An Integrated Regulatory Network Based on Comprehensive Analysis of mRNA Expression, Gene Methylation and Expression of Long Non-coding RNAs (lncRNAs) in Myelodysplastic Syndromes

Abstract Long noncoding RNAs (lncRNAs) play important roles in the occurrence and development of many diseases and can be used as targets for diagnosis and treatment. However, the expression and function of lncRNAs in the injury and repair of acute pancreatitis (AP) are unclear. To decipher lncRNAs’ regulatory roles in AP, we reanalyzed an RNA-seq dataset of 24 pancreatic tissues, including those of normal control mice (BL), those 7 days after mild AP (D7), and those 14 days after mild AP (D14). The results showed significant differences in lncRNA and mRNA expression of D7/D14 groups compared with the control group. Co-expression analysis showed that differentially expressed (DE) lncRNAs were closely related to immunity- and inflammation-related pathways by trans-regulating mRNA expression. The lncRNA–mRNA network showed that the lncRNAs Dancer, Gmm20488, Terc, Snhg3, and Snhg20 were significantly correlated with AP pathogenesis. WGCNA and cis regulation analysis also showed that AP repair-associated lncRNAs were correlated with extracellular and inflammation-related genes, which affect the repair and regeneration of pancreatic injury after AP. In conclusion, the systemic dysregulation of lncRNAs is strongly involved in remodeling AP’s gene expression regulatory network, and the lncRNA–mRNA expression network could identify targets for AP treatment and damage repair.

Download Full-text

Comprehensive analysis of long non-coding RNAs in keratinization

Journal of Dermatological Science ◽

10.1016/j.jdermsci.2016.08.414 ◽

2016 ◽

Vol 84 (1) ◽

pp. e138

Author(s):

Toshifumi Nomura

Keyword(s):

Comprehensive Analysis ◽

Non Coding Rnas

Download Full-text

The Value and Clinical Significance of ZNF582 gene Methylation in the Diagnosis of Cervical Cancer

10.21203/rs.3.rs-41008/v1 ◽

2020 ◽

Author(s):

Chunhe Zhang ◽

Shaowei Fu ◽

Luyue Wang ◽

Fang Wang ◽

Dan Wu ◽

...

Keyword(s):

Cervical Cancer ◽

Mrna Expression ◽

Promoter Methylation ◽

Zinc Finger Protein ◽

Methylation Status ◽

Cervical Lesions ◽

Gene Methylation ◽

Methylation Rate ◽

Specificity And Sensitivity ◽

Cancer Tissues

Abstract Background This study aimed to determine whether ZNF582 gene methylation and tissue protein expression can be used as a tool with high sensitivity and specificity for cervical cancer screening. We analyzed the correlation between promoter methylation of the zinc finger protein 582 (ZNF582) gene and cervical cancer and high risk HPV16/18 infection. Methods Tissue samples of normal cervical or chronic cervicitis (n=51), CIN (cervical intraepithelial neoplasia) (n=35), and cervical carcinoma (n=68) were tested for HPV16/18 infection by polymerase chain reaction (PCR). We also detected the methylation status of the ZNF582 gene promoter in the same tissues by methylation specific PCR (MSP), then analyzed the correlation between ZNF582 promoter methylation and HPV16/18 infection. Immunohistochemistry was used to analyze ZNF582 gene expression in 152 cervical tissues. We detected ZNF582 mRNA expression in cervical tissues (including cancer and non-cancer) by real-time fluorescence quantitative PCR (qRT-PCR).Results Among 93 high grade cervical lesions (CINII and above) and cervical cancer samples, 57 cases were positive for HPV16/18 infection and 36 cases were negative. ZNF582 gene methylation occurred in 9 out of 51 cases in normal cervical tissues (17.6%), 16 of 35 cases in CIN tissues (45.7%), and 50 of 68 cases in cervical cancer (73.5%). The differences in methylation rate of the three groups were statistically significant (P<0.05). The ZNF582 methylation rate in the positive HPV16/18 infection group was 73.7%, while the negative group was 63.9%. Compared with normal tissues, ZNF582 protein was highly expressed in cervical cancer tissues, but mRNA expression was low.Conclusion While ZNF582 protein is highly expressed in cervical cancer tissues, it was not sufficient for use as a standard for cervical cancer staging. On the other hand, ZNF582 promoter methylation had high specificity and sensitivity in detecting CINII and highly diseased cervical lesions and could be used as a diagnostic marker for cervical cancer of women.

Download Full-text

Comprehensive Analysis of mRNA Expression Profiling and Identification of Potential Diagnostic Biomarkers in Coronary Artery Disease

ACS Omega ◽

10.1021/acsomega.1c03171 ◽

2021 ◽

Author(s):

Jia-Xin Chen ◽

Shu He ◽

Yan-Jun Wang ◽

Xiong-Kang Gan ◽

Ya-Qing Zhou ◽

...

Keyword(s):

Coronary Artery Disease ◽

Coronary Artery ◽

Mrna Expression ◽

Expression Profiling ◽

Comprehensive Analysis ◽

Diagnostic Biomarkers ◽

Artery Disease ◽

Mrna Expression Profiling

Download Full-text

Comprehensive analysis of differentially expressed profiles of long non-coding RNAs and messenger RNAs in kaolin-induced hydrocephalus

Gene ◽

10.1016/j.gene.2019.02.041 ◽

2019 ◽

Vol 697 ◽

pp. 184-193 ◽

Cited By ~ 1

Author(s):

Yan-Hui Shi ◽

Xin-Wei He ◽

Feng-Di Liu ◽

Yi-Sheng Liu ◽

Yue Hu ◽

...

Keyword(s):

Comprehensive Analysis ◽

Differentially Expressed ◽

Messenger Rnas ◽

Non Coding Rnas

Download Full-text

Comprehensive analysis of lncRNA and mRNA expression changes in Tibetan chicken lung tissue between three developmental stages

Animal Genetics ◽

10.1111/age.12990 ◽

2020 ◽

Vol 51 (5) ◽

pp. 731-740

Author(s):

Ruixiang Tang ◽

Jiao Wang ◽

Min Zhou ◽

Yue Lan ◽

Lan Jiang ◽

...

Keyword(s):

Mrna Expression ◽

Lung Tissue ◽

Developmental Stages ◽

Comprehensive Analysis ◽

Tibetan Chicken

Download Full-text

Unique MicroRNA and mRNA Interactions in EGFR-Mutated Lung Adenocarcinoma

Journal of Clinical Medicine ◽

10.3390/jcm7110419 ◽

2018 ◽

Vol 7 (11) ◽

pp. 419 ◽

Cited By ~ 3

Author(s):

Sophia Subat ◽

Kentaro Inamura ◽

Hironori Ninomiya ◽

Hiroko Nagano ◽

Sakae Okumura ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Mrna Expression ◽

Regulatory Network ◽

Egfr Mutation ◽

Expression Profiles ◽

Integrative Analysis ◽

Future Research ◽

Mutation Status ◽

Egfr Mutated ◽

Insight Into

The EGFR gene was one of the first molecules to be selected for targeted gene therapy. EGFR-mutated lung adenocarcinoma, which is responsive to EGFR inhibitors, is characterized by a distinct oncogenic pathway in which unique microRNA (miRNA)–mRNA interactions have been observed. However, little information is available about the miRNA–mRNA regulatory network involved. Both miRNA and mRNA expression profiles were investigated using microarrays in 155 surgically resected specimens of lung adenocarcinoma with a known EGFR mutation status (52 mutated and 103 wild-type cases). An integrative analysis of the data was performed to identify the unique miRNA–mRNA regulatory network in EGFR-mutated lung adenocarcinoma. Expression profiling of miRNAs and mRNAs yielded characteristic miRNA/mRNA signatures (19 miRNAs/431 mRNAs) in EGFR-mutated lung adenocarcinoma. Five of the 19 miRNAs were previously listed as EGFR-mutation-specific miRNAs (i.e., miR-532-3p, miR-500a-3p, miR-224-5p, miR-502-3p, and miR-532-5p). An integrative analysis of miRNA and mRNA expression revealed a refined list of putative miRNA–mRNA interactions, of which 63 were potentially involved in EGFR-mutated tumors. Network structural analysis provided a comprehensive view of the complex miRNA–mRNA interactions in EGFR-mutated lung adenocarcinoma, including DUSP4 and MUC4 axes. Overall, this observational study provides insight into the unique miRNA–mRNA regulatory network present in EGFR-mutated tumors. Our findings, if validated, would inform future research examining the interplay of miRNAs and mRNAs in EGFR-mutated lung adenocarcinoma.

Download Full-text