Stratification of Pancreatic Cancer Subpopulations for Effective Immunotherapy

由于胰腺导管腺癌（PDAC）的风险增加到更高的比率， 在退伍军人相对于一般人群，迫切需要制定有效的 治疗退伍军人系统中的退伍军人PDAC的疗法。最近，癌症免疫疗法 在几种癌症中显示出很大的希望，但在PDAC中没有。部分原因是 PDAC的异质性和缺乏针对个体肿瘤亚型的免疫疗法的定制。 PDAC患者治疗分层仍处于起步阶段，并且是一种可靠的方法 还没有认识到去卷积复杂肿瘤组成对PDAC亚型的分层。 最近，我们参与了PDAC标本的全基因组测序， 根据基因组结构模式将PDAC分为四种亚型的基础 变异（Nature，2016）。其中，免疫原性亚型占178例中的30 PDAC样本在TCGA数据库中，其特征在于上调的免疫细胞 网络，这可能表明对免疫疗法的不同反应。此外该 表观基因组解卷积（EDec）方法，首先由我们的共同研究者博士。 Milosavljevic的小组提供了关于肿瘤细胞类型组成的有价值的信息， 细胞类型特异性基因表达（Cell Rep. 2016）。当应用于免疫原性亚型时 PDAC肿瘤，EDec揭示了一种免疫抑制微环境，其特征在于 Foxp 3在所有四种亚型中表达最高。癌细胞落入免疫原性 亚型也显示最高的间皮素（MSLN）表达。因此，我们假设， 具有免疫原性特征的PDAC可能是对免疫原性应答的靶亚组。 通过MSLN病毒样颗粒（VLP）疫苗接种的免疫疗法或 VLP和免疫检查点抑制剂。我们将在临床前动物中测试我们的假设 最能概括人类PDAC患者对免疫疗法的反应的模型，包括 患者来源的肿瘤异种移植物（PDX）和人源化小鼠模型。我们的初步数据 已经表明我们的抗MSLN VLP疫苗在以下情况下对MSLN高表达PDX是有效的： 人源化NSG小鼠模型（PDX-hu-NSG）。根据我们的初步结果，我们 建议通过结合三种高度免疫的方法来开发有效的癌症免疫方法。 协同创新：（1）一种新的表观遗传去卷积方法来分层PDAC肿瘤; (2)（3）MSLN-VLP疫苗加抗PD-1的联合治疗 抗体的我们提出两个具体目标。在目标1中，我们将确定免疫原性 PDAC亚型在PDX-hu-NSG模型中对MSLN-VLP疫苗应答。在这里，我们将 用EDec方法按亚型对VA PDAC进行分层，然后确定MSLN-VLP疫苗 在人源化PDX小鼠模型中的特定PDAC亚组中的功效。在目标2中，我们 确定与抗PD-1 Ab的联合治疗是否增强MSLN VLP疫苗 在癌腐殖酸模型中的反应和功效。我们还将确定特定的肿瘤浸润 这些细胞是负责有效组合疗法的细胞亚群。此外，潜在 还将评估联合治疗的副作用。我们的发现将提供临床前 评估PDAC的创新精确免疫疗法的治疗效果 人源化小鼠，而不会使患者处于危险之中。该项目将提供了解 分子、细胞和组织水平的治疗反应，这是改善 通过患者分层进行治疗的PDAC结局。

As the risk for pancreatic ductal adenocarcinoma (PDAC) has increased to a higher rate in veterans relative to that in the general population, there is an urgent need to develop effective therapies to treat PDAC for veterans in the VA system. Recently, cancer immunotherapy has shown great promise in several cancers, but not in PDAC. Part of the reason for this is the heterogeneity of PDAC and lack of tailoring of immunotherapy to individual tumor subtypes. PDAC patient stratification for therapy remains in its infancy, and a reliable method to deconvolute complex tumor composition to stratify PDAC subtypes has not been recognized. Recently, we participated in whole genome sequencing of PDAC specimens, which provides the basis for classifying PDAC into four subtypes based upon patterns of genomic structural variation (Nature, 2016). Among these, the immunogenic subtype accounts for 30% of 178 PDAC samples in the TCGA database and is characterized by upregulated immune cell networks, which could indicate differential responses to immunotherapy. In addition, the Epigenomic Deconvolution (EDec) method, first developed by our co-investigator Dr. Milosavljevic’s group, provides valuable information about cell type composition of tumors and cell-type specific gene expression (Cell Rep. 2016). When applied to immunogenic subtype PDAC tumors, EDec reveals an immunosuppressive microenvironment characterized by the highest Foxp3 expression among all four subtypes. Cancer cells falling into the immunogenic subtype also show the highest mesothelin (MSLN) expression. Therefore, we hypothesize that PDACs with an immunogenic profile could be a target subgroup that is responsive to immunotherapy either by MSLN virus-like particle (VLP) vaccination or combination therapy of VLPs and an immune checkpoint inhibitor. We will test our hypothesis in pre-clinical animal models that best recapitulate human PDAC patient’s response to immunotherapy, including patient-derived tumor xenografts (PDX) and humanized mouse models. Our preliminary data have shown that our anti-MSLN VLP vaccine is effective against MSLN-high expressing PDX in a humanized NSG mouse model (PDX-hu-NSG). Based on our strong preliminary results, we propose to develop an effective cancer immunotherapeutic approach by combining three highly synergistic innovations: (1) A novel epigenetic deconvolution method to stratify PDAC tumors; (2) PDX-hu-NSG models; and (3) Combination therapy of MSLN-VLP vaccine plus anti-PD-1 antibody. We propose two specific aims. In Aim 1, we will determine whether the immunogenic subtype of PDAC is responsive to MSLN-VLP vaccine in PDX-hu-NSG model. Here, we will use EDec method to stratify VA PDACs by subtype and then determine MSLN-VLP vaccine efficacy in specific PDAC subgroups in humanized PDX mouse model. In Aim 2, we will determine whether combination therapy with anti-PD-1 Ab enhances MSLN VLP vaccine responses and efficacy in onco-humice model. We will also determine specific tumor infiltrating subset of cells that are responsible for the effective combination therapy. Furthermore, potential side-effect of the combination therapy will also be evaluated. Our findings will provide preclinical evaluation of the therapeutic efficacy of an innovative precision immunotherapy for PDAC in humanized mice without putting patients at risk. The project will provide understanding of molecular, cellular, and tissue-level responses to therapy, a key step towards improved outcomes in PDAC through patient stratification for therapy.