MIR4435-2HG as a Novel Predictive Biomarker of Chemotherapy Response and Death in Pediatric B-cell All

Abstract

Abstract Background Although B-cell acute lymphoblastic leukemia (B-cell ALL) survival rates have improved in recent years, Hispanic children continue to have poorer survival rates. There are few tools available to identify from the time of diagnosis whether the patient will respond to induction therapy. Our objective was to identify predictive biomarkers of treatment response, which could also serve as prognostic biomarkers of relapse and death, by identifying methylated and differentially expressed genes between patients with positive minimal residual disease (MRD+) and negative minimal residual disease (MRD-). Methods Tumor blasts were separated by immunomagnetic column and subsequently DNA and RNA were extracted. DNA methylation and mRNA sequencing assays were performed on 19 bone marrows from Hispanic children with B-cell ALL. Partek Flow was used for transcript mapping and quantification, followed by differential expression analysis using DEseq2. DNA methylation analyses were performed with Partek Genomic Suite and Genome Studio. Gene expression and differential methylation were compared between patients with MRD- and MRD + at day 15 and at the end of induction chemotherapy. Overexpressed and hypomethylated genes were selected and validated by RT-qPCR in samples of validation cohort. The predictive ability of the genes was assessed by logistic regression. Survival and Cox regression analyses were performed to determine the association of genes with death. The association of genes with relapse was assessed by RT-qPCR in relapsed patient samples and validated using TARGET-PANCER data. Results DAPK1, CNKSR3, MIR4435-HG2, CTHRC1, NPDC1, SLC45A3, ITGA6, and ASCL2 were overexpressed and hypomethylated in MRD + patients. The overexpression of DAPK1, ASCL2, SCL45A3, NPDC1 and ITGA6 can predict non-response at day 15 and refractoriness. Additionally, higher expression of MIR4435-2HG increases the probability of non-response, death, and the risk of death. MIR4435-2HG is also overexpressed in relapse samples. Finally, MIR4435-2HG overexpression, together with MRD+, are associated with poorer survival, and together with overexpression of DAPK1 and ASCL2, it could improve the risk classification of patients with normal karyotype. Conclusions MIR4435-2HG is a potential predictive and prognosis biomarker in children with B-cell ALL.