Epithelial competition determines gene therapy potential to suppress Fanconi Anemia oral cancer risk.

Unlabelled: Fanconi Anemia (FA) is a heritable syndrome characterized by DNA damage repair deficits, frequent malformations and a significantly elevated risk of bone marrow failure, leukemia, and mucosal head and neck squamous cell carcinomas (HNSCC). Hematopoietic stem cell gene therapy can prevent marrow failure and lower leukemia risk, but mucosal gene therapy to lower HNSCC risk remains untested. Major knowledge gaps include an incomplete understanding of how rapidly gene-corrected cellular lineages could spread through the oral epithelium, and which delivery parameters are critical for ensuring efficient gene correction. To answer these questions, we extended an agent-based model of the oral epithelium to include the delivery of gene correction to FA cells and the competitive dynamics between cellular lineages with and without gene correction. We found that only gene-corrected lineages with substantial proliferative advantages (probability of resisting displacement out of the basal layer ≥ 0. 1) could spread on clinically relevant timelines, and that these lineages were initially at high risk of loss in the generations following correction. Delivering gene correction to many cells minimizes the risk of loss, while delivery to many distinct locations within a tissue maximizes the rate of spread. To determine the impact of mucosal gene therapy in preventing the clonal expansion of pre-cancerous mutations, we compared the expected burden of mutations in simulated tissue sections with and without gene correction. We found that when FA cells have elevated genome instability or a -dependent proliferative advantage, gene correction can substantially reduce the accumulation of pro-tumorigenic mutations. This model illustrates the power of computational frameworks to identify critical determinants of therapeutic success to enable experimental optimization and support novel and effective gene therapy applications.

Author Summary: We investigated factors influencing the success of oral mucosal gene therapy for Fanconi Anemia (FA), a genetic syndrome marked by DNA repair defects in conjunction with a heightened risk of cancer. We used a computational model of the oral epithelium to determine how gene therapy corrected cells compete with FA background cells and the best gene delivery approaches to promote effective tissue replacement by gene-corrected cells. We find that gene-corrected cells require strong proliferative advantages to spread effectively, and that initially delivering gene correction to more cells reduces the chance that these cells are stochastically eliminated before they can spread. We also demonstrate that gene correction reduces the accumulation of pro-tumorigenic mutations in an FA context, where genomic instability can elevate the mutation rate and FA-specific selective pressures could favor accelerated clonal expansion. This research provides a useful framework for guiding mucosal gene therapy experiments and the development of effective oral gene therapy protocols for cancer prevention in FA.