Abstract 313: Mechanisms of oncogenic tyrosine kinase fusion formation and selection in human cancers
Authors: Cheong Taek-Chin , Jang Ahram , Wang Qi , Leonardi Giulia C. , Lehtinen Maria K. , Harris Marian H. , Chiarle Roberto 
Published: April 2023

Abstract
Introduction: Tyrosine kinase (TK) fusions are common events in the development of resistance to targeted therapy for non-small cell lung cancer (NSCLC) and others. The mechanisms by which recurrent breakpoints are generated in solid tumors and by which they are selected are unclear. APOBEC3 proteins are the main factors for mutations in solid cancers and the mutagenic activity of APOBEC3 can activate the DNA damage response by contributing to double-strand break (DSB) formation. However, the possibility that APOBEC3 proteins could induce chromosomal translocations in solid tumors has not been investigated. In addition, mechanistic explanations on how recurrent chromosomal translocation occur in lung cancer and solid tumors in precise genomic breakpoints and with specific partners are lacking. In this work, we present a newly developed functionally active chromosomal translocation sequencing (FACTS) approach to provide insights on the mechanisms that determine the selection of oncogenic fusions in human cancers.
Methods: We applied FACTS to lung cells to map genome-wide translocations when DNA DSB is introduced in TK genes by the CRISPR/Cas9 system. We generated genomic maps of DNA breakpoints joining to anaplastic lymphoma kinase (ALK) before and after selection by high-throughput genome-wide translocation sequencing (HTGTS). We tested the effect of APOBEC3 proteins in an overexpression system or in an all seven APOBEC3 gene knockout lung cells by FACTS.
Results: Overexpression of APOBEC3 proteins significantly increased the formation of functional fusions compared to control cells. In addition, deletion of APOBEC3 genes significantly decreased the formation of functional fusions compared to APOBEC3 wild-type cells. With the FACTS data and bioinformatics analyses, we found that gene expression rather than locus accessibility dictates the selection of TK fusions and that TK fusions are likely selected from a pool of translocations occurring at the right position in transcribe genes. In addition, we found that active transcription in silent genes was sufficient to introduce the spontaneous formation of functional fusions. By using HTGTS approach, we found that breakpoints before selection did not show a preferential strand bias, but after selection the breakpoints showed a strong bias. By comparing oncogenic potential of EML4-ALK fusion variants, we found that protein stability, but not subcellular localization, is key to determining the exon usage of EML-ALK fusions. In addition, we revealed that the selection of fusion partners for each TK is more likely dictated by protein stability rather than by mRNA expression.
Conclusion: FACTS allows rapid and comprehensive mapping of functional chromosomal translocations and provides insights into the mechanisms of their formation and selection. The FACTS approach could be used to predict the oncogenic activity of fusion proteins to guide clinical decisions.
Citation Format: Taek-Chin Cheong, Ahram Jang, Qi Wang, Giulia C. Leonardi, Maria K. Lehtinen, Marian H. Harris, Roberto Chiarle. Mechanisms of oncogenic tyrosine kinase fusion formation and selection in human cancers [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 313.