Genomic Heterogeneity and Branched Evolution of Early Stage Primary Acral Melanoma Shown by Multiregional Microdissection Sequencing
Genomic Heterogeneity and Branched Evolution of Early Stage Primary Acral Melanoma Shown by Multiregional Microdissection Sequencing
复制标题
多区域显微切割测序显示早期原发性肢端黑色素瘤的基因组异质性和分支进化
DOI：
10.1016/j.jid.2019.01.019
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发表时间：
2019-07-01
影响因子：
6.5
通讯作者：
Li, Hang
中科院分区：
文献类型：
--
作者：
Zhang, Xiannian;Peng, Yang;Li, Hang
肢端黑色素瘤（AM）是一种极具侵袭性的黑色素瘤亚型，在东亚地区较为常见。AM表现出高度的肿瘤间和肿瘤内异质性，预后较差。为了将基因组异质性与表型特征和治疗效果相关联，需要一种从早期AM样本中以高特异性和敏感性从有限样本中恢复基因组信息的方法。我们采用激光捕获显微切割技术从染色组织切片中分离出仅包含几十个细胞的单个微小肿瘤巢，然后应用多重退火和基于环的扩增循环（一种最初为单细胞开发的高效全基因组扩增方法）来扩增每个肿瘤巢的全基因组以进行测序。我们能够准确地描绘出每个微小肿瘤巢的拷贝数变异和单核苷酸变异情况，并定量表征不同层面的异质性，包括肿瘤与痣之间、患者之间、同一肿瘤内不同表型之间以及具有相同表型外观的相邻肿瘤细胞簇之间的异质性。我们发现基因组异质性广泛存在，并且分支进化发生在AM发展的早期阶段。我们能够在这些具有表型可识别性的细胞簇之间构建系统发育树。
Acral melanoma (AM) is an extremely aggressive subtype of melanoma that is prevalent in eastern Asia. AM exhibits high intertumoral and intratumoral heterogeneities with poor prognosis. To associate the genomic heterogeneities with phenotypic traits and efficacy of treatments, a method is needed to recover genomic information from limited samples with high specificity and sensitivity from early stage AM specimens. We performed laser capture microdissection to isolate single micro-tumor nests, containing only dozens of cells, from stained tissue slices and then applied multiple annealing and looping-based amplification cycles, a highly efficient whole-genome amplification method originally developed for single cells, to amplify the whole genome of each tumor nest for sequencing. We were able to accurately profile the landscape of copy number alterations and single nucleotide variations of every single micro- tumor nest and to quantitatively characterize the heterogeneities at different levels, between tumor and nevi, among patients, among different phenotypes within a same tumor, and among adjacent tumor cell clusters with identical phenotypic appearance. We have found that genomic heterogeneity exists extensively and that branched evolution happens in the early stage of AM development. We are able to build the phylogenetic tree among these phenotypically addressable cell clusters.