Lay Abstract
Desmoid tumors consist of both tumor and non-tumor cells growing together. It remains unknown how the proportions and types of cells, or the interactions between them, affect the clinical behavior of a tumor. Advances in technologies called single-nuclei or single-cell RNA sequencing (sn/sc-RNAseq) now enable us to quantify the level of expression of genes in individual cells within the same tissue to compare their biological activity. These technologies have enabled significant advancement in our understanding of the behavior of other cancers. However, in desmoid tumors, we encounter a major challenge: the desmoid cells appear very similar to most of the non-tumor cells in the same area. Still, the most distinguishing feature of desmoid cells is the fact they carry a mutation in either the CTNNB1 gene or the APC gene. In this project, we propose to build a team that will work together to improve upon sn/sc-RNAseq technology by also sequencing the CTNNB1 or APC genes at the single-cell level. We will utilize this improved technology on tissues stored at the Dana-Farber Cancer Institute BioBank for desmoid tumors. We propose to combine this molecular information with clinical histories to understand the differences in gene activities between desmoid and non-desmoid cells in the same tissue and across different patients with different clinical behaviors. If successful, our study’s results will help answer whether gene activity levels can relate to spontaneous regression, and if so, which aspects of unique desmoid biology would be promising to pursue in future validation experiments.
Scientific Abstract
Desmoid tumors are fibroblastic neoplasms with differential clinical behavior often present as CTNNB1 or APC mutant cells intermixed with non-mutant cells. It remains unknown whether the cellular composition, or tumor-stromal interaction, can be used to infer tumor progression, therapeutic response, or spontaneous regression. While single-cell atlases have enabled valuable insights into the biology of many epithelial cancers, mesenchymal tumors, desmoid tumors in particular, are challenging to study because current references cannot distinguish between mutant and non-mutant fibroblasts. Since most patients present with CTNNB1 or APC mutations, we hypothesize that spontaneous regression can be detected by the transcriptional composition of desmoid tumors. We aim to test this hypothesis by concurrent genotyping of single cells to enable in sc/sn-RNAseq experiments. Here we propose to form a team of scientists and clinicians to study the clinical history of our biobank of 75 patients who donated tissues to identify cases of spontaneous regression, stable disease, and progression. Based on clinical history and onco-panel sequencing we will then nominate samples for parallel single-cell/nuclei genotyping and transcriptomics. We will then analyze the results to identify differentially expressed genes and pathways related to mutation status and clinical history. Preliminary data from 3 samples (2 tumors, and 1 adjacent normal) demonstrate the feasibility of our sequencing approach. If successful, expanding to a full project will create the first genotyped, clinically annotated single-cell reference of desmoid tumors.
