scholarly journals An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10668
Author(s):  
Juan Wang ◽  
Xiongfei Wu ◽  
Yafang Tu ◽  
Jianzhong Dang ◽  
Zhitao Cai ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Mrna Expression ◽  
Lupus Erythematosus ◽  
Expression Profiles ◽  
Inflammatory Factors ◽  
Integrated Analysis ◽  
Limited Information ◽  
Rna Seq ◽  
And Control ◽  
Upregulated Genes

Long noncoding RNAs (lncRNAs) are persistently expressed and have been described as potential biomarkers and therapeutic targets in various diseases. However, there is limited information regarding lncRNA expression in the tissue of kidney exhibiting lupus nephritis (LN)a serious complication of systemic lupus erythematosus (SLE). In this study, RNA sequencing (RNA-seq) was performed to characterize the lncRNA and mRNA expression in kidney tissues from LN (MRL/lpr) and control mice. We identified 12,979 novel lncRNAs in mouse. The expression profiles of both mRNAs and lncRNAs were differed significantly between LN and control mice. In particular, there were more upregulated lncRNAs and mRNAs than downregulated ones in the kidney tissues of LN mice. However, GO analysis showed that more downregulated genes were enriched in immune and inflammatory response-associated pathways. KEGG analysis showed that both downregulated and upregulated genes were enriched in a number of pathways, including the SLE pathway, and approximately half of these SLE-associated genes encoded inflammatory factors. Moreover, we observed that 2,181 DElncRNAs may have targeted and regulated the expression of 778 mRNAs in LN kidney tissues. The results of this study showed that 11 DElncRNAs targeted and were co-expressed with six immune and SLE-associated genes. qPCR analysis confirmed that lncRNA Gm20513 positively regulated the expression of the SLE-associated gene H2-Aa. In conclusion, the results of our study demonstrates that lncRNAs influence the progression of LN and provide some cues for further study of lncRNAs in LN. These results regarding the lncRNA-mRNAregulatory network may have important value in LN diagnosis and therapy.

Comprehensive bioinformatics analysis of mRNA expression profiles and identification of a miRNA–mRNA network associated with lupus nephritis

Lupus ◽  
2020 ◽  
Vol 29 (8) ◽  
pp. 854-861
Author(s):  
Jianbo Song ◽  
Liqin Zhao ◽  
Yuanping Li
Keyword(s):  
Lupus Nephritis ◽  
Mrna Expression ◽  
Lupus Erythematosus ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Ppi Network

Objective Lupus nephritis (LN) is one of the serious complications of systemic lupus erythematosus. The aim of this study was to identify core genes and pathways involved in the pathogenesis of LN. Methods We screened differentially expressed genes (DEGs) in LN patients using mRNA expression profile data from the Gene Expression Omnibus. The functional and pathway enrichment analysis of DEGs was performed utilizing the Database for annotation, Visualization and Integrated Discovery. Target genes with differentially expressed miRNAs (DEMIs) were predicted using the miRTarBase database, and the intersection between these target genes and DEGs was selected to be studied further. Results In total, 107 common DEGs (CDEGs) were identified from the Tub_LN group and Glom_LN group, and 66 DEMIs were identified. Fifty-three hub genes and two significant modules were identified from the protein–protein interaction (PPI) network, and a miRNA–mRNA network was constructed. The CDEGs, module genes in the PPI network and genes intersecting with the CDEGs and target genes of DEMIs were all associated with the PI3K-Akt signalling pathway. Conclusion In summary, this study reveals some crucial genes and pathways potentially involving in the pathogenesis of LN. These findings provide a new insight for the research and treatment of LN.

Integrated analysis of non-coding RNA and mRNA expression profiles of 2 pig breeds differing in muscle traits

2017 ◽  
Vol 95 (3) ◽  
pp. 1092 ◽  
Author(s):  
J. Sun ◽  
M. Xie ◽  
Z. Huang ◽  
H. Li ◽  
T. chen ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Pig Breeds ◽  
Non Coding Rna

Suppressed Immune-Related Profile Rescues Abortion-Prone Fetuses: A Novel Insight Into the CBA/J × DBA/2J Mouse Model

2019 ◽  
Vol 26 (11) ◽  
pp. 1485-1492
Author(s):  
Xiaochun Yi ◽  
Jie Zhang ◽  
Huixiang Liu ◽  
Tianxia Yi ◽  
Yuhua Ou ◽  
...  
Keyword(s):  
Immune System ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Poor Treatment ◽  
Polymerase Chain ◽  
Poor Treatment Outcome ◽  
Immune Related Genes ◽  
And Control ◽  
Upregulated Genes ◽  
Tgf Β1

The adverse clinical result and poor treatment outcome in recurrent spontaneous abortion (RSA) make it necessary to understand the pathogenic mechanism. The mating combination CBA/J × DBA/2 has been widely used as an abortion-prone model compared to DBA/2-mated CBA/J mice. Here, we used RNA-seq to get a comprehensive catalogue of genes differentially expressed between survival placenta in abortion-prone model and control. Five hundred twenty-four differentially expressed genes were obtained followed by clustering analysis, Gene Ontology analysis, and pathway analysis. We paid more attention to immune-related genes namely “immune response” and “immune system process” including 33 downregulated genes and 28 upregulated genes. Twenty-one genes contribute to suppressing immune system and 7 are against it. Six genes were validated by reverse transcription-polymerase chain reaction, namely Ccr1l1, Tlr4, Tgf-β1, Tyro3, Gzmb, and Il-1β. Furthermore, Tlr4, Tgf-β1, and Il-1β were analyzed by Western blot. Such immune profile gives us a better understanding of the complicated immune processing in RSA and immunosuppression can rescue pregnancy loss.

scholarly journals Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Wenjing Tao ◽  
Lina Sun ◽  
Hongjuan Shi ◽  
Yunying Cheng ◽  
Dongneng Jiang ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Early Stage ◽  
Expression Profiles ◽  
Sex Differentiation ◽  
Integrated Analysis

scholarly journals Integrated analysis of microRNA and mRNA expression profiles in abdominal adipose tissues in chickens

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
H. Y. Huang ◽  
R. R. Liu ◽  
G. P. Zhao ◽  
Q.H. Li ◽  
M. Q. Zheng ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Adipose Tissues

scholarly journals Integrated analysis of microRNA and mRNA expression profiles in splenomegaly induced by non-cirrhotic portal hypertension in rats

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Junji Saruwatari ◽  
Chao Dong ◽  
Teruo Utsumi ◽  
Masatake Tanaka ◽  
Matthew McConnell ◽  
...  
Keyword(s):  
Portal Hypertension ◽  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis

Integrated Analysis of MicroRNA and mRNA Expression Profiles in Rheumatoid Arthritis Synovial Monocytes

2011 ◽  
Vol 18 (4) ◽  
pp. 253 ◽  
Author(s):  
Jong Dae Ji ◽  
Tae-Hwan Kim ◽  
Bitnara Lee ◽  
Kyung-Sun Na ◽  
Sung Jae Choi ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Mrna Expression ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Synovial Monocytes
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