MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression and have been implicated in the pathogenesis of human cancer. Most current studies utilize array-based or quantitative reverse-transcription-polymerase chain reaction (RT-PCR) approaches to measure miRNA expression. However, these approaches do not interrogate all known (or predicted) miRNAs and are unable to detect mutations in miRNAs. Herein, we use next-generation sequencing approaches to comprehensively assess miRNA expression, to identify genetic variants of all miRNA genes and miRNA binding sites in a patient with AML.
Methods: This patient (AML1) was a female in her 50s. Routine cytogenetics revealed a normal 46 XX karyotype, and highresolution comparative genomic hybridization studies revealed no somatic copy number alterations at a resolution of ~5kb. We previously reported the sequence of genic regions in the cancer genome of this patient (Nature 456:66, 2008). Massively parallel sequencing of small RNAs isolated from the myeloblasts of AML1 was performed using the ABI SOLiD sequencing platform. Pooled RNA isolated from CD34+ bone marrow cells of 4 healthy volunteers (CD34) was used as control. To detect genetic variants of miRNA genes, we used 454-based sequencing of all 695 miRNA genes in the Sanger miR database (version 12.0). Finally, we analyzed the previously generated whole genome sequence for AML1 for genetic variants in the 3'-untranslated regions (3'-UTR) of all coding genes.
Results: 28×10 and 20×10 small RNA sequence reads were obtained from AML1 and CD34 respectively. 8 novel miRNAs were identified from sequences that mapped to unannotated regions of human genome. Expression of 498 known miRNAs was detected with miR-233 being the most highly expressed miRNA in both AML1 and CD34; remarkably, it represented 47.3% of all miRNA reads in AML1. MiRNA gene sequencing of AML1 leukemic blast identified several single nucleotide variants. The whole genome sequence of AML1 skin DNA was used to differentiate germline polymorphism (SNPs) from somatic mutations. 13 novel SNPs and no somatic mutation were detected. Analysis of the 3'UTR of all coding genes in leukemic blasts and skin of AML1 revealed a single somatic mutation in the 3'-UTR of TNFAIP2. This mutation results in suppression of TNFAIP2 protein expression in a miRNA dependent fashion possibly by creating a new miRNA binding site. However, no recurrent mutations in the 3'-UTR of TNFAIP2 were detected in an additional 180 patients with AML.
Conclusions: These data demonstrate the feasibility of ‘next generation’ sequencing technologies to identify novel miRNAs, accurately measure mature miRNA expression, and identify both somatic and germline genetic variants of miRNA genes and miRNA binding sites in primary cancer. Using this platform, studies are underway to comprehensively characterize miRNAs in additional human AML samples.
Citation Information: Clin Cancer Res 2010;16(14 Suppl):B12.
- Copyright © July 15, 2010, American Association for Cancer Research