Dissecting the non-mutational mechanisms of benign-to-malignant transition in colon cancer - the purpose of this proposal is to elucidate the rate-limiting non-mutational events underlying benign to…

The National Cancer Institute awarded Cold Spring Harbor Laboratory $704,182 under the Cancer Biology Research program (CFDA 93.396) on June 16, 2026, to dissect non-mutational mechanisms driving benign-to-malignant transition in colorectal cancer.

The project uses a novel mouse model that stepwise acquires mutations mirroring human colorectal cancer progression—starting with APC knockout to initiate benign polyps, then inducing KRAS G12V and TP53 loss in rare cells within established polyps with spatial and temporal precision. The recipient's preliminary findings show that while mutations are necessary, they are insufficient to drive progression to carcinoma; tumors do not advance beyond adenoma in mice lacking T cells. Spatial transcriptomic analyses reveal that KRAS G12V induces loss of homeostatic regeneration signatures and gain of fetal intestinal stem cell states associated with injury-responsive repair, and these regions are less proliferative and depleted over time. The research hypothesizes that malignant precursors in benign polyps, despite carrying necessary genetic mutations, require inflammatory signals to progress.

Work is performed in Cold Spring Harbor, New York, over the period June 16, 2026 through May 31, 2031. The project obligates $704,182 in this initial budget period.

Sanford Burnham Prebys Medical Discovery Institute serves as a sub-recipient, providing computational analysis oversight and graduate student support for single-cell and single-nuclei RNA/ATAC-Seq data analysis, gene regulatory network reverse-engineering, cellular state identification, master regulator protein discovery, cell type deconvolution, cell trajectory inference, and ligand-receptor interaction mapping from spatial transcriptomics and publicly available specimens.

Dissecting the non-mutational mechanisms of benign-to-malignant transition in colon cancer - the purpose of this proposal is to elucidate the rate-limiting non-mutational events underlying benign to malignant transition of colorectal cancer (CRC). Colon polyps are extremely common, occurring in up to 40% of adults over 50, and are the precursors to CRC. While the causative mutations and their stepwise acquisition in this polyp-to-C:arcinoma sequence are well understood, the non-mutational mechanisms are not. In this proposal, we will use a new mouse model that emulates, for the first lime, the stepwise acquisition of mutations in the distal colon to accurately model benign-to-malignant transition in human CRC. Benign polyps are initialed via knockout of the moat commonly mutated gene in human colon polyps (APC). The most common mutational events in advanced CRC (kras G120, TRP53 loss) are then induced in rare cells of established polyps WL1H spatial and temporal precision. In our preliminary studies, we have found 1HAT this model accurately emulates the histopathological progression of benign-to-malignant transition of human CRC, but not in mice that are lacking T C:ells-these tumors do not progress beyond adenoma. Spatial transcriptomic (S1) analyses of these tumors revealed that KRASG120 induces loss of signatures of homeostatic regeneration and gain of a fetal intestinal- like stem cell state, which is known to play a critical role in intestinal repair following injury and inflammation, KRASG120 regions within polyps were also less proliferative and depleted over time, consistent WI1H the slow cycling nature of injury-responsive stem cells in the C:olon. These findings establish that mutations, while necessary, are not sufficient to drive progression to CRC, at least when acquired in the stepwise sequence characteristic of human CRC. We hypothesize that malignant precursors in benign polyps despite having the necessary genetic mutations, require inflammatory signals to progress to cancer. These signals enable this transition by shifting the fitness landscape of the premalignant niche in favor of a fetal intestinal wound healing response over homeostatic regeneration. In aim 1, we will leverage our innovative model to functionally interrogate the role of the fetal intestinal state in benign-to-malignant transition by inducing 1H18 slate via 1) wounding or non-specific T cell activation, 2) knocking out its key transcriptional coordinator ( YAP), and 3) ablating cells in this slate. We will use ST data from the model to define the transcriptional regulatory networks underlying this state in progressing versus non-progressing lesions. In aim 2, we will identify rate-limiting microenvironmental factors that preferentially select for malignant precursor cells, and define the TRANSC11PLLONAL mechanism by which these factors cooperates with, oncogenic mutations. Results will be validated against ST data we have generated on human polyps with early malignancy. Impact: completion of !HIE proposal will provide a mechanistic foundation for understanding why some benign polyps progress to cancer while most do not. This knowledge may nominate new and mare specific biomarkers for early cancer detection, as well as rate-limiting events that could be targeted FUR cancer prevention.