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Yu Y, He Y, Xie Z. Accurate Identification of Spatial Domain by Incorporating Global Spatial Proximity and Local Expression Proximity. Biomolecules 2024; 14:674. [PMID: 38927077 PMCID: PMC11201407 DOI: 10.3390/biom14060674] [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: 05/03/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Accurate identification of spatial domains is essential in the analysis of spatial transcriptomics data in order to elucidate tissue microenvironments and biological functions. However, existing methods only perform domain segmentation based on local or global spatial relationships between spots, resulting in an underutilization of spatial information. To this end, we propose SECE, a deep learning-based method that captures both local and global relationships among spots and aggregates their information using expression similarity and spatial similarity. We benchmarked SECE against eight state-of-the-art methods on six real spatial transcriptomics datasets spanning four different platforms. SECE consistently outperformed other methods in spatial domain identification accuracy. Moreover, SECE produced spatial embeddings that exhibited clearer patterns in low-dimensional visualizations and facilitated a more accurate trajectory inference.
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Affiliation(s)
- Yuanyuan Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China;
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China;
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China;
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
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2
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Jahan J, Joshi S, Oca IMD, Toelle A, Lopez-Yang C, Chacon CV, Beyer AM, Garcia CA, Jarajapu YP. The role of telomerase reverse transcriptase in the mitochondrial protective functions of Angiotensin-(1-7) in diabetic CD34 + cells. Biochem Pharmacol 2024; 222:116109. [PMID: 38458330 PMCID: PMC11007670 DOI: 10.1016/j.bcp.2024.116109] [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: 10/09/2023] [Revised: 01/08/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Angiotensin (Ang)-(1-7) stimulates vasoprotective functions of diabetic (DB) CD34+ hematopoietic stem/progenitor cells partly by decreasing reactive oxygen species (ROS), increasing nitric oxide (NO) levels and decreasing TGFβ1 secretion. Telomerase reverse transcriptase (TERT) translocates to mitochondria and regulates ROS generation. Alternative splicing of TERT results in variants α-, β- and α-β-TERT, which may oppose functions of full-length (FL) TERT. This study tested if the protective functions of Ang-(1-7) or TGFβ1-silencing are mediated by mitoTERT and that diabetes decreases FL-TERT expression by inducing splicing. CD34+ cells were isolated from the peripheral blood mononuclear cells of nondiabetic (ND, n = 68) or DB (n = 74) subjects. NO and mitoROS levels were evaluated by flow cytometry. TERT splice variants and mitoDNA-lesions were characterized by qPCR. TRAP assay was used for telomerase activity. Decoy peptide was used to block mitochondrial translocation (mitoXTERT). TERT inhibitor or mitoXTERT prevented the effects of Ang-(1-7) on NO or mitoROS levels in DB-CD34+ cells. FL-TERT expression and telomerase activity were lower and mitoDNA-lesions were higher in DB cells compared to ND and were reversed by Ang-(1-7) or TGFβ1-silencing. The prevalence of TERT splice variants, with predominant β-TERT expression, was higher and the expression of FL-TERT was lower in DB cells (n = 25) compared to ND (n = 30). Ang-(1-7) or TGFβ1-silencing decreased TERT-splicing and increased FL-TERT. Blocking of β-splicing increased FL-TERT and protected mitoDNA in DB-cells. The findings suggest that diabetes induces TERT-splicing in CD34+ cells and that β-TERT splice variant largely contributes to the mitoDNA oxidative damage.
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Affiliation(s)
- Jesmin Jahan
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | - Shrinidh Joshi
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | | | - Andrew Toelle
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA
| | | | | | - Andreas M Beyer
- Department of Medicine and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Yagna Pr Jarajapu
- Department of Pharmaceutical Sciences, College of Health Professions, North Dakota State University, Fargo, ND, USA.
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3
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Tomar MS, Kumar A, Shrivastava A. Mitochondrial metabolism as a dynamic regulatory hub to malignant transformation and anti-cancer drug resistance. Biochem Biophys Res Commun 2024; 694:149382. [PMID: 38128382 DOI: 10.1016/j.bbrc.2023.149382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/02/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Glycolysis is the fundamental cellular process that permits cancer cells to convert energy and grow anaerobically. Recent developments in molecular biology have made it evident that mitochondrial respiration is critical to tumor growth and treatment response. As the principal organelle of cellular energy conversion, mitochondria can rapidly alter cellular metabolic processes, thereby fueling malignancies and contributing to treatment resistance. This review emphasizes the significance of mitochondrial biogenesis, turnover, DNA copy number, and mutations in bioenergetic system regulation. Tumorigenesis requires an intricate cascade of metabolic pathways that includes rewiring of the tricarboxylic acid (TCA) cycle, electron transport chain and oxidative phosphorylation, supply of intermediate metabolites of the TCA cycle through amino acids, and the interaction between mitochondria and lipid metabolism. Cancer recurrence or resistance to therapy often results from the cooperation of several cellular defense mechanisms, most of which are connected to mitochondria. Many clinical trials are underway to assess the effectiveness of inhibiting mitochondrial respiration as a potential cancer therapeutic. We aim to summarize innovative strategies and therapeutic targets by conducting a comprehensive review of recent studies on the relationship between mitochondrial metabolism, tumor development and therapeutic resistance.
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Affiliation(s)
- Manendra Singh Tomar
- Center for Advance Research, Faculty of Medicine, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India
| | - Ashok Kumar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS) Bhopal, Saket Nagar, Bhopal, 462020, Madhya Pradesh, India
| | - Ashutosh Shrivastava
- Center for Advance Research, Faculty of Medicine, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India.
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4
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Xu YC, Su J, Zhou JJ, Yuan Q, Han JS. Roles of MT-ND1 in Cancer. Curr Med Sci 2023; 43:869-878. [PMID: 37642864 DOI: 10.1007/s11596-023-2771-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/12/2023] [Indexed: 08/31/2023]
Abstract
The energy shift toward glycolysis is one of the hallmarks of cancer. Complex I is a vital enzyme complex necessary for oxidative phosphorylation. The mitochondrially encoded NADH: ubiquinone oxidoreductase core subunit 1 (MT-ND1) is the largest subunit coded by mitochondria of complex I. The present study summarizes the structure and biological function of MT-ND1. From databases and literature, the expressions and mutations of MT-ND1 in a variety of cancers have been reviewed. MT-ND1 may be a biomarker for cancer diagnosis and prognosis. It is also a potential target for cancer therapy.
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Affiliation(s)
- Yi-Chun Xu
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, 200065, China.
- National Engineering Research Center for Biochip, Shanghai Biochip Limited Corporation, Shanghai, 201203, China.
| | - Jun Su
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, 200065, China
- National Engineering Research Center for Biochip, Shanghai Biochip Limited Corporation, Shanghai, 201203, China
| | - Jia-Jing Zhou
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, 200065, China
| | - Qing Yuan
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, 200065, China
| | - Jun-Song Han
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai, 200065, China.
- National Engineering Research Center for Biochip, Shanghai Biochip Limited Corporation, Shanghai, 201203, China.
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5
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Smullen M, Olson MN, Murray LF, Suresh M, Yan G, Dawes P, Barton NJ, Mason JN, Zhang Y, Fernandez-Fontaine AA, Church GM, Mastroeni D, Wang Q, Lim ET, Chan Y, Readhead B. Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G. Sci Rep 2023; 13:10405. [PMID: 37369829 DOI: 10.1038/s41598-023-37541-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
Mitochondrial (MT) dysfunction has been associated with several neurodegenerative diseases including Alzheimer's disease (AD). While MT-copy number differences have been implicated in AD, the effect of MT heteroplasmy on AD has not been well characterized. Here, we analyzed over 1800 whole genome sequencing data from four AD cohorts in seven different tissue types to determine the extent of MT heteroplasmy present. While MT heteroplasmy was present throughout the entire MT genome for blood samples, we detected MT heteroplasmy only within the MT control region for brain samples. We observed that an MT variant 10398A>G (rs2853826) was significantly associated with overall MT heteroplasmy in brain tissue while also being linked with the largest number of distinct disease phenotypes of all annotated MT variants in MitoMap. Using gene-expression data from our brain samples, our modeling discovered several gene networks involved in mitochondrial respiratory chain and Complex I function associated with 10398A>G. The variant was also found to be an expression quantitative trait loci (eQTL) for the gene MT-ND3. We further characterized the effect of 10398A>G by phenotyping a population of lymphoblastoid cell-lines (LCLs) with and without the variant allele. Examination of RNA sequence data from these LCLs reveal that 10398A>G was an eQTL for MT-ND4. We also observed in LCLs that 10398A>G was significantly associated with overall MT heteroplasmy within the MT control region, confirming the initial findings observed in post-mortem brain tissue. These results provide novel evidence linking MT SNPs with MT heteroplasmy and open novel avenues for the investigation of pathomechanisms that are driven by this pleiotropic disease associated loci.
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Affiliation(s)
- Molly Smullen
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Meagan N Olson
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Liam F Murray
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Madhusoodhanan Suresh
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Guang Yan
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Pepper Dawes
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nathaniel J Barton
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jivanna N Mason
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Yucheng Zhang
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Aria A Fernandez-Fontaine
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Elaine T Lim
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Yingleong Chan
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
| | - Benjamin Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA.
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6
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Bassal MA. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. Biomolecules 2023; 13:944. [PMID: 37371524 DOI: 10.3390/biom13060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular metabolism (or energetics) and epigenetics are tightly coupled cellular processes. It is arguable that of all the described cancer hallmarks, dysregulated cellular energetics and epigenetics are the most tightly coregulated. Cellular metabolic states regulate and drive epigenetic changes while also being capable of influencing, if not driving, epigenetic reprogramming. Conversely, epigenetic changes can drive altered and compensatory metabolic states. Cancer cells meticulously modify and control each of these two linked cellular processes in order to maintain their tumorigenic potential and capacity. This review aims to explore the interplay between these two processes and discuss how each affects the other, driving and enhancing tumorigenic states in certain contexts.
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Affiliation(s)
- Mahmoud Adel Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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7
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Malayil R, Chhichholiya Y, Vasudeva K, Singh HV, Singh T, Singh S, Munshi A. Oncogenic metabolic reprogramming in breast cancer: focus on signaling pathways and mitochondrial genes. Med Oncol 2023; 40:174. [PMID: 37170010 DOI: 10.1007/s12032-023-02037-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/13/2023]
Abstract
Oncogenic metabolic reprogramming impacts the abundance of key metabolites that regulate signaling and epigenetics. Metabolic vulnerability in the cancer cell is evident from the Warburg effect. The research on metabolism in the progression and survival of breast cancer (BC) is under focus. Oncogenic signal activation and loss of tumor suppressor are important regulators of tumor cell metabolism. Several intrinsic and extrinsic factors contribute to metabolic reprogramming. The molecular mechanisms underpinning metabolic reprogramming in BC are extensive and only partially defined. Various signaling pathways involved in the metabolism play a significant role in the modulation of BC. Notably, PI3K/AKT/mTOR pathway, lactate-ERK/STAT3 signaling, loss of the tumor suppressor Ras, Myc, oxidative stress, activation of the cellular hypoxic response and acidosis contribute to different metabolic reprogramming phenotypes linked to enhanced glycolysis. The alterations in mitochondrial genes have also been elaborated upon along with their functional implications. The outcome of these active research areas might contribute to the development of novel therapeutic interventions and the remodeling of known drugs.
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Affiliation(s)
- Rhuthuparna Malayil
- Department of Human Genetics and Molecular Medicine, Central University of Punjab Bathinda, Punjab, India
| | - Yogita Chhichholiya
- Department of Human Genetics and Molecular Medicine, Central University of Punjab Bathinda, Punjab, India
| | | | - Harsh Vikram Singh
- Department of Orthopedics, All India Institute of Medical Sciences, Bathinda, India
| | - Tashvinder Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab Bathinda, Punjab, India
| | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab Bathinda, Punjab, India.
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab Bathinda, Punjab, India.
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8
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Kozakiewicz P, Grzybowska-Szatkowska L, Ciesielka M, Całka P, Osuchowski J, Szmygin P, Jarosz B, Ostrowska-Leśko M, Dudka J, Tkaczyk-Wlizło A, Ślaska B. Mitochondrial DNA Changes in Respiratory Complex I Genes in Brain Gliomas. Biomedicines 2023; 11:biomedicines11041183. [PMID: 37189801 DOI: 10.3390/biomedicines11041183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Mitochondria are organelles necessary for oxidative phosphorylation. The interest in the role of mitochondria in the process of carcinogenesis results from the fact that a respiratory deficit is found in dividing cells, especially in cells with accelerated proliferation. The study included tumor and blood material from 30 patients diagnosed with glioma grade II, III and IV according to WHO (World Health Organization). DNA was isolated from the collected material and next-generation sequencing was performed on the MiSeqFGx apparatus (Illumina). The study searched for a possible relationship between the occurrence of specific mitochondrial DNA polymorphisms in the respiratory complex I genes and brain gliomas of grade II, III and IV. The impact of missense changes on the biochemical properties, structure and functioning of the encoded protein, as well as their potential harmfulness, were assessed in silico along with their belonging to a given mitochondrial subgroup. The A3505G, C3992T, A4024G, T4216C, G5046A, G7444A, T11253C, G12406A and G13604C polymorphisms were assessed as deleterious changes in silico, indicating their association with carcinogenesis.
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Affiliation(s)
- Paulina Kozakiewicz
- Department of Radiotherapy, Oncology Centre of Lublin St. Jana z Dukli Jaczewskiego 7, 20-090 Lublin, Poland
| | | | - Marzanna Ciesielka
- Chair and Department of Forensic Medicine, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Paulina Całka
- Chair and Department of Forensic Medicine, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Jacek Osuchowski
- Chair and Department of Neurosurgery and Pediatric Neurosurgery, Medical University in Lublin, Jaczewskiego 8, 20-090 Lublin, Poland
| | - Paweł Szmygin
- Chair and Department of Neurosurgery and Pediatric Neurosurgery, Medical University in Lublin, Jaczewskiego 8, 20-090 Lublin, Poland
| | - Bożena Jarosz
- Chair and Department of Neurosurgery and Pediatric Neurosurgery, Medical University in Lublin, Jaczewskiego 8, 20-090 Lublin, Poland
| | - Marta Ostrowska-Leśko
- Chair and Department of Toxicology, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Jarosław Dudka
- Chair and Department of Toxicology, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Angelika Tkaczyk-Wlizło
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Brygida Ślaska
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
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9
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Aslebagh R, Whitham D, Channaveerappa D, Mutsengi P, Pentecost BT, Arcaro KF, Darie CC. Mass Spectrometry-Based Proteomics of Human Milk to Identify Differentially Expressed Proteins in Women with Breast Cancer versus Controls. Proteomes 2022; 10:36. [PMID: 36412635 PMCID: PMC9680319 DOI: 10.3390/proteomes10040036] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022] Open
Abstract
It is thought that accurate risk assessment and early diagnosis of breast cancer (BC) can help reduce cancer-related mortality. Proteomics analysis of breast milk may provide biomarkers of risk and occult disease. Our group works on the analysis of human milk samples from women with BC and controls to investigate alterations in protein patterns of milk that could be related to BC. In the current study, we used mass spectrometry (MS)-based proteomics analysis of 12 milk samples from donors with BC and matched controls. Specifically, we used one-dimensional (1D)-polyacrylamide gel electrophoresis (PAGE) coupled with nanoliquid chromatography tandem MS (nanoLC-MS/MS), followed by bioinformatics analysis. We confirmed the dysregulation of several proteins identified previously in a different set of milk samples. We also identified additional dysregulations in milk proteins shown to play a role in cancer development, such as Lactadherin isoform A, O-linked N-acetylglucosamine (GlcNAc) transferase, galactosyltransferase, recoverin, perilipin-3 isoform 1, histone-lysine methyltransferase, or clathrin heavy chain. Our results expand our current understanding of using milk as a biological fluid for identification of BC-related dysregulated proteins. Overall, our results also indicate that milk has the potential to be used for BC biomarker discovery, early detection and risk assessment in young, reproductively active women.
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Affiliation(s)
- Roshanak Aslebagh
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Danielle Whitham
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Devika Channaveerappa
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Panashe Mutsengi
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Brian T. Pentecost
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Kathleen F. Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003-9298, USA
| | - Costel C. Darie
- Biochemistry and Proteomics Laboratories, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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10
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Mitochondrial DNA Changes in Genes of Respiratory Complexes III, IV and V Could Be Related to Brain Tumours in Humans. Int J Mol Sci 2022; 23:ijms232012131. [PMID: 36292984 PMCID: PMC9603055 DOI: 10.3390/ijms232012131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/02/2022] [Accepted: 10/09/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial DNA changes can contribute to both an increased and decreased likelihood of cancer. This process is complex and not fully understood. Polymorphisms and mutations, especially those of the missense type, can affect mitochondrial functions, particularly if the conservative domain of the protein is concerned. This study aimed to identify the possible relationships between brain gliomas and the occurrence of specific mitochondrial DNA polymorphisms and mutations in respiratory complexes III, IV and V. The investigated material included blood and tumour material collected from 30 Caucasian patients diagnosed with WHO grade II, III or IV glioma. The mitochondrial genetic variants were investigated across the mitochondrial genome using next-generation sequencing (MiSeq/FGx system—Illumina). The study investigated, in silico, the effects of missense mutations on the biochemical properties, structure and functioning of the encoded protein, as well as their potential harmfulness. The A14793G (MTCYB), A15758G, (MT-CYB), A15218G (MT-CYB), G7444A (MT-CO1) polymorphisms, and the T15663C (MT-CYB) and G8959A (ATP6) mutations were assessed in silico as harmful alterations that could be involved in oncogenesis. The G8959A (E145K) ATP6 missense mutation has not been described in the literature so far. In light of these results, further research into the role of mtDNA changes in brain tumours should be conducted.
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11
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Evaluation of the tRNA-Leu (UUR) gene haplotype profile observed in canine mammary gland tumours based on comparative analysis with the MT-TL1 human gene. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The aetiology and pathogenesis of many canine tumours are likely to be similar to cancers found in humans. This study aimed to evaluate a plausible link between changes in the tRNA-Leu (UUR) gene and the carcinogenesis process in dogs with mammary gland tumours. The whole mitochondrial DNA (mtDNA) isolated from blood and tumour tissues of 13 dogs with malignant mammary gland tumours was sequenced. The present work is the first report showing that some polymorphisms might occur at the corresponding positions in the human and canine mtDNA genome, which in turn may provoke similar deleterious effects. The homology between the human MT-TL1 and canine tRNA-Leu (UUR) genes was 84%. After resequencing of the whole mitochondrial DNA genome with the use of the NGS technology, two polymorphisms in two haplotypes were identified: m.2683G>A (observed in 18 out of 27 samples) and m.2678_2679insG (27 out of 27 samples). The m.2683G>A polymorphism corresponded to a deleterious change at m.3243A>G, which is linked with MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis, Stroke-like episodes) syndrome and with different types of cancers in humans as well. The comparative analysis of MT-TL1 and tRNA-Leu (UUR) led us to hypothesise that the m.2678_2679insG and m.2683G>A polymorphisms might influence the dog’s condition and might be linked with tumourigenesis, as observed in humans.
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Kowal K, Tkaczyk-Wlizło A, Pierzchała M, Gawor J, Ślaska B. Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours. Vet Comp Oncol 2021; 20:256-264. [PMID: 34554638 DOI: 10.1111/vco.12772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 07/01/2021] [Accepted: 09/20/2021] [Indexed: 11/30/2022]
Abstract
The aim of this study was to determine molecular defects in mitochondrial DNA (mtDNA) with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained from 13 dogs with mammary gland tumours. The total number of mutations and polymorphisms in the analysed mitochondrial genomes was 557. We identified 383 single nucleotide polymorphisms (SNP), 32 indels (or length polymorphisms), 4 mutations, 137 heteroplasmic positions and 1 indel mutation. The highest variability (132 changes) was observed in the variable number of tandem repeats (VNTR) region. The heteroplasmy rate in VNTR varied among individuals and even between two tumours in one organism. Our previous study resulted in determination of a probable CpG island in this region, thus it is not excluded that these changes might alter mtDNA methylation. Only the ATP8 gene was not affected by any polymorphisms or mutations, whereas the COX1 gene had the highest number of polymorphisms from all protein-coding genes. One change m.13594G>A was detected in a region spanning two genes: ND5 and ND6, from which a deleterious effect was observed for the ND5 protein. Molecular changes were frequently observed in the TΨC loop, which is thought to interact with ribosomal RNA.
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Affiliation(s)
- Krzysztof Kowal
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Angelika Tkaczyk-Wlizło
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Mariusz Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Brygida Ślaska
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
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Kozakiewicz P, Grzybowska-Szatkowska L, Ciesielka M, Rzymowska J. The Role of Mitochondria in Carcinogenesis. Int J Mol Sci 2021; 22:ijms22105100. [PMID: 34065857 PMCID: PMC8151940 DOI: 10.3390/ijms22105100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022] Open
Abstract
The mitochondria are essential for normal cell functioning. Changes in mitochondrial DNA (mtDNA) may affect the occurrence of some chronic diseases and cancer. This process is complex and not entirely understood. The assignment to a particular mitochondrial haplogroup may be a factor that either contributes to cancer development or reduces its likelihood. Mutations in mtDNA occurring via an increase in reactive oxygen species may favour the occurrence of further changes both in mitochondrial and nuclear DNA. Mitochondrial DNA mutations in postmitotic cells are not inherited, but may play a role both in initiation and progression of cancer. One of the first discovered polymorphisms associated with cancer was in the gene NADH-ubiquinone oxidoreductase chain 3 (mt-ND3) and it was typical of haplogroup N. In prostate cancer, these mutations and polymorphisms involve a gene encoding subunit I of respiratory complex IV cytochrome c oxidase subunit 1 gene (COI). At present, a growing number of studies also address the impact of mtDNA polymorphisms on prognosis in cancer patients. Some of the mitochondrial DNA polymorphisms occur in both chronic disease and cancer, for instance polymorphism G5913A characteristic of prostate cancer and hypertension.
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Affiliation(s)
- Paulina Kozakiewicz
- Department of Radiotherapy, Medical University in Lublin, Chodźki 7, 20-093 Lublin, Poland; (L.G.-S.); (M.C.)
- Department of Radiotherapy, St. John’s Cancer Centre, The Regional Oncology Centre of Lublin Jaczewskiego 7, 20-090 Lublin, Poland
- Correspondence:
| | - Ludmiła Grzybowska-Szatkowska
- Department of Radiotherapy, Medical University in Lublin, Chodźki 7, 20-093 Lublin, Poland; (L.G.-S.); (M.C.)
- Department of Radiotherapy, St. John’s Cancer Centre, The Regional Oncology Centre of Lublin Jaczewskiego 7, 20-090 Lublin, Poland
| | - Marzanna Ciesielka
- Department of Radiotherapy, Medical University in Lublin, Chodźki 7, 20-093 Lublin, Poland; (L.G.-S.); (M.C.)
- Chair and Department of Forensic Medicine, Medical University in Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Jolanta Rzymowska
- Chair and Department of Biology and Genetics, Medical University of Lublin, Chodźki 4A, 20-093 Lublin, Poland;
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Pérez-Muñoz AA, de Lourdes Muñoz M, García-Hernández N, Santander-Lucio H. A New Approach to Identify the Methylation Sites in the Control Region of Mitochondrial DNA. Curr Mol Med 2021; 21:151-164. [PMID: 32484108 DOI: 10.2174/1566524020666200528154005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 11/22/2022]
Abstract
Mitochondrial DNA (mtDNA) methylation has the potential to be used as a biomarker of human development or disease. However, mtDNA methylation procedures are costly and time-consuming. Therefore, we developed a new approach based on an RT-PCR assay for the base site identification of methylated cytosine in the control region of mtDNA through a simple, fast, specific, and low-cost strategy. Total DNA was purified, and methylation was determined by RT-PCR bisulfite sequencing. This procedure included the DNA purification, bisulfite treatment and RT-PCR amplification of the control region divided into three subregions with specific primers. Sequences obtained with and without the bisulfite treatment were compared to identify the methylated cytosine dinucleotides. Furthermore, the efficiency of C to U conversion of cytosines was assessed by including a negative control. Interestingly, mtDNA methylation was observed mainly within non-Cphosphate- G (non-CpG) dinucleotides and mostly in the regions containing regulatory elements, such as OH or CSBI, CSBII, and CSBIII. This new approach will promote the generation of new information regarding mtDNA methylation patterns in samples from patients with different pathologies or that are exposed to a toxic environment in diverse human populations.
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Affiliation(s)
- Ashael Alfredo Pérez-Muñoz
- Department of Genetics and Molecular Biology, Research and Advanced Studies Center of National Polytechnic Institute (CINVESTAV of IPN), Mexico City, Mexico
| | - María de Lourdes Muñoz
- Department of Genetics and Molecular Biology, Research and Advanced Studies Center of National Polytechnic Institute (CINVESTAV of IPN), Mexico City, Mexico
| | - Normand García-Hernández
- Unidad de Investigacion Medica en Genetica Humana, Unidad Medica de Alta Especialidad Hospital de Pediatria "Dr. Silvestre Frenk Freund", Centro Medico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Heriberto Santander-Lucio
- Department of Genetics and Molecular Biology, Research and Advanced Studies Center of National Polytechnic Institute (CINVESTAV of IPN), Mexico City, Mexico
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Sepulveda-Villegas M, Rojo R, Garza-Hernandez D, de la Rosa-Garza M, Treviño V. A systematic review of genes affecting mitochondrial processes in cancer. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165846. [PMID: 32473387 DOI: 10.1016/j.bbadis.2020.165846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/01/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023]
Abstract
Malignant conversion of cancer cells requires efficient mitochondria reprogramming orchestrated by hundreds of genes. The transformation includes increased energy demand, biosynthesis of precursors, and reactive oxygen species needed to accelerate cell growth, proliferation, and survival. Reprogramming involves complex gene alterations that have not been methodically curated. Therefore, we systematically analyzed the literature of cancer-related genes in mitochondria. Through the analysis of >2500 PubMed abstracts and >1600 human genes, we identified 228 genes showing clear roles in cancer. Each gene was classified according to their homeostatic function, together with the pathological transitions that contribute to specific cancer hallmarks. The potential clinical relevance of these hallmarks and genes is discussed by representative examples and validated by detecting differences in gene expression levels across 16 different types of cancer. A compendium, including the gene functions and alterations underpinning cancer progression, can be explored at http://bioinformatica.mty.itesm.mx/MitoCancer.
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Affiliation(s)
- Maricruz Sepulveda-Villegas
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Rocio Rojo
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Debora Garza-Hernandez
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Mauricio de la Rosa-Garza
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
| | - Victor Treviño
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Av. Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico.
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Defect in Mitochondrial NADH-Dehydrogenase Genes in Canine Mast Cell Tumours. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
Recent studies have demonstrated a significant role of mitochondrial DNA (mtDNA) defects in the pathogenesis of many human and some canine tumours. The aim of this study was to identify mutations in the ND2 and ND4 mitochondrial genes in canine mast cell tumours and determine their association with the process of neoplastic transformation and the phenotypic traits of dogs. In total, 136 gene sequences from 68 biological samples, including blood and neoplastic tissue samples from 34 dogs with diagnosed MCTs, were analysed. The study consisted in DNA sequencing of the ND2 and ND4 genes as well as bioinformatics and statistical analyses. For the first time, mutations in NADH-dehydrogenase genes were detected in dogs with MCTs. In total, 22 polymorphic loci and 19 mutations in the ND2 and ND4 genes were identified. The majority of the identified mutations were homoplasmic, and tumour heteroplasmy was detected in eight nucleotide positions in three dogs. Seven of the ND2 mutations and two of the ND4 mutations caused an amino acid change. The changes in non-synonymous protein-coding SNPs did not exert an adverse effect on proteins. A statistically significant correlation of the presence of mutations/polymorphisms with the sex, age, and size of the dogs and the tumour location was demonstrated. Polymorphisms and mutations in NADH-dehydrogenase genes, including mastocyte-specific changes, in canine mast cell tumours that had not been reported earlier in the literature were identified. Some of these changes may imply that these are the hotspot mutations in canine mast cell tumours. It cannot be excluded that the molecular changes are directly associated with the development of mast cell tumours, and further investigations are needed to verify whether they can become molecular markers of MCTs in the future.
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Śmiech A, Ślaska B, Bownik A, Grzybowska-Szatkowska L, Dudka J, Łopuszyński W. Heteroplasmic Mutations and Polymorphisms in the Cyb Gene of Mitochondrial DNA in Canine Mast Cell Tumours. In Vivo 2018; 33:57-63. [PMID: 30587603 DOI: 10.21873/invivo.11439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 11/10/2022]
Abstract
AIM Identification of mutations and polymorphisms in the cytochrome b gene (Cyb) of mitochondrial DNA (mtDNA) in canine mast cell tumours and determinatiion of their association with the process of neoplastic transformation. MATERIALS AND METHODS The samples comprised tumour tissues and blood obtained from 34 dogs of various breeds. Mutations and polymorphisms in the Cyb gene were detected using amplification and sequencing methods. RESULTS Heteroplasmic mutations were detected at seven positions of mtDNA in 86% of the individuals. Blood and tumour heteroplasmy were recorded at five nucleotide positions of the Cyb gene, whereas tumour heteroplasmy was detected at two positions. Polymorphisms were detected at 14 Cyb gene positions in in the blood of 91% of dogs with mast cell tumours. CONCLUSION The presence of numerous mutations and polymorphisms of Cyb in the blood and tumour tissues and the high frequency of heteroplasmy indicate their involvement in the process of neoplastic transformation in dogs.
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Affiliation(s)
- Anna Śmiech
- Sub-Department of Pathomorphology and Forensic Veterinary Medicine, Department and Clinic of Internal Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Brygida Ślaska
- Department of Biological Bases of Animal Production, Faculty of Animal Breeding and Biology, University of Life Sciences in Lublin, Lublin, Poland
| | - Adam Bownik
- Department of Biological Bases of Animal Production, Faculty of Animal Breeding and Biology, University of Life Sciences in Lublin, Lublin, Poland
| | | | - Jarosław Dudka
- Chair and Department of Toxicology, Medical University of Lublin, Lublin, Poland
| | - Wojciech Łopuszyński
- Sub-Department of Pathomorphology and Forensic Veterinary Medicine, Department and Clinic of Internal Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
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18
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Li L, Xing R, Cui J, Li W, Lu Y. Investigation of frequent somatic mutations of MTND5 gene in gastric cancer cell lines and tissues. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:1002-1008. [PMID: 33474396 PMCID: PMC7800514 DOI: 10.1080/23802359.2018.1501287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The present study investigated the single nucleotide variants (SNVs) in mitochondrial DNA (mtDNA) of 13 paired gastric cancer tissue samples and seven gastric cancer cell lines using direct sequencing analysis of the MTND5 region. Results showed that nuclear mitochondrial pseudogenes (NUMTs) and mitochondrial copy number affected the detection of the SNV frequency in gastric cancer tissue and cell line samples using high-throughput sequencing technique. The heteroplasmic point mutation C12474T and G12835A happened in AGS and BGC823 cell lines, respectively. A total of seven SNVs were found in three paired gastric cancer tissue samples, including five heteroplasmic point mutations (A12406G, C12705T, T12882C, G12501A, and A12584G) and two homoplasmic point mutations (G12561A and C13590T). Gastric cancer tissue sample 16 exhibited the highest SNVs frequency with four SNVs (np 12406, np 12705, np 12882, and np 12501), whereas no SNVs or SNPs were detected in the tissue sample 4. SNP 12705 turned out to be an SNV in gastric cancer tissue sample 16. SNV 12338 detected by exome sequencing approach appeared to be an SNP in this study.
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Affiliation(s)
- Lian Li
- Department of Microbiology, Basic Medical College of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Rui Xing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiantao Cui
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenmei Li
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
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19
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Complete sequence of the ATP6 and ND3 mitochondrial genes in breast cancer tissue of postmenopausal women with different body mass indexes. Ann Diagn Pathol 2018; 32:23-27. [DOI: 10.1016/j.anndiagpath.2017.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/24/2017] [Accepted: 09/08/2017] [Indexed: 12/11/2022]
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20
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Jin EH, Sung JK, Lee SI, Hong JH. Mitochondrial NADH Dehydrogenase Subunit 3 ( MTND3) Polymorphisms are Associated with Gastric Cancer Susceptibility. Int J Med Sci 2018; 15:1329-1333. [PMID: 30275759 PMCID: PMC6158656 DOI: 10.7150/ijms.26881] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/01/2018] [Indexed: 11/18/2022] Open
Abstract
Accumulating evidence indicates that mitochondrial DNA alterations contribute to cancer development and progression. In this study, we evaluated the relationship between polymorphisms of mitochondrial NADH dehydrogenase subunit 3 (MTND3) and the risk of gastric cancer (GC). Five single nucleotide polymorphisms (SNPs; rs28358278, rs2853826, rs201397417, rs41467651, and rs28358275) were identified and genotyped in 377 patients with GC patients and 363 controls by direct sequencing. The rs41467651 T allele was significantly associated with GC risk [adjusted odds ratio (OR) = 2.11, 95% confidence interval (CI) = 1.25-3.55, P = 0.005). In stratified analysis, rs28358278, rs2853826, and rs41467651 were associated with subgroups of GC, with the rs28358278 G, rs2853826 T, and rs41467651 T alleles associated with an increased GC risk in females (adjusted OR = 1.70, 95% CI = 1.08-2.69, P = 0.023; adjusted OR = 1.78, 95% CI = 1.11-2.85, P = 0.016; adjusted OR = 2.07, 95% CI = 1.04-4.12, P = 0.038, respectively). The rs441467651 T allele was also related with GC risk in diffuse-type subjects compared to that of controls (adjusted OR = 2.61, 95% CI = 1.43-4.89, P = 0.002). In addition, The rs441467651 T allele was significantly related with increased GC risk regardless of lymph node metastasis (LNM), T classification, and tumor stage compared to that of controls (adjusted OR = 2.00, 95% CI = 1.12-3.55, P = 0.019 in LNM-negative subjects; adjusted OR = 2.10, 95% CI = 1.05-4.22, P = 0.0379 in LNM-positive subjects; adjusted OR = 1.82, 95% CI = 1.02-3.24, P = 0.042 in T1/T2 subjects; adjusted OR = 2.60, 95% CI = 1.29-5.24, P = 0.007 in T3/T4 subjects; adjusted OR = 1.91, 95% CI = 1.09-3.34, P = 0.025 in tumor stage I (A+B)/II (A+B+C) subjects; adjusted OR = 2.36, 95% CI = 1.12-5.13, P = 0.025 in tumor stage III (A+B+C) subjects) compared to that of controls. Our findings suggest that the rs28358278, rs2853826, and rs41467651 polymorphisms of MTND3 increase the susceptibility to GC development.
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Affiliation(s)
- Eun-Heui Jin
- Research Institute for Medical Sciences, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Jae Kyu Sung
- Department of Internal Medicine, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Sang-Il Lee
- Department of Surgery, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Jang Hee Hong
- Clinical Trials Center, Chungnam National University Hospital, Daejeon, Republic of Korea.,Department of Pharmacology, Chungnam National University College of Medicine, Daejeon, Republic of Korea
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Antolak A, Bodzoń-Kułakowska A, Cetnarska E, Pietruszka M, Marszałek-Grabska M, Kotlińska J, Suder P. Proteomic Data in Morphine Addiction Versus Real Protein Activity: Metabolic Enzymes. J Cell Biochem 2017; 118:4323-4330. [PMID: 28430368 DOI: 10.1002/jcb.26085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/20/2017] [Indexed: 01/01/2023]
Abstract
Drug dependence is an escalating problem worldwide and many efforts are being made to understand the molecular basis of addiction. The morphine model is widely used in these investigations. To date, at least 29 studies exploring the influence of morphine on mammals' proteomes have been published. Among various proteins indicated as up- or down-regulated, the expression changes of enzymes engaged in energy metabolism pathways have often been confirmed. To verify whether proteomics-indicated alterations in enzyme levels reflect changes in their activity, four enzymes: PK, MDH, Complex I, and Complex V were investigated in morphine addiction and abstinence models. After analyses of the rat brain mitochondria fraction in the model of morphine dependence, we found that one of the investigated enzymes (pyruvate kinase) showed statistically significant differences observed between morphine, control, and abstinence groups. J. Cell. Biochem. 118: 4323-4330, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Anna Antolak
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Anna Bodzoń-Kułakowska
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Ewa Cetnarska
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Monika Pietruszka
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Marta Marszałek-Grabska
- Faculty of Pharmacy, Departament of Pharmacology and Pharmacodynamics, Medical University of Lublin, Lublin, Poland
| | - Jolanta Kotlińska
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
| | - Piotr Suder
- Faculty of Materials Science and Technology, Department of Biochemistry and Neurobiology, AGH University of Science and Technology, Cracow, Poland
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22
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Mutations in the Mitochondrial ND1 Gene Are Associated with Postoperative Prognosis of Localized Renal Cell Carcinoma. Int J Mol Sci 2016; 17:ijms17122049. [PMID: 27941608 PMCID: PMC5187849 DOI: 10.3390/ijms17122049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 01/20/2023] Open
Abstract
We analyzed mutations in the mitochondrial ND1 gene to determine their association with clinicopathological parameters and postoperative recurrence of renal cell carcinoma (RCC) in Japanese patients. Among 62 RCC cases for which tumor pathology was confirmed by histopathology, ND1 sequencing revealed the presence of 30 mutation sites in 19 cases. Most mutations were heteroplasmic, with 16 of 19 cases harboring one or more heteroplasmic sites. Additionally, 12 sites had amino acid mutations, which were frequent in 10 of the cases. The 5-year recurrence-free survival (RFS) rate was significantly worse in patients with tumors >40 mm in diameter (p = 0.0091), pathological T (pT) stage ≥3 (p = 0.0122), Fuhrman nuclear atypia grade ≥III (p = 0.0070), and ND1 mutations (p = 0.0006). Multivariate analysis using these factors revealed that mutations in ND1 were significantly associated with the 5-year RFS rate (p = 0.0044). These results suggest a strong correlation between the presence of ND1 mutations in cancer tissue and postoperative recurrence of localized RCC in Japanese patients.
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Ślaska B, Grzybowska-Szatkowska L, Bugno-Poniewierska M, Gurgul A, Śmiech A, Różańska D, Dudka J. Relevance of Molecular Changes in the ND4 Gene in German Shepherd Dog Tumours. Pol J Vet Sci 2016; 19:461-469. [PMID: 27760018 DOI: 10.1515/pjvs-2016-0058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of the study was to identify polymorphisms and mutations in the mitochondrial ND4 gene and to analyse the associations between the occurrence of molecular changes in mtDNA and phenotypic traits in tumours in German Shepherd dogs. Fifty samples obtained from blood and tumour tissues of German Shepherd dogs with diagnosed tumours were analysed. DNA extraction, amplification, and sequencing of the mtDNA ND4 gene, and bioinformatics, statistical, and in silico protein coding SNP analyses were performed. ND4 mutations and/or polymorphisms were noted in eleven nucleotide positions in nearly half of the examined dogs. All the changes were substitution mutations. A majority of the changes identified were homoplasmic. In one dog with osteosarcoma, blood heteroplasmy was detected. In two positions of the ND4 gene, presence of non-synonymous mutations leading to amino acid changes in the ND4 protein was reported. Analyses carried out to determine the deleterious effect of mutations indicated an almost 97 and 62% probability that a single amino acid substitution (p.G239V and p.I401T, respectively) in the protein has a negative impact on its function. The results of statistical analyses indicate a significant association between the occurrence of mutations in three loci of the ND4 gene and the location of tumours. The mutations identified may be a result of cell adaptation to the changes in the environment occurring during carcinogenesis. The high frequency of mutations in the tumours may indicate genetic instability of mtDNA, which may also play a role in carcinogenesis.
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Śmiech A, Ślaska B, Surdyka M, Grzybowska-Szatkowska L, Łopuszyński W, Różańska D. Identification of additional mitochondrial DNA mutations in canine mast cell tumours. Acta Vet Scand 2016; 58:28. [PMID: 27146669 PMCID: PMC4855722 DOI: 10.1186/s13028-016-0210-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research has revealed the presence of somatic mutations in mitochondrial DNA (mtDNA) of certain types of tumours. As this has not been studied for canine mast cell tumours, the aim of this study was to identify mutations in the hypervariable region of mtDNA in mast cell tumours in dogs and determine their association with the process of neoplastic transformation. RESULTS Samples from 17 dogs with histopathologically confirmed mast cell tumours were analysed. The samples consisted of tumour tissues (n = 17), normal tissues (n = 17), and blood (n = 17). Amplicons of the displacement loop (D-loop) were sequenced and the obtained nucleotide sequences were subjected to bioinformatics analyses. Somatic mutations were detected in seven positions of the D-loop nucleotide sequences in 47 % of the dogs, while polymorphisms were identified in 94 % of the dogs. Most of these changes were homoplasmic, while heteroplasmy was detected in two individuals. Six new haplotypes were established as being characteristic for canine mast cell tumours. There was no association between the presence of the mutations and sex, haplotype, or malignancy grade assessed in 3 and 2-grade scales. CONCLUSIONS Differences in the frequency of somatic mutations imply their direct association with the neoplastic transformation. However, their functional consequences and clinical significance are not clear. The mutations may be used for diagnosis and prognosis of canine mast cell tumours in the future.
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