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Kamfar S, Danaei B, Rahimi S, Zeinali V. Novel blood and tissue-based mitochondrial D-loop mutations detected in an Iranian NAFLD patient cohort. Mitochondrion 2024; 77:101888. [PMID: 38697590 DOI: 10.1016/j.mito.2024.101888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is an increasingly prevalent chronic liver disease characterized by an elusive etiology. In its advanced stages, this condition can pose life-threatening implications. Mitochondrial dysfunction due to its impact on hepatic lipid homeostasis, cytokine release, ROS production, and cell death, contributes to the pathogenesis of NAFLD. Previous research reveals a direct link between NAFLD genetic predictors and mitochondrial dysfunction. The emphasis on the D-loop stems from its association with impaired mtDNA replication, underscoring its crucial role in NAFLD progression. We included 38 Iranian NAFLD patients (comprising 16 patients with non-alcoholic fatty liver [NAFL] and 22 patients with non-alcoholic steatohepatitis [NASH]), with matched blood and liver tissue samples collected from each to compare variations in the mitochondrial D-loop sequence within samples. The mitochondrial DNA (mtDNA) D-loop region was amplified using PCR, and variations were identified through sequencing. The resultant sequences were compared with the reference sequence of human mtDNA available in the MITOMAP Database for comparative analysis. In this study, 97 somatic mutations in the mtDNA D-loop region were identified in NAFLD patients. Our study revealed significant difference between the NAFLD patients and control group in 13 detected mutations (P ≤ 0.05). Novel mutations were discovered in hepatic tissues, while mutation 16220-16221ins C was found in both tissues and blood. A significant difference was found in the distribution of D310 and mt514-mt523 (CA)n repeat variations between NAFLD patients and the control group (P < 0.001). C to T and T to C transitions were the prevalent substitution among patients. Identification of the 16220-16221ins C mutation in both blood and tissue samples from NAFLD patients holds substantial promise as a potential diagnostic marker. However, further research is imperative to corroborate these findings.
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Affiliation(s)
- Sharareh Kamfar
- Pediatric Congenital Hematologic Disorders Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bardia Danaei
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samane Rahimi
- Department of Pediatric Emergency Medicine, School of Medicine, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahide Zeinali
- Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Alam MR, Alsulimani A, Haque S, Jung HR, Lee JH, Jeon CH, Kim DK. Differences in the mitochondrial microsatellite instability of Keratoacanthoma and cutaneous squamous cell carcinoma. Cancer Genet 2021; 256-257:115-121. [PMID: 34111657 DOI: 10.1016/j.cancergen.2021.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/16/2022]
Abstract
Keratoacanthoma (KA) is a common cutaneous neoplasm which often resembles typical squamous cell carcinoma (SCC) in both its clinical and historical presentation. Several studies have attempted to identify methods for distinguishing between KA and SCC, however, none of these have proven to play any obvious roles in these tumors. Given this we went on to evaluate mitochondrial microsatellite instability (mtMSI) in KA and SCC in an effort to understand these tumors better. DNA was isolated from paired normal and tumoral tissues donated by 57 KA patients and 43 SCC patients. MtMSI was then analyzed using eight microsatellite markers and was observed in 2 (3.5%) of the 57 KA patients and 8 (18.6%) of the 43 SCC patients, respectively. MtMSI was also shown to affect different locations depending on tumor type. In KA patients, mtMSI was detected at mitochondrial D514 D-loop and presented with (CA) n repeats, in contrast, all of the SCC patient experienced mtMSI at the D310 with (C)n repeats of the D-loop region. These differences in location were found to be significant, which may support the hypothesis that KA and SCC have different pathogenetic pathways. Our results also suggest that mtMSI may be a candidate for developing novel differential diagnostic methods for KA and SCC.
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Affiliation(s)
- Mohammad Rizwan Alam
- Department of Medical Genetics, School of Medicine, Keimyung University, Daegu 42601, Republic of Korea
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Hye Ra Jung
- Department of Pathology, Dongsan Medical Center, School of Medicine, Keimyung University, Daegu 42601, Republic of Korea
| | - Jae-Ho Lee
- Department of Anatomy, Keimyung University School of Medicine,1095 Dalgubeol-daero, Dalseo-gu, Daegu 42601, Republic of Korea
| | - Chang-Ho Jeon
- Department of Laboratory Medicine, Daegu Catholic University School of Medicine, Daegu, Republic of Korea
| | - Dae-Kwang Kim
- Department of Medical Genetics, School of Medicine, Keimyung University, Daegu 42601, Republic of Korea; Hanvit Institute for Medical Genetics, Daegu, Republic of Korea.
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Kamfar S, Alavian SM, Hasrak K, Houshmand M, Seifi Zarei B, Khalaj A, Homaunpur F, Saidijam M. Analysis of Mitochondrial 4977-bp Deletion and D-Loop Variation in Iranian Non-Alcoholic Fatty Liver Disease Patients. HEPATITIS MONTHLY 2019; In Press. [DOI: 10.5812/hepatmon.84553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Beadnell TC, Scheid AD, Vivian CJ, Welch DR. Roles of the mitochondrial genetics in cancer metastasis: not to be ignored any longer. Cancer Metastasis Rev 2018; 37:615-632. [PMID: 30542781 PMCID: PMC6358502 DOI: 10.1007/s10555-018-9772-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes for only a fraction of the proteins that are encoded within the nucleus, and therefore has typically been regarded as a lesser player in cancer biology and metastasis. Accumulating evidence, however, supports an increased role for mtDNA impacting tumor progression and metastatic susceptibility. Unfortunately, due to this delay, there is a dearth of data defining the relative contributions of specific mtDNA polymorphisms (SNP), which leads to an inability to effectively use these polymorphisms to guide and enhance therapeutic strategies and diagnosis. In addition, evidence also suggests that differences in mtDNA impact not only the cancer cells but also the cells within the surrounding tumor microenvironment, suggesting a broad encompassing role for mtDNA polymorphisms in regulating the disease progression. mtDNA may have profound implications in the regulation of cancer biology and metastasis. However, there are still great lengths to go to understand fully its contributions. Thus, herein, we discuss the recent advances in our understanding of mtDNA in cancer and metastasis, providing a framework for future functional validation and discovery.
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Affiliation(s)
- Thomas C Beadnell
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA
| | - Adam D Scheid
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA
| | - Carolyn J Vivian
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA
| | - Danny R Welch
- Department of Cancer Biology, The Kansas University Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
- The University of Kansas Cancer Center, 3901 Rainbow Blvd., Kansas City, KS, 66160, USA.
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Abstract
Mitochondria are essential intracellular organelles that are responsible for energy metabolism, cell growth, and differentiation, redox homeostasis, oncogenic signaling, and apoptosis. These multifunctional organelles have been implicated in cancer initiation, progression, and metastasis, relapse, and acquired drug resistance due to metabolic alterations in transformed cells. Maternally inherited mitochondrial DNA (mtDNA) is thought to contribute to cancer development and prognosis and proposed as a therapeutic target for cancer treatment. In this review, we summarize the current knowledge of mtDNA alterations, with a specific focus on somatic changes, germline variants, haplogroups, large deletions, and mtDNA content changes associated with cancer susceptibility and prognosis. We also discuss the potential of mtDNA as biomarkers of cancer detection and targets of cancer treatment. Deeper understanding of the mechanisms underlying these associations requires further investigation.
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Bussard KM, Siracusa LD. Understanding Mitochondrial Polymorphisms in Cancer. Cancer Res 2017; 77:6051-6059. [PMID: 29097610 DOI: 10.1158/0008-5472.can-17-1939] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/25/2017] [Accepted: 09/13/2017] [Indexed: 11/16/2022]
Abstract
Alterations in mitochondrial DNA (mtDNA) were once thought to be predominantly innocuous to cell growth. Recent evidence suggests that mtDNA undergo naturally occurring alterations, including mutations and polymorphisms, which profoundly affect the cells in which they appear and contribute to a variety of diseases, including cardiovascular disease, diabetes, and cancer. Furthermore, interplay between mtDNA and nuclear DNA has been found in cancer cells, necessitating consideration of these complex interactions for future studies of cancer mutations and polymorphisms. In this issue of Cancer Research, Vivian and colleagues utilize a unique mouse model, called Mitochondrial Nuclear eXchange mice, that contain the nuclear DNA from one inbred mouse strain, and the mtDNA from a different inbred mouse strain to examine the genome-wide nuclear DNA methylation and gene expression patterns of brain tissue. Results demonstrated there were alterations in nuclear DNA expression and DNA methylation driven by mtDNA. These alterations may impact disease pathogenesis. In light of these results, in this review, we highlight alterations in mtDNA, with a specific focus on polymorphisms associated with cancer susceptibility and/or prognosis, mtDNA as cancer biomarkers, and considerations for investigating the role of mtDNA in cancer progression for future studies. Cancer Res; 77(22); 6051-9. ©2017 AACR.
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Affiliation(s)
- Karen M Bussard
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.
| | - Linda D Siracusa
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, Pennsylvania
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Zhou J, Gou H, Ye Y, Zhou Y, Lu X, Ying B. Sequence variations of mitochondrial DNA D-loop region in patients with acute myeloid leukemia. Oncol Lett 2017; 14:6269-6276. [PMID: 29113277 DOI: 10.3892/ol.2017.6988] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/22/2017] [Indexed: 02/05/2023] Open
Abstract
The aim of the present study was to explore variations of the displacement (D)-loop region in patients with acute myeloid leukemia (AML) and their possible associations with AML pathogenesis. Blood or bone marrow samples from 216 patients with AML (158 AML patients in the first stage, and 58 more patients with AML-M3 for further verification), and 146 healthy controls were collected. Sanger sequencing was performed for the D-loop region ranging between nucleotide (nt)15811 and nt 775. With the exception of mitochondrial microsatellite instability (mtMSI) variations, a total of 2,630 variations in 232 loci were identified with similar variation rates/person in patients with AML and controls when compared with the revised Cambridge reference sequence (8.54±2.14 vs. 8.77±2.15; P=0.366). A positive association between AML and variation-T152C was identified, which occurred more frequently in patients with AML compared with in controls [26.6 vs. 17.1%; P=0.048; odds ratio (OR), 1.752; 95% confidence interval (CI), 1.004-3.058]. Furthermore, T152C was identified to be associated with promyelocytic leukemia-retinoic acid receptor α(PML-RARα) and French-American-British AML subtypes, with a tendency to occur in patients with AML-M3. The AML-M3 sample size was extended by 58 cases, and it was identified that the T152C variation rate was significantly higher in patients with AML-M3 compared with that of controls (41.0 vs. 17.1%; P<0.001; OR, 3.228; 95% CI, 1.714-6.079). However, no association was identified between the T152C variation and clinical characteristics, or chemotherapy response in patients with AML-M3. In addition, the mtMSIs, including D310, mt514-523 (CA)n and T16189C, demonstrated no association with AML risk. Together, the results of the present study suggest that the mitochondrial DNA D-loop region is high variable, and that T152C is associated with AML risk, particularly regarding the M3 subtype. T152C mayparticipate in AML pathogenesis and may be a diagnostic biomarker; however further studies with larger sample sizes are required in order to verify its value.
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Affiliation(s)
- Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Haimei Gou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuanxin Ye
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yi Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaojun Lu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Fesenko EE, Heydarov RN, Stepanova EV, Abramov ME, Chudinov AV, Zasedatelev AS, Mikhailovich VM. Microarray with LNA-probes for genotyping of polymorphic variants of Gilbert's syndrome gene UGT1A1(TA)n. Clin Chem Lab Med 2014; 51:1177-84. [PMID: 23241680 DOI: 10.1515/cclm-2012-0656] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 11/09/2012] [Indexed: 11/15/2022]
Abstract
BACKGROUND Gilbert's syndrome is a common metabolic dysfunction characterized by elevated levels of unconjugated bilirubin in the bloodstream. This condition is usually caused by additional (TA) insertions in a promoter region of the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene, which instead of the sequence А(TА)6TАА contains А(TА)7TАА. While the condition itself is benign, it presents elevated risk for patients treated with irinotecan, a common chemotherapy drug. METHODS The technique is based on hybridization analysis of a pre-amplified segment of the UGT1A1 gene promoter performed on a microarray. Specific probes containing locked nucleic acids (LNA) were designed and immobilized on the microarray to provide accurate identification. RESULTS A microarray has been developed to identify both common and rare variants of UGT1A1(TA)n polymorphisms. In total, 108 individuals were genotyped. Out of these, 47 (43.5%) had homozygous wild-type genotypes (TA)6/(TA)6; 41(38%) were heterozygotes (TA)6/(TA)7; and 18 (16.7%)--homozygotes (TA)7/(TA)7. In two cases (1.8%), rare genotypes (TA)5/(TA)7 and (TA)5/(TA)6 were found. The results were in full agreement with the sequencing. In addition, synthetic fragments corresponding to all human allelic variants [(TA)5, (TA)6, (TA)7, (TA)8] were successfully tested. CONCLUSIONS The developed microarray-based approach for identification of polymorphic variants of the UGT1A1 gene is a promising and reliable diagnostic tool that can be successfully implemented in clinical practice.
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Mitochondrial D-loop and cytochrome oxidase C subunit I polymorphisms among the breast cancer patients of Mizoram, Northeast India. Curr Genet 2014; 60:201-12. [PMID: 24719079 DOI: 10.1007/s00294-014-0425-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 03/23/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
Mitochondrial DNA (mtDNA) is known for its high frequencies of polymorphisms and mutations as it is prone to oxidative stress. The aim of the present study is to assess the novel mutations in mitochondrial genes from blood samples among the breast cancer patients from a less studied Northeast Indian population. D, B, L haplogroups were observed in the cancer samples and a total of 44 mtDNA D-loop sequence variations at 42 distinct nucleotide positions were found. All the sequence variations were transitional substitutions and 6 were heteroplasmic states, except for a cytosine copy number change (9C/8C) at np 303e309 in three samples examined. A total of 88 Cytochrome Oxidase C subunit I (COXI) sequence differences with respect to the Revised Cambridge Reference Sequence (rCRS) were identified including 20 missense variants with 100 % sample mutation frequency. All 20 missense mutations are highly conserved with a Cumulate Index of 100 %. Among 88 COXI mutations, 24 (13 were Non-Synonymous and 11 were Synonymous) were not previously reported (novel mutation) in the literature or the public mtDNA mutation databases. Analysis of three-dimensional structure of COXI open reading frame (ORF) predicted the effect of one single codon (96R > C, 217T > I, 224-225GG > EE and 227D > T) mutations located in the signal peptide binding position. Analysis of mitochondrial DNA mutations, as a viable alternative, has the advantage of being capable of detecting inherent risk factors for breast cancer development.
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Tipirisetti NR, Govatati S, Pullari P, Malempati S, Thupurani MK, Perugu S, Guruvaiah P, K LR, Digumarti RR, Nallanchakravarthula V, Bhanoori M, Satti V. Mitochondrial control region alterations and breast cancer risk: a study in South Indian population. PLoS One 2014; 9:e85363. [PMID: 24497926 PMCID: PMC3907410 DOI: 10.1371/journal.pone.0085363] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/26/2013] [Indexed: 01/10/2023] Open
Abstract
Background Mitochondrial displacement loop (D-loop) is the hot spot for mitochondrial DNA (mtDNA) alterations which influence the generation of cellular reactive oxygen species (ROS). Association of D-loop alterations with breast cancer has been reported in few ethnic groups; however none of the reports were documented from Indian subcontinent. Methodology We screened the entire mitochondrial D-loop region (1124 bp) of breast cancer patients (n = 213) and controls (n = 207) of south Indian origin by PCR-sequencing analysis. Haplotype frequencies for significant loci, the standardized disequilibrium coefficient (D′) for pair-wise linkage disequilibrium (LD) were assessed by Haploview Software. Principal Findings We identified 7 novel mutations and 170 reported polymorphisms in the D-loop region of patients and/or controls. Polymorphisms were predominantly located in hypervariable region I (60%) than in II (30%) of D-loop region. The frequencies of 310‘C’ insertion (P = 0.018), T16189C (P = 0.0019) variants and 310‘C’ins/16189C (P = 0.00019) haplotype were significantly higher in cases than in controls. Furthermore, strong LD was observed between nucleotide position 310 and 16189 in controls (D′ = 0.49) as compared to patients (D′ = 0.14). Conclusions Mitochondrial D-loop alterations may constitute inherent risk factors for breast cancer development. The analysis of genetic alterations in the D-loop region might help to identify patients at high risk for bad progression, thereby helping to refine therapeutic decisions in breast cancer.
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Affiliation(s)
| | - Suresh Govatati
- Department of Biochemistry, Osmania University, Hyderabad, India
| | - Priyanka Pullari
- Department of Biotechnology, Periyar University, Salem, Tamilnadu, India
| | - Sravanthi Malempati
- Department of Biochemistry, DrMRAR PG Center, Krishna University, Nuzvid, India
| | | | - Shyam Perugu
- Department of Biochemistry, Osmania University, Hyderabad, India
| | | | - Lakshmi Rao K
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | | | | | - Manjula Bhanoori
- Department of Biochemistry, Osmania University, Hyderabad, India
| | - Vishnupriya Satti
- Department of Genetics, Osmania University, Hyderabad, India
- * E-mail:
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Weigl S, Paradiso A, Tommasi S. Mitochondria and familial predisposition to breast cancer. Curr Genomics 2013; 14:195-203. [PMID: 24179442 PMCID: PMC3664469 DOI: 10.2174/1389202911314030005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 03/25/2013] [Accepted: 03/28/2013] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial genome and functional alterations are related to various diseases including cancer. In all cases, the role of these organelles is associated with defects in oxidative energy metabolism and control of tumor-induced oxidative stress. The present study examines the involvement of mitochondrial DNA in cancer and in particular in breast cancer. Furthermore, since mitochondrial DNA is maternally inherited, hereditary breast cancer has been focused on.
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Affiliation(s)
- Stefania Weigl
- National Cancer Research Centre, Istituto Tumori "Giovanni Paolo II", Bari-Italy
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12
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Verma M, Khoury MJ, Ioannidis JPA. Opportunities and challenges for selected emerging technologies in cancer epidemiology: mitochondrial, epigenomic, metabolomic, and telomerase profiling. Cancer Epidemiol Biomarkers Prev 2013; 22:189-200. [PMID: 23242141 PMCID: PMC3565041 DOI: 10.1158/1055-9965.epi-12-1263] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Remarkable progress has been made in the last decade in new methods for biologic measurements using sophisticated technologies that go beyond the established genome, proteome, and gene expression platforms. These methods and technologies create opportunities to enhance cancer epidemiologic studies. In this article, we describe several emerging technologies and evaluate their potential in epidemiologic studies. We review the background, assays, methods, and challenges and offer examples of the use of mitochondrial DNA and copy number assessments, epigenomic profiling (including methylation, histone modification, miRNAs, and chromatin condensation), metabolite profiling (metabolomics), and telomere measurements. We map the volume of literature referring to each one of these measurement tools and the extent to which efforts have been made at knowledge integration (e.g., systematic reviews and meta-analyses). We also clarify strengths and weaknesses of the existing platforms and the range of type of samples that can be tested with each of them. These measurement tools can be used in identifying at-risk populations and providing novel markers of survival and treatment response. Rigorous analytic and validation standards, transparent availability of massive data, and integration in large-scale evidence are essential in fulfilling the potential of these technologies.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Li H, Liu D, Lu J, Bai Y. Physiology and pathophysiology of mitochondrial DNA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 942:39-51. [PMID: 22399417 DOI: 10.1007/978-94-007-2869-1_2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria are the only organelles in animal cells which possess their own genomes. Mitochondrial DNA (mtDNA) alterations have been associated with various human conditions. Yet, their role in pathogenesis remains largely unclear. This review focuses on several major features of mtDNA: (1) mtDNA haplogroup, (2) mtDNA common deletion, (3) mtDNA mutations in the control region or D-loop, (4) mtDNA copy number alterations, (5) mtDNA mutations in translational machinery, (6) mtDNA mutations in protein coding genes (7) mtDNA heteroplasmy. We will also discuss their implications in various human diseases.
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Affiliation(s)
- Hongzhi Li
- Wenzhou Medical College, Wenzhou, Zhejiang, China
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Wang T, Pradhan K, Ye K, Wong LJ, Rohan TE. Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples. Front Genet 2011; 2:51. [PMID: 22303347 PMCID: PMC3268604 DOI: 10.3389/fgene.2011.00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 07/25/2011] [Indexed: 01/08/2023] Open
Abstract
Background: Both common and rare mitochondrial DNA (mtDNA) variants may contribute to genetic susceptibility to some complex human diseases. Understanding of the role of mtDNA variants will provide valuable insights into the etiology of these diseases. However, to date, there have not been any large-scale, genome-wide association studies of complete mtDNA variants and disease risk. One reason for this might be the substantial cost of sequencing the large number of samples required for genetic epidemiology studies. Next-generation sequencing of pooled mtDNA samples will dramatically reduce the cost of such studies and may represent an appealing approach for large-scale genetic epidemiology studies. However, the performance of the different designs of sequencing pooled mtDNA has not been evaluated. Methods: We examined the approach of sequencing pooled mtDNA of multiple individuals for estimating allele frequency using the Illumina genome analyzer (GA) II sequencing system. In this study the pool included mtDNA samples of 20 subjects that had been sequenced previously using Sanger sequencing. Each pool was replicated once to assess variation of the sequencing error between pools. To reduce such variation, barcoding was used for sequencing different pools in the same lane of the flow cell. To evaluate the effect of different pooling strategies pooling was done at both the pre- and post-PCR amplification step. Results: The sequencing error rate was close to that expected based on the Phred score. When only reads with Phred ≥ 20 were considered, the average error rate was about 0.3%. However, there was significant variation of the base-calling errors for different types of bases or at different loci. Using the results of the Sanger sequencing as the standard, the sensitivity of single nucleotide polymorphism detection with post-PCR pooling (about 99%) was higher than that of the pre-PCR pooling (about 82%), while the two approaches had similar specificity (about 99%). Among a total of 298 variants in the sample, the allele frequencies of 293 variants (98%) were correctly estimated with post-PCR pooling, the correlation between the estimated and the true allele frequencies being >0.99, while only 206 allele frequencies (69%) were correctly estimated in the pre-PCR pooling, the correlation being 0.89. Conclusion: Sequencing of mtDNA pooled after PCR amplification is a viable tool for screening mitochondrial variants potentially related to human diseases.
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Affiliation(s)
- Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine Bronx, NY, USA
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Komandur S, Venkatasubramanian S, Alluri RV, Rao P, Rao P, Hasan Q. Mitochondrial insertion-deletion polymorphism: role in disease pathology. Genet Test Mol Biomarkers 2011; 15:361-4. [PMID: 21476899 DOI: 10.1089/gtmb.2010.0205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIM Mitochondrial DNA (mtDNA) sequence variations are associated with a number of human diseases. The 9-bp repeat sequence, CCCCCTCTA, in the intergenic region of MTCO2 and MTTK genes of the mtDNA has been extensively used in phylogenic studies. The sequence has been reported to be polymorphic in south-east Asians in isolated cases of mt diseases. This is the first systemic study identifying the role of insertion-deletion polymorphism in human disease. RESULTS A total of 241 patients including those with cardiomyopathy, ataxias, and idiopathic neurological disorders along with 100 controls were screened; 2.9% of patients showed a single repeat (deletion) and 4.14% had three repeats (insertion), whereas all the controls had two repeats (normal). CONCLUSION This indicates that the 9-bp insertion-deletion repeat polymorphism plays a role in disease pathology, affecting the expression of the downstream genes of mtDNA and altering ATP generation.
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Affiliation(s)
- Sreelatha Komandur
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, L.B Nagar, Hyderabad, India
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Czarnecka AM, Bartnik E. The role of the mitochondrial genome in ageing and carcinogenesis. J Aging Res 2011; 2011:136435. [PMID: 21403887 PMCID: PMC3042732 DOI: 10.4061/2011/136435] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/03/2011] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial DNA mutations and polymorphisms have been the focus of intensive investigations for well over a decade in an attempt to understand how they affect fundamental processes such as cancer and aging. Initial interest in mutations occurring in mitochondrial DNA of cancer cells diminished when most were found to be the same mutations which occurred during the evolution of human mitochondrial haplogroups. However, increasingly correlations are being found between various mitochondrial haplogroups and susceptibility to cancer or diseases in some cases and successful aging in others.
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Affiliation(s)
- Anna M. Czarnecka
- Laboratory of Molecular Oncology, Department of Oncology, Military Institute of Medicine, ul. Szaserów 128, 01-141 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Morris EE, Amria MY, Kistner-Griffin E, Svenson JL, Kamen DL, Gilkeson GS, Nowling TK. A GA microsatellite in the Fli1 promoter modulates gene expression and is associated with systemic lupus erythematosus patients without nephritis. Arthritis Res Ther 2010; 12:R212. [PMID: 21087477 PMCID: PMC3046520 DOI: 10.1186/ar3189] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 10/07/2010] [Accepted: 11/18/2010] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The transcription factor Fli1 is implicated in the pathogenesis of systemic lupus erythematosus (SLE). Recently, a GA(n) polymorphic microsatellite was characterized in the mouse Fli1 promoter that modulates promoter activity and is truncated in two lupus mouse models compared to non-autoimmune prone mice. In this work, we characterize a homologous GA(n) microsatellite in the human Fli1 promoter. The purpose of this study is to determine the effect of the microsatellite length on Fli1 promoter activity in vitro and to determine if the length of the GA(n) microsatellite is associated with SLE and/or specific disease characteristics. METHODS Constructs with variable lengths of the GA(n) microsatellite in the Fli1 promoter were generated and analyzed in promoter/reporter (P/R) assays in a human T cell line. Using three SLE patient cohorts and matched controls, microsatellite length was measured and association with the presence of disease and the occurrence of specific disease manifestations was assessed. RESULTS P/R assays demonstrated that the presence of a shorter microsatellite resulted in higher Fli1 promoter activity. A significant association was observed in the lupus cohort SLE in Gullah Health (SLEIGH) between the GA(26) base pair allele and absence of nephritis. CONCLUSIONS This study demonstrates that a GA(n) microsatellite in the human Fli1 promoter is highly polymorphic. The length of the microsatellite is inversely correlated to Fli1 promoter activity in a human T cell line. Although no association between microsatellite length and lupus was observed, an association between a specific microsatellite length and patients without nephritis in the SLEIGH cohort was observed.
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Affiliation(s)
- Erin E Morris
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, 96 Jonathon Lucas St, Charleston, SC 29425, USA
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Klemba A, Kowalewska M, Kukwa W, Tonska K, Szybinska A, Mossakowska M, Scinska A, Golik P, Koper K, Radziszewski J, Kukwa A, Czarnecka AM, Bartnik E. Mitochondrial genotype in vulvar carcinoma - cuckoo in the nest. J Biomed Sci 2010; 17:73. [PMID: 20825678 PMCID: PMC2944255 DOI: 10.1186/1423-0127-17-73] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 09/08/2010] [Indexed: 01/09/2023] Open
Abstract
Vulvar squamous cell carcinoma (VSCC) is a rare female genital neoplasm. Although numerous molecular changes have been reported in VSCC, biomarkers of clinical relevance are still lacking. On the other hand, there is emerging evidence on the use of mtDNA as a diagnostic tool in oncology. In order to investigate mtDNA status in VSCC patients, haplogroup distribution analysis and D-loop sequencing were performed. The results were compared with available data for the general Polish population, cancer free-centenarians as well as patients with endometrial and head and neck cancer. The obtained data were also compared with the current status of mitochondrial databases. Significant differences in haplogroup distribution between VSCC cohort, general Polish population and cancer-free centenarians cohort were found. Moreover, a correlation between the VSCC patients haplogroup and HPV status was observed. Finally, a specific pattern of mtDNA polymorphisms was found in VSCC. Our results suggest that the mitochondrial genetic background may influence the risk of VSCC occurrence as well as susceptibility to HPV infection.
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Affiliation(s)
- Aleksandra Klemba
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, ul, Pawinskiego 5A, 02-106, Warsaw, Poland
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19
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Yacoubi Loueslati B, Troudi W, Cherni L, Rhomdhane KB, Mota-Vieira L. Germline HVR-II mitochondrial polymorphisms associated with breast cancer in Tunisian women. GENETICS AND MOLECULAR RESEARCH 2010; 9:1690-700. [PMID: 20812191 DOI: 10.4238/vol9-3gmr778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A high incidence of somatic mtDNA polymorphisms has been reported in a wide variety of human cancers; some of them have been proposed as markers for the early detection of breast cancer. However, little attention has been paid to the potential of germline mitochondrial sequence variations as genetic risk factors for cancer. We performed a case-control study of 70 unrelated Tunisian women with breast cancer and 80 healthy age- and gender-matched blood donors, taking into account clinicopathological data, to evaluate germline polymorphism of mitochondrial HVR-II region as a genetic risk factor for breast cancer. Through direct sequencing, we detected 351 polymorphisms in controls and 248 variants in patients, with 47 and 39 segregating sites, respectively. In both groups, more than 50% of the polymorphisms were due to four variants: 315 ins C, 309 ins C, 263 A>G, and 73 A>G. The HVR-II sequences were also classified into haplotypes on the basis of the polymorphisms. Fifty-nine different haplotypes were found, 20 of them shared between patients and controls. Both groups had specific haplotypes, 18 in breast cancer patients and 21 in controls. Statistical analysis revealed a weak protective effect against breast cancer risk for two mitochondrial polymorphisms - 152 T>C (odds ratio (OR) = 0.33, 95% confidence interval (CI) = 0.12-0.91) and 263 A>G (OR = 0.17, 95%CI = 0.06-0.47). In contrast, an increased risk of breast cancer was detected for the 315+C haplotype (OR = 11.66, 95%CI = 1.44-252.23). We conclude that mitochondrial variants can affect breast cancer risk. More extensive studies, involving different types of cancer and patients with different genetic makeup, will be required to improve our understanding of the effects of germline mtDNA polymorphisms on carcinogenesis.
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Affiliation(s)
- B Yacoubi Loueslati
- Department of Biology, Faculty of Sciences of Tunis, ElManar University, Tunis, Tunisia.
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20
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Rohan TE, Wong LJ, Wang T, Haines J, Kabat GC. Do alterations in mitochondrial DNA play a role in breast carcinogenesis? JOURNAL OF ONCOLOGY 2010; 2010:604304. [PMID: 20628528 PMCID: PMC2902128 DOI: 10.1155/2010/604304] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 03/01/2010] [Indexed: 01/30/2023]
Abstract
A considerable body of evidence supports a role for oxidative stress in breast carcinogenesis. Due to their role in producing energy via oxidative phosphorylation, the mitochondria are a major source of production of reactive oxygen species, which may damage DNA. The mitochondrial genome may be particularly susceptible to oxidative damage leading to mitochondrial dysfunction. Genetic variants in mtDNA and nuclear DNA may also contribute to mitochondrial dysfunction. In this review, we address the role of alterations in mtDNA in the etiology of breast cancer. Several studies have shown a relatively high frequency of mtDNA mutations in breast tumor tissue in comparison with mutations in normal breast tissue. To date, several studies have examined the association of genetic variants in mtDNA and breast cancer risk. The G10398A mtDNA polymorphism has received the most attention and has been shown to be associated with increased risk in some studies. Other variants have generally been examined in only one or two studies. Genome-wide association studies may help identify new mtDNA variants which modify breast cancer risk. In addition to assessing the main effects of specific variants, gene-gene and gene-environment interactions are likely to explain a greater proportion of the variability in breast cancer risk.
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Affiliation(s)
- Thomas E. Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx,NY 10461, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx,NY 10461, USA
| | - Jonathan Haines
- Department of Molecular Physiology & Biophysics, Vanderbilt University Medical Center, 519 Light Hall, Nashville, TN 37232-0700, USA
| | - Geoffrey C. Kabat
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx,NY 10461, USA
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21
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Czarnecka AM, Klemba A, Semczuk A, Plak K, Marzec B, Krawczyk T, Kofler B, Golik P, Bartnik E. Common mitochondrial polymorphisms as risk factor for endometrial cancer. Int Arch Med 2009; 2:33. [PMID: 19863780 PMCID: PMC2775024 DOI: 10.1186/1755-7682-2-33] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 10/28/2009] [Indexed: 01/15/2023] Open
Abstract
Endometrial carcinoma is the most commonly diagnosed gynaecological cancer in developed countries. Although the molecular genetics of this disease has been in the focus of many research laboratories for the last 20 years, relevant prognostic and diagnostic markers are still missing. At the same time mitochondrial DNA mutations have been reported in many types of cancer during the last two decades. It is therefore very likely that the mitochondrial genotype is one of the cancer susceptibility factors. To investigate the presence of mtDNA somatic mutations and distribution of inherited polymorphisms in endometrial adenocarcinoma patients we analyzed the D-loop sequence of cancer samples and their corresponding normal tissues and moreover performed mitochondrial haplogroup analysis. We detected 2 somatic mutation and increased incidence of mtDNA polymorphisms, in particular 16223C (80% patients, p = 0.005), 16126C (23%, p = 0.025) and 207A (19%, p = 0.027). Subsequent statistical analysis revealed that endometrial carcinoma population haplogroup distribution differs from the Polish population and that haplogroup H (with its defining polymorphism - C7028T) is strongly underrepresented (p = 0.003), therefore might be a cancer-protective factor. Our report supports the notion that mtDNA polymorphisms establish a specific genetic background for endometrial adenocarcinoma development and that mtDNA analysis may result in the development of new molecular tool for cancer detection.
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Affiliation(s)
- Anna M Czarnecka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.,School of Molecular Medicine, Medical University of Warsaw, Zwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Aleksandra Klemba
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Andrzej Semczuk
- II Clinic and Ward of Gynecology, Medical University of Lublin, Lublin, Poland
| | - Katarzyna Plak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Barbara Marzec
- Department of Human Genetics, Lublin University School of Medicine, Lublin, Poland
| | - Tomasz Krawczyk
- Clinical Pathology Laboratory, Monument Institute of Polish Mothers Health Center, Lodz, Poland
| | - Barbara Kofler
- Department of Pediatrics, University Hospital Salzburg, Paracelsus Medical University, Müllner Hauptstr 48, A-5020 Salzburg, Austria
| | - Pawel Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Yu M, Wan Y, Zou Q, Xi Y. High frequency of mitochondrial DNA D-loop mutations in Ewing's sarcoma. Biochem Biophys Res Commun 2009; 390:447-50. [PMID: 19785995 DOI: 10.1016/j.bbrc.2009.09.085] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Accepted: 09/22/2009] [Indexed: 01/21/2023]
Abstract
Somatic mutations and polymorphisms in the noncoding displacement (D)-loop of mitochondrial DNA (mtDNA) are present in a variety of human cancers. To investigate whether Ewing's sarcoma (EWS) harbors genetic alterations within the D-loop region and their potential association with EWS carcinogenesis, we analyzed and compared the complete mtDNA D-loop sequences from 17 pairs of tumor tissues and corresponding peripheral blood samples using the direct DNA sequencing method. Our results revealed that 12 of the 17 EWS tumor specimens (70.6%) carried 19 somatic mutations in the D-loop of mtDNA, including 11 single-base substitutions, 3 insertions and 5 deletions. Among the tested 17 patients, we screened a total of 40 germline polymorphisms including one novel sequence variant in the D-loop fragment. Most of these identified mutations and germline variations were clustered within two hypervariable segments (HVS1 and HVS2) as well as the homopolymeric C stretch between nucleotide position 303 and 309. In addition, there was no significant correlation between mtDNA D-loop mutations and various clinicopathological factors of EWS. In conclusion, our study reports for the first time that mtDNA D-loop mutations occur at a high frequency in EWS. These data provide evidence of mtDNA alterations' possible involvement in the initiation and/or progression of this rare malignancy.
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Affiliation(s)
- Man Yu
- Centre for Advanced Research in Environmental Genomics, University of Ottawa, 20 Marie Curie, Ottawa, ON, Canada.
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