The role of noncoding mutations in blood cancers

Abstract

The search for oncogenic mutations in haematological malignancies has largely focused on coding sequence variants. These variants have been critical in understanding these complex cancers in greater detail, ultimately leading to better disease monitoring, subtyping and prognostication. In contrast, the search for oncogenic variants in the noncoding genome has proven to be challenging given the vastness of the search space, the intrinsic difficulty in assessing the impact of variants that do not code for functional proteins, and our still primitive understanding of the function harboured by large parts of the noncoding genome. Recent studies have broken ground on this quest, identifying somatically acquired and recurrent mutations in the noncoding genome that activate the expression of proto-oncogenes. In this Review, we explore some of the best-characterised examples of noncoding mutations in haematological malignancies, and highlight how a significant majority of these variants impinge on gene regulation through the formation of aberrant enhancers and promoters. We delve into the challenges faced by those that embark on a search for noncoding driver mutations, and provide a framework distilled from studies that have successfully identified such variants to overcome some of the most salient hurdles. Finally, we discuss the current therapeutic strategies being explored to target the oncogenic mechanism supported by recurrent noncoding variants. We postulate that the continued discovery and functional characterisation of somatic variants in the noncoding genome will not only advance our understanding of haematological malignancies, but offer novel therapeutic avenues and provide important insights into transcriptional regulation on a broader scale.

Keywords: Enhancers and promoters; Gene regulation; Haematological malignancy; Noncoding genome.

Fig. 1.

Canonical enhancer to proximal promoter interaction. (A) Transcription factors bind cognate sequences in the enhancer, which recruits cofactors, histone acetyltransferases and larger protein complexes such as Mediator. Loop formation between the enhancer and proximal promoter of the gene allows enhancer elements to interact with RNA pol II, followed by active transcription of the target genes. Enhancer-promoter interactions can be kept insulated from other genomic loci by the CTCF/cohesin complex, which closes this interaction into an insulated genomic neighbourhood, also known as a topologically associating domain. (B) An enhancer-promoter loop can be formed through somatically acquired mutations leading to aberrant gene regulation. These can arise from mutations that nucleate de novo regulatory elements such as promoters or enhancers, by mutations in noncoding sequences bound by CTCF or by mutations of the cohesin-complex members. Such mutation may yield detectable aberrations in DNA methylation and histone modifications.

Fig. 2.

Examples of noncoding mutations in haematological malignancies and mechanisms of action. (A) Recurrent heterozygous somatic mutations of a noncoding element 5′ to TAL1 creates a de novo binding site for the transcription factor MYB in T-ALL. Recruitment of MYB and additional cofactors leads to the formation of an aberrant enhancer, as seen by an enrichment of H3K27 acetylation. This enhancer is then able to interact with the proximal promoter of TAL1 causing its monoallelic expression. (B) An endogenous NOTCH1-dependent enhancer is located 1.4 Mb away from the proximal promoter of MYC in T-ALL. Examination of primary patient samples demonstrated that this element is frequently and focally amplified in T-ALL, a cancer that frequently presents with mutations that constitutively activate NOTCH1. (C) Recurrent mutations in the 3′ UTR of NOTCH1 were identified in CLL. These mutations lead to the formation of an aberrant splice acceptor site. A truncated splice variant is created between a cryptic splice donor site in the preceding exon and this mutant splice acceptor site. This allows for the formation of transcript that excises the negative regulatory PEST domain of NOTCH1, resulting in a more stable NOTCH1 protein.

Fig. 3.

Framework for identifying novel noncoding mutations. Proposed research framework for the successful identification and functional characterisation of noncoding variants in human malignancies.