A Multimodal 3D Atlas of Colorectal Cancer Across Ages of Onset

PROJECT SUMMARY We propose the construction of a three-dimensional (3D) multimodal molecular atlas of colorectal cancer (CRC) across different ages of onset of the disease. We aim to address the emerging clinical challenge of rising early-onset CRC cases by exploring molecular differences between early-onset and later-onset

CRCs. We hypothesize that aberrant interactions between the carcinogenic microbes, tumor metabolic niche, and the tumor microenvironment lead to accelerated transitions of precancerous cell states to malignant states. Our atlas will focus on spatially mapping transitions from precancerous to cancerous

components within the same tumor, utilizing a "phylogeographic" mapping approach to create individualized and global progression trajectories between tumor subtypes (early onset CRCs, later-onset microsatellite stable CRCs, later-onset microsatellite unstable CRCs). We employ cutting-edge technologies, such as customized spatial transcriptomics, co-detection by indexing highly multiplexed

immunofluorescence microscopy, untargeted imaging mass spectrometry, and histological and autofluorescence imaging, to comprehensively characterize CRC tissue at various molecular levels and spatial scales. We employ a 3D multimodal strategy by reconstructing volumes from interleaving serial tissue sections evaluated by different technologies. Paired whole exome sequencing and single-cell

RNA-sequencing data will anchor our spatial analyses to our previous Human Tumor Atlas Network (HTAN) data. We leverage our previous success in building colorectal atlases within the HTAN and ensure that data are released for open-access use to the research community. We have a strong team with expertise in genomic profiling, multi-omic spatial analysis, biostatistics, and artificial intelligence. Our

proposal emphasizes our team's extensive track record in CRC research, with active programs in CRC, gut epithelial biology, CRC microbiome, epidemiology, and pathology. Our goal is to provide unprecedented insights into the genetic, transcriptomic, metabolomic, microbial, and architectural features of CRC in a spatially resolved manner to better understand CRCs across various age groups.