Analysis of the Irradiated Tumor and Tumor Microenvironment

摘要 肿瘤在复杂和动态的微环境中发展，影响疾病的进展和反应 到治疗，包括放射治疗(RT)。RT导致细胞命运受损，其结果是 未修复的DNA损伤，大分子损伤和对应激的不适应，最终导致细胞死亡或 永久的增殖性失活(细胞衰老)，两者都与免疫系统发生串扰。本地 基因组不稳定性、氧合作用和微生物成分的差异也会影响肿瘤对RT的反应 和免疫激活。所有这些因素及其动态交织在一起，促成了局部控制和患者 生死存亡。尽管辐射生物学方面的知识在不断增长，而且辐射向 肿瘤，RT如何随时间影响肿瘤-免疫相互作用的分子决定因素仍然在很大程度上 未定义。此外，RT如何诱导肿瘤中不同细胞成分的应激反应和适应 微环境最终影响临床结果仍然难以捉摸。同样，这样的治疗方法 结果可以通过不同的预先存在的与基因组不稳定有关的信号特征进一步改变 RT，没有得到很好的刻画。在这里，我们测试了一种新的假设，即术前放疗是可切除的 结直肠癌改变了肿瘤细胞、正常细胞、免疫之间的动态相互作用 细胞和肿瘤微生物群，以调节细胞命运决定和抗癌免疫。我们的团队 基础科学家与一群免疫学家、临床肿瘤学家、外科医生、病理学家、 物理学家和生物信息学家，创造了一个独特的环境来检验这一假说 项目2。具体地说，我们的目标是(1)建立免疫反应的时空格局，并 RT诱导大肠癌及癌旁非癌组织中的突变和转录变化 恶性结肠；(2)评估RT对基因组稳定性、细胞命运和癌症信号调节的影响 途径；以及(3)研究RT如何调节肿瘤相关微生物群。为了实现这些目标，我们将 利用分子表征试验提供的一组独特的纵向收集的CRC样本 (MCT)和最先进的创新技术，包括空间转录组(年度技术 2020)、RNAScope和其他，这将实现前所未有的(接近单细胞分辨率) 恶性肿瘤细胞、正常细胞、免疫细胞与肿瘤的动态相互作用特征 肿瘤样本中的微生物组，以及这种相互作用在放射治疗之前、期间和之后如何演变，与 特别强调以前与辐射敏感性有关的因素和过程，包括(但 不限于)基因组不稳定、缺氧、DNA损伤反应、细胞死亡和细胞衰老。

SUMMARY Tumors develop in complex and dynamic microenvironments that influence disease progression and response to treatment, including radiation therapy (RT). RT results in compromised cellular fate as a consequence of unrepaired DNA lesions, macromolecular damage and failing adaptation to stress, culminating in cell death or permanent proliferative inactivation (cell senescence), both of which crosstalk with the immune system. Local differences in genomic instability, oxygenation and microbial components can also affect tumor responses to RT and immune activation. All these factors and their dynamic intertwining contribute to local control and patient survival. Despite the growing knowledge in radiation biology and the improved precision delivery of radiation to tumors, the molecular determinants of how RT impacts the tumor-immune interaction over time are still largely undefined. Moreover, how RT-induced stress response and adaptation in distinct cell components in the tumor microenvironment ultimately influence the clinical outcome remains elusive. Likewise, how such therapeutic outcome can be further altered by distinct pre-existing signaling profiles related to genomic instability prior to RT, is not well characterized. Here, we test the novel hypothesis that pre-operative RT for resectable colorectal (CRC) cancer alters the dynamic interactions between malignant cells, normal cells, immune cells, and the tumor microbiome, to modulate cell fate decisions and anticancer immunity. Our team of basic scientists has joined forces with a group of immunologists, clinical oncologists, surgeons, pathologists, physicists, and bioinformaticians, to create a unique environment for testing this hypothesis in conjunction with Project 2. Specifically, we aim at (1) establishing the spatiotemporal landscape of the immune response and mutational and transcriptional changes within histological context induced by RT in CRC and the adjacent non- malignant colon; (2) assessing the effect of RT on genome stability, cell fate, and modulation of cancer signaling pathways; and (3) investigating how RT modulates the tumor-associated microbiome. To these aims, we will harness a unique set of longitudinally collected CRC samples provided by the Molecular Characterization Trial (MCT) and state-of-the-art, innovative technologies including spatial transcriptomics (the technology of the year 2020), RNAscope and others, which will enable for an unprecedented (at near-to-single cell resolution) characterization of the dynamic interactions between malignant cells, normal cells, immune cells and the tumor microbiome in tumor samples, and how such interactions evolve prior to, during and after radiotherapy, with special emphasis on factors and processes that have previously been linked to radiosensitivity, including (but not limited to) genomic instability, hypoxia, DNA damage responses, cell death and cellular senescence.