Aydın Efe, Woodward Eleanor L, Dushime Gladys Telliam, Gunnarsson Rebeqa, Lilljebjörn Henrik, Moura-Castro Larissa H, Fioretos Thoas, Johansson Bertil, Paulsson Kajsa, Yang Minjun
Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.
Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden.
Genes Chromosomes Cancer. 2025 Mar;64(3):e70045. doi: 10.1002/gcc.70045.
The non-coding genome, constituting 98% of human DNA, remains largely unexplored, yet holds potential for identifying new biomarkers and therapeutic targets in acute lymphoblastic leukemia (ALL). In this study, we conducted a systematic analysis of recurrent somatic non-coding single nucleotide variants (SNVs) in pediatric B-cell precursor (BCP) ALL. We leveraged whole genome sequencing (WGS) data from 345 pediatric BCP ALL cases, representing all major genetic subtypes and identified 346 mutational hotspots that harbored somatic SNVs in at least three cases. Through the integration of paired RNA sequencing along with published ChIP-seq and ATAC-seq data, we found 128 non-coding hotspots associated with differentially expressed genes nearby, which were enriched for cis-regulatory elements, demonstrating the effectiveness of multi-omics integration in distinguishing pathogenic mutations from passengers. We identified one mutational hotspot that was associated with increased expression of the leukemia-associated gene NRAS in three primary ALLs. Micro-C analysis in the leukemia cell line demonstrated interactions between the hotspot region and NRAS regulatory elements. Dual luciferase assays indicated that the mutations disrupted regulatory interactions and CRISPR-mediated deletion of the region significantly upregulated NRAS, confirming the hypothesized regulatory link. Altogether, we provide new insights into the functional roles of non-coding mutations in leukemia.
构成人类DNA 98%的非编码基因组在很大程度上仍未被探索，但在识别急性淋巴细胞白血病（ALL）的新生物标志物和治疗靶点方面具有潜力。在本研究中，我们对儿童B细胞前体（BCP）ALL中反复出现的体细胞非编码单核苷酸变异（SNV）进行了系统分析。我们利用了来自345例儿童BCP ALL病例的全基因组测序（WGS）数据，这些病例代表了所有主要的遗传亚型，并确定了346个突变热点，这些热点在至少三例病例中存在体细胞SNV。通过整合配对RNA测序以及已发表的ChIP-seq和ATAC-seq数据，我们发现了128个与附近差异表达基因相关的非编码热点，这些热点富含顺式调控元件，证明了多组学整合在区分致病突变和过客突变方面的有效性。我们在三例原发性ALL中发现了一个与白血病相关基因NRAS表达增加相关的突变热点。白血病细胞系中的Micro-C分析表明热点区域与NRAS调控元件之间存在相互作用。双荧光素酶测定表明这些突变破坏了调控相互作用，CRISPR介导的该区域缺失显著上调了NRAS，证实了假设的调控联系。总之，我们为白血病中非编码突变的功能作用提供了新的见解。
