Somatic Mutations in Nuclear and Mitochondrial Genes of Mitochondrial Proteins in Primary and Recurrent Glioblastoma
Abstract
1. Introduction
2. Results
2.1. Comparisons of Somatic mtDNA Variants in GBM-P and GBM-R Samples
2.1.1. mtDNA Variants in GBM-P Samples (Table 1)
| GBM-P | GBM-R | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene (Position) | Sequence Ontology | Nucleotide Change | Amino Acid Change | Mean VAF | In Silico Prediction | Frequency in Samples | Mean VAF | In Silico Prediction | Frequency in Samples |
| RNR2 (M:3106) | NE-CV | C/- | - | 96% | - | 10/10 | 96% | - | 9/9 |
| RNR1 (M:750) | NE-CV | A/G | - | 98% | - | 10/10 | 99% | - | 9/9 |
| ATP6 (M:8860) | MV | A/G | Thr112Ala | 100% | LB | 10/10 | 100% | LB | 9/9 |
| CYB (M:15326) | MV | A/G | Thr194Ala | 99% | - | 10/10 | 99% | - | 8/9 |
| Section between RNR1-TF genes (M:311) | US-GV | -/C | - | 52% | - | 9/10 | 51% | - | 8/9 |
| RNR2 (M:2557) | NE-CV | C/T | - | 7% | - | 5/10 | 7% | - | 5/9 |
| RNR2 (M:2523) | NE-CV | C/T | -- | 7% | - | 4/10 | |||
| Section between RNR1-TF genes (M:73) | US-GV | A/G | - | 100% | - | 4/10 | 100% | - | 4/9 |
| TF (M:621) | NE-CV | A/C | - | 5% | PB | 1/10 | |||
| CO1 (M:7356; M:7408) | MV | G/A; A/G | Val485Met; Tyr502Cys | 6%; 6% | LB | 1/10; 1/10 | |||
| Section between ATP6-ATP8 genes (M:8557) | MV, SV | G/A | Ala11Thr; Leu64= | 97% | LB | 1/10 | 97% | LB | 1/9 |
| CYB (M:15442) | SV | A/G | Leu232= | 99% | LB | 1/10 | |||
| CO2 (M:7830) | MV | A/G | Arg82His | 100% | LB | 1/10 | 100% | LB | 1/9 |
| TV (M:1619) | NE-CV | C/T | - | 10% | LB | 1/10 | |||
| ATP8 (M:8381) | MV | A/G | Thr6Ala | 97% | LB | 1/10 | 97% | LB | 1/9 |
| ND2 (M:5298) | MV | A/G | Ile277Val | 98% | LB | 1/10 | 97% | LB | 1/9 |
| ND2 (M:4794) | MV | G/A | Ala109Thr | 14% | LB | 1/9 | |||
| TI (M:4268) | NE-CV | T/C | - | 25% | PP | 1/9 | |||
| ND5 (M:13028) | MV | C/T | Pro231Leu | 9% | PP | 1/9 | |||
| ND1 (M:3502) | MV | T/C | Ser66Pro | 12% | LP | 1/9 | |||
2.1.2. mtDNA Variants in GBM-R Samples (Table 1)
2.1.3. Comparison of mtDNA Variant Numbers in GBM-P and GBM-R Samples (Table 2)
| Variant Number Change in GBM-P Versus GBM-R Samples | ||
|---|---|---|
| GBM-P | GBM-R | Observed trend |
| First pair | ||
| 27 | 9 | Decrease |
| Second pair | ||
| 9 | 10 | Increase |
| Third pair | ||
| 23 | 8 | Decrease |
| Fourth pair | ||
| 17 | 13 | Decrease |
| Fifth pair | ||
| 9 | 9 | Equal |
| Sixth pair | ||
| 18 | 20 | Increase |
| Seventh pair | ||
| 6 | 0 | Excluded |
| Eight pair | ||
| 14 | 15 | Increase |
| Ninth pair | ||
| 8 | 12 | Increase |
| Tenth pair | ||
| 5 | 8 | Increase |
2.2. Pathogenic and Likely Pathogenic Somatic Variants in Nuclear-Encoded Genes of Mitochondrial Proteins in GBM-P and GBM-R (Table 3)
| GBM-P | GBM-R | ||||||
|---|---|---|---|---|---|---|---|
| VAF | Gene | P/LP | Variant | VAF | Gene | P/LP | Variant |
| First pair | |||||||
| 15% | SLC25A13 | P | c.111del; p.Asn38fs | ||||
| 15% | FA2H | P | c.117C>A; p.Phe39Leu | ||||
| Second pair | |||||||
| NA | |||||||
| Third pair | |||||||
| 32% | WFS1 | P | c.2254G>T; p.Glu752Ter | ||||
| 26% | SDHAF2 | LP | c.260+1G>C; p.? | ||||
| Fourth pair | |||||||
| 20% | SEPSECS | P | c.1655_1656del; p.Lys552fs | ||||
| 17% | SLC22A5 | LP | c.914C>T; p.Pro305Leu | ||||
| 29% | SLC22A5 | P | c.1658+1G>A; p.? | ||||
| 22% | PLA2G6 | LP | c.120-1G>T; p.? | ||||
| Fifth pair | |||||||
| 17% | SLC22A5 | LP | c.914C>T; p.Pro305Leu | 39% | SDHB | P | c.441T>G; p.Tyr147Ter |
| 28% | DIAPH1 | P | c.3139C>T; p.Gln1047Ter | ||||
| 23% | POLG | LP | c.2841A>C; p.Lys947Asn | ||||
| 16% | COQ8B | P | c.835C>T; p.Arg279Trp | ||||
| Sixth pair | |||||||
| 22% | CPT2 | P | c.215T>A; p.Leu72Ter | ||||
| 19% | AARS2 | P | c.595C>T; p.Arg199Cys | ||||
| 25% | PDHA1 | P | c.904C>T; p.Arg302Cys | ||||
| Seventh pair | |||||||
| 34% | BCS1L | P | c.826C>T; p.Gln276Ter | 31% | SLC25A4 | P | c.111+1G>A; p.? |
| 75% | SLC52A2 | P | c.1258G>A; p.Ala420Thr | ||||
| 48% | STXBP1 | P | c.1419+5G>A; p.? | ||||
| 26% | TWNK | LP | c.1232C>T; p.Thr411Met | ||||
| Eight pair | |||||||
| 15% | FH | P | c.1391-1G>T; p.? | 32% | PC | LP | c.1826-1G>C; p.? |
| 15% | FH | P | c.1391-2A>G; p.? | 24% | POLG | P | c.178C>T; p.Gln60Ter |
| 17% | ACADS | LP | c.1086+1G>A; p.? | 19% | ACADVL | LP | c.740A>C; p.Lys247Thr |
| 26% | LONP1 | LP | c.880C>T; p.Arg294Trp | ||||
| Ninth pair | |||||||
| 31% | MFN2 | P | c.1127T>G; p.Met376Arg | 33% | CPT1A | P | c.1367C>A; p.Ser456Ter |
| 59% | SDHB | LP | c.540+1G>A; p.? | 35% | TANGO2 | P | c.262C>T; p.Arg88Ter |
| 34% | CYP24A1 | P | c.1186C>T; p.Arg396Trp | ||||
| Tenth pair | |||||||
| 24% | GDAP1 | LP | c.-67A>G; p.Lys39Arg | ||||
| 16% | GDAP1 | LP | c.117+1G>A; p.? | ||||
| GBM Designation | Gender | Age at Onset (Years) | Treatment | T1–T2 (Weeks) | Overall Survival (Weeks) |
|---|---|---|---|---|---|
| GBM 1 | man | 61 | Surgery + irradiation + TMZ | 49 | 60 |
| GBM 2 | man | 39 | Surgery + irradiation + TMZ | 40 | - |
| GBM 3 | man | 62 | Surgery + irradiation + TMZ | 58 | 62 |
| GBM 4 | woman | 61 | Surgery + irradiation + TMZ | 31 | 54 |
| GBM 5 | man | 66 | Surgery + irradiation + TMZ | 56 | - |
| GBM 6 | woman | 53 | Surgery + irradiation + TMZ | 55 | 69 |
| GBM 7 | woman | 63 | Surgery + irradiation | 30 | 43 |
| GBM 8 | woman | 45 | Surgery + irradiation + TMZ | 143 | 170 |
| GBM 9 | man | 43 | Surgery + irradiation + TMZ | 135 | 192 |
| GBM 10 | woman | 56 | AVAGLIO clinical study (STUPP + bevacizumab/placebo) | 199 | 288 |
3. Discussion
4. Materials and Methods
4.1. Subjects of the Study and Samples
4.2. Sample Preparation and Quality Check
4.3. Library Preparation
4.4. Bioinformatics for the Evaluation of mtDNA and nDNA Sequences
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
| ACMG | American College of Medical Genetics and Genomics |
| BAD | BCL2-associated agonist of cell death |
| BAX | BCL2-associated X protein |
| Bcl-2 | B-cell lymphoma 2 |
| Bcl-xL | B-cell lymphoma-extra large |
| CMA | chaperone-mediated autophagy |
| CNV | central nervous system |
| CNV | copy number variations |
| ER | endoplasmic reticulum |
| ETC | electron transport chain |
| FADH | flavin adenine dinucleotide |
| FFPE | formalin-fixed, paraffin-embedded |
| GBM | glioblastoma |
| GBM-P | primary glioblastoma |
| GBM-R | recurrent glioblastoma |
| ICGC | International Cancer Genome Consortium |
| IDH | isocitrate dehydrogenase |
| LP | likely pathogenic |
| mtDNA | mitochondrial DNA |
| NADH | nicotinamide adenine dinucleotide |
| NGS | next-generation sequencing |
| OXPHOS | oxidative phosphorylation |
| P | pathogenic |
| rCRS | revised Cambridge Reference Sequence |
| ROS | reactive oxygen species |
| rRNA | ribosomal RNA |
| SNV | included single nucleotide variant |
| TCA | tricarboxylic acid |
| TCGA | The Cancer Genome Atlas |
| UP | University of Pecs |
| VAF | variant allele frequency |
| WHO | World Health Organization |
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Tompa, M.; Galik, B.; Urban, P.; Gyenesei, A.; Kalman, B. Somatic Mutations in Nuclear and Mitochondrial Genes of Mitochondrial Proteins in Primary and Recurrent Glioblastoma. Int. J. Mol. Sci. 2026, 27, 1773. https://doi.org/10.3390/ijms27041773
Tompa M, Galik B, Urban P, Gyenesei A, Kalman B. Somatic Mutations in Nuclear and Mitochondrial Genes of Mitochondrial Proteins in Primary and Recurrent Glioblastoma. International Journal of Molecular Sciences. 2026; 27(4):1773. https://doi.org/10.3390/ijms27041773
Chicago/Turabian StyleTompa, Marton, Bence Galik, Peter Urban, Attila Gyenesei, and Bernadette Kalman. 2026. "Somatic Mutations in Nuclear and Mitochondrial Genes of Mitochondrial Proteins in Primary and Recurrent Glioblastoma" International Journal of Molecular Sciences 27, no. 4: 1773. https://doi.org/10.3390/ijms27041773
APA StyleTompa, M., Galik, B., Urban, P., Gyenesei, A., & Kalman, B. (2026). Somatic Mutations in Nuclear and Mitochondrial Genes of Mitochondrial Proteins in Primary and Recurrent Glioblastoma. International Journal of Molecular Sciences, 27(4), 1773. https://doi.org/10.3390/ijms27041773

