scholarly journals Detection and Analysis of the Hedgehog Signaling Pathway-Related Long Non-Coding RNA (lncRNA) Expression Profiles in Keloid

2018 ◽  
Vol 24 ◽  
pp. 9032-9044 ◽  
Author(s):  
Heping Huang ◽  
Shangfeng Fu ◽  
Dewu Liu
Keyword(s):  
Signaling Pathway ◽  
Hedgehog Signaling ◽  
Expression Profiles ◽  
Hedgehog Signaling Pathway ◽  
Lncrna Expression ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrheic piglets caused by Clostridium perfringens type C

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5997 ◽  
Author(s):  
Zunqiang Yan ◽  
Xiaoyu Huang ◽  
Wenyang Sun ◽  
Qiaoli Yang ◽  
Hairen Shi ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Clostridium Perfringens ◽  
Diarrheal Disease ◽  
Inflammatory Responses ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Non Coding Rna ◽  
Receptor Signaling Pathway ◽  
Type C ◽  
Long Non Coding Rna

Background Clostridium perfringens (C. perfringens) type C is the most common bacteria causing piglet diarrheal disease and it greatly affects the economy of the global pig industry. The spleen is an important immune organ in mammals; it plays an irreplaceable role in resisting and eradicating pathogenic microorganisms. Based on different immune capacity in piglets, individuals display the resistance and susceptibility to diarrhea caused by C. perfringens type C. Recently, long non-coding RNA (lncRNA) and mRNA have been found to be involved in host immune and inflammatory responses to pathogenic infections. However, little is known about spleen transcriptome information in piglet diarrhea caused by C. perfringens type C. Methods Hence, we infected 7-day-old piglets with C. perfringens type C to lead to diarrhea. Then, we investigated lncRNA and mRNA expression profiles in spleens of piglets, including control (SC), susceptible (SS), and resistant (SR) groups. Results As a result, 2,056 novel lncRNAs and 2,417 differentially expressed genes were found. These lncRNAs shared the same characteristics of fewer exons and shorter length. Bioinformatics analysis identified that two lncRNAs (ALDBSSCT0000006918 and ALDBSSCT0000007366) may be involved in five immune/inflammation-related pathways (such as Toll-like receptor signaling pathway, MAPK signaling pathway, and Jak-STAT signaling pathway), which were associated with resistance and susceptibility to C. perfringens type C infection. This study contributes to the understanding of potential mechanisms involved in the immune response of piglets infected with C. perfringens type C.

scholarly journals Aberrant expression of long non-coding RNA in thyroid neoplasms

2019 ◽  
pp. 17-25
Author(s):  
В.Д. Якушина ◽  
А.С. Танас ◽  
А.В. Лавров
Keyword(s):  
Thyroid Cancer ◽  
Signaling Pathway ◽  
In Silico ◽  
Thyroid Nodules ◽  
Differentially Expressed ◽  
Follicular Variant ◽  
Aberrant Expression ◽  
Lncrna Expression ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Актуальность. Длинные некодирующие РНК (днРНК) при раке щитовидной железы плохо изучены; не известны днРНК, общие и специфичные для фолликулярного и классического вариантов папиллярного рака, не установлены днРНК, аберрантно экспрессированные при других основных субтипах злокачественных новообразований щитовидной железы, а также при доброкачественных новообразованиях. Цель исследования - определить днРНК, аберрантно экспрессированные при фолликулярной аденоме (ФА), фолликулярном раке (ФРЩЖ), фолликулярном и классическом вариантах папиллярного рака (ПРЩЖ), анапластическом раке (АРЩЖ) щитовидной железы. Методы. Проанализирована экспрессия днРНК по данным исследований на микрочипах (8 независимых экспериментов, доступных в GEO) и секвенирования РНК (PRJEB11591 и TCGA-THCA). Исследованы 246 образцов нормальной ткани щитовидной железы, 26 - ФА, 30 - ФРЩЖ, 181 - фолликулярного варианта ПРЩЖ, 481 - классического варианта ПРЩЖ и 49 - АРЩЖ. Для классического и фолликулярного вариантов ПРЩЖ выполнена валидация дифференциальной экспрессии in silico. Потенциальные биологические функции были оценены в результате анализа обогащения коэкспрессированных генов. Результаты. Определены днРНК, дифференциально экспрессированные при ФА, ФРЩЖ, фолликулярном и классическом вариантах ПРЩЖ и АРЩЖ. Выявлены 8 днРНК, экспрессия которых изменена во всех субтипах новообразований щитовидной железы, 22 - общих для ПРЩЖ, 32 - специфичных для классического варианта ПРЩЖ, 1 - специфичная для фолликулярного варианта ПРЩЖ, и 177 - специфичных для АРЩЖ. Статистически значимо дифференциально экспрессированных днРНК в ФРЩ по сравнению с ФА не выявлено. Ранее известные онкогенные и супрессорные днРНК NR2F1-AS1, LINC00511, SLC26A4-AS1, CRNDE, RMST впервые обнаружены в новообразованиях щитовидной железы. Выявленные днРНК предположительно вовлечены в клеточную адгезию, организацию экстрацеллюлярного матрикса, образование эндодермы, регуляцию клеточного цикла и митоза, полярности клеток, сигнальные пути VEGF и WNT. Выводы. Установлены общие и специфичные паттерны экспрессии днРНК в доброкачественных и злокачественных новообразованиях щитовидной железы. Background. Long non-coding RNA (lncRNA) in thyroid cancer are poorly investigated; no lncRNAs common and specific for the follicular and classical variants of papillary cancer, as well as no lncRNAs aberrantly expressed in benign nodules or other subtypes of thyroid cancer are established. The objective of the study is to determine long noncoding RNAs aberrantly expressed in follicular adenoma (FA), follicular carcinoma (FTC), follicular and classical variants of papillary carcinoma (PTC), anaplastic carcinoma (ATC). Methods. lncRNA expression was analyzed in dataset of Microarray (8 independent experiments available in GEO) and RNA-seq studies (PRJEB11591 and TCGA-THCA). In total, 246 samples of normal thyroid tissue, 26 FAs, 30 FTCs, 181 follicular variant PTCs, 481 classic variant PTCs and 49 ATCs were examined. In silico validation was performed. Potential biological functions were assessed by enrichment analysis of coexpressed genes. Results. LncRNAs differentially expressed in FA, FTC, follicular, and classical variants of PTC, and ATC are identified. There are 8 lncRNAs common for all investigated thyroid nodules, 22 common for PTC, 32 specific for classical PTC, 1 specific for follicular variant of PTC, and 177 specific for ATC. No lncRNA significantly differentially expressed in FTC compared to FA is identified. The previously described oncogenic and suppressor lncRNAs NR2F1-AS1, LINC00511, SLC26A4-AS1, CRNDE, RMST are detected in thyroid carcinomas for the first time. Identified lncRNA are putatively involved in cell adhesion, extracellular matrix organization, endoderm formation, VEGF signaling pathway, WNT signaling pathway and cell polarity, cell cycle and mitosis. Conclusion. The general and specific patterns of lncRNA expression in benign and malignant thyroid nodules are established.

scholarly journals Characterization of Long Non-coding RNA Profile in RD and SH-SY5Y Cells Infected by CV-B5 using RNA Sequencing

2021 ◽  
Author(s):  
Wei Chen ◽  
Peiying Teng ◽  
Heng Yang ◽  
Jing Li ◽  
Fan Yang
Keyword(s):  
Signaling Pathway ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Wnt Signaling Pathway ◽  
Foot And Mouth Disease ◽  
Differentially Expressed ◽  
Host Interactions ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract Hand, foot, and mouth disease caused by Coxsackievirus B5 (CV-B5) poses considerable threats to the health of infants especially in neurological damage. And the long noncoding RNAs (lncRNAs) act pivotal factors in regulating and participating in virus-host interactions. However, the role of lncRNAs in CV-B5-host interactions has not yet been elucidated. In this study, we used the RNA sequencing to determine the expression profiles of lncRNAs in CV-B5 infected human rhabdomyosarcoma (RD) and SH-SY5Y cells. Our results identified that in the differentially expressed lncRNAs a total of 508 up-regulated and 760 down-regulated lncRNAs in RD cell, with 46.2% were lincRNAs, 28.6% were anti-sense lncRNAs, 24.1% were sense overlapping lncRNAs, and 1.0% were sense intronic lncRNAs. Moreover, 792 lncRNAs were significantly increased and 811 lncRNAs were greatly decreased in SH-SY5Y cell including 48.6% were lincRNAs, 34.7% were anti-sense lncRNAs, 16.0% were sense overlapping lncRNAs, and 0.8% were sense intronic lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway showed that the differentially expressed lncRNAs participated in the occurrence of disease in RD cell and associated with signaling pathway in SH-SY5Y cell after CVB5 infection respectively. In addition, similar results were obtained when seven lncRNAs were selected for validation using RT-qPCR assays. Moreover, we conducted the candidate lncRNA-IL12A secondary structures and found that it inhibits viral replication through Wnt signaling pathway. Our results reveal that lncRNAs can become a possible novel molecular target for the prevention and treatment of CV-B5 infection, and provided information for distinguishing neurogenic CV-B5 disease.

Long non-coding RNA expression profiles in neutrophils revealed potential biomarker for prediction of renal involvement in SLE patients

Rheumatology ◽  
2020 ◽  
Author(s):  
Bin Cai ◽  
Jingyi Cai ◽  
Zhihua Yin ◽  
Xiaoyue Jiang ◽  
Chao Yao ◽  
...  
Keyword(s):  
Disease Activity ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Renal Involvement ◽  
Differentially Expressed ◽  
Healthy Controls ◽  
Lncrna Expression ◽  
Non Coding Rna ◽  
Potential Biomarker ◽  
Long Non Coding Rna

Abstract Objective The long non-coding RNA plays an important role in inflammation and autoimmune diseases. The aim of this study is to screen and identify abnormally expressed lncRNAs in peripheral blood neutrophils of SLE patients as novel biomarkers and to explore the relationship between lncRNAs levels and clinical features, disease activity and organ damage. Methods RNA-seq technology was used to screen differentially expressed lncRNAs in neutrophils from SLE patients and healthy donors. Based on the results of screening, candidate lncRNA levels in neutrophils of 88 SLE patients, 35 other connective disease controls, and 78 healthy controls were qualified by real-time quantitative polymerase chain reaction. Results LncRNA expression profiling revealed 360 up-regulated lncRNAs and 224 down-regulated lncRNAs in neutrophils of SLE patients when compared with healthy controls. qPCR assay validated that the expression of Lnc-FOSB-1:1 was significantly decreased in neutrophils of SLE patients when compared with other CTD patients or healthy controls. It correlated negatively with SLE Disease Activity Index 2000 (SLEDAI-2K) score (r = −0.541, P < 0.001) and IFN scores (r = −0.337, P = 0.001). More importantly, decreased Lnc-FOSB-1:1 expression was associated with lupus nephritis. Lower baseline Lnc-FOSB-1:1 level was associated with higher risk of future renal involvement (within an average of 2.6 years) in patients without renal disease at baseline (P = 0.019). Conclusion LncRNA expression profile in neutrophils of SLE patients revealed differentially expressed lncRNAs. Validation study on Lnc-FOSB-1:1 suggest that it is a potential biomarker for prediction of near future renal involvement.

scholarly journals Long Non-Coding RNA Expression Profiles for the Characterization of Different Bladder Cancer Grade

2018 ◽  
Vol 50 (3) ◽  
pp. 1154-1163 ◽  
Author(s):  
Yue-Peng Cao ◽  
Jun Zhou ◽  
Wei-Jian Li ◽  
Yang Shao ◽  
Shu-Yun Zheng ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Expression Profiles ◽  
Low Grade ◽  
High Grade ◽  
Rt Pcr ◽  
Lncrna Expression ◽  
Non Coding Rna ◽  
Pathway Analyses ◽  
Long Non Coding Rna ◽  
Normal Urothelium

Background/Aims: Bladder cancer (BC) is one of the most frequent urologic tumors worldwide. However, long non-coding RNA(lncRNA) expression profiles in BC progression remain unclear. This study aimed to explore lncRNA expression profiles in different grades of bladder cancer and normal urothelium tissues. Methods: We performed high-throughput sequencing in BC tissues of different grade and obtained the expression profiles of its lncRNAs. Then, aberrantly expressed lncRNAs were validated by quantitative reverse transcription polymerase chain reaction (RT-PCR). Gene Ontology (GO) and pathway analyses were used to investigate the potential function of these lncRNAs. Co-expresson network was constructed to explore the relationship between lncRNAs and target mRNAs. Results: We identified 252 aberrantly expressed lncRNAs in high-grade BC while compared to low-grade BC, and 269 lncRNAs in high-grade BC while compared to normal urothelium. Notably, we found 33 overlapped lncRNAs. Subsequently, 7 lncRNAs were selected from the overlapped part and confirmed by RT-PCR. GO and pathway analyses showed that these dysregulated lncRNAs participated in cell migration, cell adhesion, as well as Ras signaling pathway. Co-expression network and The Cancer Genome Atlas (TCGA) data showed LUCAT1 and CCNB1 had positive relationship in regulating the progress of bladder cancer. Conclusion: Our findings revealed the significant role of lncRNAs in the development process of bladder cancer.

Long non-coding RNA expression profiles in human parathyroid tumors

2017 ◽  
Author(s):  
Annamaria Morotti ◽  
Irene Forno ◽  
Valentina Andre ◽  
Andrea Terrasi ◽  
Chiara Verdelli ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Rna Expression ◽  
Parathyroid Tumors ◽  
Non Coding Rna ◽  
Long Non Coding Rna
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