Detection of BRAF splicing variants in plasma-derived cell-free nucleic acids and extracellular vesicles of melanoma patients failing targeted therapy therapies

Authors

Michael E. Clark, Edith Cowan UniversityFollow
Helen Rizos
Michelle Pereira, Edith Cowan UniversityFollow
Ashleigh McEvoy, Edith Cowan UniversityFollow
Gabriela Marsavela, Edith Cowan UniversityFollow
Leslie Calapre, Edith Cowan UniversityFollow
Katie Meehan
Olivia Ruhen
Muhammad A. Khattak, Edith Cowan UniversityFollow
Tarek M. Meniawy, Edith Cowan UniversityFollow
Georgina Long
Matteo S. Carlino
Alexander M. Menzies
Michael Millward, Edith Cowan UniversityFollow
Melanie Ziman, Edith Cowan UniversityFollow
Elin S. Gray, Edith Cowan UniversityFollow

Author Identifier

Michael Clark

https://orcid.org/0000-0002-9748-5221

Ashleigh McEvoy

https://orcid.org/0000-0001-5692-1317

Gabriela Marsavela

https://orcid.org/0000-0002-0487-3963

Leslie Calapre

https://orcid.org/0000-0001-7595-6523

Tarek Meniawy

https://orcid.org/0000-0002-1457-6137

Muhammad Adnan Khattak

https://orcid.org/0000-0002-4633-3818

Melanie Ziman

https://orcid.org/0000-0001-7527-3538

Elin Gray

https://orcid.org/0000-0002-8613-3570

Document Type

Journal Article

Publication Title

Oncotarget

Publisher

Impact Journals

School

School of Medical and Health Sciences

RAS ID

32389

Funders

Edith Cowan University - Open Access Support Scheme 2020

Comments

Clark, M. E., Rizos, H., Pereira, M. R., McEvoy, A. C., Marsavela, G., Calapre, L., ... & Long, G. V. (2020). Detection of BRAF splicing variants in plasma-derived cell-free nucleic acids and extracellular vesicles of melanoma patients failing targeted therapy therapies. Oncotarget, 11(44), 4016-4027. https://doi.org/10.18632/oncotarget.27790

Abstract

The analysis of plasma circulating tumour nucleic acids provides a non-invasive approach to assess disease burden and the genetic evolution of tumours in response to therapy. BRAF splicing variants are known to confer melanoma resistance to BRAF inhibitors. We developed a test to screen cell-free RNA (cfRNA) for the presence of BRAF splicing variants. Custom droplet digital PCR assays were designed for the detection of BRAF splicing variants p61, p55, p48 and p41 and then validated using RNA from cell lines carrying these variants. Evaluation of plasma from patients with reported objective response to BRAF/MEK inhibition followed by disease progression was revealed by increased circulating tumour DNA (ctDNA) in 24 of 38 cases at the time of relapse. Circulating BRAF splicing variants were detected in cfRNA from 3 of these 38 patients; two patients carried the BRAF p61 variant and one the p55 variant. In all three cases the presence of the splicing variant was apparent only at the time of progressive disease. BRAF p61 was also detectable in plasma of one of four patients with confirmed BRAF splicing variants in their progressing tumours. Isolation and analysis of RNA from extracellular vesicles (EV) from resistant cell lines and patient plasma demonstrated that BRAF splicing variants are associated with EVs. These findings indicate that in addition to plasma ctDNA, RNA carried by EVs can provide important tumour specific information.

DOI

10.18632/oncotarget.27790

Related Publications

Clark, M. E. (2021). Unravelling the potential applications of extracellular vesicles for the clinical management of melanoma patients. https://ro.ecu.edu.au/theses/2485

Creative Commons License

This work is licensed under a Creative Commons Attribution 3.0 License.