Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden.
Sci Rep. 2020 Nov 9;10(1):19304. doi: 10.1038/s41598-020-74580-1.
Breast cancer (BC) is a genetically heterogeneous disease with high prevalence in Northern Europe. However, there has been no detailed investigation into the Scandinavian somatic landscape. Here, in a homogeneous Swedish cohort, we describe the somatic events underlying BC, leveraging a targeted next-generation sequencing approach. We designed a 20.5 Mb array targeting coding and regulatory regions of genes with a known role in BC (n = 765). The selected genes were either from human BC studies (n = 294) or from within canine mammary tumor associated regions (n = 471). A set of predominantly estrogen receptor positive tumors (ER + 85%) and their normal tissue counterparts (n = 61) were sequenced to ~ 140 × and 85 × mean target coverage, respectively. MuTect2 and VarScan2 were employed to detect single nucleotide variants (SNVs) and copy number aberrations (CNAs), while MutSigCV (SNVs) and GISTIC (CNAs) algorithms estimated the significance of recurrent somatic events. The significantly mutated genes (q ≤ 0.01) were PIK3CA (28% of patients), TP53 (21%) and CDH1 (11%). However, histone modifying genes contained the largest number of variants (KMT2C and ARID1A, together 28%). Mutations in KMT2C were mutually exclusive with PI3KCA mutations (p ≤ 0. 001) and half of these affect the formation of a functional PHD domain. The tumor suppressor CDK10 was deleted in 80% of the cohort while the oncogene MDM4 was amplified. Mutational signature analyses pointed towards APOBEC deaminase activity (COSMIC signature 2) and DNA mismatch repair (COSMIC signature 6). We noticed two significantly distinct patterns related to patient age; TP53 being more mutated in the younger group (29% vs 9% of patients) and CDH23 mutations were absent from the older group. The increased somatic mutation prevalence in the histone modifying genes KMT2C and ARID1A distinguishes the Swedish cohort from previous studies. KMT2C regulates enhancer activation and assists tumor proliferation in a hormone-rich environment, possibly pointing to a role in ER + BC, especially in older cases. Finally, age of onset appears to affect the mutational landscape suggesting that a larger age-diverse population incorporating more molecular subtypes should be studied to elucidate the underlying mechanisms.
乳腺癌(BC)是一种遗传异质性疾病,在北欧地区高发。然而,目前还没有对斯堪的纳维亚大陆的体细胞景观进行详细的研究。在这里,我们利用靶向下一代测序方法,在一个同质的瑞典队列中描述了乳腺癌的体细胞事件。我们设计了一个 20.5 Mb 的阵列,靶向具有已知在 BC 中作用的基因的编码和调控区域(n = 765)。所选基因要么来自人类 BC 研究(n = 294),要么来自犬乳腺肿瘤相关区域(n = 471)。一组主要是雌激素受体阳性肿瘤(ER+ 85%)及其正常组织对照(n = 61)被测序至~140×和 85×平均目标覆盖度。使用 MuTect2 和 VarScan2 检测单核苷酸变异(SNVs)和拷贝数异常(CNAs),而 MutSigCV(SNVs)和 GISTIC(CNAs)算法估计复发性体细胞事件的意义。显著突变的基因(q≤0.01)为 PIK3CA(28%的患者)、TP53(21%)和 CDH1(11%)。然而,组蛋白修饰基因包含最多的变体(KMT2C 和 ARID1A,共 28%)。KMT2C 中的突变与 PI3KCA 突变相互排斥(p≤0.001),其中一半影响功能 PHD 结构域的形成。该队列中有 80%的 CDK10 缺失,而癌基因 MDM4 扩增。突变signature 分析指向 APOBEC 脱氨酶活性(COSMIC signature 2)和 DNA 错配修复(COSMIC signature 6)。我们注意到与患者年龄相关的两个明显不同的模式;TP53 在年轻组中突变率更高(29% vs 9%的患者),而 CDH23 突变在老年组中不存在。组蛋白修饰基因 KMT2C 和 ARID1A 中体细胞突变的增加将瑞典队列与以前的研究区分开来。KMT2C 调节增强子激活,并在富含激素的环境中协助肿瘤增殖,这可能表明其在 ER+BC 中的作用,尤其是在老年病例中。最后,发病年龄似乎会影响突变谱,这表明应该研究更大年龄多样化的人群,纳入更多的分子亚型,以阐明潜在的机制。