scholarly journals TMIC-28. LONG NON-CODING RNA EXPRESSION DIFFERS BETWEEN GLIOBLASTOMA PATIENT IMMUNE CELLS AND HEALTHY VOLUNTEERS

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi253-vi253
Author(s):  
Anthony Nwankwo ◽  
Victoria Sanchez ◽  
John Lynes ◽  
Xiang Wang ◽  
Gifty Dominah ◽  
...  
Keyword(s):  
T Cells ◽  
Differential Expression ◽  
Immune Cells ◽  
Fold Change ◽  
Differentially Expressed ◽  
Preliminary Review ◽  
Lncrna Expression ◽  
Glioblastoma Patient ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract To improve glioblastoma treatment, improved characterization of the tumor’s immune microenvironment is critical. Aberrant long non-coding RNA (LncRNA) expression has been implicated in the pathogenesis of many cancers, including glioblastoma. Other studies have discovered long non-coding RNAs which regulate immunity. However, lncRNA expression has not been systematically investigated glioblastoma patient immune cells. We aimed to investigate the differential expression of LncRNA and mRNs in the T lymphocytes and monocytes of glioblastoma patients when compared to healthy controls in an unbiased fashion. CD3 and CD14 cells were sorted from PBMC samples from 3 newly diagnosed glioblastoma patients and 3 normal donors, and RNA was extracted from them. These RNA samples were run on the Arraystar Human LncRNA microarray. We found 309 LncRNAs differentially expressed in glioblastoma patient T cells, and 316 in patient monocytes (fold change >2 or £0.5, P£0.05). A preliminary review of this data has revealed upregulation of lncRNAs that have previously been reported to play a role in tumorigenesis, such as MIF12-AS1, VIM-AS1, and WEE2-AS1. Additionally, lncRNAs such as CCDC26 and Hoxa10 that have been implicated in immune cell differentiation and hyperactivity also show differential expression between the two groups. We also found differential expression of 203 mRNA in T cells and 467 in monocytes (fold change ³2 or £0.5, P£0.05). An analysis based on the Kyoto Encyclopedia of Genes and Genomes identified 42 biological pathways that have enrichment of these differentially expressed mRNAs (P£0.05), including the RIG-I-like receptor pathway and toll-like receptor pathway, both implicated in innate immunity in T-cells. This array data will form the template for future single-cell RNA sequencing of tumor-infiltrating immune cells; peripheral immune cells from glioblastoma patients; and immune cells from non-tumorous brain (epilepsy tissue) and blood samples to investigate these differences in greater detail.

scholarly journals Long non-coding RNA TCONS_00000200 as a non-invasive biomarker in patients with intracranial aneurysm

2019 ◽  
Vol 39 (11) ◽  
Author(s):  
Chenghan Wu ◽  
Hailong Song ◽  
Yinzhou Wang ◽  
Lili Gao ◽  
Yali Cai ◽  
...  
Keyword(s):  
Intracranial Aneurysm ◽  
Differential Expression ◽  
Plasma Levels ◽  
Fold Change ◽  
Differentially Expressed ◽  
Healthy Individuals ◽  
Gene Markers ◽  
Qrt Pcr ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract We performed long non-coding RNA (lncRNA) microarray assay to identify lncRNAs with differential expression between patients with intracranial aneurysm (IA) and healthy control individuals to evaluate their potential use as biomarkers of IA. Arraystar Human lncRNA Microarray v3.0 was performed to identify differentially expressed lncRNAs and mRNAs in plasma samples (4 ml). lncRNAs with the most pronounced differential expression were used to select gene markers, and results were validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Plasma levels of TCONS_00000200 (fold change: 2.28) and ENST00000511927 (fold change: 2.50) were significantly higher in IA patients than in healthy individuals (P<0.001), and plasma levels of ENST00000421997 (fold change: 0.45) and ENST00000538202 (fold change: 0.43) were significantly lower in IA patients than in healthy individuals (P<0.001). qRT-PCR confirmed the same trends of up- and down-regulation of these four lncRNAs. A receiver operating characteristic (ROC) curve for TCONS_00000200 showed that the area under the curve (AUC) was 0.963 (95% confidence interval, 0.919–1.000), optimal cut-off point was 0.0081, sensitivity was 90.0%, and specificity was 96.7%. These results indicate that the lncRNA TCONS_00000200 is differentially expressed in the plasma of IA patients and could serve as a biomarker of IA.

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.

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 Signatures with Diagnostic and Prognostic Significance in Aggressive B-Cell Lymphoma

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1759-1759 ◽  
Author(s):  
Jiayu Yu ◽  
Alyssa Bouska ◽  
Waseem Lone ◽  
Chengfeng Bi ◽  
Tayla Heavican ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Fold Change ◽  
Differentially Expressed ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Aggressive B Cell Lymphoma

Abstract Diffuse large B-cell lymphoma (DLBCL) displays significant heterogeneity with regard to clinical, pathological, and genetic features. Using gene expression profiling, we have delineated 3 molecular subgroups within DLBCL: germinal center B cells (GCB-DLBCL), activated B cells (ABC-DLBCL), and primary mediastinal B-cell lymphoma (PMBL),while these defined subgroups show characteristic mutation profiles and oncogenic pathways, a small set of cases of DLBCL still remain "unclassifiable" (UC). Burkitt lymphoma (BL) is characterized by the t(8;14)(q24;q32) with distinct morphological and immunophenotypic features. The diagnostic distinction between BL and DLBCL is challenging in a subset of cases that have overlapping morphological, immunohistochemical, and even molecular features, but is crucial for effective therapy. The identification of long non-coding RNA (lncRNA) has added another critical component to cancer biology. LncRNAs are defined as a distinct set of non-protein coding transcripts longer than 200 nucleotides. The functions of a few lncRNAs have been recently elucidated of which some are thought to regulate gene-specific transcription. The goal of the current study was to identify reliable lncRNA signatures for the BL and DLBCL subgroups and evaluate their usefulness as prognostic biomarkers. We examined the expression of lncRNAs from our earlier studies using Affymetrix-HG-U133 plus 2 arrays to distinguish unique gene expression profiles between BL and DLBCL (PMID: 27292966). In the initial analysis, we compared BL (n=77) with DLBCL (n=474) and identified 275 differentially expressed lncRNAs (p=0.005, fold change>1.5). There was high expression of TCL6 and DDX-AS11 in BL. We confirmed the microarray results for TCL6 and DDX-AS11 by qRT-PCR in a subset of cases. We further tested whether expression of TCL6 and DDX-AS11 was regulated by the MYC oncogene and observed significant downregulation of these transcripts upon CRISPR/cas9 mediated deletion of the MYC promoter in the Raji cell line. We also sought to identify GCB-DLBCL and ABC-DLBCL associated lncRNAs. We observed 36 lncRNAs highly expressed in ABC-DLBCL and 40 lncRNAs highly expressed in GCB-DLBCL (P=0.005, fold change>1.5). Of the differentially expressed lncRNAs, lnc00487 and DUBR were upregulated in GCB-DLBCL, whereas lnc00944 and FUT8 were upregulated ABC-DLBCL. The observed expression differences were validated in ABC-DLBCL and GCB-DLBCL cell lines. The differentially expressed LncRNAs were also validated in other DLBCL cohorts. LncRNA00487 expression was associated with superior clinical outcome in DLBCL series treated with Rituximab (R)-CHOP (p=0.01), and gene expression and overall survival (OS) were validated in another DLBCL series treated with R-CHOP (PMID:22437443). In the present study, we found that lncRNAs are differentially expressed in aggressive B cell lymphoma and could be useful as diagnostic or prognostic markers. They may play an important role in lymphoma biology and further studies of their functions are warranted. Disclosures No relevant conflicts of interest to declare.

scholarly journals Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma

Head & Neck ◽  
2018 ◽  
Vol 40 (7) ◽  
pp. 1555-1564 ◽  
Author(s):  
Sulsal-Ul Haque ◽  
Liang Niu ◽  
Damaris Kuhnell ◽  
Jacob Hendershot ◽  
Jacek Biesiada ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Differential Expression ◽  
Squamous Cell ◽  
Prognostic Value ◽  
Neck Squamous Cell Carcinoma ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals Long-non Coding RNAs Related to Fat Deposition in Pigs Included lncRNA Corresponding to Human MALAT1

2021 ◽  
Author(s):  
Katarzyna Piórkowska ◽  
Kacper Żukowski ◽  
Katarzyna Ropka-Molik ◽  
Mirosław Tyra
Keyword(s):  
Regulatory Elements ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Sequencing Method ◽  
Non Coding Rnas ◽  
Potential Interactions ◽  
Long Non Coding Rna ◽  
Generation Sequencing

Obesity is a problem in the last decades since the development of different technologies forced the submission of a faster pace of life, resulting in nutrition style changes. In turn, domestic pigs are an excellent animal model in recognition of adiposity-related processes, corresponding to the size of individual organs, the distribution of body fat in the organism, and similar metabolism. The present study applied the next-generation sequencing method to identify adipose tissue (AT) transcriptomic signals related to increased fat content by identifying differentially expressed genes (DEGs), included long-non coding RNA molecules. The Freiburg RNA tool was applied to recognise predicting hybridisation energy of RNA-RNA interactions. The results indicated several long non-coding RNAs (lncRNAs) whose expression was significantly positively or negatively associated with fat deposition. lncRNAs play an essential role in regulating gene expression by sponging miRNA, binding transcripts, facilitating translation, or coding other smaller RNA regulatory elements. In the pig fat tissue of obese group, increased expression of lncRNAs corresponding to human MALAT1 was observed that previously recognised in the obesity-related context. Moreover, hybridisation energy analyses pinpointed numerous potential interactions between identified differentially expressed lncRNAs, and obesity-related genes and miRNAs expressed in AT.

scholarly journals Identification of Immune-Related Prognostic mRNA and lncRNA in Patients with Hepatocellular Carcinoma

2022 ◽  
Vol 2022 ◽  
pp. 1-16
Author(s):  
Dan Chen ◽  
Xiaoting Li ◽  
Hui Li ◽  
Kai Wang ◽  
Xianghua Tian
Keyword(s):  
Hepatocellular Carcinoma ◽  
Flow Cytometry ◽  
T Cells ◽  
Regression Analysis ◽  
Survival Analysis ◽  
Immune Cells ◽  
Cox Regression ◽  
Differentially Expressed ◽  
Cox Regression Analysis ◽  
Immune Related Genes

Background. As the most common hepatic malignancy, hepatocellular carcinoma (HCC) has a high incidence; therefore, in this paper, the immune-related genes were sought as biomarkers in liver cancer. Methods. In this study, a differential expression analysis of lncRNA and mRNA in The Cancer Genome Atlas (TCGA) dataset between the HCC group and the normal control group was performed. Enrichment analysis was used to screen immune-related differentially expressed genes. Cox regression analysis and survival analysis were used to determine prognostic genes of HCC, whose expression was detected by molecular experiments. Finally, important immune cells were identified by immune cell infiltration and detected by flow cytometry. Results. Compared with the normal group, 1613 differentially expressed mRNAs (DEmRs) and 1237 differentially expressed lncRNAs (DElncRs) were found in HCC. Among them, 143 immune-related DEmRs and 39 immune-related DElncRs were screened out. These genes were mainly related to MAPK cascade, PI3K-AKT signaling pathway, and TGF-beta. Through Cox regression analysis and survival analysis, MMP9, SPP1, HAGLR, LINC02202, and RP11-598F7.3 were finally determined as the potential diagnostic biomarkers for HCC. The gene expression was verified by RT-qPCR and western blot. In addition, CD4 + memory resting T cells and CD8 + T cells were identified as protective factors for overall survival of HCC, and they were found highly expressed in HCC through flow cytometry. Conclusion. The study explored the dysregulation mechanism and potential biomarkers of immune-related genes and further identified the influence of immune cells on the prognosis of HCC, providing a theoretical basis for the prognosis prediction and immunotherapy in HCC patients.

scholarly journals Overexpression of long non coding RNA OR3A4 is associated with altered p38 signalling, morphological and phenotypic changes, and reduced immunogenicity in Barretts Oesophagus

2021 ◽  
Author(s):  
Thomas Nieto ◽  
Yash Sinha ◽  
Qin Qin Zhuang ◽  
Mathew Coleman ◽  
Joanne D Stockton ◽  
...  
Keyword(s):  
T Cells ◽  
P38 Mapk ◽  
Significant Risk ◽  
Oesophageal Adenocarcinoma ◽  
Cellular Phenotype ◽  
Over Expression ◽  
Non Coding Rna ◽  
P38 Mapk Inhibitor ◽  
Long Non Coding Rna ◽  
Mapk Inhibitor

Background: Barretts Oesophagus (BO) presents a particular pathological dilemma, in that patients who have no dysplasia within their BO experience a small but significant risk of malignant progression each year. Screening programmes have attempted to reduce the mortality from BO associated oesophageal adenocarcinoma but cannot predict which BO patients will progress to invasive malignancy. We have previously identified the long non coding RNA, OR3A4, is differentially hypomethylated in progressive BO. We aimed to understand its role in BO pathogenicity Methods: The stable BO cell line CP-A, as well as the oesophageal adenocarcinoma cells line OE-33 was transfected with a lentiviral OR3A4 over-expression vector, and underwent high resolution microscopy, immunofluorescence, RT-qPCR, RNA sequencing, and targeted drug screening with the p38-MAPK inhibitor domipramod to understand the effects of OR3A4 expression on progression. We then compared progressive vs. non-progressive BO samples using quantitative multi-fluorophore (Vectra) immunohistochemistry. Results: Over-expression of OR3A4 in CP-A lines resulted in a hyperproliferative, dysplastic cellular phenotype, with strong over-expression of MAPK and anti-apoptotic pathways at the RNA and protein level, which was sensitive to the p38-MAPK inhibitor domipramod. Vectra immunohistochemistry demonstrated that progressive BO had reduced visibility associated with a reduction in CD8+ T-cells and CD68+ macrophages and reduced CD4+ T-cells in the stomal compartment. Conclusion: The overexpression of OR3A4, which we have previously shown is associated with progressive BO leads to a proliferative dysplastic cellular phenotype associated with increased, reversible MAPK signalling and loss of immune visibility.

scholarly journals Differential long non-coding RNA expression profile and function analysis in primary Sjogren’s syndrome

2021 ◽  
Author(s):  
Xiaochan Chen ◽  
Qi Cheng ◽  
Yan Du ◽  
Lei Liu ◽  
Huaxiang Wu
Keyword(s):  
B Cells ◽  
Primary Sjögren’S Syndrome ◽  
Differentially Expressed ◽  
Expression Level ◽  
Primary Sjogren’S Syndrome ◽  
Primary Sjögren's Syndrome ◽  
Cerna Network ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Healthy Persons

Abstract Background: Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease characterized by abnormal immune cell activation. This study aimed to investigate differentially expressed long non-coding RNA (lncRNA) in peripheral blood mononuclear cells (PBMCs) in patients with pSS to identify lncRNAs that affect pSS pathogenesis. Methods: Total RNA was extrated from PBMCs of 30 patients with pSS and 15 healthy persons. Transcriptome sequencing was used to screen differentially expressed lncRNAs and mRNAs in 8 RNA samples from the discovery cohort. The differentially expressed mRNAs underwent functional enrichment analysis. A protein interaction relationship (PPI) and ceRNA network was constructed. Real-time PCR was used to validate screened lncRNAs in all 45 RNA samples. Results: 1180 lncRNAs and 640 mRNAs were differentially expressed in pSS patients (fold change > 2 in healthy persons). The PPI network was constructed with 640 mRNAs and a ceRNA network with four key lncRNAs (GABPB1-AS1, PSMA3-AS1, LINC00847 and SNHG1). RT-PCR revealed that GABPB1-AS1 and PSMA3-AS1 were significantly upregulated 3.0-and 1.4-fold in the pSS group, respectively. The GABPB1-AS1 expression level was positively correlated with the percentage of B cells and IgG levels. Conclusions: GABPB1-AS1 was significently upregulated in pSS patients, and its expression level is positively correlated with the percentage of B cells and IgG levels. GABPB1-AS1 may be involved in the pathogenesis of pSS.

Sign in / Sign up

Export Citation Format

Share Document