A microbiome-informed platform for the development and testing of bacterial therapies for colorectal cancer

项目摘要 有一个明显的当务之急是开发有效的、成本效益高的疗法来对抗 癌症对社会构成了挑战。在这里，我们通过综合开发来满足这一需求 对多种癌症类型有效的工程细胞，特别强调 结直肠癌(CRC)这种癌症是导致癌症死亡的第二大常见原因。 在美国，每年有超过5万名美国人死亡。最近的研究表明 基因工程在更有效的癌症方面取得重大进展的力量 心理治疗。基因工程细胞的引入，如嵌合抗原受体T (CAR T)细胞，已经显示出治疗许多类型的B细胞恶性肿瘤的巨大希望，但是 不幸的是，将CAR T细胞靶向实体肿瘤仍然具有挑战性。在这个项目中，我们将 使用合成生物学的工具来制造基于细菌的新的工程疗法 而不是哺乳动物细胞。某些细菌物种已经显示出一种有用的“栖息”能力。 并选择性地在不感染健康组织的情况下定植实体肿瘤。这种肿瘤靶向 将在拟议的工作中利用财产，直接向 最需要它们的地方：肿瘤的固体核心。之前，我们开发了一种 细菌治疗，并在转移性疾病的动物模型中进行了测试。与其他 利用细菌细胞，这种“裂解菌株”不需要特殊的基因 对编码货物的分泌进行修改，在以下情况下将其释放到环境中 细胞爆裂了。最初，我们将对裂解菌株进行基因改造，以产生广泛的 用于测试的治疗学，包括毒素(来自细菌、动植物)、酶、 抗生素和凋亡肽。接下来我们将分析来自人类的肿瘤微生物组 样本，因为我们假设本地细菌种群的组成将提供 独特的签名(类似于指纹)，可用于将肿瘤分成不同的 子类型。我们希望使用这些指纹来识别其他具有更好适应性的物种 用于治疗结直肠癌的治疗性交付。一旦确定，我们将开发两种体外检测方法，用于 测试候选菌株。我们将使用微流控技术来创造高吞吐量 细菌与癌细胞共培养体系。同时，我们将发展一种共同培养 用于从相同的人类肿瘤样本中产生细菌和有机物的系统 它以前曾被用于菌株鉴定和指纹分析。最后，我们将测试 在结直肠癌动物模型中最有希望的治疗方法，以确定其在治疗前的疗效 临床模型。

Project Summary There is a clear imperative to develop potent, cost effective therapeutics to confront the challenge cancer poses to society. Here we address this need by developing synthetically engineered cells effective against a broad range of cancer types with a special emphasis on colorectal cancer (CRC). This cancer type is the second most common cause of cancer death in the US, with more than 50,000 Americans dying every year. Recent research demonstrates the power of genetic engineering to make significant advances towards more efficacious cancer therapy. The introduction of genetically engineered cells, such as chimeric antigen receptor T (CAR T) cells, has shown great promise for treating many types of B cell malignancies, but unfortunately targeting CAR T cells to solid tumors remains challenging. In this project we will use the tools of synthetic biology to make new engineered therapies based on bacterial rather than mammalian cells. Certain bacterial species have demonstrated a useful ability to “home in” and selectively colonize solid tumors without infecting healthy tissue. This tumor targeting property will be exploited in the proposed work to deliver safe, effective therapies directly to the locations where they are needed most: the solid core of tumors. Previously we developed a bacterial therapeutic and tested it in an animal model of metastatic disease. In contrast to other approaches utilizing bacterial cells, this “lysis strain” does not require specialized genetic modifications for the secretion of encoded cargo, it simply releases it into the environment when the cells burst. Initially we will genetically modify the lysis strain to produce a wide range of therapeutics for testing, including toxins (from bacteria, animals and plants), enzymes, antibiotics, and apoptotic peptides. Next we will analyze the tumor microbiome from human samples since we hypothesize that the native bacterial population's composition will provide a unique signature (analogous to a fingerprint) that can be used to divide tumors into distinct subtypes. We expect to use these fingerprints to identify other species with superior suitability for therapeutic delivery in treating CRC. Once identified we will develop two in vitro assays for testing the candidate strains. We will use microfluidic technology to create a high throughput co-culturing system for bacteria and a cancer cell line. In parallel, we will develop a co-culturing system for bacteria and organoids that are generated from the same human tumor samples which had been previously used for strain identification and fingerprinting. Lastly we will test the most promising therapies in an animal model of colorectal cancer to determine efficacy in a pre- clinical model.