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Figure 4. Analysis of non-coding variants and shared mutations between monoclonal B-cell lymphocytosis (MBL)/chronic lymphocytic leukemia (CLL) and poly- morphonuclear (PMN) cell samples in the present cohort. (A) Topology of the 106 relevant non-coding variants identified in the present study. The majority con- cerned gene promoter sites. (B) Recurrent non-coding variants in genes relevant to CLL. The BIRC3, BCL6 and BTG2 genes are known to be associated with various types of cancer. (C) Topology of shared mutations between MBL/CLL and PMN samples. Intergenic mutations predominated, followed by intronic mutations.
WGS in MBL and ultra-stable CLL
AB
C
lack of any obvious impact of the identified mutations on disease progression after a prolonged follow up highlights the fact that the mere presence of a given driver mutation does not axiomatically equate with disease progression, as previously reported.31,44 Additional studies are required in order to clarify this phenomenon.
Chronic lymphocytic leukemia cases have been shown to harbor detrimental gene mutations in subclones not vis- ible at diagnosis that are progressively selected, e.g. fol- lowing the use of chemotherapy.45,46 Such mutations were identified by targeted re-sequencing, yet only in a minor fraction of the present cohort. In this context, it has been recently proposed that sequence depths greater than 4000X will be essential in order to robustly identify all subclonal mutations and predict aggressive cases.12 Arguably, the absence of such driver mutations when applying highly sensitive methods may potentially help to identify individuals with very indolent disease for whom less frequent, if any follow up will be warranted.
Whole-genome sequencing revealed that the non-cod-
ing mutome commonly targets gene pathways and cellu- lar processes involved in CLL pathobiology. A sizeable proportion of variants affected the promoter sites of genes previously associated with cancer, e.g. BTG2, BCL6, BACH2 and TCL1A. Interestingly, all 4 genes have been recently reported as non-IG targets of the SHM process in patients with lymphomas,47 implicating this otherwise normal process in the emergence of CLL-like clones. Additional studies need to be performed to address the relevance of such mutations; however, since AID-related mutations are common in CLL,16 they may indeed be rel- evant to disease pathogenesis. We did not identify any “poor-prognostic” 3’ UTR NOTCH1 mutations;9 howev- er, we did discover two NCVs targeting indirectly the BIRC3 gene. We also found a number of variants within the promoter sites of genes implicated in pathways rele- vant to CLL biology, including the PI3K-AKT and NF-κB pathways as well as the spliceosome machinery. Furthermore, we identified TF binding motif breaking events that may arise due to NCVs; most concerned the
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