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Lin WR, Chiang JM, Lim SN, Su MY, Chen TH, Huang SW, Chen CW, Wu RC, Tsai CL, Lin YH, Alison MR, Hsieh SY, Yu JS, Chiu CT, Yeh CT. Dynamic bioenergetic alterations in colorectal adenomatous polyps and adenocarcinomas. EBioMedicine 2019; 44:334-345. [PMID: 31122841 PMCID: PMC6606928 DOI: 10.1016/j.ebiom.2019.05.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Energy metabolism in carcinogenesis is poorly understood. It is widely accepted the majority of colorectal cancers (CRCs) arise from adenomatous polyps (APs). We aimed to characterize the bioenergetic alterations in APs and CRCs. METHODS Fifty-six APs, 93 CRCs and adjacent normal mucosae were tested. Oxygen consumption rate (OCR) was measured representing mitochondrial oxidative phosphorylation (OxPhos), and extracellular acidification rate (ECAR)was measured representing glycolysis. Mitochondrial DNA (mtDNA) variants and mutations were studied. Over-expressed metabolic genes in APs were identified by microarray and validated by qRT-PCR, Western blots and immunohistochemistry. Identified genes were knocked down in WiDr and colo205 CRC cell lines, and their expression was analyzed in APs/CRCs with enhanced glycolysis. FINDINGS ECAR, not OCR, was significantly increased in APs. While no difference of ECAR was found between CRCs and normal mucosae, OCR was significantly reduced in CRCs. OCR/ECAR ratio was decreased in APs over 1 cm, APs with a villous component and CRCs, indicating their glycolytic tendencies. The number of mtDNA mutations was increased in APs and CRCs, but not correlated with metabolic profiles. Two metabolic genes ALDOB and SLC16A4 were up-regulated in APs. Both ALDOB-knockdown and SLC16A4-knockdown CRC cell lines showed increased basal motichondrial OxPhos and decreased basal glycolysis. Moreover, the increase of mitochondrial ATP-linked respiration and the decrease of glycolytic capacity were showed in SLC16A4-knockdown cells. Finally, APs/CRCs with enhanced glycolysis had increased SLC16A4 expression. INTERPRETATION ATP production shifts from OxPhos to glycolysis in the process of AP enlargement and villous transformation. OxPhos defects are present in CRCs but not in APs. APs and CRCs tend to accumulate mtDNA mutations, but these are not correlated with bioenergetic profiles. Finally, the ALDOB and SLC16A4 may contribute to the glycolytic shift in APs/CRCs.
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Affiliation(s)
- Wey-Ran Lin
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan; Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
| | - Jy-Ming Chiang
- Department of Proctology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Siew-Na Lim
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ming-Yao Su
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Tsung-Hsing Chen
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Shu-Wei Huang
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chun-Wei Chen
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ren-Chin Wu
- Department of Pathology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yang-Hsiang Lin
- Chang Gung University College of Medicine, Taoyuan, Taiwan; Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Malcolm R Alison
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Tang Chiu
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chau-Ting Yeh
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Chang Gung University College of Medicine, Taoyuan, Taiwan; Liver Research Center, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
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Skonieczna K, Malyarchuk B, Jawień A, Marszałek A, Banaszkiewicz Z, Jarmocik P, Grzybowski T. Mitogenomic differences between the normal and tumor cells of colorectal cancer patients. Hum Mutat 2018; 39:691-701. [PMID: 29330893 DOI: 10.1002/humu.23402] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 12/18/2017] [Accepted: 01/05/2018] [Indexed: 12/13/2022]
Abstract
So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are "drivers" or "passengers" of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorectal cancer patients. Minority variant mutations were detected at the 1% level. We showed that somatic mutations frequently occur in colorectal cancer cells (75%) and are randomly distributed across the mitochondrial genome. Mutational signatures of somatic mitogenome mutations suggest that they might arise through nucleotide deamination due to oxidative stress. The majority of somatic mutations localized within the coding region (in positions not known from the human phylogeny) and was potentially pathogenic to cell metabolism. Further analysis suggested that the relaxation of negative selection in the mitogenomes of colorectal cancer cells may allow accumulation of somatic mutations. Thus, a shift in glucose metabolism from oxidative phosphorylation to glycolysis may create advantageous conditions for accumulation of mtDNA mutations. Considering the fact that the presence of somatic mtDNA mutations was not associated with any clinicopathological features, we suggested that mtDNA somatic mutations are "passengers" rather than the cause of colorectal carcinogenesis.
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Affiliation(s)
- Katarzyna Skonieczna
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Arkadiusz Jawień
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Andrzej Marszałek
- Department of Pathology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland.,Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Zbigniew Banaszkiewicz
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Paweł Jarmocik
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
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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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Srinivasainagendra V, Sandel MW, Singh B, Sundaresan A, Mooga VP, Bajpai P, Tiwari HK, Singh KK. Migration of mitochondrial DNA in the nuclear genome of colorectal adenocarcinoma. Genome Med 2017; 9:31. [PMID: 28356157 PMCID: PMC5370490 DOI: 10.1186/s13073-017-0420-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Here we report the discovery of increased copies of nuclear mtDNA (NUMT) in colorectal adenocarcinomas, which supports link between mtDNA and genomic instability in the nucleus. We name this phenomenon of nuclear occurrence of mitochondrial component as numtogenesis. We provide a description of NUMT abundance and distribution in tumor versus matched blood-derived normal genomes. Methods Whole-genome sequence data were obtained for colon adenocarcinoma and rectum adenocarcinoma patients participating in The Cancer Genome Atlas, via the Cancer Genomics Hub, using the GeneTorrent file acquisition tool. Data were analyzed to determine NUMT proportion and distribution on a genome-wide scale. A NUMT suppressor gene was identified by comparing numtogenesis in other organisms. Results Our study reveals that colorectal adenocarcinoma genomes, on average, contains up to 4.2-fold more somatic NUMTs than matched normal genomes. Women colorectal tumors contained more NUMT than men. NUMT abundance in tumor predicted parallel abundance in blood. NUMT abundance positively correlated with GC content and gene density. Increased numtogenesis was observed with higher mortality. We identified YME1L1, a human homolog of yeast YME1 (yeast mitochondrial DNA escape 1) to be frequently mutated in colorectal tumors. YME1L1 was also mutated in tumors derived from other tissues. We show that inactivation of YME1L1 results in increased transfer of mtDNA in the nuclear genome. Conclusions Our study demonstrates increased somatic transfer of mtDNA in colorectal tumors. Our study also reveals sex-based differences in frequency of NUMT occurrence and that NUMT in blood reflects NUMT in tumors, suggesting NUMT may be used as a biomarker for tumorigenesis. We identify YME1L1 as the first NUMT suppressor gene in human and demonstrate that inactivation of YME1L1 induces migration of mtDNA to the nuclear genome. Our study reveals that numtogenesis plays an important role in the development of cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0420-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vinodh Srinivasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Michael W Sandel
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA.,Present address: Department of Biological and Environmental Sciences, School of Natural Sciences and Mathematics, University of West Alabama, Livingston, Alabama, USA
| | - Bhupendra Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Aishwarya Sundaresan
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Ved P Mooga
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Prachi Bajpai
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA.
| | - Keshav K Singh
- Departments of Genetics, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA. .,Departments of Pathology, Environmental Health, Center for Free Radical Biology, Center for Aging and UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, 35294, USA. .,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, 35294, USA. .,Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Suite 620, 720 20th St. South, Birmingham, AL, 35294, USA.
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5
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Can Mitochondria DNA Provide a Novel Biomarker for Evaluating the Risk and Prognosis of Colorectal Cancer? DISEASE MARKERS 2017; 2017:5189803. [PMID: 28408773 PMCID: PMC5376434 DOI: 10.1155/2017/5189803] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/14/2017] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) was one of the most frequent cancers worldwide. Accurate risk and prognosis evaluation could obtain better quality of life and longer survival time for the patients. Current research hotspot was focus on the gene biomarker to evaluate the risk and prognosis. Mitochondrion contains its own DNA and regulates self-replicating so that it can be as a candidate biomarker for evaluating the risk and prognosis of colorectal cancer. But there were already huge controversies on this issue. The review was to summarize current viewpoints of the controversial issues and described our understanding from the four aspects including mtDNA copy number, mitochondrial displacement loop, mtDNA variation, and mtDNA microsatellite instability, wishing the summary of the mtDNA in colorectal cancer could provide a meaningful reference or a valuable direction in the future studies.
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Zhou HY, Shu HY, Dai J, Li HC, Tang L, Wang HW, Ni B. Maternal genetic backgrounds contribute to the genetic susceptibility of tongue cancer patients in Hunan, central of China. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:347-352. [PMID: 28278694 DOI: 10.1080/24701394.2016.1278539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations played crucial roles on affecting the susceptibility to cancer. In this study, to investigate whether mitochondrial DNA mutations contributed to the genetic susceptibility of Chinese tongue cancer patients, mtDNA control regions of 105 Chinese tongue cancer patients were amplified and sequenced, the mutations were recorded by comparing with the revised Cambridge Reference Sequence (rCRS), which were attributed to certain mtDNA haplogroups based on the specific variations motif of each patients. The Miao Chinese group (a Chinese ethnic minority) from surrounding region has no essential difference with tongue cancer group, which was taken as the matched control group with principal component analysis by taking the haplogroups frequency of 105 tongue cancer individuals and 354 healthy individuals of eight groups from the similar geographic regions as input factors. This was supported by the smallest genetic distance between tongue cancer and Miao_2 groups. Further, the statistical analysis based on mtDNA variations of hypervariable sequence I (HVSI) indicated that 13 variations including 16,124, 16,148, 16,182C, 16,183C, 16,227, 16,266A, 16,249, 16,272, 16,291, 16,327, 16,335, 16,497, and 16,519 have significant differences between tongue cancer group and matched control group. Comparison of mtDNA haplogroups between tongue cancer and control groups indicated that mtDNA haplogroups C, F2*, and M10 have significant differences. It's worth noting that 16,327 and 16,291 was the defining variation of haplogroups C and F2*, respectively. Our results suggested that mitochondrial DNA may play a crucial role for the maternal genetic susceptibility of tongue cancer patients from Hunan, central of China.
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Affiliation(s)
- Hai-Yan Zhou
- a Key Laboratory of Genetics and Birth Health of Hunan Province , Family Planning Institute of Hunan Province , Changsha , Hunan Province , China
| | - Hong-Ying Shu
- a Key Laboratory of Genetics and Birth Health of Hunan Province , Family Planning Institute of Hunan Province , Changsha , Hunan Province , China
| | - Jie Dai
- b Department of Head & Neck (Oncoplastic Surgery) , Hunan Cancer Hospital , Changsha , Hunan Province , China
| | - Hong-Chao Li
- b Department of Head & Neck (Oncoplastic Surgery) , Hunan Cancer Hospital , Changsha , Hunan Province , China
| | - Li Tang
- c Department of Reproduction and Genetics , The First Affiliated Hospital of Kunming Medical University , Kunming , Yunnan Province , China.,d Department of Reproduction and Genetics, The First People's Hospital of Yunnan Province , Kunming , Yunnan Province , China
| | - Hua-Wei Wang
- c Department of Reproduction and Genetics , The First Affiliated Hospital of Kunming Medical University , Kunming , Yunnan Province , China
| | - Bin Ni
- a Key Laboratory of Genetics and Birth Health of Hunan Province , Family Planning Institute of Hunan Province , Changsha , Hunan Province , China
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Santorsola M, Calabrese C, Girolimetti G, Diroma MA, Gasparre G, Attimonelli M. A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest. Hum Genet 2015; 135:121-36. [PMID: 26621530 PMCID: PMC4698288 DOI: 10.1007/s00439-015-1615-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/12/2015] [Indexed: 02/07/2023]
Abstract
Assigning a pathogenic role to mitochondrial DNA (mtDNA) variants and unveiling the potential involvement of the mitochondrial genome in diseases are challenging tasks in human medicine. Assuming that rare variants are more likely to be damaging, we designed a phylogeny-based prioritization workflow to obtain a reliable pool of candidate variants for further investigations. The prioritization workflow relies on an exhaustive functional annotation through the mtDNA extraction pipeline MToolBox and includes Macro Haplogroup Consensus Sequences to filter out fixed evolutionary variants and report rare or private variants, the nucleotide variability as reported in HmtDB and the disease score based on several predictors of pathogenicity for non-synonymous variants. Cutoffs for both the disease score as well as for the nucleotide variability index were established with the aim to discriminate sequence variants contributing to defective phenotypes. The workflow was validated on mitochondrial sequences from Leber’s Hereditary Optic Neuropathy affected individuals, successfully identifying 23 variants including the majority of the known causative ones. The application of the prioritization workflow to cancer datasets allowed to trim down the number of candidate for subsequent functional analyses, unveiling among these a high percentage of somatic variants. Prioritization criteria were implemented in both standalone (http://sourceforge.net/projects/mtoolbox/) and web version (https://mseqdr.org/mtoolbox.php) of MToolBox.
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Affiliation(s)
- Mariangela Santorsola
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E.Orabona 4, 70126, Bari, Italy.,Department of Science and Technologies, University of Sannio, Via Port'Arsa 11, 82100, Benevento, Italy
| | - Claudia Calabrese
- Department of Medical and Surgical Sciences, Medical Genetics, University of Bologna Medical School, via Massarenti 9, 40138, Bologna, Italy
| | - Giulia Girolimetti
- Department of Medical and Surgical Sciences, Medical Genetics, University of Bologna Medical School, via Massarenti 9, 40138, Bologna, Italy
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E.Orabona 4, 70126, Bari, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences, Medical Genetics, University of Bologna Medical School, via Massarenti 9, 40138, Bologna, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E.Orabona 4, 70126, Bari, Italy.
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Venderbosch S, van Vliet S, Craenmehr MHC, Simmer F, de Haan AFJ, Punt CJA, Koopman M, Nagtegaal ID. Mitochondrial microsatellite instability in patients with metastatic colorectal cancer. Virchows Arch 2015; 466:495-502. [PMID: 25697538 PMCID: PMC4422840 DOI: 10.1007/s00428-015-1733-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/02/2015] [Indexed: 12/20/2022]
Abstract
Mitochondrial microsatellite instability (mtMSI), a change in length in mtDNA microsatellite sequences between normal and tumor tissue, has been described as a frequent occurrence in colorectal cancer (CRC). We evaluated the prevalence and prognostic value of mtMSI and its relation to nuclear microsatellite instability (MSI) in patients with metastatic CRC (mCRC). At six loci (D310, D514, D16184, ND1, ND5, and COX1), the mitochondrial DNA sequence was analyzed in normal and tumor tissue, and the mtMSI status was determined. We evaluated the prevalence and outcome in terms of overall survival (OS) in 83 CRC patients with a MSI tumor (including 39 patients with Lynch syndrome) and in 99 mCRC patients with a microsatellite stable (MSS) tumor. A meta-analysis was performed to compare our findings with existing data. mtMSI at the D-loop region was found in 54.4 % (99 out of 182) of all patients. Prevalence of mtMSI was most pronounced at the D310 locus (50.5 %). Prevalence of mtMSI at the D-loop region was not different among patients with MSI compared to MSS tumors. There was no effect of mtMSI on prognosis in patients with MSI or MSS tumors. Prevalence of mtMSI was high in mCRC patients with both MSI and MSS tumors, but there was no correlation with prognosis. mtMSI was particularly present at the D310 locus.
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Affiliation(s)
- S. Venderbosch
- Department of Pathology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
- Department of Medical Oncology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - S. van Vliet
- Department of Pathology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - M. H. C. Craenmehr
- Department of Pathology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - F. Simmer
- Department of Pathology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - A. F. J. de Haan
- Department for Health Evidence, Section Biostatistics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C. J. A. Punt
- Department of Medical Oncology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - M. Koopman
- Department of Medical Oncology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - I. D. Nagtegaal
- Department of Pathology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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Venesio T, Balsamo A, Errichiello E, Ranzani GN, Risio M. Oxidative DNA damage drives carcinogenesis in MUTYH-associated-polyposis by specific mutations of mitochondrial and MAPK genes. Mod Pathol 2013; 26:1371-81. [PMID: 23599153 DOI: 10.1038/modpathol.2013.66] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 12/29/2022]
Abstract
MUTYH is a DNA-base-excision-repair gene implicated in the activation of nuclear and mitochondrial cell-death pathways. MUTYH germline mutations cause an inherited polyposis, MUTYH-associated-polyposis, characterized by multiple adenomas and increased susceptibility to colorectal cancer. Since this carcinogenesis remains partially unknown, we searched for nuclear and mitochondrial gene alterations that may drive the tumorigenic process. Ninety-six adenomas and 7 carcinomas from 12 MUTYH-associated-polyposis and 13 classical/attenuated adenomatous polyposis patients were investigated by sequencing and pyrosequencing for the presence of mutations in KRAS, BRAF, MT-CO1/MT-CO2 and MT-TD genes. KRAS mutations were identified in 24% MUTYH-associated-polyposis vs 15% classical/attenuated familial polyposis adenomas; mutated MUTYH-associated-polyposis adenomas exhibited only c.34G>T transversions in codon 12, an alteration typically associated with oxidative DNA damage, or mutations in codon 13; neither of these mutations was found in classical/attenuated familial polyposis adenomas (P<0.001). Mutated MUTYH-associated-polyposis carcinomas showed KRAS c.34G>T transversions, prevalently occurring with BRAFV600E; none of the classical/attenuated familial polyposis carcinomas displayed these alterations. Comparing mitochondrial DNA from lymphocytes and adenomas of the same individuals, we detected variants in 82% MUTYH-associated-polyposis vs 38% classical/attenuated familial polyposis patients (P=0.040). MT-CO1/MT-CO2 missense mutations, which cause aminoacid changes, were only found in MUTYH-associated-polyposis lesions and were significantly associated with KRAS mutations (P=0.0085). We provide evidence that MUTYH-associated-polyposis carcinogenesis is characterized by the occurrence of specific mutations in both KRAS and phylogenetically conserved genes of mitochondrial DNA which are involved in controlling oxidative phosphorylation; this implies the existence of a colorectal tumorigenesis in which changes in mitochondrial functions cooperate with RAS-induced malignant transformation.
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Affiliation(s)
- Tiziana Venesio
- Unit of Pathology, Institute for Cancer Research and Treatment, Candiolo, (Torino), Italy
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Chen T, Liu Q, Jiang L, Liu C, Ou Q. Mitochondrial COX2 G7598A mutation may have a modifying role in the phenotypic manifestation of aminoglycoside antibiotic-induced deafness associated with 12S rRNA A1555G mutation in a Han Chinese pedigree. Genet Test Mol Biomarkers 2013; 17:122-30. [PMID: 23256547 PMCID: PMC3552164 DOI: 10.1089/gtmb.2012.0251] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recent studies suggest that certain mitochondrial haplogroup markers and some specific variants in mitochondrial haplogroup may also influence the phenotypic expression of particular mitochondrial disorders. In this report, the clinical, genetic, and molecular characterization were identified in a Chinese pedigree with the aminoglycoside antibiotic (AmAn)-induced deafness and nonsyndromic hearing loss (NSHL). The pathogenic gene responsible for this hereditary NSHL pedigree was determined by Microarray chip, which possessed the nine NSHL hot-spot mutations, including GJB2 (35delG, 176dell6bp, 235de1C, and 299delAT), GJB3 (538C>T), SLC26A4 (IVS7-2A>G and 2168A>G), and mitochondrial DNA (mtDNA) 12S rRNA (C1494T and A1555G). Only the homoplasmic A1555G mutation was detected, which was confirmed by direct sequencing. Also, real-time amplification refractory mutation system quantitative polymerase chain reaction methodology was performed to calculate the A1555G mutation load. The proband's complete mtDNA genome were amplified and direct sequencing was performed to determine the mitochondrial haplogroup and private mutations. The proband's mitochondrial haplogroup belonges to M7b1 and a private mutation MTCOX2 G7598A (p.Ala 5 Thr) is found. Phylogenetic analysis of COX2 polypeptide sequences demonstrates that the alanine residue is relatively conserved, but owing to the missense mutation (p.Ala 5 Thr), its side chain hydrophobicity will be changed, and what is more, as it is adjacent to a glutamine residue, which is highly conserved and hydrophilic, in an evolutionary stable domain; G7598A (p.Ala 5 Thr) may alter the protein secondary structure and physiological function of COX2 and, thus, aggravate the mitochondrial dysfunction conferred by the A1555G mutation. Furthermore, the G7598A mutation is absent in 100 unrelated healthy controls; therefore, G7598A (p.Ala 5 Thr) in the mitochondrial haplogoup M7b1 may have a modifying role, enhancing its penetrance and severity, in the AmAn-induced deafness and NSHL associated with 12S rRNA A1555G mutation in the Han Chinese pedigree.
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Affiliation(s)
- Tianbin Chen
- First Clinical College, Fujian Medical University, Fuzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- The First Affiliated Hospital of Fujian Medical University Clinical Transformation Base of Biochip Beijing National Engineering Research Center, Fuzhou, China
| | - Qicai Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- The First Affiliated Hospital of Fujian Medical University Clinical Transformation Base of Biochip Beijing National Engineering Research Center, Fuzhou, China
| | - Ling Jiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- The First Affiliated Hospital of Fujian Medical University Clinical Transformation Base of Biochip Beijing National Engineering Research Center, Fuzhou, China
| | - Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- The First Affiliated Hospital of Fujian Medical University Clinical Transformation Base of Biochip Beijing National Engineering Research Center, Fuzhou, China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- The First Affiliated Hospital of Fujian Medical University Clinical Transformation Base of Biochip Beijing National Engineering Research Center, Fuzhou, China
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Iommarini L, Calvaruso MA, Kurelac I, Gasparre G, Porcelli AM. Complex I impairment in mitochondrial diseases and cancer: Parallel roads leading to different outcomes. Int J Biochem Cell Biol 2013; 45:47-63. [DOI: 10.1016/j.biocel.2012.05.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/03/2012] [Accepted: 05/24/2012] [Indexed: 02/06/2023]
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13
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[Energy metabolism pathway related genes and adaptive evolution of tumor cells]. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2012; 33:557-65. [PMID: 23266974 DOI: 10.3724/sp.j.1141.2012.06557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The proliferation of tumor cells is an extremely energy-consuming process. However, different from normal cells, tumor cells generate energy via glycolysis even under aerobic conditions, which is one of the ten hallmarks of tumor cells. The switch of energy metabolism results in a series of physiological changes in tumor cells, including rapid generation of ATP and abundant biomass for cell proliferation, which form the basis of tumor cells to successfully adapt to their extreme microenvironment (e.g. lack of oxygen). In this review, we will introduce recent progress in studying somatic mutations on the energy metabolism related genes in tumors, with special focus on the potential factors involving in the "switch" and to decipher the genetic adaptive footprint of the "switch" from the angle of molecular evolution.
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14
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Li H, Hong ZH. Mitochondrial DNA mutations in human tumor cells. Oncol Lett 2012; 4:868-872. [PMID: 23162613 DOI: 10.3892/ol.2012.874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 08/20/2012] [Indexed: 02/02/2023] Open
Abstract
Mitochondria play significant roles in cellular energy metabolism, free radical generation and apoptosis. The dysfunction of mitochondria is correlated with the origin and progression of tumors; thus, mutations in the mitochondrial genome that affect mitochondrial function may be one of the causal factors of tumorigenesis. Although the role of mitochondrial DNA (mtDNA) mutations in carcinogenesis has been investigated extensively by various approaches, the conclusions remain controversial to date. This review briefly summarizes the recent progress in this field.
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Affiliation(s)
- Hui Li
- Department of Genetics and Developmental Biology, Southeast University School of Medicine; ; The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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15
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Derenko M, Malyarchuk B, Denisova G, Perkova M, Rogalla U, Grzybowski T, Khusnutdinova E, Dambueva I, Zakharov I. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS One 2012; 7:e32179. [PMID: 22363811 PMCID: PMC3283723 DOI: 10.1371/journal.pone.0032179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/22/2012] [Indexed: 12/21/2022] Open
Abstract
With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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16
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Wang CY, Zhao ZB. Somatic mtDNA mutations in lung tissues of pesticide-exposed fruit growers. Toxicology 2012; 291:51-5. [DOI: 10.1016/j.tox.2011.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 10/12/2011] [Accepted: 10/27/2011] [Indexed: 12/24/2022]
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17
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Skonieczna K, Malyarchuk BA, Grzybowski T. The landscape of mitochondrial DNA variation in human colorectal cancer on the background of phylogenetic knowledge. Biochim Biophys Acta Rev Cancer 2011; 1825:153-9. [PMID: 22178219 DOI: 10.1016/j.bbcan.2011.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/21/2011] [Accepted: 11/23/2011] [Indexed: 01/07/2023]
Abstract
Recently, an increasing number of studies indicate that mutations in mitochondrial genome may contribute to cancer development or metastasis. Hence, it is important to determine whether the mitochondrial DNA might be a good, clinically applicable marker of cancer. This review describes hereditary as well as somatic mutations reported in mitochondrial DNA of colorectal cancer cells. We showed here that the entire mitochondrial genome mutational spectra are different in colorectal cancer and non-tumor cells. We also placed the described mutations on the phylogenetic context, which highlighted the recurrent problem of data quality. Therefore, the most important rules for adequately assessing the quality of mitochondrial DNA sequence analysis in cancer have been summarized. As follows from this review, neither the reliable spectrum of mtDNA somatic mutations nor the association between hereditary mutations and colorectal cancer risk have been resolved. This indicates that only high resolution studies on mtDNA variability, followed by a proper data interpretation employing phylogenetic knowledge may finally verify the utility of mtDNA sequence (if any) in clinical practice.
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Affiliation(s)
- Katarzyna Skonieczna
- Department of Molecular and Forensic Genetics, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Sklodowskiej-Curie Street, 85-094 Bydgoszcz, Poland
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Liu J, Wang LD, Sun YB, Li EM, Xu LY, Zhang YP, Yao YG, Kong QP. Deciphering the Signature of Selective Constraints on Cancerous Mitochondrial Genome. Mol Biol Evol 2011; 29:1255-61. [DOI: 10.1093/molbev/msr290] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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