Genome-Wide Analysis of mRNA and Long Noncoding RNA Profiles in Chronic Actinic Dermatitis

Chronic actinic dermatitis (CAD), a photosensitive dermatosis, is characterized by inflammatory lesions, especially on sun-exposed skin. However, its pathogenesis remains unclear. In this study, second-generation RNA sequencing and comprehensive bioinformatics analyses of mRNAs and long noncoding RNAs (lncRNAs) were performed to determine the transcriptome profiles of patients with CAD. A total 6889 annotated lncRNAs, 341 novel lncRNAs, and 65091 mRNAs were identified. Interestingly, patients with CAD and healthy controls showed distinct transcriptome profiles. Indeed, 198 annotated (81.48%) and 45 novel (18.52%) lncRNAs were differentially expressed between the two groups. GO, KEGG, and RGSEA analyses of lncRNAs showed that inflammatory and immune response related pathways played crucial roles in the pathogenetic mechanism of CAD. In addition, we unveiled key differentially expressed lncRNAs, including lncRNA RP11-356I2.4 which plays a role probably by regulating TNFAIP3 and inflammation. qRT-PCR data validated the differentially expressed genes. The newly identified lncRNAs may have potential roles in the development of CAD; these findings lay a solid foundation for subsequent functional exploration of lncRNAs and mRNAs as therapeutic targets for CAD.

Download Full-text

Comprehensive Analysis of Differentially Expressed Long Noncoding RNA-mRNA in the Adenoma-Carcinoma Sequence of DNA Mismatch Repair Proficient Colon Cancer

Journal of Oncology ◽

10.1155/2021/9977695 ◽

2021 ◽

Vol 2021 ◽

pp. 1-15

Author(s):

Wenkun Li ◽

Qian Li ◽

Jiang Ge ◽

Yun Wang ◽

Nanshan Li ◽

...

Keyword(s):

Colon Cancer ◽

Mismatch Repair ◽

Noncoding Rna ◽

Intraepithelial Neoplasia ◽

Roc Curves ◽

Differentially Expressed ◽

Low Grade ◽

Large Set ◽

Network Analyses ◽

Qrt Pcr

DNA proficient mismatch repair colon cancer (pMMR CC) is the most common subtype of sporadic CC. We aimed to investigate the role of long noncoding RNAs (lncRNAs) in pMMR CC carcinogenesis. In the present study, we conducted transcriptomic analysis of lncRNAs-mRNAs in five low-grade intraepithelial neoplasia (LGIN), five high-grade intraepithelial neoplasia (HGIN), four pMMR CC, and five normal control (NC) tissues. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway, and coexpression network analyses were performed to elucidate the functions of lncRNAs and mRNAs as well as their interactions. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate five dysregulated lncRNAs in a large set of colon tissues. Receiver-operating characteristic (ROC) curves were employed to evaluate the performance of the candidate lncRNAs. A set of 5783 differentially expressed lncRNAs and 4483 differentially expressed mRNAs were detected among the LGIN, HGIN, pMMR CC, and NC samples. These differentially expressed lncRNAs and mRNAs were assigned to 275 significant GO terms and 179 significant KEGG enriched pathways. qRT-PCR confirmed that the expression of five selected lncRNAs (ENST00000521815, ENST00000603052, ENST00000609220, NR_026543, and ENST00000545920) were consistent with the microarray data. ROC analysis showed that four lncRNAs (ENST00000521815, ENST00000603052, ENST00000609220, and NR_026543) had larger area under the ROC curve (AUC) values compared to serum carcinoembryonic antigens, thereby distinguishing NC from pMMR CC. In conclusion, several lncRNAs play various roles in the adenoma-carcinoma sequence and may serve as potential biomarkers for the early diagnosis of pMMR CC.

Download Full-text

Aberrant Expression Profile of Long Noncoding RNA in Human Sinonasal Squamous Cell Carcinoma by Microarray Analysis

BioMed Research International ◽

10.1155/2016/1095710 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

Ling-zhao Meng ◽

Ju-gao Fang ◽

Jing-wu Sun ◽

Fan Yang ◽

Yong-xiang Wei

Keyword(s):

Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Pathway Analysis ◽

Expression Profile ◽

Squamous Cell ◽

Noncoding Rna ◽

Differentially Expressed ◽

Aberrant Expression ◽

Qrt Pcr ◽

Signal Network

Objectives. This study aimed to identify aberrantly expressed long noncoding RNAs (lncRNAs) profile of sinonasal squamous cell carcinoma (SSCC) and explore their potential functions. Methods. We investigated lncRNA and mRNA expression in SSCC and paired adjacent noncancerous tissues obtained from 6 patients with microarrays. Gene ontology (GO) analysis and pathway analysis were utilized to investigate the gene function. Gene signal-network and lncRNA-mRNA network were depicted. Quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to validate 5 lncRNAs in a second set of paired SSCC and adjacent noncancerous tissues obtained from 22 additional patients. Results. We identified significantly differentially expressed lncRNAs (n=3146) and mRNAs (n=2208) in SSCC relative to noncancerous tissues. The GO annotation indicated that there are some core gene products that may be attributed to the progress of SSCC. The pathway analysis identified many pathways associated with cancer. The results of lncRNA-mRNA network and gene signal-network implied some core lncRNAs/mRNAs might play important roles in SSCC pathogenesis. The results of qRT-PCR showed that all of the 5 lncRNAs were differentially expressed and consistent with the microarray results. Conclusion. Our study is the first screening and analysis of lncRNAs expression profile in SSCC and may offer new insights into pathogenesis of this disease.

Download Full-text

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

BioMed Research International ◽

10.1155/2015/618924 ◽

2015 ◽

Vol 2015 ◽

pp. 1-13 ◽

Cited By ~ 15

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.

Download Full-text

Long noncoding RNA expression profile of mouse cementoblasts under compressive force

The Angle Orthodontist ◽

10.2319/061118-438.1 ◽

2019 ◽

Vol 89 (3) ◽

pp. 455-463 ◽

Cited By ~ 3

Author(s):

Hao Liu ◽

Yiping Huang ◽

Yingying Zhang ◽

Yineng Han ◽

Yixin Zhang ◽

...

Keyword(s):

Expression Profile ◽

Long Noncoding Rna ◽

Functional Annotation ◽

Noncoding Rna ◽

Compressive Loading ◽

Compressive Force ◽

Differentially Expressed ◽

Rna Seq ◽

Lncrna Expression ◽

Qrt Pcr

ABSTRACT Objectives: To investigate the long noncoding RNA (lncRNA) expression profile of cementoblasts under compressive force. Materials and Methods: Mouse cementoblasts were exposed to compression (1.5 g/cm2) for 8 hours. RNA sequencing (RNA-seq) was performed to compare the transcriptomes of the compressed and control cells. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate five of the differentially expressed lncRNAs of interest. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also performed. Results: A total of 70 lncRNAs and 521 mRNAs were differentially regulated in cementoblasts subjected to compressive loading. Among the differentially expressed lncRNAs, 57 were upregulated and 13 downregulated. The expression levels of the five selected lncRNAs (Prkcz2, Hklos, Trp53cor1, Gdap10, and Ak312-ps) were validated by qRT-PCR and consistent with the RNA-seq results. GO functional annotation demonstrated upregulation of genes associated with cellular response to hypoxia and apoptotic processes during compressive loading. KEGG analysis identified the crucial pathways involving the hypoxia-inducing factor-1α, forkhead box O, and mammalian target of rapamycin signaling pathways. Conclusions: Mechanical compression changes the lncRNA expression profile of cementoblasts, providing important references for further investigation into the role and regulation of lncRNAs in compressed cementoblasts and root resorption during orthodontic treatment.

Download Full-text

Differential Expression Profiles of Long Noncoding RNA and mRNA of Osteogenically Differentiated Mesenchymal Stem Cells in Ankylosing Spondylitis

The Journal of Rheumatology ◽

10.3899/jrheum.151181 ◽

2016 ◽

Vol 43 (8) ◽

pp. 1523-1531 ◽

Cited By ~ 24

Author(s):

Zhongyu Xie ◽

Jinteng Li ◽

Peng Wang ◽

Yuxi Li ◽

Xiaohua Wu ◽

...

Keyword(s):

Stem Cells ◽

Mesenchymal Stem Cells ◽

Ankylosing Spondylitis ◽

Osteogenic Differentiation ◽

Noncoding Rna ◽

Bioinformatics Analysis ◽

Expression Profiles ◽

Differentially Expressed ◽

Qrt Pcr ◽

Pcr Assays

Objective.We previously demonstrated that mesenchymal stem cells (MSC) from patients with ankylosing spondylitis (AS; ASMSC) have a greater osteogenic differentiation capacity than MSC from healthy donors (HDMSC) and that this difference underlies the pathogenesis of pathological osteogenesis in AS. Here we compared expression levels of long noncoding RNA (lncRNA) and mRNA between osteogenically differentiated ASMSC and HDMSC and explored the precise mechanism underlying abnormal osteogenic differentiation in ASMSC.Methods.HDMSC and ASMSC were induced with osteogenic differentiation medium for 10 days. Microarray analyses were then performed to identify lncRNA and mRNA differentially expressed between HDMSC and ASMSC, which were then subjected to bioinformatics analysis and confirmed by quantitative real-time PCR (qRT-PCR) assays. In addition, coding-non-coding gene co-expression (CNC) networks were constructed to examine the relationships between the lncRNA and mRNA expression patterns.Results.A total of 520 lncRNA and 665 mRNA were differentially expressed in osteogenically differentiated ASMSC compared with HDMSC. Bioinformatics analysis revealed 64 signaling pathways with significant differences, including transforming growth factor-β signaling. qRT-PCR assays confirmed the reliability of the microarray data. The CNC network indicated that 4 differentially expressed lncRNA, including lnc-ZNF354A-1, lnc-LIN54-1, lnc-FRG2C-3, and lnc-USP50-2 may be involved in the abnormal osteogenic differentiation of ASMSC.Conclusion.Our study characterized the differential lncRNA and mRNA expression profiles of osteogenically differentiated ASMSC and identified 4 lncRNA that may participate in the abnormal osteogenic differentiation of ASMSC. These results provide insight into the pathogenesis of pathological osteogenesis in AS.

Download Full-text

Integrative analysis of miRNA-mRNA network in high altitude retinopathy by bioinformatics analysis

Bioscience Reports ◽

10.1042/bsr20200776 ◽

2021 ◽

Author(s):

Tong Su ◽

Chufeng Gu ◽

Deji Draga ◽

Chuandi Zhou ◽

Thashi Lhamo ◽

...

Keyword(s):

High Altitude ◽

Bioinformatics Analysis ◽

Cell Model ◽

Expression Profiles ◽

Oxygen Deficiency ◽

Differentially Expressed ◽

Hub Genes ◽

Bioinformatics Analyses ◽

Effective Prevention ◽

Qrt Pcr

High-altitude retinopathy (HAR) is an ocular manifestation of acute oxygen deficiency at high altitudes. Although the pathophysiology of HAR has been revealed by many studies in recent years, the molecular mechanism is not yet clear. Our study aimed to systematically identify the genes and miRNA and explore the potential biomarkers associated with HAR by integrated bioinformatics analysis. The mRNA and miRNA expression profiles were obtained from the GEO database. We performed Gene Ontology (GO) functional annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Potential target gene analysis and miRNA-mRNA network analysis were also conducted. Quantitative RT-PCR (qRT-PCR) was used to validate the results of the bioinformatics analysis. Through a series of bioinformatics analyses and experiments, we selected 16 differentially expressed miRNAs (DE-miRNAs) and 157 differentially expressed genes (DEGs) related to AMS and constructed a miRNA-mRNA network containing 240 relationship pairs. The hub genes were filtered from the PPI network: IL7R, FOS, IL10, FCGR2A, DDX3X, CDK1, BCL11B and HNRNPH1, which were all downregulated in the AMS group. Then, 9 upregulated DE-miRNAs and 8 hub genes were verified by qRT-PCR in our hypoxia-induced HAR cell model. The expression of miR-3177-3p, miR-369-3p, miR-603, miR-495, miR-4791, miR-424-5p, FOS, IL10 and IL7R was consistent with our bioinformatics results. In conclusion, FOS, IL10, IL-7R and 7 DE-miRNAs may participate in the development of HAR. Our findings will contribute to the identification of biomarkers and promote the effective prevention and treatment of HAR in the future.

Download Full-text

Identification of Long Noncoding RNA Expression Profiles in HPV-Negative Cervical Cancer

Gynecologic and Obstetric Investigation ◽

10.1159/000510030 ◽

2020 ◽

Vol 85 (5) ◽

pp. 377-387

Author(s):

Shiyin Ooi ◽

Yuandong Liao ◽

Pan Liu ◽

Ganlin Xu ◽

Tianyu Liu ◽

...

Keyword(s):

Cervical Cancer ◽

Noncoding Rna ◽

Expression Profiles ◽

Noncoding Rnas ◽

Cell Counting ◽

Migration And Invasion ◽

Bioinformatics Analyses ◽

Qrt Pcr ◽

Potential Biomarker ◽

Normal Cervix

Aim: HPV-negative cervical cancer (CC) usually appears more aggressive and causes poorer survival outcomes compared to HPV-positive cases. However, the research in regard to HPV-negative CC is rare, and the related molecular mechanism underlying remains unclear. We intended to explore the expression profiles of long noncoding RNAs (lncRNAs) and identify the tumor-associated lncRNAs which might be used as the potential biomarker for HPV-negative CC. Methods: Bioinformatics analyses were utilized to construct the expression profiles of lncRNAs, Gene Ontology, and KEGG analyses and draw the lncRNA-mRNA co-expression network in HPV-negative CC. The expression levels of the top 5 marked-up tumor-associated lncRNAs were detected by qRT-PCR. The effect of LINC00115 on CC growth and metastasis was studied by Cell Counting Kit-8 and transwell assays. Results: In comparison to normal cervix (NC), 2,052 lncRNAs were differentially expressed in HPV-negative CC. It demonstrated that LINC00115 was significantly upregulated in HPV-negative CC cells compared to NC, and it could promote proliferation, migration, and invasion of HPV-negative CC cells. Conclusion: LINC00115 might be a potential biomarker for HPV-negative CC.

Download Full-text

Long non-coding RNA expression profiling in the lungs of pulmonary arterial hypertension rats with acute inflammation

Pulmonary Circulation ◽

10.1177/2045894019879393 ◽

2019 ◽

Vol 9 (4) ◽

pp. 204589401987939

Author(s):

Yue Yang ◽

Yanan Cao ◽

Gang Qin ◽

Lu Wang ◽

Qian Li ◽

...

Keyword(s):

Pulmonary Arterial Hypertension ◽

Arterial Hypertension ◽

Acute Inflammation ◽

Expression Profiles ◽

Differentially Expressed ◽

Control Group ◽

Messenger Rnas ◽

Bioinformatics Analyses ◽

Qrt Pcr ◽

Pulmonary Arterial

Background We performed RNA-sequencing to investigate the changes and expression profiles in long non-coding RNAs (lncRNAs) and their potential functional roles in the lungs of pulmonary arterial hypertension rats responding to acute inflammation. Methods To establish a pulmonary arterial hypertension rat model, monocrotaline was injected intraperitoneally and lipopolysaccharide was given to induce acute inflammation. Selected lncRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatics analyses were carried out to predict the potential biological roles of key lncRNAs. Results Twenty-eight lncRNAs and seven mRNAs with elevated expression and 202 lncRNAs and 36 mRNAs with decreased expression were found in the lung tissues of lipopolysaccharide-treated pulmonary arterial hypertension rats compared with control group. The qRT-PCR validation results were consistent with the bioinformatics analysis. Gene ontology analyses showed that the mRNAs and lncRNAs were differentially expressed in different pathways regarding biological process, cellular components, and molecular function. The functions of differentially expressed messenger RNAs (DEmRNAs) and DElncRNAs were indicated by Kyoto Encyclopedia of Genes and Genomes enrichment. Conclusion The DEmRNAs co-expressed with DElncRNAs were obviously enriched in inflammation. DElncRNAs and DEmRNAs in the lungs of pulmonary arterial hypertension rats changed with acute inflammation may provide new insights into the pathogenesis of pulmonary arterial hypertension.

Download Full-text

Seminal Plasma piRNA Array Analysis Identifies Possible Biomarker piRNAs for the Diagnosis of Asthenozoospermia

10.21203/rs.3.rs-149605/v1 ◽

2021 ◽

Author(s):

ling he ◽

Xing wu ◽

rong wu ◽

ping guo ◽

Wan sun ◽

...

Keyword(s):

Logistic Regression ◽

Small Rna ◽

Metal Ion ◽

Roc Analysis ◽

Characteristic Curve ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Bioinformatics Analyses ◽

Diagnostic Efficacy ◽

Qrt Pcr

Abstract Asthenozoospermia (AZS) is characterized by reduced sperm motility, and its pathogenesis remains poorly understood. Piwi-interacting RNAs (piRNAs) have been recognized to play important roles in spermatogenesis. However, little is known about the correlation of piRNAs with AZS. In this study, small RNA sequencing was performed on samples from AZS patients and fertile controls. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate the small RNA-seq results. Bioinformatics analyses were performed to predict the functions of differentially expressed piRNAs. Logistic regression models were constructed, and receiver operating characteristic curve (ROC) analysis was used to evaluate their diagnostic performance. A total of 114 upregulated and 169 downregulated piRNAs were detected in AZS patients. GO and KEGG analyses showed that the differentially expressed piRNAs were mainly associated with transcription, signal transduction, cell differentiation, metal ion binding and focal adhesion. These results were verified by qRT-PCR of 8 selected piRNAs. Among the differentially expressed piRNAs tested, piR-hsa-32694, piR-hsa-26591, piR-hsa-18725, piR-hsa-18586 and piR-hsa-2912 produced qRT-PCR results consistent with the sequencing results in AZS compared with controls in the first cohort, whereas the other three genes did not show significant differences in expression. piR-hsa-32694, piR-hsa-26591, piR-hsa-18725, and piR-hsa-18586 were significantly upregulated in AZS. The diagnostic power of the four piRNAs was further analysed using ROC analysis; piR-hsa-26591 exhibited an area under the ROC curve (AUC) of 0.913 (95% CI: 0.795-0.994). Logistic regression modelling and subsequent ROC analysis indicated that the combination of the 4 piRNAs reached good diagnostic efficacy (AUC: 0.935).

Download Full-text