A high-resolution landscape of mutations in the BCL6 super-enhancer in normal human B cells

Abstract

The super-enhancers (SEs) of lineage-specific genes in B cells are off-target sites of somatic hypermutation. However, the inability to detect sufficient numbers of mutations in normal human B cells has precluded the generation of a high-resolution mutational landscape of SEs. Here we captured and sequenced 12 B cell SEs at single-nucleotide resolution from 10 healthy individuals across diverse ethnicities. We detected a total of approximately 9,000 subclonal mutations (allele frequencies <0.1%); of these, approximately 8,000 are present in the BCL6 SE alone. Within the BCL6 SE, we identified 3 regions of clustered mutations in which the mutation frequency is ∼7 × 10−4. Mutational spectra show a predominance of C > T/G > A and A > G/T > C substitutions, consistent with the activities of activation-induced-cytidine deaminase (AID) and the A-T mutator, DNA polymerase η, respectively, in mutagenesis in normal B cells. Analyses of mutational signatures further corroborate the participation of these factors in this process. Single base substitution signatures SBS85, SBS37, and SBS39 were found in the BCL6 SE. While SBS85 is a denoted signature of AID in lymphoid cells, the etiologies of SBS37 and SBS39 are unknown. Our analysis suggests the contribution of error-prone DNA polymerases to the latter signatures. The high-resolution mutation landscape has enabled accurate profiling of subclonal mutations in B cell SEs in normal individuals. By virtue of the fact that subclonal SE mutations are clonally expanded in B cell lymphomas, our studies also offer the potential for early detection of neoplastic alterations.

Molecular origins of mutational spectra produced by the environmental carcinogen N-nitrosodimethylamine and SN1 chemotherapeutic agents

“…During tumor outgrowth, promotional events, such as an activated immune system, cause additional diversity among the heterogeneous population of cells in the malignant mass. As shown here with NDMA, and in work on other agents ( 49 , 61 , 62 ), the founder spectrum can be a highly distinctive genetic fingerprint. Indeed, that fingerprint could help to identify which agents, among the many to which people are exposed, contribute to the causation of specific human cancers.…”

Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing

“…However, the need for consensus sequences for each DNA strand requires the sequencing of multiple PCR replicates, which translates into extremely high costs if the targeted region is large ( Kennedy et al 2014 ). The most commonly used strategy to target genomic regions for DS is based on consecutive rounds of hybridization captures and enrichment ( Schmitt et al 2015 ; Krimmel et al 2016 ; Loeb et al 2019 ; Salk et al 2019 ; Shen et al 2019 ). Our DS library preparation approach used restriction enzymes to fragment DNA, followed by size selection.…”

Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing

“…For example, what would define the optimal subset of the genome to be used for drug and chemical safety testing? For some applications, a diverse, genome-representative panel makes the most sense; for others it might be preferable to enrich for regions that are predisposed to certain mutagenic processes ( 42 ) or have unique repair biology ( 35 ).…”