Integration of epidemiology, pathology, immunology and outcomes in colorectal cancer

结直肠癌流行病学、病理学、免疫学和结果的整合

• 批准号: 10709493
• 负责人: STEPHEN B GRUBER
• 金额: $ 65.01万
• 依托单位: BECKMAN RESEARCH INSTITUTE/CITY OF HOPE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-22 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10709493
• 关键词: Address; Age; Algorithms; Artificial Intelligence; CD3 Antigens; CD8-Positive T-Lymphocytes; California; Cancer Prognosis; Characteristics; Clinical; Clinical Data; Colorectal Cancer; Colorectal Neoplasms; Computers; Computing Methodologies; Crohn' s disease; Data; Detection; Diagnosis; Ensure; Epidemiology; Expression Profiling; Failure; Florida; Genetic; Goals; Histology; Image; Image Analysis; Immune; Immune response; Immune system; Immunologics; Immunology; Immunotherapy; Israel; Location; Lymphocyte; Lymphoid; Machine Learning; Maps; Measures; Methods; Microsatellite Instability; Microscopic; Modeling; Molecular; New York; Other Genetics; Outcome; Pathologic; Pathologist; Pathology; Patients; Pattern; Performance; Persons; Physicians; Population; Population Heterogeneity; Predictive Value; Process; Prognosis; Proteins; Puerto Rico; Reaction; Recording of previous events; Reproducibility; Research; Sampling; Slide; Solid Neoplasm; Spain; Spatial Distribution; Specimen; Statistical Methods; System; TNM; Technology; Testing; Training; Tumor-Infiltrating Lymphocytes; Validation; Visual; accurate diagnosis; cancer diagnosis; cancer survival; clinical predictors; clinically relevant; colon cancer patients; colorectal cancer treatment; deep learning; design; digital; digital imaging; driver mutation; effective therapy; epidemiologic data; ethnic diversity; immunoreaction; immunoregulation; improved; improved outcome; insight; learning strategy; low income country; machine learning algorithm; machine learning prediction algorithm; medical specialties; novel; prediction algorithm; predictive modeling; prognostic; prognostic model; prognostic value; protein expression; racial diversity; response; sex; survival prediction; task analysis; tool; treatment response; tumor; whole slide imaging

ABSTRACT Machine learning has the potential to transform pathologic diagnosis and to address very limited accessibility of expert pathology in low-income countries. Routine histology images of solid tumors contain an immense number of visual features that can be extracted and processed by artificial intelligence tools like machine learning, which excels at basic image analysis tasks such as tumor detection. In addition, machine learning can also predict clinically relevant features directly from histology images including microsatellite instability and immune features that independently predict prognosis response to therapy. This large, multicultural, racially and ethnically diverse study uses images of whole slides from routinely collected clinical specimens and applies computational pathology methods and digital spatial expression profiling to quantifiably improve CRC diagnosis, prognosis and predictive models together with clinical, epidemiologic and genetic data. The study goals will be accomplished through three specific aims. In Aim 1, we will apply novel machine learning algorithms from whole slide images to reproducibly identify MSI, histopathologic and immune features of colorectal cancer in racially/ethnically diverse populations. We will study H&E slides from 6,751 CRC cases, digitizing existing slides from 5,551 CRC cases and 1,200 new cases of CRC with contemporaneous clinical and epidemiologic data. Then, we will apply deep learning methods to accurately identify histopathologic features and immune characteristics of CRC. We will use a robust training validation, and testing design (70%/15%/15%) to ensure the rigor and reproducibility of our findings. In Aim 2, we will test whether machine learning algorithms that predict MSI and immune features related to CRC prognosis improve with the addition of clinical, epidemiologic, and germline genetic data. We will use machine learning statistical methods to test whether algorithms developed in Aim 1 improve prediction of overall survival and response to therapy with the addition of supplemental information beyond whole slide digital images. Finally, in Aim 3, we will compare the information derived from digital spatial profiling of expressed proteins in colorectal tumors with the information derived from Immunoscore quantification of lymphocyte populations at the tumor center (CT) and the invasive margin (IM), and explore whether these measures improve the models developed in Aims 1 and 2 in a subset of samples. We will perform GeoMx digital spatial profiling of 56 proteins expressed in 150 Stage I-III TNM colorectal cancers to compare the performance of digital spatial profiling to Immunoscore, a scoring system relying exclusively on expression patterns of CD3+ and CD8+ T cells. This study takes advantage of pathologic, epidemiologic, clinical, immunologic and germline genetic data from racially/ethnically diverse CRC patients from California, Detroit, New York, Florida, Puerto Rico, Israel and Spain. Our overarching goal is to improve the efficient diagnosis of colorectal cancer with clinically impactful immune profiles.

摘要 机器学习有可能改变病理诊断，并解决非常有限的可获得性 低收入国家的专家病理学。实体肿瘤的常规组织学图像包含大量的 可以由机器学习等人工智能工具提取和处理的视觉特征，这些工具 擅长基本的图像分析任务，如肿瘤检测。此外，机器学习还可以预测 直接来自组织学图像的临床相关特征，包括微卫星不稳定性和免疫特征 它们独立地预测治疗的预后反应。这个规模庞大、多元文化、种族和民族多元化的 研究使用了常规收集的临床标本的整个幻灯片的图像，并应用计算 病理方法和数字空间表达谱可定量改善结直肠癌的诊断、预后和 预测模型与临床、流行病学和遗传数据相结合。研究目标将会实现 通过三个具体目标。在目标1中，我们将从整个幻灯片图像中应用新的机器学习算法 重复性鉴定人种/人种中结直肠癌的MSI、组织病理学和免疫特征 不同的人群。我们将研究6751个CRC案例的H&E幻灯片，将5551个CRC的现有幻灯片数字化 有同期临床和流行病学数据的结直肠癌病例和1,200例新病例。那么，我们会申请 深入学习方法，准确识别结直肠癌的组织病理学特征和免疫特征。我们 将使用强大的培训验证和测试设计(70%/15%/15%)，以确保 我们的发现。在目标2中，我们将测试预测MSI和免疫特征的机器学习算法 与结直肠癌相关的预后随着临床、流行病学和生殖系遗传学数据的增加而改善。我们会 使用机器学习统计方法来测试在目标1中开发的算法是否提高了对 整体存活率和对治疗的反应，增加了整个幻灯片数字之外的补充信息 图像。最后，在目标3中，我们将比较来自EXPRESS数字空间剖面图的信息 结直肠肿瘤中的蛋白质与淋巴细胞免疫印迹定量信息 肿瘤中心(CT)和浸润性边缘(IM)的人群，并探索这些措施是否有所改善 在目标1和目标2中开发的模型是在样本子集中开发的。我们将执行GeoMx数字空间剖面图 比较150例I-III期结直肠癌组织中56种蛋白表达的数字空间表现 免疫评分系统完全依赖于CD3+和CD8+T细胞的表达模式。 这项研究利用了病理、流行病学、临床、免疫学和生殖系遗传数据 来自加利福尼亚州、底特律、纽约、佛罗里达州、波多黎各、以色列和西班牙的种族/民族多样化的CRC患者。 我们的首要目标是通过临床有效的免疫来提高结直肠癌的诊断效率。 配置文件。

项目成果

Transformer-based biomarker prediction from colorectal cancer histology: A large-scale multicentric study.

• DOI: 10.1016/j.ccell.2023.08.002
• 发表时间: 2023-09-11
• 期刊: CANCER CELL
• 影响因子: 50.3
• 作者: Wagner, Sophia J.;Reisenbuechler, Daniel;West, Nicholas P.;Niehues, Jan Moritz;Zhu, Jiefu;Foersch, Sebastian;Veldhuizen, Gregory Patrick;Quirke, Philip;Grabsch, Heike I.;van den Brandt, Piet A.;Hutchins, Gordon G. A.;Richman, Susan D.;Yuan, Tanwei;Langer, Rupert;Jenniskens, Josien C. A.;Offermans, Kelly;Mueller, Wolfram;Gray, Richard;Gruber, Stephen B.;Greenson, Joel K.;Rennert, Gad;Bonner, Joseph D.;Schmolze, Daniel;Jonnagaddala, Jitendra;Hawkins, Nicholas J.;Ward, Robyn L.;Morton, Dion;Seymour, Matthew;Magill, Laura;Nowak, Marta;Hay, Jennifer;Koelzer, Viktor H.;Church, David N.;Matek, Christian;Geppert, Carol;Peng, Chaolong;Zhi, Cheng;Ouyang, Xiaoming;James, Jacqueline A.;Loughrey, Maurice B.;Salto-Tellez, Manuel;Brenner, Hermann;Hoffmeister, Michael;Truhn, Daniel;Schnabel, Julia A.;Boxberg, Melanie;Peng, Tingying;Kather, Jakob Nikolas
• 通讯作者: Kather, Jakob Nikolas