Deep sequencing reveals the mitochondrial DNA variation landscapes of breast-to-brain metastasis blood samples

Abstract

Breast-to-brain metastasis (BBM) often represents a terminal event, due to the inability of many systemic treatments to cross the blood–brain barrier (BBB), rendering the brain a sanctuary site for tumour cells. Identifying genetic variations that can predict the patients who will develop BBM would allow targeting of adjuvant treatments to reduce risk while disease bulk is minimal. Germ-line genetic variations may contribute to whether a BBM forms by influencing the primary tumour subtype that presents, or by influencing the host response to the tumour or treatment regimen, or by facilitating transition of tumour cells across the BBB and establish a viable brain metastasis. The role of mitochondrial DNA (mtDNA) variants specifically in BBM is underexplored. Consequently, using a sensitive deep sequencing approach, we characterized the mtDNA variation landscapes of blood samples derived from 13 females who were diagnosed with early-onset breast cancer and later went on to develop BBM. We also predicted the potential pathogenic significance of variations identified in all mtDNA-encoded oxidative phosphorylation (OXPHOS) proteins using 3D protein structural mapping and analysis, to identify variations worthy of follow-up. From the 70 variations found in protein coding regions, we reveal novel links between three specific mtDNA variations and altered OXPHOS structure and function in 23% of the BBM samples. Further studies are required to confirm the origin of mtDNA variations, and whether they correlate with (1) the predicted alterations in mitochondrial function and (2) increased risk of developing breast-to-brain metastasis using a much larger cohort of samples.

Keywords:

• mtDNA
• breast cancer
• breast-to-brain metastasis
• 3D protein structural mapping and analysis
• OXPHOS and long PCR

Acknowledgements

We would also like to gratefully thank John E. McGeehan for his discussion during the design of the project and comments and guidance on the structural section of this work; Geoffrey J. Pilkington and Helen L. Fillmore for the use of the Brain Tumour Research Centre facilities; Sajid Rafiq and Will Tapper for their discussions during the design of the project; and Nikki J. Graham and Lorraine T. Duncan for providing the patient blood DNA samples and associated clinical details.

Disclosure statement

The authors declare no conflict of interest. The founding sponsors had no role in the design of the study; in the collection, analyses or interpretation of data; in the writing of the manuscript; and in the decision to publish the results.

Additional information

Funding

Running costs were provided by the Institute of Biomedical and Biomolecular Science (IBBS-fund) and REM’s salary was supported by the charity Brain Tumour Research (Taylan's Project).