Background
Methods
Patient selection
Mitochondrial genomic sequencing
Next-generation sequencing data analysis
Sequence kernel association test (SKAT) analysis
Functional annotation of nonsynonymous alleles in protein-coding genes
Functional annotation of alleles in transfer RNA (tRNA) genes
Validation of selected alleles detected by next-generation sequencing
Heteroplasmic fraction (HF) calculation
Statistical analyses
Results
Spectrum of mitochondrial genome mutant alleles
Mitochondrial mutant allele burdens in patients with gout and non-gout controls
Mitochondrial alleles by allele groups
Gene | Group 1 | Group 2 | Group 3 | ||||
---|---|---|---|---|---|---|---|
Gout n (%) | Non-gout n (%) |
P
| Gout n (%) |
P
| Non-gout n (%) |
P
| |
MT-ATP6
| 40 (76.92) | 69 (66.35) | 0.175 | 10 (19.23) | 9.03 × 10−6 | 25 (24.04) | 1.14 × 10−4 |
MT-ATP8
| 4 (7.69) | 12 (11.54) | 0.455 | 2 (3.85) | 1.10 × 10−1 | 12 (11.54) | 8.86 × 10−3 |
MT-CO1
| 26 (50.00) | 48 (46.15) | 0.650 | 14 (26.92) | 5.56 × 10−8 | 39 (37.50) | 3.41 × 10−7 |
MT-CO2
| 14 (26.92) | 20 (19.23) | 0.273 | 12 (23.08) | 7.34 × 10−7 | 20 (19.23) | 7.07 × 10−4 |
MT-CO3
| 42 (80.77) | 78 (75.00) | 0.420 | 6 (11.54) | 1.12 × 10−3 | 17 (16.35) | 2.01 × 10− 3 |
MT-CYB
| 52 (100.00) | 104 (100.00) | 1.000 | 10 (19.23) | 9.03 × 10−6 | 40 (38.46) | 2.15 × 10−7 |
MT-ND1
| 33 (63.46) | 57 (54.81) | 0.302 | 9 (17.31) | 3.09 × 10−5 | 19 (18.27) | 1.01 × 10−3 |
MT-ND2
| 37 (71.15) | 69 (66.35) | 0.544 | 8 (15.38) | 1.04 × 10−4 | 22 (21.15) | 3.46 × 10− 4 |
MT-ND3
| 46 (88.46) | 88 (84.62) | 0.515 | 2 (3.85) | 1.10 × 10−1 | 17 (16.35) | 2.01 × 10−3 |
MT-ND4
| 52 (100.00) | 104 (100.00) | 1.000 | 7 (13.46) | 3.44 × 10−2 | 30 (28.85) | 1.64 × 10−5 |
MT-ND4L
| 11 (21.15) | 19 (18.27) | 0.667 | 0 (0.00) | 1.000 | 9 (8.65) | 2.98× 10−2 |
MT-ND5
| 46 (88.46) | 99 (95.19) | 0.182 | 15 (28.85) | 8.35 × 10−9 | 32 (30.77) | 7.24 × 10−6 |
MT-ND6
| 31 (59.62) | 57 (54.81) | 0.568 | 9 (17.31) | 3.09 × 10−5 | 18 (17.31) | 1.42 × 10−3 |
MT-RNR1
| 35 (67.31) | 74 (71.15) | 0.622 | 4 (7.69) | 1.14 × 10−2 | 20 (19.23) | 7.07 × 10−4 |
MT-RNR2
| 52 (100.00) | 104 (100.00) | 1.000 | 5 (9.62) | 3.60 × 10−3 | 25 (24.04) | 1.14 × 10−4 |
MT-TRNA
a
| 26 (50.00) | 54 (51.92) | 0.821 | 18 (34.62) | 1.78 × 10−10 | 28 (26.92) | 3.62 × 10−5 |
Association of mitochondrial genes with gout
Functional annotation of positively associated MT-CO3 alleles
Gene | Position | Mutation | Amino acid change | HF (%) | Impacta | Published disease association |
---|---|---|---|---|---|---|
MT-CO3
| 9438 | G➔A | G78S | 42.05 | ** | LHON [26] |
MT-CO3
| 9490 | C➔T | A95V | 99.23 | ** | |
MT-CO3
| 9755 | G➔C | E183D | 99.59 | * | |
MT-CO3
| 9856 | T➔C | I217T | 99.71 | ** | LVNC [27] |
MT-CO3
b
| 9957 | T➔C | F251 L | 99.35 59.92 | ** |
Functional annotation of positively associated MT-TA, MT-TC, MT-TH, MT-TQ, MT-TS2, MT-TT, and MT-TW alleles
Gene | Position | Mutation | Locationa | Nucleotide numberb | HF (%) | Absent in control | Fre (%)c | CI (%) | Alterationd | Published disease association |
---|---|---|---|---|---|---|---|---|---|---|
MT-TQ
e
| 4386 | T➔C | D-loop | 15 | 99.8599.61 | + | 1.89 | 64.71 | ||
MT-TW
| 5528 | T➔C | D-loop | 18 | 70.53 | + | 0.00 | 11.76 | ||
MT-TW
| 5557 | T➔C | V region | 48 | 80.18 | + | 0.15 | 47.06 | ||
MT-TW
| 5563 | G➔A | T-loop | 55 | 51.92 | + | 0.30 | 11.76 | ||
MT-TA
| 5601 | C➔T | T-loop | 59 | 77.10 | + | 1.37 | 47.06 | ||
MT-TA
| 5628 | T➔C | AC stem | 31 | 99.61 | + | 0.15 | 94.12 | + | |
MT-TC
| 5783 | G➔A | T-stem | 50 | 99.58 | + | 0.04 | 94.12 | + | |
MT-TC
| 5814 | T→C | D-stem | 13 | 59.30 | + | 0.37 | 88.24 | + | Encephalomyopathy [42] |
MT-TH
| 12,172 | A→G | AC loop | 38 | 99.67 | + | 1.15 | 88.24 | + | |
MT-TH
| 12,178 | C→T | V region | 44 | 71.81 | + | 0.00 | 64.71 | + | |
MT-TS2
| 12,234 | A→G | AC stem | 42 | 55.90 | + | 0.30 | 58.82 | ||
MT-TS2
| 12,239 | C→T | V region | 48 | 66.70 | + | 0.96 | 64.71 | ||
MT-TS2
| 12,248 | A→G | T-loop | 57 | 99.59 | + | 0.11 | 100.00 | ||
MT-TT
| 15,894 | G→A | ACC stem | 7 | 99.52 | + | 0.04 | 88.24 | + | |
MT-TT
| 15,940 | T→C | T-loop | 59 | 65.31 | + | 0.11 | 41.18 |
Validation of selected alleles detected by next-generation sequencing
Association between mitochondrial potentially pathogenic alleles and patient phenotypes
Variables | Potentially pathogenic MT-CO3 alleles |
P
| |
---|---|---|---|
+ | – | ||
Number (percentage) | 4 (7.69) | 48 (92.31) | |
Age (years; mean ± SD) | 50.00 ± 12.99 | 51.73 ± 10.77 | 0.798 |
Uric acid (mg/dl; mean ± SD) | 6.60 ± 2.07 | 7.71 ± 1.63 | 0.236 |
BMI (kg/m2; mean ± SD) | 23.87 ± 2.09 | 26.70 ± 3.74 | 0.118 |
Diabetes mellitus (n (%)) | 1 (25.00) | 3 (6.25) | 0.281 |
Fasting glucose (mg/dl; mean ± SD) | 98.50 ± 14.89 | 99.90 ± 19.31 | 0.973 |
Total cholesterol (mg/dl; mean ± SD) | 192.20 ± 45.17 | 191.00 ± 39.92 | 0.693 |
HDL (mg/dl; mean ± SD) | 61.00 ± 12.41 | 47.17 ± 12.60 | 0.034 |
LDL (mg/dl; mean ± SD) | 119.30 ± 34.81 | 119.50 ± 38.81 | 0.918 |
Triglycerides (mg/dl; mean ± SD) | 137.80 ± 86.89 | 159.10 ± 100.30 | 0.706 |