scholarly journals High-throughput RNA sequencing from paired lesional- and non-lesional skin reveals major alterations in the psoriasis circRNAome

2019 ◽  
Author(s):  
Liviu-Ionut Moldovan ◽  
Thomas Birkballe Hansen ◽  
Morten Trillingsgaard Venø ◽  
Trine Line Hauge Okholm ◽  
Thomas Levin Andersen ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Mirna Expression ◽  
Binding Sites ◽  
Negative Impact ◽  
Expression Patterns ◽  
Circular Rnas ◽  
Altered Expression ◽  
Lesional Skin ◽  
Inflammatory Skin

AbstractBackgroundPsoriasis is a chronic inflammatory skin disease characterized by hyperproliferation and abnormal differentiation of keratinocytes. It is one of the most prevalent chronic inflammatory skin condition in adults worldwide, with a considerable negative impact on quality of life. Circular RNAs (circRNAs) are a recently identified type of non-coding RNA with diverse cellular functions related to their exceptional stability. In particular, some circRNAs can bind and regulate microRNAs (miRNAs), a group of RNAs that play a role in the pathogenesis of psoriasis. The aim of this study was to characterize the circRNAome in psoriasis and to assess potential correlations to miRNA expression patterns.ResultsUsing high-throughput RNA-sequencing (RNA-seq) and NanoString nCounter technology, we found a substantial down-regulation of circRNA expression in lesional skin compared to non-lesional skin from psoriasis patients. We saw that this mainly applies to the epidermis by analyzing laser capture microdissected tissues and by RNA chromogenicin situhybridization (CISH). We also found that the majority of the circRNAs were downregulated independent of their corresponding linear host genes. The observed downregulation of circRNAs in psoriasis was not due to altered expression levels of factors known to affect circRNA biogenesis, nor because lesional skin contained an increased number of inflammatory cells such as lymphocytes. Finally, we saw that the overall differences in available miRNA binding sites on the circRNAs between lesional and non-lesional skin did not correlate with differences in miRNA expression patterns.ConclusionsWe have performed the first genome-wide circRNA profiling of paired lesional and non-lesional skin from psoriasis patients and revealed that circRNAs are much less abundant in the lesional samples. Whether this is a cause or a consequence of the disease remains to be revealed, however, we found no evidence that the loss of miRNA binding sites on the circRNAs could explain differences in miRNA expression reported between lesional and non-lesional skin.

scholarly journals High-throughput RNA sequencing from paired lesional- and non-lesional skin reveals major alterations in the psoriasis circRNAome

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Liviu-Ionut Moldovan ◽  
Thomas Birkballe Hansen ◽  
Morten Trillingsgaard Venø ◽  
Trine Line Hauge Okholm ◽  
Thomas Levin Andersen ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Mirna Expression ◽  
Binding Sites ◽  
Expression Patterns ◽  
Psoriatic Skin ◽  
Altered Expression ◽  
Lesional Skin ◽  
Inflammatory Skin ◽  
Laser Capture

Abstract Background Psoriasis is a chronic inflammatory skin disease characterized by hyperproliferation and abnormal differentiation of keratinocytes. It is one of the most prevalent chronic inflammatory skin conditions in adults worldwide, with a considerable negative impact on quality of life. Circular RNAs (circRNAs) are a recently identified type of non-coding RNA with diverse cellular functions related to their exceptional stability. In particular, some circRNAs can bind and regulate microRNAs (miRNAs), a group of RNAs that play a role in the pathogenesis of psoriasis. The aim of this study was to characterize the circRNAome in psoriasis and to assess potential correlations to miRNA expression patterns. Methods We used high-throughput RNA-sequencing (RNA-seq), NanoString nCounter technology and RNA chromogenic in situ hybridization (CISH) to profile the circRNA expression in paired lesional and non-lesional psoriatic skin from patients with psoriasis vulgaris. In addition, 799 miRNAs were profiled using NanoString nCounter technology and laser capture microdissection was used to study the dermis and epidermis separately. Results We found a substantial down-regulation of circRNA expression in lesional skin compared to non-lesional skin. We observed that this mainly applies to the epidermis by analyzing laser capture microdissected tissues. We also found that the majority of the circRNAs were downregulated independently of their corresponding linear host genes. The observed downregulation of circRNAs in psoriasis was neither due to altered expression levels of factors known to affect circRNA biogenesis, nor because lesional skin contained an increased number of inflammatory cells such as lymphocytes. Finally, we observed that the overall differences in available miRNA binding sites on the circRNAs between lesional and non-lesional skin did not correlate with differences in miRNA expression patterns. Conclusions We have performed the first genome-wide circRNA profiling of paired lesional and non-lesional skin from patients with psoriasis and revealed that circRNAs are much less abundant in the lesional samples. Whether this is a cause or a consequence of the disease remains to be revealed, however, we found no evidence that the loss of miRNA binding sites on the circRNAs could explain differences in miRNA expression between lesional and non-lesional skin.

Altered expression patterns of circular RNAs between implantation sites and interimplantation sites in early pregnant mice

2018 ◽  
Vol 234 (6) ◽  
pp. 9862-9872 ◽  
Author(s):  
Shuang Zhang ◽  
Yubin Ding ◽  
Junlin He ◽  
Juanjuan Zhang ◽  
Xueqing Liu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Circular Rnas ◽  
Altered Expression ◽  
Pregnant Mice ◽  
Implantation Sites

scholarly journals Small RNA Sequencing Reveals Differentially Expressed miRNAs in Necrotizing Enterocolitis in Rats

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Ren-qiang Yu ◽  
Min Wang ◽  
Shan-yu Jiang ◽  
Ying-hui Zhang ◽  
Xiao-yu Zhou ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Signaling Pathway ◽  
Rna Sequencing ◽  
Necrotizing Enterocolitis ◽  
Small Rna ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Wnt Signaling Pathway ◽  
Differentially Expressed ◽  
Small Rna Sequencing

Necrotizing enterocolitis (NEC) is the leading cause of death due to gastrointestinal disease in preterm infants. The role of miRNAs in NEC is still unknown. The objective of this study was to identify differentially expressed (DE) miRNAs in rats with NEC and analyze their possible roles. In this study, a NEC rat model was established using Sprague-Dawley rat pups. Small RNA sequencing was used to analyze the miRNA expression profiles in the NEC and control rats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify target mRNAs for the DE miRNAs and to explore their potential roles. The DE miRNAs were verified by real-time quantitative PCR (RT-qPCR). The status of intestinal injury and the elevated levels of inflammatory cytokines in the NEC group confirmed that the NEC model was successfully established. The 16 miRNAs were found to be differentially expressed between the NEC group and the control group of rats. Bioinformatics analysis indicated that the parental genes of the DE miRNAs were predominantly implicated in the phosphorylation, cell migration, and protein phosphorylation processes. Moreover, the DE miRNAs were mainly found to be involved in the pathways of axon guidance, endocytosis, and focal adhesion, as well as in the Wnt signaling pathway, which is related to colitis. The expression patterns of the candidate miRNAs (rno-miR-27a-5p and rno-miR-187-3p), as assessed by RT-qPCR, were in accordance with the expression patterns obtained by miRNA-sequencing. The miRNA/mRNA/pathway network revealed that rno-miR-27a-5p and rno-miR-187-3p might be involved in NEC via the Wnt signaling pathway. We found an altered miRNA expression pattern in rats with NEC. We hypothesize that rno-miR-27a-5p and rno-miR-187-3p might mediate the NEC pathophysiological processes via the Wnt signaling pathway.

Mirna Expression Profile of Microvesicles Derived From K562 Cells

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4411-4411
Author(s):  
Wei Xiong ◽  
Xiaomei Chen ◽  
Fang Liu ◽  
Xiangjun Chen ◽  
Cong Lu ◽  
...  
Keyword(s):  
Expression Profile ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Leukemia Cell ◽  
K562 Cells ◽  
Mirna Expression Profile ◽  
Leukemia Cell Line ◽  
Normal Cells ◽  
Altered Expression ◽  
Mirnas Expression

Abstract Abstract 4411 MicroRNAs (miRNAs) are small non-coding RNA sequences of about 22nt and play an important role in disease progression including carcinogenesis. Recent evidences reveal that genetic exchange of miRNAs between cells can be accomplished through microvesicles(MVs). MVs are small exosomes of endocytic origin released not only by activated platelets but also by hematologic malignancies such as leukemia. Sheded from the plasma membrane MVs move into the extracellular environment to facilitate communication between cells. MVs containing miRNAs would enable intercellular cross-talk in vivo. This prompted us to investigate specific variations of miRNA expression patterns in MVs derived from leukemia. We examined the miRNA expression profile of MVs both from chronic myeloid leukemia cell line K562 and normal human volunteers’ peripheral blood. Agilent miRNA microarray was employed for detection and then real-time PCR for verification. Bioinformatic software tools were used to predict the target genes of identified microRNAs and define their function. Our study figures out miRNAs of MVs from leukemia and normal cells and characterizes specific miRNAs expression. We found that MVs from K562 cells express 348 miRNAs of 888 miRNAs. While 77 miRNAs displayed down regulation, 134 were upregulated. Interestingly, most of the miRNAs dysregulated in MVs display up regulated expression, suggesting their prevalent roles as tumor promotors. Among the aberrantly expressed miRNAs, miR-1290 was identified whose expression levels was more than 900 times than that of normal cell derived MVs. While the expression of miR-125a-3p was up-regulated by more than 300 times. And miR-654-5p, miR-654-5p, miR-1268 and miR-1246 were up-regulated more than 200 times. Five of the disregulated miRNAs (miR-1290, miR-125a-3p, let-7a, let-7f, miR-26a) were further assayed and validated by Q-RT-PCR results which correlated well with the microarray data. Of note, upexpression of miR-663, miR-1237, miR-149, miR-634, miR-1181, miR-92b, miR-130b as well as downregulation of let-7a, let-7f, miR-26a, miR-26a, miR-26b, miR-266, miR-126, miR-93, miR-451, miR-103, miR-107, miR-27a were similar to what was previously reported about leukemia, thus supporting the general roles of these miRNAs as tumor suppressors or oncomiRNAs in leukemia. Meanwhile we noticed a reduced expression of miR-1237, miR-365, miR-223b, miR-27b, miR-151-5p, miR-23a, miR-21, miR-30e, miR-361-5p, miR-484, miR-185, miR-374a, miR-197 in our study, as recently stated in solid tumor, thus suggesting that significantly lower abundance of these miRNAs is shared in leukemia. In addition to identify the already known leukemia-associated miRNAs, we had checked out dozens of novel miRNAs without any articles published until now, namely miR-502-3p, miR-718, miR-877, miR-1470, miR-720, miR-1267, miR-127, miR-767-3p, miR-1974-v14.0, miR-361-5p, miR-374b and so on. Using bioinformatic tools (TargetScan), we predicted potential targets for those miRNAs that exhibited altered expression in MVs from leukemia cells. Of particular interest, we found that hsa-miR-125a-3p which was refered above may regulate 34 potential genes of which five are located around the chromosome open reading frame. We hypothesised that miR-125a-3p may participate in the modulation of leukemia through these genes by affecting chromosome. Taken together, our study identifies miRNAs of MVs from leukemia and normal cells and characterizes specific miRNAs expression. These findings highlight a number of miRNAs from leukemia-derived MVs that may contribute to the development of hematopoietic malignancies. Further investigation will reveal the function of these differentially expressed miRNAs and may provide potential targets for novel therapeutic strategies. Disclosures: No relevant conflicts of interest to declare.

Elucidating the role of long intergenic non-coding RNA 339 in human endometrium and endometriosis

2021 ◽  
Author(s):  
Sarah J Holdsworth-Carson ◽  
Molly Churchill ◽  
Jacqueline F Donoghue ◽  
Sally Mortlock ◽  
Jenny N Fung ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cell Lines ◽  
Expression Patterns ◽  
In Situ Hybridisation ◽  
Immune Defense ◽  
Human Endometrium ◽  
Altered Expression ◽  
Non Coding Rna

Abstract Endometriosis is a complex disease, influenced by genetic factors. Genetic markers associated with endometriosis exist at chromosome 1p36.12 and lead to altered expression of the long intergenic non-coding RNA 339 (LINC00339), however the role of LINC00339 in endometriosis pathophysiology remains unknown. The aim of this work was to characterise the expression patterns of LINC00339 mRNA in endometrium and endometriotic lesions in situ and to determine the functional role of LINC00339 in human endometrium. We employed RNA-sequencing, quantitative RT-PCR and in situ hybridisation to investigate the abundance of LINC00339 transcripts in endometrium and endometrial cell lines and to describe the pattern and localisation of LINC00339 expression in endometrium and endometriotic lesions. LINC00339 mRNA expression was manipulated (overexpressed and silenced) in endometrial stomal cell lines and RNA-sequencing data from overexpression models were analysed using online bioinformatics platforms (STRING and Ingenuity Pathway Analysis) to determine functional processes. We demonstrated the expression of LINC00339 in endometriotic lesions for the first time; we found LINC00339 expression was restricted to the lesion foci and absent in surrounding non-lesion tissue. Furthermore, manipulation of LINC00339 expression in endometrial stromal cell lines significantly impacted the expression of genes involved in immune defense pathways. These studies identify a novel mechanism for LINC00339 activity in endometrium and endometriosis, paving the way for future work, which is essential for understanding the pathogenesis of endometriosis.

scholarly journals SMARTer single cell total RNA sequencing

2018 ◽  
Author(s):  
Verboom Karen ◽  
Everaert Celine ◽  
Bolduc Nathalie ◽  
Livak J. Kenneth ◽  
Yigit Nurten ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Transcript Level ◽  
Cellular Heterogeneity ◽  
Circular Rnas ◽  
Rna Seq ◽  
Sequencing Data ◽  
Total Rna ◽  
Sequencing Experiment

AbstractSingle cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3’ end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.

scholarly journals Identification and comparison of circular RNAs in preeclampsia

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11299
Author(s):  
Zepeng Ping ◽  
Ling Ai ◽  
Huaxiang Shen ◽  
Xing Zhang ◽  
Huling Jiang ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Gestational Hypertension ◽  
Interaction Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Circular Rnas ◽  
Pathway Enrichment Analysis ◽  
Sequencing Data ◽  
Mortality And Morbidity ◽  
Specific Syndrome

Background Preeclampsia (PE) is a pregnancy-specific syndrome, belongs to the gestational hypertension diseases category and is considered among the causes of maternal and perinatal mortality and morbidity. However, the pathogenesis of PE is still vague. Methods In the present study, the circular RNA (circRNA) expression patterns of normal pregnant women and PE patients were investigated using whole RNA sequencing. Results A total of 151 differential expressed circRNAs were identified including 121 upregulated and 30 downregulated ones. Functional and pathway enrichment analysis was conducted on the differentially expressed circRNAs using Gene Ontology and KEGG databases. The results of this analysis indicated that several crucial biological processes and pathways were enriched in PE patients. circRNA–microRNA (miRNA) interaction analysis indicated that the reported differentially expresse circRNAs may be associated with some regulatory functions through miRNAs in PE patients. Two ceRNAs networks were constructed according to the targeting relationship between circRNAs/miRNAs and miRNAs/mRNAs. One sub-network contained one upregulated circRNA, four downregulated miRNAs and five upregulated mRNAs, and another sub-network contained 10 downregulated circRNAs, 21 upregulated miRNAs and 15 downregulated mRNAs. Conclusion CircRNA expression patterns have been investigated and this analysis revealed their potential regulatory mechanisms in PE patients. We constructed the ceRNAs (competing endogenous RNA) to reveal the potential molecular roles of dysregulated circRNAs in the PE patients using RNA sequencing data. circRNA_13301 was the only one upregulated circRNA in ceRNA being targeted by four miRNAs.

scholarly journals SMARTer single cell total RNA sequencing

2019 ◽  
Vol 47 (16) ◽  
pp. e93-e93 ◽  
Author(s):  
Karen Verboom ◽  
Celine Everaert ◽  
Nathalie Bolduc ◽  
Kenneth J Livak ◽  
Nurten Yigit ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
Expression Patterns ◽  
Cancer Cell Lines ◽  
Cellular Heterogeneity ◽  
Circular Rnas ◽  
Rna Seq ◽  
Total Rna

Abstract Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3′ end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation and on two other cancer cell lines sorted in microplates. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.

scholarly journals Identification of microRNA expression patterns and definition of a microRNA/mRNA regulatory network in distinct molecular groups of multiple myeloma

Blood ◽  
2009 ◽  
Vol 114 (25) ◽  
pp. e20-e26 ◽  
Author(s):  
Marta Lionetti ◽  
Marta Biasiolo ◽  
Luca Agnelli ◽  
Katia Todoerti ◽  
Laura Mosca ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Mirna Expression ◽  
Plasma Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Target Prediction ◽  
Primary Tumors ◽  
Altered Expression ◽  
Genome Wide ◽  
Definition Of

Abstract To date, little evidence of miRNA expression/deregulation in multiple myeloma has been reported. To characterize miRNA in the context of the major multiple myeloma molecular types, we generated miRNA expression profiles of highly purified malignant plasma cells from 40 primary tumors. Furthermore, transcriptional profiles, available for all patients, were used to investigate the occurrence of miRNA/predicted target mRNA pair anticorrelations, and the miRNA and genome-wide DNA data were integrated in a subset of patients to evaluate the influence of allelic imbalances on miRNA expression. Differential miRNA expression patterns were identified, which were mainly associated with the major IGH translocations; particularly, t(4;14) patients showed specific overexpression of let-7e, miR-125a-5p, and miR-99b belonging to a cluster at 19q13.33. The occurrence of other lesions (ie, 1q gain, 13q and 17p deletions, and hyperdiploidy) was slightly characterized by specific miRNA signatures. Furthermore, the occurrence of several allelic imbalances or loss of heterozygosity was found significantly associated with the altered expression of miRNAs located in the involved regions, such as let-7b at 22q13.31 or miR-140-3p at 16q22. Finally, the integrative analysis based on computational target prediction and miRNA/mRNA profiling defined a network of putative functional miRNA-target regulatory relations supported by expression data.

scholarly journals Circular RNAs regulate cancer-related signaling pathways and serve as potential diagnostic biomarkers for human cancers

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Pranavi Garlapati ◽  
Jinjie Ling ◽  
Paul J. Chiao ◽  
Jie Fu
Keyword(s):  
Signaling Pathways ◽  
Rna Sequencing ◽  
Cell Lines ◽  
Cancer Cell ◽  
High Throughput ◽  
Circular Rnas ◽  
Gene Expressions ◽  
Diagnostic Biomarkers ◽  
Cellular Components ◽  
Cell Signaling Pathways

AbstractCircular RNAs (circRNAs) are RNAs that have an important role in various pathological processes, including cancer. After the usage of high-throughput RNA sequencing, many circRNAs were found to be differentially expressed in various cancer cell lines and regulate cell signaling pathways by modulating particular gene expressions. Understanding their role in these pathways and what cancers they are found in can set the stage for identifying diagnostic and prognostic biomarkers and therapeutic targets of cancer. This paper will discuss which circRNAs are found in different cancers and what mechanisms they use to upregulate or downregulate certain cellular components.

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