Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in mediating targeted therapy dosage challenges

• Published in: bioRxiv
• Main Authors: Song, Kai, Minami, Jenna K, Crosson, William P, Salazar, Jesus, Pazol, Eli, Senaratne, Niroshi T, Rao, Nagesh, Paraiso, Kim, Graeber, Thomas G
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 24.11.2021
• Subjects: Copy number; Drug addiction; Drug dosages; Drug resistance; Kinases; MEK inhibitors; Melanoma; Plasticity
• DOI: 10.1101/2021.11.23.468420

Cancer cells display two modes of focal amplifications (FAs), extrachromosomal DNA/double-minutes (ecDNA/DMs) and intrachromosomal homogenously staining regions (HSRs). Understanding the plasticity of these two modes is critical for preventing targeted therapy resistance. We developed a combined BRAF plus MEK inhibitor resistance melanoma model that bears high BRAF amplifications through both DM and HSR modes, and investigated FA dynamics in the context of drug resistance plasticity. Cells harboring FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of pre-existing subpopulations. We found that copy number plasticity is not exclusive to DMs. Single cell-derived clones with HSRs also exhibit BRAF copy number and corresponding HSR length plasticity that allows them to respond to dose reduction and recover from drug addiction. Upon kinase inhibitor escalation, we observed reproducible selection for cells with BRAF kinase domain duplications residing on DMs. In sum, the plasticity of FAs allows cancer cells to respond to drug dose changes through a myriad of mechanisms. These mechanisms include increases or decreases in DMs, shortening of HSRs, acquisition of secondary resistance mechanisms, and expression of alternative slicing oncogene variants. These results highlight the challenges in targeting the cellular vulnerabilities tied to focal amplifications. Competing Interest Statement T.G.G. reports receiving an honorarium from Amgen, having consulting and equity agreements with Auron Therapeutics, Boundless Bio, Coherus BioSciences, and Trethera Corporation. The lab of T.G.G. has a research agreement with BridgeBio Pharma, and has completed a research agreement with ImmunoActiva.