Identification of sequence polymorphisms in the D-loop region of mitochondrial DNA as a risk factor for lung cancer

Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses

Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.

Molecular fingerprints of nuclear genome and mitochondrial genome for early diagnosis of lung adenocarcinoma

BACKGROUND

Lung adenocarcinoma (LUAD) is the most prevalent subtype of lung cancer with high morbidity and mortality rates. Due to the heterogeneity of LUAD, its characteristics remain poorly understood. Exploring the clinical and molecular characteristics of LUAD is challenging but vital for early diagnosis.

METHODS

This observational and validation study enrolled 80 patients and 13 healthy controls. Nuclear and mtDNA-captured sequencings were performed.

RESULTS

This study identified a spectrum of nuclear and mitochondrial genome mutations in early-stage lung adenocarcinoma and explored their association with diagnosis. The correlation coefficient for somatic mutations in cfDNA and patient-matched tumor tissues was high in nuclear and mitochondrial genomes. The mutation number of highly mutated genes was evaluated, and the Least Absolute Shrinkage and Selection Operator (LASSO) established a diagnostic model. Receiver operating characteristic (ROC) curve analysis explored the diagnostic ability of the two panels. All models were verified in the testing cohort, and the mtDNA panel demonstrated excellent performance. This study identified somatic mutations in the nuclear and mitochondrial genomes, and detecting mutations in cfDNA displayed good diagnostic performance for early-stage LUAD. Moreover, detecting somatic mutations in the mitochondria may be a better tool for diagnosing early-stage LUAD.

CONCLUSIONS

This study identified specific and sensitive diagnostic biomarkers for early-stage LUAD by focusing on nuclear and mitochondrial genome mutations. This also further developed an early-stage LUAD-specific mutation gene panel for clinical utility. This study established a foundation for further investigation of LUAD molecular pathogenesis.

Variants in the Control Region of Mitochondrial Genome Associated with type 2 Diabetes in a Cohort of Mexican Mestizos

BACKGROUND

According to the International Diabetes Federation, Mexico is seventh place in the prevalence of type 2 diabetes (T2D) worldwide. Mitochondrial DNA variant association studies in multifactorial diseases like T2D are scarce in Mexican populations.

AIM OF THE STUDY

The objective of this study was to analyze the association between 18 variants in the mtDNA control region and T2D and related metabolic traits in a Mexican mestizo population from Mexico City.

METHODS

This study included 1001 participants divided into 477 cases with T2D and 524 healthy controls aged between 42 and 62 years and 18 mtDNA variants with frequencies >15%.

RESULTS

Association analyses matched by age and sex showed differences in the distribution between cases and controls for variants m.315_316insC (p = 1.18 × 10^-6), m.489T>C (p = 0.009), m.16362T>C (p = 0.001), and m.16519T>C (p = 0.004). The associations between T2D and variants m.315_316ins (OR = 6.13, CI = 3.42-10.97, p = 1.97 × 10^-6), m.489T>C (OR = 1.45, CI = 1.00-2.11, p = 0.006), m.16362T>C (OR = 2.17, CI = 1.57-3.00, p = 0.001), and m.16519T>C (OR = 1.69, CI = 1.23-2.33, p = 0.006) were significant after performing logistic regression models adjusted for age, sex, and diastolic blood pressure. Metabolic traits in the control group through linear regressions, adjusted for age, sex and BMI, and corrected for multiple comparisons showed nominal association between glucose and variants m.263A>G (p <0.050), m.16183A>C (p <0.010), m.16189T>C (p <0.020), and m.16223C>T (p <0.024); triglycerides, and cholesterol and variant m.309_310insC (p <0.010 and p <0.050 respectively); urea, and creatinine, and variant m.315_316insC (p <0.007, and p <0.004 respectively); diastolic blood pressure and variants m.235A>G (p <0.016), m.263A>G (p <0.013), m.315_316insC (p <0.043), and m.16111C>T (p <0.022).

CONCLUSION

These results demonstrate a strong association between variant m.315_316insC and T2D and a nominal association with T2D traits.

The SNPs of mitochondrial DNA displacement loop region and mitochondrial DNA copy number associated with risk of polymyositis and dermatomyositis

Oxidative damage-induced mitochondrial dysfunction may activate muscle catabolism and autophagy pathways to initiate muscle weakening in idiopathic inflammatory myopathies (IIMs). In this study, Single nucleotide polymorphisms (SNPs) in the mitochondrial displacement loop (D-loop) and mitochondrial DNA (mtDNA) copy number were assessed and their association with the risk of polymyositis and dermatomyositis (PM/DM) was evaluated. Excessive D-loop SNPs (8.779 ± 1.912 vs. 7.972 ± 1.903, p = 0.004) correlated positively with mtDNA copy number (0.602 ± 0.457 vs. 0.300 ± 0.118, p < 0.001). Compared with that of the controls, the mtDNA of PM/DM patients showed D-loop SNP accumulation. In addition, the distribution frequencies of 16304C (p = 0.047) and 16519C (p = 0.043) were significantly higher in the patients with PM/DM. Subsequent analysis showed that reactive oxygen species (ROS) generation was increased in PM/DM patients compared with that in the controls (18,477.756 ± 13,574.916 vs. 14,484.191 ± 5703.097, p = 0.012). Further analysis showed that the PM/DM risk-related allele 16304C was significantly associated with lower IL-4 levels (p = 0.021), while 16519C had a trend to be associated with higher IL-2 expression (p = 0.064). The allele 16519C was associated with a positive antinuclear antibody (ANA) status in PM/DM patients (p = 0.011). Our findings suggest that mitochondrial D-loop SNPs could be potential biomarkers for PM/DM risk and these SNPs associated with cytokine expression may be involved in the development of PM/DM. Further, mtDNA copy number-mediated mitochondrial dysfunction may precede the onset of PM/DM.

Mitochondrial DNA sequence variation and risk of glioma

BACKGROUND

Malignant gliomas are the most common primary adult brain tumors, with a poor prognosis and ill-defined etiology. Mitochondrial DNA (mtDNA) sequence variation has been linked with certain cancers; however, research on glioma is lacking.

METHODS

We examined the association of common (minor allele frequency ≥ 5%) germline mtDNA variants and haplogroups with glioma risk in 1,566 glioma cases and 1,017 controls from a US case-control study, and 425 glioma cases and 1,534 matched controls from the UK Biobank cohort (UKB). DNA samples were genotyped using the UK Biobank array that included a set of common and rare mtDNA variants. Risk associations were examined separately for glioblastoma (GBM) and lower grade tumors (non-GBM).

RESULTS

In the US study, haplogroup W was inversely associated with glioma when compared with haplogroup H (OR = 0.43, 95%CI: 0.23-0.79); this association was not demonstrated in the UKB (OR = 1.07, 95%CI: 0.47-2.43). In the UKB, the variant m.3010G > A was significantly associated with GBM (OR = 1.32; 95%CI: 1.01-1.73; p = 0.04), but not non-GBM (1.23; 95%CI: 0.78-1.95; p = 0.38); no similar association was observed in the US study. In the US study, the variant m.14798 T > C, was significantly associated with non-GBM (OR = 0.72; 95%CI: 0.53-0.99), but not GBM (OR = 0.86; 95%CI: 0.66-1.11), whereas in the UKB, a positive association was observed between this variant and GBM (OR = 1.46; 95%CI: 1.06-2.02) but not non-GBM (OR = 0.92; 95%CI: 0.52-1.63). None of these associations were significant after adjustment for multiple testing.

CONCLUSION

The association of inherited mtDNA variation, including rare and singleton variants, with glioma risk merits further study.

Mitochondrial DNA sequence variation and risk of meningioma

BACKGROUND

Risk factors for meningioma include female gender, African American race, high body mass index (BMI), and exposure to ionizing radiation. Although genome-wide association studies (GWAS) have identified two nuclear genome risk loci for meningioma (rs12770228 and rs2686876), the relation between mitochondrial DNA (mtDNA) sequence variants and meningioma is unknown.

METHODS

We examined the association of 42 common germline mtDNA variants (minor allele frequency ≥ 5%), haplogroups, and genes with meningioma in 1080 controls and 478 meningioma cases from a case-control study conducted at medical centers in the southeastern United States. Associations were examined separately for meningioma overall and by WHO grade (n = 409 grade I and n = 69 grade II/III).

RESULTS

Overall, meningioma was significantly associated with being female (OR 2.85; 95% CI 2.21-3.69), self-reported African American race (OR 2.38, 95% CI 1.41-3.99), and being overweight (OR 1.48; 95% CI 1.11-1.97) or obese (OR 1.70; 95% CI 1.25-2.31). The variant m.16362T > C (rs62581341) in the mitochondrial control region was positively associated with grade II/III meningiomas (OR 2.33; 95% CI 1.14-4.77), but not grade I tumors (OR 0.99; 95% CI 0.64-1.53). Haplogroup L, a marker for African ancestry, was associated with meningioma overall (OR 2.92; 95% CI 1.01-8.44). However, after stratifying by self-reported race, this association was only apparent among the few self-reported Caucasians with this haplogroup (OR 6.35; 95% CI 1.56-25.9). No other mtDNA variant, haplogroup, or gene was associated with meningioma.

CONCLUSION

Common mtDNA variants and major mtDNA haplogroups do not appear to have associations with the odds of developing meningioma.

Role of Mitochondrial DNA in Inflammatory Airway Diseases

The mitochondrial genome is a small, circular, and highly conserved piece of DNA which encodes only 13 protein subunits yet is vital for electron transport in the mitochondrion and, therefore, vital for the existence of multicellular life on Earth. Despite this importance, mitochondrial DNA (mtDNA) is located in one of the least-protected areas of the cell, exposing it to high concentrations of intracellular reactive oxygen species (ROS) and threat from exogenous substances and pathogens. Until recently, the quality control mechanisms which ensured the stability of the nuclear genome were thought to be minimal or nonexistent in the mitochondria, and the thousands of redundant copies of mtDNA in each cell were believed to be the primary mechanism of protecting these genes. However, a vast network of mechanisms has been discovered that repair mtDNA lesions, replace and recycle mitochondrial chromosomes, and conduct alternate RNA processing for previously undescribed mitochondrial proteins. New mtDNA/RNA-dependent signaling pathways reveal a mostly undiscovered biochemical landscape in which the mitochondria interface with their host cells/organisms. As the myriad ways in which the function of the mitochondrial genome can affect human health have become increasingly apparent, the use of mitogenomic biomarkers (such as copy number and heteroplasmy) as toxicological endpoints has become more widely accepted. In this article, we examine several pathologies of human airway epithelium, including particle exposures, inflammatory diseases, and hyperoxia, and discuss the role of mitochondrial genotoxicity in the pathogenesis and/or exacerbation of these conditions. © 2021 American Physiological Society. Compr Physiol 11:1485-1499, 2021.

Role of Mitochondrial DNA (mtDNA) Variations in Cancer Development: A Systematic Review

mtDNA is the closed circular, ds-DNA present in mitochondria of eukaryotic cells and are inherited maternally. Besides being the power house of the cell, mitochondria are also responsible for the regulation of redox homeostasis, signaling, metabolism, immunity, survival and apoptosis. Lack of a 'Systematic Review' on mtDNA variations and cancers encouraged us to perform the present study. Pubmed', 'Embase' and 'Cochrane Library' databases were searched using keywords 'Mitochondrial DNA' OR 'mtDNA' OR 'mDNA' AND 'polymorphism' AND 'cancer' AND 'risk' to retrieve literature. Polymorphisms occupy first rank among mtDNA variations followed by CNV, MSI, mutations and hold a great potential to emerge as key predictors for human cancers.

Identification of sequence polymorphisms in the displacement loop region of mitochondrial DNA as a risk factor for gastroenteropancreatic neuroendocrine neoplasm

BACKGROUND

Gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN) are relatively rare tumors that arise from the diffuse neuroendocrine system, and the biggest advances in molecular biology have helped in understanding these biological diversity of tumors over the past decades. It is important to determine the carcinogenesis of GEP-NEN from the perspective of genetic backgrounds.

METHODS

Mitochondrial DNA (mtDNA) of peripheral blood from 66 GEP-NEN patients and from 75 healthy controls without history of any cancer were examined for single nucleotide polymorphisms (SNPs) and mutations in the displacement loop (D-loop) region.

RESULTS

Single nucleotide polymorphisms were detected in 148 sites within the 982 bp mitochondria D-loop region from blood samples of healthy controls and GEP-NEN patients. SNPs with a rare allele frequency >5% in either controls or GEP-NEN patients were used for cancer risk analysis; a total of 23 SNPs were selected. When individual SNPs of GEP-NEN patients compared with healthy controls were analyzed, a statistically significant increase in the SNP frequency was observed for 73G, 150T, 151T, 492C, 16257A, 16261T, and 16399G in GEP-NEN patients (P<.05). It was also observed that the SNP frequency for 489C and 16519C significantly decreased in GEP-NEN patients compared with controls (P<.05).

CONCLUSION

In summary, SNPs in the mutations of the mitochondrial D-loop may be valuable markers for GEP-NEN risk evaluation. Analysis of the genetic polymorphisms in the D-loop may be useful for diagnosis of high-risk individuals.

Relationship between mutations of mitochondrial DNA control region and tumors

The mitochondrion is the main place of cell respiration and participates in the process of cell apoptosis and proliferation, nucleic acid synthesis, and the production of free radicals. Mitochondrial DNA (mtDNA) is susceptible to the attack by oxygen free radicals and their products, and tends to develop somatic mutations, because of the lack of protection by histones and complete repair system. Somatic mutations in mtDNA will finally promote tumorigenesis. The control region of mtDNA is a region with a high mutation frequency. The association between control region mutations and tumorigenesis has attracted wide attention. Therefore, it is of great significance to elucidate the relationship between mtDNA control region mutations and tumorigenesis.

Identification of sequence polymorphisms in the D-Loop region of mitochondrial DNA as a risk factor for colon cancer

The accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-Loop) of mitochondrial DNA (mtDNA) has been identified for their association with cancer risk in a number of cancers. We investigated the colon cancer risk profile of D-Loop SNPs in a case-control study. The frequent alleles of nucleotides 73G/A, 146T/C, 195T/C, 324C/G, 16261C/T, and 16304T/C as well as the minor allele of 309C/C insert were significantly associated with an increased risk for colon cancer. In conclusion, SNPs in the mtDNA D-Loop were found to be valuable markers for colon cancer risk evaluation.

Single nucleotide polymorphisms in the D-loop region of mitochondrial DNA is associated with colorectal cancer outcome

Single nucleotide polymorphisms (SNPs) in the displacement loop (D-Loop) of mitochondrial DNA (mtDNA) has been identified for their association with the risk and outcome in many cancers. We have identified risk associated D-loop SNPs for colorectal cancer previously, in the present study, we evaluate their prognostic value for postoperative survival of colorectal cancer (CRC). The minor haplotype of nucleotides 16290T and frequent haplotype of nucleotide 16298T in the hypervariable segment 1 (HV1) region of the D-loop were identified for their association with high survival rate of CRC. After adjusted with COX proportional hazard model, the nucleotide site of 16290 was identified as independent predictor for CRC (RR, 0.379; 95% CI, 0.171-0.839; p = 0.017). In conclusion, SNPs in the mtDNA D-Loop were found to be valuable markers for colorectal cancer outcome evaluation.

Nonsense and missense mutation of mitochondrial ND6 gene promotes cell migration and invasion in human lung adenocarcinoma

Background

Previous study showed that mitochondrial ND6 (mitND6) gene missense mutation resulted in NADH dehydrogenase deficiency and was associated with tumor metastasis in several mouse tumor cell lines. In the present study, we investigated the possible role of mitND6 gene nonsense and missense mutations in the metastasis of human lung adenocarcinoma.

Methods

The presence of mitND6 gene mutations was screened by DNA sequencing of tumor tissues from 87 primary lung adenocarcinoma patients and the correlation of the mutations with the clinical features was analyzed. In addition, we constructed cytoplasmic hybrid cells with denucleared primary lung adenocarcinoma cell as the mitochondria donor and mitochondria depleted lung adenocarcinoma A549 cell as the nuclear donor. Using these cells, we studied the effects of mitND6 gene nonsense and missense mutations on cell migration and invasion through wounding healing and matrigel-coated transwell assay. The effects of mitND6 gene mutations on NADH dehydrogenase activity and ROS production were analyzed by spectrophotometry and flow cytometry.

Results

mitND6 gene nonsense and missense mutations were detected in 11 of 87 lung adenocarcinoma specimens and was correlated with the clinical features including age, pathological grade, tumor stage, lymph node metastasis and survival rate. Moreover, A549 cell containing mitND6 gene nonsense and missense mutation exhibited significantly lower activity of NADH dehydrogenase, higher level of ROS, higher capacity of cell migration and invasion, and higher pAKT and pERK1/ERK2 expression level than cells with the wild type mitND6 gene. In addition, NADH dehydrogenase inhibitor rotenone was found to significantly promote the migration and invasion of A549 cells.

Conclusions

Our data suggest that mitND6 gene nonsense and missense mutation might promote cell migration and invasion in lung adenocarcinoma, probably by NADH dehydrogenase deficiency induced over-production of ROS.

Gene mutations in the D-loop region of mitochondrial DNA in oral squamous cell carcinoma

The present study aimed to investigate gene mutations in the displacement‑loop (D‑loop) region of mitochondrial DNA (mtDNA) in patients with oral squamous cell carcinoma (OSCC) in order to examine the role of gene mutation in mtDNA in OSCC tumorigenesis. mtDNA was obtained from cancer tissues, paracancerous tissues and normal mucosal tissues of thirty patients with OSCC. The D‑loop region of the mtDNA was amplified using polymerase chain reaction, sequenced and then analyzed by Chromas software and BLAST to identify the mutation sites. Mutations in the D‑loop region were observed in the cancer tissue samples of eight out of thirty cases with OSCC, with a mutation rate of 27%. There were nine mutations in total, including one point mutation, two base deletions, three insertion mutations and three heterozygous mutations. In these mutations, base deletions were different from each other and heterozygous mutations did not have the same mutation form; however, the three insertion mutations were the same, consisting of an insertion of a C base. One case contained a T/A heterozygous mutation as well as base insertion of C. The eight cases with mutations in the D‑loop region consisted of three cases of tongue cancer, two cases of soft palate cancer, one case of floor of the mouth cancer, one case of oropharyngeal cancer and one case of lip cancer. This study demonstrated mutations in the mtDNA D‑loop region in OSCC cells; however, the association between occurrences of OSCC and mtDNA mutations requires further investigation.

Single nucleotide polymorphisms in the mitochondrial displacement loop region predict malignant melanoma outcome: a study in Chinese Han population

BACKGROUND

Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been identified to be associated with cancer risk and disease outcome. In this study, we investigated whether the SNPs in mitochondrial D-loop were associated with the outcome of malignant melanoma (MM) in Chinese Han population.

METHODS

The D-loop region of mtDNA was sequenced for 75 MM patients recorded in the Fourth Hospital of Hebei Medical University between 2003 and 2009. The 5-year survival curve were calculated with the Kaplan-Meier method and compared by the log-rank test at each SNP site, a multivariate survival analysis was also performed with the Cox proportional hazards method.

RESULTS

The SNP sites of nucleotides T204C, A235G and T16519C were identified for prediction of post-operational survival by the log-rank test. In an overall multivariate analysis, the T204C and A235G alleles were identified as independent predictors of MM outcome.

CONCLUSION

Genetic polymorphisms in the D-loop are independent prognostic markers for patients with MM. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can help identify patient subgroups at high risk of a poor disease outcome.

The influence of mtDNA deletion on lung cancer cells under the conditions of hypoxia and irradiation

PURPOSE

This study was to evaluate the influence of mtDNA deletion on the lung cancer cells under the conditions of hypoxia or irradiation.

METHOD

The treatment conditions of lung cancer cell lines with (A549) and without mtDNA (ρ0A549: obtained by inducing from A549) included 2 h of hypoxia and 4 Gy irradiation (group 1: without treatment; group 2: 2 h of hypoxia; group 3: 4 Gy irradiation; group 4: 2 h of hypoxia plus 4 Gy irradiation). The Human OneArray™ microarray was used to hybridize with the Cy5-labeled aRNA in microarray sample preparation. Differentially expressed genes (DEGs) between the lung cancer cells with and without mtDNA were identified using NOISeq package in R. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the online tool of DAVID.

RESULT

In the KEGG pathway analysis of down-regulated DEGs, nineteen pathways were simultaneously enriched in the four groups, which were mainly metabolism- and biosynthesis-related pathways. Nine lung cancer-related pathways were enriched in group 4, and more cancer-associated DEGs, such as MYC, MAX, and E2F1 were found in group 4 than in the other groups.

CONCLUSION

The mtDNA deletion could inhibit the biosynthesis and metabolism of lung cancer cells and promote the effect of hypoxia and radiation on lung cancer cells. MYC might be the key gene of the cooperation of hypoxia and radiation and MYC, MAX, and E2F1 might play roles in hypoxia- and radiation-induced cell death in lung cancer cells without mtDNA.

Mitochondrial DNA haplogroup N is associated good outcome of gastric cancer

Accumulation of mutations and single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been identified for their association with cancer risk and disease outcome in a variety of cancers. We have identified cancer risk-associated D-loop SNPs in gastric cancer patients. In this study, we evaluated the predictive value of these SNPs for cancer outcome. Two SNP sites of nucleotides 489C/T and 523-524AC/del were identified for statistically significant prediction of postoperative survival in gastric cancer by univariate analysis with log-rank test. In addition, the mitochondrial DNA haplogroup N (489T) contributed to the good survival of gastric cancer patients compared with the mitochondrial DNA haplogroup M (489C) genotype (relative risk, 1.753; 95 %CI, 1.005-3.060; p = 0.048) by multivariate analysis with COX hazards model. In conclusion, analysis of genetic polymorphisms in the mitochondrial D-loop can help identify subgroups of patients who are at a high risk of a poor disease outcome.

Mitochondrial DNA variants and risk of familial breast cancer: an exploratory study

To assess if mitochondrial DNA (mtDNA) variants are associated with mutations in BRCA susceptibility genes and to investigate the possible role of mitochondrial alterations as susceptibility markers in familial breast cancer (BC), 22 patients with or without BRCA1/BRCA2 mutations, 14 sporadic BC patients and 20 healthy subjects were analyzed. In the D-loop and in the MTND4 region, variants significantly associated with BRCA1 carriers were identified. Moreover, examination of mitochondrial haplogroups revealed X as the most significantly frequent haplogroup in BRCA1 carriers (P=0.005), and H as significantly linked to BRCA2 carriers (P=0.05). Our data suggest the involvement of the mitochondrial genome in the pathogenetic and molecular mechanism of familial BC disease.

Single nucleotide polymorphisms in the mitochondrial displacement loop and age-at-onset of renal cell carcinoma

The accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described in various types of cancers, and their association with cancer risk and disease outcome has been extensively identified. In the present study, we investigated the association between age-at-onset and SNPs in the mitochondrial D-loop using a population-based series of renal cell carcinoma(RCC). The SNP sites of nucleotides 16293A/G were identified for their association with age-at-onset using the log-rank test. The age-at-onset of patients with the minor allele G genotype was significantly lower than that of patients with the A genotype at the 16293 site (p < 0.001). Genetic polymorphisms in the D-loop are predictive markers of age-at-onset in RCC patients. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop may help identify RCC patient subgroups at high risk of early onset.

Single nucleotide polymorphisms in the mitochondrial displacement loop region and outcome of malignant fibrous histiocytoma

PURPOSE

Single nucleotide polymorphisms (SNPs) in the mitochondrial DNA displacement-loop (D-loop) region have been reported to be associated with cancer risk and disease outcome in several types of cancer. In this study, we investigated whether the SNPs in mitochondrial D-loop were associated with the outcome of malignant fibrous histiocytoma (MFH).

EXPERIMENTAL DESIGN

The D-loop region of mtDNA was sequenced for 80 MFH patients. The 3 years survival curve were calculated with the Kaplan-Meier method and compared by the log-rank test at each SNP site, a multivariate survival analysis was also performed with the Cox proportional hazards method.

RESULTS

The SNP sites of nucleotides 152T/C, 16,390G/A, 16,290C/T, 16,304T/C and the AC deletion at sites 523 and 524 were identified for prediction of post-operational survival by the log-rank test. In an overall multivariate analysis, the 16,290 and 16,390 alleles were identified as independent predictors of MFH outcome. The length of survival for patients with the rare allele 16,390A genotype was significantly shorter than that for patients with the frequent allele 16,390Gat the site 16,390. The same was seen for the rare allele 16,290T genotype when compared with matched allele 16,290C at the site 16,290 in MFH patients.

CONCLUSIONS

These results suggested that SNPs in the D-loop are independent prognostic markers for patients with MFH. The analysis of genetic polymorphisms in the D-loop can help identify patient subgroups at higher risk of a poor disease outcome.

Identification of sequence polymorphisms in the mitochondrial displacement loop as risk factors for sporadic and familial breast cancer

The accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described for different types of cancers, and the association of these SNPs with cancer risk and disease outcome has been exhaustively studied. We sequenced a region of approximately 1 kb flanking the majority of the D-Loop in the DNA from the blood of breast cancer patients and the controls to identify cancer risk-associated D-loop SNPs. The D-loop region of mtDNA was sequenced from 92 sporadic breast cancer patients, 60 familial breast cancer patients and 41 relatives, and 93 healthy controls. Paired and unpaired Student's t tests were used as appropriate to determine the differences in SNP distribution within the D-loop region and in the number of SNPs per patient among the groups. The χ (2) test was used to analyze dichotomous values, such as the presence or absence of an individual SNP among each group, and the clinical characteristics between every two groups. The distribution frequencies of 315C/Cinsert, 524C/del, 16247A/del, 16248C/del, 16249T/C, 16257C/A, 16258A/del, 16259C/del, 16262C/del, 16268C/del, 16279C/del, 16280A/del, 16297T/C, and 16300A/del were significantly different between sporadic breast cancer patients and the normal controls. The SNP sites at nucleotides 310, 315, and 16362 were identified as cancer risk-associated SNPs specific for familial breast cancer. The N haplogroup, defined as 489T, was identified as a specific risk-associated SNP for families of breast cancer patients by comparing familial breast cancer patients with their relatives. The analysis of genetic polymorphisms in the D-loop may help to predict cancer risk for familial breast cancer and thereby help to detect and refine therapeutic decisions earlier.

Identification of sequence polymorphisms in the D-loop region of mitochondrial DNA as risk biomarkers for malignant fibrous histiocytoma

Single nucleotide polymorphisms (SNPs) in the mitochondrial DNA Displacement-loop (D-loop) region particularly in a highly polymorphic homopolymeric C stretch named D310 have been reported to be associated with cancer risk in several types of cancer. In order to evaluate the frequency of D-loop SNPs in a large series of malignant fibrous histiocytoma (MFH) and establish correlations with cancer risk, we sequenced the D-loop of 92 MFH patients and analyzed their use as predictive biomarkers for MFH risk. The minor alleles of nucleotides 73G, 151T were associated with an increased risk for MFH patients, whereas the alleles of nucleotides 16,298C, 152C, and insertion of C at the site 315 (located within the D310) were associated with a decreased risk for MFH patients. These results suggest that SNPs in the mitochondrial D-loop should be considered as a biomarker which may be useful for the early detection of MFH in individuals at risk of this cancer.

Single nucleotide polymorphisms in the D-loop region of mitochondrial DNA is associated with renal cell carcinoma outcome

Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described in various types of cancers and might be associated with cancer risk and disease outcome. We identified 14 SNPs with a frequency higher than 5% and 5 SNPs associated with the risk of renal cell carcinoma (RCC) in a case-control study previously. In the present study, we assessed the relationship of these SNPs and the outcome of RCC patients, a SNP of 262C/T was identified by the log-rank test for statistically significant prediction of RCC survival. In an overall multivariate analysis, allele 262 was identified as an independent predictor of RCC outcome. The length of survival of patients with 262T was significantly shorter than that of patients with allele 262C (relative risk, 2.136, 95%CI, 1.863-2.449; p = 0.000). The analysis of genetic polymorphisms in the mitochondrial D-loop can help identify patients subgroup at high risk of a poor disease outcome.

Sequence polymorphisms in the D-loop region of mitochondrial DNA and outcome of non-Hodgkin lymphoma

Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) might be associated with cancer risk and disease outcome. We have identified 140 SNPs including 26 SNPs with frequency distribution of minor allele greater than 5% in a case-control study for non-Hodgkin lymphoma patients previously. In this study, we assessed the predictive power of D-loop SNPs in NHL patients. Five SNP sites were identified by log-rank test for statistically significant prediction of NHL survival in a univariate analysis. In an overall multivariate analysis, allele 16304 was identified as an independent predictor of NHL outcome. The survival time of NHL patients with 16304C was significantly shorter than that of patients with 16304T (relative risk, 0.513; 95% CI, 0.266-0.989; p = 0.046). The analysis of genetic polymorphisms in the mitochondrial D-loop can help identify subgroups of patients who are at a high risk of a poor disease outcome.

Detecting the somatic mutations spectrum of Chinese lung cancer by analyzing the whole mitochondrial DNA genomes

To detect the somatic mutations and character its spectrum in Chinese lung cancer patients. In this study, we sequenced the whole mitochondrial DNA (mtDNA) genomes for 10 lung cancer patients including the primary cancerous, matched paracancerous normal and distant normal tissues. By analyzing the 30 whole mtDNA genomes, eight somatic mutations were identified from five patients investigated, which were confirmed with the cloning and sequencing of the somatic mutations. Five of the somatic mutations were detected among control region and the rests were found at the coding region. Heterogeneity was the main character of the somatic mutations in Chinese lung cancer patients. Further potential disease-related screening showed that, except the C deletion at position 309 showed AD-weakly associated, most of them were not disease-related. Although the role of aforementioned somatic mutations was unknown, however, considering the relative higher frequency of somatic mutations among the whole mtDNA genomes, it hints that detecting the somatic mutation(s) from the whole mtDNA genomes can serve as a useful tool for the Chinese lung cancer diagnostic to some extent.

Single nucleotide polymorphisms in the mitochondrial displacement loop and age at onset of non-Hodgkin lymphoma

OBJECTIVE

Single nucleotide polymorphisms (SNPs) accumulated frequently in the mitochondrial displacement loop (D-loop) in many cancers. We had identified cancer risk-associated SNPs in the D-loop of non-Hodgkin lymphoma (NHL) patients previously, in this study, we investigated the association of age at onset and D-loop SNPs in NHL patients.

MATERIALS AND METHODS

The D-loop region of mtDNA was sequenced for 133 NHL patients recorded at the Fourth Hospital of Hebei Medical University. The Kaplan-Meier method was used to identify age at onset-associated SNPs in the D-loop of NHL patients. The Cox proportional hazards model was used to identify independent risk factors for age at onset.

RESULTS

The SNP sites of nucleotides 146C/T, 151T/C, 194T/C, 315C/C insert, 523Del/A, and 525Del/C were identified for their association with age at onset, by the logrank test. In an overall multivariate analysis, allele 146 (relative risk, 0.403; 95% confidence interval [CI]: 0.182-0.895) (P = 0.026), allele 151 (relative risk, 0.378; 95% CI: 0.165-0.868) (P = 0.022), and allele 315 (relative risk, 3.554; 95% CI: 1.344-9.400) (P = 0.011) were identified as independent predictors for age at onset in NHL patients.

CONCLUSION

SNPs in the D-loop can predict age at onset in NHL patients. Analysis of the D-loop SNPs can help identify NHL patient subgroups at high risk of early onset.

Identification of sequence polymorphisms in the D-loop region of mitochondrial DNA as a risk factor for non-Hodgkin lymphoma

Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) may be associated with an increased cancer risk. We investigated the non-Hodgkin lymphoma (NHL) risk profile of D-loop SNPs in a case-control study. The minor alleles of nucleotides 73A/G, 263A/G, 315C/C insert were associated with a decreased risk for NHL. The minor alleles of the nucleotides 200G/A were specifically associated with the risk of diffuse large B-cell lymphoma, whereas the minor allele of nucleotides 16362C/T and 249Del/A was specifically associated with the decreased risk of T-cell lymphoma. In conclusion, SNPs in mtDNA are potential modifiers of NHL risk. The analysis of genetic polymorphisms in the mitochondrial D-loop can help identify subgroups of patients who are at a high risk of developing NHL.

Identification of sequence polymorphisms in the displacement loop region of mitochondrial DNA as a risk factor for renal cell carcinoma

The accumulation of single-nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) may be associated with an increased cancer risk. In this case-control study, the SNPs in the mitochondrial D-loop of renal cell carcinoma (RCC) patients were identified and their association with cancer risk was evaluated. The minor alleles of nucleotides 16293A/G, 262A/G and 488T/C were associated with an increased risk, whereas the minor alleles of nucleotides 16298T/C and 16319G/A were associated with a decreased risk for RCC. Moreover, the nucleotides 16293, 262, 16298 and 16319 were identified as specifically associated with the risk of clear cell RCC (ccRCC), whereas 262 and 488 were specifically associated with papillary RCC and renal oncocytoma. In conclusion, SNPs in mtDNA are potential modifiers of RCC. The analysis of genetic polymorphisms in the mitochondrial D-loop may help identify the patient subgroups at a high risk of developing RCC.

Mitochondrial D-loop mutations and polymorphisms are connected with canine malignant cancers

Abstract The aim of the conducted investigations was to identify differences in the D-loop nucleotide sequence between neoplastic tissue, normal tissue, and blood and to determine their correlation with the type of cancer in dogs. In 62.5% of the analyzed tumors of epithelial origin and 25% tumors of mesenchymal origin, substitution was detected within the D-loop sequence between the neoplastic tissue, normal tissue, and blood. Two mutations occurring in the carcinogenic process in position T15620C have been identified in epithelioma glandulae sebacei and carcinoma planoepithelialae keratodes. Blood and cancer heteroplasmy was diagnosed for carcinoma planoepithelialae keratodes and "Comedo" carcinoma. The results of the study indicate that polymorphic changes in the D-loop sequence promote carcinogenesis in dogs. Heteroplasmy diagnosed in blood and tumor cells and absence thereof in normal tissue may imply mtDNA recombination. High prevalence of mtDNA mutations in canine tumors may suggest mtDNA genetic instability, which is likely to play a role in carcinogenesis.