Comprehensive atlas of advanced adenomas and their surrounding primed colon: A multi-omics evaluation and clinical impact assessment

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SUMMARY Colon adenomas account for 80-85% of the CRC precancerous lesions and can progress to CRC. Yet, the majority of these early lesions remain in an indolent early state, and only 5-10% are aggressive and progress to CRC. Although the adenoma progression sequence was initially proposed to be driven mainly by the serial accumulation of gene mutations and epigenetic alterations in colon epithelial cells, based on increasingly detailed analyses of the ‘cancer-causing’ alterations that characterize CRC, it has becoming apparent that these same alterations can also be found in indolent adenomas and even in the histologically normal colon epithelium. These observations indicate that DNA alterations alone are not sufficient to drive adenoma progression. Emerging studies indicate that factors that mediate adenoma progression can be derived from histologically normal colon tissue ‘primed’ to foster adenoma progression into cancer. We hypothesize that the adenoma progression is driven by both cell-autonomous and non-autonomous mechanisms and the ‘primed’ colon promotes adenoma progression by providing a permissive tissue environment. We further hypothesize that the distinct features of a ‘primed’ colon may be developed as biomarkers to predict the likelihood of adenoma progression to cancer. AIM 1A: To identify molecular signatures of adenoma progression (‘aggressive’ or ‘indolent’) by performing a mutli-omics evaluation of a unique collection of adenomas followed longitudinally with defined progression outcomes; AIM 1B: To determine the ‘aggressiveness’ of adenomas in an independent cohort using the molecular signature of progression derived from Aim 1A. AIM 2: To directly determine the distinct features of a ‘primed’ colon that associate with adenoma progression. (1) increased senescent fibroblast load and associated SASP factor expression; (2) oncogenic immune microenvironment; (3) increased cancer driver gene mutation burden; (4) altered CRC associated methylome, and (5) the dysbiotic CRC-associated microbiome state. AIM 3A: To identify and evaluate DNA methylation-based tissue biomarkers to determine whether they predict the risk of aggressive adenoma occurrence using a highly precise and sensitive droplet digital PCR method. AIM 3B: To determine if the cancer driver gene mutation burden in the primed colon associates with aggressive adenoma occurrence using a high fidelity and ultra-deep sequencing method. This translational Project 1 will provide an unprecedented high-quality characterization of the early lesion and the surrounding primed colon that enables its progression. This project aligns with the expertise of the investigators involved, the access to precious sample biorepositories and the infrastructure provided by the U54 mechanism. The significance findings from Project 1 will be functionally interrogated in Project 2&3 and other U54 projects, leading to an iterative process to advance our understanding of the adenoma biology and the development of personalized biomarkers for CRC prevention.