Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci

Huihuang Yan, Shulan Tian, Geffen Kleinstern, Zhiquan Wang, Jeong Heon Lee, Nicholas J. Boddicker, James R. Cerhan, Neil E. Kay, Esteban Braggio, Susan L. Slager

Research output: Contribution to journalArticlepeer-review

Abstract

Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ∼ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.

Original languageEnglish
Pages (from-to)2761-2774
Number of pages14
JournalHuman Molecular Genetics
Volume29
Issue number16
DOIs
StatePublished - 15 Aug 2020
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by National Institutes of Health grants [R01 CA235026, R01 CA200703 and P50 CA097274 to SLS]; and by Mayo CCaTS grant [UL1TR000135 to SLS].

Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press. All rights reserved.

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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