Abstract 5177: Nilotinib suppresses the myofibroblastic cancer-associated fibroblast phenotype

Abstract

Abstract Background: Cancer-associated fibroblasts (CAFs) modulate the tumor immune microenvironment and are an exciting target for improving response to immunotherapy. Major roles of CAFs in the immune microenvironment include deposition of extracellular matrix (ECM) to prevent immune cell infiltration, a function associated with myofibroblastic CAFs (myCAFs), and production of cytokines to alter the immune milieu, associated with inflammatory CAFs (iCAFs). Recently we have demonstrated the potential for tyrosine kinase inhibitors (TKIs) to alter CAF phenotypes. Here we investigate the ability of dasatinib and nilotinib to alter the immune regulatory functions of CAFs. Methods: Bulk RNA sequencing comparing the effects of nilotinib and dasatinib on primary-derived patient CAFs was performed. CAFs from two rectal cancer patient tumors were isolated, cultured, and treated for 96 hours with 2.5μM nilotinib, 100nM dasatinib, or control feeding media. RNA isolation, library preparation, sequencing, data processing, and differential expression analysis was done through the University of Wisconsin - Madison Gene Expression Center, Biotechnology Center, and Bioinformatics Resource. Gene set enrichment analyses were done using GSEA 4.2.3 (Broad Institute) and all other analyses done in R. Results: The primary variance in samples is between CAF lines (RC1 and RC2), followed by treatments. RNA expression markers for myCAFs significantly associate with the Gene Ontology molecular function ECM structural constituent (q < 0.001). Nilotinib decreased expression of this gene set in RC1 (q < 0.001), while dasatinib treatment increased these genes in RC2, though not significantly (q = 0.2). Both dasatinib and nilotinib downregulated immune-related hallmark gene sets including IL6/JAK/STAT3 signaling (RC2 dasatinib q < 0.05, q < 0.001 for others) and TNFα signaling through NFκB (RC1 dasatinib q < 0.001, RC2 niltoinib q < 0.05, others q = 0.001,). Additionally, dasatinib induced increased expression of genes involved in myogenesis in both CAF lines (RC1 q = 0.001, RC2 q < 0.001), while nilotinib significantly decreased these genes in RC1 (q = 0.001). MYOCD is a transcription factor involved in myogenesis that regulates important myCAF genes such as ACTA2 and TAGLN. Nilotinib treatment decreased expression of MYOCD (RC1 log2FC -1.3 q < 0.001, RC2 -0.75 q < 0.05) and its target genes in both lines, whereas dasatinib did not significantly alter expression. Conclusions: CAFs derived from different cancers harbor different transcriptional profiles and have different responses to TKIs. Dasatinib treatment led to an increase in expression of ECM genes associated with the myCAF phenotype, while nilotinib decreased this phenotype, potentially by inhibiting MYOCD expression. Further investigation into the mechanisms by which nilotinib treatment decreases expression of ECM genes and whether these trends continue in vivo are warranted. Citation Format: Katherine Anne Johnson, Yousef Gadalla, Cheri A. Pasch, Dustin A. Deming. Nilotinib suppresses the myofibroblastic cancer-associated fibroblast phenotype. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5177.