Linkage of genetic drivers and strain-specific germline variants confound mouse cancer genome analyses
Linkage of genetic drivers and strain-specific germline variants confound mouse cancer genome analyses
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遗传驱动因素和品系特异性种系变异的联系混淆了小鼠癌症基因组分析
DOI：
10.1038/s41467-020-18095-3
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发表时间：
2020
影响因子：
16.6
通讯作者：
Saur D
中科院分区：
文献类型：
--
作者：
Mueller S;Lange S;Collins KAN;Krebs S;Blum H;Schneider G;Saur D
Niknafs等人使用具有工程化KrasG 12 D和Trp 53 R172 H突变的小鼠模型（KPC模型）描述了胰腺癌的进化轨迹。作为另一个方面，该研究报告了Nlrp 1基因座的频繁纯合缺失，这被解释为胰腺癌中的体细胞驱动事件。我们观察到，这种Nlrp 1改变的起源是菌株特异性种系变异，对其生物学相关性的解释产生了深远的影响。除了这个特定的基因座，我们表明，菌株特异性生殖系变异是一个普遍的混淆基因组分析小鼠模型的癌症。与Niknafs等人1一致，我们还在我们自己的KPC小鼠队列中观察到Nlrp 1基因座的频繁变化。然而，Nlrp 1的变化总是与一系列不寻常的特征。首先，在所有受影响的癌症中，缺失涵盖了11号染色体上完全相同的基因组区域（图1a，d）。独立癌症中的这些相同断点并不反映肿瘤抑制基因座处体细胞损失的典型“阶梯式”模式（图1a显示了重叠拷贝数分布的这种模式）。其次，在Trp 53突变小鼠中诱导的其他癌症实体中也可以发现完全相同的缺失，如我们自己的研究（胰腺癌、骨肉瘤、肺腺癌、皮肤鳞状细胞癌）以及通过对公开可用的数据集（淋巴瘤、肝细胞癌2-4）的重新分析所揭示的。在不同的癌症、模型、实体和实验室中，体细胞获得绝对相同的纯合缺失是相当不可能的。第三，我们观察到Nlrp 1基因座的改变，只有在小鼠模型与工程突变或floxed Trp 53等位基因（Trp 53 ENG）。更具体地说，Nlrp 1基因座的改变只在Trp 53 ENG杂合子肿瘤中检测到，而在与Trp 53 ENG纯合子杂交的小鼠中从未检测到（n= 0/27，自身队列）。人类在这个位点只有一个基因，NLRP 1。在小鼠参考基因组（基于品系C57 BL/6 J）中，Nlrp 1基因座包含三个相关基因：Nlrp 1a、Nlrp 1b和Nlrp 1c-ps。重要的是，Trp 53和Nlrp 1基因座在11号染色体上仅相隔1.5 Mb，导致两个基因座之间的紧密遗传连锁。基因工程改造的Trp 53等位基因是在129 S相关背景下产生的（Trp 53 ENG-129 S）。我们检查了129 S基因组中的Nlrp 1基因座（Nlrp 1129 S），发现C57 BL/6 J序列的部分在129 S参考组装体5中没有基因组比对（图1 B）。我们还分析了来自一项研究的阵列比较基因组杂交（aCGH）数据，该研究检查了不同小鼠品系之间的种系拷贝数变异（CNV）6。我们发现，129 S相关小鼠品系的基因组含有Nlrp 1基因座的纯合缺失，这与KPC肿瘤（图1c，d）和上述所有其他癌症实体中的Nlrp 1基因座缺失相同。使用纳米孔长读测序（图1 B），我们证实了我们（以及Niknafs等人1）使用的工程化Trp 53 R172 H小鼠系7中存在菌株特异性Nlrp 1129 S基因座变体。因此，Nlrp 1基因座缺失的起源不是肿瘤演变过程中的体细胞获得和随后的选择，而是预先存在的菌株特异性种系变异。在确定Trp 53 ENG-129 S等位基因与Nlrp 1129 S基因座（Trp 53 ENG-129 S; Nlrp 1129 S）遗传连锁后，我们询问了第二等位基因在种系中的状态。这个考虑很重要，因为我们将小鼠保持在混合的129 S; C57 BL/6 J背景下（类似于…
Niknafs et al. describe evolutionary trajectories in pancreatic cancer using mouse models with engineered KrasG12D and Trp53R172H mutations (KPC model). As an additional aspect, the study reports frequent homozygous deletions at the Nlrp1 locus, which are interpreted as a somatic driver event in pancreatic cancer. We observed that the origin of this Nlrp1 alteration is strain-specific germline variation, having profound impact on the interpretation of its biological relevance. Beyond this specific locus, we show that strain-specific germline variation is a general confounder of genome analyses in mouse models of cancer. In line with Niknafs et al. 1, we also observed frequent changes at the Nlrp1 locus in our own cohorts of KPC mice. However, Nlrp1 changes were invariably associated with a series of unusual characteristics. First, the deletion encompasses the exact same genomic region on chromosome 11 in all affected cancers (Fig. 1 a, d). These identical breakpoints in independent cancers do not reflect the typical “stepped” pattern of somatic losses at tumor suppressor loci (Fig. 1 a shows such a pattern of overlaid copy number profiles). Second, the exact same deletion can also be found in other cancer entities induced in Trp53 mutant mice, as revealed in our own studies (pancreatic cancer, osteosarcoma, lung adenocarcinoma, cutaneous squamous cell carcinoma) as well as through re-analysis of publicly available datasets (lymphomas, hepatocellular carcinomas 2–4). Somatic acquisition of absolutely identical homozygous deletions in different cancers, models, entities, and laboratories is rather unlikely. Third, we observed Nlrp1 locus alterations only in mouse models with engineered mutant or floxed Trp53 alleles (Trp53ENG). More specifically, Nlrp1 locus alterations were only detected in heterozygous Trp53ENG tumors, but never in mice, which were crossed to Trp53ENG homozygosity (n= 0/27, own cohort).These seeming inconsistencies prompted us to examine the locus in detail. Humans have only one gene at this locus, NLRP1. In the mouse reference genome (based on strain C57BL/6J) the Nlrp1 locus comprises three related genes: Nlrp1a, Nlrp1b, and Nlrp1c-ps. Importantly, Trp53 and the Nlrp1 locus are separated by only 1.5 Mb on chromosome 11, causing tight genetic linkage between both loci. The genetically engineered Trp53 allele was generated on a 129S-related background (Trp53ENG-129S). We examined the Nlrp1 locus in 129S genomes (Nlrp1129S) and found that parts of the C57BL/6J sequence have no genomic alignment in the 129S reference assembly 5 (Fig. 1 b). We also analyzed array comparative genomic hybridization (aCGH) data from a study examining germline copy number variation (CNV) between different mouse strains 6. We found that genomes of 129S-related mouse strains contain homozygous deletions of the Nlrp1 locus that were identical to Nlrp1 locus deletions in KPC tumors (Fig. 1 c, d) and all other cancer entities mentioned above. Using nanopore long-read sequencing (Fig. 1 b), we confirmed the presence of the strain-specific Nlrp1129S locus variant in the engineered Trp53R172H mouse line 7 used by us (and by Niknafs et al. 1). Thus, the origin of the Nlrp1 locus deletion is not somatic acquisition followed by selection during tumor evolution, but a pre-existing strain-specific germline variant. After identifying that the Trp53ENG-129S allele is genetically linked to the Nlrp1129S locus (Trp53ENG-129S; Nlrp1129S), we interrogated the status of the second allele in the germline. This consideration is important, because we kept the mice on a mixed 129S; C57BL/6J background (similar to …
影响因子：
50.3
作者：
Hingorani, SR;Wang, LF;Tuveson, DA
通讯作者：
Tuveson, DA
影响因子：
14.8
作者：
Friedrich, Mathias J.;Rad, Lena;Rad, Roland
通讯作者：
Rad, Roland
影响因子：
14.8
作者：
Lange, Sebastian;Engleitner, Thomas;Rad, Roland
通讯作者：
Rad, Roland