Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells

Abstract

Mitochondria are small organelles that play an essential role in the energy production of eukaryotic cells. Defects in their genomes are associated with diseases, such as aging and cancer. Here, we analyzed the mitochondrial genomes of 532 whole-genome sequencing samples from cancers and normal clonally expanded single cells. We show that the mitochondria of normal cells accumulate mutations with age and that most of the mitochondrial mutations found in cancer are the result of healthy mutation accumulation. We also show that the normal HSPCs of patients with leukemia have an increased mitochondrial mutation load. Finally, we show that secondary pediatric cancers and chemotherapy treatments do not impact the mitochondrial mutation load and mtDNA copy numbers of most cells, suggesting that damage to the mitochondrial genome is not a major driver for carcinogenesis. Overall, these findings may contribute to our understanding of mitochondrial genomes and their role in cancer.

Keywords: Cancer; Genomics; Stem cells research.

Graphical abstract

Figure 1

Accumulation of mitochondrial substitutions in normal stem cells with age (A)The mitochondrial read coverage is shown per donor, with each dot showing a single sample (536 samples; 89 donors). The color of the dots indicates the sample group. Samples below the dashed red line were removed for having a low mitochondrial read coverage. Donors were ordered on the x axis based on the sample groups of their samples. (B–D) The number of mitochondrial base substitutions per clone is plotted against the donor age for normal HSPCS (blood stem cells) (B) (33 mutations; 62 samples; 14 donors), normal colon stem cells (SCs) (C) (26 mutations; 19 samples; 5 donors), and normal intestinal stem cells (D) (20 mutations; 22 samples; 10 donors). Each clone is a clonally expanded single cell. p values show the significance of the age of the donor on the number of substitutions (generalized linear model). The red line indicates the mean fitted number of mutations at that age. The dark gray background shows the 95% confidence interval of the model, whereas the light gray background shows the 95% prediction interval. The prediction intervals show the predicted intervals that contain the mutation load of 95% of all cells in the population. A small amount of jitter was added to the dots to prevent them from completely overlapping. The color of the dots indicates the donor.

Figure 2

Effect of age and cell type on mtDNA copy number (A–C) The mtDNA copy number is plotted against the donor age for normal HSPCs (A) (62 samples; 14 donors), normal colon stem cells (B) (19 samples; 5 donors), and normal intestinal stem cells (C) (22 samples; 10 donors). p values show the significance of the age of the donor on the mtDNA copy number (linear mixed-effects model). The red line indicates the mean fitted number of mutations at that age. The dark gray background shows the 95% confidence interval of the model, whereas the light gray background shows the 95% prediction interval. The prediction intervals show the predicted intervals that contain the mutation load of 95% of all cells in the population. A small amount of jitter was added to the dots to prevent them from completely overlapping. The color of the dots indicates the donor.

Figure 3

Comparison of mitochondrial substitutions between normal stem cells and cancers (A) The number of mitochondrial base substitutions per clone is plotted against the donor age for normal HSPCs from healthy donors (33 mutations; 62 samples; 14 donors) and blood cancers (418 mutations; 264 samples; 264 donors). The p value shows the significance of the difference in the number of substitutions between normal HSPCs and blood cancer (generalized linear model). The color of the dots and lines indicates the sample type. The trend lines indicate the mean fitted number of mutations at that age and sample type. The shaded backgrounds show the 95% confidence intervals of the model. A small amount of jitter was added to the dots to prevent them from completely overlapping. (B and C) 7-Spectrum of mitochondrial base substitutions for HSPCs from healthy donors (33 mutations; 62 samples; 14 donors) (B) and blood cancers (418 mutations; 264 samples; 264 donors) (C). A spectrum separated into light and heavy strands is also shown. The total number of base substitutions is indicated. (D) The number of mitochondrial base substitutions per clone is plotted against the donor age for normal colon stem cells (26 mutations; 19 samples; 5 donors) and colon cancers (224 mutations; 59 samples; 59 donors). The p value shows the significance of the difference in the number of substitutions between normal colon and colon cancer (generalized linear model). The color of the dots and lines indicates the sample type. The trend lines indicate the mean fitted number of mutations at that age and sample type. The shaded backgrounds show the 95% confidence intervals of the model. A small amount of jitter was added to the dots to prevent them from completely overlapping. (E and F) 7-Spectrum of mitochondrial base substitutions for normal colon stem cells (24 mutations; 19 samples; 5 donors) (E) and colon cancers (224 mutations; 59 samples; 59 donors) (F). A spectrum separated into light and heavy strands is also shown. The total number of base substitutions is indicated.

Figure 4

The effects of cancer and treatment on mitochondrial genomes (A) The number of mitochondrial base substitutions per clone is plotted against the donor age for HSPCs from healthy donors (33 mutations; 62 samples; 14 donors) and HSPCs at either diagnosis, follow-up during remission, or a diagnosis of a genetically unrelated secondary cancer (144 mutations; 202 samples; 28 donors). The p values show the significance of the difference in the number of substitutions between HSPCs from healthy donors and HSPCs from patients with leukemia (generalized linear model). The color of the dots and lines indicates the sample type. The trend lines indicate the mean fitted number of mutations at that age and sample type. The shaded backgrounds show the 95% confidence intervals of the model. A small amount of jitter was added to the dots to prevent them from completely overlapping. (B) The number of mitochondrial base substitutions per clone is plotted against the donor age for HSPCs from healthy donors (33 mutations; 62 samples; 14 donors) and secondary pediatric leukemias (8 mutations; 16 samples; 16 donors). The p values show the significance of the difference in the number of substitutions between HSPCs from healthy donors and secondary leukemias that are genetically unrelated from the original cancer (generalized linear model). A small amount of jitter was added to the dots to prevent them from completely overlapping. (C) The number of mitochondrial base substitutions per clone is shown for clonally expanded cord blood cells from healthy donors treated with different chemotherapies and X-ray. The color of the dots indicates the donor. CTRL = Control (2 mutations; 19 samples; 6 donors), CAR = carboplatin (0 mutations; 3 samples; 1 donor), CIS = cisplatin (3 mutations; 4 samples; 2 donors), CYTA = Cytarabine (3 mutations; 6 samples; 2 donors), DOX = Doxorubucin (2 mutations; 5 samples; 2 donors), MAPH = Maphosphamide (0 mutations; 3 samples; 1 donor), RAD = X-ray (2 mutations; 9 samples; 4 donors), VINCRIS = Vincristine (0 mutations; 6 samples; 2 donors), GCV = Ganciclovir (0 mutations; 3 samples; 2 donors), FC = Foscarnet (0 mutations; 2 samples; 1 donor), GCV + FC (0 mutations; 3 samples; 1 donor). The p value shows the significance of the difference in the number of base substitutions per clone between treatments (one-way ANOVA). (D) Comparison of the mtDNA copy numbers between clonally expanded cord blood cells from healthy donors treated with different chemotherapies and X-ray. The color of the dots indicates the donor. CTRL = Control (19 samples; 6 donors), CAR = carboplatin (3 samples; 1 donor), CIS = cisplatin (4 samples; 2 donors), CYTA = Cytarabine (6 samples; 2 donors), DOX = Doxorubucin (5 samples; 2 donors), MAPH = Maphosphamide (3 samples; 1 donor), RAD = X-ray (9 samples; 4 donors), VINCRIS = Vincristine (6 samples; 2 donors), GCV = Ganciclovir (3 samples; 2 donors), FC = Foscarnet (2 samples; 1 donor), GCV + FC (3 samples; 1 donor). The p value shows the significance of the difference in the mtDNA copy numbers per clone between treatments (one-way ANOVA).