`Analysis of neo-antigens and immune profiles of Asian breast cancer patients, focusing on common germline deletion of APOBEC3B cytosine deaminase

乳腺癌是女性最常见的癌症，在亚洲，随着生活方式因素的改变，乳腺癌发病率正以每年3%的速度增长，这是因为越来越多的西方化和都市化。对包括乳腺癌在内的常见癌症的基因组变化进行了大量的分类，但这主要是在欧洲血统的女性身上完成的。在多种族亚裔人群中，乳腺癌的分子图谱一直受到限制，部分原因是成本高，而且无法获得大量高质量、经过临床注释的肿瘤样本。了解亚洲乳腺癌基因组基础的目标现在可以实现，因为新的DNA测序技术以显著降低的成本提供了高通量和准确的数据。我们决定将重点放在APOBEC3B(A3B)缺失生殖系携带者中发生的乳腺癌，这在亚洲人中比高加索人常见三倍。APOBEC(载脂蛋白B mRNA编辑酶，催化多肽样)家族是进化上保守的胞嘧啶脱氨酶，与病毒和细菌感染的内在突变相关。最近，据报道，生殖系A3B缺失与乳腺癌风险增加有关，并与具有超突变表型和激活免疫信号的乳腺癌相关。然而，在一定程度上，由于种系突变在高加索人群中不太常见，而且到目前为止，大多数大型测序项目都是在高加索样本集合中进行的，因此关于乳腺癌中的A3B的信息仍然有限，特别是在亚洲乳腺癌样本中。肿瘤浸润性免疫细胞在免疫监测中发挥作用，免疫检查点抑制剂如抗PD-1和抗CTLA-4抗体已被证明在治疗黑色素瘤、非小细胞肺癌、肾细胞癌和其他癌症方面具有显著的疗效。然而，只有一小部分患者受益，而且似乎突变负荷较高的癌症更有可能受益于免疫激活，从而增加了肿瘤浸润性免疫细胞。事实上，由于错配修复缺陷而导致高突变负荷的结直肠癌患者表现出更好的免疫相关客观应答率和无进展生存率，提示高体细胞突变负荷可能是免疫检查点抑制剂的潜在预测生物标志物。到目前为止，关于乳腺癌对免疫检查点治疗的肿瘤反应的数据有限。在欧洲血统的女性中，大多数乳腺癌是绝经后乳腺癌，这种癌症更有可能是雌激素受体阳性，突变负荷较低。然而，对于乳腺癌的一部分，例如，那些患有三阴性乳腺癌、BRCA1或BRCA2胚系改变和A3B胚系突变的乳腺癌，有更高的突变负荷。值得注意的是，亚洲乳腺癌样本中的突变负载尚未在亚洲女性中进行系统测试。自2012年以来，我们已经建立了以新鲜冷冻格式收集的以医院为基础的乳腺癌样本队列，所有样本都与深入的风险因素信息、30个乳腺癌易感基因的全面小组测序以及A3B种系状态分析有关，因此为这次合作提供了一个独特的机会。在这个项目中，我们建议对A3B基因野生型、1个拷贝缺失或2个拷贝缺失的女性队列中的突变情况和免疫反应进行系统分析，并确定生殖系A3B状态与抗肿瘤反应相关。我们相信，这项工作将有助于更好地了解亚洲女性常见的生殖系变化，并可能为未来亚洲乳腺癌患者的免疫治疗研究奠定基础。

Breast cancer is the most common cancer among women, and in Asia, breast cancer incidence is increasing at 3% per annum because of increasing "westernization" and urbanization, along with changes in lifestyle factors. Much effort to catalogue the genomic alterations in common types of cancers including breast cancer, but this has mainly been done in women of European descent. Molecular profiling of breast cancer in multi-ethnic Asian populations has been limited in part because of cost and unavailability of large collections of good quality, clinically annotated tumour samples. The goal of understanding the genomic basis of Asian breast cancers can now be realized because newer DNA sequencing technologies provide high-throughput and accurate data at a significantly reduced cost. We have decided to focus on breast cancers arising in germline carriers of APOBEC3B (A3B) deletion, which is three times more common in Asians compared to Caucasians. The APOBEC ("apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like") family of proteins are evolutionarily conserved cytosine deaminases associated with intrinsic mutations in response to viral and bacterial infection. Recently, germline A3B deletions were reported to be associated with increased risk to breast cancer, and breast cancers that have a hypermutator phenotype and activated immune signature. However, in part because germline mutations are less common in Caucasian populations and the majority of large sequencing projects have thus far been conducted in Caucasian sample collections, there remains limited information about A3B in breast cancers, particularly in Asian breast cancer samples. Tumour-infiltrating immune cells play a role in immunesurveillance and immune checkpoint inhibitors such as anti-PD-1 and anti-CTLA-4 antibodies have been shown to elicit remarkable response in treatment of melanoma, non-small-cell lung cancer, renal-cell carcinoma, and other cancers. However, only a small fraction of patients benefit and it appears that cancers with higher mutation load are more likely benefit due to immune activation and consequently increased tumour-infiltrating immune cells. Indeed, colorectal patients with high mutation burden because of mismatch repair deficiency showed better immune-related objective response rate and progression-free survival, suggesting that high somatic mutation burden may be a predictive potential biomarker to immune checkpoint inhibitors. To date, there has been limited data of tumour response to immune checkpoint therapy in breast cancer. The majority of breast cancers in women of European descent are post menopausal breast cancer which is more likely to be positive for estrogen receptor and have a lower mutational load. However, for a subset of breast cancers, for example, those with triple negative breast cancers, with BRCA1 or BRCA2 germline alterations, and with A3B germline mutations, there is higher mutational load. Notably, the mutational load in Asian breast cancer samples, where A3B germline mutations are 3 times more common, has not yet been systematically tested in Asian women.Since 2012, we have established hospital-based cohort of breast cancer samples collected in fresh frozen format and all samples are associated with in depth risk factor information, sequencing for a comprehensive panel of 30 breast cancer predisposition genes, and A3B germline status analysis, thus providing a unique opportunity for this collaboration. In this project, we propose to conduct a systematic analysis of the mutational profile and immune response in a cohort of women with either wild-type, 1 copy deletion or 2 copy deletion of A3B and determine germline A3B status is associated with anti-tumour response. We believe that this work will lead to a better understanding of a common germline alteration in Asian women and may lay the grounds for future studies on immunotherapy in Asian breast cancer patients.