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Paiva I, Seguin J, Grgurina I, Singh AK, Cosquer B, Plassard D, Tzeplaeff L, Le Gras S, Cotellessa L, Decraene C, Gambi J, Alcala-Vida R, Eswaramoorthy M, Buée L, Cassel JC, Giacobini P, Blum D, Merienne K, Kundu TK, Boutillier AL. Dysregulated expression of cholesterol biosynthetic genes in Alzheimer's disease alters epigenomic signatures of hippocampal neurons. Neurobiol Dis 2024; 198:106538. [PMID: 38789057 DOI: 10.1016/j.nbd.2024.106538] [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: 12/29/2023] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Aging is the main risk factor of cognitive neurodegenerative diseases such as Alzheimer's disease, with epigenome alterations as a contributing factor. Here, we compared transcriptomic/epigenomic changes in the hippocampus, modified by aging and by tauopathy, an AD-related feature. We show that the cholesterol biosynthesis pathway is severely impaired in hippocampal neurons of tauopathic but not of aged mice pointing to vulnerability of these neurons in the disease. At the epigenomic level, histone hyperacetylation was observed at neuronal enhancers associated with glutamatergic regulations only in the tauopathy. Lastly, a treatment of tau mice with the CSP-TTK21 epi-drug that restored expression of key cholesterol biosynthesis genes counteracted hyperacetylation at neuronal enhancers and restored object memory. As acetyl-CoA is the primary substrate of both pathways, these data suggest that the rate of the cholesterol biosynthesis in hippocampal neurons may trigger epigenetic-driven changes, that may compromise the functions of hippocampal neurons in pathological conditions.
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Affiliation(s)
- Isabel Paiva
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France.
| | - Jonathan Seguin
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Iris Grgurina
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Akash Kumar Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India
| | - Brigitte Cosquer
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Damien Plassard
- University of Strasbourg, CNRS UMR7104, Inserm U1258 - GenomEast Platform - IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Laura Tzeplaeff
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Stephanie Le Gras
- University of Strasbourg, CNRS UMR7104, Inserm U1258 - GenomEast Platform - IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67404 Illkirch, France
| | - Ludovica Cotellessa
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Postnatal Brain, Lille Neuroscience & Cognition, UMR-S1172, FHU 1000 Days for Health, 59000 Lille, France
| | - Charles Decraene
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Johanne Gambi
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Rafael Alcala-Vida
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Muthusamy Eswaramoorthy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, UMR-S1172 LilNCog - Lille Neuroscience & Cognition, Lille, France; Alzheimer and Tauopathies, LabEx DISTALZ, France
| | - Jean-Christophe Cassel
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Paolo Giacobini
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Postnatal Brain, Lille Neuroscience & Cognition, UMR-S1172, FHU 1000 Days for Health, 59000 Lille, France
| | - David Blum
- University of Lille, Inserm, CHU Lille, UMR-S1172 LilNCog - Lille Neuroscience & Cognition, Lille, France; Alzheimer and Tauopathies, LabEx DISTALZ, France
| | - Karine Merienne
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India
| | - Anne-Laurence Boutillier
- University of Strasbourg, Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France; CNRS, UMR7364 - Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Strasbourg F-67000, France.
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2
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Laird M, Ku JC, Raiten J, Sriram S, Moore M, Li Y. Mitochondrial metabolism regulation and epigenetics in hypoxia. Front Physiol 2024; 15:1393232. [PMID: 38915781 PMCID: PMC11194441 DOI: 10.3389/fphys.2024.1393232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/13/2024] [Indexed: 06/26/2024] Open
Abstract
The complex and dynamic interaction between cellular energy control and gene expression modulation is shown by the intersection between mitochondrial metabolism and epigenetics in hypoxic environments. Poor oxygen delivery to tissues, or hypoxia, is a basic physiological stressor that sets off a series of reactions in cells to adapt and endure oxygen-starved environments. Often called the "powerhouse of the cell," mitochondria are essential to cellular metabolism, especially regarding producing energy through oxidative phosphorylation. The cellular response to hypoxia entails a change in mitochondrial metabolism to improve survival, including epigenetic modifications that control gene expression without altering the underlying genome. By altering the expression of genes involved in angiogenesis, cell survival, and metabolism, these epigenetic modifications help cells adapt to hypoxia. The sophisticated interplay between mitochondrial metabolism and epigenetics in hypoxia is highlighted by several important points, which have been summarized in the current article. Deciphering the relationship between mitochondrial metabolism and epigenetics during hypoxia is essential to understanding the molecular processes that regulate cellular adaptation to reduced oxygen concentrations.
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Affiliation(s)
- Madison Laird
- Western Michigan University Homer Stryker School of Medicine, Kalamazoo, MI, United States
| | - Jennifer C. Ku
- Western Michigan University Homer Stryker School of Medicine, Kalamazoo, MI, United States
| | - Jacob Raiten
- Western Michigan University Homer Stryker School of Medicine, Kalamazoo, MI, United States
| | - Sashwat Sriram
- Western Michigan University Homer Stryker School of Medicine, Kalamazoo, MI, United States
| | - Megan Moore
- Western Michigan University Homer Stryker School of Medicine, Kalamazoo, MI, United States
| | - Yong Li
- Department of Orthopaedic Surgery, Biomedical Engineering, Western Michigan University Homer Stryker School of Medicine, Kalamazoo, MI, United States
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Yuan L, Jiang H, Jia Y, Liao Y, Shao C, Zhou Y, Li J, Liao Y, Huang H, Pan Y, Wen W, Zhao X, Chen L, Jing X, Pan C, Wang W, Yao S, Zhang C. Fatty Acid Oxidation Supports Lymph Node Metastasis of Cervical Cancer via Acetyl-CoA-Mediated Stemness. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308422. [PMID: 38520724 DOI: 10.1002/advs.202308422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/18/2024] [Indexed: 03/25/2024]
Abstract
Accumulating evidence indicates that metabolic reprogramming of cancer cells supports the energy and metabolic demands during tumor metastasis. However, the metabolic alterations underlying lymph node metastasis (LNM) of cervical cancer (CCa) have not been well recognized. In the present study, it is found that lymphatic metastatic CCa cells have reduced dependency on glucose and glycolysis but increased fatty acid oxidation (FAO). Inhibition of carnitine palmitoyl transferase 1A (CPT1A) significantly compromises palmitate-induced cell stemness. Mechanistically, FAO-derived acetyl-CoA enhances H3K27 acetylation (H3K27Ac) modification level in the promoter of stemness genes, increasing stemness and nodal metastasis in the lipid-rich nodal environment. Genetic and pharmacological loss of CPT1A function markedly suppresses the metastatic colonization of CCa cells in tumor-draining lymph nodes. Together, these findings propose an effective method of cancer therapy by targeting FAO in patients with CCa and lymph node metastasis.
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Affiliation(s)
- Li Yuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Hongye Jiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Yan Jia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Yuandong Liao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Caixia Shao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Yijia Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Jiaying Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Yan Liao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Hua Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Weijia Wen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Xueyuan Zhao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Linna Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Xu Jing
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, 17165, Sweden
| | - Chaoyun Pan
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
| | - Chunyu Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, 510080, China
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4
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Orešković D, Madero Pohlen A, Cvitković I, Alen JF, Raguž M, Álvarez-Sala de la Cuadra A, Bazarra Castro GJ, Bušić Z, Konstantinović I, Ledenko V, Martínez Macho C, Müller D, Žarak M, Jovanov-Milosevic N, Chudy D, Marinović T. Chronic hyperglycemia and intracranial meningiomas. BMC Cancer 2024; 24:488. [PMID: 38632533 PMCID: PMC11022447 DOI: 10.1186/s12885-024-12243-4] [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: 12/27/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Meningiomas are among the most common primary tumors of the central nervous system. Previous research into the meningioma histological appearance, genetic markers, transcriptome and epigenetic landscape has revealed that benign meningiomas significantly differ in their glucose metabolism compared to aggressive lesions. However, a correlation between the systemic glucose metabolism and the metabolism of the tumor hasn't yet been found. We hypothesized that chronic levels of glycaemia (approximated with glycated hemoglobin (HbA1c)) are different in patients with aggressive and benign meningiomas. The study encompassed 71 patients with de novo intracranial meningiomas, operated on in three European hospitals, two in Croatia and one in Spain. Our results show that patients with WHO grade 2 meningiomas had significantly higher HbA1c values compared to patients with grade 1 lesions (P = 0.0290). We also found a significant number of patients (19/71; 26.7%) being hyperglycemic, harboring all the risks that such a condition entails. Finally, we found a significant correlation between our patients' age and their preoperative HbA1c levels (P = 0.0008, ρ(rho) = 0.388), suggesting that older meningioma patients are at a higher risk of having their glycaemia severely dysregulated. These findings are especially important considering the current routine and wide-spread use of corticosteroids as anti-edematous treatment. Further research in this area could lead to better understanding of meningiomas and have immediate clinical impact.
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Affiliation(s)
- D Orešković
- Department of Neurosurgery, Clinical Hospital Dubrava, Zagreb, Croatia.
| | - A Madero Pohlen
- Department of Neurosurgery, University Hospital de la Princesa, Madrid, Spain
| | - I Cvitković
- Department of Neurosurgery, University Hospital Center Split, Split, Croatia
| | - J F Alen
- Department of Neurosurgery, University Hospital de la Princesa, Madrid, Spain
| | - M Raguž
- Department of Neurosurgery, Clinical Hospital Dubrava, Zagreb, Croatia
| | | | - G J Bazarra Castro
- Department of Neurosurgery, University Hospital de la Princesa, Madrid, Spain
| | - Z Bušić
- Department of Neurosurgery, University Hospital Center Split, Split, Croatia
| | - I Konstantinović
- Department of Neurosurgery, University Hospital Center Split, Split, Croatia
| | - V Ledenko
- Department of Neurosurgery, University Hospital Center Split, Split, Croatia
| | - C Martínez Macho
- Department of Neurosurgery, University Hospital de la Princesa, Madrid, Spain
| | - D Müller
- Department of Pathology, Clinical Hospital Dubrava, Zagreb, Croatia
| | - M Žarak
- Clinical Department of Laboratory Diagnostics, Clinical Hospital Dubrava, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - N Jovanov-Milosevic
- Department of Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Centre of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, Croatian Institute for Brain Research, University of Zagreb, Zagreb, Croatia
| | - D Chudy
- Department of Neurosurgery, Clinical Hospital Dubrava, Zagreb, Croatia
- Scientific Centre of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, Croatian Institute for Brain Research, University of Zagreb, Zagreb, Croatia
| | - T Marinović
- Department of Neurosurgery, Clinical Hospital Dubrava, Zagreb, Croatia
- Department of Neurology and Neurosurgery, Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
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5
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Ren J, Ren B, Liu X, Cui M, Fang Y, Wang X, Zhou F, Gu M, Xiao R, Bai J, You L, Zhao Y. Crosstalk between metabolic remodeling and epigenetic reprogramming: A new perspective on pancreatic cancer. Cancer Lett 2024; 587:216649. [PMID: 38311052 DOI: 10.1016/j.canlet.2024.216649] [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: 07/18/2023] [Revised: 09/21/2023] [Accepted: 01/13/2024] [Indexed: 02/06/2024]
Abstract
Pancreatic cancer is a highly malignant solid tumor with a poor prognosis and a high mortality rate. Thus, exploring the mechanisms underlying the development and progression of pancreatic cancer is critical for identifying targets for diagnosis and treatment. Two important hallmarks of cancer-metabolic remodeling and epigenetic reprogramming-are interconnected and closely linked to regulate one another, creating a complex interaction landscape that is implicated in tumorigenesis, invasive metastasis, and immune escape. For example, metabolites can be involved in the regulation of epigenetic enzymes as substrates or cofactors, and alterations in epigenetic modifications can in turn regulate the expression of metabolic enzymes. The crosstalk between metabolic remodeling and epigenetic reprogramming in pancreatic cancer has gained considerable attention. Here, we review the emerging data with a focus on the reciprocal regulation of metabolic remodeling and epigenetic reprogramming. We aim to highlight how these mechanisms could be applied to develop better therapeutic strategies.
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Affiliation(s)
- Jie Ren
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Bo Ren
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Xiaohong Liu
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Ming Cui
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Yuan Fang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Xing Wang
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Feihan Zhou
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Minzhi Gu
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Ruiling Xiao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Jialu Bai
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100023, PR China; Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing 100023, PR China; National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing 100023, PR China.
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6
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Freij K, Cleveland B, Biga P. Maternal dietary choline levels cause transcriptome shift due to genotype-by-diet interactions in rainbow trout (Oncorhynchus mykiss). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101193. [PMID: 38309055 DOI: 10.1016/j.cbd.2024.101193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
The objective of this study was to identify metabolic regulatory mechanisms affected by choline availability in rainbow trout (Oncorhynchus mykiss) broodstock diets associated with increased offspring growth performance. Three customized diets were formulated to have different levels of choline: (a) 0 % choline supplementation (Low Choline: 2065 ppm choline), (b) 0.6 % choline supplementation (Medium Choline: 5657 ppm choline), and (c) 1.2 % choline supplementation (High Choline: 9248 ppm choline). Six all-female rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning at 22 months post-hatch; their offspring were fed a commercial diet. Experimental broodstock diet did not affect overall choline, fatty acid, or amino acid content in the oocytes (p > 0.05), apart from tyrosine (p ≤ 0.05). Offspring body weights from the High and Low Choline diets did not differ from those in the Medium Choline diet (p > 0.05); however, family-by-diet and sire-by-diet interactions on offspring growth were detected (p ≤ 0.05). The High Choline diet did not improve growth performance in the six broodstock families at final harvest (520-days post-hatch, or dph). Numerous genes associated with muscle development and lipid metabolism were identified as affected by broodstock diet, including myosin, troponin C, and fatty acid binding proteins, which were associated with key signaling pathways of lipid metabolism, muscle cell development, muscle cell proliferation, and muscle cell differentiation. These findings indicate that supplementing broodstock diets with choline does regulate expression of genes related to growth and nutrient partitioning but does not lead to growth benefits in rainbow trout families selected for disease resistance.
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Affiliation(s)
- Khalid Freij
- Department of Biology, The University of Alabama at Birmingham, Birmingham 35294, AL, USA. https://twitter.com/FreijKhalid
| | - Beth Cleveland
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service (ARS-USDA), Kearneysville 25430, WV, USA
| | - Peggy Biga
- Department of Biology, The University of Alabama at Birmingham, Birmingham 35294, AL, USA.
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7
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Cheng B, Fu X. The Role of Stem Cell on Wound Healing After Revascularization-Healing Following Revascularization-Unlocking Skin Potential. INT J LOW EXTR WOUND 2024; 23:63-69. [PMID: 37899578 DOI: 10.1177/15347346231210709] [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] [Indexed: 10/31/2023]
Abstract
Wound healing is a complex and dynamic process involving a series of cellular and molecular events. Revascularization, the restoration of blood flow to ischemic or damaged tissue, is a key step in wound healing. Adequate vascularization has been recognized as a necessary factor for successful tissue regeneration. In the later stage of revascularization and tissue remodeling in wound healing, stem cells regulate other repair cells and matrix formation by influencing the maturation of blood vessels. The reductive oxidation (REDOX) state may be a key mechanism through stem/progenitor cells to influence endothelial cells to mature blood vessels and improve the quality of healing. Mitochondria may play an important role in this process.
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Affiliation(s)
- Biao Cheng
- Department of Burns and Plastic Surgery, General Hospital of Southern Theater Command of PLA, Guangzhou, China
| | - Xiaobing Fu
- Research Center for Tissue Repair and Regeneration Affiliated to the Medical Innovation Research Department, PLA General Hospital and PLA Medical College; Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, Beijing, P. R. China
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8
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Cheng KCL, Frost JM, Sánchez-Luque FJ, García-Canãdas M, Taylor D, Yang WR, Irayanar B, Sampath S, Patani H, Agger K, Helin K, Ficz G, Burns KH, Ewing A, García-Pérez JL, Branco MR. Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation. Epigenetics Chromatin 2023; 16:39. [PMID: 37845773 PMCID: PMC10578016 DOI: 10.1186/s13072-023-00514-6] [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: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells. RESULTS Here we show that vitC increases the expression of several TE families, including evolutionarily young LINE-1 (L1) elements, in mouse ESCs. We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we did not detect increased somatic insertion rates in vitC-treated cells. Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism. CONCLUSION VitC directly modulates the expression of mouse L1s and other TEs through epigenetic mechanisms, with potential for downstream effects related to the multiple emerging roles of L1s in cellular function.
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Affiliation(s)
- Kevin C L Cheng
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jennifer M Frost
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Francisco J Sánchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Marta García-Canãdas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Darren Taylor
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Branavy Irayanar
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Swetha Sampath
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Hemalvi Patani
- Barts Cancer Institute, Faculty of Medicine and Dentistry, QMUL, London, EC1M 6BQ, UK
| | - Karl Agger
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
- The Institute of Cancer Research, London, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Faculty of Medicine and Dentistry, QMUL, London, EC1M 6BQ, UK
| | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Adam Ewing
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - José L García-Pérez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Miguel R Branco
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK.
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9
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Di Pietrantonio N, Cappellacci I, Mandatori D, Baldassarre MPA, Pandolfi A, Pipino C. Role of Epigenetics and Metabolomics in Predicting Endothelial Dysfunction in Type 2 Diabetes. Adv Biol (Weinh) 2023; 7:e2300172. [PMID: 37616517 DOI: 10.1002/adbi.202300172] [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: 05/04/2023] [Revised: 06/15/2023] [Indexed: 08/26/2023]
Abstract
Type 2 diabetes (T2D) is a worldwide health problem and cardiovascular disease (CVD) is a leading cause of morbidity and mortality in T2D patients, making the prevention of CVD onset a major priority. It is therefore crucial to optimize diagnosis and treatment to reduce this burden. Endothelial dysfunction is one of the most important prognostic factors for CVD progression, thus novel approaches to identify the early phase of endothelial dysfunction may lead to specific preventive measures to reduce the occurrence of CVD. Nowadays, multiomics approaches have provided unprecedented opportunities to stratify T2D patients into endotypes, improve therapeutic treatment and outcome and amend the survival prediction. Among omics strategies, epigenetics and metabolomics are gaining increasing interest. Recently, a dynamic correlation between metabolic pathways and gene expression through chromatin remodeling, such as DNA methylation, has emerged, indicating new perspectives on the regulatory networks impacting cellular processes. Thus, a better understanding of epigenetic-metabolite relationships can provide insight into the physiological processes altered early in the endothelium that ultimately head to disease development. Here, recent studies on epigenetics and metabolomics related to CVD prevention potentially useful to identify disease biomarkers, as well as new therapies hopefully targeting the early phase of endothelial dysfunction are highlighted.
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Affiliation(s)
- Nadia Di Pietrantonio
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Ilaria Cappellacci
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Domitilla Mandatori
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Maria Pompea Antonia Baldassarre
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Department of Medicine and Aging Sciences, "G. d'Annunzio" University Chieti-Pescara, Chieti, 66100, Italy
| | - Assunta Pandolfi
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
| | - Caterina Pipino
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
- Center for Advanced Studies and Technology-CAST, "G. d'Annunzio" University of Chieti-Pescara, Chieti, 66100, Italy
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10
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García-Velázquez L, Massieu L. The proteomic effects of ketone bodies: implications for proteostasis and brain proteinopathies. Front Mol Neurosci 2023; 16:1214092. [PMID: 37575967 PMCID: PMC10413579 DOI: 10.3389/fnmol.2023.1214092] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/07/2023] [Indexed: 08/15/2023] Open
Abstract
A growing body of evidence supports the beneficial effects of the ketone bodies (KBs), acetoacetate and β-hydroxybutyrate (BHB), on diverse physiological processes and diseases. Hence, KBs have been suggested as therapeutic tools for neurodegenerative diseases. KBs are an alternative fuel during fasting and starvation as they can be converted to Ac-CoA to produce ATP. A ketogenic diet (KD), enriched in fats and low in carbohydrates, induces KB production in the liver and favors their use in the brain. BHB is the most abundant KB in the circulation; in addition to its role as energy fuel, it exerts many actions that impact the set of proteins in the cell and tissue. BHB can covalently bind to proteins in lysine residues as a new post-translational modification (PTM) named β-hydroxybutyrylation (Kbhb). Kbhb has been identified in many proteins where Kbhb sites can be critical for binding to other proteins or cofactors. Kbhb is mostly found in proteins involved in chromatin structure, DNA repair, regulation of spliceosome, transcription, and oxidative phosphorylation. Histones are the most studied family of proteins with this PTM, and H3K9bhb is the best studied histone mark. Their target genes are mainly related to cell metabolism, chromatin remodeling and the control of circadian rhythms. The role of Kbhb on physiological processes is poorly known, but it might link KB metabolism to cell signaling and genome regulation. BHB also impacts the proteome by influencing proteostasis. This KB can modulate the Unfolded Protein Response (UPR) and autophagy, two processes involved in the maintenance of protein homeostasis through the clearance of accumulated unfolded and damaged proteins. BHB can support proteostasis and regulate the UPR to promote metabolism adaptation in the liver and prevent cell damage in the brain. Also, BHB stimulates autophagy aiding to the degradation of accumulated proteins. Protein aggregation is common to proteinopathies like Alzheimer's (AD) and Parkinson's (PD) diseases, where the KD and BHB treatment have shown favorable effects. In the present review, the current literature supporting the effects of KBs on proteome conformation and proteostasis is discussed, as well as its possible impact on AD and PD.
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Affiliation(s)
| | - Lourdes Massieu
- Department of Molecular Neuropathology, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), México City, Mexico
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11
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Carlberg C, Raczyk M, Zawrotna N. Vitamin D: A master example of nutrigenomics. Redox Biol 2023; 62:102695. [PMID: 37043983 PMCID: PMC10119805 DOI: 10.1016/j.redox.2023.102695] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Nutrigenomics attempts to characterize and integrate the relation between dietary molecules and gene expression on a genome-wide level. One of the biologically active nutritional compounds is vitamin D3, which activates via its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) the nuclear receptor VDR (vitamin D receptor). Vitamin D3 can be synthesized endogenously in our skin, but since we spend long times indoors and often live at higher latitudes where for many winter months UV-B radiation is too low, it became a true vitamin. The ligand-inducible transcription factor VDR is expressed in the majority of human tissues and cell types, where it modulates the epigenome at thousands of genomic sites. In a tissue-specific fashion this results in the up- and downregulation of primary vitamin D target genes, some of which are involved in attenuating oxidative stress. Vitamin D affects a wide range of physiological functions including the control of metabolism, bone formation and immunity. In this review, we will discuss how the epigenome- and transcriptome-wide effects of 1,25(OH)2D3 and its receptor VDR serve as a master example in nutrigenomics. In this context, we will outline the basis of a mechanistic understanding for personalized nutrition with vitamin D3.
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12
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Staneva D, Vasileva B, Podlesniy P, Miloshev G, Georgieva M. Yeast Chromatin Mutants Reveal Altered mtDNA Copy Number and Impaired Mitochondrial Membrane Potential. J Fungi (Basel) 2023; 9:jof9030329. [PMID: 36983497 PMCID: PMC10058930 DOI: 10.3390/jof9030329] [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: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are multifunctional, dynamic organelles important for stress response, cell longevity, ageing and death. Although the mitochondrion has its genome, nuclear-encoded proteins are essential in regulating mitochondria biogenesis, morphology, dynamics and function. Moreover, chromatin structure and epigenetic mechanisms govern the accessibility to DNA and control gene transcription, indirectly influencing nucleo-mitochondrial communications. Thus, they exert crucial functions in maintaining proper chromatin structure, cell morphology, gene expression, stress resistance and ageing. Here, we present our studies on the mtDNA copy number in Saccharomyces cerevisiae chromatin mutants and investigate the mitochondrial membrane potential throughout their lifespan. The mutants are arp4 (with a point mutation in the ARP4 gene, coding for actin-related protein 4-Arp4p), hho1Δ (lacking the HHO1 gene, coding for the linker histone H1), and the double mutant arp4 hho1Δ cells with the two mutations. Our findings showed that the three chromatin mutants acquired strain-specific changes in the mtDNA copy number. Furthermore, we detected the disrupted mitochondrial membrane potential in their chronological lifespan. In addition, the expression of nuclear genes responsible for regulating mitochondria biogenesis and turnover was changed. The most pronounced were the alterations found in the double mutant arp4 hho1Δ strain, which appeared as the only petite colony-forming mutant, unable to grow on respiratory substrates and with partial depletion of the mitochondrial genome. The results suggest that in the studied chromatin mutants, hho1Δ, arp4 and arp4 hho1Δ, the nucleus-mitochondria communication was disrupted, leading to impaired mitochondrial function and premature ageing phenotype in these mutants, especially in the double mutant.
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Affiliation(s)
- Dessislava Staneva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Bela Vasileva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Petar Podlesniy
- CiberNed (Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas), 28029 Barcelona, Spain
| | - George Miloshev
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Milena Georgieva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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13
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Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
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Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
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14
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Tabe Y, Konopleva M. Resistance to energy metabolism - targeted therapy of AML cells residual in the bone marrow microenvironment. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2023; 6:138-150. [PMID: 37065866 PMCID: PMC10099600 DOI: 10.20517/cdr.2022.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/07/2023] [Accepted: 03/01/2023] [Indexed: 04/18/2023]
Abstract
In response to the changing availability of nutrients and oxygen in the bone marrow microenvironment, acute myeloid leukemia (AML) cells continuously adjust their metabolic state. To meet the biochemical demands of their increased proliferation, AML cells strongly depend on mitochondrial oxidative phosphorylation (OXPHOS). Recent data indicate that a subset of AML cells remains quiescent and survives through metabolic activation of fatty acid oxidation (FAO), which causes uncoupling of mitochondrial OXPHOS and facilitates chemoresistance. For targeting these metabolic vulnerabilities of AML cells, inhibitors of OXPHOS and FAO have been developed and investigated for their therapeutic potential. Recent experimental and clinical evidence has revealed that drug-resistant AML cells and leukemic stem cells rewire metabolic pathways through interaction with BM stromal cells, enabling them to acquire resistance against OXPHOS and FAO inhibitors. These acquired resistance mechanisms compensate for the metabolic targeting by inhibitors. Several chemotherapy/targeted therapy regimens in combination with OXPHOS and FAO inhibitors are under development to target these compensatory pathways.
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Affiliation(s)
- Yoko Tabe
- Department of Laboratory Medicine, Juntendo University, Tokyo 112-8421, Japan
- Department of Medicine (Oncology) and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Marina Konopleva
- Department of Medicine (Oncology) and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence to: Prof. Marina Konopleva, Department of Medicine (Oncology) and Molecular Pharmacology, Albert Einstein College of Medicine and Montefiore Medical Center,1300 Morris Park Avenue, NY 10461, USA; Department of Leukemia, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA. E-mail:
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15
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Zhou D, Sun MH, Jiang WJ, Li XH, Lee SH, Heo G, Choi J, Kim KS, Cui XS. Knock-down of YME1L1 induces mitochondrial dysfunction during early porcine embryonic development. Front Cell Dev Biol 2023; 11:1147095. [PMID: 37123411 PMCID: PMC10133515 DOI: 10.3389/fcell.2023.1147095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
YME1L1, a mitochondrial metalloproteinase, is an Adenosine triphosphate (ATP)-dependent metalloproteinase and locates in the mitochondrial inner membrane. The protease domain of YME1L1 is oriented towards the mitochondrial intermembrane space, which modulates the mitochondrial GTPase optic atrophy type 1 (OPA1) processing. However, during embryonic development, there is no report yet about the role of YME1L1 on mitochondrial biogenesis and function in pigs. In the current study, the mRNA level of YME1L1 was knocked down by double strand RNA microinjection to the 1-cell stage embryos. The expression patterns of YME1L1 and its related proteins were performed by immunofluorescence and western blotting. To access the biological function of YME1L1, we first counted the preimplantation development rate, diameter, and total cell number of blastocyst on day-7. First, the localization of endogenous YME1L1 was found in the punctate structures of the mitochondria, and the expression level of YME1L1 is highly expressed from the 4-cell stage. Following significant knock-down of YME1L1, blastocyst rate and quality were decreased, and mitochondrial fragmentation was induced. YME1L1 knockdown induced excessive ROS production, lower mitochondrial membrane potential, and lower ATP levels. The OPA1 cleavage induced by YME1L1 knockdown was prevented by double knock-down of YME1L1 and OMA1. Moreover, cytochrome c, a pro-apoptotic signal, was released from the mitochondria after the knock-down of YME1L1. Taken together, these results indicate that YME1L1 is essential for regulating mitochondrial fission, function, and apoptosis during porcine embryo preimplantation development.
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Affiliation(s)
| | | | | | | | | | | | | | - Kwan-Suk Kim
- *Correspondence: Xiang-Shun Cui, ; Kwan-Suk Kim,
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Chu DT, Thi YVN, Chew NW. Histone modifications in fat metabolism and obesity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:135-152. [PMID: 37019590 DOI: 10.1016/bs.pmbts.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The World Health Organization (WHO) has identified the obesity epidemic as one of the leading causes of overall morbidity and mortality. Obesity affects individual health, and quality of life and has negative long-term economic implications on society and the entire country. In recent years, studies on histone modifications in fat metabolism and obesity have received great attention. Processes such as methylation, histone modification, chromatin remodeling, and microRNA expression are mechanisms in epigenetic regulation. These processes play a particularly important role in cell development and differentiation through gene regulation. In this chapter, we discuss the types of histone modifications in adipose tissue under different conditions, the role of histone modifications in adipose tissue development, and the relationship between histone modifications and biosynthesis in the body. In addition, the chapter provides detailed information on histone modifications in obesity, the relationship between histone modifications and food consumption status, and the role of histone modifications in overweight and obesity.
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17
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Li C, Yin Z, Xiao R, Huang B, Cui Y, Wang H, Xiang Y, Wang L, Lei L, Ye J, Li T, Zhong Y, Guo F, Xia Y, Fang P, Liang K. G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes. Genome Biol 2022; 23:259. [PMID: 36522639 PMCID: PMC9753424 DOI: 10.1186/s13059-022-02830-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/02/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which have been proposed to physically interact with transcription factors and chromatin remodelers to regulate cell type-specific transcriptome and shape chromatin landscapes. RESULTS Based on the direct interaction between G4 and natural porphyrins, we establish genome-wide approaches to profile where the iron-liganded porphyrin hemin can bind in the chromatin. Hemin promotes genome-wide G4 formation, impairs transcription initiation, and alters chromatin landscapes, including decreased H3K27ac and H3K4me3 modifications at promoters. Interestingly, G4 status is not involved in the canonical hemin-BACH1-NRF2-mediated enhancer activation process, highlighting an unprecedented G4-dependent mechanism for metabolic regulation of transcription. Furthermore, hemin treatment induces specific gene expression profiles in hepatocytes, underscoring the in vivo potential for metabolic control of gene transcription by porphyrins. CONCLUSIONS These studies demonstrate that G4 functions as a sensor for natural porphyrin metabolites in cells, revealing a G4-dependent mechanism for metabolic regulation of gene transcription and chromatin landscapes, which will deepen our knowledge of G4 biology and the contribution of cellular metabolites to gene regulation.
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Affiliation(s)
- Conghui Li
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Zhinang Yin
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Ruijing Xiao
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Beili Huang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Yali Cui
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Honghong Wang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Ying Xiang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Lingrui Wang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Lingyu Lei
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Jiaqin Ye
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Tianyu Li
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Youquan Zhong
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Fangteng Guo
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Yuchen Xia
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, 430071 China
| | - Pingping Fang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Kaiwei Liang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
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18
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Fuchs S, van Helden RW, Wiendels M, de Graaf MN, Orlova VV, Mummery CL, van Meer BJ, Mayr T. On-chip analysis of glycolysis and mitochondrial respiration in human induced pluripotent stem cells. Mater Today Bio 2022; 17:100475. [DOI: 10.1016/j.mtbio.2022.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 11/08/2022]
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19
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Hao Y, Lu L, Liu A, Lin X, Xiao L, Kong X, Li K, Liang F, Xiong J, Qu L, Li Y, Li J. Integrating bioinformatic strategies in spatial life science research. Brief Bioinform 2022; 23:bbac415. [PMID: 36198665 PMCID: PMC9677476 DOI: 10.1093/bib/bbac415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/27/2022] [Indexed: 12/14/2022] Open
Abstract
As space exploration programs progress, manned space missions will become more frequent and farther away from Earth, putting a greater emphasis on astronaut health. Through the collaborative efforts of researchers from various countries, the effect of the space environment factors on living systems is gradually being uncovered. Although a large number of interconnected research findings have been produced, their connection seems to be confused, and many unknown effects are left to be discovered. Simultaneously, several valuable data resources have emerged, accumulating data measuring biological effects in space that can be used to further investigate the unknown biological adaptations. In this review, the previous findings and their correlations are sorted out to facilitate the understanding of biological adaptations to space and the design of countermeasures. The biological effect measurement methods/data types are also organized to provide references for experimental design and data analysis. To aid deeper exploration of the data resources, we summarized common characteristics of the data generated from longitudinal experiments, outlined challenges or caveats in data analysis and provided corresponding solutions by recommending bioinformatics strategies and available models/tools.
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Affiliation(s)
- Yangyang Hao
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Liang Lu
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Xue Lin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Li Xiao
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Xiaoyue Kong
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Kai Li
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Fengji Liang
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Jianghui Xiong
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Lina Qu
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Yinghui Li
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
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20
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Liu Y, Chen C, Wang X, Sun Y, Zhang J, Chen J, Shi Y. An Epigenetic Role of Mitochondria in Cancer. Cells 2022; 11:cells11162518. [PMID: 36010594 PMCID: PMC9406960 DOI: 10.3390/cells11162518] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are not only the main energy supplier but are also the cell metabolic center regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These metabolites include acetyl-CoA, α-ketoglutarate (α-KG), S-adenosyl methionine (SAM), NAD+, and O-linked beta-N-acetylglucosamine (O-GlcNAc), which are the main substrates for DNA methylation and histone post-translation modifications, essential for gene transcriptional regulation and cell fate determination. Tumorigenesis is attributed to many factors, including gene mutations and tumor microenvironment. Mitochondria and epigenetics play essential roles in tumor initiation, evolution, metastasis, and recurrence. Targeting mitochondrial metabolism and epigenetics are promising therapeutic strategies for tumor treatment. In this review, we summarize the roles of mitochondria in key metabolites required for epigenetics modification and in cell fate regulation and discuss the current strategy in cancer therapies via targeting epigenetic modifiers and related enzymes in metabolic regulation. This review is an important contribution to the understanding of the current metabolic-epigenetic-tumorigenesis concept.
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Affiliation(s)
- Yu’e Liu
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chao Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
| | - Xinye Wang
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yihong Sun
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Juxiang Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
- Correspondence: (J.C.); (Y.S.)
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai 200092, China
- Correspondence: (J.C.); (Y.S.)
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21
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Wu S, Zhang H, Gao C, Chen J, Li H, Meng Z, Bai J, Shen Q, Wu H, Yin T. Hyperglycemia Enhances Immunosuppression and Aerobic Glycolysis of Pancreatic Cancer Through Upregulating Bmi1-UPF1-HK2 Pathway. Cell Mol Gastroenterol Hepatol 2022; 14:1146-1165. [PMID: 35863742 PMCID: PMC9606831 DOI: 10.1016/j.jcmgh.2022.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Accumulating evidence strongly suggests that hyperglycemia promotes the progression of pancreatic cancer (PC). Approximately 80% of patients with PC are intolerant to hyperglycemic conditions. In this study, we define the role of Bmi1, a stemness-related oncogene, in controlling the Warburg effect, and immune suppression under hyperglycemia conditions. METHODS The diabetes mellitus model was established by intraperitoneal injection of streptozotocin. The role of the hyperglycemia-Bmi1-HK2 axis in glycolysis-related immunosuppression was examined in both orthotopic and xenograft in vivo models. Evaluation of immune infiltrates was carried out by flow cytometry. Human PC cell lines, SW1990, BxPC-3, and CFPAC-1, were used for mechanistic in vitro studies. RESULTS Through bioinformatics analysis, we found that hyperglycemia was strongly related to aerobic glycolysis, immunosuppression, and cancer cell stemness. High glucose condition in the tumor microenvironment promotes immune suppression by upregulating glycolysis in PC cells, which can be rescued via knockdown Bmi1 expression or after 2-deoxy-D-glucose treatment. Through gain-/loss-of-function assessments, we found that Bmi1 upregulated the expression of UPF1, which enhanced the stability of HK2 mRNA and thereby increased the expression of HK2. The role of the hyperglycemia-Bmi-HK2 pathway in the inhibition of antitumor immunity was further verified via the immune-competent and immunodeficient mice model. We also demonstrated that hyperglycemia promotes the expression of Bmi1 by elevating the intracellular acetyl-CoA levels and histone H4 acetylation levels. CONCLUSIONS Our results suggest that the previously unreported Bmi1-UPF1-HK2 pathway contributes to PC progression and immunosuppression, which may bring in new targets for developing effective therapies to treat patients with PC.
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Affiliation(s)
- Shihong Wu
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoxiang Zhang
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenggang Gao
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoshun Chen
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hehe Li
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zibo Meng
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
| | - Jianwei Bai
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Shen
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Heshui Wu
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Yin
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,Correspondence Address correspondence to: Tao Yin, MD, PhD, Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China. Tel: +86 027-85351631.
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22
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Gong M, Shi R, Liu Y, Ke J, Liu X, Du HZ, Liu CM. Abnormal microglial polarization induced by Arid1a deletion leads to neuronal differentiation deficits. Cell Prolif 2022; 55:e13314. [PMID: 35854653 DOI: 10.1111/cpr.13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/03/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE Microglia, the prototypical innate immune cells of the central nervous system (CNS), are highly plastic and assume their phenotypes dependent on intrinsically genetic, epigenetic regulation or extrinsically microenvironmental cues. Microglia has been recognized as key regulators of neural stem/progenitor cells (NSPCs) and brain functions. Chromatin accessibility is implicated in immune cell development and functional regulation. However, it is still unknown whether and how chromatin remodelling regulates the phenotypic plasticity of microglia and exerts what kind of effects on NSPCs. METHODS We investigated the role of chromatin accessibility in microglia by deleting chromatin remodelling gene Arid1a using microglia-specific Cx3cr1-cre and Cx3cr1-CreERT2 mice. RNA-seq and ATAC-seq were performed to dissect the molecular mechanisms. In addition, we examined postnatal M1/M2 microglia polarization and analysed neuronal differentiation of NSPCs. Finally, we tested the effects of microglial Arid1a deletion on mouse behaviours. RESULTS Increased chromatin accessibility upon Arid1a ablation resulted in enhanced M1 microglial polarization and weakened M2 polarization, which led to abnormal neurogenesis and anxiety-like behaviours. Switching the polarization state under IL4 stimulation could rescue abnormal neurogenesis, supporting an essential role for chromatin remodeler ARID1A in balancing microglial polarization and brain functions. CONCLUSIONS Our study identifies ARID1A as a central regulator of microglia polarization, establishing a mechanistic link between chromatin remodelling, neurogenesis and mouse behaviours, and highlights the potential development of innovative therapeutics exploiting the innate regenerative capacity of the nervous system.
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Affiliation(s)
- Maolei Gong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ruoxi Shi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yijun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Ke
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Hong-Zhen Du
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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23
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Activation of the Mitochondrial Unfolded Protein Response: A New Therapeutic Target? Biomedicines 2022; 10:biomedicines10071611. [PMID: 35884915 PMCID: PMC9313171 DOI: 10.3390/biomedicines10071611] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction is a key hub that is common to many diseases. Mitochondria’s role in energy production, calcium homeostasis, and ROS balance makes them essential for cell survival and fitness. However, there are no effective treatments for most mitochondrial and related diseases to this day. Therefore, new therapeutic approaches, such as activation of the mitochondrial unfolded protein response (UPRmt), are being examined. UPRmt englobes several compensation processes related to proteostasis and antioxidant mechanisms. UPRmt activation, through an hormetic response, promotes cell homeostasis and improves lifespan and disease conditions in biological models of neurodegenerative diseases, cardiopathies, and mitochondrial diseases. Although UPRmt activation is a promising therapeutic option for many conditions, its overactivation could lead to non-desired side effects, such as increased heteroplasmy of mitochondrial DNA mutations or cancer progression in oncologic patients. In this review, we present the most recent UPRmt activation therapeutic strategies, UPRmt’s role in diseases, and its possible negative consequences in particular pathological conditions.
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24
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Thomas GE, Egan G, García-Prat L, Botham A, Voisin V, Patel PS, Hoff FW, Chin J, Nachmias B, Kaufmann KB, Khan DH, Hurren R, Wang X, Gronda M, MacLean N, O'Brien C, Singh RP, Jones CL, Harding SM, Raught B, Arruda A, Minden MD, Bader GD, Hakem R, Kornblau S, Dick JE, Schimmer AD. The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness. Nat Cell Biol 2022; 24:872-884. [PMID: 35668135 PMCID: PMC9203277 DOI: 10.1038/s41556-022-00925-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 04/22/2022] [Indexed: 11/21/2022]
Abstract
Mitochondrial metabolites regulate leukaemic and normal stem cells by affecting epigenetic marks. How mitochondrial enzymes localize to the nucleus to control stem cell function is less understood. We discovered that the mitochondrial metabolic enzyme hexokinase 2 (HK2) localizes to the nucleus in leukaemic and normal haematopoietic stem cells. Overexpression of nuclear HK2 increases leukaemic stem cell properties and decreases differentiation, whereas selective nuclear HK2 knockdown promotes differentiation and decreases stem cell function. Nuclear HK2 localization is phosphorylation-dependent, requires active import and export, and regulates differentiation independently of its enzymatic activity. HK2 interacts with nuclear proteins regulating chromatin openness, increasing chromatin accessibilities at leukaemic stem cell-positive signature and DNA-repair sites. Nuclear HK2 overexpression decreases double-strand breaks and confers chemoresistance, which may contribute to the mechanism by which leukaemic stem cells resist DNA-damaging agents. Thus, we describe a non-canonical mechanism by which mitochondrial enzymes influence stem cell function independently of their metabolic function. Thomas, Egan et al. report that hexokinase 2 localizes to the nucleus of leukaemic and normal haematopoietic cells to maintain stemness by interacting with nuclear proteins and modulating chromatin accessibility independently of its kinase activity.
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Affiliation(s)
- Geethu Emily Thomas
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Grace Egan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Laura García-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron Botham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Veronique Voisin
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Parasvi S Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fieke W Hoff
- Department of Pediatric Hematology/Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Jordan Chin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Boaz Nachmias
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dilshad H Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cristiana O'Brien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rashim P Singh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Courtney L Jones
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shane M Harding
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gary D Bader
- Terrence Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario, Canada
| | - Razq Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Steve Kornblau
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
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25
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Liu D, Benzaquen J, Morris LGT, Ilié M, Hofman P. Mutations in KMT2C, BCOR and KDM5C Predict Response to Immune Checkpoint Blockade Therapy in Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:cancers14112816. [PMID: 35681795 PMCID: PMC9179442 DOI: 10.3390/cancers14112816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Efficient biomarkers are urgently needed to predict response to immune checkpoint blockade (ICB) therapy for non-small cell lung cancer (NSCLC), particularly NSCLC with low tumor mutational burden (TMB). Here, we show that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, are associated with the ICB response in NSCLC, including NSCLC with low TMB level. Furthermore, this association is further improved by a combined use of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 expression. These data suggest that KMT2C/BCOR/KDM5C mutation status has the potential to serve as a predictive biomarker for ICB therapy in NSCLC. Abstract Efficient predictive biomarkers are urgently needed to identify non-small cell lung cancer (NSCLC) patients who could benefit from immune checkpoint blockade (ICB) therapy. Since chromatin remodeling is required for DNA repair process, we asked whether mutations in chromatin remodeling genes could increase tumor mutational burden (TMB) and predict response to ICB therapy in NSCLC. Analysis of seven ICB-treated NSCLC cohorts revealed that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, were significantly associated with ICB response, and combined mutations of these three genes further enhance this association. NSCLC patients with KMT2C/BCOR/KDM5C mutations had comparable clinical outcomes to TMB-high patients in terms of objective response rate, durable clinical benefit and overall survival. Although KMT2C/BCOR/KDM5C mutations were positively correlated with TMB levels in NSCLC, the association of this mutation with better ICB response was independent of tumor TMB and programmed death-ligand 1 (PD-L1) level, and combination of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 further improve the prediction of ICB response in NSCLC patients. Cancer Genome Atlas (TCGA) pan-cancer analysis suggested that the association of KMT2C/BCOR/KDM5C mutations with ICB response observed here might not result from DNA repair defects. In conclusion, our data indicate that KMT2C/BCOR/KDM5C mutation has the potential to serve as a predictive biomarker, alone or combined with PD-L1 expression or TMB, for ICB therapy in NSCLC.
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Affiliation(s)
- Dingxie Liu
- Bluewater Biotech LLC, New Providence, NJ 07974, USA
- Correspondence: (D.L.); (P.H.)
| | - Jonathan Benzaquen
- Department of Pneumology, Pasteur Hospital, FHU OncoAge, 06000 Nice, France; (J.B.); (M.I.)
| | - Luc G. T. Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Marius Ilié
- Department of Pneumology, Pasteur Hospital, FHU OncoAge, 06000 Nice, France; (J.B.); (M.I.)
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, CHU Nice, FHU OncoAge, University Côte d’Azur, 06100 Nice, France
- Team 4, IRCAN, UMR 7284/U10181, FHU OncoAge, University Côte d’Azur, 06107 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), CHU of Nice, FHU OncoAge, University Côte d’Azur, 06100 Nice, France
- Correspondence: (D.L.); (P.H.)
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26
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Wang L, Shannar AAF, Wu R, Chou P, Sarwar MS, Kuo HC, Peter RM, Wang Y, Su X, Kong AN. Butyrate Drives Metabolic Rewiring and Epigenetic Reprogramming in Human Colon Cancer Cells. Mol Nutr Food Res 2022; 66:e2200028. [PMID: 35429118 DOI: 10.1002/mnfr.202200028] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/23/2022] [Indexed: 12/16/2022]
Abstract
SCOPE Butyrate (B) is a short-chain fatty acid produced by dietary fiber, known to inhibit histone deacetylases (HDACs) and possess cancer-preventive/anticancer effects. However, the role of B in metabolic rewiring, epigenomic reprogramming, transcriptomic network, NRF2 signaling, and eliciting cancer-preventive effects in colorectal cancer (CRC) HCT116 cell remains unclear. METHODS AND RESULTS Sodium butyrate (NaB) dose-dependently inhibits the growth of CRC HCT116 cells. NaB inhibits NRF2/NRF2-target genes and blocks NRF2-ARE signaling. NaB increases NRF2 negative regulator KEAP1 expression through inhibiting its promoter methylation. Associative analysis of DEGs (differentially expressed genes) from RNA-seq and DMRs (differentially methylated regions) from CpG methyl-seq identified the tumor suppressor gene ABCA1 and tumor promote gene EGR3 are correlated with their promoters' CpG methylation indicating NaB regulates cancer markers through modulating their promoter methylation. NaB activated the mitochondrial tricarboxylic acid (TCA) cycle while inhibited the methionine metabolism which are both tightly coupled to the epigenetic machinery. NaB regulates the epigenetic enzymes/genes including DNMT1, HAT1, KDM1A, KDM1B, and TET1. Altogether, B's regulation of metabolites coupled to the epigenetic enzymes illustrates the potential underlying biological connectivity between metabolomics and epigenomics. CONCLUSION B regulates KEAP1/NRF2 signaling, drives metabolic rewiring, CpG methylomic, and transcriptomic reprogramming contributing to the overall cancer-prevention/anticancer effect in the CRC cell model.
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Affiliation(s)
- Lujing Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
| | - Ahmad Abdel Fat Shannar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Pochung Chou
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
| | - Md Shahid Sarwar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Hsiao-Chen Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
| | - Rebecca Mary Peter
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08854, USA
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08903, USA.,Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08903, USA.,Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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Van Dyck L, Güiza F, Derese I, Pauwels L, Casaer MP, Hermans G, Wouters PJ, Van den Berghe G, Vanhorebeek I. DNA methylation alterations in muscle of critically ill patients. J Cachexia Sarcopenia Muscle 2022; 13:1731-1740. [PMID: 35274472 PMCID: PMC9178166 DOI: 10.1002/jcsm.12970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/15/2021] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Intensive care unit (ICU)-acquired weakness can persist beyond ICU stay and has been associated with long-term functional impairment of ICU survivors. Recently, DNA methylation alterations were found in the blood of ICU patients, partially explaining long-term developmental impairment of critically ill children. As illness-induced aberrant DNA methylation theoretically could also be involved in long-term weakness, we investigated whether the DNA methylation signature in muscle of adult critically ill patients differs from that in muscle of healthy controls. METHODS Genome-wide methylation was determined (Infinium® HumanMethylationEPIC BeadChips) in DNA extracted from skeletal muscle biopsies that had been collected on Day 8 ± 1 in ICU from 172 EPaNIC-trial patients [66% male sex, median age 62.7 years, median body mass index (BMI) 25.9 kg/m2 ] and 20 matched healthy controls (70% male sex, median age 58.0 years, median BMI 24.4 kg/m2 ). Methylation status of individual cytosine-phosphate-guanine (CpG) sites of patients and controls was compared with F-tests, using the Benjamini-Hochberg false discovery rate to correct for multiple comparisons. Differential methylation of DNA regions was assessed with bump hunting, with 1000 permutations assessing uncertainty, expressed as family-wise error rate. Gene expression was investigated for 10 representative affected genes. RESULTS In DNA from ICU patients, 565 CpG sites, associated with 400 unique genes, were differentially methylated as compared with controls (average difference 3.2 ± 0.1% ranging up to 16.9%, P < 0.00005). Many of the associated genes appeared highly relevant for muscle structure and function/weakness, including genes involved in myogenesis, muscle regeneration, nerve/muscle membrane excitability, muscle denervation/re-innervation, axon guidance/myelination/degeneration/regeneration, synapse function, ion channelling with especially calcium signalling, metabolism (glucose, protein, and fat), insulin signalling, neuroendocrine hormone regulation, mitochondrial function, autophagy, apoptosis, oxidative stress, Wnt signalling, transcription regulation, muscle fat infiltration during regeneration, and fibrosis. In patients as compared with controls, we also identified two hypomethylated regions, spanning 18 and 3 CpG sites in the promoters of the HIC1 and NADK2 genes, respectively (average differences 5.8 ± 0.01% and 12.1 ± 0.04%, family-wise error rate <0.05). HIC1 and NADK2 play important roles in muscle regeneration and postsynaptic acetylcholine receptors and in mitochondrial processes, respectively. Nine of 10 investigated genes containing DNA methylation alterations were differentially expressed in patients as compared with controls (P ≤ 0.03). CONCLUSIONS Critically ill patients present with a different DNA methylation signature in skeletal muscle as compared with healthy controls, which in theory could provide a biological basis for long-term persistence of weakness in ICU survivors. TRIAL REGISTRATION ClinicalTrials.gov: NCT00512122, registered on 31 July 2007.
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Affiliation(s)
- Lisa Van Dyck
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Fabian Güiza
- Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Inge Derese
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Lies Pauwels
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Michaël P Casaer
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Greet Hermans
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Pieter J Wouters
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Greet Van den Berghe
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Ilse Vanhorebeek
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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28
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Calciolari B, Scarpinello G, Tubi LQ, Piazza F, Carrer A. Metabolic control of epigenetic rearrangements in B cell pathophysiology. Open Biol 2022; 12:220038. [PMID: 35580618 PMCID: PMC9113833 DOI: 10.1098/rsob.220038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Both epigenetic and metabolic reprogramming guide lymphocyte differentiation and can be linked, in that metabolic inputs can be integrated into the epigenome to inform cell fate decisions. This framework has been thoroughly investigated in several pathophysiological contexts, including haematopoietic cell differentiation. In fact, metabolite availability dictates chromatin architecture and lymphocyte specification, a multi-step process where haematopoietic stem cells become terminally differentiated lymphocytes (effector or memory) to mount the adaptive immune response. B and T cell precursors reprogram their cellular metabolism across developmental stages, not only to meet ever-changing energetic demands but to impose chromatin accessibility and regulate the function of master transcription factors. Metabolic control of the epigenome has been extensively investigated in T lymphocytes, but how this impacts type-B life cycle remains poorly appreciated. This assay will review our current understanding of the connection between cell metabolism and epigenetics at crucial steps of B cell maturation and how its dysregulation contributes to malignant transformation.
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Affiliation(s)
- Beatrice Calciolari
- Department of Biology (DiBio), of the University of Padova, Padova, Italy,Department of Medicine (DIMED), Hematology and Clinical Immunology Section, of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Greta Scarpinello
- Department of Surgical, Oncological and Gastroenterological Sciences (DiSCOG), of the University of Padova, Padova, Italy
| | - Laura Quotti Tubi
- Department of Medicine (DIMED), Hematology and Clinical Immunology Section, of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Francesco Piazza
- Department of Medicine (DIMED), Hematology and Clinical Immunology Section, of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Alessandro Carrer
- Department of Biology (DiBio), of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
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29
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L M, C H, V V, J L, M M, E Q, T C, M DN, F M. A plant-based diet differentially affects the global hepatic methylome in rainbow trout depending on genetic background. Epigenetics 2022; 17:1726-1737. [PMID: 35345978 PMCID: PMC9621033 DOI: 10.1080/15592294.2022.2058226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Replacing fish meal and oil in trout diets with plant-derived ingredients is a contemporary challenge to move towards more sustainable aquaculture practices. However, such dietary replacement causes hepatic metabolic changes that have not yet been elucidated. Here, we aimed to decipher the effect of a 100% plant-based diet on the hepatic global DNA methylation landscape in trout and assess whether changes depend on fish genetic background. We analysed the global methylome and the expression of DNA (de)methylation-related genes of three isogenic lines that exhibit similar growth when fed a marine resource-based diet (M diet), but differ in their responses to a plant-based diet (V diet). Our results revealed that the V diet induced a decrease in 5-cytosine combined with an increase in 5-hydroxymethylcytosine in two of the three analysed lines. For one of these 2 affected lines, when fed the M diet but at the same feed intake of the V diet (MR), no methylome differences were highlighted between M and MR or between MR and V-fed trout whereas for the other affected line, M fed trout displayed a divergent methylome profile from MR and V fed fish. DNA (de)methylation-related genes were also affected by the V or MR diets. Our findings showed that the global hepatic methylome of trout is affected by a V diet, depending on genetic background. This latter effect seems to be due to either a decreased feed intake alone or combined with the effect of the dietary composition per se.
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Affiliation(s)
- Marandel L
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Heraud C
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Véron V
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Laithier J
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Marchand M
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Quillet E
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Callet T
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
| | - Dupont-Nivet M
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Médale F
- INRAE, Univ Pau & Pays Adour, E2S UPPA, UMR 1419, Nutrition, Métabolisme, Aquaculture, Saint Pée sur Nivelle, France
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Kamerzell TJ, Mikell B, Chen L, Elias H, Dawn B, MacRae C, Middaugh CR. The structural basis of histone modifying enzyme specificity and promiscuity: Implications for metabolic regulation and drug design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:189-243. [PMID: 35534108 DOI: 10.1016/bs.apcsb.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Histone modifying enzymes regulate chromatin architecture through covalent modifications and ultimately control multiple aspects of cellular function. Disruption of histone modification leads to changes in gene expression profiles and may lead to disease. Both small molecule inhibitors and intermediary metabolites have been shown to modulate histone modifying enzyme activity although our ability to identify successful drug candidates or novel metabolic regulators of these enzymes has been limited. Using a combination of large scale in silico screens and in vivo phenotypic analysis, we identified several small molecules and intermediary metabolites with distinctive HME activity. Our approach using unsupervised learning identifies the chemical fingerprints of both small molecules and metabolites that facilitate recognition by the enzymes active sites which can be used as a blueprint to design novel inhibitors. Furthermore, this work supports the idea that histone modifying enzymes sense intermediary metabolites integrating genes, environment and cellular physiology.
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Affiliation(s)
- Tim J Kamerzell
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States; Division of Internal Medicine, HCA MidWest Health, Overland Park, KS, United States; Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States; Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States; Applied AI Technologies, LLC, Overland Park, KS, United States.
| | - Brittney Mikell
- Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Lei Chen
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Harold Elias
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Buddhadeb Dawn
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Calum MacRae
- Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
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Neurons undergo pathogenic metabolic reprogramming in models of familial ALS. Mol Metab 2022; 60:101468. [PMID: 35248787 PMCID: PMC8958550 DOI: 10.1016/j.molmet.2022.101468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/21/2022] Open
Abstract
Objectives Methods Results Conclusions Our work is the first to perform a comprehensive and quantitative analysis of intermediary metabolism in neurons in the setting of fALS causing gene products. Because the cardinal feature of ALS is death of motor neurons, these new studies are directly relevant to the pathogenesis of ALS. Our functional interrogations begin to unpack how metabolic re-wiring is induced by fALS genes and it will be very interesting, in the future, to gain insight in amino acid fueling of the TCA cycle. We suspect pleiotropic effects of amino acid fueling, and this may lead to very targeted therapeutic interventions.
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32
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Yuan Y, Li H, Pu W, Chen L, Guo D, Jiang H, He B, Qin S, Wang K, Li N, Feng J, Wen J, Cheng S, Zhang Y, Yang W, Ye D, Lu Z, Huang C, Mei J, Zhang HF, Gao P, Jiang P, Su S, Sun B, Zhao SM. Cancer metabolism and tumor microenvironment: fostering each other? SCIENCE CHINA. LIFE SCIENCES 2022; 65:236-279. [PMID: 34846643 DOI: 10.1007/s11427-021-1999-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023]
Abstract
The changes associated with malignancy are not only in cancer cells but also in environment in which cancer cells live. Metabolic reprogramming supports tumor cell high demand of biogenesis for their rapid proliferation, and helps tumor cell to survive under certain genetic or environmental stresses. Emerging evidence suggests that metabolic alteration is ultimately and tightly associated with genetic changes, in particular the dysregulation of key oncogenic and tumor suppressive signaling pathways. Cancer cells activate HIF signaling even in the presence of oxygen and in the absence of growth factor stimulation. This cancer metabolic phenotype, described firstly by German physiologist Otto Warburg, insures enhanced glycolytic metabolism for the biosynthesis of macromolecules. The conception of metabolite signaling, i.e., metabolites are regulators of cell signaling, provides novel insights into how reactive oxygen species (ROS) and other metabolites deregulation may regulate redox homeostasis, epigenetics, and proliferation of cancer cells. Moreover, the unveiling of noncanonical functions of metabolic enzymes, such as the moonlighting functions of phosphoglycerate kinase 1 (PGK1), reassures the importance of metabolism in cancer development. The metabolic, microRNAs, and ncRNAs alterations in cancer cells can be sorted and delivered either to intercellular matrix or to cancer adjacent cells to shape cancer microenvironment via media such as exosome. Among them, cancer microenvironmental cells are immune cells which exert profound effects on cancer cells. Understanding of all these processes is a prerequisite for the development of a more effective strategy to contain cancers.
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Affiliation(s)
- Yiyuan Yuan
- Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China
| | - Huimin Li
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wang Pu
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences and School of Life Sciences, Fudan University, Shanghai, 200032, China
| | - Leilei Chen
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences and School of Life Sciences, Fudan University, Shanghai, 200032, China
| | - Dong Guo
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Hongfei Jiang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China
| | - Bo He
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Siyuan Qin
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Na Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jingwei Feng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Jing Wen
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shipeng Cheng
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yaguang Zhang
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Weiwei Yang
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Dan Ye
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences and School of Life Sciences, Fudan University, Shanghai, 200032, China.
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
| | - Canhua Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
| | - Jun Mei
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hua-Feng Zhang
- CAS Centre for Excellence in Cell and Molecular Biology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ping Gao
- School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, 510006, China.
| | - Peng Jiang
- Tsinghua University School of Life Sciences, and Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
| | - Bing Sun
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shi-Min Zhao
- Obstetrics & Gynecology Hospital of Fudan University, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China.
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Nasr M, Abd-Allah H, Ahmed-Farid OAH, Bakeer RM, Hassan NS, Ahmed RF. A comparative study between curcumin and curcumin nanoemulsion on high-fat, high-fructose diet-induced impaired spermatogenesis in rats. J Pharm Pharmacol 2022; 74:268-281. [DOI: 10.1093/jpp/rgab172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Abstract
Objectives
Curcumin is a promising nutraceutical with reported diverse therapeutic properties, but of limited oral bioavailability. The current manuscript investigates the role of encapsulation of curcumin in nanoemulsion form in counteracting the adverse effect of chronic ingestion of a high-fat high-fructose diet (HFHF) by juvenile male rats regarding testicular abnormalities and declined spermatogenesis.
Methods
Curcumin nanoemulsion was administered orally to Wistar rats at a dose of 5 or 10 mg/kg and compared with curcumin powder, followed by a pharmacological and histological assessment.
Key findings
Results demonstrated that curcumin nanoemulsion was superior to curcumin powder, particularly in enhancing the percentage progressive motility of spermatozoa, normalization of essential and non-essential amino acids in semen, normalization of serum leptin and testosterone levels, as well as normalization of oxidative and nitrosative parameters. It was also proven to reduce testicular DNA fragmentation, while elevating testicular cellular energy. In addition, curcumin nanoemulsion administered at a dose of 10 mg/kg induced the highest level of spermatogenesis, delineated by histological examination of the seminiferous tubules.
Conclusions
It can be concluded that curcumin nanoemulsion administered at a dose of 10 mg/kg successfully ameliorates the adverse effects of a HFHF on spermatogenesis.
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Affiliation(s)
- Maha Nasr
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Hend Abd-Allah
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Omar A H Ahmed-Farid
- Department of Physiology, National Organization for Drug Control and Research, Giza, Egypt
| | - Rofanda M Bakeer
- Department of Pathology, Faculty of Medicine, Helwan University, Helwan, Egypt
| | - Nabila S Hassan
- Department of Pathology, Medical Research and Clinical Studies Institute, National Research Centre, Giza, Egypt
| | - Rania F Ahmed
- Department of Pharmacology, Medical Research and Clinical Studies Institute, National Research Centre, Giza, Egypt
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Tan J, Li H, Ji C, Zhang L, Zhao C, Tang L, Zhang C, Sun Z, Tan W, Yuan Q. Electron transfer-triggered imaging of EGFR signaling activity. Nat Commun 2022; 13:594. [PMID: 35105871 PMCID: PMC8807759 DOI: 10.1038/s41467-022-28213-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
In vivo electron transfer processes are closely related to the activation of signaling pathways, and, thus, affect various life processes. Indeed, the signaling pathway activation of key molecules may be associated with certain diseases. For example, epidermal growth factor receptor (EGFR) activation is related to the occurrence and development of tumors. Hence, monitoring the activation of EGFR-related signaling pathways can help reveal the progression of tumor development. However, it is challenging for current detection methods to monitor the activation of specific signaling pathways in complex biochemical reactions. Here we designed a highly sensitive and specific nanoprobe that enables in vivo imaging of electronic transfer over a broad range of spatial and temporal scales. By using the ferrocene-DNA polymer “wire”, the electrons transferred in a biochemical reaction can flow to persistent luminescent nanoparticles and change their electron distribution, thereby altering the optical signal of the particles. This electron transfer-triggered imaging probe enables mapping the activation of EGFR-related signaling pathways in a temporally and spatially precise manner. By offering precise visualization of signaling activity, this approach may offer a general platform not only for understanding molecular mechanisms in various biological processes but also for promoting disease therapies and drug evaluation. Here, the authors design a nanoprobe for in vivo imaging of electronic transfer, consisting of a ferrocene-DNA polymer to transfer electrons to luminescent nanoparticles, changing their optical signal. Using this probe, they map activation of EGFR signalling during tumour treatment.
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Affiliation(s)
- Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Hao Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Chenxuan Zhao
- Department of Chemistry, ZJU-NHU United R&D Center, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liming Tang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Caixin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Zhijun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China.
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China. .,The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.
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Wang L, Wu R, Sargsyan D, Su S, Kuo HC, Li S, Chou P, Sarwar MS, Phadnis A, Wang Y, Su X, Kong AN. Nfe2l2 Regulates Metabolic Rewiring and Epigenetic Reprogramming in Mediating Cancer Protective Effect by Fucoxanthin. AAPS J 2022; 24:30. [PMID: 35043283 DOI: 10.1208/s12248-022-00679-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fucoxanthin (FX) is a carotenoid with many pharmaceutical properties due to its antioxidant/anti-inflammatory and epigenetic effects. NFE2L2 is involved in the defense against oxidative stress/inflammation-mediated diseases, like anticancer effects elicited by phytochemicals including FX. However, the role of FX and NFE2L2 in metabolic rewiring, epigenomic reprogramming, and transcriptomic network in blocking pro-tumorigenic signaling and eliciting cancer-protective effects remains unknown. Herein, we utilized multi-omics approaches to evaluate the role of NFE2L2 and the impact of FX on tumor promoter TPA-induced skin cell transformation. FX blocked TPA-induced ROS and oxidized GSSG/reduced GSH in Nfe2l2wild-type(WT) but not Nfe2l2-knockdown (KD) cells. Both Nfe2l2 KD and TPA altered cellular metabolisms and metabolites which are tightly coupled to epigenetic machinery. The suppressive effects of FX on TPA-enhancedSAM/SAH was abrogated by Nfe2l2 KD indicating Nfe2l2 plays a critical role in FX-mediated metabolic rewiring and its potential consequences on epigenetic reprogramming. Epigenomic CpG methyl-seq revealed that FX attenuated TPA-induced differentially methylated regions (DMRs) of Uhrf1 and Dnmt1 genes. Transcriptomic RNA-seq showed that FX abrogated TPA-induced differentially expressed genes (DEGs) of Nfe2l2-related genes Nqo1, Ho1, and Keap1. Associative analysis of DEGs and DMRs identified that the mRNA expressions of Uhrf1 and Dnmt1 were correlated with the promoter CpG methylation status. Chromatin immunoprecipitation assay showed that FX restored Uhrf1 expression by regulating H3K27Me3 enrichment in the promoter region. In this context, FX/Nfe2l2's redox signaling drives metabolic rewiring causing epigenetic and transcriptomic reprogramming potentially contributing to the protection of TPA-induced JB6 cellular transformation skin cancer model. Graphical abstract.
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Affiliation(s)
- Lujing Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Shan Su
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Hsiao-Chen Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Shanyi Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Pochung Chou
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Md Shahid Sarwar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Ameya Phadnis
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, 08903, USA.,Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, New Jersey, 08903, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, 08903, USA.,Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, New Jersey, 08903, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA.
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Zhao Y, Zhu W, Chen H, Yan K, Wu J, Huang Q. Glioma stem cells and their microenvironment: A narrative review on docking and transformation. GLIOMA 2022. [DOI: 10.4103/glioma.glioma_5_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Mishra P, Beura S, Ghosh R, Modak R. Nutritional Epigenetics: How Metabolism Epigenetically Controls Cellular Physiology, Gene Expression and Disease. Subcell Biochem 2022; 100:239-267. [PMID: 36301497 DOI: 10.1007/978-3-031-07634-3_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The regulation of gene expression is a dynamic process that is influenced by both internal and external factors. Alteration in the epigenetic profile is a key mechanism in the regulation process. Epigenetic regulators, such as enzymes and proteins involved in posttranslational modification (PTM), use different cofactors and substrates derived from dietary sources. For example, glucose metabolism provides acetyl CoA, S-adenosylmethionine (SAM), α- ketoglutarate, uridine diphosphate (UDP)-glucose, adenosine triphosphate (ATP), nicotinamide adenine dinucleotide (NAD+), and fatty acid desaturase (FAD), which are utilized by chromatin-modifying enzymes in many intermediary metabolic pathways. Any alteration in the metabolic status of the cell results in the alteration of these metabolites, which causes dysregulation in the activity of chromatin regulators, resulting in the alteration of the epigenetic profile. Such long-term or repeated alteration of epigenetic profile can lead to several diseases, like cancer, insulin resistance and diabetes, cognitive impairment, neurodegenerative disease, and metabolic syndromes. Here we discuss the functions of key nutrients that contribute to epigenetic regulation and their role in pathophysiological conditions.
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Affiliation(s)
- Pragyan Mishra
- Infection and Epigenetics Group, School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Shibangini Beura
- Infection and Epigenetics Group, School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Ritu Ghosh
- Infection and Epigenetics Group, School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Rahul Modak
- Infection and Epigenetics Group, School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India.
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Tandem Mass Tag labelling quantitative acetylome analysis of differentially modified proteins during mycoparasitism of Clonostachys chloroleuca 67-1. Sci Rep 2021; 11:22383. [PMID: 34789861 PMCID: PMC8599485 DOI: 10.1038/s41598-021-01956-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022] Open
Abstract
Lysine acetylation (Kac) is an important post-translational modification (PTM) of proteins in all organisms, but its functions have not been extensively explored in filamentous fungi. In this study, a Tandem Mass Tag (TMT) labelling lysine acetylome was constructed, and differentially modified Kac proteins were quantified during mycoparasitism and vegetative growth in the biocontrol fungus Clonostachys chloroleuca 67–1, using liquid chromatography-tandem mass spectrometry (LC–MS/MS). A total of 1448 Kac sites were detected on 740 Kac proteins, among which 126 sites on 103 proteins were differentially regulated. Systematic bioinformatics analyses indicate that the modified Kac proteins were from multiple subcellular localizations and involved in diverse functions including chromatin assembly, glycometabolism and redox activities. All Kac sites were characterized by 10 motifs, including the novel CxxKac motif. The results suggest that Kac proteins may have effects of broadly regulating protein interaction networks during C. chloroleuca parasitism to Sclerotinia sclerotiorum sclerotia. This is the first report of a correlation between Kac events and the biocontrol activity of C. chloroleuca. Our findings provide insight into the molecular mechanisms underlying C. chloroleuca control of plant fungal pathogens regulated by Kac proteins.
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Exogenous mitochondrial transfer and endogenous mitochondrial fission facilitate AML resistance to OxPhos inhibition. Blood Adv 2021; 5:4233-4255. [PMID: 34507353 PMCID: PMC8945617 DOI: 10.1182/bloodadvances.2020003661] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/09/2021] [Indexed: 01/03/2023] Open
Abstract
Acute myeloid leukemia (AML) cells are highly dependent on oxidative phosphorylation (OxPhos) for survival, and they continually adapt to fluctuations in nutrient and oxygen availability in the bone marrow (BM) microenvironment. We investigated how the BM microenvironment affects the response to OxPhos inhibition in AML by using a novel complex I OxPhos inhibitor, IACS-010759. Cellular adhesion, growth, and apoptosis assays, along with measurements of expression of mitochondrial DNA and generation of mitochondrial reactive oxygen species indicated that direct interactions with BM stromal cells triggered compensatory activation of mitochondrial respiration and resistance to OxPhos inhibition in AML cells. Mechanistically, inhibition of OxPhos induced transfer of mitochondria derived from mesenchymal stem cells (MSCs) to AML cells via tunneling nanotubes under direct-contact coculture conditions. Inhibition of OxPhos also induced mitochondrial fission and increased functional mitochondria and mitophagy in AML cells. Mitochondrial fission is known to enhance cell migration, so we used electron microscopy to observe mitochondrial transport to the leading edge of protrusions of AML cells migrating toward MSCs. We further demonstrated that cytarabine, a commonly used antileukemia agent, increased mitochondrial transfer of MSCs to AML cells triggered by OxPhos inhibition. Our findings indicate an important role of exogenous mitochondrial trafficking from BM stromal cells to AML cells as well as endogenous mitochondrial fission and mitophagy in the compensatory adaptation of leukemia cells to energetic stress in the BM microenvironment.
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Abstract
Even with strict implementation of preventive measures, surgical site infections (SSIs) remain among the most prevalent health care-associated infections. New strategies to prevent SSIs would thus have a huge impact, also in light of increasing global rates of antimicrobial drug resistance. Considering the indispensable role of innate immune cells in host defense in surgical wounds, enhancing their function may represent a potential strategy for prevention of SSIs. Trained immunity is characterized by metabolic, epigenetic, and functional reprogramming of innate immune cells. These functional changes take place at multiple levels, namely, at the level of bone marrow precursors, circulating innate immune cells, and resident tissue macrophages. Experimental studies have shown that induction of trained immunity can protect against various infections. Increasing evidence suggests that it may also lower the risk and severity of SSIs. This may occur through several different mechanisms. First, trained immunity enhances local host defense against soft tissue infections, including those caused by Staphylococcus aureus, the most common cause of SSIs. Second, training effects on nonimmune cells such as fibroblasts have been shown to improve wound repair. Third, trained immunity may prevent or reverse the postoperative immunoparalysis that contributes to risk of infections following surgery. There are multiple approaches to inducing trained immunity, such as vaccination with the bacillus Calmette-Guérin (BCG) tuberculosis vaccine, topical administration of β-glucan, or treatment with the Toll-like receptor 7 agonist imiquimod. Clinical-experimental studies should establish if and how induction of trained immunity can best help prevent SSIs and what patient groups would most benefit.
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Dietary Patterns Influence Target Gene Expression through Emerging Epigenetic Mechanisms in Nonalcoholic Fatty Liver Disease. Biomedicines 2021; 9:biomedicines9091256. [PMID: 34572442 PMCID: PMC8468830 DOI: 10.3390/biomedicines9091256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) refers to the pathologic buildup of extra fat in the form of triglycerides in liver cells without excessive alcohol intake. NAFLD became the most common cause of chronic liver disease that is tightly associated with key aspects of metabolic disorders, including insulin resistance, obesity, diabetes, and metabolic syndrome. It is generally accepted that multiple mechanisms and pathways are involved in the pathogenesis of NAFLD. Heredity, sedentary lifestyle, westernized high sugar saturated fat diet, metabolic derangements, and gut microbiota, all may interact on a on genetically susceptible individual to cause the disease initiation and progression. While there is an unquestionable role for gene-diet interaction in the etiopathogenesis of NAFLD, it is increasingly apparent that epigenetic processes can orchestrate many aspects of this interaction and provide additional mechanistic insight. Exciting research demonstrated that epigenetic alterations in chromatin can influence gene expression chiefly at the transcriptional level in response to unbalanced diet, and therefore predispose an individual to NAFLD. Thus, further discoveries into molecular epigenetic mechanisms underlying the link between nutrition and aberrant hepatic gene expression can yield new insights into the pathogenesis of NAFLD, and allow innovative epigenetic-based strategies for its early prevention and targeted therapies. Herein, we outline the current knowledge of the interactive role of a high-fat high-calories diet and gene expression through DNA methylation and histone modifications on the pathogenesis of NAFLD. We also provide perspectives on the advancement of the epigenomics in the field and possible shortcomings and limitations ahead.
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42
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Tortelote GG, Colón-Leyva M, Saifudeen Z. Metabolic programming of nephron progenitor cell fate. Pediatr Nephrol 2021; 36:2155-2164. [PMID: 33089379 PMCID: PMC10734399 DOI: 10.1007/s00467-020-04752-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/30/2020] [Accepted: 08/31/2020] [Indexed: 11/28/2022]
Abstract
Metabolic pathways are one of the first responses at the cellular level to maternal/fetal interface stressors. Studies have revealed the previously unrecognized contributions of intermediary metabolism to developmental programs. Here, we provide an overview of cellular metabolic pathways and the cues that modulate metabolic states. We discuss the developmental and physiological implications of metabolic reprogramming and the key role of metabolites in epigenetic and epiproteomic modifications during embryonic development and with respect to kidney development and nephrogenesis.
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Affiliation(s)
- Giovane G Tortelote
- Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue SL37, Room 5534, New Orleans, LA, 70112, USA
| | - Mariel Colón-Leyva
- Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue SL37, Room 5534, New Orleans, LA, 70112, USA
| | - Zubaida Saifudeen
- Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Avenue SL37, Room 5534, New Orleans, LA, 70112, USA.
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Abstract
The genetic information of human cells is stored in the context of chromatin, which is subjected to DNA methylation and various histone modifications. Such a 'language' of chromatin modification constitutes a fundamental means of gene and (epi)genome regulation, underlying a myriad of cellular and developmental processes. In recent years, mounting evidence has demonstrated that miswriting, misreading or mis-erasing of the modification language embedded in chromatin represents a common, sometimes early and pivotal, event across a wide range of human cancers, contributing to oncogenesis through the induction of epigenetic, transcriptomic and phenotypic alterations. It is increasingly clear that cancer-related metabolic perturbations and oncohistone mutations also directly impact chromatin modification, thereby promoting cancerous transformation. Phase separation-based deregulation of chromatin modulators and chromatin structure is also emerging to be an important underpinning of tumorigenesis. Understanding the various molecular pathways that underscore a misregulated chromatin language in cancer, together with discovery and development of more effective drugs to target these chromatin-related vulnerabilities, will enhance treatment of human malignancies.
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Affiliation(s)
- Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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Placental Glucose Transporters and Response to Bisphenol A in Pregnancies from of Normal and Overweight Mothers. Int J Mol Sci 2021; 22:ijms22126625. [PMID: 34205666 PMCID: PMC8233759 DOI: 10.3390/ijms22126625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Bisphenol A (BPA) is a synthetic phenol extensively used in the manufacture of polycarbonate plastics and epoxy resins and a component of liquid and food storages. Among health disorders potentially attributed to BPA, the effects on metabolism have been especially studied. BPA represents a hazard in prenatal life because of its presence in tissues and fluids during pregnancy. Our recent study in rats fed with BPA showed a placental increase in glucose type 1 transporter (GLUT-1), suggesting a higher uptake of glucose. However, the role of BPA on GLUT transporters in pregnant women with metabolic dysfunction has not yet been investigated. In this study, placental tissue from 26 overweight (OW) women and 32 age-matched normal weight (NW) pregnant women were examined for expression of GLUT1 and GLUT4. Placental explants from OW and NW mothers were exposed to BPA 1 nM and 1 μM and tested for GLUTs expression. The data showed a different response of placental explants to BPA in GLUT1 expression with an increase in NW mothers and a decrease in OW ones. GLUT4 expression was lower in the explants from OW than NW mothers, while no difference was showed between OW and NW in placental biopsies for any of the transporters.
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Abstract
Alterations in cardiac energy metabolism contribute to the severity of heart failure. However, the energy metabolic changes that occur in heart failure are complex and are dependent not only on the severity and type of heart failure present but also on the co-existence of common comorbidities such as obesity and type 2 diabetes. The failing heart faces an energy deficit, primarily because of a decrease in mitochondrial oxidative capacity. This is partly compensated for by an increase in ATP production from glycolysis. The relative contribution of the different fuels for mitochondrial ATP production also changes, including a decrease in glucose and amino acid oxidation, and an increase in ketone oxidation. The oxidation of fatty acids by the heart increases or decreases, depending on the type of heart failure. For instance, in heart failure associated with diabetes and obesity, myocardial fatty acid oxidation increases, while in heart failure associated with hypertension or ischemia, myocardial fatty acid oxidation decreases. Combined, these energy metabolic changes result in the failing heart becoming less efficient (ie, a decrease in cardiac work/O2 consumed). The alterations in both glycolysis and mitochondrial oxidative metabolism in the failing heart are due to both transcriptional changes in key enzymes involved in these metabolic pathways, as well as alterations in NAD redox state (NAD+ and nicotinamide adenine dinucleotide levels) and metabolite signaling that contribute to posttranslational epigenetic changes in the control of expression of genes encoding energy metabolic enzymes. Alterations in the fate of glucose, beyond flux through glycolysis or glucose oxidation, also contribute to the pathology of heart failure. Of importance, pharmacological targeting of the energy metabolic pathways has emerged as a novel therapeutic approach to improving cardiac efficiency, decreasing the energy deficit and improving cardiac function in the failing heart.
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Affiliation(s)
- Gary D Lopaschuk
- Cardiovascular Research Centre, University of Alberta, Edmonton, Canada (G.D.L., Q.G.K.)
| | - Qutuba G Karwi
- Cardiovascular Research Centre, University of Alberta, Edmonton, Canada (G.D.L., Q.G.K.)
| | - Rong Tian
- Mitochondria and Metabolism Center, University of Washington, Seattle (R.T.)
| | - Adam R Wende
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham (A.R.W.)
| | - E Dale Abel
- Division of Endocrinology and Metabolism, University of Iowa Carver College of Medicine, Iowa City (E.D.A.).,Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine, Iowa City (E.D.A.)
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Sakagami H, Nakatani S, Enomoto A, Ota S, Kaneko M, Sugimoto M, Horiuchi M, Toeda K, Oizumi T. Multi-Omics Analysis of Anti-Inflammatory Action of Alkaline Extract of the Leaves of Sasa sp. J Clin Med 2021; 10:jcm10102100. [PMID: 34068182 PMCID: PMC8152990 DOI: 10.3390/jcm10102100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
Efficient utilization of alkaline extracts of several plants for the treatment of oral diseases has been reported. To investigate the mechanism of anti-inflammatory activity of alkaline extract of the leaves of Sasa sp. (SE), multi-omics analysis using metabolomics and DNA array was performed. Human gingival fibroblasts (HGFs) were treated for IL-1β to induce inflammation (detected by PGE2 production in culture medium) in the presence or absence of SE. Both IL-1β and SE showed slight hormetic growth stimulation against HGF. SE inhibited PGE2 production dose- and time-dependently. Its inhibitory action was more pronounced by first treating the cells with SE, rather than with IL-1β. At 3 h after IL-1β treatment, 18 amino acids (except cysteine and glutamic acid), total glutathione (GSH, GSSG, Cys-GSH disulfide), Met-sulfoxide, 5-oxoproline, and SAM declined, whereas DNA expressions of AKT, CASP3, and CXCL3 were elevated. These changes were reversed by simultaneous treatment with SE. The present study suggests that the anti-inflammatory action of SE is mediated via various metabolic pathways for cell survival, apoptosis, and leukocyte recruitment.
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Affiliation(s)
- Hiroshi Sakagami
- Meikai University Research Institute of Odontology (M-RIO), Meikai University School of Dentistry, 1-1 Keyakidai, Sakado, Saitama 350-0283, Japan
- Correspondence: ; Tel.: +81-049-279-2758
| | - Sachie Nakatani
- Graduate School of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan;
| | - Ayame Enomoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.E.); (S.O.); (M.K.); (M.S.)
| | - Sana Ota
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.E.); (S.O.); (M.K.); (M.S.)
| | - Miku Kaneko
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.E.); (S.O.); (M.K.); (M.S.)
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.E.); (S.O.); (M.K.); (M.S.)
- Research and Development Center for Minimally Invasive Therapies, Institute of Medical Science, Tokyo Medical University, Shinjuku, Tokyo 160-0022, Japan
| | - Misaki Horiuchi
- Daiwa Biological Research Institute Co., Ltd., Sakado 3-2-1, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (M.H.); (K.T.); (T.O.)
| | - Kazuki Toeda
- Daiwa Biological Research Institute Co., Ltd., Sakado 3-2-1, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (M.H.); (K.T.); (T.O.)
| | - Takaaki Oizumi
- Daiwa Biological Research Institute Co., Ltd., Sakado 3-2-1, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (M.H.); (K.T.); (T.O.)
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47
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Costa Dos Santos G, Renovato-Martins M, de Brito NM. The remodel of the "central dogma": a metabolomics interaction perspective. Metabolomics 2021; 17:48. [PMID: 33969452 PMCID: PMC8106972 DOI: 10.1007/s11306-021-01800-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND In 1957, Francis Crick drew a linear diagram on a blackboard. This diagram is often called the "central dogma." Subsequently, the relationships between different steps of the "central dogma" have been shown to be considerably complex, mostly because of the emerging world of small molecules. It is noteworthy that metabolites can be generated from the diet through gut microbiome metabolism, serve as substrates for epigenetic modifications, destabilize DNA quadruplexes, and follow Lamarckian inheritance. Small molecules were once considered the missing link in the "central dogma"; however, recently they have acquired a central role, and their general perception as downstream products has become reductionist. Metabolomics is a large-scale analysis of metabolites, and this emerging field has been shown to be the closest omics associated with the phenotype and concomitantly, the basis for all omics. AIM OF REVIEW Herein, we propose a broad updated perspective for the flux of information diagram centered in metabolomics, including the influence of other factors, such as epigenomics, diet, nutrition, and the gut- microbiome. KEY SCIENTIFIC CONCEPTS OF REVIEW Metabolites are the beginning and the end of the flux of information.
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Affiliation(s)
- Gilson Costa Dos Santos
- Laboratory of NMR Metabolomics, IBRAG, Department of Genetics, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
| | - Mariana Renovato-Martins
- Department of Cellular and Molecular Biology, IB, Federal Fluminense University, Niterói, 24210-200, Brazil
| | - Natália Mesquita de Brito
- Laboratory of Cellular and Molecular Pharmacology, IBRAG, Department of Cell Biology, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
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48
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Cifani P, Li Z, Luo D, Grivainis M, Intlekofer AM, Fenyö D, Kentsis A. Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. J Proteome Res 2021; 20:1835-1848. [PMID: 33749263 PMCID: PMC8341206 DOI: 10.1021/acs.jproteome.0c00638] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent studies have revealed diverse amino acid, post-translational, and noncanonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. Using synthetic standards and controlled chemical labeling experiments, we demonstrate its high specificity and sensitivity for the discovery of substoichiometric protein modifications in complex cellular extracts. SAMPEI mapping of mouse macrophage differentiation revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation. SAMPEI's robust parametrization and versatility are expected to facilitate the discovery of biological modifications of diverse macromolecules. SAMPEI is implemented as a Python package and is available open-source from BioConda and GitHub (https://github.com/FenyoLab/SAMPEI).
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Zhi Li
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Danmeng Luo
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Mark Grivainis
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Andrew M Intlekofer
- Human Oncology & Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, and Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, New York 10021, United States
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Sar P, Dalai S. CRISPR/Cas9 in epigenetics studies of health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:309-343. [PMID: 34127198 DOI: 10.1016/bs.pmbts.2021.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetics is the heritable phenotypic changes without altering the genotype. Epigenetic processes are such as histone methylation, acetylation, ubiquitination, sumoylation, phosphorylation, ADP ribosylation, DNA methylation and non-coding RNAs interactions associated with structural changes in chromatin. The change of structure is either open chromatin for "active" state or closed chromatin for "inactive" state, that regulates important biological phenomenon like chromatin condensation, gene expression, DNA repair, cellular development, differentiation and homeostasis, etc. However, dysregulation of epigenetic patterns causes diseases like cancer, diabetes, neurological disorder, infectious diseases, autoimmunity etc. Besides, the most important clinical uses of Epigenetics studies are i. identification of disease biomarkers and ii. development of their therapeutics. Epigenetic therapies include epi-drugs, combinatorial therapy, nanocarriers, plant-derived products that are being used for changing the epigenetic pattern to reverse gene expression. However, the developed epi- drugs cause off-target gene and transposable elements activation; promote mutagenesis and carcinogenesis in normal cells, are the major hurdles regarding their clinical use. Therefore, advanced epigenetic therapeutics are required to develop target-specific epigenetic modifications to reverse gene expression pattern. CRISPR-Cas9 (Clustered Regularly Interspaced Palindrome Repeats-associated protein 9) system-mediated gene activation mechanism paves new methods of target-specific epigenetic therapeutics to cure diseases. In this chapter, we discuss how CRISPR/Cas9 and dCas9 have recently been engineered for epigenome editing. Different strategies have been discussed used for epigenome editing based on their efficacy and complexity. Last but not least we have discussed the limitations, different uses of CRISPR/Cas9 and dCas9 in the area of genetic engineering.
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Affiliation(s)
- Pranati Sar
- Institute of Science, NIRMA University, Ahmedabad, India.
| | - Sarat Dalai
- Institute of Science, NIRMA University, Ahmedabad, India.
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Masalha W, Daka K, Woerner J, Pompe N, Weber S, Delev D, Krüger MT, Schnell O, Beck J, Heiland DH, Grauvogel J. Metabolic alterations in meningioma reflect the clinical course. BMC Cancer 2021; 21:211. [PMID: 33648471 PMCID: PMC7923818 DOI: 10.1186/s12885-021-07887-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Meningiomas are common brain tumours that are usually defined by benign clinical course. However, some meningiomas undergo a malignant transformation and recur within a short time period regardless of their World Health Organization (WHO) grade. The current study aimed to identify potential markers that can discriminate between benign and malignant meningioma courses. Methods We profiled the metabolites from 43 patients with low- and high-grade meningiomas. Tumour specimens were analyzed by nuclear magnetic resonance analysis; 270 metabolites were identified and clustered with the AutoPipe algorithm. Results We observed two distinct clusters marked by alterations in glycine/serine and choline/tryptophan metabolism. Glycine/serine cluster showed significantly lower WHO grades and proliferation rates. Also progression-free survival was significantly longer in the glycine/serine cluster. Conclusion Our findings suggest that alterations in glycine/serine metabolism are associated with lower proliferation and more recurrent tumours. Altered choline/tryptophan metabolism was associated with increases proliferation, and recurrence. Our results suggest that tumour malignancy can be reflected by metabolic alterations, which may support histological classifications to predict the clinical outcome of patients with meningiomas. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07887-5.
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Affiliation(s)
- Waseem Masalha
- Department of Neurosurgery, University Medical Center Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Karam Daka
- Department of Neurosurgery, University Medical Center Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jakob Woerner
- Institute of Physical Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg im Breisgau, Germany
| | - Nils Pompe
- Institute of Physical Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg im Breisgau, Germany
| | - Daniel Delev
- Department of Neurosurgery, RWTH University, Aachen, Germany
| | - Marie T Krüger
- Department of Neurosurgery, Cantonal Hospital St.Gallen, st. gallen, Switzerland
| | - Oliver Schnell
- Department of Neurosurgery, University Medical Center Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jürgen Beck
- Department of Neurosurgery, University Medical Center Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Dieter Henrik Heiland
- Department of Neurosurgery, University Medical Center Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Juergen Grauvogel
- Department of Neurosurgery, University Medical Center Freiburg, Breisacher Straße 64, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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