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.

Mitochondrial DNA abnormalities provide mechanistic insight and predict reactive oxygen species-stimulating drug efficacy

“…A three-dimensional (3D) protein structure mapping and analysis approach (developed and validated by Lloyd and McGeehan) [ 38 – 40 ] was used to predict the functional impact of all non-synonymous identified in mtDNA protein coding regions.…”

Mitochondrial DNA abnormalities provide mechanistic insight and predict reactive oxygen species-stimulating drug efficacy

“…Variations in the mitochondrial genome were identi ed by comparing the obtained sequences with the NCBI Human Mitochondrial Reference Sequence (NC_012920.1; https://www.ncbi.nlm.nih.gov/nuccore/251831106/) using the Nucleotide BLAST software (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Identi ed mtDNA variations were annotated and their disease association was analysed using online tools and databases including MitoWheel In silico three-dimensional protein structure mapping and analysis of variations A three-dimensional (3D) protein structure mapping and analysis approach (developed and validated by Lloyd and McGeehan) [37][38][39] was used to predict the functional impact of all non-synonymous identi ed in mtDNA protein coding regions.…”

“…In silico three-dimensional protein structure mapping and analysis of variations A three-dimensional (3D) protein structure mapping and analysis approach (developed and validated by Lloyd and McGeehan) [37][38][39] was used to predict the functional impact of all non-synonymous identi ed in mtDNA protein coding regions. Brie y, the human mtDNA-encoded protein sequences were used to identify the most homologous OXPHOS complexes I, III, IV and V available from the RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank; http://www.rcsb.org/).…”

Mitochondria Autoimmunity and MNRR1 in Breast Carcinogenesis: A Review

“…ATP synthase generates ATP against a proton gradient in response to electron transport in the mitochondria. The relevance of autoantibodies to a gene product of MT-ATP8 in BC is suggested by the study of McGeehan et al who reported mtDNA variations including MT-ATP8 in blood samples derived from a small group of women who were diagnosed with early-onset BC and later went on to develop breast to brain metastasis [41]. Further research into the significance of the autoreactivity of mitochondrial ribosomal RNA associated with the diagnosis of BC is warranted, in particular in relation to the role of small mitochondrial peptides encoded by 16S mitochondrial ribosomal RNA.…”