Mitochondrial DNA point mutations and relative copy number in 1363 disease and control human brains

Abstract

Mitochondria play a key role in common neurodegenerative diseases and contain their own genome: mtDNA. Common inherited polymorphic variants of mtDNA have been associated with several neurodegenerative diseases, and somatic deletions of mtDNA have been found in affected brain regions. However, there are conflicting reports describing the role of rare inherited variants and somatic point mutations in neurodegenerative disorders, and recent evidence also implicates mtDNA levels. To address these issues we studied 1363 post mortem human brains with a histopathological diagnosis of Parkinson's disease (PD), Alzheimer's disease (AD), Frontotemporal dementia - Amyotrophic Lateral Sclerosis (FTD-ALS), Creutzfeldt Jacob disease (CJD), and healthy controls. We obtained high-depth whole mitochondrial genome sequences using off target reads from whole exome sequencing to determine the association of mtDNA variation with the development and progression of disease, and to better understand the development of mtDNA mutations and copy number in the aging brain. With this approach, we found a surprisingly high frequency of heteroplasmic mtDNA variants in 32.3% of subjects. However, we found no evidence of an association between rare inherited variants of mtDNA or mtDNA heteroplasmy and disease. In contrast, we observed a reduction in the amount of mtDNA copy in both AD and CJD. Based on these findings, single nucleotide variants of mtDNA are unlikely to play a major role in the pathogenesis of these neurodegenerative diseases, but mtDNA levels merit further investigation.

Keywords: Dementia; Mitochondrial; Mutation; Neurodegeneration; Somatic.

Fig. 1

Phylogenetic tree of the 1363 mtDNA sequenced derived from the MRC Brain Tissue Resource. Major haplogroups are shown

Fig. 2

Circos plot summarizing all of the genetic data from 1363 sequences derived form the MRC Brain Tissue Resource. From outside the circle to inside: (1) mtDNA position, (2) mtDNA genes, (3) mtDNA Complex, (4) frequency of variants in 40,440 mitochondrial sequences in NCBI-GenBank, (5) mean read depth of 1363 samples per base, (6) Total variants in all 1363 samples [circles], (7) Total Rare variants in 1363 samples [triangles], (8) Total novel variants in 1363 samples [squares]. Colour code for circles (6) – (8): Red - AD, green - ALS-FTD, blue - CJD, yellow - DLB-PD, grey - others; from inner to outer, HF increasing. Key – AD –Alzheimer’s disease, CJD – Creutzfeldt Jacob Disease, DLB-PD – Dementia with Lewy Bodies or Parkinson’s disease, FTD-ALS – Frontotemporal Dementia or Amyotrophic Lateral Sclerosis

Fig. 3

The distribution and nature of major heteroplasmic mtDNA variation within 1363 cases from the MRC Brain Bank Tissue Resource. a Top left – The mean number of heteroplasmic variants per sample in each cohort. b Top right - The distribution of heteroplasmic fraction (ratio of mutant to wild-type allele) for heteroplasmic variants for each disease cohort. c Bottom left – The mean number of heteroplasmic point mutations by age for each disease cohort. d Bottom right – The mean heteroplasmic fraction by age for each disease cohort. Key – AD –Alzheimer’s disease, CJD – Creutzfeldt Jacob Disease, DLB-PD – Dementia with Lewy Bodies or Parkinson’s disease, FTD-ALS – Frontotemporal Dementia or Amyotrophic Lateral Sclerosis

Fig. 4

The relative mtDNA copy number in each disease cohort. a Top – Relative copy number of each cohort calculated as the ratio between the mean mtDNA read depth and the mean exome read depth as previously described [5]. ** (P < 0.01). b Bottom - The association between relative mtDNA copy number and age for all CJD cases (n = 182) with the Spearman Rank ρ and p-value shown. Key – AD –Alzheimer’s disease, CJD – Creutzfeldt Jacob Disease, DLB-PD – Dementia with Lewy Bodies or Parkinson’s disease, FTD-ALS – Frontotemporal Dementia or Amyotrophic Lateral Sclerosis