High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of  chemoresistance in leukemias.
Aberrant DNA methylation at CpG dinucleotides is a hallmark of cancer and is associated with the emergence of resistance to anti cancer treatment, though molecular mechanisms and biological significance remain elusive. Genome scale methylation maps by currently used methods are based on chemical modification of DNA and are best suited for analyses of methylation at CpG rich regions (CpG islands). We report the first high coverage whole genome map in cancer using the long read nanopore technology, which allows simultaneous DNA sequence and methylation analyses on native DNA. We analyzed clonal epigenomic/genomic evolution in Acute Myeloid Leukemias (AMLs) at diagnosis and relapse, after chemotherapy. Long read sequencing coupled to a novel computational method allowed definition of differential methylation at unprecedented resolution (>99% CpGs), extending analyses of CpG islands to sparse CpGs, which represent half of all differentially methylated regions. We showed that therelapse methylome is characterized by hypermethylation at both CpG islands and sparse CpGs. Hypermethylated genes, however, only accounted for <5% of all differentially expressed genes (DEGs) in the relapsed AMLs and were not enriched for chemoresistance genes. A few under expressed transcription factors (1 to 6 in the different AMLs) hyper methylated at sparse CpGs support 40% DEGs and are highly enriched in chemoresistance genes. Hypermethylated regions at sparse CpGs were poorly conserved in the relapsed AMLs, under represented at their genomic positions and showed high methylation entropy, as compared to CpG islands. Relapsed AMLs carried a few patient specific structural variants and DNA mutations, apparently not involved in drug resistance. Thus, drug resistance in AMLs is due to the selection of random epigenetic alterations at sparse CpGs of a few transcription factors, which then induce reprogramming of the relapsing phenotype, independently of clonal genomic evolution.