Institute of Pathology, University Medicine of Rostock, Strempelstrasse, Rostock, Germany.
Centogene AG, Am Strande, Rostock, Germany; Arcensus GmbH, Goethestrasse, Rostock, Germany.
Lab Invest. 2023 Jul;103(7):100132. doi: 10.1016/j.labinv.2023.100132. Epub 2023 Mar 24.
To test the traditional model of tumor progression, Darwinian-type evolution, against the more recent Big Bang model, we selected 6 microsatellite-stable colorectal standard-type adenocarcinomas and their synchronous lymph node and liver metastases. Somatic genomic variants were identified by whole-exome sequencing (WES) of large tumor fragments from the primaries and 1 liver metastasis each, and used to design targeted resequencing next-generation sequencing (NGS) panels, 1 per case. Targeted deep resequencing (mean coverage, 2725; median, 2222) was performed with DNA from punch samples (1-mm tissue microarrayer needles) obtained from different regions of the primaries and their metastases. In total, 255 genomic variants were interrogated in 108 punch samples. Clonal heterogeneity was infrequent: a pattern of clonal heterogeneity consistent with a role in metastasis formation was observed only in 1 case in a single gene (p. Asp604Tyr of the PTPRT gene). However, when comparing variant allele frequencies (VAFs) of genomic variants in adjacent positions on chromosomes ("matched genomic variant loci") across punch samples, differences that exceeded 2 SD of the NGS assay variations (ad hoc dubbed VAF dysbalance) were observed in 7.1% of the punch samples (2.6%-12.0% per case), which indicates an intricate intermixing of mutated and nonmutated tumor cells ("intrinsic heterogeneity"). Additional OncoScan array analyses on a subset of the punch samples (31 in total) showed gross genomic aberrations as a possible explanation in only some (39.2%) of the matched genomic variant loci with VAF dysbalance. Our study provides a fairly direct (statistical model-free) view of the genomic states of microsatellite-stable colorectal carcinomas and their metastases, and suggests that Darwinian-type tumor evolution is not the key pathway of the metastasizing disease; instead, we recorded an "intrinsic" genomic heterogeneity, which may echo an initial Big Bang-like event.
为了验证肿瘤演进的传统达尔文式模型与最近提出的大爆炸模型，我们选择了 6 例微卫星稳定的结直肠标准型腺癌及其同步的淋巴结和肝转移灶。通过对原发灶和 1 个肝转移灶的大肿瘤片段进行全外显子组测序（WES），鉴定了体细胞基因组变异，并设计了靶向重测序下一代测序（NGS）面板，每个病例 1 个。对来自原发灶及其转移灶不同区域的穿刺样本（1mm 组织微阵列针）的 DNA 进行靶向深度重测序（平均覆盖度 2725，中位数 2222）。总共在 108 个穿刺样本中检测了 255 个基因组变异。克隆异质性罕见：仅在 1 例中观察到与转移形成相关的克隆异质性模式，即 PTPRT 基因的 p.Asp604Tyr 点突变。然而，当比较染色体上相邻位置（“匹配基因组变异位点”）的基因组变异等位基因频率（VAF）时，在 7.1%的穿刺样本（每个病例 2.6%-12.0%）中观察到超过 NGS 检测变异的 2 个标准差的差异（临时称为 VAF 失衡），这表明突变和非突变肿瘤细胞的复杂混合（“固有异质性”）。在一组穿刺样本（共 31 个）中进行的额外 OncoScan 阵列分析表明，在具有 VAF 失衡的匹配基因组变异位点中，只有部分（39.2%）可由大片段基因组异常解释。我们的研究提供了一种直接的（无统计模型）观察微卫星稳定结直肠癌及其转移灶基因组状态的方法，表明达尔文式肿瘤演进不是转移疾病的关键途径；相反，我们记录了一种“内在”的基因组异质性，这可能反映了最初的大爆炸事件。
