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Pratama AM, Sharma M, Naidu S, Bömmel H, Prabhuswamimath SC, Thati M, Wihadmadyatami H, Bachhuka A, Karnati S. Peroxisomes and PPARs: Emerging role as master regulators of cancer metabolism. Mol Metab 2024:102044. [PMID: 39368612 DOI: 10.1016/j.molmet.2024.102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 09/16/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024] Open
Abstract
Cancer is a disease characterized by the acquisition of a multitude of unique traits. It has long been understood that cancer cells divert significantly from normal cell metabolism. The most obvious of metabolic changes is that cancer cells strongly rely on glucose conversion by aerobic glycolysis. In addition, they also regularly develop mechanisms to use lipids and fatty acids for their energy needs. Peroxisomes lie central to these adaptive changes of lipid metabolism. Peroxisomes are metabolic organelles that take part in over 50 enzymatic reactions crucial for cellular functioning. Thus, they are essential for an effective and comprehensive use of lipids' energy supplied to cells. Cancer cells display a substantial increase in the biogenesis of peroxisomes and an increased expression of proteins necessary for the enzymatic functions provided by peroxisomes. Moreover, the enzymatic conversion of FAs in peroxisomes is a significant source of reactive oxygen and nitrogen species (ROS/RNS) that strongly impact cancer malignancy. Important regulators in peroxisomal FA oxidation and ROS/RNS generation are the transcription factors of the peroxisome proliferator-activated receptor (PPAR) family. This review describes the metabolic changes in tumorigenesis and cancer progression influenced by peroxisomes. We will highlight the ambivalent role that peroxisomes and PPARs play in the different stages of tumor development and summarize our current understanding of how to capitalize on the comprehension of peroxisomal biology for cancer treatment.
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Affiliation(s)
- Anggi Muhtar Pratama
- University of Würzburg, Institute of Anatomy and Cell Biology, Würzburg, Germany
| | - Mansi Sharma
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, India
| | - Srivatsava Naidu
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, India
| | - Heike Bömmel
- University of Würzburg, Institute of Anatomy and Cell Biology, Würzburg, Germany
| | - Samudyata C Prabhuswamimath
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, 570 015, Karnataka, India
| | - Madhusudhan Thati
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Hevi Wihadmadyatami
- Department of Anatomy, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Akash Bachhuka
- Department of Electronics, Electric, and Automatic Engineering, Rovira I Virgili University (URV), Tarragona, 43003, Spain.
| | - Srikanth Karnati
- University of Würzburg, Institute of Anatomy and Cell Biology, Würzburg, Germany.
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Wang J, Wu Q, Wang X, Liu H, Chen M, Xu L, Zhang Z, Li K, Li W, Zhong J. Targeting Macrophage Phenotypes and Metabolism as Novel Therapeutic Approaches in Atherosclerosis and Related Cardiovascular Diseases. Curr Atheroscler Rep 2024; 26:573-588. [PMID: 39133247 PMCID: PMC11392985 DOI: 10.1007/s11883-024-01229-z] [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] [Accepted: 07/22/2024] [Indexed: 08/13/2024]
Abstract
PURPOSE OF THE REVIEW Macrophage accumulation and activation function as hallmarks of atherosclerosis and have complex and intricate dynamics throughout all components and stages of atherosclerotic plaques. In this review, we focus on the regulatory roles and underlying mechanisms of macrophage phenotypes and metabolism in atherosclerosis. We highlight the diverse range of macrophage phenotypes present in atherosclerosis and their potential roles in progression and regression of atherosclerotic plaque. Furthermore, we discuss the challenges and opportunities in developing therapeutic strategies for preventing and treating atherosclerotic cardiovascular disease. RECENT FINDINGS Dysregulation of macrophage polarization between the proinflammatory M1 and anti-inflammatory M2 phenotypealters the immuno-inflammatory response during atherosclerosis progression, leading to plaque initiation, growth, and ultimately rupture. Altered metabolism of macrophage is a key feature for their function and the subsequent progression of atherosclerotic cardiovascular disease. The immunometabolism of macrophage has been implicated to macrophage activation and metabolic rewiring of macrophages within atherosclerotic lesions, thereby shifting altered macrophage immune-effector and tissue-reparative function. Targeting macrophage phenotypes and metabolism are potential therapeutic strategies in the prevention and treatment of atherosclerosis and atherosclerotic cardiovascular diseases. Understanding the precise function and metabolism of specific macrophage subsets and their contributions to the composition and growth of atherosclerotic plaques could reveal novel strategies to delay or halt development of atherosclerotic cardiovascular diseases and their associated pathophysiological consequences. Identifying biological stimuli capable of modulating macrophage phenotypes and metabolism may lead to the development of innovative therapeutic approaches for treating patients with atherosclerosis and coronary artery diseases.
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Affiliation(s)
- Juan Wang
- Beijing Key Laboratory of Hypertension, Heart Center of Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
| | - Qiang Wu
- Senior Department of Cardiology, the Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
- Journal of Geriatric Cardiology Editorial Office, Chinese PLA General Hospital, Beijing, China
| | - Xinyu Wang
- Beijing Key Laboratory of Hypertension, Heart Center of Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Hongbin Liu
- Department of Cardiology, the Second Medical Center, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Mulei Chen
- Beijing Key Laboratory of Hypertension, Heart Center of Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Li Xu
- Beijing Key Laboratory of Hypertension, Heart Center of Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ze Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Kuibao Li
- Beijing Key Laboratory of Hypertension, Heart Center of Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Weiming Li
- Beijing Key Laboratory of Hypertension, Heart Center of Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
| | - Jiuchang Zhong
- Beijing Key Laboratory of Hypertension, Heart Center of Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
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Li D, Zhang Z, Wang L. Emerging role of tumor microenvironmental nutrients and metabolic molecules in ferroptosis: Mechanisms and clinical implications. Biomed Pharmacother 2024; 179:117406. [PMID: 39255738 DOI: 10.1016/j.biopha.2024.117406] [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: 06/15/2024] [Revised: 08/22/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
In recent years, ferroptosis has gradually attracted increasing attention because of its important role in tumors. Ferroptosis resistance is an important cause of tumor metastasis, recurrence and drug resistance. Exploring the initiating factors and specific mechanisms of ferroptosis has become a key strategy to block tumor progression and improve drug sensitivity. As the external space in direct contact with tumor cells, the tumor microenvironment has a great impact on the biological function of tumor cells. The relationships between abnormal environmental characteristics (hypoxia, lactic acid accumulation, etc.) in the microenvironment and ferroptosis of tumor cells has not been fully characterized. This review focuses on the characteristics of the tumor microenvironment and summarizes the mechanisms of ferroptosis under different environmental factors, aiming to provide new insights for subsequent targeted therapy. Moreover, considering the presence of anticancer drugs in the microenvironment, we further summarize the mechanisms of ferroptosis to provide new strategies for the sensitization of tumor cells to drugs.
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Affiliation(s)
- Dongyu Li
- Department of VIP In-Patient Ward, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Zhe Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Lei Wang
- Department of Vascular and Thyroid Surgery, the First Hospital of China Medical University, Shenyang, Liaoning 110001, China.
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4
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Zuber J, Palm W. Modelling and deciphering tumour metabolism in CRISPR screens. Nat Rev Cancer 2024:10.1038/s41568-024-00758-8. [PMID: 39354071 DOI: 10.1038/s41568-024-00758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Affiliation(s)
- Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Wilhelm Palm
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.
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Fang J, Singh S, Wells B, Wu Q, Jin H, Janke LJ, Wan S, Steele JA, Connelly JP, Murphy AJ, Wang R, Davidoff AM, Ashcroft M, Pruett-Miller SM, Yang J. The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells. RESEARCH SQUARE 2024:rs.3.rs-4390765. [PMID: 38853928 PMCID: PMC11160912 DOI: 10.21203/rs.3.rs-4390765/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
3D cellular-specific epigenetic and transcriptomic reprogramming is critical to organogenesis and tumorigenesis. Here we dissect the distinct cell fitness in 2D (normoxia vs. chronic hypoxia) vs 3D (normoxia) culture conditions for a MYC-driven murine liver cancer model. We identify over 600 shared essential genes and additional context-specific fitness genes and pathways. Knockout of the VHL-HIF1 pathway results in incompatible fitness defects under normoxia vs. 1% oxygen or 3D culture conditions. Moreover, deletion of each of the mitochondrial respiratory electron transport chain complex has distinct fitness outcomes. Notably, multicellular organogenesis signaling pathways including TGFb-SMAD specifically constrict the uncontrolled cell proliferation in 3D while inactivation of epigenetic modifiers (Bcor, Kmt2d, Mettl3 and Mettl14) has opposite outcomes in 2D vs. 3D. We further identify a 3D-dependent synthetic lethality with partial loss of Prmt5 due to a reduction of Mtap expression resulting from 3D-specific epigenetic reprogramming. Our study highlights unique epigenetic, metabolic and organogenesis signaling dependencies under different cellular settings.
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Affiliation(s)
- Jie Fang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shivendra Singh
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brennan Wells
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Qiong Wu
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Laura J. Janke
- Department of Pathology and Division of Comparative Pathology, St. Jude Children’s Research Hospital, TN 38105, USA
| | - Shibiao Wan
- Bioinformatics and Systems Biology Core and Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical Center, Omaha, NE 68198-5805, USA
| | - Jacob A. Steele
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jon P. Connelly
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Andrew J. Murphy
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ruoning Wang
- Center for Childhood Cancer Research, Hematology/Oncology & BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Department of Pediatrics at The Ohio State University, Columbus, OH 43025, USA
| | - Andrew M. Davidoff
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, TN 38105
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
| | - Margaret Ashcroft
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, TN 38105
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Wyant GA, Jiang Q, Singh M, Qayyum S, Levrero C, Maron BA, Kaelin WG. Induction of DEPP1 by HIF Mediates Multiple Hallmarks of Ischemic Cardiomyopathy. Circulation 2024; 150:770-786. [PMID: 38881449 PMCID: PMC11361356 DOI: 10.1161/circulationaha.123.066628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/22/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND HIF (hypoxia inducible factor) regulates many aspects of cardiac function. We and others previously showed that chronic HIF activation in the heart in mouse models phenocopies multiple features of ischemic cardiomyopathy in humans, including mitochondrial loss, lipid accumulation, and systolic cardiac dysfunction. In some settings, HIF also causes the loss of peroxisomes. How, mechanistically, HIF promotes cardiac dysfunction is an open question. METHODS We used mice lacking cardiac pVHL (von Hippel-Lindau protein) to investigate how chronic HIF activation causes multiple features of ischemic cardiomyopathy, such as autophagy induction and lipid accumulation. We performed immunoblot assays, RNA sequencing, mitochondrial and peroxisomal autophagy flux measurements, and live cell imaging on isolated cardiomyocytes. We used CRISPR-Cas9 gene editing in mice to validate a novel mediator of cardiac dysfunction in the setting of chronic HIF activation. RESULTS We identify a previously unknown pathway by which cardiac HIF activation promotes the loss of mitochondria and peroxisomes. We found that DEPP1 (decidual protein induced by progesterone 1) is induced under hypoxia in a HIF-dependent manner and localizes inside mitochondria. DEPP1 is both necessary and sufficient for hypoxia-induced autophagy and triglyceride accumulation in cardiomyocytes ex vivo. DEPP1 loss increases cardiomyocyte survival in the setting of chronic HIF activation ex vivo, and whole-body Depp1 loss decreases cardiac dysfunction in hearts with chronic HIF activation caused by VHL loss in vivo. CONCLUSIONS Our findings identify DEPP1 as a key component in the cardiac remodeling that occurs with chronic ischemia.
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Affiliation(s)
- Gregory A. Wyant
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA (G.A.W., Q.J., C.L., W.G.K.)
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA (G.A.W., M.S., S.Q.)
| | - Qinqin Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA (G.A.W., Q.J., C.L., W.G.K.)
| | - Madhu Singh
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA (G.A.W., M.S., S.Q.)
| | - Shariq Qayyum
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA (G.A.W., M.S., S.Q.)
| | - Clara Levrero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA (G.A.W., Q.J., C.L., W.G.K.)
| | - Bradley A. Maron
- Department of Cardiovascular Medicine (B.A.M.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - William G. Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA (G.A.W., Q.J., C.L., W.G.K.)
- Department of Medicine (W.G.K.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD (W.G.K.)
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7
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Diwan A. The Case for Restoring Organelles to Treat Ischemic Cardiomyopathy: Is DEPP1 an Attractive Target? Circulation 2024; 150:787-790. [PMID: 39226384 PMCID: PMC11373883 DOI: 10.1161/circulationaha.124.070750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Affiliation(s)
- Abhinav Diwan
- Departments of Medicine, Cell Biology and Physiology, Obstetrics and Gynecology, and Neurology; Center for Cardiovascular Research; and Hope Center for Neurologic Disorders, Washington University School of Medicine, St Louis, MO. John Cochran Veterans Affairs Medical Center, St Louis, MO
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Arroyo AB, Tyrkalska SD, Bastida-Martínez E, Monera-Girona AJ, Cantón-Sandoval J, Bernal-Carrión M, García-Moreno D, Elías-Arnanz M, Mulero V. Peds1 deficiency in zebrafish results in myeloid cell apoptosis and exacerbated inflammation. Cell Death Discov 2024; 10:388. [PMID: 39209813 PMCID: PMC11362147 DOI: 10.1038/s41420-024-02141-w] [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: 01/30/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Plasmalogens are glycerophospholipids with a vinyl ether bond that confers unique properties. Recent identification of the gene encoding PEDS1, the desaturase generating the vinyl ether bond, enables evaluation of the role of plasmalogens in health and disease. Here, we report that Peds1-deficient zebrafish larvae display delayed development, increased basal inflammation, normal hematopoietic stem and progenitor cell emergence, and cell-autonomous myeloid cell apoptosis. In a sterile acute inflammation model, Peds1-deficient larvae exhibited impaired inflammation resolution and tissue regeneration, increased interleukin-1β and NF-κB expression, and elevated ROS levels at the wound site. Abnormal immune cell recruitment, neutrophil persistence, and fewer but predominantly pro-inflammatory macrophages were observed. Chronic skin inflammation worsened in Peds1-deficient larvae but was mitigated by exogenous plasmalogen, which also alleviated hyper-susceptibility to bacterial infection, as did pharmacological inhibition of caspase-3 and colony-stimulating factor 3-induced myelopoiesis. Overall, our results highlight an important role for plasmalogens in myeloid cell biology and inflammation.
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Affiliation(s)
- Ana B Arroyo
- Inmunidad, Inflamación y Cáncer. Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, 30120, Murcia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Sylwia D Tyrkalska
- Inmunidad, Inflamación y Cáncer. Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, 30120, Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Antonio J Monera-Girona
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Joaquín Cantón-Sandoval
- Inmunidad, Inflamación y Cáncer. Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, 30120, Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Martín Bernal-Carrión
- Inmunidad, Inflamación y Cáncer. Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, 30120, Murcia, Spain
| | - Diana García-Moreno
- Inmunidad, Inflamación y Cáncer. Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, 30120, Murcia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain.
| | - Victoriano Mulero
- Inmunidad, Inflamación y Cáncer. Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria Pascual Parrilla, 30120, Murcia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto de Salud Carlos III, 28029, Madrid, Spain.
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Rogers ZJ, Colombani T, Khan S, Bhatt K, Nukovic A, Zhou G, Woolston BM, Taylor CT, Gilkes DM, Slavov N, Bencherif SA. Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402557. [PMID: 38874400 PMCID: PMC11321643 DOI: 10.1002/advs.202402557] [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: 03/14/2024] [Revised: 04/11/2024] [Indexed: 06/15/2024]
Abstract
In oxygen (O2)-controlled cell culture, an indispensable tool in biological research, it is presumed that the incubator setpoint equals the O2 tension experienced by cells (i.e., pericellular O2). However, it is discovered that physioxic (5% O2) and hypoxic (1% O2) setpoints regularly induce anoxic (0% O2) pericellular tensions in both adherent and suspension cell cultures. Electron transport chain inhibition ablates this effect, indicating that cellular O2 consumption is the driving factor. RNA-seq analysis revealed that primary human hepatocytes cultured in physioxia experience ischemia-reperfusion injury due to cellular O2 consumption. A reaction-diffusion model is developed to predict pericellular O2 tension a priori, demonstrating that the effect of cellular O2 consumption has the greatest impact in smaller volume culture vessels. By controlling pericellular O2 tension in cell culture, it is found that hypoxia vs. anoxia induce distinct breast cancer transcriptomic and translational responses, including modulation of the hypoxia-inducible factor (HIF) pathway and metabolic reprogramming. Collectively, these findings indicate that breast cancer cells respond non-monotonically to low O2, suggesting that anoxic cell culture is not suitable for modeling hypoxia. Furthermore, it is shown that controlling atmospheric O2 tension in cell culture incubators is insufficient to regulate O2 in cell culture, thus introducing the concept of pericellular O2-controlled cell culture.
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Affiliation(s)
- Zachary J. Rogers
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Thibault Colombani
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Saad Khan
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
| | - Khushbu Bhatt
- Department of Pharmaceutical SciencesNortheastern UniversityBostonMA02115USA
| | - Alexandra Nukovic
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Guanyu Zhou
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | | | - Cormac T. Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of MedicineUniversity College DublinBelfieldDublinD04 V1W8Ireland
| | - Daniele M. Gilkes
- Department of OncologyThe Sidney Kimmel Comprehensive Cancer CenterThe Johns Hopkins University School of MedicineBaltimoreMD21321USA
- Cellular and Molecular Medicine ProgramThe Johns Hopkins University School of MedicineBaltimoreMD21321USA
- Department of Chemical and Biomolecular EngineeringThe Johns Hopkins UniversityBaltimoreMD21218USA
- Johns Hopkins Institute for NanoBioTechnologyThe Johns Hopkins UniversityBaltimoreMD21218USA
| | - Nikolai Slavov
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
- Departments of BioengineeringBiologyChemistry and Chemical BiologySingle Cell Center and Barnett InstituteNortheastern UniversityBostonMA02115USA
- Parallel Squared Technology InstituteWatertownMA02472USA
| | - Sidi A. Bencherif
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
- Harvard John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
- Biomechanics and Bioengineering (BMBI)UTC CNRS UMR 7338University of Technology of CompiègneSorbonne UniversityCompiègne60203France
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10
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Sussman JH, Kim N, Kemp SB, Traum D, Katsuda T, Kahn BM, Xu J, Kim IK, Eskandarian C, Delman D, Beatty GL, Kaestner KH, Simpson AL, Stanger BZ. Multiplexed Imaging Mass Cytometry Analysis Characterizes the Vascular Niche in Pancreatic Cancer. Cancer Res 2024; 84:2364-2376. [PMID: 38695869 PMCID: PMC11250934 DOI: 10.1158/0008-5472.can-23-2352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/22/2024] [Accepted: 04/26/2024] [Indexed: 06/01/2024]
Abstract
Oncogenesis and progression of pancreatic ductal adenocarcinoma (PDAC) are driven by complex interactions between the neoplastic component and the tumor microenvironment, which includes immune, stromal, and parenchymal cells. In particular, most PDACs are characterized by a hypovascular and hypoxic environment that alters tumor cell behavior and limits the efficacy of chemotherapy and immunotherapy. Characterization of the spatial features of the vascular niche could advance our understanding of inter- and intratumoral heterogeneity in PDAC. In this study, we investigated the vascular microenvironment of PDAC by applying imaging mass cytometry using a 26-antibody panel on 35 regions of interest across 9 patients, capturing more than 140,000 single cells. The approach distinguished major cell types, including multiple populations of lymphoid and myeloid cells, endocrine cells, ductal cells, stromal cells, and endothelial cells. Evaluation of cellular neighborhoods identified 10 distinct spatial domains, including multiple immune and tumor-enriched environments as well as the vascular niche. Focused analysis revealed differential interactions between immune populations and the vasculature and identified distinct spatial domains wherein tumor cell proliferation occurs. Importantly, the vascular niche was closely associated with a population of CD44-expressing macrophages enriched for a proangiogenic gene signature. Taken together, this study provides insights into the spatial heterogeneity of PDAC and suggests a role for CD44-expressing macrophages in shaping the vascular niche. Significance: Imaging mass cytometry revealed that pancreatic ductal cancers are composed of 10 distinct cellular neighborhoods, including a vascular niche enriched for macrophages expressing high levels of CD44 and a proangiogenic gene signature.
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Affiliation(s)
- Jonathan H. Sussman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nathalia Kim
- Department of Biomedical and Molecular Sciences/School of Computing, Queen’s University, Kingston, Ontario, Canada
| | - Samantha B Kemp
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Daniel Traum
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | - Takeshi Katsuda
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Benjamin M. Kahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Jason Xu
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Il-Kyu Kim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Cody Eskandarian
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
| | - Devora Delman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gregory L. Beatty
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Klaus H. Kaestner
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
| | - Amber L. Simpson
- Department of Biomedical and Molecular Sciences/School of Computing, Queen’s University, Kingston, Ontario, Canada
| | - Ben Z. Stanger
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA
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11
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Lee RG, Rudler DL, Rackham O, Filipovska A. Interorganelle phospholipid communication, a house not so divided. Trends Endocrinol Metab 2024:S1043-2760(24)00168-1. [PMID: 38972781 DOI: 10.1016/j.tem.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/09/2024]
Abstract
The presence of membrane-bound organelles with specific functions is one of the main hallmarks of eukaryotic cells. Organelle membranes are composed of specific lipids that govern their function and interorganelle communication. Discoveries in cell biology using imaging and omic technologies have revealed the mechanisms that drive membrane remodeling, organelle contact sites, and metabolite exchange. The interplay between multiple organelles and their interdependence is emerging as the next frontier for discovery using 3D reconstruction of volume electron microscopy (vEM) datasets. We discuss recent findings on the links between organelles that underlie common functions and cellular pathways. Specifically, we focus on the metabolism of ether glycerophospholipids that mediate organelle dynamics and their communication with each other, and the new imaging techniques that are powering these discoveries.
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Affiliation(s)
- Richard G Lee
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre (QEIIMC), Nedlands, WA, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Danielle L Rudler
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre (QEIIMC), Nedlands, WA, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Oliver Rackham
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre (QEIIMC), Nedlands, WA, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia; Curtin Medical School, Curtin University, Bentley, WA, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
| | - Aleksandra Filipovska
- Australian Research Council (ARC) Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre (QEIIMC), Nedlands, WA, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia; The University of Western Australia Centre for Child Health Research, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia.
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12
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Li Q, Xia Z, Wu Y, Ma Y, Zhang D, Wang S, Fan J, Xu P, Li X, Bai L, Zhou X, Xue M. Lysophospholipid acyltransferase-mediated formation of saturated glycerophospholipids maintained cell membrane integrity for hypoxic adaptation. FEBS J 2024; 291:3191-3210. [PMID: 38602252 DOI: 10.1111/febs.17132] [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: 11/10/2023] [Revised: 01/11/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
Adaptation to hypoxia has attracted much public interest because of its clinical significance. However, hypoxic adaptation in the body is complicated and difficult to fully explore. To explore previously unknown conserved mechanisms and key proteins involved in hypoxic adaptation in different species, we first used a yeast model for mechanistic screening. Further multi-omics analyses in multiple species including yeast, zebrafish and mice revealed that glycerophospholipid metabolism was significantly involved in hypoxic adaptation with up-regulation of lysophospholipid acyltransferase (ALE1) in yeast, a key protein for the formation of dipalmitoyl phosphatidylcholine [DPPC (16:0/16:0)], which is a saturated phosphatidylcholine. Importantly, a mammalian homolog of ALE1, lysophosphatidylcholine acyltransferase 1 (LPCAT1), enhanced DPPC levels at the cell membrane and exhibited the same protective effect in mammalian cells under hypoxic conditions. DPPC supplementation effectively attenuated growth restriction, maintained cell membrane integrity and increased the expression of epidermal growth factor receptor under hypoxic conditions, but unsaturated phosphatidylcholine did not. In agreement with these findings, DPPC treatment could also repair hypoxic injury of intestinal mucosa in mice. Taken together, ALE1/LPCAT1-mediated DPPC formation, a key pathway of glycerophospholipid metabolism, is crucial for cell viability under hypoxic conditions. Moreover, we found that ALE1 was also involved in glycolysis to maintain sufficient survival conditions for yeast. The present study offers a novel approach to understanding lipid metabolism under hypoxia and provides new insights into treating hypoxia-related diseases.
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Affiliation(s)
- Qiang Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Zhengchao Xia
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yi Wu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yi Ma
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
| | - Di Zhang
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Sihan Wang
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jingxin Fan
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Pingxiang Xu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xiaorong Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Lu Bai
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xuelin Zhou
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Ming Xue
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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13
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Janssen Daalen JM, Meinders MJ, Mathur S, van Hees HWH, Ainslie PN, Thijssen DHJ, Bloem BR. Randomized controlled trial of intermittent hypoxia in Parkinson's disease: study rationale and protocol. BMC Neurol 2024; 24:212. [PMID: 38909201 PMCID: PMC11193237 DOI: 10.1186/s12883-024-03702-3] [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: 04/02/2024] [Accepted: 05/31/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a neurodegenerative disease for which no disease-modifying therapies exist. Preclinical and clinical evidence suggest that repeated exposure to intermittent hypoxia might have short- and long-term benefits in PD. In a previous exploratory phase I trial, we demonstrated that in-clinic intermittent hypoxia exposure is safe and feasible with short-term symptomatic effects on PD symptoms. The current study aims to explore the safety, tolerability, feasibility, and net symptomatic effects of a four-week intermittent hypoxia protocol, administered at home, in individuals with PD. METHODS/DESIGN This is a two-armed double-blinded randomized controlled trial involving 40 individuals with mild to moderate PD. Participants will receive 45 min of normobaric intermittent hypoxia (fraction of inspired oxygen 0.16 for 5 min interspersed with 5 min normoxia), 3 times a week for 4 weeks. Co-primary endpoints include nature and total number of adverse events, and a feasibility-tolerability questionnaire. Secondary endpoints include Movement Disorders Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) part II and III scores, gait tests and biomarkers indicative of hypoxic dose and neuroprotective pathway induction. DISCUSSION This trial builds on the previous phase I trial and aims to investigate the safety, tolerability, feasibility, and net symptomatic effects of intermittent hypoxia in individuals with PD. Additionally, the study aims to explore induction of relevant neuroprotective pathways as measured in plasma. The results of this trial could provide further insight into the potential of hypoxia-based therapy as a novel treatment approach for PD. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT05948761 (registered June 20th, 2023).
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Affiliation(s)
- Jules M Janssen Daalen
- Radboud University Medical Center, Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands.
- Radboud University Medical Center, Department of Medical BioSciences, Nijmegen, The Netherlands.
| | - Marjan J Meinders
- Radboud University Medical Center, Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | | | - Hieronymus W H van Hees
- Radboud University Medical Center, Department of Pulmonary Diseases, Nijmegen, The Netherlands
| | - Philip N Ainslie
- University of British Columbia, Center for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, Kelowna, Canada
| | - Dick H J Thijssen
- Radboud University Medical Center, Department of Medical BioSciences, Nijmegen, The Netherlands
| | - Bastiaan R Bloem
- Radboud University Medical Center, Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands.
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14
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Zhang M, Wang Y, Di J, Zhang X, Liu Y, Zhang Y, Li B, Qi S, Cao X, Liu L, Liu S, Xu F. High coverage of targeted lipidomics revealed lipid changes in the follicular fluid of patients with insulin-resistant polycystic ovary syndrome and a positive correlation between plasmalogens and oocyte quality. Front Endocrinol (Lausanne) 2024; 15:1414289. [PMID: 38904043 PMCID: PMC11187234 DOI: 10.3389/fendo.2024.1414289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024] Open
Abstract
Background Polycystic ovary syndrome with insulin resistance (PCOS-IR) is the most common endocrine and metabolic disease in women of reproductive age, and low fertility in PCOS patients may be associated with oocyte quality; however, the molecular mechanism through which PCOS-IR affects oocyte quality remains unknown. Methods A total of 22 women with PCOS-IR and 23 women without polycystic ovary syndrome (control) who underwent in vitro fertilization and embryo transfer were recruited, and clinical information pertaining to oocyte quality was analyzed. Lipid components of follicular fluid (FF) were detected using high-coverage targeted lipidomics, which identified 344 lipid species belonging to 19 lipid classes. The exact lipid species associated with oocyte quality were identified. Results The number (rate) of two pronuclear (2PN) zygotes, the number (rate) of 2PN cleaved embryos, and the number of high-quality embryos were significantly lower in the PCOS-IR group. A total of 19 individual lipid classes and 344 lipid species were identified and quantified. The concentrations of the 19 lipid species in the normal follicular fluid (control) ranged between 10-3 mol/L and 10-9 mol/L. In addition, 39 lipid species were significantly reduced in the PCOS-IR group, among which plasmalogens were positively correlated with oocyte quality. Conclusions This study measured the levels of various lipids in follicular fluid, identified a significantly altered lipid profile in the FF of PCOS-IR patients, and established a correlation between poor oocyte quality and plasmalogens in PCOS-IR patients. These findings have contributed to the development of plasmalogen replacement therapy to enhance oocyte quality and have improved culture medium formulations for oocyte in vitro maturation (IVM).
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Affiliation(s)
- Meizi Zhang
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Yuanyuan Wang
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Jianyong Di
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Xuanlin Zhang
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Ye Liu
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Yixin Zhang
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Bowen Li
- LipidAll Technologies Company Limited, Changzhou, Jiangsu, China
| | - Simeng Qi
- LipidAll Technologies Company Limited, Changzhou, Jiangsu, China
| | - Xiaomin Cao
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Li Liu
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Shouzeng Liu
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Fengqin Xu
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
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15
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Enström A, Carlsson R, Buizza C, Lewi M, Paul G. Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model. Mol Cell Proteomics 2024; 23:100782. [PMID: 38705386 PMCID: PMC11176767 DOI: 10.1016/j.mcpro.2024.100782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 04/09/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024] Open
Abstract
Cellular communication within the brain is imperative for maintaining homeostasis and mounting effective responses to pathological triggers like hypoxia. However, a comprehensive understanding of the precise composition and dynamic release of secreted molecules has remained elusive, confined primarily to investigations using isolated monocultures. To overcome these limitations, we utilized the potential of TurboID, a non-toxic biotin ligation enzyme, to capture and enrich secreted proteins specifically originating from human brain pericytes in spheroid cocultures with human endothelial cells and astrocytes. This approach allowed us to characterize the pericyte secretome within a more physiologically relevant multicellular setting encompassing the constituents of the blood-brain barrier. Through a combination of mass spectrometry and multiplex immunoassays, we identified a wide spectrum of different secreted proteins by pericytes. Our findings demonstrate that the pericytes secretome is profoundly shaped by their intercellular communication with other blood-brain barrier-residing cells. Moreover, we identified substantial differences in the secretory profiles between hypoxic and normoxic pericytes. Mass spectrometry analysis showed that hypoxic pericytes in coculture increase their release of signals related to protein secretion, mTOR signaling, and the complement system, while hypoxic pericytes in monocultures showed an upregulation in proliferative pathways including G2M checkpoints, E2F-, and Myc-targets. In addition, hypoxic pericytes show an upregulation of proangiogenic proteins such as VEGFA but display downregulation of canonical proinflammatory cytokines such as CXCL1, MCP-1, and CXCL6. Understanding the specific composition of secreted proteins in the multicellular brain microvasculature is crucial for advancing our knowledge of brain homeostasis and the mechanisms underlying pathology. This study has implications for the identification of targeted therapeutic strategies aimed at modulating microvascular signaling in brain pathologies associated with hypoxia.
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Affiliation(s)
- Andreas Enström
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Robert Carlsson
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Carolina Buizza
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Marvel Lewi
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Gesine Paul
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden; Department of Neurology, Scania University Hospital, Lund, Sweden; Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
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16
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Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Bidault G, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Liang L, Pereira C, Dale M, Shun-Shion AS, Baird HJ, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Nathan JA, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ. Limited oxygen in standard cell culture alters metabolism and function of differentiated cells. EMBO J 2024; 43:2127-2165. [PMID: 38580776 PMCID: PMC11148168 DOI: 10.1038/s44318-024-00084-7] [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: 01/12/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/07/2024] Open
Abstract
The in vitro oxygen microenvironment profoundly affects the capacity of cell cultures to model physiological and pathophysiological states. Cell culture is often considered to be hyperoxic, but pericellular oxygen levels, which are affected by oxygen diffusivity and consumption, are rarely reported. Here, we provide evidence that several cell types in culture actually experience local hypoxia, with important implications for cell metabolism and function. We focused initially on adipocytes, as adipose tissue hypoxia is frequently observed in obesity and precedes diminished adipocyte function. Under standard conditions, cultured adipocytes are highly glycolytic and exhibit a transcriptional profile indicative of physiological hypoxia. Increasing pericellular oxygen diverted glucose flux toward mitochondria, lowered HIF1α activity, and resulted in widespread transcriptional rewiring. Functionally, adipocytes increased adipokine secretion and sensitivity to insulin and lipolytic stimuli, recapitulating a healthier adipocyte model. The functional benefits of increasing pericellular oxygen were also observed in macrophages, hPSC-derived hepatocytes and cardiac organoids. Our findings demonstrate that oxygen is limiting in many terminally-differentiated cell types, and that considering pericellular oxygen improves the quality, reproducibility and translatability of culture models.
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Affiliation(s)
- Joycelyn Tan
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sam Virtue
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Olivia J Conway
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Guillaume Bidault
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Christopher Gribben
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Fatima Lugtu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ioannis Kamzolas
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - James R Krycer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Lu Liang
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Martin Dale
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Harry Jm Baird
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - James A Horscroft
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Alice P Sowton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Marcella Ma
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stefania Carobbio
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Andrew J Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC, 27834, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain.
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
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17
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Benej M, Papandreou I, Denko NC. Hypoxic adaptation of mitochondria and its impact on tumor cell function. Semin Cancer Biol 2024; 100:28-38. [PMID: 38556040 PMCID: PMC11320707 DOI: 10.1016/j.semcancer.2024.03.004] [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: 01/09/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
Mitochondria are the major sink for oxygen in the cell, consuming it during ATP production. Therefore, when environmental oxygen levels drop in the tumor, significant adaptation is required. Mitochondrial activity is also a major producer of biosynthetic precursors and a regulator of cellular oxidative and reductive balance. Because of the complex biochemistry, mitochondrial adaptation to hypoxia occurs through multiple mechanisms and has significant impact on other cellular processes such as macromolecule synthesis and gene regulation. In tumor hypoxia, mitochondria shift their location in the cell and accelerate the fission and quality control pathways. Hypoxic mitochondria also undergo significant changes to fundamental metabolic pathways of carbon metabolism and electron transport. These metabolic changes further impact the nuclear epigenome because mitochondrial metabolites are used as enzymatic substrates for modifying chromatin. This coordinated response delivers physiological flexibility and increased tumor cell robustness during the environmental stress of low oxygen.
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Affiliation(s)
- Martin Benej
- Department of Radiation Oncology, OSU Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Ohio State University, Columbus, OH, USA
| | - Ioanna Papandreou
- Department of Radiation Oncology, OSU Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Ohio State University, Columbus, OH, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Nicholas C Denko
- Department of Radiation Oncology, OSU Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Ohio State University, Columbus, OH, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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18
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Kotrys AV, Durham TJ, Guo XA, Vantaku VR, Parangi S, Mootha VK. Single-cell analysis reveals context-dependent, cell-level selection of mtDNA. Nature 2024; 629:458-466. [PMID: 38658765 PMCID: PMC11078733 DOI: 10.1038/s41586-024-07332-0] [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: 03/18/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
Heteroplasmy occurs when wild-type and mutant mitochondrial DNA (mtDNA) molecules co-exist in single cells1. Heteroplasmy levels change dynamically in development, disease and ageing2,3, but it is unclear whether these shifts are caused by selection or drift, and whether they occur at the level of cells or intracellularly. Here we investigate heteroplasmy dynamics in dividing cells by combining precise mtDNA base editing (DdCBE)4 with a new method, SCI-LITE (single-cell combinatorial indexing leveraged to interrogate targeted expression), which tracks single-cell heteroplasmy with ultra-high throughput. We engineered cells to have synonymous or nonsynonymous complex I mtDNA mutations and found that cell populations in standard culture conditions purge nonsynonymous mtDNA variants, whereas synonymous variants are maintained. This suggests that selection dominates over simple drift in shaping population heteroplasmy. We simultaneously tracked single-cell mtDNA heteroplasmy and ancestry, and found that, although the population heteroplasmy shifts, the heteroplasmy of individual cell lineages remains stable, arguing that selection acts at the level of cell fitness in dividing cells. Using these insights, we show that we can force cells to accumulate high levels of truncating complex I mtDNA heteroplasmy by placing them in environments where loss of biochemical complex I activity has been reported to benefit cell fitness. We conclude that in dividing cells, a given nonsynonymous mtDNA heteroplasmy can be harmful, neutral or even beneficial to cell fitness, but that the 'sign' of the effect is wholly dependent on the environment.
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Affiliation(s)
- Anna V Kotrys
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoyan A Guo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Venkata R Vantaku
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sareh Parangi
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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19
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Xiao C, Wang R, Fu R, Yu P, Guo J, Li G, Wang Z, Wang H, Nie J, Liu W, Zhai J, Li C, Deng C, Chen D, Zhou L, Ning C. Piezo-enhanced near infrared photocatalytic nanoheterojunction integrated injectable biopolymer hydrogel for anti-osteosarcoma and osteogenesis combination therapy. Bioact Mater 2024; 34:381-400. [PMID: 38269309 PMCID: PMC10806218 DOI: 10.1016/j.bioactmat.2024.01.003] [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] [Received: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
Preventing local tumor recurrence while promoting bone tissue regeneration is an urgent need for osteosarcoma treatment. However, the therapeutic efficacy of traditional photosensitizers is limited, and they lack the ability to regenerate bone. Here, a piezo-photo nanoheterostructure is developed based on ultrasmall bismuth/strontium titanate nanocubes (denoted as Bi/SrTiO3), which achieve piezoelectric field-driven fast charge separation coupling with surface plasmon resonance to efficiently generate reactive oxygen species. These hybrid nanotherapeutics are integrated into injectable biopolymer hydrogels, which exhibit outstanding anticancer effects under the combined irradiation of NIR and ultrasound. In vivo studies using patient-derived xenograft models and tibial osteosarcoma models demonstrate that the hydrogels achieve tumor suppression with efficacy rates of 98.6 % and 67.6 % in the respective models. Furthermore, the hydrogel had good filling and retention capabilities in the bone defect region, which exerted bone repair therapeutic efficacy by polarizing and conveying electrical stimuli to the cells under mild ultrasound radiation. This study provides a comprehensive and clinically feasible strategy for the overall treatment and tissue regeneration of osteosarcoma.
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Affiliation(s)
- Cairong Xiao
- School of Materials Science and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510641, China
| | - Renxian Wang
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Beijing, 100035, China
- JST Sarcopenia Research Centre, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Rumin Fu
- School of Materials Science and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510641, China
| | - Peng Yu
- School of Materials Science and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510641, China
| | - Jianxun Guo
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Guangping Li
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Zhengao Wang
- School of Materials Science and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510641, China
| | - Honggang Wang
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Jingjun Nie
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Weifeng Liu
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Peking University, Beijing, 100035, China
| | - Jinxia Zhai
- School of Materials Science and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510641, China
| | - Changhao Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University and Guangdong Key Laboratory of Stomatology, Guangzhou, Guangdong, 510055, China
| | - Chunlin Deng
- School of Materials Science and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510641, China
| | - Dafu Chen
- Laboratory of Bone Tissue Engineering, Beijing Laboratory of Biomedical Materials, National Center for Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Lei Zhou
- Guangzhou Key Laboratory of Spine Disease Prevention and Treatment, Department of Spine Surgery, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510150, China
| | - Chengyun Ning
- School of Materials Science and Engineering, National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510641, China
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20
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Michl J, White B, Monterisi S, Bodmer WF, Swietach P. Phenotypic screen of sixty-eight colorectal cancer cell lines identifies CEACAM6 and CEACAM5 as markers of acid resistance. Proc Natl Acad Sci U S A 2024; 121:e2319055121. [PMID: 38502695 PMCID: PMC10990159 DOI: 10.1073/pnas.2319055121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Elevated cancer metabolism releases lactic acid and CO2 into the under-perfused tumor microenvironment, resulting in extracellular acidosis. The surviving cancer cells must adapt to this selection pressure; thus, targeting tumor acidosis is a rational therapeutic strategy to manage tumor growth. However, none of the major approved treatments are based explicitly on disrupting acid handling, signaling, or adaptations, possibly because the distinction between acid-sensitive and acid-resistant phenotypes is not clear. Here, we report pH-related phenotypes of sixty-eight colorectal cancer (CRC) cell lines by measuring i) extracellular acidification as a readout of acid production by fermentative metabolism and ii) growth of cell biomass over a range of extracellular pH (pHe) levels as a measure of the acid sensitivity of proliferation. Based on these measurements, CRC cell lines were grouped along two dimensions as "acid-sensitive"/"acid-resistant" versus "low metabolic acid production"/"high metabolic acid production." Strikingly, acid resistance was associated with the expression of CEACAM6 and CEACAM5 genes coding for two related cell-adhesion molecules, and among pH-regulating genes, of CA12. CEACAM5/6 protein levels were strongly induced by acidity, with a further induction under hypoxia in a subset of CRC lines. Lack of CEACAM6 (but not of CEACAM5) reduced cell growth and their ability to differentiate. Finally, CEACAM6 levels were strongly increased in human colorectal cancers from stage II and III patients, compared to matched samples from adjacent normal tissues. Thus, CEACAM6 is a marker of acid-resistant clones in colorectal cancer and a potential motif for targeting therapies to acidic regions within the tumors.
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Affiliation(s)
- Johanna Michl
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Bobby White
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Stefania Monterisi
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Walter F. Bodmer
- Department of Oncology, University of Oxford, OxfordOX3 7DQ, United Kingdom
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
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21
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Plessner M, Thiele L, Hofhuis J, Thoms S. Tissue-specific roles of peroxisomes revealed by expression meta-analysis. Biol Direct 2024; 19:14. [PMID: 38365851 PMCID: PMC10873952 DOI: 10.1186/s13062-024-00458-1] [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: 09/14/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Peroxisomes are primarily studied in the brain, kidney, and liver due to the conspicuous tissue-specific pathology of peroxisomal biogenesis disorders. In contrast, little is known about the role of peroxisomes in other tissues such as the heart. In this meta-analysis, we explore mitochondrial and peroxisomal gene expression on RNA and protein levels in the brain, heart, kidney, and liver, focusing on lipid metabolism. Further, we evaluate a potential developmental and heart region-dependent specificity of our gene set. We find marginal expression of the enzymes for peroxisomal fatty acid oxidation in cardiac tissue in comparison to the liver or cardiac mitochondrial β-oxidation. However, the expression of peroxisome biogenesis proteins in the heart is similar to other tissues despite low levels of peroxisomal fatty acid oxidation. Strikingly, peroxisomal targeting signal type 2-containing factors and plasmalogen biosynthesis appear to play a fundamental role in explaining the essential protective and supporting functions of cardiac peroxisomes.
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Affiliation(s)
- Matthias Plessner
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Leonie Thiele
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Julia Hofhuis
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sven Thoms
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany.
- Department of Child and Adolescent Health, University Medical Center, Göttingen, Germany.
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22
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Janssen Daalen JM, Koopman WJH, Saris CGJ, Meinders MJ, Thijssen DHJ, Bloem BR. The Hypoxia Response Pathway: A Potential Intervention Target in Parkinson's Disease? Mov Disord 2024; 39:273-293. [PMID: 38140810 DOI: 10.1002/mds.29688] [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: 07/14/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder for which only symptomatic treatments are available. Both preclinical and clinical studies suggest that moderate hypoxia induces evolutionarily conserved adaptive mechanisms that enhance neuronal viability and survival. Therefore, targeting the hypoxia response pathway might provide neuroprotection by ameliorating the deleterious effects of mitochondrial dysfunction and oxidative stress, which underlie neurodegeneration in PD. Here, we review experimental studies regarding the link between PD pathophysiology and neurophysiological adaptations to hypoxia. We highlight the mechanistic differences between the rescuing effects of chronic hypoxia in neurodegeneration and short-term moderate hypoxia to improve neuronal resilience, termed "hypoxic conditioning". Moreover, we interpret these preclinical observations regarding the pharmacological targeting of the hypoxia response pathway. Finally, we discuss controversies with respect to the differential effects of hypoxia response pathway activation across the PD spectrum, as well as intervention dosing in hypoxic conditioning and potential harmful effects of such interventions. We recommend that initial clinical studies in PD should focus on the safety, physiological responses, and mechanisms of hypoxic conditioning, as well as on repurposing of existing pharmacological compounds. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Jules M Janssen Daalen
- Center of Expertise for Parkinson and Movement Disorders, Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands, Nijmegen, The Netherlands
- Department of Neurology, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
- Department of Physiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Christiaan G J Saris
- Department of Neurology, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjan J Meinders
- Center of Expertise for Parkinson and Movement Disorders, Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands, Nijmegen, The Netherlands
| | - Dick H J Thijssen
- Department of Physiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bastiaan R Bloem
- Center of Expertise for Parkinson and Movement Disorders, Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands, Nijmegen, The Netherlands
- Department of Neurology, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
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23
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An X, Mao L, Wang Y, Xu Q, Liu X, Zhang S, Qiao Z, Li B, Li F, Kuang Z, Wan N, Liang X, Duan Q, Feng Z, Yang X, Liu S, Nevo E, Liu J, Storz JF, Li K. Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors. Nat Ecol Evol 2024; 8:339-351. [PMID: 38195998 DOI: 10.1038/s41559-023-02275-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.
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Affiliation(s)
- Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qinqin Xu
- Department of Medical Oncology, Qinghai Provincial People's Hospital, Xining, China
| | - Xi Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shangzhe Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhenglei Qiao
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Fang Li
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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24
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Meisel JD, Miranda M, Skinner OS, Wiesenthal PP, Wellner SM, Jourdain AA, Ruvkun G, Mootha VK. Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism. Cell 2024; 187:659-675.e18. [PMID: 38215760 PMCID: PMC10919891 DOI: 10.1016/j.cell.2023.12.010] [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: 02/20/2023] [Revised: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/14/2024]
Abstract
The electron transport chain (ETC) of mitochondria, bacteria, and archaea couples electron flow to proton pumping and is adapted to diverse oxygen environments. Remarkably, in mice, neurological disease due to ETC complex I dysfunction is rescued by hypoxia through unknown mechanisms. Here, we show that hypoxia rescue and hyperoxia sensitivity of complex I deficiency are evolutionarily conserved to C. elegans and are specific to mutants that compromise the electron-conducting matrix arm. We show that hypoxia rescue does not involve the hypoxia-inducible factor pathway or attenuation of reactive oxygen species. To discover the mechanism, we use C. elegans genetic screens to identify suppressor mutations in the complex I accessory subunit NDUFA6/nuo-3 that phenocopy hypoxia rescue. We show that NDUFA6/nuo-3(G60D) or hypoxia directly restores complex I forward activity, with downstream rescue of ETC flux and, in some cases, complex I levels. Additional screens identify residues within the ubiquinone binding pocket as being required for the rescue by NDUFA6/nuo-3(G60D) or hypoxia. This reveals oxygen-sensitive coupling between an accessory subunit and the quinone binding pocket of complex I that can restore forward activity in the same manner as hypoxia.
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Affiliation(s)
- Joshua D Meisel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Maria Miranda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Owen S Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Presli P Wiesenthal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sandra M Wellner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexis A Jourdain
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Vamsi K Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA.
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25
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Wang J, Zhang X, Chen H, Ren H, Zhou M, Zhao Y. Engineered stem cells by emerging biomedical stratagems. Sci Bull (Beijing) 2024; 69:248-279. [PMID: 38101962 DOI: 10.1016/j.scib.2023.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/24/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023]
Abstract
Stem cell therapy holds immense potential as a viable treatment for a widespread range of intractable disorders. As the safety of stem cell transplantation having been demonstrated in numerous clinical trials, various kinds of stem cells are currently utilized in medical applications. Despite the achievements, the therapeutic benefits of stem cells for diseases are limited, and the data of clinical researches are unstable. To optimize tthe effectiveness of stem cells, engineering approaches have been developed to enhance their inherent abilities and impart them with new functionalities, paving the way for the next generation of stem cell therapies. This review offers a detailed analysis of engineered stem cells, including their clinical applications and potential for future development. We begin by briefly introducing the recent advances in the production of stem cells (induced pluripotent stem cells (iPSCs), embryonic stem cells (ESCs), mesenchymal stem cells (MSCs) and hematopoietic stem cells (HSCs)). Furthermore, we present the latest developments of engineered strategies in stem cells, including engineered methods in molecular biology and biomaterial fields, and their application in biomedical research. Finally, we summarize the current obstacles and suggest future prospects for engineered stem cells in clinical translations and biomedical applications.
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Affiliation(s)
- Jinglin Wang
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaoxuan Zhang
- Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hanxu Chen
- Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Haozhen Ren
- Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Min Zhou
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
| | - Yuanjin Zhao
- Department of Vascular Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China; Division of Hepatobiliary Surgery and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Shenzhen Research Institute, Southeast University, Shenzhen 518038, China.
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26
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Solanki S, Shah YM. Hypoxia-Induced Signaling in Gut and Liver Pathobiology. ANNUAL REVIEW OF PATHOLOGY 2024; 19:291-317. [PMID: 37832943 DOI: 10.1146/annurev-pathmechdis-051122-094743] [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] [Indexed: 10/15/2023]
Abstract
Oxygen (O2) is essential for cellular metabolism and biochemical reactions. When the demand for O2 exceeds the supply, hypoxia occurs. Hypoxia-inducible factors (HIFs) are essential to activate adaptive and survival responses following hypoxic stress. In the gut (intestines) and liver, the presence of oxygen gradients or physiologic hypoxia is necessary to maintain normal homeostasis. While physiologic hypoxia is beneficial and aids in normal functions, pathological hypoxia is harmful as it exacerbates inflammatory responses and tissue dysfunction and is a hallmark of many cancers. In this review, we discuss the role of gut and liver hypoxia-induced signaling, primarily focusing on HIFs, in the physiology and pathobiology of gut and liver diseases. Additionally, we examine the function of HIFs in various cell types during gut and liver diseases, beyond intestinal epithelial and hepatocyte HIFs. This review highlights the importance of understanding hypoxia-induced signaling in the pathogenesis of gut and liver diseases and emphasizes the potential of HIFs as therapeutic targets.
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Affiliation(s)
- Sumeet Solanki
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA;
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA;
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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27
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Bennett NK, Lee M, Orr AL, Nakamura K. Systems-level analyses dissociate genetic regulators of reactive oxygen species and energy production. Proc Natl Acad Sci U S A 2024; 121:e2307904121. [PMID: 38207075 PMCID: PMC10801874 DOI: 10.1073/pnas.2307904121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/20/2023] [Indexed: 01/13/2024] Open
Abstract
Respiratory chain dysfunction can decrease ATP and increase reactive oxygen species (ROS) levels. Despite the importance of these metabolic parameters to a wide range of cellular functions and disease, we lack an integrated understanding of how they are differentially regulated. To address this question, we adapted a CRISPRi- and FACS-based platform to compare the effects of respiratory gene knockdown on ROS to their effects on ATP. Focusing on genes whose knockdown is known to decrease mitochondria-derived ATP, we showed that knockdown of genes in specific respiratory chain complexes (I, III, and CoQ10 biosynthesis) increased ROS, whereas knockdown of other low ATP hits either had no impact (mitochondrial ribosomal proteins) or actually decreased ROS (complex IV). Moreover, although shifting metabolic conditions profoundly altered mitochondria-derived ATP levels, it had little impact on mitochondrial or cytosolic ROS. In addition, knockdown of a subset of complex I subunits-including NDUFA8, NDUFB4, and NDUFS8-decreased complex I activity, mitochondria-derived ATP, and supercomplex level, but knockdown of these genes had differential effects on ROS. Conversely, we found an essential role for ether lipids in the dynamic regulation of mitochondrial ROS levels independent of ATP. Thus, our results identify specific metabolic regulators of cellular ATP and ROS balance that may help dissect the roles of these processes in disease and identify therapeutic strategies to independently target energy failure and oxidative stress.
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Affiliation(s)
- Neal K. Bennett
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA94158
| | - Megan Lee
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA94158
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Adam L. Orr
- Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY10021
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY10021
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA94158
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Graduate Program in Biomedical Sciences, University of California, San Francisco, CA94143
- Graduate Program in Neuroscience, University of California San Francisco, San Francisco, CA94158
- Department of Neurology, University of California, San Francisco, CA94158
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Wedan RJ, Longenecker JZ, Nowinski SM. Mitochondrial fatty acid synthesis is an emergent central regulator of mammalian oxidative metabolism. Cell Metab 2024; 36:36-47. [PMID: 38128528 PMCID: PMC10843818 DOI: 10.1016/j.cmet.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
Contrary to their well-known functions in nutrient breakdown, mitochondria are also important biosynthetic hubs and express an evolutionarily conserved mitochondrial fatty acid synthesis (mtFAS) pathway. mtFAS builds lipoic acid and longer saturated fatty acids, but its exact products, their ultimate destination in cells, and the cellular significance of the pathway are all active research questions. Moreover, why mitochondria need mtFAS despite their well-defined ability to import fatty acids is still unclear. The identification of patients with inborn errors of metabolism in mtFAS genes has sparked fresh research interest in the pathway. New mammalian models have provided insights into how mtFAS coordinates many aspects of oxidative mitochondrial metabolism and raise questions about its role in diseases such as obesity, diabetes, and heart failure. In this review, we discuss the products of mtFAS, their function, and the consequences of mtFAS impairment across models and in metabolic disease.
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Affiliation(s)
- Riley J Wedan
- Department of Metabolism and Nutritional Programming, The Van Andel Institute, Grand Rapids, MI 49503, USA; College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jacob Z Longenecker
- Department of Metabolism and Nutritional Programming, The Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sara M Nowinski
- Department of Metabolism and Nutritional Programming, The Van Andel Institute, Grand Rapids, MI 49503, USA.
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Dong HQ, Hu XY, Liang SJ, Wang RS, Cheng P. Selection of reference genes in liproxstatin-1-treated K562 Leukemia cells via RT-qPCR and RNA sequencing. Mol Biol Rep 2024; 51:55. [PMID: 38165476 DOI: 10.1007/s11033-023-08912-5] [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: 09/15/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Reverse transcription quantitative polymerase chain reaction (RT-qPCR) can accurately detect relative gene expression levels in biological samples. However, widely used reference genes exhibit unstable expression under certain conditions. METHODS AND RESULTS Here, we compared the expression stability of eight reference genes (RPLP0, RPS18, RPL13, EEF1A1, β-actin, GAPDH, HPRT1, and TUBB) commonly used in liproxstatin-1 (Lip-1)-treated K562 cells using RNA-sequencing and RT-qPCR. The expression of EEF1A1, ACTB, GAPDH, HPRT1, and TUBB was considerably lower in cells treated with 20 μM Lip-1 than in the control, and GAPDH also showed significant downregulation in the 10 μM Lip-1 group. Meanwhile, when we used geNorm, NormFinder, and BestKeeper to compare expression stability, we found that GAPDH and HPRT1 were the most unstable reference genes among all those tested. Stability analysis yielded very similar results when geNorm or BestKeeper was used but not when NormFinder was used. Specifically, geNorm and BestKeeper identified RPL13 and RPLP0 as the most stable genes under 20 μM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable under 10 μM Lip-1 treatment. TUBB and EEF1A1 were the most stable genes in both treatment groups according to the results obtained using NormFinder. An assumed most stable gene was incorporated into each software to validate the accuracy. The results suggest that NormFinder is not an appropriate algorithm for this study. CONCLUSIONS Stable reference genes were recognized using geNorm and BestKeeper but not NormFinder. Overall, RPL13 and RPLP0 were the most stable reference genes under 20 μM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable genes under 10 μM Lip-1 treatment.
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Affiliation(s)
- Hai-Qun Dong
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Xue-Ying Hu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Shi-Jing Liang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Hematology, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Ren-Sheng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| | - Peng Cheng
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
- Key Laboratory of Hematology, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, 530021, China.
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Cao Y, Zeng T, Han W, Ma X, Gu T, Chen L, Tian Y, Xu W, Yin J, Li G, Lu L, Gun S. Comparative analysis of liver transcriptome reveals adaptive responses to hypoxia environmental condition in Tibetan chicken. Anim Biosci 2024; 37:28-38. [PMID: 37641844 PMCID: PMC10766467 DOI: 10.5713/ab.23.0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown. METHODS RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]). RESULTS A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds. CONCLUSION This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals.
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Affiliation(s)
- Yongqing Cao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wei Han
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Xueying Ma
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy Agricultural and Animal Husbandry Sciences, Lhasa 850004,
China
| | - Tiantian Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Jianmei Yin
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Guohui Li
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Lizhi Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
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Abstract
Cancers undergo sequential changes to proton (H+) concentration and sensing that are consequences of the disease and facilitate its further progression. The impact of protonation state on protein activity can arise from alterations to amino acids or their titration. Indeed, many cancer-initiating mutations influence pH balance, regulation or sensing in a manner that enables growth and invasion outside normal constraints as part of oncogenic transformation. These cancer-supporting effects become more prominent when tumours develop an acidic microenvironment owing to metabolic reprogramming and disordered perfusion. The ensuing intracellular and extracellular pH disturbances affect multiple aspects of tumour biology, ranging from proliferation to immune surveillance, and can even facilitate further mutagenesis. As a selection pressure, extracellular acidosis accelerates disease progression by favouring acid-resistant cancer cells, which are typically associated with aggressive phenotypes. Although acid-base disturbances in tumours often occur alongside hypoxia and lactate accumulation, there is now ample evidence for a distinct role of H+-operated responses in key events underpinning cancer. The breadth of these actions presents therapeutic opportunities to change the trajectory of disease.
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Affiliation(s)
- Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
| | - Ebbe Boedtkjer
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Stine Falsig Pedersen
- Department of Biology, University of Copenhagen, University of Copenhagen, Faculty of Science, København, Denmark.
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Dong P, Du X, Yang T, Li D, Du Y, Wei Y, Sun J. PEX13 is a potential immunotherapeutic indicator and prognostic biomarker for various tumors including PAAD. Oncol Lett 2023; 26:512. [PMID: 37920431 PMCID: PMC10618920 DOI: 10.3892/ol.2023.14099] [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] [Received: 04/07/2023] [Accepted: 09/07/2023] [Indexed: 11/04/2023] Open
Abstract
The peroxisome serves a significant role in the occurrence and development of cancers. Specifically, the peroxisomal biogenesis factor 13 (PEX13) is crucial to the occurrence of peroxisomes. However, the biological function of PEX13 in cancers remains unclear. To address this, various portals and databases such as The Cancer Genome Atlas Program, The Genotype-Tissue Expression project, the Gene Expression Profiling Interactive Analysis 2, cBioPortal, the Genomic Identification of Significant Targets In Cancer 2.0, Tumor Immune Estimation Resource 2, SangerBox, LinkedOmics, DAVID and STRING were applied to extract and analyze PEX13 data in tumors. The correlations between PEX13 and prognosis, genetic alterations, PEX13-related gene enrichment analysis, weighted gene co-expression network analysis (WGCNA), protein interaction, long non-coding (lnc)RNA/circular (circ)RNA-micro (mi)RNA network and tumor immunity were explored in various tumors. The lncRNA-miRNA-PEX13 and circRNA-miRNA-PEX13 regulatory networks were identified via miRabel, miRDB, TargetScan and ENCORI portals and Cytoscape tool. In vitro assays were applied to verify the biological functions of PEX13 in pancreatic adenocarcinoma (PAAD) cells. The findings revealed that PEX13 is upregulated in various tumors and high PEX13 mRNA expression is associated with poor prognosis in patients with multiple cancers. Genetic alterations in PEX13 such as amplification, mutation and deep deletion have been found in multiple cancers. PEX13-related genes were associated with T cell receptor, signaling pathway and hippo signaling pathway through 'biological process' subontology of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Through WGCNA analysis, it was discovered that PEX13 hub genes were mainly enriched in the Rap1, ErbB and AMPK signaling pathways in PAAD. Immune analysis showed that PEX13 was significantly related to tumor infiltration immune cells, immune checkpoint genes, microsatellite instability, TMB and tumor purity in a variety of tumors. Cell Counting Kit-8, wound healing, Transwell and colony formation assays displayed that PEX13 knockdown could suppress PAAD cell proliferation, migration, invasion, and colony formation in vitro, respectively. Overall, PEX13 is a potential predictor of immunotherapeutic and prognostic biomarkers in various malignant tumors, including ACC, KICH, LGG, LIHC and PAAD.
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Affiliation(s)
- Penggang Dong
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
- Department of Hepatobiliary Surgery, Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Xuezhi Du
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Ting Yang
- Central Laboratory, Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Dandan Li
- Central Laboratory, Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Yunyi Du
- Department of Oncology, Changzhi People's Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Yaqing Wei
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Jinjin Sun
- Department of Hepatopancreatobiliary Surgery, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
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33
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Bennett NK, Lee M, Orr AL, Nakamura K. Systems-level analyses dissociate genetic regulators of reactive oxygen species and energy production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.562276. [PMID: 37904938 PMCID: PMC10614765 DOI: 10.1101/2023.10.14.562276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Respiratory chain dysfunction can decrease ATP and increase reactive oxygen species (ROS) levels. Despite the importance of these metabolic parameters to a wide range of cellular functions and disease, we lack an integrated understanding of how they are differentially regulated. To address this question, we adapted a CRISPRi- and FACS- based platform to compare the effects of respiratory gene knockdown on ROS to their effects on ATP. Focusing on genes whose knockdown is known to decrease mitochondria-derived ATP, we showed that knockdown of genes in specific respiratory chain complexes (I, III and CoQ10 biosynthesis) increased ROS, whereas knockdown of other low ATP hits either had no impact (mitochondrial ribosomal proteins) or actually decreased ROS (complex IV). Moreover, although shifting metabolic conditions profoundly altered mitochondria-derived ATP levels, it had little impact on mitochondrial or cytosolic ROS. In addition, knockdown of a subset of complex I subunits-including NDUFA8, NDUFB4, and NDUFS8-decreased complex I activity, mitochondria-derived ATP and supercomplex level, but knockdown of these genes had differential effects on ROS. Conversely, we found an essential role for ether lipids in the dynamic regulation of mitochondrial ROS levels independent of ATP. Thus, our results identify specific metabolic regulators of cellular ATP and ROS balance that may help dissect the roles of these processes in disease and identify therapeutic strategies to independently target energy failure and oxidative stress.
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Affiliation(s)
- Neal K. Bennett
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Megan Lee
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, 94158, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Adam L. Orr
- Appel Alzheimer’s Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, 94158, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Graduate Programs in Neuroscience and Biomedical Sciences, University of California San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, 94158, USA
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An Y, Talwar CS, Park KH, Ahn WC, Lee SJ, Go SR, Cho JH, Kim DY, Kim YS, Cho S, Kim JH, Kim TJ, Woo EJ. Design of hypoxia responsive CRISPR-Cas9 for target gene regulation. Sci Rep 2023; 13:16763. [PMID: 37798384 PMCID: PMC10556097 DOI: 10.1038/s41598-023-43711-9] [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: 03/08/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
The CRISPR-Cas9 system is a widely used gene-editing tool, offering unprecedented opportunities for treating various diseases. Controlling Cas9/dCas9 activity at specific location and time to avoid undesirable effects is very important. Here, we report a conditionally active CRISPR-Cas9 system that regulates target gene expression upon sensing cellular environmental change. We conjugated the oxygen-sensing transcription activation domain (TAD) of hypoxia-inducing factor (HIF-1α) with the Cas9/dCas9 protein. The Cas9-TAD conjugate significantly increased endogenous target gene cleavage under hypoxic conditions compared with that under normoxic conditions, whereas the dCas9-TAD conjugate upregulated endogenous gene transcription. Furthermore, the conjugate system effectively downregulated the expression of SNAIL, an essential gene in cancer metastasis, and upregulated the expression of the tumour-related genes HNF4 and NEUROD1 under hypoxic conditions. Since hypoxia is closely associated with cancer, the hypoxia-dependent Cas9/dCas9 system is a novel addition to the molecular tool kit that functions in response to cellular signals and has potential application for gene therapeutics.
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Affiliation(s)
- Yan An
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Chandana S Talwar
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Kwang-Hyun Park
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Woo-Chan Ahn
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Su-Jin Lee
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Seong-Ryeong Go
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Jin Hwa Cho
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Do Yon Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Yong-Sam Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Sayeon Cho
- Laboratory of Molecular and Pharmacological Cell Biology, College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jeong-Hoon Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea
| | - Tae-Jip Kim
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Eui-Jeon Woo
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea.
- Department of Bioscience, University of Science and Technology, Daejeon, 305-333, Republic of Korea.
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Rogers ZJ, Colombani T, Khan S, Bhatt K, Nukovic A, Zhou G, Woolston BM, Taylor CT, Gilkes DM, Slavov N, Bencherif SA. Controlling pericellular oxygen tension in cell culture reveals distinct breast cancer responses to low oxygen tensions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560369. [PMID: 37873449 PMCID: PMC10592900 DOI: 10.1101/2023.10.02.560369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Oxygen (O2) tension plays a key role in tissue function and pathophysiology. O2-controlled cell culture, in which the O2 concentration in an incubator's gas phase is controlled, is an indispensable tool to study the role of O2 in vivo. For this technique, it is presumed that the incubator setpoint is equal to the O2 tension that cells experience (i.e., pericellular O2). We discovered that physioxic (5% O2) and hypoxic (1% O2) setpoints regularly induce anoxic (0.0% O2) pericellular tensions in both adherent and suspension cell cultures. Electron transport chain inhibition ablates this effect, indicating that cellular O2 consumption is the driving factor. RNA-seq revealed that primary human hepatocytes cultured in physioxia experience ischemia-reperfusion injury due to anoxic exposure followed by rapid reoxygenation. To better understand the relationship between incubator gas phase and pericellular O2 tensions, we developed a reaction-diffusion model that predicts pericellular O2 tension a priori. This model revealed that the effect of cellular O2 consumption is greatest in smaller volume culture vessels (e.g., 96-well plate). By controlling pericellular O2 tension in cell culture, we discovered that MCF7 cells have stronger glycolytic and glutamine metabolism responses in anoxia vs. hypoxia. MCF7 also expressed higher levels of HIF2A, CD73, NDUFA4L2, etc. and lower levels of HIF1A, CA9, VEGFA, etc. in response to hypoxia vs. anoxia. Proteomics revealed that 4T1 cells had an upregulated epithelial-to-mesenchymal transition (EMT) response and downregulated reactive oxygen species (ROS) management, glycolysis, and fatty acid metabolism pathways in hypoxia vs. anoxia. Collectively, these results reveal that breast cancer cells respond non-monotonically to low O2, suggesting that anoxic cell culture is not suitable to model hypoxia. We demonstrate that controlling atmospheric O2 tension in cell culture incubators is insufficient to control O2 in cell culture and introduce the concept of pericellular O2-controlled cell culture.
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Affiliation(s)
- Zachary J. Rogers
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Thibault Colombani
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Saad Khan
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
| | - Khushbu Bhatt
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Alexandra Nukovic
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Guanyu Zhou
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Benjamin M. Woolston
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Cormac T. Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Daniele M. Gilkes
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21321, USA
- Cellular and Molecular Medicine Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21321, USA
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA 02115 USA
- Parallel Squared Technology Institute, Watertown, MA 02135 USA
| | - Sidi A. Bencherif
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Biomechanics and Bioengineering (BMBI), UTC CNRS UMR 7338, University of Technology of Compiègne, Sorbonne University, 60203 Compiègne, France
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Lobel GP, Jiang Y, Simon MC. Tumor microenvironmental nutrients, cellular responses, and cancer. Cell Chem Biol 2023; 30:1015-1032. [PMID: 37703882 PMCID: PMC10528750 DOI: 10.1016/j.chembiol.2023.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Abstract
Over the last two decades, the rapidly expanding field of tumor metabolism has enhanced our knowledge of the impact of nutrient availability on metabolic reprogramming in cancer. Apart from established roles in cancer cells themselves, various nutrients, metabolic enzymes, and stress responses are key to the activities of tumor microenvironmental immune, fibroblastic, endothelial, and other cell types that support malignant transformation. In this article, we review our current understanding of how nutrient availability affects metabolic pathways and responses in both cancer and "stromal" cells, by dissecting major examples and their regulation of cellular activity. Understanding the relationship of nutrient availability to cellular behaviors in the tumor ecosystem will broaden the horizon of exploiting novel therapeutic vulnerabilities in cancer.
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Affiliation(s)
- Graham P Lobel
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yanqing Jiang
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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37
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Fan D, Ma Y, Qi Y, Yang X, Zhao H. TMEM189 as a target gene of MiR-499a-5p regulates breast cancer progression through the ferroptosis pathway. J Clin Biochem Nutr 2023; 73:154-160. [PMID: 37700851 PMCID: PMC10493215 DOI: 10.3164/jcbn.22-130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/08/2023] [Indexed: 09/14/2023] Open
Abstract
MicroRNA (miR)-499a-5p has been reported to regulate the progression of various tumours. However, the role of miR-499a-5p in breast cancer is unclear. The purpose of this study was to investigate the role and mechanism of miR-499a-5p in breast cancer. The growth effect of miR-499a-5p on breast cancer cells was investigated by the CCK-8 assay, wound healing assay and Transwell invasion assay. The luciferase activity assay was used to verify the downstream targets of miR-499a-5p. The levels of GSH, MDA, and ROS were detected by kits. Quantitative real-time PCR and Western blot were used to determine the expression levels of TMEM189, COX-2, GPX4, and other related genes in cells. miR-499a-5p was down-regulated in MDA-MB-231 cells and was shown to reduced the viability, migration and invasion of MDA-MB-231 cells. Further studies revealed that TMEM189 is a target of miR-499a-5p. miR-499a-5p inhibited breast cancer cell growth by downregulating TMEM189. Furthermore, the down-regulation of TMEM189 promotes ferroptosis in breast cancer cells. The low expression of TMEM189 inhibited the development of breast cancer through the ferroptosis pathway. We have demonstrated for the first time that miR-499a-5p inhibits breast cancer progression by targeting the TMEM189-mediated ferroptosis pathway.
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Affiliation(s)
- Dong Fan
- Department of General Surgery, The Second Affiliated Hospital of the Air Force Medical University, No. 1, Xinsi Road, Baqiao District, Xi’an, Shaanxi 710038, China
| | - Yue Ma
- Department of Anesthesia operating room, The Second Affiliated Hospital of the Air Force Medical University, No. 1, Xinsi Road, Baqiao District, Xi’an, Shaanxi 710038, China
| | - Yujuan Qi
- Department of General Surgery, The Second Affiliated Hospital of the Air Force Medical University, No. 1, Xinsi Road, Baqiao District, Xi’an, Shaanxi 710038, China
| | - Xiaozhou Yang
- Department of General Surgery, The Second Affiliated Hospital of the Air Force Medical University, No. 1, Xinsi Road, Baqiao District, Xi’an, Shaanxi 710038, China
| | - Huadong Zhao
- Department of General Surgery, The Second Affiliated Hospital of the Air Force Medical University, No. 1, Xinsi Road, Baqiao District, Xi’an, Shaanxi 710038, China
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Ehrenreich H, Gassmann M, Poustka L, Burtscher M, Hammermann P, Sirén AL, Nave KA, Miskowiak K. Exploiting moderate hypoxia to benefit patients with brain disease: Molecular mechanisms and translational research in progress. NEUROPROTECTION 2023; 1:9-19. [PMID: 37671067 PMCID: PMC7615021 DOI: 10.1002/nep3.15] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/07/2023]
Abstract
Hypoxia is increasingly recognized as an important physiological driving force. A specific transcriptional program, induced by a decrease in oxygen (O2) availability, for example, inspiratory hypoxia at high altitude, allows cells to adapt to lower O2 and limited energy metabolism. This transcriptional program is partly controlled by and partly independent of hypoxia-inducible factors. Remarkably, this same transcriptional program is stimulated in the brain by extensive motor-cognitive exercise, leading to a relative decrease in O2 supply, compared to the acutely augmented O2 requirement. We have coined the term "functional hypoxia" for this important demand-responsive, relative reduction in O2 availability. Functional hypoxia seems to be critical for enduring adaptation to higher physiological challenge that includes substantial "brain hardware upgrade," underlying advanced performance. Hypoxia-induced erythropoietin expression in the brain likely plays a decisive role in these processes, which can be imitated by recombinant human erythropoietin treatment. This article review presents hints of how inspiratory O2 manipulations can potentially contribute to enhanced brain function. It thereby provides the ground for exploiting moderate inspiratory plus functional hypoxia to treat individuals with brain disease. Finally, it sketches a planned multistep pilot study in healthy volunteers and first patients, about to start, aiming at improved performance upon motor-cognitive training under inspiratory hypoxia.
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Affiliation(s)
- Hannelore Ehrenreich
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Max Gassmann
- Institute of Veterinary Physiology and Zürich Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland
| | - Luise Poustka
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Martin Burtscher
- Faculty of Sports Science, University of Innsbruck, Innsbruck, Austria
| | | | - Anna-Leena Sirén
- Departments of Neurophysiology and Neurosurgery, University of Würzburg, Würzburg, Germany
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Kamilla Miskowiak
- Psychiatric Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Psychology, University of Copenhagen, Copenhagen, Denmark
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Zhang R, Yang A, Zhang L, He L, Gu X, Yu C, Lu Z, Wang C, Zhou F, Li F, Ji L, Xing J, Guo H. MFN2 deficiency promotes cardiac response to hypobaric hypoxia by reprogramming cardiomyocyte metabolism. Acta Physiol (Oxf) 2023; 239:e14018. [PMID: 37401731 DOI: 10.1111/apha.14018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
AIM Under hypobaric hypoxia (HH), the heart triggers various defense mechanisms including metabolic remodeling against lack of oxygen. Mitofusin 2 (MFN2), located at the mitochondrial outer membrane, is closely involved in the regulation of mitochondrial fusion and cell metabolism. To date, however, the role of MFN2 in cardiac response to HH has not been explored. METHODS Loss- and gain-of-function approaches were used to investigate the role of MFN2 in cardiac response to HH. In vitro, the function of MFN2 in the contraction of primary neonatal rat cardiomyocytes under hypoxia was examined. Non-targeted metabolomics and mitochondrial respiration analyses, as well as functional experiments were performed to explore underlying molecular mechanisms. RESULTS Our data demonstrated that, following 4 weeks of HH, cardiac-specific MFN2 knockout (MFN2 cKO) mice exhibited significantly better cardiac function than control mice. Moreover, restoring the expression of MFN2 clearly inhibited the cardiac response to HH in MFN2 cKO mice. Importantly, MFN2 knockout significantly improved cardiac metabolic reprogramming during HH, resulting in reduced capacity for fatty acid oxidation (FAO) and oxidative phosphorylation, and increased glycolysis and ATP production. In vitro data showed that down-regulation of MFN2 promoted cardiomyocyte contractility under hypoxia. Interestingly, increased FAO through palmitate treatment decreased contractility of cardiomyocyte with MFN2 knockdown under hypoxia. Furthermore, treatment with mdivi-1, an inhibitor of mitochondrial fission, disrupted HH-induced metabolic reprogramming and subsequently promoted cardiac dysfunction in MFN2-knockout hearts. CONCLUSION Our findings provide the first evidence that down-regulation of MFN2 preserves cardiac function in chronic HH by promoting cardiac metabolic reprogramming.
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Affiliation(s)
- Ru Zhang
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China
- Department of Aerospace Physiology, Air Force Medical University, Xi'an, China
| | - Ailin Yang
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China
| | - Lin Zhang
- Department of Aerospace Physiology, Air Force Medical University, Xi'an, China
| | - Linjie He
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China
| | - Xiaoming Gu
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China
| | - Caiyong Yu
- Military Medical Innovation Center, Air Force Medical University, Xi'an, China
| | - Zhenxing Lu
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Chuang Wang
- College of Basic Medicine, Air Force Medical University, Xi'an, China
| | - Feng Zhou
- Department of General Surgery, The 71st Group Army Hospital of the People's Liberation Army, Xuzhou, China
| | - Fei Li
- Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Lele Ji
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China
- Experimental Teaching Center of Basic Medicine, Air Force Medical University, Xi'an, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China
| | - Haitao Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China
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40
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Pilon M, Ruiz M. PAQR proteins and the evolution of a superpower: Eating all kinds of fats: Animals rely on evolutionarily conserved membrane homeostasis proteins to compensate for dietary variation. Bioessays 2023; 45:e2300079. [PMID: 37345585 DOI: 10.1002/bies.202300079] [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: 05/05/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
Recently published work showed that members of the PAQR protein family are activated by cell membrane rigidity and contribute to our ability to eat a wide variety of diets. Cell membranes are primarily composed of phospholipids containing dietarily obtained fatty acids, which poses a challenge to membrane properties because diets can vary greatly in their fatty acid composition and could impart opposite properties to the cellular membranes. In particular, saturated fatty acids (SFAs) can pack tightly and form rigid membranes (like butter at room temperature) while unsaturated fatty acids (UFAs) form more fluid membranes (like vegetable oils). Proteins of the PAQR protein family, characterized by the presence of seven transmembrane domains and a cytosolic N-terminus, contribute to membrane homeostasis in bacteria, yeasts, and animals. These proteins respond to membrane rigidity by stimulating fatty acid desaturation and incorporation of UFAs into phospholipids and explain the ability of animals to thrive on diets with widely varied fat composition. Also see the video abstract here: https://youtu.be/6ckcvaDdbQg.
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Affiliation(s)
- Marc Pilon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Mario Ruiz
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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41
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Joshi PR, Sadre S, Guo XA, McCoy JG, Mootha VK. Lipoylation is dependent on the ferredoxin FDX1 and dispensable under hypoxia in human cells. J Biol Chem 2023; 299:105075. [PMID: 37481209 PMCID: PMC10470009 DOI: 10.1016/j.jbc.2023.105075] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/24/2023] Open
Abstract
Iron-sulfur clusters (ISC) are essential cofactors that participate in electron transfer, environmental sensing, and catalysis. Amongst the most ancient ISC-containing proteins are the ferredoxin (FDX) family of electron carriers. Humans have two FDXs- FDX1 and FDX2, both of which are localized to mitochondria, and the latter of which is itself important for ISC synthesis. We have previously shown that hypoxia can eliminate the requirement for some components of the ISC biosynthetic pathway, but FDXs were not included in that study. Here, we report that FDX1, but not FDX2, is dispensable under 1% O2 in cultured human cells. We find that FDX1 is essential for production of the lipoic acid cofactor, which is synthesized by the ISC-containing enzyme lipoyl synthase. While hypoxia can rescue the growth phenotype of either FDX1 or lipoyl synthase KO cells, lipoylation in these same cells is not rescued, arguing against an alternative biosynthetic route or salvage pathway for lipoate in hypoxia. Our work reveals the divergent roles of FDX1 and FDX2 in mitochondria, identifies a role for FDX1 in lipoate synthesis, and suggests that loss of lipoic acid can be tolerated under low oxygen tensions in cell culture.
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Affiliation(s)
- Pallavi R Joshi
- Broad Institute, Cambridge, Massachusetts, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shayan Sadre
- Broad Institute, Cambridge, Massachusetts, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaoyan A Guo
- Broad Institute, Cambridge, Massachusetts, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason G McCoy
- Broad Institute, Cambridge, Massachusetts, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Vamsi K Mootha
- Broad Institute, Cambridge, Massachusetts, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.
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Honsho M, Fujiki Y. Asymmetric Distribution of Plasmalogens and Their Roles-A Mini Review. MEMBRANES 2023; 13:764. [PMID: 37755186 PMCID: PMC10534842 DOI: 10.3390/membranes13090764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
Plasmalogens are a unique family of cellular glycerophospholipids that contain a vinyl-ether bond. The synthesis of plasmalogens is initiated in peroxisomes and completed in the endoplasmic reticulum. Plasmalogens are transported to the post-Golgi compartment, including endosomes and plasma membranes, in a manner dependent on ATP, but not vesicular transport. Plasmalogens are preferentially localized in the inner leaflet of the plasma membrane in a manner dependent on P4-type ATPase ATP8B2, that associates with the CDC50 subunit. Plasmalogen biosynthesis is spatiotemporally regulated by a feedback mechanism that senses the amount of plasmalogens in the inner leaflet of the plasma membrane and controls the stability of fatty acyl-CoA reductase 1 (FAR1), the rate-limiting enzyme for plasmalogen biosynthesis. The physiological consequences of such asymmetric localization and homeostasis of plasmalogens are discussed in this review.
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Affiliation(s)
- Masanori Honsho
- Department of Neuroinflammation and Brain Fatigue Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Yukio Fujiki
- Institute of Rheological Functions of Food-Kyushu University Collaboration Program, Kyushu University, Fukuoka 811-2501, Japan
- Graduate School of Science, University of Hyogo, Himeji 671-2280, Japan
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43
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Melero A, Jiménez-Rojo N. Cracking the membrane lipid code. Curr Opin Cell Biol 2023; 83:102203. [PMID: 37437490 DOI: 10.1016/j.ceb.2023.102203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/14/2023]
Abstract
Why has nature acquired such a huge lipid repertoire? Although it would be theoretically possible to make a lipid bilayer fulfilling barrier functions with only one glycerophospholipid, there are diverse and numerous different lipid species. Lipids are heterogeneously distributed across the evolutionary tree with lipidomes evolving in parallel to organismal complexity. Moreover, lipids are different between organs and tissues and even within the same cell, different organelles have characteristic lipid signatures. At the molecular level, membranes are asymmetric and laterally heterogeneous. This lipid asymmetry at different scales indicates that these molecules may play very specific molecular functions in biology. Some of these roles have been recently uncovered: lipids have been shown to be essential in processes such as hypoxia and ferroptosis or in protein sorting and trafficking but many of them remain still unknown. In this review we will discuss the importance of understanding lipid diversity in biology across scales and we will share a toolbox with some of the emerging technologies that are helping us to uncover new lipid molecular functions in cell biology and, step by step, crack the membrane lipid code.
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Affiliation(s)
- Alejandro Melero
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Noemi Jiménez-Rojo
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain; Instituto Biofisika (UPV/EHU, CSIC), 48940, Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
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Copeland CA, Olenchock BA, Ziehr D, McGarrity S, Leahy K, Young JD, Loscalzo J, Oldham WM. MYC overrides HIF-1α to regulate proliferating primary cell metabolism in hypoxia. eLife 2023; 12:e82597. [PMID: 37428010 DOI: 10.7554/elife.82597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
Hypoxia requires metabolic adaptations to sustain energetically demanding cellular activities. While the metabolic consequences of hypoxia have been studied extensively in cancer cell models, comparatively little is known about how primary cell metabolism responds to hypoxia. Thus, we developed metabolic flux models for human lung fibroblast and pulmonary artery smooth muscle cells proliferating in hypoxia. Unexpectedly, we found that hypoxia decreased glycolysis despite activation of hypoxia-inducible factor 1α (HIF-1α) and increased glycolytic enzyme expression. While HIF-1α activation in normoxia by prolyl hydroxylase (PHD) inhibition did increase glycolysis, hypoxia blocked this effect. Multi-omic profiling revealed distinct molecular responses to hypoxia and PHD inhibition, and suggested a critical role for MYC in modulating HIF-1α responses to hypoxia. Consistent with this hypothesis, MYC knockdown in hypoxia increased glycolysis and MYC over-expression in normoxia decreased glycolysis stimulated by PHD inhibition. These data suggest that MYC signaling in hypoxia uncouples an increase in HIF-dependent glycolytic gene transcription from glycolytic flux.
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Affiliation(s)
- Courtney A Copeland
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - Benjamin A Olenchock
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - David Ziehr
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
- Department of Medicine, Massachusetts General Hospital, Boston, United States
| | - Sarah McGarrity
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
- Center for Systems Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kevin Leahy
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - Jamey D Young
- Departments of Chemical & Biomolecular Engineering and Molecular Physiology & Biophysics, Vanderbilt University, Nashville, United States
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - William M Oldham
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
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45
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Mu H, Wan W, Song J, Kuang R, Deng T. Mitochondrial Lipid Peroxidation and Microsomal Drug-metabolizing Enzyme Activity of Rat Hepatotoxicity under Heavy Metals from Slag Waste Exposure. Cell Biochem Biophys 2023:10.1007/s12013-023-01134-3. [PMID: 37268808 DOI: 10.1007/s12013-023-01134-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 06/04/2023]
Abstract
Heavy metals from slag waste (HMSWs) have attracted much attention because of their serious toxicity to the environment and human organs, especially hepatotoxicity. The aim of this study was to explore the effects of different HMSWs exposure on mitochondrial lipid peroxidation, microsomal drug metabolizing enzyme activities as well as their relationship in the rat liver injury. Based on toxicogenomic analysis, heavy metals including iron, copper, cobalt, nickel and manganese, might interfere with pathophysiological processes such as oxidative stress, cell death, and energy metabolism regulation in vivo, and participate in the regulation of HIF-1 signaling pathway, peroxisomes, drug metabolism-cytochrome P450, ferroptosis, and other signaling pathways. HMSWs exposure caused weight loss, and significantly increased lactate dehydrogenase (LDH), malondialdehyde (MDA), alanine transaminase (ALT), and aspartate transaminase (AST) in different groups of rat liver, suggesting the presence of mitochondrial lipid peroxidation damage. In addition, the ratios of AST/ALT and ALT/LDH were down-regulated, especially the ALT/LDH ratios were less than 1, indicating that hepatic ischemic injury occurred in the process of liver injury. The superoxide dismutase (SOD) and mitochondrial membrane potential (MMP) activities in rats also showed significant decreases, indicating the occurrence of hepatic oxidative/antioxidant dysfunction imbalance. Further decision tree analysis of live biochemical abnormalities suggested that AST > 58.78 U/gprot and MDA > 173.2 nmol/mgprot could be used for hepatotoxicity warning. Liver microsomal cytochrome P4501A2 (CYP1A2) and 3A1 (CYP3A1) enzymes were also involved in the hepatotoxic process of heavy metals. These results suggest that lipid peroxidation damage and metabolic damage in liver mitochondria and peroxisomes, may be one of the key events in heavy metal-induced liver injury.
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Affiliation(s)
- Haishuo Mu
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Wangjun Wan
- Technology Center of Hangzhou Customs, Hangzhou, China
| | - Jingwu Song
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Rong Kuang
- NMPA Key Laboratory for Animal Alternative Testing Technology of Cosmetics, Zhejiang Institute for Food and Drug Control, Hangzhou, China
| | - Tongle Deng
- College of Life Sciences, China Jiliang University, Hangzhou, China.
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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47
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Farese RV, Walther TC. Glycerolipid Synthesis and Lipid Droplet Formation in the Endoplasmic Reticulum. Cold Spring Harb Perspect Biol 2023; 15:a041246. [PMID: 36096640 PMCID: PMC10153804 DOI: 10.1101/cshperspect.a041246] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
More than 60 years ago, Eugene Kennedy and coworkers elucidated the endoplasmic reticulum (ER)-based pathways of glycerolipid synthesis, including the synthesis of phospholipids and triacylglycerols (TGs). The reactions of the Kennedy pathway were identified by studying the conversion of lipid intermediates and the isolation of biochemical enzymatic activities, but the molecular basis for most of these reactions was unknown. With recent progress in the cell biology, biochemistry, and structural biology in this area, we have a much more mechanistic understanding of this pathway and its reactions. In this review, we provide an overview of molecular aspects of glycerolipid synthesis, focusing on recent insights into the synthesis of TGs. Further, we go beyond the Kennedy pathway to describe the mechanisms for storage of TG in cytosolic lipid droplets and discuss how overwhelming these pathways leads to ER stress and cellular toxicity, as seen in diseases linked to lipid overload and obesity.
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Affiliation(s)
- Robert V Farese
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Center for Causes and Prevention of Cardiovascular Disease (CAP-CVD), Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Center for Causes and Prevention of Cardiovascular Disease (CAP-CVD), Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute Boston, Boston, Massachusetts 02115, USA
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Chen Z, Ho IL, Soeung M, Yen EY, Liu J, Yan L, Rose JL, Srinivasan S, Jiang S, Edward Chang Q, Feng N, Gay JP, Wang Q, Wang J, Lorenzi PL, Veillon LJ, Wei B, Weinstein JN, Deem AK, Gao S, Genovese G, Viale A, Yao W, Lyssiotis CA, Marszalek JR, Draetta GF, Ying H. Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis. Nat Commun 2023; 14:2194. [PMID: 37069167 PMCID: PMC10110566 DOI: 10.1038/s41467-023-37924-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
Mitochondria are hubs where bioenergetics, redox homeostasis, and anabolic metabolism pathways integrate through a tightly coordinated flux of metabolites. The contributions of mitochondrial metabolism to tumor growth and therapy resistance are evident, but drugs targeting mitochondrial metabolism have repeatedly failed in the clinic. Our study in pancreatic ductal adenocarcinoma (PDAC) finds that cellular and mitochondrial lipid composition influence cancer cell sensitivity to pharmacological inhibition of electron transport chain complex I. Profiling of patient-derived PDAC models revealed that monounsaturated fatty acids (MUFAs) and MUFA-linked ether phospholipids play a critical role in maintaining ROS homeostasis. We show that ether phospholipids support mitochondrial supercomplex assembly and ROS production; accordingly, blocking de novo ether phospholipid biosynthesis sensitized PDAC cells to complex I inhibition by inducing mitochondrial ROS and lipid peroxidation. These data identify ether phospholipids as a regulator of mitochondrial redox control that contributes to the sensitivity of PDAC cells to complex I inhibition.
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Affiliation(s)
- Ziheng Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - I-Lin Ho
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Soeung
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Er-Yen Yen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jintan Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Liang Yan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Johnathon L Rose
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanjana Srinivasan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shan Jiang
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Q Edward Chang
- The Oncology Research for Biologics and Immunotherapy Translation (ORBIT), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ningping Feng
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason P Gay
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucas J Veillon
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bo Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Angela K Deem
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sisi Gao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wantong Yao
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph R Marszalek
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology (TRACTION), The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Abubakar SD, Takaki M, Haeno H. Computational modeling of locoregional recurrence with spatial structure identifies tissue-specific carcinogenic profiles. Front Oncol 2023; 13:1116210. [PMID: 37091178 PMCID: PMC10117647 DOI: 10.3389/fonc.2023.1116210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
IntroductionLocal and regional recurrence after surgical intervention is a significant problem in cancer management. The multistage theory of carcinogenesis precisely places the presence of histologically normal but mutated premalignant lesions surrounding the tumor - field cancerization, as a significant cause of cancer recurrence. The relationship between tissue dynamics, cancer initiation and cancer recurrence in multistage carcinogenesis is not well known.MethodsThis study constructs a computational model for cancer initiation and recurrence by combining the Moran and branching processes in which cells requires 3 or more mutations to become malignant. In addition, a spatial structure-setting is included in the model to account for positional relativity in cell turnover towards malignant transformation. The model consists of a population of normal cells with no mutation; several populations of premalignant cells with varying number of mutations and a population of malignant cells. The model computes a stage of cancer detection and surgery to eliminate malignant cells but spares premalignant cells and then estimates the time for malignant cells to re-emerge.ResultsWe report the cellular conditions that give rise to different patterns of cancer initiation and the conditions favoring a shorter cancer recurrence by analyzing premalignant cell types at the time of surgery. In addition, the model is fitted to disease-free clinical data of 8,957 patients in 27 different cancer types; From this fitting, we estimate the turnover rate per month, relative fitness of premalignant cells, growth rate and death rate of cancer cells in each cancer type.DiscussionOur study provides insights into how to identify patients who are likely to have a shorter recurrence and where to target the therapeutic intervention.
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Affiliation(s)
| | - Mitsuaki Takaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroshi Haeno
- Research Institute for Biomedical Science, Tokyo University of Science, Noda, Japan
- *Correspondence: Hiroshi Haeno,
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Carlsson R, Enström A, Paul G. Molecular Regulation of the Response of Brain Pericytes to Hypoxia. Int J Mol Sci 2023; 24:5671. [PMID: 36982744 PMCID: PMC10053233 DOI: 10.3390/ijms24065671] [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: 02/19/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
The brain needs sufficient oxygen in order to function normally. This is achieved by a large vascular capillary network ensuring that oxygen supply meets the changing demand of the brain tissue, especially in situations of hypoxia. Brain capillaries are formed by endothelial cells and perivascular pericytes, whereby pericytes in the brain have a particularly high 1:1 ratio to endothelial cells. Pericytes not only have a key location at the blood/brain interface, they also have multiple functions, for example, they maintain blood-brain barrier integrity, play an important role in angiogenesis and have large secretory abilities. This review is specifically focused on both the cellular and the molecular responses of brain pericytes to hypoxia. We discuss the immediate early molecular responses in pericytes, highlighting four transcription factors involved in regulating the majority of transcripts that change between hypoxic and normoxic pericytes and their potential functions. Whilst many hypoxic responses are controlled by hypoxia-inducible factors (HIF), we specifically focus on the role and functional implications of the regulator of G-protein signaling 5 (RGS5) in pericytes, a hypoxia-sensing protein that is regulated independently of HIF. Finally, we describe potential molecular targets of RGS5 in pericytes. These molecular events together contribute to the pericyte response to hypoxia, regulating survival, metabolism, inflammation and induction of angiogenesis.
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Affiliation(s)
- Robert Carlsson
- Translational Neurology Group, Department of Clinical Science, Wallenberg Neuroscience Centre and Wallenberg Centre for Molecular Medicine, Lund University, 22184 Lund, Sweden
| | - Andreas Enström
- Translational Neurology Group, Department of Clinical Science, Wallenberg Neuroscience Centre and Wallenberg Centre for Molecular Medicine, Lund University, 22184 Lund, Sweden
| | - Gesine Paul
- Translational Neurology Group, Department of Clinical Science, Wallenberg Neuroscience Centre and Wallenberg Centre for Molecular Medicine, Lund University, 22184 Lund, Sweden
- Department of Neurology, Scania University Hospital, 22185 Lund, Sweden
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