Evolving DNA methylation and gene expression markers of B-cell chronic lymphocytic leukemia are present in pre-diagnostic blood samples more than 10 years prior to diagnosis

Abstract

BackgroundB-cell chronic lymphocytic leukemia (CLL) is a common type of adult leukemia. It often follows an indolent course and is preceded by monoclonal B-cell lymphocytosis, an asymptomatic condition, however it is not known what causes subjects with this condition to progress to CLL. Hence the discovery of prediagnostic markers has the potential to improve the identification of subjects likely to develop CLL and may also provide insights into the pathogenesis of the disease of potential clinical relevance.ResultsWe employed peripheral blood buffy coats of 347 apparently healthy subjects, of whom 28 were diagnosed with CLL 2.0–15.7 years after enrollment, to derive for the first time genome-wide DNA methylation, as well as gene and miRNA expression, profiles associated with the risk of future disease. After adjustment for white blood cell composition, we identified 722 differentially methylated CpG sites and 15 differentially expressed genes (Bonferroni-corrected p < 0.05) as well as 2 miRNAs (FDR < 0.05) which were associated with the risk of future CLL. The majority of these signals have also been observed in clinical CLL, suggesting the presence in prediagnostic blood of CLL-like cells. Future CLL cases who, at enrollment, had a relatively low B-cell fraction (<10%), and were therefore less likely to have been suffering from undiagnosed CLL or a precursor condition, showed profiles involving smaller numbers of the same differential signals with intensities, after adjusting for B-cell content, generally smaller than those observed in the full set of cases. A similar picture was obtained when the differential profiles of cases with time-to-diagnosis above the overall median period of 7.4 years were compared with those with shorted time-to-disease. Differentially methylated genes of major functional significance include numerous genes that encode for transcription factors, especially members of the homeobox family, while differentially expressed genes include, among others, multiple genes related to WNT signaling as well as the miRNAs miR-150-5p and miR-155-5p.ConclusionsOur findings demonstrate the presence in prediagnostic blood of future CLL patients, more than 10 years before diagnosis, of CLL-like cells which evolve as preclinical disease progresses, and point to early molecular alterations with a pathogenetic potential.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4117-4) contains supplementary material. Note to Editor: If Journal regulations permit, the Supplementary material should be available to all without any additional authorisation.

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

“…Expanding WES panels to include the UTRs of protein-coding transcripts harboring nuORFs could extend clinical access to an expanded pool of potential neoantigens. Among the nuORFs transcribed and translated in cancer-specific manner in melanoma, GBM or CLL, were a 5' uORF in ARHGAP44, a 5' ouORF in RRAS2, and nuORFs in SOX2-OT lincRNA, each derived from a gene involved in cancer biology (Georgiadis et al 2017;Rodríguez et al 2012;Su et al 2017). Multiple additional cancer-specific nuORFs were derived from novel transcripts .…”

“…In particular, 13 nuORFs were strongly upregulated in CLL compared to GTEx and other cancer samples (Figure 4k). For example, we found a CLL-specific 5'uORF in the ARHGAP44 locus, a gene which has been shown to be upregulated in CLL patients up to 10 years prior to diagnosis (Georgiadis et al 2017). The ARHGAP44 5' uORF is translated from a 5'UTR of a CLL-specific ARHGAP44 transcript isoform, not expressed in healthy B cells and different from the isoform expressed in other tissues, such as melanoma (Figure 4l).…”

Methylation alteration of SHANK1 as a predictive, diagnostic and prognostic biomarker for chronic lymphocytic leukemia

“…Some such changes have already shown clinical relevance, such as BRCA1 in breast cancer, MGMT in glioblastoma multiform, and SEPT9 , which has been approved by the Food and Drug Administration (FDA) for the diagnosis of colon cancer. Since global DNA methylation is similar in resting and proliferative compartments [12], aberrant methylation patterns may be an early event in CLL, as suggested by its occurrence in blood samples collected years before diagnosis of mature B-cells neoplasm [3] and CLL [4].…”

“…Aberrant methylation patterns, which represent a molecular hallmark of cancer, are early events in tumor development, and they might represent early diagnostic biomarkers. It has been shown that methylome alterations would predict the diagnosis several years prior to the clinical appearance of the disease, thus proving to be potential markers for carrying out large-scale screening tests [3, 4]. Besides, aberrant methylation changes might represent a specific signature of different types of leukemia, depending on the originating cell [5].…”

Advances in Epigenetics and Epigenomics in Chronic Lymphocytic Leukemia

“…Georgiadis and colleagues provided evidence that CLLlike changes at DNA methylation and transcriptome profiles existed more than 10 years before CLL diagnosis [14]. These findings suggest that the path from normal counterpart to malignant transformation and further clonal evolution is a long, multi-step process, in which DNA methylation can be viewed not only as a contributor to disease pathogenesis but also as a tool for understanding pre-malignant evolutionary trajectory.…”