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Transcriptome analysis of intestine from alk-SMase knockout mice reveals the effect of alk-SMase
Jiang Zhu1, Lingqi Wang1,2, Zhongwu Guo3
1Medical Laboratory Technology College, Daqing Campus of Harbin Medical University, Daqing, 163319, Heilongjiang, China.
Objective:
Intestinal alkaline sphingomyelinase (alk-SMase) generates ceramide and inactivates platelet-activating factor associated with digestion and inhibition of cancer. There is few study to analyze the correlated function and characterize the genes related to alk-SMase comprehensively. We characterised transcriptome landscapes of intestine tissues from alk-SMase knockout (KO) mice aiming to identify novel associated genes and research targets.
Methods:
We performed the high-resolution RNA sequencing of alk-SMase KO mice and compared them to wild type (WT) mice. Differentially expressed genes (DEGs) for the training group were screened. Functional enrichment analysis of the DEGs between KO mice and WT mice was implemented using the Database for Annotation, Visualization and Integrated Discovery (DAVID). An integrated protein-protein interaction (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) network was chose to study the relationship of differentially expressed gene. Moreover, quantitative real-time polymerase chain reaction (qPCR) was further used to validate the accuracy of RNA-seq technology.
Results:
Our RNA-seq data found 97 differentially expressed mRNAs between the WT mice and alk-SMase gene NPP7 KO mice, in which 32 were significantly up-regulated and 65 were down-regulated, including protein coding genes, non-coding RNAs. Notably, the results of gene ontology functional enrichment analysis indicated that DEGs were functionally associated with the immune response, regulation of cell proliferation and development related terms. Additionally, an integrated network analysis was shown that some modules was significantly related to alk-SMase and with accordance of previously results. We chose 6 of these genes randomly were validated the accuracy of RNA-seq technology using qPCR and 2 genes showed difference significantly (P < 0.05).
Conclusions:
We investigated the potential biological significant of alk-SMase with high resolution genome-wide transcriptome of alk-SMase knockout mice. The results revealed new insight into the functional modules related to alk-SMase was involved in the intestinal related diseases.
Insights
This study characterized the transcriptome of intestinal alkaline sphingomyelinase (alk-SMase) knockout mice, revealing novel genes and pathways involved in intestinal functions and diseases. The findings provide new insights into alk-SMase
Area of Science:
- Genomics and Molecular Biology
- Gastroenterology
- Biochemistry
Background:
- Intestinal alkaline sphingomyelinase (alk-SMase) plays roles in digestion, ceramide generation, and platelet-activating factor inactivation.
- Its involvement in cancer inhibition is recognized, but comprehensive gene characterization is lacking.
- Understanding alk-SMase's functional network is crucial for identifying therapeutic targets.
Purpose of the Study:
- To comprehensively characterize the transcriptome of alk-SMase knockout mice.
- To identify novel genes and functional modules associated with alk-SMase.
- To gain insights into alk-SMase's role in intestinal biology and disease.
Main Methods:
- High-resolution RNA sequencing was performed on intestine tissues from alk-SMase knockout (KO) and wild-type (WT) mice.
- Differentially expressed genes (DEGs) were identified and subjected to functional enrichment analysis (DAVID).
- Integrated protein-protein interaction (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) network analyses were conducted. Quantitative real-time polymerase chain reaction (qPCR) was used for validation.
Main Results:
- 97 differentially expressed mRNAs were identified between KO and WT mice (32 up-regulated, 65 down-regulated).
- Functional enrichment analysis revealed DEGs are associated with immune response, cell proliferation, and development.
- Network analysis identified modules significantly related to alk-SMase function, with 2 validated by qPCR.
Conclusions:
- Genome-wide transcriptome analysis of alk-SMase KO mice provides novel insights into its biological significance.
- Identified functional modules highlight alk-SMase's involvement in intestinal-related diseases.
- This study establishes a foundation for further research into alk-SMase's role in gut health and pathology.
