellular mechanisms that underlie muscle growth and development and how these are altered by external stressors are crucial in maintaining and improving meat quality. This study investigated circular RNAs (circRNAs) as an emerging aspect of gene regulation. We used data mining to identify circRNAs and characterize their expression profiles within RNAseq data collected from thermally challenged turkey poults of the RBC2 and F-lines. From sequences of 28 paired-end libraries, 8924 unique circRNAs were predicted of which 1629 were common to all treatment groups. Expression analysis identified significant differentially expressed circRNAs (DECs) in comparisons between thermal treatments (41 DECs) and between genetic lines (117 DECs). No intersection was observed between the DECs and differentially expressed gene transcripts indicating that the DECs are not simply the result of expression changes in the parental genes. Comparative analyses based on the chicken microRNA (miRNA) database suggest potential interactions between turkey circRNAs and miRNAs. Additional studies are needed to reveal the functional significance of the predicted circRNAs and their role in muscle development in response to thermal challenge. The DECs identified in this study provide an important framework for future investigation.

20 Profiling circRNA and lncRNA Expression in Key Bovine Metabolic Tissues

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 9-9
Author(s):  
Jian Wang ◽  
Hui-Zeng Sun ◽  
Eóin O’Hara ◽  
Hong Chen ◽  
Leluo Guan
Keyword(s):  
Signaling Pathway ◽  
Balance Control ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Adipose Tissues ◽  
Mitofusin 2 ◽  
Tissue Specific ◽  
Lncrna Expression ◽  
Non Coding Rnas ◽  
Subcutaneous Adipose

Abstract CircRNAs and lncRNAs are non-coding RNAs that regulate many biological processes at the cellular level. However, knowledge of their function and expression patterns in cattle remains scarce. We investigated circRNA and lncRNA expression profiles in four key metabolic tissues of beef cattle (rumen, liver, muscle, and subcutaneous adipose) using RNA-Seq. Bioinformatic analysis of 189 samples collected from 48 cattle identified 19,766 circRNAs and 10,615 lncRNAs across all four tissues. PCA revealed the expression profiles of both circ- and lncRNA were clearly separated by tissue, suggesting their expression patterns are tissue dependent. Moreover, both datasets contained large numbers of transcripts that were unique to each tissue, underlining the divergence in function across metabolic sites. Further functional analysis of tissue specific circRNAs using the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that lysine degradation, peroxisome, insulin resistance, and ubiquitin-mediated proteolysis unique to the rumen, liver, muscle, and adipose tissues, respectively. The same analysis of the lncRNAs revealed that purine metabolism, fatty acid degradation, cAMP signaling pathway, and AGE-RAGE signaling pathway in diabetic complications were uniquely enriched in the rumen, liver, muscle, and subcutaneous adipose tissues, respectively. Together, these results revealed tissue specific metabolic pathways that may be regulated by the multiple non-coding RNAs. More specifically, circDLG1 and lncMSTRG.12092.8 were predicted to regulate the expression of Lymphocyte Antigen 6 Family Member G5B (LY6G5B) and pyruvate kinase M1/2 (PKM), Adenylate Kinase 1 (AK1), and Mitofusin 2 (MFN2), respectively, indicating regulatory roles in host immune response, glycolysis, energy balance control, and mitochondrial fusion, all of which may contribute to regulation of energy metabolism. Our findings show that expression profiles of circRNAs and lncRNAs differ among metabolic tissues, and these transcripts may play crucial roles in regulating metabolism in cattle.

scholarly journals Roles of Non-Coding RNAs on Anaplastic Thyroid Carcinomas

Cancers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3159
Author(s):  
Plabon Kumar Das ◽  
Saharia Yeasmin Asha ◽  
Ichiro Abe ◽  
Farhadul Islam ◽  
Alfred K. Lam
Keyword(s):  
Gene Expression ◽  
Tumour Progression ◽  
Regulation Of Gene Expression ◽  
Survival Rates ◽  
Human Leukocyte ◽  
Anaplastic Thyroid Cancer ◽  
Therapeutic Interventions ◽  
Poor Survival ◽  
Human Carcinomas ◽  
Non Coding Rnas

Anaplastic thyroid cancer (ATC) remains as one of the most aggressive human carcinomas with poor survival rates in patients with the cancer despite therapeutic interventions. Novel targeted and personalized therapies could solve the puzzle of poor survival rates of patients with ATC. In this review, we discuss the role of non-coding RNAs in the regulation of gene expression in ATC as well as how the changes in their expression could potentially reshape the characteristics of ATCs. A broad range of miRNA, such as miR-205, miR-19a, miR-17-3p and miR-17-5p, miR-618, miR-20a, miR-155, etc., have abnormal expressions in ATC tissues and cells when compared to those of non-neoplastic thyroid tissues and cells. Moreover, lncRNAs, such as H19, Human leukocyte antigen (HLA) complex P5 (HCP5), Urothelial carcinoma-associated 1 (UCA1), Nuclear paraspeckle assembly transcript 1 (NEAT1), etc., participate in transcription and post-transcriptional regulation of gene expression in ATC cells. Dysregulations of these non-coding RNAs were associated with development and progression of ATC by modulating the functions of oncogenes during tumour progression. Thus, restoration of the abnormal expression of these miRNAs and lncRNAs may serve as promising ways to treat the patients with ATC. In addition, siRNA mediated inhibition of several oncogenes may act as a potential option against ATC. Thus, non-coding RNAs can be useful as prognostic biomarkers and potential therapeutic targets for the better management of patients with ATC.

scholarly journals Systematic Identification and Analysis of Light-Responsive Circular RNA and Co-expression Networks in Lettuce (Lactuca sativa)

2020 ◽  
Vol 10 (7) ◽  
pp. 2397-2410
Author(s):  
Zhenchao Yang ◽  
Zhao Yang ◽  
Yingge Xie ◽  
Qi Liu ◽  
Yanhao Mei ◽  
...  
Keyword(s):  
Light Intensity ◽  
Lactuca Sativa ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Circular Rna ◽  
Rna Seq ◽  
Chlorophyll Metabolism ◽  
Plant Hormone Signaling ◽  
And Function

Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase chain reaction (PCR) to validate the candidate circRNA molecules. We then combined bioinformatics approach to explore the function of the parental genes of circRNA, including network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We identified 1650 circRNAs in lettuce, of which 1508 (86.40%) were derived from exons. Using real-time PCR, we characterized 10 validated differentially expressed circRNAs and their parental genes, all of which showed expression patterns consistent with RNA-Seq data. Interestingly, the expression of circRNA was, in some cases, inversely correlated with the expression of the parental gene. Furthermore, analysis of the circRNA–microRNA–mRNA network suggests that circRNAs may be involved in plant hormone signaling and chlorophyll metabolism during photoreactivity. These findings provide an essential reference basis for studying circRNAs’ biological mechanisms in light-treated plants.

scholarly journals Integrated miRNA-mRNA analysis reveals the roles of miRNAs in the replanting benefit of Achyranthes bidentata roots

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yan Hui Yang ◽  
Ming Jie Li ◽  
Yan Jie Yi ◽  
Rui Fang Li ◽  
Cui Xiang Li ◽  
...  
Keyword(s):  
Mirna Target ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
First Year ◽  
Achyranthes Bidentata ◽  
Yield And Quality ◽  
Post Transcriptional Regulation

AbstractThe yield and quality of the medicinal plant Achyranthes bidentata can be increased when it is replanted into a field cultivated previously with the same crop, however, fundamental aspects of its biology (so-called “replanting benefit”) still remain to be elucidated. miRNAs are sRNA molecules involved in the post-transcriptional regulation of gene expression in plant biological processes. Here, 267 conserved and 36 novel miRNAs were identified in A. bidentata roots. We compared the miRNA content of the roots (R1) from first-year planting with that of the roots (R2) of second-year replanting, and screened 21 differentially expressed (DE) miRNAs. Based on in silico functional analysis, integrated miRNA-mRNA datasets allowed the identification of 10 miRNA-target family modules, which might participate in the benefit. The expression profiles of the miRNA-target modules were potentially correlated with the presence of the replanting benefit. The indication was that the miRNA-responsive continuous monoculture could reprogram miRNA-mRNA expression patterns, which possibly promote the root growth and development, enhance its transport activity and strengthen its tolerance to various stresses, thereby improving A. bidentata productivity as observed in the replanting benefit. Our study provides basic data for further research on the molecular mechanisms of the benefit in A. bidentata.

scholarly journals Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks

2018 ◽  
Author(s):  
Kevin Walters ◽  
Radmir Sarsenov ◽  
Wen Siong Too ◽  
Roseanna K. Hare ◽  
Ian C. Paterson ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Therapeutic Potential ◽  
Tumour Progression ◽  
Expression Profiles ◽  
Critical Role ◽  
Multiple Cancer ◽  
Protein Coding ◽  
Cancer Types ◽  
Non Coding Rnas ◽  
Pan Cancer

AbstractLong non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes in diseases such as cancer, although the functions of most remain poorly understood. To address this, here we apply a novel strategy to integrate gene expression profiles across 32 cancer types, and cluster human lncRNAs based on their pan-cancer protein-coding gene associations. By doing so, we derive 16 lncRNA modules whose unique properties allow simultaneous inference of function, disease specificity and regulation for over 800 lncRNAs. Remarkably, modules could be grouped into just four functional themes: transcription regulation, immunological, extracellular, and neurological, with module generation frequently driven by lncRNA tissue specificity. Notably, three modules associated with the extracellular matrix represented potential networks of lncRNAs regulating key events in tumour progression. These included a tumour-specific signature of 33 lncRNAs that may play a role in inducing epithelialmesenchymal transition through modulation of TGFβ signalling, and two stromal-specific modules comprising 26 lncRNAs linked to a tumour suppressive microenvironment, and 12 lncRNAs related to cancer-associated fibroblasts. At least one member of the 12-lncRNA signature was experimentally supported by siRNA knockdown, which resulted in attenuated differentiation of quiescent fibroblasts to a cancer-associated phenotype. Overall, the study provides a unique pan-cancer perspective on the lncRNA functional landscape, acting as a global source of novel hypotheses on lncRNA contribution to tumour progression.Author SummaryThe established view of protein production is that genomic DNA is transcribed into RNA, which is then translated into protein. Proteins play a critical role in shaping the function of each individual cell in the human body yet they represent less than 2% of human genomic sequence whilst up to 90% of the genome is transcribed. To explain this disparity, the existence of thousands of long non-coding RNAs (lncRNAs) has emerged that do not encode proteins but perform function as an RNA molecule. Most lncRNAs have yet to be assigned a specific biological role, so to address this we apply a novel computational approach to characterise the function of >800 lncRNAs through consistent association with protein coding genes across multiple cancer types. By doing so, we discover 16 “modules” of closely related lncRNAs that share broad functional themes, the most compelling of which consists of 12 lncRNAs that could regulate activation of specific cells neighbouring the tumour, leading to accelerated tumour progression and invasion. Overall, the study provides the most robust view of the lncRNA-protein coding gene landscape to date, adding to growing evidence that lncRNAs are key regulators of cancer, and have therapeutic potential comparable to proteins.

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