Dynamic alterations of the transcriptome-wide m6A methylome in cytogenetically normal acute myeloid leukaemia during initial diagnosis and relapse

Abstract

Accumulating studies have indicated that N6-methyladenosine (m⁶A) plays an important role in acute myeloid leukaemia (AML). However, little is known about the m⁶A methylome at a transcriptome-wide scale in AML patients. We obtained three pairs of bone marrow (BM) samples from cytogenetically normal AML patients at the timepoints of diagnosis (AML) and relapse (R_AML) and three BM samples from healthy donors used as normal controls (NCs). Methylated RNA immunoprecipitation next-generation sequencing (MeRIP-Seq) was conducted to identify differences in the m⁶A methylomes between AML and NC and between R_AML and AML. We identified a total of 11,076 and 11,962 differential m⁶A peaks in AML and R_AML group, respectively. These dysregulated m⁶A peaks were detected on all chromosomes, especially chr1, chr19 and chr17, and were mainly enriched in 3' untranslated regions, stop codon and coding sequence regions. Moreover, GO and KEGG analyses indicated that m⁶A -modified genes were significantly enriched in cancer-related biological functions and pathways. Additionally, we identified a link between the m⁶A methylome and RNA transcriptome via combined analyses of MeRIP-seq and RNA-seq data. In addition, 5 genes, HSPG2, HOMER3, TSPO2, CXCL12 and FUT1 regulated by m⁶A modification potentially, were shown to be related to the prognosis of AML patients. Additionally, we detected the mRNA expression of major m6A regulators and potential target mRNA on the leukemogenesis and found that the expression of IGF2BP2, HSPG2 and HOMER3 were upregulated in AML at the time of diagnosis. Moreover, their expression became downregulated after remission and then elevated again at relapse. Our study provides the first data on the differential m⁶A methylome in AML patients during initial diagnosis and relapse. This study demonstrates a novel relationship between m⁶A modification and AML relapse and paves the way for further studies aimed at elucidating the epigenic mechanisms involved in the relapse of AML.

Keywords: Acute myeloid leukaemia; MeRIP-seq; RNA-seq; Relapse; m(6)A.