Notch1 is one of the major driving oncogene in T-ALL. About 55% of T-ALL patients occurred Notch1 mutation in the trans-membrane region and the intracellular PEST domain, which resulted abnormal activation of the Notch signaling pathway. Overexpression of ICN1 by retroviral infection in hematopoietic progenitor cells or thymocytes promote T ALL tumorigenesis, which was made to set up mouse T-ALL model. Over the past decades, the molecular mechanism of Notch1-correlated T-ALL has been extensively investigated. However, the precise pathogenesis of Notch1-correlated T-ALL is still unknown. Recent years, ncRNAs, including lncRNAs, have been found to be related with humorous number of biological regulatory functions. lncRNA NALT activating Notch signaling pathway promoted cell proliferation in T-ALL[13]. lncRNA-IUR acted as a tumor suppressors by suppressing the STAT5-CD71 pathway in Bcr-Abl-mediated tumorigenesis of T-ALL[14]. To further confirm the significant differences in the expression of lncRNAs and mRNAs, we removed the spleen from T-ALL leukemia mice and C57BL/6 mice and performed deep RNA sequence to study the different expression of lncRNAs and mRNAs. We found that lncRNAs’ expression altered significantly in the spleen of Notch1-correlated T-ALL leukemia mice compared with that of C57BL/6 mice which was the first time to report the altered expression of lncRNAs. 1873 lncRNAs and 5626 mRNAs were differentially expressed in the spleen from T-ALL leukemia mice compared with that of C57BL/6 mice.
we performed GO terms enrichment to study the biological functions of differently expressed mRNAs. The most enriched GO terms for differentially expressed mRNAs were related to melanocyte differentiation, myosin complex and translation repressor activity in biological processes, cellular component or molecular function. To understand the function of differentially expressed mRNAs further, we performed KEGG pathway analysis and found that 303 pathways were significantly enriched among the altered transcripts. Acute myeloid leukemia, Protein export ad Glycosaminoglycan biosynthesis-keratan sulfate were the 3 significantly enriched pathways. Apoptosis, Notch signaling pathway and PI3K-Akt signaling pathway which was closely related with the pathology process of T-ALL was involved in the enriched pathways[15]. Furthermore, we constructed co-expression network to investigate the relation between lncRNAs and the coding genes.
Competing endogenous RNAs (ceRNAs) was raised that ceRNA molecules could sponge miRNA through miRNA response elements (MREs) and regulate gene expression. Numbers of molecules could act as ceRNAs, including lncRNAs, circRNAs or pseudogene. Wang et al found that lncRNA CHRF regulates cardiac hypertrophy by targeting miR-489[16]. circRNA MTO1 sponges miR-9 to suppress hepatocellular carcinoma progression[17]. Chan et al found that A FTH1 gene:pseudogene, can sponge miRNAs to regulates tumorigenesis in prostate cancer[18]. In this study, a lncRNA-associated ceRNA network analysis was perform and showed that 71 differentially expressed lncRNAs and 123 expressed mRNAs were selected, which predicted 11 miRNAs sharing binding sites with the differentially expressed lncRNAs and mRNAs.
Nice differentially expressed lncRNAs from ceRNA network prediction were selected to confirm deep RNA sequence results by qRT-PCR. We selected ten pairs of mice spleen which contain both T-ALL leukemia mice or C57BL/6 mice to further validation. All of the nice downregulated lncRNAs expression were consistent with RNA sequence results. NONMMUT117521.1 was located in intron of ECE-1 which has endopeptidase activity and membrane-bound metalloprotease. Bao et al found that ECE-1 promoted Ischemia/Reperfusion-Induced Injury[19]. ENSMUST00000195494 was located in Pfkfb3 which participated in the glucose metabolism and promoted cell proliferation, apoptosis and autophage in many types of cancer[20]. NONMMUT008951.2 was located in Bcl11a which inhibited proliferation and promoted apoptosis in B lymphoma cell lines[21]. NONMMUT026003.2, in the ceRNA network of differentially expressed lncRNAs, was located Bcl6 which participated humorous of processes, including inflammatory response, growth and differentiation[22].
This study provides the first Notch1-correlated ceRNA network prediction of lncRNAs and mRNAs which needed some studies to explore the roles of these differentially expressed lncRNAs. Because of the limitation of mice model, patients’ samples addition is valuable.