Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia
Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia
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DOI：
10.1002/gcc.22054
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发表时间：
2013-06-01
影响因子：
3.7
通讯作者：
Borkhardt, Arndt
中科院分区：
文献类型：
--
作者：
Chen, Cai;Bartenhagen, Christoph;Borkhardt, Arndt
近单倍体（2329条染色体）是儿童急性淋巴细胞白血病（ALL）中与特别差的结果相关的细胞遗传学数量畸变。相比之下，高超二倍体（5167条染色体）具有良好的预后。近单倍体的正确分类和适当的风险分层经常受到明显高的超二倍体克隆的存在的阻碍，这些克隆是由原始近单倍体克隆的核内复制产生的。我们评估了下一代测序（NGS），以区分高超二倍体白血病克隆的近单倍体和真正的高超二倍体起源。对5例高超二倍体ALL病例和来源于近单倍体克隆的高超二倍体细胞系MHH-CALL-2进行了单亲同二体性检测。NGS显示MHH-CALL-2的所有二体染色体，但没有一个患者，是单亲起源的，因此可靠地区分这些亚型。MHH-CALL-2的全外显子组和全基因组测序揭示了预测对63个基因的蛋白质功能有害的纯合非同义编码突变，其中包括已知的癌症相关基因，如FANCA、NF 1、TCF 7 L2、CARD 11、EP 400、组蛋白脱甲基酶和转移酶（KDM 6 B、KDM 1A、PRDM 11）。其中只有八个也是，但异源，突变的高超二倍体患者。MHH-CALL-2的结构变异包括纯合缺失（MTAP/CDKN 2A/CDKN 2B/ANRIL）、纯合倒位（NCKAP 5）和不平衡易位（FAM 189 A1）。总之，序列变异为MHH-CALL-2提供了通常在癌症发展期间获得的能力，例如，细胞周期控制丧失、增殖增强、缺乏DNA修复、细胞死亡逃避和表观遗传基因调控紊乱。近单倍体ALL的预后最可能是由于大量有害纯合突变的完全缺失。(c)2013 Wiley Periodicals，Inc.
Near haploidy (2329 chromosomes) is a numerical cytogenetic aberration in childhood acute lymphoblastic leukemia (ALL) associated with particularly poor outcome. In contrast, high hyperdiploidy (5167 chromosomes) has a favorable prognosis. Correct classification and appropriate risk stratification of near haploidy is frequently hampered by the presence of apparently high hyperdiploid clones that arise by endoreduplication of the original near haploid clone. We evaluated next-generation-sequencing (NGS) to distinguish between high hyperdiploid leukemic clones of near haploid and true high hyperdiploid origin. Five high hyperdiploid ALL cases and the high hyperdiploid cell line MHH-CALL-2, derived from a near haploid clone, were tested for uniparental isodisomy. NGS showed that all disomic chromosomes of MHH-CALL-2, but none of the patients, were of uniparental origin, thus reliably discriminating these subtypes. Whole-exome- and whole-genome-sequencing of MHH-CALL-2 revealed homozygous non-synonymous coding mutations predicted to be deleterious for the protein function of 63 genes, among them known cancer-associated genes, such as FANCA, NF1, TCF7L2, CARD11, EP400, histone demethylases, and transferases (KDM6B, KDM1A, PRDM11). Only eight of these were also, but heterozygously, mutated in the high hyperdiploid patients. Structural variations in MHH-CALL-2 include a homozygous deletion (MTAP/CDKN2A/CDKN2B/ANRIL), a homozygous inversion (NCKAP5), and an unbalanced translocation (FAM189A1). Together, the sequence variations provide MHH-CALL-2 with capabilities typically acquired during cancer development, e.g., loss of cell cycle control, enhanced proliferation, lack of DNA repair, cell death evasion, and disturbance of epigenetic gene regulation. Poorer prognosis of near haploid ALL most likely results from full penetrance of a large array of detrimental homozygous mutations. (c) 2013 Wiley Periodicals, Inc.