Characterizing and predicting colitis in immune checkpoint blockade-treated cancer patients

项目总结 首次批准使用ipilimumab(抗CTLA-4)和nivolumab(抗PD-1)联合治疗 与仅使用nivolumab相比，2015年的黑色素瘤实现了更长的无进展生存期(11.5比6.9 月)，53%的患者在4年后仍然活着，其中71%的患者仍然无需治疗。然而，安全是 更广泛地实施这一成功组合的最大障碍，因为更多的 与单独使用nivolumab相比，严重的免疫相关不良事件(IrAEs)。尤其是与免疫相关的 结肠炎(Ircoltis)是最常见的疾病，10-15%的患者在接受抗结肠炎治疗后发展为结肠炎。 CTLA-4单独或联合使用。这种肠结肠炎危及生命，需要立即用高剂量的 剂量类固醇或生物制品，如抗肿瘤坏死因子，以及伊匹单抗或免疫治疗停止。这些 安全方面的担忧阻碍了CTLA-4靶向剂的开发，并可能降低了它们的 疗效归因于联合治疗推荐剂量较低和疗程有限。的确有 因此迫切需要全面研究肠炎的性质，找出是否存在潜在的危险因素 可以识别和缓解，以获得更大的安全性和联合治疗的有效性。 我们已经组建了一支独特的炎症性肠病(IBD)科学家和临床医生团队， 专门从事黑色素瘤免疫治疗的免疫学家、微生物组专家和内科肿瘤学家 分析结直肠组织病变、肠道微生物组和外周血液生物标志物，这些生物标志物可以预测或 有助于肠结肠炎的发展。通过比较我们已经从研究生物标本中学到的东西 IBD患者，即他们在单细胞水平上的遗传亚群、肠道微生物群和预测性免疫 签名，我们的目标是确定转录、免疫病理、血清学和肠道微生物组的特征 并利用这一知识为更好的治疗选择。 我们将通过确定黑色素瘤患者在治疗过程中的肠道活检组织的特征来解决肠结肠炎。 细胞RNA测序和多重免疫组织化学图谱，我们将联系免疫亚群和 与IBD病变中发现的标记物相比较。我们还将检测外周血血清标志物 (用ELISA法检测抗微生物和抗GM-CSF自身抗体，用Olink法检测可溶性细胞因子和蛋白质分析物 我们最近发现的在IBD发生之前可以检测到的危险因素)，以及 分析它们预测肠炎的能力。从治疗前和治疗过程中收集的粪便中，我们 将通过16S和元基因组测序来分析患有或不患有黑色素瘤患者的肠道微生物组 将其与IBD中已知的结肠炎结构进行比较，并从功能上评估IBD中的细菌群落 灵知生学模型。最后，我们将结合我们的研究结果，建立一个比较肠梗阻的机制模型。 对IBD，提出癌症免疫治疗患者危险因素的新分层，并提供未来 治疗机会，如可操作的组织基因组和蛋白质靶点或粪便移植。

PROJECT SUMMARY The first combination immunotherapy of ipilimumab (anti-CTLA-4) and nivolumab (anti-PD-1) approved for melanoma in 2015 has achieved longer progression-free survival compared to nivolumab alone (11.5 vs. 6.9 months), with 53% of patients still alive at 4 years, of whom 71% remain treatment free. Yet, safety is the biggest barrier to broader implementation of this successful combination, due to much greater occurrence of serious immune-related adverse events (irAEs) compared to nivolumab alone. In particular, immune-related colitis (irColitis) is the most common occurrence, with 10-15% of patients developing it upon receiving anti- CTLA-4 alone or in combinations. Such irColitis is life-threatening and requires immediate treatment with high- dose steroids or biologics such as anti-TNF, as well as ipilimumab or immunotherapy discontinuation. These safety concerns have hampered the development of CTLA-4 targeting agents and may have reduced their efficacy due to lower recommended dosing in combination therapy and limited treatment course. There is therefore an urgent need to comprehensively study the nature of irColitis and find whether potential risk factors could be identified and mitigated for greater safety and efficacy of combination treatments. We have assembled a unique team of inflammatory bowel disease (IBD) scientists and clinicians, tumor immunologists, microbiome specialists, and medical oncologists specializing in immunotherapy of melanoma to analyze colorectal tissue lesions, the gut microbiome, and peripheral blood biomarkers that could predict or contribute to development of irColitis. By comparing what we already learned from studying biospecimens of IBD patients, i.e., their genetic subsets at the single cell level, gut microbiome, and predictive immune signatures, we aim to characterize the transcriptomic, immunopathologic, serologic, and gut microbiome landscape of irColitis and leverage this knowledge for better therapeutic options. We will address irColitis by characterizing gut biopsies of melanoma patients during treatment using single- cell RNA sequencing and multiplex immunohistochemistry mapping, and we will relate immune subsets and markers discovered to those found in IBD lesions. We will also measure peripheral blood serologic markers (anti-microbial and anti-GM-CSF autoantibodies by ELISA, soluble cytokine and protein analytes with Olink proximity extension assay) that we recently found to be risk factors detectable prior to development of IBD, and analyze them for their capacity to predict irColitis. From stool collected before and throughout treatment, we will analyze by 16S and metagenomic sequencing the gut microbiome of melanoma patients with or without irColitis to compare it to known colitogenic structure in IBD, and functionally assess bacterial communities in gnotobiotic models. Finally, we will integrate our findings to establish a mechanistic model of irColitis compared to IBD, to propose novel stratifications of cancer immunotherapy patients by risk factors, and to offer future therapeutic opportunities, such as actionable tissue genomic and protein targets or fecal transplants.