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Wang H, Li X, Zhang Q, Fu C, Jiang W, Xue J, Liu S, Meng Q, Ai L, Zhi X, Deng S, Liang W. Autophagy in Disease Onset and Progression. Aging Dis 2024; 15:1646-1671. [PMID: 37962467 PMCID: PMC11272186 DOI: 10.14336/ad.2023.0815] [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: 05/03/2023] [Accepted: 08/15/2023] [Indexed: 11/15/2023] Open
Abstract
Autophagy is a biological phenomenon whereby components of cells can self-degrade using autophagosomes. During this process, cells can clear dysfunctional organelles or unwanted elements. Autophagy can recycle unnecessary biomolecules into new components or sometimes, even destroy the cells themselves. This cellular process was first observed in 1962 by Keith R. Porter et al. Since then, autophagy has been studied for over 60 years, and much has been learned on the topic. Nevertheless, the process is still not fully understood. It has been proven, for example, that autophagy can be a positive force for maintaining good health by removing older or damaged cells. By contrast, autophagy is also involved in the onset and progression of various conditions caused by pathogenic infections. These diseases generally involve several important organs in the human body, including the liver, kidney, heart, and central nervous system. The regulation of the defects of autophagy defects may potentially be used to treat some diseases. This review comprehensively discusses recent research frontiers and topics of interest regarding autophagy-related diseases.
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Affiliation(s)
- Hao Wang
- Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, Guangdong, China.
| | - Xiushen Li
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, Guangdong, China.
| | - Qi Zhang
- Department of Obstetrics and Gynecology, Shenzhen University General Hospital, Shenzhen, Guangdong, China.
| | - Chengtao Fu
- School of Medicine, Huzhou University, Zhejiang, China.
| | - Wenjie Jiang
- Department of Artificial Intelligence and Data Science, Hebei University of Technology, Tianjin, China.
| | - Jun Xue
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
| | - Shan Liu
- Bioimaging Core of Shenzhen Bay Laboratory Shenzhen, China.
| | - Qingxue Meng
- Technology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
| | - Lisha Ai
- Department of Teaching and Research, Shenzhen University General Hospital, Shenzhen, Guangdong, China.
| | - Xuejun Zhi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
| | - Shoulong Deng
- National Health Commission of China (NHC) Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China.
| | - Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China.
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Haque PS, Kapur N, Barrett TA, Theiss AL. Mitochondrial function and gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 2024; 21:537-555. [PMID: 38740978 DOI: 10.1038/s41575-024-00931-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Mitochondria are dynamic organelles that function in cellular energy metabolism, intracellular and extracellular signalling, cellular fate and stress responses. Mitochondria of the intestinal epithelium, the cellular interface between self and enteric microbiota, have emerged as crucial in intestinal health. Mitochondrial dysfunction occurs in gastrointestinal diseases, including inflammatory bowel diseases and colorectal cancer. In this Review, we provide an overview of the current understanding of intestinal epithelial cell mitochondrial metabolism, function and signalling to affect tissue homeostasis, including gut microbiota composition. We also discuss mitochondrial-targeted therapeutics for inflammatory bowel diseases and colorectal cancer and the evolving concept of mitochondrial impairment as a consequence versus initiator of the disease.
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Affiliation(s)
- Parsa S Haque
- Division of Gastroenterology and Hepatology, Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Neeraj Kapur
- Department of Medicine, Division of Digestive Diseases and Nutrition, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Terrence A Barrett
- Department of Medicine, Division of Digestive Diseases and Nutrition, University of Kentucky College of Medicine, Lexington, KY, USA
- Lexington Veterans Affairs Medical Center Kentucky, Lexington, KY, USA
| | - Arianne L Theiss
- Division of Gastroenterology and Hepatology, Department of Medicine and the Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, USA.
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, USA.
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3
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Hassan HM, Elsaed WM, Elzeiny D, Habotta OA, Eleraky ES, Nashar EME, Alghamdi MA, Aldahhan RA, Alzahrani MA, Saleh Alamari AM, Hamza E. Modulatory effects of Moringa oleifera leaf extract on sodium nitrate-induced experimental colitis via regulation of P53, Ki-67 and PCNA biomarkers. Tissue Cell 2024; 88:102327. [PMID: 38493756 DOI: 10.1016/j.tice.2024.102327] [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: 11/08/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Ulcerative colitis is a risk factor for colorectal carcinoma. Different mechanisms are related to colitis like apoptosis and hyperproliferation. Moringa oleifera leaves extract (MO) provides a promising option to overcome the risk. PURPOSE To examine the colonic changes in a rat model of colitis induced by sodium nitrate (SN) and study the effects of MO. STUDY DESIGN Eight adult male rats were allocated in each of the three group; control (distilled water), SN (100 mg/kg/day, orally via gastric gavage), and SN + MO (100 mg/kg/day, orally via gastric gavage). METHODS Body weight was measured after the end of the experiment. Colonic homogenates were tested for levels of oxidative stress indicators. Immunohistochemistry for P53, PCNA and Ki-67 was performed. Fresh colon specimens were used for quantitative real-time PCR for assessment of P53, PCNA and Ki-67 gene expression. RESULTS SN group revealed a significant decreased weight (p = 0.002). MDA and NO levels were higher with SN administration than with MO co-administration (p= 0.04, 0.01 respectively). GSH level was reduced in SN group (p = 0.02) and significantly increased with MO intake (p = 0.04). SN-induced colonic destructive changes were reversed with MO. P53, PCNA and Ki-67 levels of gene expression were reduced in SN + MO group than SN group (P = 0.007, 0.02, 0.001 respectively). CONCLUSION MO protected the colonic mucosa against SN-induced changes regulating apoptosis, and cell proliferation.
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Affiliation(s)
- Hend M Hassan
- Human Anatomy and Embryology Department, Faculty of Medicine, Mansoura University, Egypt; Human Anatomy and Embryology Department, Faculty of Medicine, New Mansoura University, Egypt.
| | - Wael M Elsaed
- Human Anatomy and Embryology Department, Faculty of Medicine, Mansoura University, Egypt; Human Anatomy and Embryology Department, National Mansoura University, Gamasa, Egypt.
| | - Dina Elzeiny
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Mansoura University, Egypt; Department of Medical Biochemistry and Molecular Biology, New Mansoura University, Egypt.
| | - Ola Ali Habotta
- Forensic Medicine and Toxicology Department, Faculty of Veterinary Medicine, Mansoura University, Egypt.
| | - Elshimaa S Eleraky
- Department of Internal Medicine, Faculty of Medicine, Horus University, Damietta, Egypt.
| | - Eman Mohamed El Nashar
- Department of Anatomy, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia.
| | - Mansour Abdullah Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia; Genomics and Personalized Medicine Unit, The Center for Medical and Health Research, King Khalid University, Abha 62529, Saudi Arabia.
| | - Rashid A Aldahhan
- Department of Anatomy, College of Medicine, Imam Abdulrahman Bin Faisal University, P.O. Box 2114, Dammam 31451, Saudi Arabia.
| | - Mohammed Attieh Alzahrani
- Internal Medicine Department, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia.
| | | | - Eman Hamza
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Mansoura University, Egypt; Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Horus University, New Damietta, Egypt.
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Sánchez-Quintero MJ, Rodríguez-Díaz C, Rodríguez-González FJ, Fernández-Castañer A, García-Fuentes E, López-Gómez C. Role of Mitochondria in Inflammatory Bowel Diseases: A Systematic Review. Int J Mol Sci 2023; 24:17124. [PMID: 38069446 PMCID: PMC10707203 DOI: 10.3390/ijms242317124] [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: 11/11/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Mitochondria are key cellular organelles whose main function is maintaining cell bioenergetics by producing ATP through oxidative phosphorylation. However, mitochondria are involved in a much higher number of cellular processes. Mitochondria are the home of key metabolic pathways like the tricarboxylic acid cycle and β-oxidation of fatty acids, as well as biosynthetic pathways of key products like nucleotides and amino acids, the control of the redox balance of the cell and detoxifying the cell from H2S and NH3. This plethora of critical functions within the cell is the reason mitochondrial function is involved in several complex disorders (apart from pure mitochondrial disorders), among them inflammatory bowel diseases (IBD). IBD are a group of chronic, inflammatory disorders of the gut, mainly composed of ulcerative colitis and Crohn's disease. In this review, we present the current knowledge regarding the impact of mitochondrial dysfunction in the context of IBD. The role of mitochondria in both intestinal mucosa and immune cell populations are discussed, as well as the role of mitochondrial function in mechanisms like mucosal repair, the microbiota- and brain-gut axes and the development of colitis-associated colorectal cancer.
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Affiliation(s)
- María José Sánchez-Quintero
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; (M.J.S.-Q.); (C.R.-D.); (A.F.-C.)
- Unidad de Gestión Clínica Cardiología y Cirugía Cardiovascular, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Rodríguez-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; (M.J.S.-Q.); (C.R.-D.); (A.F.-C.)
- Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Francisco J. Rodríguez-González
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; (M.J.S.-Q.); (C.R.-D.); (A.F.-C.)
- Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Alejandra Fernández-Castañer
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; (M.J.S.-Q.); (C.R.-D.); (A.F.-C.)
- Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
| | - Eduardo García-Fuentes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; (M.J.S.-Q.); (C.R.-D.); (A.F.-C.)
- Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos López-Gómez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590 Málaga, Spain; (M.J.S.-Q.); (C.R.-D.); (A.F.-C.)
- Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Málaga, Spain
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5
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Degtyareva NP, Placentra VC, Gabel SA, Klimczak LJ, Gordenin DA, Wagner BA, Buettner GR, Mueller GA, Smirnova TI, Doetsch PW. Changes in metabolic landscapes shape divergent but distinct mutational signatures and cytotoxic consequences of redox stress. Nucleic Acids Res 2023; 51:5056-5072. [PMID: 37078607 PMCID: PMC10250236 DOI: 10.1093/nar/gkad305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/17/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
Mutational signatures discerned in cancer genomes, in aging tissues and in cells exposed to toxic agents, reflect complex processes underlying transformation of cells from normal to dysfunctional. Due to its ubiquitous and chronic nature, redox stress contributions to cellular makeover remain equivocal. The deciphering of a new mutational signature of an environmentally-relevant oxidizing agent, potassium bromate, in yeast single strand DNA uncovered a surprising heterogeneity in the mutational signatures of oxidizing agents. NMR-based analysis of molecular outcomes of redox stress revealed profound dissimilarities in metabolic landscapes following exposure to hydrogen peroxide versus potassium bromate. The predominance of G to T substitutions in the mutational spectra distinguished potassium bromate from hydrogen peroxide and paraquat and mirrored the observed metabolic changes. We attributed these changes to the generation of uncommon oxidizing species in a reaction with thiol-containing antioxidants; a nearly total depletion of intracellular glutathione and a paradoxical augmentation of potassium bromate mutagenicity and toxicity by antioxidants. Our study provides the framework for understanding multidimensional processes triggered by agents collectively known as oxidants. Detection of increased mutational loads associated with potassium bromate-related mutational motifs in human tumors may be clinically relevant as a biomarker of this distinct type of redox stress.
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Affiliation(s)
- Natalya P Degtyareva
- Mutagenesis and DNA Repair Regulation Group, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC27709, USA
| | - Victoria C Placentra
- Mutagenesis and DNA Repair Regulation Group, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC27709, USA
| | - Scott A Gabel
- Nuclear Magnetic Resonance Research Core Facility, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC27709, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC27709, USA
| | - Dmitry A Gordenin
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC27709, USA
| | - Brett A Wagner
- Free Radical and Radiation Biology, ESR Facility, Department of Radiation Oncology, The University of Iowa, Iowa City, IA52242, USA
| | - Garry R Buettner
- Free Radical and Radiation Biology, ESR Facility, Department of Radiation Oncology, The University of Iowa, Iowa City, IA52242, USA
| | - Geoffrey A Mueller
- Nuclear Magnetic Resonance Research Core Facility, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC27709, USA
| | | | - Paul W Doetsch
- Mutagenesis and DNA Repair Regulation Group, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC27709, USA
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6
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Sanchez-Contreras M, Sweetwyne MT, Tsantilas KA, Whitson JA, Campbell MD, Kohrn BF, Kim HJ, Hipp MJ, Fredrickson J, Nguyen MM, Hurley JB, Marcinek DJ, Rabinovitch PS, Kennedy SR. The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging. eLife 2023; 12:e83395. [PMID: 36799304 PMCID: PMC10072880 DOI: 10.7554/elife.83395] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low-frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue- and mutation type-dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.
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Affiliation(s)
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Brenden F Kohrn
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Hyeon Jeong Kim
- Department of Biology, University of WashingtonSeattleUnited States
| | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Megan M Nguyen
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - James B Hurley
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - David J Marcinek
- Department of Radiology, University of WashingtonSeattleUnited States
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
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7
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Mikhailova AG, Mikhailova AA, Ushakova K, Tretiakov EO, Iliushchenko D, Shamansky V, Lobanova V, Kozenkov I, Efimenko B, Yurchenko AA, Kozenkova E, Zdobnov EM, Makeev V, Yurov V, Tanaka M, Gostimskaya I, Fleischmann Z, Annis S, Franco M, Wasko K, Denisov S, Kunz WS, Knorre D, Mazunin I, Nikolaev S, Fellay J, Reymond A, Khrapko K, Gunbin K, Popadin K. A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand. Nucleic Acids Res 2022; 50:10264-10277. [PMID: 36130228 PMCID: PMC9561281 DOI: 10.1093/nar/gkac779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/02/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are responsible for aerobic respiration, it is expected that mtDNA mutational spectrum is affected by oxidative damage. Assuming that oxidative damage increases with age, we analyse mtDNA mutagenesis of different species in regards to their generation length. Analysing, (i) dozens of thousands of somatic mtDNA mutations in samples of different ages (ii) 70053 polymorphic synonymous mtDNA substitutions reconstructed in 424 mammalian species with different generation lengths and (iii) synonymous nucleotide content of 650 complete mitochondrial genomes of mammalian species we observed that the frequency of AH > GH substitutions (H: heavy strand notation) is twice bigger in species with high versus low generation length making their mtDNA more AH poor and GH rich. Considering that AH > GH substitutions are also sensitive to the time spent single-stranded (TSSS) during asynchronous mtDNA replication we demonstrated that AH > GH substitution rate is a function of both species-specific generation length and position-specific TSSS. We propose that AH > GH is a mitochondria-specific signature of oxidative damage associated with both aging and TSSS.
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Affiliation(s)
- Alina G Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Alina A Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Kristina Ushakova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Evgeny O Tretiakov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Dmitrii Iliushchenko
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Victor Shamansky
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Valeria Lobanova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Ivan Kozenkov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Bogdan Efimenko
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Elena Kozenkova
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vsevolod Makeev
- Vavilov Institute of General Genetics RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
| | - Valerian Yurov
- Institute of Physics, Mathematics and Information Technology, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
| | - Masashi Tanaka
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Irina Gostimskaya
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Zoe Fleischmann
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Sofia Annis
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Melissa Franco
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Kevin Wasko
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Stepan Denisov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Wolfram S Kunz
- Department of Epileptology and Institute of Experimental Epileptology and Cognition Research, University Bonn, Bonn, Germany
| | - Dmitry Knorre
- The A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow State University, Moscow, Russian Federation
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology (Skoltech), Skolkovo, Russian Federation
- Fomin Clinic, Moscow, Russian Federation
- Medical Genomics LLC, Moscow, Russian Federation
| | - Sergey Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Jacques Fellay
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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8
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Liu L, Liu Y, Zhou X, Xu Z, Zhang Y, Ji L, Hong C, Li C. Analyzing the metabolic fate of oral administration drugs: A review and state-of-the-art roadmap. Front Pharmacol 2022; 13:962718. [PMID: 36278150 PMCID: PMC9585159 DOI: 10.3389/fphar.2022.962718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The key orally delivered drug metabolism processes are reviewed to aid the assessment of the current in vivo/vitro experimental systems applicability for evaluating drug metabolism and the interaction potential. Orally administration is the most commonly used state-of-the-art road for drug delivery due to its ease of administration, high patient compliance and cost-effectiveness. Roles of gut metabolic enzymes and microbiota in drug metabolism and absorption suggest that the gut is an important site for drug metabolism, while the liver has long been recognized as the principal organ responsible for drugs or other substances metabolism. In this contribution, we explore various experimental models from their development to the application for studying oral drugs metabolism of and summarized advantages and disadvantages. Undoubtedly, understanding the possible metabolic mechanism of drugs in vivo and evaluating the procedure with relevant models is of great significance for screening potential clinical drugs. With the increasing popularity and prevalence of orally delivered drugs, sophisticated experimental models with higher predictive capacity for the metabolism of oral drugs used in current preclinical studies will be needed. Collectively, the review seeks to provide a comprehensive roadmap for researchers in related fields.
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Mazumder S, Bindu S, De R, Debsharma S, Pramanik S, Bandyopadhyay U. Emerging role of mitochondrial DAMPs, aberrant mitochondrial dynamics and anomalous mitophagy in gut mucosal pathogenesis. Life Sci 2022; 305:120753. [PMID: 35787999 DOI: 10.1016/j.lfs.2022.120753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 12/22/2022]
Abstract
Gastroduodenal inflammation and ulcerative injuries are increasing due to expanding socio-economic stress, unhealthy food habits-lifestyle, smoking, alcoholism and usage of medicines like non-steroidal anti-inflammatory drugs. In fact, gastrointestinal (GI) complications, associated with the prevailing COVID-19 pandemic, further, poses a challenge to global healthcare towards safeguarding the GI tract. Emerging evidences have discretely identified mitochondrial dysfunctions as common etiological denominators in diseases. However, it is worth realizing that mitochondrial dysfunctions are not just consequences of diseases. Rather, damaged mitochondria severely aggravate the pathogenesis thereby qualifying as perpetrable factors worth of prophylactic and therapeutic targeting. Oxidative and nitrosative stress due to endogenous and exogenous stimuli triggers mitochondrial injury causing production of mitochondrial damage associated molecular patterns (mtDAMPs), which, in a feed-forward loop, inflicts inflammatory tissue damage. Mitochondrial structural dynamics and mitophagy are crucial quality control parameters determining the extent of mitopathology and disease outcomes. Interestingly, apart from endogenous factors, mitochondria also crosstalk and in turn get detrimentally affected by gut pathobionts colonized during luminal dysbiosis. Although mitopathology is documented in various pre-clinical/clinical studies, a comprehensive account appreciating the mitochondrial basis of GI mucosal pathologies is largely lacking. Here we critically discuss the molecular events impinging on mitochondria along with the interplay of mitochondria-derived factors in fueling mucosal pathogenesis. We specifically emphasize on the potential role of aberrant mitochondrial dynamics, anomalous mitophagy, mitochondrial lipoxidation and ferroptosis as emerging regulators of GI mucosal pathogenesis. We finally discuss about the prospect of mitochondrial targeting for next-generation drug discovery against GI disorders.
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Affiliation(s)
- Somnath Mazumder
- Department of Zoology, Raja Peary Mohan College, 1 Acharya Dhruba Pal Road, Uttarpara, West Bengal 712258, India
| | - Samik Bindu
- Department of Zoology, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal 736101, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, West Bengal 700135, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India; Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal 700091, India.
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10
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Ji X, Guo W, Gu X, Guo S, Zhou K, Su L, Yuan Q, Liu Y, Guo X, Huang Q, Xing J. Mutational profiling of mtDNA control region reveals tumor-specific evolutionary selection involved in mitochondrial dysfunction. EBioMedicine 2022; 80:104058. [PMID: 35594659 PMCID: PMC9121266 DOI: 10.1016/j.ebiom.2022.104058] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/06/2022] [Accepted: 04/28/2022] [Indexed: 11/05/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) mutations alter mitochondrial function in oxidative metabolism and play an important role in tumorigenesis. A series of studies have demonstrated that the mtDNA control region (mtCTR), which is essential for mtDNA replication and transcription, represents a mutational hotspot in human tumors. However, a comprehensive pan-cancer evolutionary pattern analysis of mtCTR mutations is urgently needed. Methods We generated a comprehensive combined dataset containing 10026 mtDNA somatic mutations from 4664 patients, covering 20 tumor types based on public and private next-generation sequencing data. Findings Our results demonstrated a significantly higher and much more variable mutation rate in mtCTR than in the coding region across different tumor types. Moreover, our data showed a remarkable distributional bias of tumor somatic mutations between the hypervariable segment (HVS) and non-HVS, with a significantly higher mutation density and average mutation sites in HVS. Importantly, the tumor-specific mutational pattern between mtCTR HVS and non-HVS was identified, which was classified into three evolutionary selection types (relaxed, moderate, and strict constraint types). Analysis of substitution patterns revealed that the prevalence of CH > TH in non-HVS greatly contributed to the mutational selection pattern of mtCTR across different tumor types. Furthermore, we found that the mutational pattern of mtCTR in the four tumor types was clearly associated with mitochondrial biogenesis, mitochondrial oxidative metabolism, and the overall survival of patients. Interpretation Our results suggest that somatic mutations in mtCTR may be shaped by tumor-specific selective pressure and are involved in tumorigenesis. Fundings National Natural Science Foundation of China [grants 82020108023, 81830070, 81872302], and Autonomous Project of State Key Laboratory of Cancer Biology, China [grants CBSKL2019ZZ06, CBSKL2019ZZ27].
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11
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Abstract
Mitochondria are the main source of energy used to maintain cellular homeostasis. This aspect of mitochondrial biology underlies their putative role in age-associated tissue dysfunction. Proper functioning of the electron transport chain (ETC), which is partially encoded by the extra-nuclear mitochondrial genome (mtDNA), is key to maintaining this energy production. The acquisition of de novo somatic mutations that interrupt the function of the ETC have long been associated with aging and common diseases of the elderly. Yet, despite over 30 years of study, the exact role(s) mtDNA mutations play in driving aging and its associated pathologies remains under considerable debate. Furthermore, even fundamental aspects of age-related mtDNA mutagenesis, such as when mutations arise during aging, where and how often they occur across tissues, and the specific mechanisms that give rise to them, remain poorly understood. In this review, we address the current understanding of the somatic mtDNA mutations, with an emphasis of when, where, and how these mutations arise during aging. Additionally, we highlight current limitations in our knowledge and critically evaluate the controversies stemming from these limitations. Lastly, we highlight new and emerging technologies that offer potential ways forward in increasing our understanding of somatic mtDNA mutagenesis in the aging process.
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Affiliation(s)
- Monica Sanchez-Contreras
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
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12
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Su L, Guo S, Guo W, Ji X, Liu Y, Zhang H, Huang Q, Zhou K, Guo X, Gu X, Xing J. mitoDataclean: A machine learning approach for the accurate identification of cross-contamination-derived tumor mitochondrial DNA mutations. Int J Cancer 2022; 150:1677-1689. [PMID: 35001369 DOI: 10.1002/ijc.33927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/03/2021] [Accepted: 12/22/2021] [Indexed: 11/06/2022]
Abstract
Next-generation sequencing (NGS) of mitochondrial DNA (mtDNA) has widespread applications in aging and cancer studies. However, cross-contamination of mtDNA constitutes a major concern. Previous methods for the detection of mtDNA contamination mainly focus on haplogroup-level phylogeny, but neglect haplotype-level differences, leading to limited sensitivity and accuracy. In this study, we present mitoDataclean, a random-forest-based machine learning package for accurate identification of cross-contamination, evaluation of contamination levels and detection of contamination-derived variants in mtDNA NGS data. Comprehensive optimization of mitoDataclean revealed that training simulation with mixtures of small haplogroup distance and low polymorphic difference was critical for optimal modeling. Compared with existing methods, mitoDataclean exhibited significantly improved sensitivity and accuracy for the detection of sample contamination in simulated data. In addition, mitoDataclean achieved area under the curve values of 0.91 and 0.97 for discerning genuine and contamination-derived mtDNA variants in a simulated Western dataset and private sequencing contamination data, respectively, suggesting that this tool may be applicable for different populations and samples with different sources of contamination. Finally, mitoDataclean was further evaluated in several private and public datasets and showed a robust ability for contamination detection. Altogether, our study demonstrates that mitoDataclean may be used for accurate detection of contaminated samples and contamination-derived variants in mtDNA NGS data. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Liping Su
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Shanshan Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Wenjie Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiaoying Ji
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Yang Liu
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Huanqin Zhang
- College of Medical Technology, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Qichao Huang
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Kaixiang Zhou
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiwen Gu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
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13
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Sanchez-Contreras M, Sweetwyne MT, Kohrn BF, Tsantilas KA, Hipp MJ, Schmidt EK, Fredrickson J, Whitson JA, Campbell MD, Rabinovitch PS, Marcinek DJ, Kennedy SR. A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA. Nucleic Acids Res 2021; 49:11103-11118. [PMID: 34614167 PMCID: PMC8565317 DOI: 10.1093/nar/gkab901] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) cause maternally inherited diseases, while somatic mutations are linked to common diseases of aging. Although mtDNA mutations impact health, the processes that give rise to them are under considerable debate. To investigate the mechanism by which de novo mutations arise, we analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing. We observe distinct mutational gradients in G→A and T→C transitions delimited by the light-strand origin and the mitochondrial Control Region (mCR). The gradient increases unequally across the mtDNA with age and is lost in the absence of DNA polymerase γ proofreading activity. In addition, high-resolution analysis of the mCR shows that important regulatory elements exhibit considerable variability in mutation frequency, consistent with them being mutational ‘hot-spots’ or ‘cold-spots’. Collectively, these patterns support genome replication via a deamination prone asymmetric strand-displacement mechanism as the fundamental driver of mutagenesis in mammalian DNA. Moreover, the distribution of mtDNA single nucleotide polymorphisms in humans and the distribution of bases in the mtDNA across vertebrate species mirror this gradient, indicating that replication-linked mutations are likely the primary source of inherited polymorphisms that, over evolutionary timescales, influences genome composition during speciation.
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Affiliation(s)
- Monica Sanchez-Contreras
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth K Schmidt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Matthew D Campbell
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David J Marcinek
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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14
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Kłos P, Dabravolski SA. The Role of Mitochondria Dysfunction in Inflammatory Bowel Diseases and Colorectal Cancer. Int J Mol Sci 2021; 22:11673. [PMID: 34769108 PMCID: PMC8584106 DOI: 10.3390/ijms222111673] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Inflammatory bowel disease (IBD) is one of the leading gut chronic inflammation disorders, especially prevalent in Western countries. Recent research suggests that mitochondria play a crucial role in IBD development and progression to the more severe disease-colorectal cancer (CRC). In this review, we focus on the role of mitochondrial mutations and dysfunctions in IBD and CRC. In addition, main mitochondria-related molecular pathways involved in IBD to CRC transition are discussed. Additionally, recent publications dedicated to mitochondria-targeted therapeutic approaches to cure IBD and prevent CRC progression are discussed.
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Affiliation(s)
- Patrycja Kłos
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 72 Al. Powstańców Wlkp., 70-111 Szczecin, Poland;
| | - Siarhei A. Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], 7/11 Dovatora Str., 210026 Vitebsk, Belarus
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15
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Liu L, Tian C, Dong B, Xia M, Cai Y, Hu R, Chu X. Models to evaluate the barrier properties of mucus during drug diffusion. Int J Pharm 2021; 599:120415. [PMID: 33647411 DOI: 10.1016/j.ijpharm.2021.120415] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/07/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
Mucus is widely disseminated in the nasal cavity, oral cavity, respiratory tract, eyes, gastrointestinal tract, and reproductive tract to prevent the invasion of pathogenic bacteria and toxins. The mucus layer through its continuous secretion can prevent the passage of macromolecular substances such as pathogenic bacteria and toxins, thereby reducing the occurrence of inflammation. Without a doubt, mucus also hinders oral absorption. The physiological and biochemical properties of intestinal mucus and the different types of mucus barrier models need to be predominated. To find ways to increase the bioavailability of drugs in the future, this article summarizes mucus composition, barrier properties, mucus models, and mucoadhesive/mucopenetrating particles to highlight the information they can afford. Collectively, the review seeks to provide a state-of-the-art roadmap for researchers who must contend with this critical barrier to drug delivery.
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Affiliation(s)
- Liu Liu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Chunling Tian
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Baoqi Dong
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Mengqiu Xia
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Ye Cai
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Rongfeng Hu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei 230012, China
| | - Xiaoqin Chu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei 230012, China.
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16
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Wu Z, Zuo M, Zeng L, Cui K, Liu B, Yan C, Chen L, Dong J, Shangguan F, Hu W, He H, Lu B, Song Z. OMA1 reprograms metabolism under hypoxia to promote colorectal cancer development. EMBO Rep 2021; 22:e50827. [PMID: 33314701 PMCID: PMC7788456 DOI: 10.15252/embr.202050827] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Many cancer cells maintain enhanced aerobic glycolysis due to irreversible defective mitochondrial oxidative phosphorylation (OXPHOS). This phenomenon, known as the Warburg effect, is recently challenged because most cancer cells maintain OXPHOS. However, how cancer cells coordinate glycolysis and OXPHOS remains largely unknown. Here, we demonstrate that OMA1, a stress-activated mitochondrial protease, promotes colorectal cancer development by driving metabolic reprogramming. OMA1 knockout suppresses colorectal cancer development in AOM/DSS and xenograft mice models of colorectal cancer. OMA1-OPA1 axis is activated by hypoxia, increasing mitochondrial ROS to stabilize HIF-1α, thereby promoting glycolysis in colorectal cancer cells. On the other hand, under hypoxia, OMA1 depletion promotes accumulation of NDUFB5, NDUFB6, NDUFA4, and COX4L1, supporting that OMA1 suppresses OXPHOS in colorectal cancer. Therefore, our findings support a role for OMA1 in coordination of glycolysis and OXPHOS to promote colorectal cancer development and highlight OMA1 as a potential target for colorectal cancer therapy.
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Affiliation(s)
- Zhida Wu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Meiling Zuo
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Ling Zeng
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Kaisa Cui
- Wuxi Cancer InstituteAffiliated Hospital of Jiangnan UniversityWuxiJiangsuChina
- Laboratory of Cancer EpigeneticsWuxi School of MedicineJiangnan UniversityWuxiJiangsuChina
| | - Bing Liu
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Chaojun Yan
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Li Chen
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Jun Dong
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Fugen Shangguan
- Attardi Institute of Mitochondrial BiomedicineSchool of Life SciencesWenzhou Medical UniversityWenzhouZhejiangChina
| | - Wanglai Hu
- School of Basic Medical ScienceAnhui Medical UniversityHefeiAnhuiChina
| | - He He
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
| | - Bin Lu
- Attardi Institute of Mitochondrial BiomedicineSchool of Life SciencesWenzhou Medical UniversityWenzhouZhejiangChina
| | - Zhiyin Song
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhanHubeiChina
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17
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Saini N, Gordenin DA. Hypermutation in single-stranded DNA. DNA Repair (Amst) 2020; 91-92:102868. [PMID: 32438271 PMCID: PMC7234795 DOI: 10.1016/j.dnarep.2020.102868] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
Regions of genomic DNA can become single-stranded in the course of normal replication and transcription as well as during DNA repair. Abnormal repair and replication intermediates can contain large stretches of persistent single-stranded DNA, which is extremely vulnerable to DNA damaging agents and hypermutation. Since such single-stranded DNA spans only a fraction of the genome at a given instance, hypermutation in these regions leads to tightly-spaced mutation clusters. This phenomenon of hypermutation in single-stranded DNA has been documented in several experimental models as well as in cancer genomes. Recently, hypermutated single-stranded RNA viral genomes also have been documented. Moreover, indications of hypermutation in single-stranded DNA may also be found in the human germline. This review will summarize key current knowledge and the recent developments in understanding the diverse mechanisms and sources of ssDNA hypermutation.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.
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18
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Delgado-Deida Y, Alula KM, Theiss AL. The influence of mitochondrial-directed regulation of Wnt signaling on tumorigenesis. Gastroenterol Rep (Oxf) 2020; 8:215-223. [PMID: 32665853 PMCID: PMC7333924 DOI: 10.1093/gastro/goaa025] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/26/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are dynamic organelles that play a key role in integrating cellular signaling. Mitochondrial alterations are evident in all stages of tumorigenesis and targeting mitochondrial pathways has emerged as an anticancer therapeutic strategy. The Wnt-signaling pathway regulates many fundamental cellular functions such as proliferation, survival, migration, stem-cell maintenance, and mitochondrial metabolism and dynamics. Emerging evidence demonstrates that mitochondrial-induced regulation of Wnt signaling provides an additional mechanism to influence cell-fate decisions. Crosstalk between mitochondria and Wnt signaling presents a feedforward loop in which Wnt activation regulates mitochondrial function that, in turn, drives Wnt signaling. In this mini-review, we will discuss the recent evidence revealing the mitochondrial control of Wnt signaling and its implications for tumorigenesis and anticancer therapeutic targeting.
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Affiliation(s)
- Yaritza Delgado-Deida
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kibrom M Alula
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Arianne L Theiss
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
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19
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Increased levels of 5',8-Cyclopurine DNA lesions in inflammatory bowel diseases. Redox Biol 2020; 34:101562. [PMID: 32413746 PMCID: PMC7225727 DOI: 10.1016/j.redox.2020.101562] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/14/2020] [Accepted: 04/27/2020] [Indexed: 12/19/2022] Open
Abstract
Chronic inflammation is estimated to be a causative factor in a variety of diseases. Under inflammatory conditions reactive oxygen species (ROS) and nitrogen species (RNS) are released leading to DNA damage accumulation and genomic instability. Purine 5′,8-cyclo-2′-deoxynucleosides (cPu) are oxidative DNA lesions, exclusively derived from the attack of HO• radicals, which are known to have cytotoxic and mutagenic properties. Herein, we have analyzed the presence of cPu in genomic DNA isolated from fresh colon and visceral adipose tissue biopsies collected from inflammatory bowel diseases (IBD)-affected patients and severely obese subjects, respectively, versus what observed in the control specimens. In colon biopsies, characterized by a higher gene expression level of inducible nitric oxide synthase (iNOS), a significant increase of 8-oxo-7,8-dihydro-2′-deoxyadenosine (8-oxo-dA) and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) lesions and an accumulation of both diastereomeric cPu have been detected. In contrast, the 8-oxo-dA and 8-oxo-dG levels were extremely lower compared to the colon tissues values and no accumulation of cPu, in the inflamed visceral adipose tissue biopsies isolated from bariatric patients versus the lean counterpart was reported. In addition, in adipose tissue undetectable levels of iNOS have been found. These data suggest a potential involvement of cPu in the colon cancer susceptibility observed in IBD patients.
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20
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Abstract
The gastrointestinal microbiome plays a pivotal role in physiological homeostasis of the intestine as well as in the pathophysiology of diseases including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). Emerging evidence suggests that gut microbiota signal to the mitochondria of mucosal cells, including epithelial cells and immune cells. Gut microbiota signaling to mitochondria has been shown to alter mitochondrial metabolism, activate immune cells, induce inflammasome signaling, and alter epithelial barrier function. Both dysbiosis of the gut microbiota and mitochondrial dysfunction are associated with chronic intestinal inflammation and CRC. This review discusses mitochondrial metabolism of gut mucosal cells, mitochondrial dysfunction, and known gut microbiota-mediated mitochondrial alterations during IBD and CRC.
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Affiliation(s)
- Dakota N. Jackson
- Department of Internal Medicine, Division of Gastroenterology, Baylor Scott & White Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Arianne L. Theiss
- Department of Internal Medicine, Division of Gastroenterology, Baylor Scott & White Research Institute, Baylor University Medical Center, Dallas, TX, USA,CONTACT Arianne L. Theiss Division of Gastroenterology, Baylor Research Institute, Baylor University Medical Center, 250 Hoblitzelle, 3500 Gaston Avenue, Dallas, TX75246, USA
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21
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Siska PJ, Singer K, Evert K, Renner K, Kreutz M. The immunological Warburg effect: Can a metabolic-tumor-stroma score (MeTS) guide cancer immunotherapy? Immunol Rev 2020; 295:187-202. [PMID: 32157706 DOI: 10.1111/imr.12846] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022]
Abstract
The "glycolytic switch" also known as the "Warburg effect" is a key feature of tumor cells and leads to the accumulation of lactate and protons in the tumor environment. Intriguingly, non-malignant lymphocytes or stromal cells such as tumor-associated macrophages and cancer-associated fibroblasts contribute to the lactate accumulation in the tumor environment, a phenomenon described as the "Reverse Warburg effect." Localized lactic acidosis has a strong immunosuppressive effect and mediates an immune escape of tumors. However, some tumors do not display the Warburg phenotype and either rely on respiration or appear as a mosaic of cells with different metabolic properties. Based on these findings and on the knowledge that T cell infiltration is predictive for patient outcome, we suggest a metabolic-tumor-stroma score to determine the likelihood of a successful anti-tumor immune response: (a) a respiring tumor with high T cell infiltration ("hot"); (b) a reverse Warburg type with respiring tumor cells but glycolytic stromal cells; (c) a mixed type with glycolytic and respiring compartments; and (d) a glycolytic (Warburg) tumor with low T cell infiltration ("cold"). Here, we provide evidence that these types can be independent of the organ of origin, prognostically relevant and might help select the appropriate immunotherapy approach.
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Affiliation(s)
- Peter J Siska
- Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Katrin Singer
- Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Katja Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Kathrin Renner
- Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
| | - Marina Kreutz
- Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.,Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
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Salk JJ, Kennedy SR. Next-Generation Genotoxicology: Using Modern Sequencing Technologies to Assess Somatic Mutagenesis and Cancer Risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:135-151. [PMID: 31595553 PMCID: PMC7003768 DOI: 10.1002/em.22342] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 05/09/2023]
Abstract
Mutations have a profound effect on human health, particularly through an increased risk of carcinogenesis and genetic disease. The strong correlation between mutagenesis and carcinogenesis has been a driving force behind genotoxicity research for more than 50 years. The stochastic and infrequent nature of mutagenesis makes it challenging to observe and to study. Indeed, decades have been spent developing increasingly sophisticated assays and methods to study these low-frequency genetic errors, in hopes of better predicting which chemicals may be carcinogens, understanding their mode of action, and informing guidelines to prevent undue human exposure. While effective, widely used genetic selection-based technologies have a number of limitations that have hampered major advancements in the field of genotoxicity. Emerging new tools, in the form of enhanced next-generation sequencing platforms and methods, are changing this paradigm. In this review, we discuss rapidly evolving sequencing tools and technologies, such as error-corrected sequencing and single cell analysis, which we anticipate will fundamentally reshape the field. In addition, we consider a variety emerging applications for these new technologies, including the detection of DNA adducts, inference of mutational processes based on genomic site and local sequence contexts, and evaluation of genome engineering fidelity, as well as other cutting-edge challenges for the next 50 years of environmental and molecular mutagenesis research. Environ. Mol. Mutagen. 61:135-151, 2020. © 2019 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Jesse J. Salk
- Department of Medicine, Division of Medical OncologyUniversity of Washington School of MedicineSeattleWashington
- TwinStrand BiosciencesSeattleWashington
| | - Scott R. Kennedy
- Department of PathologyUniversity of WashingtonSeattleWashington
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Protective effect of methylene blue on TNBS-induced colitis in rats mediated through the modulation of inflammatory and apoptotic signalling pathways. Arch Toxicol 2019; 93:2927-2942. [DOI: 10.1007/s00204-019-02548-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 01/16/2023]
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