Construction of a 14-lncRNA risk score system predicting survival of children with acute myelocytic leukemia.

Abstract

Acute myelocytic leukemia (AML) is a frequent type of acute leukemia. The present study was performed to build a risk score system for the prognostic prediction of AML. AML RNA-sequencing data from samples from 111 children were downloaded from The Cancer Genome Atlas database. Using the DEseq and edgeR packages, the differentially expressed long non-coding RNAs (DE-lncRNAs) between bad and good prognosis groups were identified. A survival package was used to screen prognosis-associated lncRNAs and clinical factors. The optimal lncRNA combination was selected using the penalized package, and the risk-score system was built and evaluated. After the lncRNA-mRNA expression correlation network was constructed, the potential pathways involving the key lncRNAs were enriched using Gene Set Enrichment Analysis. Among the 61 DE-lncRNAs, 48 lncRNAs were significantly associated with prognosis. Relapse was an independent prognostic factor. The optimal 14-lncRNA risk score system was constructed. After 730 differentially expressed mRNAs were identified between the good and bad prognosis groups divided using a prognostic index, the lncRNA-mRNA expression correlation network was constructed. Enrichment analysis showed that semaphorin-3C [SEMA3C; regulated by probable leucine-tRNA ligase, mitochondrial (LARS2-AS1)] and secreted frizzled-related protein 5 [SFRP5; mediated by WASH complex subunit 5 (WASHC5)-antisense RNA 1 (AS1)] were involved in axon guidance and the Wnt signaling pathway, respectively. A 14-lncRNA (including paired box protein Pax8-AS1 and MYB AS1) risk-score system might be effective in predicting the prognosis of AML. Axon guidance (involving SEMA3C and LARS2-AS1) and the Wnt signaling pathway (involving SFRP5 and WASHC5-AS1) might be two important pathways affecting the prognosis of AML.