mRNA/lncRNA expression patterns and the function of fibrinogen‐like protein 2 in Meishan pig endometrium during the preimplantation phases

2019 ◽  
Vol 86 (4) ◽  
pp. 354-369 ◽  
Author(s):  
Yueying Wang ◽  
Renwu Hua ◽  
Songyi Xue ◽  
Wenchao Li ◽  
Lihang Wu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Lncrna Expression ◽  
Meishan Pig

Abstract 2459: Clinicopathological subgroups of glioblastoma patients are characterized by specific lncRNA expression patterns

2018 ◽  
Author(s):  
Marek Vecera ◽  
Romana Butova ◽  
Radim Lipina ◽  
Stefan Reguli ◽  
Martin Smrcka ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Lncrna Expression

scholarly journals Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Alexandra Kalmár ◽  
Zsófia Brigitta Nagy ◽  
Orsolya Galamb ◽  
István Csabai ◽  
András Bodor ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Differential Expression ◽  
Colorectal Adenoma ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Aberrant Expression ◽  
Array Data ◽  
Lncrna Expression ◽  
Qrt Pcr ◽  
Mrna Targets

Abstract Background Long non-coding RNAs (lncRNAs) play a fundamental role in colorectal cancer (CRC) development, however, lncRNA expression profiles in CRC and its precancerous stages remain to be explored. We aimed to study whole genomic lncRNA expression patterns in colorectal adenoma–carcinoma transition and to analyze the underlying functional interactions of aberrantly expressed lncRNAs. Methods LncRNA expression levels of colonic biopsy samples (20 CRCs, 20 adenomas (Ad), 20 healthy controls (N)) were analyzed with Human Transcriptome Array (HTA) 2.0. Expression of a subset of candidates was verified by qRT-PCR and in situ hybridization (ISH) analyses. Furthermore, in silico validation was performed on an independent HTA 2.0, on HGU133Plus 2.0 array data and on the TCGA COAD dataset. MiRNA targets of lncRNAs were predicted with miRCODE and lncBase v2 algorithms and miRNA expression was analyzed on miRNA3.0 Array data. MiRNA-mRNA target prediction was performed using miRWALK and c-Met protein levels were analyzed by immunohistochemistry. Comprehensive lncRNA-mRNA-miRNA co-expression pattern analysis was also performed. Results Based on our HTA results, a subset of literature-based CRC-associated lncRNAs showed remarkable expression changes already in precancerous colonic lesions. In both Ad vs. normal and CRC vs. normal comparisons 16 lncRNAs, including downregulated LINC02023, MEG8, AC092834.1, and upregulated CCAT1, CASC19 were identified showing differential expression during early carcinogenesis that persisted until CRC formation (FDR-adjusted p < 0.05). The intersection of CRC vs. N and CRC vs. Ad comparisons defines lncRNAs characteristic of malignancy in colonic tumors, where significant downregulation of LINC01752 and overexpression of UCA1 and PCAT1 were found. Two candidates with the greatest increase in expression in the adenoma-carcinoma transition were further confirmed by qRT-PCR (UCA1, CCAT1) and by ISH (UCA1). In line with aberrant expression of certain lncRNAs in tumors, the expression of miRNA and mRNA targets showed systematic alterations. For example, UCA1 upregulation in CRC samples occurred in parallel with hsa-miR-1 downregulation, accompanied by c-Met target mRNA overexpression (p < 0.05). Conclusion The defined lncRNA sets may have a regulatory role in the colorectal adenoma-carcinoma transition. A subset of CRC-associated lncRNAs showed significantly differential expression in precancerous samples, raising the possibility of developing adenoma-specific markers for early detection of colonic lesions.

scholarly journals Long Noncoding RNA Expression Signatures of Metastatic Nasopharyngeal Carcinoma and Their Prognostic Value

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Wei Zhang ◽  
Lin Wang ◽  
Fang Zheng ◽  
Ruhai Zou ◽  
Changqing Xie ◽  
...  
Keyword(s):  
Nasopharyngeal Carcinoma ◽  
Disease Progression ◽  
Noncoding Rna ◽  
Prognostic Value ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Lncrna Expression ◽  
Genome Wide ◽  
Independent Panel ◽  
Metastatic Nasopharyngeal Carcinoma

Long noncoding RNAs (lncRNAs) have recently been found to play important roles in various cancer types. The elucidation of genome-wide lncRNA expression patterns in metastatic nasopharyngeal carcinoma (NPC) could reveal novel mechanisms underlying NPC carcinogenesis and progression. In this study, lncRNA expression profiling was performed on metastatic and primary NPC tumors, and the differentially expressed lncRNAs between these samples were identified. A total of 33,045 lncRNA probes were generated for our microarray based on authoritative data sources, including RefSeq, UCSC Knowngenes, Ensembl, and related literature. Using these probes, 8,088 lncRNAs were found to be significantly differentially expressed (≥2-fold). To identify the prognostic value of these differentially expressed lncRNAs, four lncRNAs (LOC84740, ENST00000498296, AL359062, and ENST00000438550) were selected; their expression levels were measured in an independent panel of 106 primary NPC samples via QPCR. Among these lncRNAs, ENST00000438550 expression was demonstrated to be significantly correlated with NPC disease progression. A survival analysis showed that a high expression level of ENST00000438550 was an independent indicator of disease progression in NPC patients (P=0.01). In summary, this study may provide novel diagnostic and prognostic biomarkers for NPC, as well as a novel understanding of the mechanism underlying NPC metastasis and potential targets for future treatment.

scholarly journals Identification of lncRNAs associated with the pathogenesis of ankylosing spondylitis

2020 ◽  
Author(s):  
Dan Huang ◽  
Jian Liu ◽  
Lei Wan ◽  
Yanyan Fang ◽  
Yan Long ◽  
...  
Keyword(s):  
Ankylosing Spondylitis ◽  
Autoimmune Disease ◽  
Control Patient ◽  
Pearson Correlation ◽  
Expression Patterns ◽  
Rna Seq ◽  
Peripheral Blood Mononuclear ◽  
Lncrna Expression ◽  
Qrt Pcr ◽  
And Control

Abstract Background Ankylosing spondylitis (AS) is a chronic autoimmune disease affecting the sacroiliac joint. To date, few studies have examined the association between long non-coding RNAs (lncRNAs) and AS pathogenesis. As such, we herein sought to characterize patterns of AS-related lncRNA expression and to evaluate the potential role played by these lncRNAs in this complex autoimmune context. Methods We conducted an RNA-seq analysis of peripheral blood mononuclear cell samples isolated from five AS patients and corresponding controls. These data were then leveraged to characterize AS-related lncRNA expression patterns. We further conducted GO and KEGG enrichment analyses of the parental genes encoding these lncRNAs, and we confirmed the validity of our RNA-seq data by assessing the expression of six lncRNAs via qRT-PCR in 15 AS and control patient samples. Pearson correlation analyses were additionally employed to examine the associations between the expression levels of these six lncRNAs and patient clinical index values. Results We detected 56575 total lncRNAs in AS and control patient samples during our initial RNA-seq analysis, of which 200 and 70 were found to be up- and down-regulated (FC > 2 or < 0.05; P < 0.05), respectively, in AS samples relative to controls. In qRT-PCR validation assays, we confirmed the significant upregulation of NONHSAT118801.2, ENST00000444046, and NONHSAT183847.1 and the significant downregulation of NONHSAT205110.1, NONHSAT105444.2, and NONHSAT051856.2 in AS patient samples. We further found the expression of NONHSAT118801.2 and NONHSAT183847.1 to be positively correlated with disease severity. Conclusion Overall, our findings highlight several lncRNAs that are specifically expressed in the context of AS, indicating that they may play key functions in the pathogenesis of this autoimmune disease. Specifically, we determined that NONHSAT118801.2 and NONHSAT183847.1 may be valuable biomarkers of AS.

scholarly journals Identification of a prognostic long noncoding RNA signature in lung squamous cell carcinoma: a population-based study with a mean follow-up of 3.5 years

2021 ◽  
Vol 79 (1) ◽  
Author(s):  
Rongjiong Zheng ◽  
Mengdi Zheng ◽  
Mingming Wang ◽  
Feijie Lu ◽  
Meiling Hu
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Patient Survival ◽  
Expression Patterns ◽  
Lung Squamous Cell Carcinoma ◽  
Multidimensional Data ◽  
Cox Regression Analysis ◽  
Lncrna Expression ◽  
Patient Prognosis

Abstract Background Lung squamous cell carcinoma (LSCC) is a form of cancer that is associated with high rates of relapse, poor responsiveness to therapy, and a relatively poor prognosis. The relationship between long non-coding RNA (lncRNA) expression and LSCC patient prognosis remains to be established. Methods In the present study, we discovered that lncRNAs were differentially expressed in LSCC tumor tissues relative to normal control tissues, and we explored the prognostic relevance of these lncRNA expression patterns using data from the Cancer Genome Atlas (TCGA). Results These multidimensional data were analyzed in order to identify lncRNA signatures that were associated with LSCC patient survival outcomes. Kaplan-Meier survival curves revealed prognostic capabilities for three of these lncRNAs (LINC02555, APCDD1L-DT and OTX2-AS1). A Cox regression analysis revealed this three-lncRNA signature to be significantly associated with patient survival. Further GO and KEGG analyses revealed that the predicted target genes of these three lncRNAs were also potentially involved in cancer-associated pathways. Conclusions Together these results thus indicate that this novel three-lncRNA signature can be used to predict LSCC patient prognosis.

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 Identification of a prognostic three-long noncoding RNA signature in lung squamous cell carcinoma via bioinformatic analysis

2020 ◽  
Author(s):  
Rongjiong Zheng ◽  
Mengdi Zheng ◽  
Mingming Wang ◽  
Meiling Hu
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Patient Survival ◽  
Expression Patterns ◽  
Lung Squamous Cell Carcinoma ◽  
Multidimensional Data ◽  
Cox Regression Analysis ◽  
Lncrna Expression ◽  
Patient Prognosis

Abstract Background Lung squamous cell carcinoma (LSCC) is a form of cancer that is associated with high rates of relapse, poor responsiveness to therapy, and a relatively poor prognosis. The relationship between long non-coding RNA (lncRNA) expression and LSCC patient prognosis remains to be established. Methods In the present study, we discovered that lncRNAs were differentially expressed in LSCC tumor tissues relative to normal control tissues, and we explored the prognostic relevance of these lncRNA expression patterns using data from the Cancer Genome Atlas (TCGA). Results These multidimensional data were analyzed in order to identify lncRNA signatures that were associated with LSCC patient survival outcomes. Kaplan-Meier survival curves revealed prognostic capabilities for three of these lncRNAs (LINC02555, APCDD1L-DT and OTX2-AS1). A Cox regression analysis revealed this three-lncRNA signature to be significantly associated with patient survival. Further GO and KEGG analyses revealed that the predicted target genes of these three lncRNAs were also potentially involved in cancer-associated pathways. Conclusions Together these results thus indicate that this novel three-lncRNA signature can be used to predict LSCC patient prognosis.

scholarly journals Identification of lncRNAs associated with the pathogenesis of ankylosing spondylitis

2021 ◽  
Author(s):  
Dan Huang ◽  
Jian Liu ◽  
Lei Wan ◽  
Yanyan Fang ◽  
Yan Long ◽  
...  
Keyword(s):  
Ankylosing Spondylitis ◽  
Autoimmune Disease ◽  
Control Patient ◽  
Pearson Correlation ◽  
Expression Patterns ◽  
Rna Seq ◽  
Peripheral Blood Mononuclear ◽  
Lncrna Expression ◽  
Qrt Pcr ◽  
And Control

Abstract Background: Ankylosing spondylitis (AS) is a chronic autoimmune disease affecting the sacroiliac joint. To date, few studies have examined the association between long non-coding RNAs (lncRNAs) and AS pathogenesis. As such, we herein sought to characterize patterns of AS-related lncRNA expression and to evaluate the potential role played by these lncRNAs in this complex autoimmune context. Methods: We conducted a RNA-seq analysis of peripheral blood mononuclear cell (PBMC) samples isolated from five AS patients and corresponding controls. These data were then leveraged to characterize AS-related lncRNA expression patterns. We further conducted GO and KEGG enrichment analyses of the parental genes encoding these lncRNAs, and we confirmed the validity of our RNA-seq data by assessing the expression of six lncRNAs via qRT-PCR in 15 AS and control patient samples. Pearson correlation analyses were additionally employed to examine the associations between the expression levels of these six lncRNAs and patient clinical index values. Results: We detected 56575 total lncRNAs in AS and control patient samples during our initial RNA-seq analysis, of which 200 and 70 were found to be up- and down-regulated (FC > 2 or < 0.05; P<0.05), respectively, in AS samples relative to controls. In qRT-PCR validation assays, we confirmed the significant upregulation of NONHSAT118801.2, ENST00000444046, and NONHSAT183847.1 and the significant downregulation of NONHSAT205110.1, NONHSAT105444.2, and NONHSAT051856.2 in AS patient samples. We further found the expression of NONHSAT118801.2 and NONHSAT183847.1 to be positively correlated with disease severity. Conclusion: Overall, our findings highlight several lncRNAs that are specifically expressed in PBMCs of AS patients, indicating that they may play key functions in the pathogenesis of this autoimmune disease. Specifically, we determined that NONHSAT118801.2 and NONHSAT183847.1 may influence the occurrence and development of AS.

scholarly journals Identification of lncRNAs associated with the pathogenesis of ankylosing spondylitis

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dan Huang ◽  
Jian Liu ◽  
Lei Wan ◽  
Yanyan Fang ◽  
Yan Long ◽  
...  
Keyword(s):  
Ankylosing Spondylitis ◽  
Autoimmune Disease ◽  
Control Patient ◽  
Pearson Correlation ◽  
Expression Patterns ◽  
Rna Seq ◽  
Peripheral Blood Mononuclear ◽  
Lncrna Expression ◽  
Qrt Pcr ◽  
And Control

Abstract Background Ankylosing spondylitis (AS) is a chronic autoimmune disease affecting the sacroiliac joint. To date, few studies have examined the association between long non-coding RNAs (lncRNAs) and AS pathogenesis. As such, we herein sought to characterize patterns of AS-related lncRNA expression and to evaluate the potential role played by these lncRNAs in this complex autoimmune context. Methods We conducted a RNA-seq analysis of peripheral blood mononuclear cell (PBMC) samples isolated from five AS patients and corresponding controls. These data were then leveraged to characterize AS-related lncRNA expression patterns. We further conducted GO and KEGG enrichment analyses of the parental genes encoding these lncRNAs, and we confirmed the validity of our RNA-seq data by assessing the expression of six lncRNAs via qRT-PCR in 15 AS and control patient samples. Pearson correlation analyses were additionally employed to examine the associations between the expression levels of these six lncRNAs and patient clinical index values. Results We detected 56,575 total lncRNAs in AS and control patient samples during our initial RNA-seq analysis, of which 200 and 70 were found to be up- and down-regulated (FC > 2 or < 0.05; P < 0.05), respectively, in AS samples relative to controls. In qRT-PCR validation assays, we confirmed the significant upregulation of NONHSAT118801.2, ENST00000444046, and NONHSAT183847.1 and the significant downregulation of NONHSAT205110.1, NONHSAT105444.2, and NONHSAT051856.2 in AS patient samples. We further found the expression of NONHSAT118801.2 and NONHSAT183847.1 to be positively correlated with disease severity. Conclusion Overall, our findings highlight several lncRNAs that are specifically expressed in PBMCs of AS patients, indicating that they may play key functions in the pathogenesis of this autoimmune disease. Specifically, we determined that NONHSAT118801.2 and NONHSAT183847.1 may influence the occurrence and development of AS.

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