Transcriptome analysis of intestine from alk-SMase knockout mice reveals the effect of alk-SMase

Jiang Zhu; Lingqi Wang; Zhongwu Guo; Tao Zhang; Ping Zhang

doi:10.1186/s12935-022-02764-y

Transcriptome analysis of intestine from alk-SMase knockout mice reveals the effect of alk-SMase

Cancer Cell Int. 2022 Nov 9;22(1):344. doi: 10.1186/s12935-022-02764-y.

Authors

Jiang Zhu^#¹, Lingqi Wang^#^{1

2}, Zhongwu Guo³, Tao Zhang¹, Ping Zhang⁴

Affiliations

¹ Medical Laboratory Technology College, Daqing Campus of Harbin Medical University, Daqing, 163319, Heilongjiang, China.
² Department of Laboratory Diagnosis, The fifth Affiliated Hospital of Harbin Medical University, Daqing, 163319, Heilongjiang, China.
³ General Surgery, Daqing Oil General Hospital, Daqing, 163319, Heilongjiang, China.
⁴ International School of Public Health and One Health, Hainan Medical University, Haikou, 571199, Hainan, China. 035040@hrbmu.edu.cn.

^# Contributed equally.

Abstract

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.

Keywords: Alk-SMase; Gene knockout; Genome-wide; RNA-seq.

Abstract

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