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de Souza FG, Silva CS, de Araújo GS, Santana-da-Silva MN, Gobbo AR, da Silva MB, Pinto P, da Costa PF, Salgado CG, Ribeiro-Dos-Santos Â, Cavalcante GC. Mitochondrial variants of complex I genes associated with leprosy clinical subtypes. Sci Rep 2024; 14:6365. [PMID: 38493220 PMCID: PMC10944465 DOI: 10.1038/s41598-024-57191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/15/2024] [Indexed: 03/18/2024] Open
Abstract
Leprosy is a chronic bacterial infection mainly caused by Mycobacterium leprae that primarily affects skin and peripheral nerves. Due to its ability to absorb carbon from the host cell, the bacillus became dependent on energy production, mainly through oxidative phosphorylation. In fact, variations in genes of Complex I of oxidative phosphorylation encoded by mtDNA have been associated with several diseases in humans, including bacterial infections, which are possible influencers in the host response to leprosy. Here, we investigated the presence of variants in the mtDNA genes encoding Complex I regarding leprosy, as well as the analysis of their pathogenicity in the studied cohort. We found an association of 74 mitochondrial variants with either of the polar forms, Pole T (Borderline Tuberculoid) or Pole L (Borderline Lepromatous and Lepromatous) of leprosy. Notably, six variants were exclusively found in both clinical poles of leprosy, including m.4158A>G and m.4248T>C in MT-ND1, m.13650C>A, m.13674T>C, m.12705C>T and m.13263A>G in MT-ND5, of which there are no previous reports in the global literature. Our observations reveal a substantial number of mutations among different groups of leprosy, highlighting a diverse range of consequences associated with mutations in genes across these groups. Furthermore, we suggest that the six specific variants exclusively identified in the case group could potentially play a crucial role in leprosy susceptibility and its clinical differentiation. These variants are believed to contribute to the instability and dysregulation of oxidative phosphorylation during the infection, further emphasizing their significance.
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Affiliation(s)
- Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Caio S Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Gilderlanio S de Araújo
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Mayara N Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Angélica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Moisés Batista da Silva
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Giovanna C Cavalcante
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
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de Souza FG, da Silva MB, de Araújo GS, Silva CS, Pinheiro AHG, Cáceres-Durán MÁ, Santana-da-Silva MN, Pinto P, Gobbo AR, da Costa PF, Salgado CG, Ribeiro-Dos-Santos Â, Cavalcante GC. Whole mitogenome sequencing uncovers a relation between mitochondrial heteroplasmy and leprosy severity. Hum Genomics 2023; 17:110. [PMID: 38062538 PMCID: PMC10704783 DOI: 10.1186/s40246-023-00555-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND In recent years, the mitochondria/immune system interaction has been proposed, so that variants of mitochondrial genome and levels of heteroplasmy might deregulate important metabolic processes in fighting infections, such as leprosy. METHODS We sequenced the whole mitochondrial genome to investigate variants and heteroplasmy levels, considering patients with different clinical forms of leprosy and household contacts. After sequencing, a specific pipeline was used for preparation and bioinformatics analysis to select heteroplasmic variants. RESULTS We found 116 variants in at least two of the subtypes of the case group (Borderline Tuberculoid, Borderline Lepromatous, Lepromatous), suggesting a possible clinical significance to these variants. Notably, 15 variants were exclusively found in these three clinical forms, of which five variants stand out for being missense (m.3791T > C in MT-ND1, m.5317C > A in MT-ND2, m.8545G > A in MT-ATP8, m.9044T > C in MT-ATP6 and m.15837T > C in MT-CYB). In addition, we found 26 variants shared only by leprosy poles, of which two are characterized as missense (m.4248T > C in MT-ND1 and m.8027G > A in MT-CO2). CONCLUSION We found a significant number of variants and heteroplasmy levels in the leprosy patients from our cohort, as well as six genes that may influence leprosy susceptibility, suggesting for the first time that the mitogenome might be involved with the leprosy process, distinction of clinical forms and severity. Thus, future studies are needed to help understand the genetic consequences of these variants.
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Affiliation(s)
- Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Moisés Batista da Silva
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Gilderlanio S de Araújo
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Caio S Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Andrey Henrique Gama Pinheiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Angélica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
| | - Giovanna C Cavalcante
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
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de Souza FG, Cavalcante GC. Mitochondria in Mycobacterium Infection: From the Immune System to Mitochondrial Haplogroups. Int J Mol Sci 2022; 23:ijms23179511. [PMID: 36076909 PMCID: PMC9455157 DOI: 10.3390/ijms23179511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
In humans, mitochondria play key roles in the regulation of cellular functions, such as the regulation of the innate immune response and are targets of several pathogenic viruses and bacteria. Mycobacteria are intracellular pathogens that infect cells important to the immune system of organisms and target mitochondria to meet their energy demands. In this review, we discuss the main mechanisms by which mitochondria regulate the innate immune response of humans to mycobacterial infection, especially those that cause tuberculosis and leprosy. Notably, the importance of mitochondrial haplogroups and ancestry studies for mycobacterial diseases is also discussed.
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Song Y, Hussain T, Wang J, Liao Y, Yue R, Sabir N, Zhao D, Zhou X. Mitochondrial Transcription Factor A Regulates Mycobacterium bovis-Induced IFN-β Production by Modulating Mitochondrial DNA Replication in Macrophages. J Infect Dis 2020; 221:438-448. [PMID: 31495880 DOI: 10.1093/infdis/jiz461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/06/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Mycobacterium bovis persistently survives in macrophages by developing multiple strategies to evade host immune responses, and the early induction of interferon-β (IFN-β) is one of these critical strategies. The mitochondrial transcription factor A (TFAM) plays a vital role in mitochondrial DNA (mtDNA) metabolism and has been suggested to influence IFN-β production in response to viral infection. However, its role in the production of IFN-β by M. bovis has not been elucidated. METHODS In the current study, we investigated the role of TFAM in the production of IFN-β in M. bovis-infected macrophages. RESULTS We found that knockdown of TFAM expression significantly reduced M. bovis-induced IFN-β production, mtDNA copy numbers and cytosolic mtDNA were increased in murine macrophages with M. bovis infection, cytosolic mtDNA contributed to IFN-β production, and TFAM was required for the increase in mtDNA copy numbers induced by M. bovis. We also observed that TFAM affected the intracellular survival of M. bovis. CONCLUSIONS Our results suggest that TFAM plays an essential role in M. bovis-induced IFN-β production by regulating mtDNA copy numbers. This might be a new strategy adopted by M. bovis for its intracellular survival.
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Affiliation(s)
- Yinjuan Song
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Tariq Hussain
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jie Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yi Liao
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruichao Yue
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Naveed Sabir
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Deming Zhao
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiangmei Zhou
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Skonieczna K, Jawień A, Marszałek A, Grzybowski T. Mitogenome germline mutations and colorectal cancer risk in Polish population. Arch Med Sci 2020; 16:366-373. [PMID: 32190148 PMCID: PMC7069428 DOI: 10.5114/aoms.2018.80893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION To date, several nuclear DNA variants have been shown to be associated with increased risk of developing colorectal cancer. Despite the fact that mitochondria play an important role in carcinogenesis, little is known about inherited mitochondrial DNA mutations that could be involved in this disease. Thus, potential associations between inherited mutations in the entire mitochondrial genomes and colorectal cancer were analysed in this study. MATERIAL AND METHODS Two hundred mitogenome sequences determined for colorectal cancer patients and healthy individuals from Poland were used to investigate the association between mtDNA alleles or haplogroups and colorectal cancer. Additional mtDNA control region haplotypes determined for 1353 individuals from the general Polish population were used for comparison of haplogroup and certain allele frequencies between case and control groups. RESULTS The non-R clades together with their diagnostic T alleles at positions 12705 and 16223 were observed with higher frequencies in healthy individuals than in colorectal cancer patients. Nevertheless, the differences of the R macrohaplogroup (as well as 12705 or 16223 alleles) frequencies between cases and controls were statistically insignificant after Bonferroni correction. Most of the non-R clades were of Asian and African origin, but none of them were prevalent in the control group. Moreover, neither mtDNA alleles nor haplogroups were associated with clinicopathological parameters of colorectal cancer patients. CONCLUSIONS Contrary to some previous reports, the findings of this study do not support the hypothesis that mitochondrial DNA variants contribute to inherited predisposition to colorectal cancer.
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Affiliation(s)
- Katarzyna Skonieczna
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Arkadiusz Jawień
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Andrzej Marszałek
- Department of Pathology, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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Li X, Zhou TC, Wu CH, Tao LL, Bi R, Chen LJ, Deng DY, Liu C, Otecko NO, Tang Y, Lai X, Zhang L, Wei J. Correlations between mitochondrial DNA haplogroup D5 and chronic hepatitis B virus infection in Yunnan, China. Sci Rep 2018; 8:869. [PMID: 29343698 PMCID: PMC5772044 DOI: 10.1038/s41598-018-19184-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial abnormality is frequently reported in individuals with hepatitis B virus (HBV) infection, but the associated hosts’ mitochondrial genetic factors remain obscure. We hypothesized that mitochondria may affect host susceptibility to HBV infection. In this study, we aimed to detect the association between chronic HBV infection and mitochondrial DNA in Chinese from Yunnan, Southwest China. A total of 272 individuals with chronic HBV infection (CHB), 310 who had never been infected by HBV (healthy controls, HC) and 278 with a trace of HBV infection (spontaneously recovered, SR) were analysed for mtDNA sequence variations and classified into respective haplogroups. Haplogroup frequencies were compared between HBV infected patients, HCs and SRs. Haplogroup D5 presented a higher frequency in CHBs than in HCs (P = 0.017, OR = 2.87, 95% confidence interval [CI] = (1.21–6.81)) and SRs (P = 0.049, OR = 2.90, 95% CI = 1.01–8.35). The network of haplogroup D5 revealed a distinct distribution pattern between CHBs and non-CHBs. A trend of higher viral load among CHBs with haplogroup D5 was observed. Our results indicate the risk potential of mtDNA haplogroup D5 in chronic HBV infection in Yunnan, China.
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Affiliation(s)
- Xiao Li
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Tai-Cheng Zhou
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Chang-Hui Wu
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Li-Lin Tao
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China
| | - Li-Jun Chen
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - De-Yao Deng
- Clinical Laboratory of the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Chang Liu
- Clinical Laboratory of the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yang Tang
- The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, 650000, China
| | - Xin Lai
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Liang Zhang
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China.
| | - Jia Wei
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China.
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Nucleoside reverse transcriptase inhibitor-induced rat oocyte dysfunction and low fertility mediated by autophagy. Oncotarget 2017; 9:3895-3907. [PMID: 29423092 PMCID: PMC5790509 DOI: 10.18632/oncotarget.23243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Abstract
Low fertility is one of the most common side effects caused by nucleoside reverse transcriptase inhibitors (NRTIs), whereas the molecular mechanism underlying this process were largely unclear. This study was conducted to investigate whether autophagy plays a role in NRTIs-induced oocyte dysfunction and low fertility in female rat. Both in vivo and in vitro experiments were conducted. For the in vivo experiment, female adult Sprague-Dawley rats were subjected to zidovudine (AZT) and lamivudine (3TC) intragastric treatment for 3, 6, 9, and 12 weeks; a control was also set. Oocytes were collected for maturation evaluation, in vitro fertilization and mitochondrial function assays, and apoptosis and autophagy analysis. For the in vitro experiment, oocytes were collected and assigned to the control, 3-methyladenine (3-MA, an effective autophagy inhibitor), AZT, AZT+3-MA, 3TC, and 3TC+3-MA groups. The oocytes were cultured with the abovementioned drugs for 24, 48, and 72 h and then, subjected to the same assays as in the in vivo study. The results showed a significant time-dependent decrease in oocyte maturation-related maker levels, oocyte cleavage rate, blastocyst formation rate, mitochondrial DNA copy number and adenosine triphosphate level, and apoptosis, and a significant increase in the reactive oxygen species levels (all P-values < 0.05), in both the in vivo and the in vitro experiments. These changes, except for the changes in the oocyte maturation-related markers, were partially attenuated by 3-MA. In conclusion, we demonstrated that NRTIs can cause rat oocyte dysfunction and low fertility, and this damage was, at least partially, mediated by autophagy.
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Wang D, Li GD, Fan Y, Zhang DF, Bi R, Yu XF, Long H, Li YY, Yao YG. The mtDNA replication-related genes TFAM and POLG are associated with leprosy in Han Chinese from Southwest China. J Dermatol Sci 2017; 88:349-356. [PMID: 28958595 DOI: 10.1016/j.jdermsci.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND The pathogen Mycobacterium leprae of leprosy is heavily dependent on the host energy metabolites and nutritional products for survival. Previously we and others have identified associations of several mitochondrion-related genes and mitochondrial DNA (mtDNA) copy number alterations with leprosy and/or its subtype. We hypothesized that genetic variants of mtDNA replication-related genes would affect leprosy. OBJECTIVE We aimed to identify genetic associations between the mtDNA replication-related genes TFAM, POLG and leprosy. METHODS Genetic association study was performed in 2898 individuals from two independent sample sets in Yunnan Province, China. We first screened 7 tag SNPs of TFAM and POLG in 527 leprosy cases and 583 controls (Sample I). Expression quantitative trait loci (eQTL) analysis and differential mRNA expression were analyzed to discern potential effect of risk variants. The entire exon region of TFAM and POLG were further analyzed in 798 leprosy cases and 990 controls (Sample II; 4327 East Asians from the ExAC dataset was included as a reference control) by using targeted gene sequencing for fine mapping potentially causal variants. RESULTS Two tag SNPs of TFAM (rs1049432, P=0.007) and POLG (rs3176238, P=0.006) were associated with multibacillary leprosy (MB) in Sample I and the significance survived correction for multiple comparisons. SNPs rs1937 of TFAM (which was linked with rs1049432) and rs61756401 of POLG were associated with leprosy, whereas no potentially causative coding variants were identified in Sample II. The eQTL analysis showed that rs1049432 was a significant cis eQTL for TFAM in nerve tissue (P=1.20×10-12), and rs3176238 was a significant cis eQTL for POLG in nerve (P=3.90×10-13) and skin tissues (P=2.50×10-11). Consistently, mRNA level of POLG was differentially expressed in leprotic skin lesions. CONCLUSIONS Genetic variants of TFAM and POLG were associated with leprosy in Han Chinese, presumably by affecting gene expression.
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Affiliation(s)
- Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Guo-Dong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Xiu-Feng Yu
- Wenshan Institute of Dermatology, Wenshan, Yunnan, 663000, China
| | - Heng Long
- Wenshan Institute of Dermatology, Wenshan, Yunnan, 663000, China
| | - Yu-Ye Li
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Common variants in the PARL and PINK1 genes increase the risk to leprosy in Han Chinese from South China. Sci Rep 2016; 6:37086. [PMID: 27876828 PMCID: PMC5120299 DOI: 10.1038/srep37086] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/24/2016] [Indexed: 01/04/2023] Open
Abstract
Leprosy is a chronic infectious and neurological disease caused by Mycobacterium leprae, an unculturable pathogen with massive genomic decay and dependence on host metabolism. We hypothesized that mitochondrial genes PARL and PINK1 would confer risk to leprosy. Thirteen tag SNPs of PARL and PINK1 were analyzed in 3620 individuals with or without leprosy from China. We also sequenced the entire exons of PARL, PINK1 and PARK2 in 80 patients with a family history of leprosy by using the next generation sequencing technology (NGS). We found that PARL SNP rs12631031 conferred a risk to leprosy (Padjusted = 0.019) and multibacillary leprosy (MB, Padjusted = 0.020) at the allelic level. rs12631031 and rs7653061 in PARL were associated with leprosy and MB (dominant model, Padjusted < 0.05) at the genotypic level. PINK1 SNP rs4704 was associated with leprosy at the genotypic level (Padjusted = 0.004). We confirmed that common variants in PARL and PINK1 were associated with leprosy in patients underwent NGS. Furthermore, PARL and PINK1 could physically interact with each other and were involved in the highly connected network formed by reported leprosy susceptibility genes. Together, our results showed that PARL and PINK1 genetic variants are associated with leprosy.
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Li GD, Wang D, Zhang DF, Xiang Q, Feng JQ, Li XA, Li YY, Yao YG. Fine mapping of the GWAS loci identifies SLC35D1 and IL23R as potential risk genes for leprosy. J Dermatol Sci 2016; 84:322-329. [PMID: 27712858 DOI: 10.1016/j.jdermsci.2016.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 01/16/2023]
Abstract
BACKGROUND Previous genome-wide association study (GWAS) identified two new leprosy associated loci (1p31.3 [rs3762318] and 6q24.3 [rs2275606]). However, there were insufficient validations in independent populations. OBJECTIVE To validate the association and to map the potentially causal variants/genes underlying the association between the confirmed GWAS hit and leprosy. METHODS We genotyped 10 variants in the regions encompassing the two loci in 1110 Han Chinese subjects with and without leprosy, followed by expression quantitative trait loci (eQTL), mRNA expression profiling, and network analysis. We further sequenced the exon region of four genes that were located in the confirmed GWAS hit region in 80 leprosy patients and 99 individuals without leprosy. RESULTS We validated the positive association of rs3762318 with multibacillary leprosy (P=7.5×10-4), whereas the association of rs2275606 could not be validated. eQTL analysis showed that both the GWAS locus rs3762318 and one surrounding positively associated SNP rs2144658 (P=1.8×10-3) significantly affected the mRNA expression of a nearby gene SLC35D1, which might be involved in metabolism. Moreover, SLC35D1 was differentially expressed in skin tissues of leprosy patients, and the differential expression pattern was consistent among leprosy subtypes. Rare damaging missense variants in IL23R were significantly enriched in leprosy patients. CONCLUSION Our results supported the positive association between the GWAS reported rs3762318 and leprosy, and SLC35D1 and IL23R might be the causal genes.
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Affiliation(s)
- Guo-Dong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Qun Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Jia-Qi Feng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Xiao-An Li
- Yuxi City Center for Disease Control and Prevention, Yuxi, Yunnan 653100, China
| | - Yu-Ye Li
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.
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EMPOP-quality mtDNA control region sequences from Kashmiri of Azad Jammu & Kashmir, Pakistan. Forensic Sci Int Genet 2016; 25:125-131. [PMID: 27591488 DOI: 10.1016/j.fsigen.2016.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 01/13/2023]
Abstract
The mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were generated through Sanger sequencing method for 317 self-identified Kashmiris from all districts of Azad Jammu & Kashmir Pakistan. The population sample set showed a total of 251 haplotypes, with a relatively high haplotype diversity (0.9977) and a low random match probability (0.54%). The containing matrilineal lineages belonging to three different phylogeographic origins of Western Eurasian (48.9%), South Asian (47.0%) and East Asian (4.1%). The present study was compared to previous data from Pakistan and other worldwide populations (Central Asia, Western Asia, and East & Southeast Asia). The dataset is made available through EMPOP under accession number EMP00679 and will serve as an mtDNA reference database in forensic casework in Pakistan.
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Ma K, Li H, Cao Y, Zhao X, Liu W, Zhao X. Haplotype diversity in mitochondrial genome in a Chinese Han population. J Hum Genet 2016; 61:903-906. [PMID: 27305984 DOI: 10.1038/jhg.2016.74] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/08/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022]
Abstract
Investigations into the use of mitochondrial genome (mtGenome) typing by massively parallel sequencing technologies are well underway in many areas, including forensic genetics. Previous studies have demonstrated that mtGenome sequencing data generated from Ion torrent personal genome machine (PGM) system were highly viable and reliable in forensic research. In this study, 145 whole mtGenomes from unrelated Chinese Han population were sequenced using the Ion PGM system. Results showed that 145 distinct haplotypes were obtained at a relatively high coverage with limited strand bias. The distribution of variants across the entire mtGenomes was illustrated and 70.74% of the variants were observed outside of the control region. An overall increase in the number of unique haplotypes as well as haplotype diversity were observed by detection of mtGenome compared with hypervariable region I/II (HV I/II) and control region (CR). This study demonstrates the substantially higher degree of haplotype resolution with whole-mtGenome sequences in comparison to HV I/II or CR that historically targeted for forensic testing, which shows the potential value of mtGenome typing in forensic testing in the future.
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Affiliation(s)
- Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuejun Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Xueying Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
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Spadafora D, Kozhukhar N, Alexeyev MF. Presequence-Independent Mitochondrial Import of DNA Ligase Facilitates Establishment of Cell Lines with Reduced mtDNA Copy Number. PLoS One 2016; 11:e0152705. [PMID: 27031233 PMCID: PMC4816344 DOI: 10.1371/journal.pone.0152705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/17/2016] [Indexed: 01/10/2023] Open
Abstract
Due to the essential role played by mitochondrial DNA (mtDNA) in cellular physiology and bioenergetics, methods for establishing cell lines with altered mtDNA content are of considerable interest. Here, we report evidence for the existence in mammalian cells of a novel, low- efficiency, presequence-independent pathway for mitochondrial protein import, which facilitates mitochondrial uptake of such proteins as Chlorella virus ligase (ChVlig) and Escherichia coli LigA. Mouse cells engineered to depend on this pathway for mitochondrial import of the LigA protein for mtDNA maintenance had severely (up to >90%) reduced mtDNA content. These observations were used to establish a method for the generation of mouse cell lines with reduced mtDNA copy number by, first, transducing them with a retrovirus encoding LigA, and then inactivating in these transductants endogenous Lig3 with CRISPR-Cas9. Interestingly, mtDNA depletion to an average level of one copy per cell proceeds faster in cells engineered to maintain mtDNA at low copy number. This makes a low-mtDNA copy number phenotype resulting from dependence on mitochondrial import of DNA ligase through presequence-independent pathway potentially useful for rapidly shifting mtDNA heteroplasmy through partial mtDNA depletion.
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Affiliation(s)
- Domenico Spadafora
- Department of Pharmacology, University of South Alabama, 307 University Blvd, Mobile, Alabama, 36688, United States of America
| | - Natalia Kozhukhar
- Department of Physiology and Cell Biology, 307 University Blvd, University of South Alabama, Mobile, Alabama, 36688, United States of America
| | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, 307 University Blvd, University of South Alabama, Mobile, Alabama, 36688, United States of America
- Center for Lung Biology, University of South Alabama, 307 University Blvd, Mobile, Alabama, 36688, United States of America
- * E-mail:
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Kang L, Wang CC, Chen F, Yao D, Jin L, Li H. Northward genetic penetration across the Himalayas viewed from Sherpa people. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:342-9. [PMID: 24617465 DOI: 10.3109/19401736.2014.895986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Himalayas have been suggested as a natural barrier for human migrations, especially the northward dispersals from the Indian Subcontinent to Tibetan Plateau. However, although the majority of Sherpa have a Tibeto-Burman origin, considerable genetic components from Indian Subcontinent have been observed in Sherpa people living in Tibet. The western Y chromosomal haplogroups R1a1a-M17, J-M304, and F*-M89 comprise almost 17% of Sherpa paternal gene pool. In the maternal side, M5c2, M21d, and U from the west also count up to 8% of Sherpa people. Those lineages with South Asian origin indicate that the Himalayas have been permeable to bidirectional gene flow.
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Affiliation(s)
- Longli Kang
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Chuan-Chao Wang
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Feng Chen
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Dali Yao
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Li Jin
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Hui Li
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and.,b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
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15
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Xiang YL, Zhang DF, Wang D, Li YY, Yao YG. Common variants of OPA1 conferring genetic susceptibility to leprosy in Han Chinese from Southwest China. J Dermatol Sci 2015; 80:133-41. [PMID: 26360011 DOI: 10.1016/j.jdermsci.2015.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Leprosy is an ancient chronic infection caused by Mycobacterium leprae. Onset of leprosy was highly affected by host nutritional condition and energy production, (partially) due to genomic loss and parasitic life style of M. leprae. The optic atrophy 1 (OPA1) gene plays an essential role in mitochondria, which function in cellular energy supply and innate immunity. OBJECTIVE To investigate the potential involvement of OPA1 in leprosy. METHODS We analyzed 7 common genetic variants of OPA1 in 1110 Han Chinese subjects with and without leprosy, followed by mRNA expression profiling and protein-protein interaction (PPI) network analysis. RESULTS We observed positive associations between OPA1 variants rs9838374 (Pgenotypic=0.003) and rs414237 (Pgenotypic=0.002) with lepromatous leprosy. expression quantitative trait loci (eQTL) analysis showed that the leprosy-related risk allele C of rs414237 is correlated with lower OPA1 mRNA expression level. Indeed, we identified a decrease of OPA1 mRNA expression in both with patients and cellular model of leprosy. In addition, the PPI analysis showed that OPA1 protein was actively involved in the interaction network of M. leprae induced differentially expressed genes. CONCLUSION Our results indicated that OPA1 variants confer risk of leprosy and may affect OPA1 expression, mitochondrial function and antimicrobial pathways.
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Affiliation(s)
- Yang-Lin Xiang
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China; Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
| | - Yu-Ye Li
- Department of Dermatology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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Mitochondrial DNA Haplogroup A Decreases the Risk of Drug Addiction but Conversely Increases the Risk of HIV-1 Infection in Chinese Addicts. Mol Neurobiol 2015; 53:3873-3881. [PMID: 26162319 DOI: 10.1007/s12035-015-9323-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/24/2015] [Indexed: 01/19/2023]
Abstract
Drug addiction is one of the most serious social problems in the world today and addicts are always at a high risk of acquiring HIV infection. Mitochondrial impairment has been reported in both drug addicts and in HIV patients undergoing treatment. In this study, we aimed to investigate whether mitochondrial DNA (mtDNA) haplogroup could affect the risk of drug addiction and HIV-1 infection in Chinese. We analyzed mtDNA sequence variations of 577 Chinese intravenous drug addicts (289 with HIV-1 infection and 288 without) and compared with 2 control populations (n = 362 and n = 850). We quantified the viral load in HIV-1-infected patients with and without haplogroup A status and investigated the potential effect of haplogroup A defining variants m.4824A > G and m.8794C > T on the cellular reactive oxygen species (ROS) levels by using an allotopic expression assay. mtDNA haplogroup A had a protective effect against drug addiction but appeared to confer an increased risk of HIV infection in addicts. HIV-1-infected addicts with haplogroup A had a trend for a higher viral load, although the mean viral load was similar between carriers of haplogroup A and those with other haplogroup. Hela cells overexpressing allele m.8794 T showed significantly decreased ROS levels as compared to cells with the allele m.8794C (P = 0.03). Our results suggested that mtDNA haplogroup A might protect against drug addiction but increase the risk of HIV-1 infection. The contradictory role of haplogroup A might be caused by an alteration in mitochondrial function due to a particular mtDNA ancestral variant.
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Zhang AM, Ma K, Song Y, Feng Y, Duan H, Zhao P, Wang B, Xu G, Li Z, Xia X. Mitochondrial DNAs decreased and correlated with clinical features in HCV patients from Yunnan, China. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2516-9. [PMID: 26099975 DOI: 10.3109/19401736.2015.1036255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hepatitis C was the most popular chronic infectious liver disease worldwide. It was identified that Hepatitis C virus (HCV) infection could lead to mitochondrial dysfunction, though the mechanism was not fully understood. To investigate whether mtDNA copy number could be affected by HCV infection and be associated with clinical features of HCV patients, mtDNA copy numbers were analyzed in 242 patients with HCV infection and 226 matched control samples. The results suggested that mtDNA copy numbers significantly decreased in HCV patients (68.80 ± 3.33) than in control samples (81.54 ± 4.50) (p = 0.022). When males/females were separated from total patients to compare mtDNA copy numbers with gender matched controls, mtDNA copy numbers still significantly decreased in male HCV patients (p = 0.002). Further analysis indicated that level of high-density lipoprotein cholesterol (HDL-C) was negatively correlated with mtDNA copy numbers in total HCV patients (r = -0.128, p = 0.047), and this correlation was more significant in male HCV patients (r = -0.266, p = 0.030). Intriguingly, aspartate amino-transferase (AST) showed positive correlation with mtDNA copy numbers (r = 0.260, p = 0.034) in male HCV patients. Our results indicated that mtDNA copy numbers depleted and correlated with clinical features in male HCV patients.
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Affiliation(s)
- A-Mei Zhang
- a Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming, Yunnan , China
| | - Ke Ma
- a Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming, Yunnan , China
| | - Yuzhu Song
- a Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming, Yunnan , China
| | - Yue Feng
- a Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming, Yunnan , China
| | - Haiping Duan
- b Department of Clinical Laboratory , The People's Hospital of LuXi County in Yunnan Province , Yunnan , China
| | - Ping Zhao
- c Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense , Second Military Medical University , Shanghai , China , and
| | - Binghui Wang
- a Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming, Yunnan , China
| | - Gang Xu
- c Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense , Second Military Medical University , Shanghai , China , and
| | - Zheng Li
- d Department of Clinical Laboratory , The First People's Hospital of Yunnan Province , Yunnan , China
| | - Xueshan Xia
- a Faculty of Life Science and Technology , Kunming University of Science and Technology , Kunming, Yunnan , China
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18
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Mitochondrial DNA: A disposable genome? Biochim Biophys Acta Mol Basis Dis 2015; 1852:1805-9. [PMID: 26071375 DOI: 10.1016/j.bbadis.2015.05.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 01/21/2023]
Abstract
In mammalian cells, mitochondria are the only organelles besides the nucleus that house genomic DNA. The mammalian mitochondrial genome is represented by prokaryotic-type, circular, highly compacted DNA molecules. Today, more than a half-century after their discovery, the biology of these small and redundant molecules remains much less understood than that of their nuclear counterparts. One peculiarity of the mitochondrial genome that emerged in recent years is its disposable nature, as evidenced by cells abandoning a fraction of their mitochondrial DNA (mtDNA) in response to various stimuli with little or no physiological consequence. Here, we review some recent developments in the field of mtDNA biology and discuss emerging questions on the disposability and indispensability of mtDNA.
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Chen S, Li Z, He Y, Zhang F, Li H, Liao Y, Wei Z, Wan G, Xiang X, Hu M, Xia K, Chen X, Tang J. Elevated mitochondrial DNA copy number in peripheral blood cells is associated with childhood autism. BMC Psychiatry 2015; 15:50. [PMID: 25884388 PMCID: PMC4367837 DOI: 10.1186/s12888-015-0432-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/27/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Several lines of evidence indicate mitochondrial impairment in the pathophysiology of autism. As one of the most common biomarkers for mitochondrial dysfunction, mitochondrial DNA (mtDNA) copy number has also been linked to autism, but the relationship between mtDNA copy number and autism was still obscured. In this study, we performed a case-control study to investigate whether mtDNA copy number in peripheral blood cells is related to patients with autism. METHODS Relative mtDNA copy number in peripheral blood cells was measured by using real-time polymerase chain reaction method. The participants in this study included 78 patients with childhood autism and 83 typically developing children. RESULTS We observed children with autism had significantly elevated relative mtDNA copy number than healthy controls (Beta = -0.173, P = 0.0003). However, there were no significant correlations between mtDNA copy number and clinical features (paternal age, maternal age, age of onset, illness of duration, CARS score and ABC score) in childhood autism. CONCLUSION We show that elevated mtDNA copy number in peripheral blood is associated with autism, indicating that there may be mitochondrial dysfunction in children with autism.
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Affiliation(s)
- Shan Chen
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China.
| | - Zongchang Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Ying He
- Institute of Mental Health of the Second Xiangya Hospital, National Laboratory for Psychiatric Disease Diagnosis and Treatment, Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Central South University, Changsha, China.
| | - Fengyu Zhang
- Institute of Mental Health of the Second Xiangya Hospital, National Laboratory for Psychiatric Disease Diagnosis and Treatment, Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Central South University, Changsha, China. .,The National Clinical Research Center for Psychiatric and Psychological Diseases, Changsha, China. .,Division of Clinical Sciences, Lieber Institute for Brain Development, John Hopkins University Medical Campus, 855 N. Wolfe Street, Suite 300, Baltimore, 21205, MD, USA.
| | - Hong Li
- Institute of Mental Health of the Second Xiangya Hospital, National Laboratory for Psychiatric Disease Diagnosis and Treatment, Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Central South University, Changsha, China.
| | - Yanhui Liao
- Institute of Mental Health of the Second Xiangya Hospital, National Laboratory for Psychiatric Disease Diagnosis and Treatment, Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Central South University, Changsha, China.
| | - Zhen Wei
- Department of Women's Health Care, The Affiliated Shenzhen Maternal and Child Health Care Hospital, Nanfang University of Medical Science, Shenzhen, China.
| | - Guobin Wan
- Department of Women's Health Care, The Affiliated Shenzhen Maternal and Child Health Care Hospital, Nanfang University of Medical Science, Shenzhen, China.
| | - Xi Xiang
- BGI Ark Biotechnology Co., Ltd., Shenzhen, Guangdong, China.
| | - Maolin Hu
- Institute of Mental Health of the Second Xiangya Hospital, National Laboratory for Psychiatric Disease Diagnosis and Treatment, Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Central South University, Changsha, China.
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China.
| | - Xiaogang Chen
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China. .,Institute of Mental Health of the Second Xiangya Hospital, National Laboratory for Psychiatric Disease Diagnosis and Treatment, Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Central South University, Changsha, China. .,The National Clinical Research Center for Psychiatric and Psychological Diseases, Changsha, China.
| | - Jinsong Tang
- Institute of Mental Health of the Second Xiangya Hospital, National Laboratory for Psychiatric Disease Diagnosis and Treatment, Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Central South University, Changsha, China. .,The National Clinical Research Center for Psychiatric and Psychological Diseases, Changsha, China. .,Division of Clinical Sciences, Lieber Institute for Brain Development, John Hopkins University Medical Campus, 855 N. Wolfe Street, Suite 300, Baltimore, 21205, MD, USA.
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20
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Hao XD, Chen P, Wang Y, Li SX, Xie LX. Mitochondrial DNA copy number, but not haplogroup is associated with keratoconus in Han Chinese population. Exp Eye Res 2015; 132:59-63. [PMID: 25613073 DOI: 10.1016/j.exer.2015.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 12/31/2014] [Accepted: 01/18/2015] [Indexed: 10/24/2022]
Abstract
Oxidative stress may play a role in the pathogenesis of keratoconus (KC). Mitochondrial DNA (mtDNA) is closely related to mitochondrion function, and variations may affect the generation of reactive oxygen species (ROS) and be involved in the pathogenesis of KC. To test whether mtDNA background and copy number confer genetic susceptibility to KC in the Han Chinese population, we performed this association study. We analyzed mtDNA sequence variations in 210 KC patients and 309 matched individuals from China, and classified each subject by haplogroup. Mitochondrial DNA copy number was measured in a subset of these subjects (193 patients and 103 controls). Comparison of matrilineal components of the cases and control populations revealed no significant difference. However, measurement of mtDNA copy number showed that KC patients had significantly lower mtDNA copy numbers than controls (P = 0.0002), even when age, gender, and mtDNA background were considered. Our results suggest that mtDNA copy number, but not haplogroup, is associated with keratoconus, and may contribute to its pathogenesis.
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Affiliation(s)
- Xiao-Dan Hao
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China.
| | - Peng Chen
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China.
| | - Ye Wang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China.
| | - Su-Xia Li
- Shandong Eye Hospital, Shandong Eye Institute, Shandong Academy of Medical Sciences, Jinan, China.
| | - Li-Xin Xie
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China.
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21
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Wang D, Xu L, Lv L, Su LY, Fan Y, Zhang DF, Bi R, Yu D, Zhang W, Li XA, Li YY, Yao YG. Association of the LRRK2 genetic polymorphisms with leprosy in Han Chinese from Southwest China. Genes Immun 2014; 16:112-9. [PMID: 25521227 DOI: 10.1038/gene.2014.72] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/19/2014] [Accepted: 10/27/2014] [Indexed: 12/31/2022]
Abstract
Leprosy is a chronic infectious and neurological disease that is caused by infection of Mycobacterium leprae (M. leprae). A recent genome-wide association study indicated a suggestive association of LRRK2 genetic variant rs1873613 with leprosy in Chinese population. To validate this association and further identify potential causal variants of LRRK2 with leprosy, we genotyped 13 LRRK2 variants in 548 leprosy patients and 1078 healthy individuals from Yunnan Province and (re-)analyzed 3225 Han Chinese across China. Variants rs1427267, rs3761863, rs1873613, rs732374 and rs7298930 were significantly associated with leprosy per se and/or paucibacillary leprosy (PB). Haplotype A-G-A-C-A was significantly associated with leprosy per se (P=0.018) and PB (P=0.020). Overexpression of the protective allele (Thr2397) of rs3761863 in HEK293 cells led to a significantly increased nuclear factor of activated T-cells' activity compared with allele Met2397 after lipopolysaccharides stimulation. Allele Thr2397 could attenuate 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine-induced autophagic activity in U251 cells. These data suggest that the protective effect of LRRK2 variant p.M2397T on leprosy might be mediated by increasing immune response and decreasing neurotoxicity after M. leprae loading. Our findings confirm that LRRK2 is a susceptible gene to leprosy in Han Chinese population.
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Affiliation(s)
- D Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - L Xu
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - L Lv
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - L-Y Su
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Y Fan
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - D-F Zhang
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - R Bi
- 1] Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - D Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - W Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - X-A Li
- Yuxi City Center for Disease Control and Prevention, Yuxi, Yunnan, China
| | - Y-Y Li
- Department of Dermatology, the First Affiliated Hospital of Kunming Medical College, Kunming, Yunnan, China
| | - Y-G Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Xu Y, Lu S. Transforming growth factor-β1-induced epithelial to mesenchymal transition increases mitochondrial content in the A549 non-small cell lung cancer cell line. Mol Med Rep 2014; 11:417-21. [PMID: 25323156 DOI: 10.3892/mmr.2014.2678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 07/30/2014] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial genome DNA copy number is critical for the functional maintenance of the mitochondria and energy acquisition for cell metabolism. Epithelial to mesenchymal transition (EMT) is an important process during embryonic development and has also been hypothesized to exhibit a significant role in cancer cell invasion and metastasis. In the present study, EMT was induced in the A549 non-small cell lung cancer (NSCLC) cell line, using transforming growth factor-β1 (TGF-β1) and changes in mitochondrial content, mitochondrial DNA (mtDNA) copy number and protein cytochrome c (Cyt c) were determined by reverse transcription-quantitative polymerase chain reaction and western blot analysis, respectively. mtDNA copy number and Cyt c protein levels were observed to increase following the induction of EMT in NSCLC cells. Results of the current study indicate that energy metabolism is adapted to facilitate EMT in NSCLC cells.
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Affiliation(s)
- Yunhua Xu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, P.R. China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, P.R. China
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Genetic structure of Qiangic populations residing in the western Sichuan corridor. PLoS One 2014; 9:e103772. [PMID: 25090432 PMCID: PMC4121179 DOI: 10.1371/journal.pone.0103772] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/02/2014] [Indexed: 12/20/2022] Open
Abstract
The Qiangic languages in western Sichuan (WSC) are believed to be the oldest branch of the Sino-Tibetan linguistic family, and therefore, all Sino-Tibetan populations might have originated in WSC. However, very few genetic investigations have been done on Qiangic populations and no genetic evidences for the origin of Sino-Tibetan populations have been provided. By using the informative Y chromosome and mitochondrial DNA (mtDNA) markers, we analyzed the genetic structure of Qiangic populations. Our results revealed a predominantly Northern Asian-specific component in Qiangic populations, especially in maternal lineages. The Qiangic populations are an admixture of the northward migrations of East Asian initial settlers with Y chromosome haplogroup D (D1-M15 and the later originated D3a-P47) in the late Paleolithic age, and the southward Di-Qiang people with dominant haplogroup O3a2c1*-M134 and O3a2c1a-M117 in the Neolithic Age.
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He Y, Tang J, Li Z, Li H, Liao Y, Tang Y, Tan L, Chen J, Xia K, Chen X. Leukocyte mitochondrial DNA copy number in blood is not associated with major depressive disorder in young adults. PLoS One 2014; 9:e96869. [PMID: 24809340 PMCID: PMC4014566 DOI: 10.1371/journal.pone.0096869] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/12/2014] [Indexed: 01/02/2023] Open
Abstract
Background Major depressive disorder (MDD) is the leading cause of disability worldwide, and has significant genetic predisposition. Mitochondria may have a role in MDD and so mitochondrial DNA (mtDNA) has been suggested as a possible biomarker for this disease. We aimed to test whether the mtDNA copy number of peripheral blood leukocytes is related to MDD in young adults. Methods A case-control study was conducted with 210 MDD patients and 217 healthy controls (HC). The mtDNA copy number was measured by quantitative polymerase chain reaction (qPCR) method. Depression severity was assessed by the Hamilton-17 Depression Rating Scale (HDRS-17). Results We found no significant differences in mtDNA copy number between MDD patients and HC, though the power analysis showed that our sample size has enough power to detect the difference. There were also no significant correlations between mtDNA copy number and the clinical characteristics (such as age, age of onset, episodes, Hamilton Depression Rating Scale (HDRS) score and Global Assessment of Function Scale (GAF) score) in MDD patients. Conclusion Our study suggests that leukocyte mtDNA copy number is unlikely to contribute to MDD, but it doesn’t mean that we can exclude the possibility of involvement of mitochondria in the disease. Further studies are required to elucidate whether mtDNA can be a biomarker of MDD.
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Affiliation(s)
- Ying He
- Institute of Mental Health, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jinsong Tang
- Institute of Mental Health, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zongchang Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hong Li
- Institute of Mental Health, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yanhui Liao
- Institute of Mental Health, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yanqing Tang
- Department of Psychiatry, First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Liwen Tan
- Institute of Mental Health, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jindong Chen
- Institute of Mental Health, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Xiaogang Chen
- Institute of Mental Health, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China; The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China; Key Laboratory of Psychiatry and Mental Health of Hunan Province, Central South University, Changsha, Hunan, China; The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
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25
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Horan MP, Cooper DN. The emergence of the mitochondrial genome as a partial regulator of nuclear function is providing new insights into the genetic mechanisms underlying age-related complex disease. Hum Genet 2013; 133:435-58. [DOI: 10.1007/s00439-013-1402-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/23/2013] [Indexed: 12/17/2022]
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Zhang DF, Huang XQ, Wang D, Li YY, Yao YG. Genetic variants of complement genes ficolin-2, mannose-binding lectin and complement factor H are associated with leprosy in Han Chinese from Southwest China. Hum Genet 2013; 132:629-40. [PMID: 23423485 DOI: 10.1007/s00439-013-1273-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/05/2013] [Indexed: 10/27/2022]
Abstract
The complement system plays multiple roles in host defense against infection and is supposed to confer genetic susceptibility to leprosy. We aimed to examine whether genetic variants of the Ficolin-2 (FCN2), Mannose-binding lectin (MBL2) and Complement factor H (CFH) genes, which are involved in activation and regulation of the complement system, are associated with leprosy in Han Chinese from Southwest China. 527 leprosy patients and 583 matched controls were recruited from Yunnan Province, China, and were analyzed in this study. We sequenced the promoter region of the FCN2 and MBL2 genes and exon 8 of the FCN2 gene and genotyped three tag SNPs of the CFH gene. Association analysis was performed to discern potential effect of these three genes with leprosy and its subtypes. Luciferase assay was used to characterize the role of different promoter alleles of the FCN2 and MBL2 genes. Genetic variants of FCN2 (rs3811140 and rs7851696), MBL2 (rs11003125, rs7100749, rs11003124 and rs7096206) and CFH (rs1065489 and rs3753395) were significantly associated with leprosy and its subtypes. Haplotypes/genotypes representing low FCN2 and MBL2 transcriptional activity conferred risk to paucibacillary leprosy. Our data confirmed the expected positive association of complement genes with leprosy susceptibility and clinical outcomes in Han Chinese.
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Affiliation(s)
- Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China
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