Background There is growing evidence for the inherited basis of susceptibility to childhood acute lymphoblastic leukemia (ALL). Genome-wide association studies have identified non-coding ALL risk variants at the ARID5B gene locus, but their exact functional effects and the molecular mechanism linking ARID5B to B-ALL leukemogenesis remain largely unknown. Methods We performed targeted sequencing of ARID5B in germline DNA of 5,008 children with ALL. Variants were evaluated for association with ALL susceptibility using 3,644 subjects from the UK10K cohort as non-ALL controls, under an additive model. Cis-regulatory elements in ARID5B were systematically identified using CRISPRi enhancer screen in ALL cells. Disruption of transcription factor binding by ARID5B variant was predicted informatically and then confirmed using chromatin immunoprecipitation and co-immunoprecipitation. ARID5B variant association with hematological traits was examined using UK Biobank dataset. All statistical tests are two-sided. Results We identified 54 common variants in ARID5B significantly associated with leukemia risk, all of which were non-coding. Six cis-regulatory elements at the ARID5B locus were discovered using CRISPR-based high-throughput enhancer screening. Strikingly, the top ALL risk variant (rs7090445, P=5.57 × 10-45) is located precisely within the strongest enhancer element, which is also distally tethered to the ARID5B promoter. The variant allele disrupts the MEF2C binding motif sequence, resulting in reduced MEF2C affinity and decreased local chromosome accessibility. MEF2C influences ARID5B expression in ALL, likely via a transcription factor complex with RUNX1. Using the UK Biobank dataset (n = 349,861), we showed that rs7090445 was also associated with lymphocyte percentage and count in the general population (P=8.6 × 10-22 and 2.1 × 10-18, respectively). Conclusion Our results indicate that ALL risk variants in ARID5B function by modulating cis-regulatory elements at this locus.

中文翻译：

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ARID5B介导的急性淋巴细胞白血病遗传易感性的分子机制

背景 越来越多的证据表明儿童急性淋巴细胞白血病 (ALL) 的易感性具有遗传基础。全基因组关联研究已经确定了 ARID5B 基因位点的非编码 ALL 风险变异，但它们的确切功能效应和将 ARID5B 与 B-ALL 白血病发生联系起来的分子机制在很大程度上仍然未知。方法 我们对 5,008 名 ALL 儿童的种系 DNA 中的 ARID5B 进行了靶向测序。在附加模型下，使用来自 UK10K 队列的 3,644 名受试者作为非 ALL 对照，评估变体与 ALL 易感性的关联。在 ALL 细胞中使用 CRISPRi 增强子筛选系统地鉴定了 ARID5B 中的顺式调节元件。通过信息预测 ARID5B 变体对转录因子结合的破坏，然后使用染色质免疫沉淀和免疫共沉淀进行确认。使用 UK Biobank 数据集检查了 ARID5B 变异与血液学特征的关联。所有统计检验都是双面的。结果我们在 ARID5B 中鉴定出 54 个与白血病风险显着相关的常见变异，所有这些变异都是非编码的。使用基于 CRISPR 的高通量增强子筛选发现了 ARID5B 位点的六个顺式调控元件。引人注目的是，最高 ALL 风险变体 (rs7090445, P=5.57 × 10-45) 恰好位于最强的增强子元件内，该元件也在远端与 ARID5B 启动子相连。变异等位基因破坏了 MEF2C 结合基序序列，导致 MEF2C 亲和力降低和局部染色体可及性降低。MEF2C 可能通过与 RUNX1 的转录因子复合物影响 ALL 中的 ARID5B 表达。使用 UK Biobank 数据集 (n = 349,861)，我们发现 rs7090445 也与一般人群中的淋巴细胞百分比和计数相关（分别为 P=8.6 × 10-22 和 2.1 × 10-18）。结论 我们的结果表明 ARID5B 中的所有风险变异通过调节该位点的顺式调控元件发挥作用。