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Lin CH, Chin Y, Zhou M, Sobol RW, Hung MC, Tan M. Protein lipoylation: mitochondria, cuproptosis, and beyond. Trends Biochem Sci 2024; 49:729-744. [PMID: 38714376 DOI: 10.1016/j.tibs.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/09/2024]
Abstract
Protein lipoylation, a crucial post-translational modification (PTM), plays a pivotal role in mitochondrial function and emerges as a key player in cell death through cuproptosis. This novel copper-driven cell death pathway is activated by excessive copper ions binding to lipoylated mitochondrial proteins, disrupting energy production and causing lethal protein aggregation and cell death. The intricate relationship among protein lipoylation, cellular energy metabolism, and cuproptosis offers a promising avenue for regulating essential cellular functions. This review focuses on the mechanisms of lipoylation and its significant impact on cell metabolism and cuproptosis, emphasizing the key genes involved and their implications for human diseases. It offers valuable insights into targeting dysregulated cellular metabolism for therapeutic purposes.
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Affiliation(s)
- Cheng-Han Lin
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Yeh Chin
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School and Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Mien-Chie Hung
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan.
| | - Ming Tan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan.
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2
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Li L, Zhou H, Zhang C. Cuproptosis in cancer: biological implications and therapeutic opportunities. Cell Mol Biol Lett 2024; 29:91. [PMID: 38918694 PMCID: PMC11201306 DOI: 10.1186/s11658-024-00608-3] [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: 03/13/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Cuproptosis, a newly identified copper (Cu)-dependent form of cell death, stands out due to its distinct mechanism that sets it apart from other known cell death pathways. The molecular underpinnings of cuproptosis involve the binding of Cu to lipoylated enzymes in the tricarboxylic acid cycle. This interaction triggers enzyme aggregation and proteotoxic stress, culminating in cell death. The specific mechanism of cuproptosis has yet to be fully elucidated. This newly recognized form of cell death has sparked numerous investigations into its role in tumorigenesis and cancer therapy. In this review, we summarized the current knowledge on Cu metabolism and its link to cancer. Furthermore, we delineated the molecular mechanisms of cuproptosis and summarized the roles of cuproptosis-related genes in cancer. Finally, we offered a comprehensive discussion of the most recent advancements in Cu ionophores and nanoparticle delivery systems that utilize cuproptosis as a cutting-edge strategy for cancer treatment.
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Affiliation(s)
- Liping Li
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, People's Republic of China
| | - Houfeng Zhou
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, People's Republic of China
| | - Chenliang Zhang
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
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3
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Arribas-Carreira L, Castro M, García F, Navarrete R, Bravo-Alonso I, Zafra F, Ugarte M, Richard E, Pérez B, Rodríguez-Pombo P. Metabolic Rewiring and Altered Glial Differentiation in an iPSC-Derived Astrocyte Model Derived from a Nonketotic Hyperglycinemia Patient. Int J Mol Sci 2024; 25:2814. [PMID: 38474060 DOI: 10.3390/ijms25052814] [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: 01/25/2024] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The pathophysiology of nonketotic hyperglycinemia (NKH), a rare neuro-metabolic disorder associated with severe brain malformations and life-threatening neurological manifestations, remains incompletely understood. Therefore, a valid human neural model is essential. We aimed to investigate the impact of GLDC gene variants, which cause NKH, on cellular fitness during the differentiation process of human induced pluripotent stem cells (iPSCs) into iPSC-derived astrocytes and to identify sustainable mechanisms capable of overcoming GLDC deficiency. We developed the GLDC27-FiPS4F-1 line and performed metabolomic, mRNA abundance, and protein analyses. This study showed that although GLDC27-FiPS4F-1 maintained the parental genetic profile, it underwent a metabolic switch to an altered serine-glycine-one-carbon metabolism with a coordinated cell growth and cell cycle proliferation response. We then differentiated the iPSCs into neural progenitor cells (NPCs) and astrocyte-lineage cells. Our analysis showed that GLDC-deficient NPCs had shifted towards a more heterogeneous astrocyte lineage with increased expression of the radial glial markers GFAP and GLAST and the neuronal markers MAP2 and NeuN. In addition, we detected changes in other genes related to serine and glycine metabolism and transport, all consistent with the need to maintain glycine at physiological levels. These findings improve our understanding of the pathology of nonketotic hyperglycinemia and offer new perspectives for therapeutic options.
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Affiliation(s)
- Laura Arribas-Carreira
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
| | - Margarita Castro
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Fernando García
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Rosa Navarrete
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Irene Bravo-Alonso
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Francisco Zafra
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Magdalena Ugarte
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Belén Pérez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
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Zhang P, Chen H, Zhang Y, Liu Y, Zhu G, Zhao W, Shang Q, He J, Zhou Z, Shen G, Yu X, Zhang Z, Chen G, Yu F, Liang D, Tang J, Liu Z, Cui J, Jiang X, Ren H. Dry and wet experiments reveal diagnostic clustering and immune landscapes of cuproptosis patterns in patients with ankylosing spondylitis. Int Immunopharmacol 2024; 127:111326. [PMID: 38091828 DOI: 10.1016/j.intimp.2023.111326] [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: 02/24/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024]
Abstract
Cuproptosis is a new manner of mitochondrial cell death induced by copper. There is evidence that serum copper has a crucial impact on ankylosing spondylitis (AS) by copper-induced inflammatory response. However, the molecular mechanisms of cuproptosis modulators in AS remain unknown. We aimed to use a bioinformatics-based method to comprehensively investigate cuproptosis-related subtype identification and immune microenvironment infiltration of AS. Additionally, we further verified the results by in vitro experiments, in which peripheral blood and fibroblast cells from AS patients were used to evaluate the functions of significant cuproptosis modulators on AS. Finally, eight significant cuproptosis modulators were identified by analysis of differences between controls and AS cases from GSE73754 dataset. Eight prognostic cuproptosis modulators (LIPT1, DLD, PDHA1, PDHB, SLC31A1, ATP7A, MTF1, CDKN2A) were identified using a random forest model for prediction of AS risk. A nomogram model of the 8 prognostic cuproptosis modulators was then constructed; the model could be beneficial in clinical settings, as indicated by decision curve analysis. Consensus clustering analysis was used to divide AS patients into two cuproptosis subtypes (clusterA & B) according to significant cuproptosis modulators. The cuproptosis score of each sample was calculated by principal component analysis to quantify cuproptosis subtypes. The cuproptosis scores were higher in clusterB than in clusterA. Additionally, cases in clusterA were closely associated with the immunity of activated B cells, Activated CD4 T cell, Type17 T helper cell and Type2 T helper cell, while cases in clusterB were linked to Mast cell, Neutrophil, Plasmacytoid dendritic cell immunity, indicating that clusterB may be more correlated with AS. Notably, key cuproptosis genes including ATP7A, MTF1, SLC31A1 detected by RT-qPCR with peripheral blood exhibited significantly higher expression levels in AS cases than controls; LIPT1 showed the opposite results; High MTF1 expression is correlated with increased osteogenic capacity. In general, this study of cuproptosis patterns may provide promising biomarkers and immunotherapeutic strategies for future AS treatment.
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Affiliation(s)
- Peng Zhang
- The Second Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Honglin Chen
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - You Zhang
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yu Liu
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Guangye Zhu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou 215007, China
| | - Wenhua Zhao
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Qi Shang
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jiahui He
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou 510130, China
| | - Zelin Zhou
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Gengyang Shen
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Xiang Yu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Zhida Zhang
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou 510130, China
| | - Guifeng Chen
- Shanghai 9th Peoples Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200011, China
| | - Fuyong Yu
- Qianxinan Autonomous Prefecture Hospital of TCM, Xingyi 562400, China
| | - De Liang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jingjing Tang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Zhixiang Liu
- Affiliated Huadu Hospital, Southern Medical University, Guangzhou 510800, China
| | - Jianchao Cui
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Xiaobing Jiang
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Hui Ren
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
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5
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Yuan J, Kitchener AC, Lackey LB, Sun T, Jiangzuo Q, Tuohetahong Y, Zhao L, Yang P, Wang G, Huang C, Wang J, Hou W, Liu Y, Chen W, Mi D, Murphy WJ, Li G. The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids. Proc Natl Acad Sci U S A 2024; 121:e2310763120. [PMID: 38165928 PMCID: PMC10786289 DOI: 10.1073/pnas.2310763120] [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: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 01/04/2024] Open
Abstract
Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.
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Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, EdinburghEH1 1JF, United Kingdom
- School of Geosciences, University of Edinburgh, EdinburghEH9 3PX, United Kingdom
| | | | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing100044, China
| | | | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development Collaborative Innovation Center, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong723099, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wenhui Hou
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
| | - Da Mi
- Xi’an Haorui Genomics Technology Co., Ltd., Xi’an710116, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an710049, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77843
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
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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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Li J, Tuo D, Guo G, Gan J. Aberrant expression of cuproptosis‑related gene LIPT1 is associated with metabolic dysregulation of fatty acid and prognosis in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:15763-15779. [PMID: 37668796 DOI: 10.1007/s00432-023-05325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
PURPOSE Lipoyltransferase 1 (LIPT1) has been recently identified as a cuproptosis‑related gene. As a key enzyme of lipoic acid metabolism, LIPT1 has been revealed to play important roles in hereditary diseases involved with lipoic acid biosynthesis defects, while its roles in hepatocellular carcinoma (HCC) remain to be elucidated. Hence, we aimed to explore the roles and mechanisms of LIPT1 in HCC progression. METHODS The expression of LIPT1 in HCC tissues and its clinical significance for HCC were evaluated by bioinformatic analysis and in our patient cohort. The influences of LIPT1 on the growth, migration, and lipid metabolism of HCC cells were assessed in vitro. The underlying mechanisms were explored using gene set enrichment analysis (GSEA) and molecular experiments. RESULTS LIPT1 expression was significantly elevated in HCC tissues compared to the normal tissues, and such upregulation was associated with more malignant pathological features and poor prognosis of patients with HCC. LIPT1 silencing significantly inhibited cell proliferation, migration, and lipid content. GSEA revealed that LIPT1 upregulation was significantly associated with various cancer-associated signaling pathways, including the PI3K-AKT signaling pathway and the Wnt/β-catenin pathway. Further molecular experiments indicated that LIPT1 silencing repressed the expression of peroxisome proliferator-activated receptor gamma (PPARγ) and inactivated the AKT/GSK-3β/β-catenin signaling axis. CONCLUSIONS Upregulation of LIPT1 is involved in metabolic dysregulation of fatty acid and poor prognosis of HCC patients, which suggests that LIPT1 plays an important role in reprogramming lipid metabolism and could act as a potential prognostic marker and therapeutic target for HCC.
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Affiliation(s)
- Jinping Li
- Department of Histology and Embryology of School of Preclinical Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China.
| | - Dayun Tuo
- Department of Histology and Embryology of School of Preclinical Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Gunan Guo
- Department of Histology and Embryology of School of Preclinical Medicine, Guilin Medical University, Guilin, Guangxi, People's Republic of China
- School of Stomatology, Zhaoqing Medical College, Zhaoqing, Guangdong, People's Republic of China
| | - Jinfeng Gan
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, People's Republic of China.
- Guangxi Health Commission Key Laboratory of Tumor Immunology and Receptor-Targeted Drug Basic Research, Guilin Medical University, Guilin, Guangxi, People's Republic of China.
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Krokidis MG, Vrahatis AG, Lazaros K, Skolariki K, Exarchos TP, Vlamos P. Machine Learning Analysis of Alzheimer's Disease Single-Cell RNA-Sequencing Data across Cortex and Hippocampus Regions. Curr Issues Mol Biol 2023; 45:8652-8669. [PMID: 37998721 PMCID: PMC10670182 DOI: 10.3390/cimb45110544] [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: 09/30/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Advancements in molecular biology have revolutionized our understanding of complex diseases, with Alzheimer's disease being a prime example. Single-cell sequencing, currently the most suitable technology, facilitates profoundly detailed disease analysis at the cellular level. Prior research has established that the pathology of Alzheimer's disease varies across different brain regions and cell types. In parallel, only machine learning has the capacity to address the myriad challenges presented by such studies, where the integration of large-scale data and numerous experiments is required to extract meaningful knowledge. Our methodology utilizes single-cell RNA sequencing data from healthy and Alzheimer's disease (AD) samples, focused on the cortex and hippocampus regions in mice. We designed three distinct case studies and implemented an ensemble feature selection approach through machine learning, also performing an analysis of distinct age-related datasets to unravel age-specific effects, showing differential gene expression patterns within each condition. Important evidence was reported, such as enrichment in central nervous system development and regulation of oligodendrocyte differentiation between the hippocampus and cortex of 6-month-old AD mice as well as regulation of epinephrine secretion and dendritic spine morphogenesis in 15-month-old AD mice. Our outcomes from all three of our case studies illustrate the capacity of machine learning strategies when applied to single-cell data, revealing critical insights into Alzheimer's disease.
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Affiliation(s)
- Marios G. Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece; (A.G.V.); (K.L.); (K.S.); (T.P.E.); (P.V.)
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9
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Deng X, Chen X, Luo Y, Que J, Chen L. Intratumor microbiome derived glycolysis-lactate signatures depicts immune heterogeneity in lung adenocarcinoma by integration of microbiomic, transcriptomic, proteomic and single-cell data. Front Microbiol 2023; 14:1202454. [PMID: 37664112 PMCID: PMC10469687 DOI: 10.3389/fmicb.2023.1202454] [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: 04/08/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Microbiome plays roles in lung adenocarcinoma (LUAD) development and anti-tumor treatment efficacy. Aberrant glycolysis in tumor might promote lactate production that alter tumor microenvironment, affecting microbiome, cancer cells and immune cells. We aimed to construct intratumor microbiome score to predict prognosis of LUAD patients and thoroughly investigate glycolysis and lactate signature's association with LUAD immune cell infiltration. Methods The Cancer Genome Atlas-LUAD (TCGA-LUAD) microbiome data was downloaded from cBioPortal and analyzed to examine its association with overall survival to create a prognostic scoring model. Gene Set Enrichment Analysis (GSEA) was used to find each group's major mechanisms involved. Our study then investigated the glycolysis and lactate pattern in LUAD patients based on 19 genes, which were correlated with the tumor microenvironment (TME) phenotypes and immunotherapy outcomes. We developed a glycolysis-lactate risk score and signature to accurately predict TME phenotypes, prognosis, and response to immunotherapy. Results Using the univariate Cox regression analysis, the abundance of 38 genera were identified with prognostic values and a lung-resident microbial score (LMS) was then developed from the TCGA-LUAD-microbiome dataset. Glycolysis hallmark pathway was significantly enriched in high-LMS group and three distinct glycolysis-lactate patterns were generated. Patients in Cluster1 exhibited unfavorable outcomes and might be insensitive to immunotherapy. Glycolysis-lactate score was constructed for predicting prognosis with high accuracy and validated in external cohorts. Gene signature was developed and this signature was elevated in epithelial cells especially in tumor mass on single-cell level. Finally, we found that the glycolysis-lactate signature levels were consistent with the malignancy of histological subtypes. Discussion Our study demonstrated that an 18-microbe prognostic score and a 19-gene glycolysis-lactate signature for predicting prognosis of LUAD patients. Our LMS, glycolysis-lactate score and glycolysis-lactate signature have potential roles in precision therapy of LUAD patients.
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Affiliation(s)
| | | | | | - Jun Que
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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10
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Chen S, Zhou Z, Wang Y, Chen S, Jiang J. Machine learning-based identification of cuproptosis-related markers and immune infiltration in severe community-acquired pneumonia. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:618-628. [PMID: 37279744 PMCID: PMC10363779 DOI: 10.1111/crj.13633] [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: 03/17/2023] [Revised: 04/24/2023] [Accepted: 05/06/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND Severe community-acquired pneumonia (SCAP) is one of the world's most common diseases and a major etiology of acute respiratory distress syndrome (ARDS). Cuproptosis is a novel form of regulated cell death that can occur in various diseases. METHODS Our study explored the degree of immune cell infiltration during the onset of severe CAP and identified potential biomarkers related to cuproptosis. Gene expression matrix was obtained from GEO database indexed GSE196399. Three machine learning algorithms were applied: The least absolute shrinkage and selection operator (LASSO), the random forest, and the support vector machine-recursive feature elimination (SVM-RFE). Immune cell infiltration was quantified by single-sample gene set enrichment analysis (ssGSEA) scoring. Nomogram was constructed to verify the applicability of using cuproptosis-related genes to predict the onset of severe CAP and its deterioration toward ARDS. RESULTS Nine cuproptosis-related genes were differentially expressed between the severe CAP group and the control group: ATP7B, DBT, DLAT, DLD, FDX1, GCSH, LIAS, LIPT1, and SLC31A1. All 13 cuproptosis-related genes were involved in immune cell infiltration. A three-gene diagnostic model was constructed to predict the onset of severe CAP: GCSH, DLD, and LIPT1. CONCLUSION Our study confirmed the involvement of the newly discovered cuproptosis-related genes in the progression of SCAP.
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Affiliation(s)
- Shuyang Chen
- Department of Pulmonary and Critical Care Medicine, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Zheng Zhou
- Department of Pulmonary and Critical Care Medicine, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Yajun Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Shujing Chen
- Department of Pulmonary and Critical Care Medicine, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jinjun Jiang
- Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan UniversityShanghaiChina
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11
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Liang P, Chen J, Yao L, Hao Z, Chang Q. A Deep Learning Approach for Prognostic Evaluation of Lung Adenocarcinoma Based on Cuproptosis-Related Genes. Biomedicines 2023; 11:biomedicines11051479. [PMID: 37239150 DOI: 10.3390/biomedicines11051479] [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: 04/25/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Lung adenocarcinoma represents a significant global health challenge. Despite advances in diagnosis and treatment, the prognosis remains poor for many patients. In this study, we aimed to identify cuproptosis-related genes and to develop a deep neural network model to predict the prognosis of lung adenocarcinoma. We screened differentially expressed genes from The Cancer Genome Atlas data through differential analysis of cuproptosis-related genes. We then used this information to establish a prognostic model using a deep neural network, which we validated using data from the Gene Expression Omnibus. Our deep neural network model incorporated nine cuproptosis-related genes and achieved an area under the curve of 0.732 in the training set and 0.646 in the validation set. The model effectively distinguished between distinct risk groups, as evidenced by significant differences in survival curves (p < 0.001), and demonstrated significant independence as a standalone prognostic predictor (p < 0.001). Functional analysis revealed differences in cellular pathways, the immune microenvironment, and tumor mutation burden between the risk groups. Furthermore, our model provided personalized survival probability predictions with a concordance index of 0.795 and identified the drug candidate BMS-754807 as a potentially sensitive treatment option for lung adenocarcinoma. In summary, we presented a deep neural network prognostic model for lung adenocarcinoma, based on nine cuproptosis-related genes, which offers independent prognostic capabilities. This model can be used for personalized predictions of patient survival and the identification of potential therapeutic agents for lung adenocarcinoma, which may ultimately improve patient outcomes.
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Affiliation(s)
- Pengchen Liang
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
- School of Microelectronics, Shanghai University, Shanghai 201800, China
| | - Jianguo Chen
- School of Software Engineering, Sun Yat-sen University, Zhuhai 528478, China
| | - Lei Yao
- School of Microelectronics, Shanghai University, Shanghai 201800, China
| | - Zezhou Hao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Qing Chang
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
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12
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Li D, Gao Z, Li Q, Liu X, Liu H. Cuproptosis-a potential target for the treatment of osteoporosis. Front Endocrinol (Lausanne) 2023; 14:1135181. [PMID: 37214253 PMCID: PMC10196240 DOI: 10.3389/fendo.2023.1135181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/10/2023] [Indexed: 05/24/2023] Open
Abstract
Osteoporosis is an age-related disease of bone metabolism marked by reduced bone mineral density and impaired bone strength. The disease causes the bones to weaken and break more easily. Osteoclasts participate in bone resorption more than osteoblasts participate in bone formation, disrupting bone homeostasis and leading to osteoporosis. Currently, drug therapy for osteoporosis includes calcium supplements, vitamin D, parathyroid hormone, estrogen, calcitonin, bisphosphates, and other medications. These medications are effective in treating osteoporosis but have side effects. Copper is a necessary trace element in the human body, and studies have shown that it links to the development of osteoporosis. Cuproptosis is a recently proposed new type of cell death. Copper-induced cell death regulates by lipoylated components mediated via mitochondrial ferredoxin 1; that is, copper binds directly to the lipoylated components of the tricarboxylic acid cycle, resulting in lipoylated protein accumulation and subsequent loss of iron-sulfur cluster proteins, leading to proteotoxic stress and eventually cell death. Therapeutic options for tumor disorders include targeting the intracellular toxicity of copper and cuproptosis. The hypoxic environment in bone and the metabolic pathway of glycolysis to provide energy in cells can inhibit cuproptosis, which may promote the survival and proliferation of various cells, including osteoblasts, osteoclasts, effector T cells, and macrophages, thereby mediating the osteoporosis process. As a result, our group tried to explain the relationship between the role of cuproptosis and its essential regulatory genes, as well as the pathological mechanism of osteoporosis and its effects on various cells. This study intends to investigate a new treatment approach for the clinical treatment of osteoporosis that is beneficial to the treatment of osteoporosis.
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Affiliation(s)
- Dinglin Li
- Department of Integrated Traditional Chinese and Western Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhonghua Gao
- Department of Geriatrics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Li
- Department of Integrated Traditional Chinese and Western Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangjie Liu
- Department of Geriatrics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Liu
- Department of Integrated Traditional Chinese and Western Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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13
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Sawant Dessai A, Kalhotra P, Novickis AT, Dasgupta S. Regulation of tumor metabolism by post translational modifications on metabolic enzymes. Cancer Gene Ther 2023; 30:548-558. [PMID: 35999357 PMCID: PMC9947196 DOI: 10.1038/s41417-022-00521-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/05/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Metabolic reprogramming is a hallmark of cancer development, progression, and metastasis. Several metabolic pathways such as glycolysis, tricarboxylic acid (TCA) cycle, lipid metabolism, and glutamine catabolism are frequently altered to support cancer growth. Importantly, the activity of the rate-limiting metabolic enzymes in these pathways are specifically modulated in cancer cells. This is achieved by transcriptional, translational, and post translational regulations that enhance the expression, activity, stability, and substrate sensitivity of the rate-limiting enzymes. These mechanisms allow the enzymes to retain increased activity supporting the metabolic needs of rapidly growing tumors, sustain their survival in the hostile tumor microenvironments and in the metastatic lesions. In this review, we primarily focused on the post translational modifications of the rate-limiting enzymes in the glucose and glutamine metabolism, TCA cycle, and fatty acid metabolism promoting tumor progression and metastasis.
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Affiliation(s)
- Abhisha Sawant Dessai
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Poonam Kalhotra
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Aaron T Novickis
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Subhamoy Dasgupta
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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14
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Wongkittichote P, Chhay C, Zerafati-Jahromi G, Weisenberg JL, Mian A, Jensen LT, Grange DK. Novel LIAS variants in a patient with epilepsy and profound developmental disabilities. Mol Genet Metab 2023; 138:107373. [PMID: 36680912 DOI: 10.1016/j.ymgme.2023.107373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Multiple mitochondrial enzymes employ lipoic acid as a coenzyme. Pathogenic variants in LIAS, encoding lipoic acid synthase (LIAS), are associated with autosomal recessive LIAS-related disorder (OMIM# 614462). This disorder is characterized by infantile-onset hypotonia, profound psychomotor delay, epileptic encephalopathy, nonketotic hyperglycinemia, and lactic acidosis. We present the case of a 20-year-old female who experienced developmental deficits at the age of 6 months and began to have seizures at 3 years of age. Exome sequencing revealed compound heterozygous novel variants in LIAS, designated c.277delC (p.Leu93Ter) and c.542A > T (p.Asp181Val). The p.Leu93Ter variant is predicted to cause loss of function due to the severe truncation of the encoded protein. To examine the p.Asp181Val variant, functional analysis was performed using Baker's yeast (Saccharomyces cerevisiae) lacking LIP5, the homologue of human LIAS. Wild-type LIAS promoted oxidative growth of the lip5∆ yeast strain. In contrast, lip5∆ yeast expressing p.Asp181Val exhibited poor growth, similar to known pathogenic variants, p.Asp215Glu and p.Met310Thr. Our work has expanded the phenotypic and genotypic spectrum of LIAS-related disorder and established the use of the yeast model as a system for functional study of novel missense variants in LIAS.
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Affiliation(s)
- Parith Wongkittichote
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chanseyha Chhay
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Gazelle Zerafati-Jahromi
- Division of Pediatric Neurology, Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Judith L Weisenberg
- Division of Pediatric Neurology, Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Ali Mian
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Laran T Jensen
- Division of Pediatric Neurology, Department of Neurology, Washington University School of Medicine, St Louis, MO, USA.
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA.
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15
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Zhu H, Wan Q, Tan J, Ouyang H, Pan X, Li M, Zhao Y. A novel prognostic signature of cuproptosis-related genes and the prognostic value of FDX1 in gliomas. Front Genet 2022; 13:992995. [PMID: 36579333 PMCID: PMC9792093 DOI: 10.3389/fgene.2022.992995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Background: Gliomas are the most common malignant tumors of the central nervous system, with extremely bad prognoses. Cuproptosis is a novel form of regulated cell death. The impact of cuproptosis-related genes on glioma development has not been reported. Methods: The TCGA, GTEx, and CGGA databases were used to retrieve transcriptomic expression data. We employed Cox's regressions to determine the associations between clinical factors and cuproptosis-related gene expression. Overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) were evaluated using the Kaplan-Meier method. We also used the least absolute shrinkage and selection operator (LASSO) regression technique. Results: The expression levels of all 10 CRGs varied considerably between glioma tumors and healthy tissues. In glioma patients, the levels of CDKN2A, FDX1, DLD, DLAT, LIAS, LIPT1, and PDHA1 were significantly associated with the OS, disease-specific survival, and progression-free interval. We used LASSO Cox's regression to create a prognostic model; the risk score was (0.882340) *FDX1 expression + (0.141089) *DLD expression + (-0.333875) *LIAS expression + (0.356469) *LIPT1 expression + (-0.123851) *PDHA1 expression. A high-risk score/signature was associated with poor OS (hazard ratio = 3.50, 95% confidence interval 2, -4.55, log-rank p < 0.001). Cox's regression revealed that the FDX1 level independently predicted prognosis; FDX1 may control immune cell infiltration of the tumor microenvironment. Conclusion: The CRG signature may be prognostic in glioma patients, and the FDX1 level may independently predict glioma prognosis. These data may afford new insights into treatment.
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Affiliation(s)
- HuaXin Zhu
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qinsi Wan
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jiacong Tan
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Hengyang Ouyang
- Huankui Academy, Nanchang University, Nanchang, Jiangxi, China
| | - Xinyi Pan
- Huankui Academy, Nanchang University, Nanchang, Jiangxi, China
| | - MeiHua Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China,*Correspondence: MeiHua Li, ; YeYu Zhao,
| | - YeYu Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China,*Correspondence: MeiHua Li, ; YeYu Zhao,
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16
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Liu Y, Luo G, Yan Y, Peng J. A pan-cancer analysis of copper homeostasis-related gene lipoyltransferase 1: Its potential biological functions and prognosis values. Front Genet 2022; 13:1038174. [PMID: 36330439 PMCID: PMC9623413 DOI: 10.3389/fgene.2022.1038174] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/05/2022] [Indexed: 11/23/2022] Open
Abstract
As a key copper homeostasis-related molecule, lipoyltransferase 1 (LIPT1) is an essential enzyme for the activation of mitochondrial 2-ketoacid dehydrogenase, participating in fatty acylation. However, the biological significances of LIPT1 in the pan-cancer are unclear. Here, we comprehensively analyzed the functional characteristics of LIPT1 in human cancers and its roles in immune response. We found that LIPT1 was down-regulated in some cancers. And LIPT1 overexpression is associated with favorable prognosis in these patients, such as breast cancer, clear cell renal cell carcinoma, ovarian cancer and gastric cancer. We also explored the mutational status and methylation levels of LIPT1 in human cancers. Gene enrichment analysis indicated that abnormally expressed LIPT1 was significantly associated with immune cells infiltration, such as B cells, CD8+ T cells and cancer-associated fibroblast cells. The result from single cell sequencing reflected the important roles of LIPT1 in the regulation of several biological behaviors of cancer cells, such as DNA damage response and cell apoptosis. Taken together, our research could provide a comprehensive overview about the significances of LIPT1 in human pan-cancer progression, prognosis and immune.
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Affiliation(s)
- Ying Liu
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Gengqiu Luo
- Department of Pathology, Xiangya Hospital, Basic School of Medicine, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yuanliang Yan,
| | - Jinwu Peng
- Department of Pathology, Xiangya Hospital, Basic School of Medicine, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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17
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Yan C, Niu Y, Ma L, Tian L, Ma J. System analysis based on the cuproptosis-related genes identifies LIPT1 as a novel therapy target for liver hepatocellular carcinoma. J Transl Med 2022; 20:452. [PMID: 36195876 PMCID: PMC9531858 DOI: 10.1186/s12967-022-03630-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Liver hepatocellular carcinoma (LIHC) ranks sixth among the most common types of cancer with a high mortality rate. Cuproptosis is a newly discovered type of cell death in tumor, which is characterized by accumulation of intracellular copper leading to the aggregation of mitochondrial lipoproteins and destabilization of proteins. Thus, understanding the exact effects of cuproptosis-related genes in LIHC and determining their prognosticvalue is critical. However, the prognostic model of LIHC based on cuproptosis-related genes has not been reported. METHODS Firstly, we downloaded transcriptome data and clinical information of LIHC patients from TCGA and GEO (GSE76427), respectively. We then extracted the expression of cuproptosis-related genes and established a prognostic model by lasso cox regression analysis. Afterwards, the prediction performance of the model was evaluated by Kaplan-Meier survival analysis and receiver operating characteristic curve (ROC). Then, the prognostic model and the expression levels of the three genes were validated using the dataset from GEO. Subsequently, we divided LIHC patients into two subtypes by non-negative matrix factorization (NMF) classification and performed survival analysis. We constructed a Sankey plot linking different subtypes and prognostic models. Next, we calculate the drug sensitivity of each sample from patients in the high-risk group and low-risk group by the R package pRRophetic. Finally, we verified the function of LIPT1 in LIHC. RESULTS Using lasso cox regression analysis, we developed a prognostic risk model based on three cuproptosis-related genes (GCSH, LIPT1 and CDKN2A). Both in the training and in the test sets, the overall survival (OS) of LIHC patients in the low-risk group was significantly longer than that in the high-risk group. By performing NMF cluster, we identified two molecular subtypes of LIHC (C1 and C2), with C1 subtype having significantly longer OS and PFS than C2 subtype. The ROC analysis indicated that our model had a precisely predictive capacity for patients with LIHC. The multivariate Cox regression analysis indicated that the risk score is an independent predictor. Subsequently, we identified 71 compounds with IC50 values that differed between the high-risk and low-risk groups. Finally, we determined that knockdown of LIPT1 gene expression inhibited proliferation and invasion of hepatoma cells. CONCLUSION In this study, we developed a novel prognostic model for hepatocellular carcinoma based on cuproptosis-related genes that can effectively predict the prognosis of LIHC patients. The model may be helpful for clinicians to make clinical decisions for patients with LIHC and provide valuable insights for individualized treatment. Two distinct subtypes of LIHC were identified based on cuproptosis-related genes, with different prognosis and immune characteristics. In addition, we verified that LIPT1 may promote proliferation, invasion and migration of LIHC cells. LIPT1 might be a new potential target for therapy of LIHC.
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Affiliation(s)
- Cheng Yan
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, Henan China
| | - Yandie Niu
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, Henan China
| | - Liukai Ma
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, Henan China
| | - Lifang Tian
- grid.495434.b0000 0004 1797 4346School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, Henan China
| | - Jiahao Ma
- School of Pharmacy, Key Laboratory of Nano-Carbon Modified Film Technology of Henan Province, Diagnostic Laboratory of Animal Diseases, Xinxiang University, Xinxiang, Henan, China.
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18
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Bai WD, Liu JY, Li M, Yang X, Wang YL, Wang GJ, Li SC. A Novel Cuproptosis-Related Signature Identified DLAT as a Prognostic Biomarker for Hepatocellular Carcinoma Patients. World J Oncol 2022; 13:299-310. [PMID: 36406193 PMCID: PMC9635792 DOI: 10.14740/wjon1529] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common type of liver cancers, with more than a million cases per year by 2025. Cuproptosis is a novel form of programmed cell death, and is caused by mitochondrial lipoylation and destabilization of iron-sulfur proteins triggered by copper, which was considered as a key player in various biological processes. However, the roles of cuproptosis-related genes (CRGs) in HCC remain largely unknown. METHODS In the present study, we constructed and validated a four CRGs signature for predicting the overall survival (OS) of HCC patients in both The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. RESULTS Patients with high CRGs risk score showed shorter OS than those with low CRGs risk score. Functional analysis suggested that the CRGs-based prognostic signature was associated with metabolism remodeling which facilitated liver cancer progression. In addition, reduced infiltration of CD8+ T cells and increased macrophages were found in HCCs from patients with high CRGs risk score. As one of the four CRGs, higher expression of dihydrolipoamide S-acetyltransferase (DLAT) was accompanied by higher expression of program death ligand 1 (PD-L1) in HCC. Further, we confirmed that DLAT was up-regulated and correlated with poor prognosis in a clinical HCC cohort. CONCLUSION In conclusion, our study constructed a four CRGs signature prognostic model and identified DLAT as an independent prognostic factor for HCC, thus providing new clues for understanding the association between cuproptosis and HCC.
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Affiliation(s)
- Wen Dong Bai
- Department of Hematology, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China,These authors contributed equally to this work
| | - Jun Yu Liu
- Department of Gastroenterology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510060, China,These authors contributed equally to this work
| | - Miao Li
- School of Rehabilitation Medicine, Xinjiang Medical University, Urumqi, Xinjiang, China,These authors contributed equally to this work
| | - Xi Yang
- Department of Medical Service, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China
| | - Yu Lan Wang
- Depatment of Pathology, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China
| | - Guang Jun Wang
- Department of Medical Service, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China,Corresponding Author: Guang Jun Wang, Department of Medical Service, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China. ; Shi Chao Li, Department of Pathology, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China.
| | - Shi Chao Li
- Depatment of Pathology, General Hospital of Xinjiang Military Command, Urumqi, Xinjiang, China,Corresponding Author: Guang Jun Wang, Department of Medical Service, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China. ; Shi Chao Li, Department of Pathology, General Hospital of Xinjiang Military Command, 830000 Urumqi, Xinjiang, China.
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19
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Lv H, Liu X, Zeng X, Liu Y, Zhang C, Zhang Q, Xu J. Comprehensive Analysis of Cuproptosis-Related Genes in Immune Infiltration and Prognosis in Melanoma. Front Pharmacol 2022; 13:930041. [PMID: 35837286 PMCID: PMC9273972 DOI: 10.3389/fphar.2022.930041] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 12/16/2022] Open
Abstract
Skin cutaneous melanoma (SKCM, hereafter referred to as melanoma) is the most lethal skin cancer with increasing incidence. Regulated cell death plays an important role in tumorigenesis and serves as an important target for almost all treatment strategies. Cuproptosis is the most recently identified copper-dependent regulated cell death form that relies on mitochondria respiration. However, its role in tumorigenesis remains unknown. The correlation of cuproptosis-related genes with tumor prognosis is far to be understood, either. In the present study, we explored the correlation between cuproptosis-related genes with the prognosis of melanoma by accessing and analyzing a public database and found 11 out 12 genes were upregulated in melanoma tissues and three genes (LIPT1, PDHA1, and SLC31A1) have predictive value for the prognosis. The subgroup of melanoma patients with higher cuproptosis-related gene expression showed longer overall survival than those with lower gene expression. We chose LIPT1 for further exploration. LIPT1 expression was increased in melanoma biopsies and was an independent favorable prognostic indicator for melanoma patients. Moreover, LIPT1 expression was positively correlated with PD-L1 expression and negatively associated with Treg cell infiltration. The melanoma patients with higher LIPT1 expression showed longer overall survival than those with lower LIPT1 expression after receiving immunotherapy, indicating the prognostic predictive value of LIPT1. Finally, a pan-cancer analysis indicated that LIPT1 was differentially expressed in diverse cancers as compared to normal tissues and correlated with the expression of multiple immune checkpoints, especially PD-L1. It could serve as a favorable prognosis indicator in some cancer types. In conclusion, our study demonstrated the prognostic value of cuproptosis-related genes, especially LIPT1, in melanoma, and revealed the correlation between LIPT1 expression and immune infiltration in melanoma, thus providing new clues on the prognostic assessment of melanoma patients and providing a new target for the immunotherapy of melanoma.
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Affiliation(s)
- Haozhen Lv
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuanhao Zeng
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yating Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Canjing Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qi Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Qi Zhang, ; Jinhua Xu,
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Dermatology, Shanghai, China
- *Correspondence: Qi Zhang, ; Jinhua Xu,
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Hou L, Guo S, Ding D, Du B, Wang X. Neuroendocrinal and molecular basis of flight performance in locusts. Cell Mol Life Sci 2022; 79:325. [PMID: 35644827 PMCID: PMC11071871 DOI: 10.1007/s00018-022-04344-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/22/2022] [Accepted: 05/02/2022] [Indexed: 11/03/2022]
Abstract
Insect flight is a complex physiological process that involves sensory and neuroendocrinal control, efficient energy metabolism, rhythmic muscle contraction, and coordinated wing movement. As a classical study model for insect flight, locusts have attracted much attention from physiologists, behaviorists, and neuroendocrinologists over the past decades. In earlier research, scientists made extensive efforts to explore the hormone regulation of metabolism related to locust flight; however, this work was hindered by the absence of molecular and genetic tools. Recently, the rapid development of molecular and genetic tools as well as multi-omics has greatly advanced our understanding of the metabolic, molecular, and neuroendocrinal basis of long-term flight in locusts. Novel neural and molecular factors modulating locust flight and their regulatory mechanisms have been explored. Moreover, the molecular mechanisms underlying phase-dependent differences in locust flight have also been revealed. Here, we provide a systematic review of locust flight physiology, with emphasis on recent advances in the neuroendocrinal, genetic, and molecular basis. Future research directions and potential challenges are also addressed.
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Affiliation(s)
- Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ding Ding
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baozhen Du
- Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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21
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Anthony RM, MacLeay JM, Gross KL. Alpha-Lipoic Acid as a Nutritive Supplement for Humans and Animals: An Overview of Its Use in Dog Food. Animals (Basel) 2021; 11:ani11051454. [PMID: 34069383 PMCID: PMC8158713 DOI: 10.3390/ani11051454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary A review of human and animal studies involving alpha-lipoic acid supplementation was conducted to determine the utility of alpha-lipoic acid in dog food. The present literature shows that alpha-lipoic acid has utility as a nutritive additive at concentrations of 2.7–4.94 mg/kg body weight/day and improves antioxidant capacity in dogs. Abstract Alpha-lipoic acid (a-LA) is used as a nutritive additive in dog food. Therefore, we performed a systematic review of studies published to date in PubMed, Google Scholar, Cochrane Library and MedlinePlus involving alpha-lipoic acid supplementation, which included human clinical trials as well as animal studies, to evaluate its utility as a supplement in foods for healthy, adult dogs. While an upper limit of alpha-lipoic acid intake in humans has not been conclusively determined, the levels for oral intake of a-LA have been better defined in animals, and distinct differences based on species have been described. The maximum tolerated oral dose of a-LA in dogs has been reported as 126 mg/kg body weight and the LD50 as 400 to 500 mg/kg body weight. The antioxidant, anti-inflammatory and neuro-protective benefits of alpha-lipoic acid in dogs were observed at concentrations much lower than the maximum tolerated dose or proposed LD50. At concentrations of 2.7–4.94 mg/kg body weight/day, alpha-lipoic acid is well tolerated and posed no health risks to dogs while providing improved antioxidant capacity. This review thereby supports the utility of alpha-lipoic acid as an effective nutritive additive in dog food.
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22
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Guo S, Yang P, Liang B, Zhou F, Hou L, Kang L, Wang X. Aging features of the migratory locust at physiological and transcriptional levels. BMC Genomics 2021; 22:257. [PMID: 33838645 PMCID: PMC8037904 DOI: 10.1186/s12864-021-07585-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background Non-Drosophila insects provide diverse aging types and important complementary systems for studies of aging biology. However, little attention has been paid to the special roles of non-Drosophila insects in aging research. Here, the aging-related features of the migratory locust, Locusta migratoria, were determined at the physiological, cellular, and transcriptional levels. Results In physiological assessments, the flight performance and sperm state of locusts displayed clear aging-related decline in male adults. Transcriptional analyses demonstrated locusts have similar aging-related genes with model species. However, different from those of Drosophila and mammals, the organ-specific aging transcriptional features of locusts were characterized by intensive expression changes in flight muscle and fat body and little transcriptional changes in brain. The predominant transcriptional characteristics of flight muscle and fat body aging were changes in expression of mitochondrion-related genes and detoxification and phagocytosis genes, respectively. Cellular assessments revealed the incidence of mitochondrial abnormalities significantly increased in aged flight muscle, and apoptotic signals and nuclear abnormalities were enhanced in aged fat body but not in brain. In addition, some well-known aging genes and locust aging-related genes (i.e., IAP1, PGRP-SA, and LIPT1), whose roles in aging regulation were rarely reported, were demonstrated to affect lifespan, metabolism, and flight ability of locusts after RNAi. Conclusion This study revealed multi-level aging signatures of locust, thus laying a foundation for further investigation of aging mechanisms in this famous insect in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07585-3.
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Affiliation(s)
- Siyuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bo Liang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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23
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Altered Metabolic Flexibility in Inherited Metabolic Diseases of Mitochondrial Fatty Acid Metabolism. Int J Mol Sci 2021; 22:ijms22073799. [PMID: 33917608 PMCID: PMC8038842 DOI: 10.3390/ijms22073799] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 12/14/2022] Open
Abstract
In general, metabolic flexibility refers to an organism's capacity to adapt to metabolic changes due to differing energy demands. The aim of this work is to summarize and discuss recent findings regarding variables that modulate energy regulation in two different pathways of mitochondrial fatty metabolism: β-oxidation and fatty acid biosynthesis. We focus specifically on two diseases: very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) and malonyl-CoA synthetase deficiency (acyl-CoA synthetase family member 3 (ACSF3)) deficiency, which are both characterized by alterations in metabolic flexibility. On the one hand, in a mouse model of VLCAD-deficient (VLCAD-/-) mice, the white skeletal muscle undergoes metabolic and morphologic transdifferentiation towards glycolytic muscle fiber types via the up-regulation of mitochondrial fatty acid biosynthesis (mtFAS). On the other hand, in ACSF3-deficient patients, fibroblasts show impaired mitochondrial respiration, reduced lipoylation, and reduced glycolytic flux, which are compensated for by an increased β-oxidation rate and the use of anaplerotic amino acids to address the energy needs. Here, we discuss a possible co-regulation by mtFAS and β-oxidation in the maintenance of energy homeostasis.
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24
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Broomfield AA, Padidela R, Wilkinson S. Pulmonary Manifestations of Endocrine and Metabolic Diseases in Children. Pediatr Clin North Am 2021; 68:81-102. [PMID: 33228944 DOI: 10.1016/j.pcl.2020.09.011] [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] [Indexed: 11/25/2022]
Abstract
Advances in technology, methodology, and deep phenotyping are increasingly driving the understanding of the pathologic basis of disease. Improvements in patient identification and treatment are impacting survival. This is true in endocrinology and inborn errors of metabolism, where disease-modifying therapies are developing. Inherent to this evolution is the increasing awareness of the respiratory manifestations of these rare diseases. This review updates clinicians, stratifying diseases spirometerically; pulmonary hypertension and diseases with a predisposition to recurrent pulmonary infection are discussed. This division is artificial; many diseases have multiple pathologic effects on respiration. This review does not cover the impact of obesity.
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Affiliation(s)
- Alexander A Broomfield
- Willink Biochemical Genetics Unit, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
| | - Raja Padidela
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK; Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Stuart Wilkinson
- Respiratory Department Royal Manchester Children's Hospital, Manchester University, NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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25
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Pietikäinen LP, Rahman MT, Hiltunen JK, Dieckmann CL, Kastaniotis AJ. Genetic dissection of the mitochondrial lipoylation pathway in yeast. BMC Biol 2021; 19:14. [PMID: 33487163 PMCID: PMC7831266 DOI: 10.1186/s12915-021-00951-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/06/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lipoylation of 2-ketoacid dehydrogenases is essential for mitochondrial function in eukaryotes. While the basic principles of the lipoylation processes have been worked out, we still lack a thorough understanding of the details of this important post-translational modification pathway. Here we used yeast as a model organism to characterize substrate usage by the highly conserved eukaryotic octanoyl/lipoyl transferases in vivo and queried how amenable the lipoylation system is to supplementation with exogenous substrate. RESULTS We show that the requirement for mitochondrial fatty acid synthesis to provide substrates for lipoylation of the 2-ketoacid dehydrogenases can be bypassed by supplying the cells with free lipoic acid (LA) or octanoic acid (C8) and a mitochondrially targeted fatty acyl/lipoyl activating enzyme. We also provide evidence that the S. cerevisiae lipoyl transferase Lip3, in addition to transferring LA from the glycine cleavage system H protein to the pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase (KGD) E2 subunits, can transfer this cofactor from the PDH complex to the KGD complex. In support of yeast as a model system for human metabolism, we demonstrate that the human octanoyl/lipoyl transferases can substitute for their counterparts in yeast to support respiratory growth and protein lipoylation. Like the wild-type yeast enzyme, the human lipoyl transferase LIPT1 responds to LA supplementation in the presence of the activating enzyme LplA. CONCLUSIONS In the yeast model system, the eukaryotic lipoylation pathway can use free LA and C8 as substrates when fatty/lipoic acid activating enzymes are targeted to mitochondria. Lip3 LA transferase has a wider substrate specificity than previously recognized. We show that these features of the lipoylation mechanism in yeast are conserved in mammalian mitochondria. Our findings have important implications for the development of effective therapies for the treatment of LA or mtFAS deficiency-related disorders.
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Affiliation(s)
- Laura P Pietikäinen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland
| | - M Tanvir Rahman
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland
| | - Carol L Dieckmann
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, FI-90014, Oulu, Finland.
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26
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Ma Q, Liu Y, Fang H, Wang P, Ahammed GJ, Zai W, Shi K. An Essential Role of Mitochondrial α-Ketoglutarate Dehydrogenase E2 in the Basal Immune Response Against Bacterial Pathogens in Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:579772. [PMID: 33193523 PMCID: PMC7661389 DOI: 10.3389/fpls.2020.579772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/18/2020] [Indexed: 06/01/2023]
Abstract
Plants intensely modulate respiration when pathogens attack, but the function of mitochondrial respiration-related genes in plant-bacteria interaction is largely unclear. Here, the functions of α-ketoglutarate dehydrogenase (α-kGDH) E2 subunit and alternative oxidase (AOX) were investigated in the interaction between tomato and the virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst). Pst inoculation suppressed the transcript abundance of α-kGDH E2, but enhanced AOX expression and salicylic acid (SA) accumulation. Gene silencing and transient overexpression approaches revealed that plant susceptibility to Pst was significantly reduced by silencing α-kGDH E2 in tomato, but increased by overexpressing α-kGDH E2 in Nicotiana benthamiana, whereas silencing or overexpressing of AOX1a did not affect plant defense. Moreover, silencing octanoyltransferase (LIP2), engaged in the lipoylation of α-kGDH E2, significantly reduced disease susceptibility and hydrogen peroxide accumulation. Use of transgenic NahG tomato plants that cannot accumulate SA as well as the exogenous SA application experiment evidenced that α-kGDH E2 acts downstream of SA defense pathway. These results demonstrate tomato α-kGDH E2 plays a negative role in plant basal defense against Pst in an AOX-independent pathway but was associated with lipoylation and SA defense pathways. The findings help to elucidate the mechanisms of mitochondria-involved plant basal immunity.
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Affiliation(s)
- Qiaomei Ma
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yaru Liu
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Hanmo Fang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Ping Wang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Golam Jalal Ahammed
- College of Forestry, Henan University of Science and Technology, Luoyang, China
| | - Wenshan Zai
- Wenzhou Vocational College of Science & Technology, Wenzhou, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, China
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27
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Increased antioxidant response in medium-chain acyl-CoA dehydrogenase deficiency: does lipoic acid have a protective role? Pediatr Res 2020; 88:556-564. [PMID: 32045933 DOI: 10.1038/s41390-020-0801-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/30/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency (MCADD) is the most frequent fatty acid oxidation (FAO) defect in humans. MCAD-deficient fibroblasts are more resistant to oxidative stress-induced cell death than other FAO defects and healthy controls. METHODS Herein we investigate the antioxidant response and mitochondrial function in fibroblasts from MCAD-deficient patients (c.985 A>G/c.985 A>G) and healthy controls. RESULTS MCAD-deficient fibroblasts showed increased level of mitochondrial superoxide, while lipids were less oxidatively damaged, and higher amount of manganese superoxide dismutase were detected compared to healthy controls, showing forceful antioxidant system in MCADD. We showed increased maximal respiration and reserve capacity in MCAD-deficient fibroblasts compared to controls, indicating more capacity through the tricarboxylic acid (TCA) cycle and subsequently respiratory chain. This led us to study the pyruvate dehydrogenase complex (PDC), the key enzyme in the glycolysis releasing acetyl-CoA to the TCA cycle. MCAD-deficient fibroblasts displayed not only significantly increased PDC but also increased lipoylated PDC protein levels compared to healthy controls. CONCLUSIONS Based on these findings, we raise the interesting hypothesis that increased PDC-bound lipoic acid, synthesized from accumulated octanoic acid in MCADD, may affect the cellular antioxidant pool in MCADD.
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28
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Lavatelli A, de Mendoza D, Mansilla MC. Defining Caenorhabditis elegans as a model system to investigate lipoic acid metabolism. J Biol Chem 2020; 295:14973-14986. [PMID: 32843480 DOI: 10.1074/jbc.ra120.013760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/22/2020] [Indexed: 11/06/2022] Open
Abstract
Lipoic acid (LA) is a sulfur-containing cofactor that covalently binds to a variety of cognate enzymes that are essential for redox reactions in all three domains of life. Inherited mutations in the enzymes that make LA, namely lipoyl synthase, octanoyltransferase, and amidotransferase, result in devastating human metabolic disorders. Unfortunately, because many aspects of this essential pathway are still obscure, available treatments only serve to alleviate symptoms. We envisioned that the development of an organismal model system might provide new opportunities to interrogate LA biochemistry, biology, and physiology. Here we report our investigations on three Caenorhabditis elegans orthologous proteins involved in this post-translational modification. We established that M01F1.3 is a lipoyl synthase, ZC410.7 an octanoyltransferase, and C45G3.3 an amidotransferase. Worms subjected to RNAi against M01F1.3 and ZC410.7 manifest larval arrest in the second generation. The arrest was not rescued by LA supplementation, indicating that endogenous synthesis of LA is essential for C. elegans development. Expression of the enzymes M01F1.3, ZC410.7, and C45G3.3 completely rescue bacterial or yeast mutants affected in different steps of the lipoylation pathway, indicating functional overlap. Thus, we demonstrate that, similarly to humans, C. elegans is able to synthesize LA de novo via a lipoyl-relay pathway, and suggest that this nematode could be a valuable model to dissect the role of protein mislipoylation and to develop new therapies.
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Affiliation(s)
- Antonela Lavatelli
- Laboratory of Microbial Physiology, Institute of Molecular and Cellular Biology of Rosario, National Scientific and Technical Research Council, Rosario, Santa Fe, Argentina; Department of Microbiology, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Santa Fe, Argentina
| | - Diego de Mendoza
- Laboratory of Microbial Physiology, Institute of Molecular and Cellular Biology of Rosario, National Scientific and Technical Research Council, Rosario, Santa Fe, Argentina; Department of Microbiology, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Santa Fe, Argentina
| | - María Cecilia Mansilla
- Laboratory of Microbial Physiology, Institute of Molecular and Cellular Biology of Rosario, National Scientific and Technical Research Council, Rosario, Santa Fe, Argentina; Department of Microbiology, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Santa Fe, Argentina.
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29
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Bailey PSJ, Ortmann BM, Martinelli AW, Houghton JW, Costa ASH, Burr SP, Antrobus R, Frezza C, Nathan JA. ABHD11 maintains 2-oxoglutarate metabolism by preserving functional lipoylation of the 2-oxoglutarate dehydrogenase complex. Nat Commun 2020; 11:4046. [PMID: 32792488 PMCID: PMC7426941 DOI: 10.1038/s41467-020-17862-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
2-oxoglutarate (2-OG or α-ketoglutarate) relates mitochondrial metabolism to cell function by modulating the activity of 2-OG dependent dioxygenases involved in the hypoxia response and DNA/histone modifications. However, metabolic pathways that regulate these oxygen and 2-OG sensitive enzymes remain poorly understood. Here, using CRISPR Cas9 genome-wide mutagenesis to screen for genetic determinants of 2-OG levels, we uncover a redox sensitive mitochondrial lipoylation pathway, dependent on the mitochondrial hydrolase ABHD11, that signals changes in mitochondrial 2-OG metabolism to 2-OG dependent dioxygenase function. ABHD11 loss or inhibition drives a rapid increase in 2-OG levels by impairing lipoylation of the 2-OG dehydrogenase complex (OGDHc)-the rate limiting step for mitochondrial 2-OG metabolism. Rather than facilitating lipoate conjugation, ABHD11 associates with the OGDHc and maintains catalytic activity of lipoyl domain by preventing the formation of lipoyl adducts, highlighting ABHD11 as a regulator of functional lipoylation and 2-OG metabolism.
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Affiliation(s)
- Peter S J Bailey
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Brian M Ortmann
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Anthony W Martinelli
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Jack W Houghton
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Stephen P Burr
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - James A Nathan
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK.
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30
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Kastaniotis AJ, Autio KJ, R Nair R. Mitochondrial Fatty Acids and Neurodegenerative Disorders. Neuroscientist 2020; 27:143-158. [PMID: 32644907 DOI: 10.1177/1073858420936162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fatty acids in mitochondria, in sensu stricto, arise either as β-oxidation substrates imported via the carnitine shuttle or through de novo synthesis by the mitochondrial fatty acid synthesis (mtFAS) pathway. Defects in mtFAS or processes involved in the generation of the mtFAS product derivative lipoic acid (LA), including iron-sulfur cluster synthesis required for functional LA synthase, have emerged only recently as etiology for neurodegenerative disease. Intriguingly, mtFAS deficiencies very specifically affect CNS function, while LA synthesis and attachment defects have a pleiotropic presentation beyond neurodegeneration. Typical mtFAS defect presentations include optical atrophy, as well as basal ganglia defects associated with dystonia. The phenotype display of patients with mtFAS defects can resemble the presentation of disorders associated with coenzyme A (CoA) synthesis. A recent publication links these processes together based on the requirement of CoA for acyl carrier protein maturation. MtFAS defects, CoA synthesis- as well as Fe-S cluster-deficiencies share lack of LA as a common symptom.
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Affiliation(s)
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Remya R Nair
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, UK
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31
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Ni M, Solmonson A, Pan C, Yang C, Li D, Notzon A, Cai L, Guevara G, Zacharias LG, Faubert B, Vu HS, Jiang L, Ko B, Morales NM, Pei J, Vale G, Rakheja D, Grishin NV, McDonald JG, Gotway GK, McNutt MC, Pascual JM, DeBerardinis RJ. Functional Assessment of Lipoyltransferase-1 Deficiency in Cells, Mice, and Humans. Cell Rep 2020; 27:1376-1386.e6. [PMID: 31042466 PMCID: PMC7351313 DOI: 10.1016/j.celrep.2019.04.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 02/21/2019] [Accepted: 03/28/2019] [Indexed: 12/31/2022] Open
Abstract
Inborn errors of metabolism (IEMs) link metabolic defects to human phenotypes. Modern genomics has accelerated IEM discovery, but assessing the impact of genomic variants is still challenging. Here, we integrate genomics and metabolomics to identify a cause of lactic acidosis and epilepsy. The proband is a compound heterozygote for variants in LIPT1, which encodes the lipoyltransferase required for 2-ketoacid dehydrogenase (2KDH) function. Metabolomics reveals abnormalities in lipids, amino acids, and 2-hydroxyglutarate consistent with loss of multiple 2KDHs. Homozygous knockin of a LIPT1 mutation reduces 2KDH lipoylation in utero and results in embryonic demise. In patient fibroblasts, defective 2KDH lipoylation and function are corrected by wild-type, but not mutant, LIPT1 alleles. Isotope tracing reveals that LIPT1 supports lipogenesis and balances oxidative and reductive glutamine metabolism. Altogether, the data extend the role of LIPT1 in metabolic regulation and demonstrate how integrating genomics and metabolomics can uncover broader aspects of IEM pathophysiology.
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Affiliation(s)
- Min Ni
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ashley Solmonson
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunxiao Pan
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chendong Yang
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dan Li
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashley Notzon
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ling Cai
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gerardo Guevara
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brandon Faubert
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hieu S Vu
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Jiang
- Department of Molecular and Cellular Endocrinology, City of Hope, Duarte, CA 91010, USA
| | - Bookyung Ko
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Noriko Merida Morales
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jimin Pei
- Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gonçalo Vale
- Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dinesh Rakheja
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nick V Grishin
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Garrett K Gotway
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Markey C McNutt
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Juan M Pascual
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Vemuri S, Srivastava R, Mir Q, Hashemikhabir S, Dong XC, Janga SC. SliceIt: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome. Methods 2020; 178:104-113. [PMID: 31494246 PMCID: PMC7056568 DOI: 10.1016/j.ymeth.2019.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/25/2019] [Accepted: 09/01/2019] [Indexed: 12/26/2022] Open
Abstract
Several protein-RNA cross linking protocols have been established in recent years to delineate the molecular interaction of an RNA Binding Protein (RBP) and its target RNAs. However, functional dissection of the role of the RBP binding sites in modulating the post-transcriptional fate of the target RNA remains challenging. CRISPR/Cas9 genome editing system is being commonly employed to perturb both coding and noncoding regions in the genome. With the advancements in genome-scale CRISPR/Cas9 screens, it is now possible to not only perturb specific binding sites but also probe the global impact of protein-RNA interaction sites across cell types. Here, we present SliceIt (http://sliceit.soic.iupui.edu/), a database of in silico sgRNA (single guide RNA) library to facilitate conducting such high throughput screens. SliceIt comprises of ~4.8 million unique sgRNAs with an estimated range of 2-8 sgRNAs designed per RBP binding site, for eCLIP experiments of >100 RBPs in HepG2 and K562 cell lines from the ENCODE project. SliceIt provides a user friendly environment, developed using advanced search engine framework, Elasticsearch. It is available in both table and genome browser views facilitating the easy navigation of RBP binding sites, designed sgRNAs, exon expression levels across 53 human tissues along with prevalence of SNPs and GWAS hits on binding sites. Exon expression profiles enable examination of locus specific changes proximal to the binding sites. Users can also upload custom tracks of various file formats directly onto genome browser, to navigate additional genomic features in the genome and compare with other types of omics profiles. All the binding site-centric information is dynamically accessible via "search by gene", "search by coordinates" and "search by RBP" options and readily available to download. Validation of the sgRNA library in SliceIt was performed by selecting RBP binding sites in Lipt1 gene and designing sgRNAs. Effect of CRISPR/Cas9 perturbations on the selected binding sites in HepG2 cell line, was confirmed based on altered proximal exon expression levels using qPCR, further supporting the utility of the resource to design experiments for perturbing protein-RNA interaction networks. Thus, SliceIt provides a one-stop repertoire of guide RNA library to perturb RBP binding sites, along with several layers of functional information to design both low and high throughput CRISPR/Cas9 screens, for studying the phenotypes and diseases associated with RBP binding sites.
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Affiliation(s)
- Sasank Vemuri
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Seyedsasan Hashemikhabir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - X Charlie Dong
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, United States
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, United States; Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, United States.
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Cronan JE. Progress in the Enzymology of the Mitochondrial Diseases of Lipoic Acid Requiring Enzymes. Front Genet 2020; 11:510. [PMID: 32508887 PMCID: PMC7253636 DOI: 10.3389/fgene.2020.00510] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Three human mitochondrial diseases that directly affect lipoic acid metabolism result from heterozygous missense and nonsense mutations in the LIAS, LIPT1, and LIPT2 genes. However, the functions of the proteins encoded by these genes in lipoic acid metabolism remained uncertain due to a lack of biochemical analysis at the enzyme level. An exception was the LIPT1 protein for which a perplexing property had been reported, a ligase lacking the ability to activate its substrate. This led to several models, some contradictory, to accommodate the role of LIPT1 protein activity in explaining the phenotypes of the afflicted neonatal patients. Recent evidence indicates that this LIPT1 protein activity is a misleading evolutionary artifact and that the physiological role of LIPT1 is in transfer of lipoic acid moieties from one protein to another. This and other new biochemical data now define a straightforward pathway that fully explains each of the human disorders specific to the assembly of lipoic acid on its cognate enzyme proteins.
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Affiliation(s)
- John E Cronan
- B103 Chemical and Life Sciences Laboratory, Departments of Microbiology and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Yu Q, Tai YY, Tang Y, Zhao J, Negi V, Culley MK, Pilli J, Sun W, Brugger K, Mayr J, Saggar R, Saggar R, Wallace WD, Ross DJ, Waxman AB, Wendell SG, Mullett SJ, Sembrat J, Rojas M, Khan OF, Dahlman JE, Sugahara M, Kagiyama N, Satoh T, Zhang M, Feng N, Gorcsan J, Vargas SO, Haley KJ, Kumar R, Graham BB, Langer R, Anderson DG, Wang B, Shiva S, Bertero T, Chan SY. BOLA (BolA Family Member 3) Deficiency Controls Endothelial Metabolism and Glycine Homeostasis in Pulmonary Hypertension. Circulation 2020; 139:2238-2255. [PMID: 30759996 DOI: 10.1161/circulationaha.118.035889] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Deficiencies of iron-sulfur (Fe-S) clusters, metal complexes that control redox state and mitochondrial metabolism, have been linked to pulmonary hypertension (PH), a deadly vascular disease with poorly defined molecular origins. BOLA3 (BolA Family Member 3) regulates Fe-S biogenesis, and mutations in BOLA3 result in multiple mitochondrial dysfunction syndrome, a fatal disorder associated with PH. The mechanistic role of BOLA3 in PH remains undefined. METHODS In vitro assessment of BOLA3 regulation and gain- and loss-of-function assays were performed in human pulmonary artery endothelial cells using siRNA and lentiviral vectors expressing the mitochondrial isoform of BOLA3. Polymeric nanoparticle 7C1 was used for lung endothelium-specific delivery of BOLA3 siRNA oligonucleotides in mice. Overexpression of pulmonary vascular BOLA3 was performed by orotracheal transgene delivery of adeno-associated virus in mouse models of PH. RESULTS In cultured hypoxic pulmonary artery endothelial cells, lung from human patients with Group 1 and 3 PH, and multiple rodent models of PH, endothelial BOLA3 expression was downregulated, which involved hypoxia inducible factor-2α-dependent transcriptional repression via histone deacetylase 1-mediated histone deacetylation. In vitro gain- and loss-of-function studies demonstrated that BOLA3 regulated Fe-S integrity, thus modulating lipoate-containing 2-oxoacid dehydrogenases with consequent control over glycolysis and mitochondrial respiration. In contexts of siRNA knockdown and naturally occurring human genetic mutation, cellular BOLA3 deficiency downregulated the glycine cleavage system protein H, thus bolstering intracellular glycine content. In the setting of these alterations of oxidative metabolism and glycine levels, BOLA3 deficiency increased endothelial proliferation, survival, and vasoconstriction while decreasing angiogenic potential. In vivo, pharmacological knockdown of endothelial BOLA3 and targeted overexpression of BOLA3 in mice demonstrated that BOLA3 deficiency promotes histological and hemodynamic manifestations of PH. Notably, the therapeutic effects of BOLA3 expression were reversed by exogenous glycine supplementation. CONCLUSIONS BOLA3 acts as a crucial lynchpin connecting Fe-S-dependent oxidative respiration and glycine homeostasis with endothelial metabolic reprogramming critical to PH pathogenesis. These results provide a molecular explanation for the clinical associations linking PH with hyperglycinemic syndromes and mitochondrial disorders. These findings also identify novel metabolic targets, including those involved in epigenetics, Fe-S biogenesis, and glycine biology, for diagnostic and therapeutic development.
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Affiliation(s)
- Qiujun Yu
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Yi-Yin Tai
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Ying Tang
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Jingsi Zhao
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Vinny Negi
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Miranda K Culley
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Jyotsna Pilli
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Wei Sun
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Karin Brugger
- Department of Pediatrics, Paracelsus Medical University Salzburg, Austria (K.B., J.M.)
| | - Johannes Mayr
- Department of Pediatrics, Paracelsus Medical University Salzburg, Austria (K.B., J.M.)
| | - Rajeev Saggar
- Department of Medicine, University of Arizona, Phoenix (Rajeev Saggar)
| | - Rajan Saggar
- Departments of Medicine and Pathology, David Geffen School of Medicine, University of California, Los Angeles (Rajan Saggar, W.D.W., D.J.R.)
| | - W Dean Wallace
- Departments of Medicine and Pathology, David Geffen School of Medicine, University of California, Los Angeles (Rajan Saggar, W.D.W., D.J.R.)
| | - David J Ross
- Departments of Medicine and Pathology, David Geffen School of Medicine, University of California, Los Angeles (Rajan Saggar, W.D.W., D.J.R.)
| | - Aaron B Waxman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (A.B.W., K.J.H.)
| | - Stacy G Wendell
- Department of Pharmacology and Chemical Biology (S.G.W.), University of Pittsburgh, PA
- Health Sciences Metabolomics and Lipidomics Core (S.G.W., S.J.M.), University of Pittsburgh, PA
| | - Steven J Mullett
- Health Sciences Metabolomics and Lipidomics Core (S.G.W., S.J.M.), University of Pittsburgh, PA
| | - John Sembrat
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Mauricio Rojas
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Omar F Khan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge (O.F.K., R.L., D.G.A.)
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta (J.E.D.)
| | - Masataka Sugahara
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Nobuyuki Kagiyama
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Taijyu Satoh
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Manling Zhang
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Ning Feng
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - John Gorcsan
- Division of Cardiology, Department of Medicine, Washington University in St. Louis, MO (J.G.)
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, MA (S.O.V.)
| | - Kathleen J Haley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (A.B.W., K.J.H.)
| | - Rahul Kumar
- Program in Translational Lung Research, University of Colorado Denver, Aurora, CO (R.K., B.B.G.)
| | - Brian B Graham
- Program in Translational Lung Research, University of Colorado Denver, Aurora, CO (R.K., B.B.G.)
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge (O.F.K., R.L., D.G.A.)
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge (R.L., D.G.A.)
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge (O.F.K., R.L., D.G.A.)
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge (R.L., D.G.A.)
| | - Bing Wang
- Molecular Therapy Lab, Stem Cell Research Center, University of Pittsburgh School of Medicine, PA (B.W.)
| | - Sruti Shiva
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
| | - Thomas Bertero
- Université Côte d'Azur, CNRS UMR7275, IPMC, Sophia-Antipolis, France (T.B.)
| | - Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Center for Metabolism and Mitochondrial Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology and Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, PA (Q.Y., Y.-Y.T., Y.T., J.Z., V.N., M.K.C., J.P., W.S., J.S., M.R., M.S., N.K., T.S., M.Z., N.F., S.S., S.Y.C.)
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Singh AK, Upadhyay RC, Chandra G, Kumar S, Malakar D, Singh SV, Singh MK. Genome-wide expression analysis of the heat stress response in dermal fibroblasts of Tharparkar (zebu) and Karan-Fries (zebu × taurine) cattle. Cell Stress Chaperones 2020; 25:327-344. [PMID: 32062819 PMCID: PMC7058763 DOI: 10.1007/s12192-020-01076-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/14/2020] [Accepted: 01/23/2020] [Indexed: 11/26/2022] Open
Abstract
The present study sought to evaluate mRNA expression profiles in the cultured dermal fibroblasts of Tharparkar (zebu) and Karan-Fries (zebu, Tharparkar × taurine, Holstein Friesian) cattle in response to heat stress. Bioinformatics' analysis identified temperature-regulated biological processes and pathways. Biological processes overrepresented among the earliest genes induced by temperature stress include regulation of stress responses, protein repair, metabolism, protein transport, cell division, and apoptosis. The present microarray platform contains 51,338 synthesized oligonucleotide probes corresponding to at least 36,713 unigenes. A total of 11,183 and 8126 transcripts were differentially expressed with a fold change of ≥ 2 in Tharparkar and Karan-Fries cattle, respectively. Randomly selected real-time validation showed 83.33% correlation with microarray data. Functional annotation and pathway study of the differentially expressed transcripts or genes (DEGs) reveal that upregulated genes significantly (P < 0.05) affect protein processing and NOD-like receptor pathways (NLRs), while downregulated genes were significantly (P < 0.05) found to be associated with cell cycle, metabolism, and protein transport. Gene expression changes include activation of heat shock factors (HSFs), increased expression of heat shock proteins (HSPs), and apoptosis, while decreasing protein synthesis and another metabolism. These findings provide insights into the underlying mechanism of the physiology of heat stress in Tharparkar and Karan-Fries cattle. Understanding the biology and mechanisms of heat stress is critical to developing approaches to ameliorate current production issues for improving animal performance and agriculture economics in tropical climatic conditions. In conclusion, the present study indicates that heat stress differentially affects the expression of the significant number of genes associated with stress response, metabolism, apoptosis, and protein transport in dermal fibroblasts of Tharparkar and Karan-Fries cattle.
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Affiliation(s)
- A. K. Singh
- Department of Veterinary Physiology & Biochemistry, College of Veterinary Science & Animal Husbandry, Rewa, Madhya Pradesh 486 001 India
- Dairy Cattle Physiology Division, ICAR- National Dairy Research Institute, Karnal, Haryana 132 001 India
| | - R. C. Upadhyay
- Dairy Cattle Physiology Division, ICAR- National Dairy Research Institute, Karnal, Haryana 132 001 India
| | - Gulab Chandra
- Dairy Cattle Physiology Division, ICAR- National Dairy Research Institute, Karnal, Haryana 132 001 India
- Department of Veterinary Physiology & Biochemistry, College of Veterinary & Animal Sciences, SVBPUAT, Meerut, U.P. 250 110 India
| | - Sudarshan Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana 132 001 India
| | - D. Malakar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana 132 001 India
| | - S. V. Singh
- Dairy Cattle Physiology Division, ICAR- National Dairy Research Institute, Karnal, Haryana 132 001 India
| | - M. K. Singh
- Department of Poultry Science, DUVASU, Mathura, U.P. 281 001 India
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Respiratory complications of metabolic disease in the paediatric population: A review of presentation, diagnosis and therapeutic options. Paediatr Respir Rev 2019; 32:55-65. [PMID: 31101546 DOI: 10.1016/j.prrv.2019.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/21/2022]
Abstract
Inborn errors of metabolism (IEMs) whilst individually rare, as a group constitute a field which is increasingly demands on pulmonologists. With the advent of new therapies such as enzyme replacement and gene therapy, early diagnosis and treatment of these conditions can impact on long term outcome, making their timely recognition and appropriate investigation increasingly important. Conversely, with improved treatment, survival of these patients is increasing, with the emergence of previously unknown respiratory phenotypes. It is thus important that pulmonologists are aware of and appropriately monitor and manage these complications. This review aims to highlight the respiratory manifestations which can occur. It isdivided into conditions resulting primarily in obstructive airway and lung disease, restrictive lung disease such as interstitial lung disease or pulmonary alveolar proteinosis and pulmonary hypertension, whilst acknowledging that some diseases have the potential to cause all three. The review focuses on general phenotypes of IEMs, their known respiratory complications and the basic metabolic investigations which should be performed where an IEM is suspected.
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Wehbe Z, Behringer S, Alatibi K, Watkins D, Rosenblatt D, Spiekerkoetter U, Tucci S. The emerging role of the mitochondrial fatty-acid synthase (mtFASII) in the regulation of energy metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1629-1643. [PMID: 31376476 DOI: 10.1016/j.bbalip.2019.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/17/2019] [Accepted: 07/28/2019] [Indexed: 11/30/2022]
Abstract
Malonyl-CoA synthetase (ACSF3) catalyzes the first step of the mitochondrial fatty acid biosynthesis (mtFASII). Mutations in ACSF3 cause CMAMMA a rare inborn error of metabolism. The clinical phenotype is very heterogeneous, with some patients presenting with neurologic manifestations. In some children, presenting symptoms such as coma, ketoacidosis and hypoglycemia are suggestive of an intermediary metabolic disorder. The overall pathophysiological mechanisms are not understood. In order to study the role of mtFASII in the regulation of energy metabolism we performed a comprehensive metabolic phenotyping with Seahorse technology proteomics in fibroblasts from healthy controls and ACSF3 patients. SILAC-based proteomics and lipidomic analysis were performed to investigate the effects of hypofunctional mtFASII on proteome and lipid homeostasis of complex lipids. Our data clearly confirmed an impaired mitochondrial flexibility characterized by reduced mitochondrial respiration and glycolytic flux due to a lower lipoylation degree. These findings were accompanied by the adaptational upregulation of β-oxidation and by the reduction of anaplerotic amino acids as compensatory mechanism to address the required energy need. Finally, lipidomic analysis demonstrated that the content of the bioactive lipids sphingomyelins and cardiolipins was strongly increased. Our data clearly demonstrate the role of mtFASII in metabolic regulation. Moreover, we show that mtFASII acts as mediator in the lipid-mediated signaling processes in the regulation of energy homeostasis and metabolic flexibility.
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Affiliation(s)
- Zeinab Wehbe
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, 79106 Freiburg, Germany; University of Freiburg, Faculty of Biology, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Sidney Behringer
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, 79106 Freiburg, Germany
| | - Khaled Alatibi
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, 79106 Freiburg, Germany; University of Freiburg, Faculty of Biology, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - David Watkins
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1 Montreal, Quebec, Canada
| | - David Rosenblatt
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1 Montreal, Quebec, Canada
| | - Ute Spiekerkoetter
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, 79106 Freiburg, Germany
| | - Sara Tucci
- Department of General Pediatrics, Center for Pediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, 79106 Freiburg, Germany.
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Affiliation(s)
- Boa Kim
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Zolt Arany
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia
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Reply to Bailey et al.: New perspectives on the novel role of the Poldip2/ACSM1 axis in a functional mammalian lipoylation salvage pathway. Proc Natl Acad Sci U S A 2018; 115:E7460-E7461. [PMID: 30042216 DOI: 10.1073/pnas.1807968115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Protein moonlighting elucidates the essential human pathway catalyzing lipoic acid assembly on its cognate enzymes. Proc Natl Acad Sci U S A 2018; 115:E7063-E7072. [PMID: 29987032 DOI: 10.1073/pnas.1805862115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The lack of attachment of lipoic acid to its cognate enzyme proteins results in devastating human metabolic disorders. These mitochondrial disorders are evident soon after birth and generally result in early death. The mutations causing specific defects in lipoyl assembly map in three genes, LIAS, LIPT1, and LIPT2 Although physiological roles have been proposed for the encoded proteins, only the LIPT1 protein had been studied at the enzyme level. LIPT1 was reported to catalyze only the second partial reaction of the classical lipoate ligase mechanism. We report that the physiologically relevant LIPT1 enzyme activity is transfer of lipoyl moieties from the H protein of the glycine cleavage system to the E2 subunits of the 2-oxoacid dehydrogenases required for respiration (e.g., pyruvate dehydrogenase) and amino acid degradation. We also report that LIPT2 encodes an octanoyl transferase that initiates lipoyl group assembly. The human pathway is now biochemically defined.
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Stowe RC, Sun Q, Elsea SH, Scaglia F. LIPT1 deficiency presenting as early infantile epileptic encephalopathy, Leigh disease, and secondary pyruvate dehydrogenase complex deficiency. Am J Med Genet A 2018; 176:1184-1189. [DOI: 10.1002/ajmg.a.38654] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Robert C. Stowe
- Department of Pediatrics, Section of Pediatric Neurology and Developmental NeuroscienceBaylor College of MedicineHouston Texas
| | - Qin Sun
- Department of Molecular and Human GeneticsBaylor College of MedicineHouston Texas
| | - Sarah H. Elsea
- Department of Molecular and Human GeneticsBaylor College of MedicineHouston Texas
| | - Fernando Scaglia
- Department of Molecular and Human GeneticsBaylor College of MedicineHouston Texas
- Texas Children's HospitalHouston Texas
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Poldip2 is an oxygen-sensitive protein that controls PDH and αKGDH lipoylation and activation to support metabolic adaptation in hypoxia and cancer. Proc Natl Acad Sci U S A 2018; 115:1789-1794. [PMID: 29434038 PMCID: PMC5828627 DOI: 10.1073/pnas.1720693115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The present work establishes that the addition of the prosthetic group lipoic acid to catabolic enzymes is a dynamically regulated posttranslational modification that increases metabolic plasticity under hypoxia and in cancer cells. We show that that the polymerase-δ interacting protein 2 (Poldip2) is an oxygen-sensitive protein that regulates the lipoylation and activation of the pyruvate and α-ketoglutarate dehydrogenase complexes. Additionally, our work reveals that mitochondrial peptidases participate in an integrated response needed for metabolic adaptation. This study positions Poldip2 as a key regulator of mitochondrial function and cell metabolism. Although the addition of the prosthetic group lipoate is essential to the activity of critical mitochondrial catabolic enzymes, its regulation is unknown. Here, we show that lipoylation of the pyruvate dehydrogenase and α-ketoglutarate dehydrogenase (αKDH) complexes is a dynamically regulated process that is inhibited under hypoxia and in cancer cells to restrain mitochondrial respiration. Mechanistically, we found that the polymerase-δ interacting protein 2 (Poldip2), a nuclear-encoded mitochondrial protein of unknown function, controls the lipoylation of the pyruvate and α-KDH dihydrolipoamide acetyltransferase subunits by a mechanism that involves regulation of the caseinolytic peptidase (Clp)-protease complex and degradation of the lipoate-activating enzyme Ac-CoA synthetase medium-chain family member 1 (ACSM1). ACSM1 is required for the utilization of lipoic acid derived from a salvage pathway, an unacknowledged lipoylation mechanism. In Poldip2-deficient cells, reduced lipoylation represses mitochondrial function and induces the stabilization of hypoxia-inducible factor 1α (HIF-1α) by loss of substrate inhibition of prolyl-4-hydroxylases (PHDs). HIF-1α–mediated retrograde signaling results in a metabolic reprogramming that resembles hypoxic and cancer cell adaptation. Indeed, we observe that Poldip2 expression is down-regulated by hypoxia in a variety of cell types and basally repressed in triple-negative cancer cells, leading to inhibition of lipoylation of the pyruvate and α-KDH complexes and mitochondrial dysfunction. Increasing mitochondrial lipoylation by forced expression of Poldip2 increases respiration and reduces the growth rate of cancer cells. Our work unveils a regulatory mechanism of catabolic enzymes required for metabolic plasticity and highlights the role of Poldip2 as key during hypoxia and cancer cell metabolic adaptation.
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Peska L, Buza K, Koller J. Drug-target interaction prediction: A Bayesian ranking approach. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2017; 152:15-21. [PMID: 29054256 DOI: 10.1016/j.cmpb.2017.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/28/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND OBJECTIVE In silico prediction of drug-target interactions (DTI) could provide valuable information and speed-up the process of drug repositioning - finding novel usage for existing drugs. In our work, we focus on machine learning algorithms supporting drug-centric repositioning approach, which aims to find novel usage for existing or abandoned drugs. We aim at proposing a per-drug ranking-based method, which reflects the needs of drug-centric repositioning research better than conventional drug-target prediction approaches. METHODS We propose Bayesian Ranking Prediction of Drug-Target Interactions (BRDTI). The method is based on Bayesian Personalized Ranking matrix factorization (BPR) which has been shown to be an excellent approach for various preference learning tasks, however, it has not been used for DTI prediction previously. In order to successfully deal with DTI challenges, we extended BPR by proposing: (i) the incorporation of target bias, (ii) a technique to handle new drugs and (iii) content alignment to take structural similarities of drugs and targets into account. RESULTS Evaluation on five benchmark datasets shows that BRDTI outperforms several state-of-the-art approaches in terms of per-drug nDCG and AUC. BRDTI results w.r.t. nDCG are 0.929, 0.953, 0.948, 0.897 and 0.690 for G-Protein Coupled Receptors (GPCR), Ion Channels (IC), Nuclear Receptors (NR), Enzymes (E) and Kinase (K) datasets respectively. Additionally, BRDTI significantly outperformed other methods (BLM-NII, WNN-GIP, NetLapRLS and CMF) w.r.t. nDCG in 17 out of 20 cases. Furthermore, BRDTI was also shown to be able to predict novel drug-target interactions not contained in the original datasets. The average recall at top-10 predicted targets for each drug was 0.762, 0.560, 1.000 and 0.404 for GPCR, IC, NR, and E datasets respectively. CONCLUSIONS Based on the evaluation, we can conclude that BRDTI is an appropriate choice for researchers looking for an in silico DTI prediction technique to be used in drug-centric repositioning scenarios. BRDTI Software and supplementary materials are available online at www.ksi.mff.cuni.cz/∼peska/BRDTI.
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Affiliation(s)
- Ladislav Peska
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic; Brain Imaging Centre, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Krisztian Buza
- Brain Imaging Centre, Hungarian Academy of Sciences, Budapest, Hungary; Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - Júlia Koller
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
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Lebigot E, Gaignard P, Dorboz I, Slama A, Rio M, de Lonlay P, Héron B, Sabourdy F, Boespflug-Tanguy O, Cardoso A, Habarou F, Ottolenghi C, Thérond P, Bouton C, Golinelli-Cohen MP, Boutron A. Impact of mutations within the [Fe-S] cluster or the lipoic acid biosynthesis pathways on mitochondrial protein expression profiles in fibroblasts from patients. Mol Genet Metab 2017; 122:85-94. [PMID: 28803783 DOI: 10.1016/j.ymgme.2017.08.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/01/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022]
Abstract
Lipoic acid (LA) is the cofactor of the E2 subunit of mitochondrial ketoacid dehydrogenases and plays a major role in oxidative decarboxylation. De novo LA biosynthesis is dependent on LIAS activity together with LIPT1 and LIPT2. LIAS is an iron‑sulfur (Fe-S) cluster-containing mitochondrial protein, like mitochondrial aconitase (mt-aco) and some subunits of respiratory chain (RC) complexes I, II and III. All of them harbor at least one [Fe-S] cluster and their activity is dependent on the mitochondrial [Fe-S] cluster (ISC) assembly machinery. Disorders in the ISC machinery affect numerous Fe-S proteins and lead to a heterogeneous group of diseases with a wide variety of clinical symptoms and combined enzymatic defects. Here, we present the biochemical profiles of several key mitochondrial [Fe-S]-containing proteins in fibroblasts from 13 patients carrying mutations in genes encoding proteins involved in either the lipoic acid (LIPT1 and LIPT2) or mitochondrial ISC biogenesis (FDX1L, ISCA2, IBA57, NFU1, BOLA3) pathway. Ten of them are new patients described for the first time. We confirm that the fibroblast is a good cellular model to study these deficiencies, except for patients presenting mutations in FDX1L and a muscular clinical phenotype. We find that oxidative phosphorylation can be affected by LA defects in LIPT1 and LIPT2 patients due to excessive oxidative stress or to another mechanism connecting LA and respiratory chain activity. We confirm that NFU1, BOLA3, ISCA2 and IBA57 operate in the maturation of [4Fe-4S] clusters and not in [2Fe-2S] protein maturation. Our work suggests a functional difference between IBA57 and other proteins involved in maturation of [Fe-S] proteins. IBA57 seems to require BOLA3, NFU1 and ISCA2 for its stability and NFU1 requires BOLA3. Finally, our study establishes different biochemical profiles for patients according to their mutated protein.
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Affiliation(s)
- E Lebigot
- Biochemistry Department, Hôpital de Bicêtre, Hôpitaux universitaires Paris-Sud, Assistance Publique - Hôpitaux de Paris, 94270 Le Kremlin Bicêtre, France; Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - P Gaignard
- Biochemistry Department, Hôpital de Bicêtre, Hôpitaux universitaires Paris-Sud, Assistance Publique - Hôpitaux de Paris, 94270 Le Kremlin Bicêtre, France
| | - I Dorboz
- Inserm U1141, Paris Diderot University, Sorbonne Paris Cité, DHU PROTECT, Hôpital Robert Debré, Paris, France
| | - A Slama
- Biochemistry Department, Hôpital de Bicêtre, Hôpitaux universitaires Paris-Sud, Assistance Publique - Hôpitaux de Paris, 94270 Le Kremlin Bicêtre, France
| | - M Rio
- Reference Center of Inherited Metabolic Diseases, Hôpital Necker Enfants Malades, Institut Imagine, Assistance Publique - Hôpitaux de Paris, Université Paris-Descartes, 75015 Paris, France
| | - P de Lonlay
- Reference Center of Inherited Metabolic Diseases, Hôpital Necker Enfants Malades, Institut Imagine, Assistance Publique - Hôpitaux de Paris, Université Paris-Descartes, 75015 Paris, France
| | - B Héron
- Neuropediatrics Department, Hôpital Trousseau, Assistance Publique - Hôpitaux de Paris, 75012 Paris, GCR Concer-LD Sorbonne Universités UPMC, Univ 06, Paris, France
| | - F Sabourdy
- Metabolic Biochemistry Department, Hôpital des Enfants, 31059 Toulouse cedex, France
| | - O Boespflug-Tanguy
- Inserm U1141, Paris Diderot University, Sorbonne Paris Cité, DHU PROTECT, Hôpital Robert Debré, Paris, France; Neuropediatrics Department, Hôpital Robert Debré, Assistance Publique - Hôpitaux de Paris, 75019 Paris, France
| | - A Cardoso
- Biochemistry Department, Hôpital de Bicêtre, Hôpitaux universitaires Paris-Sud, Assistance Publique - Hôpitaux de Paris, 94270 Le Kremlin Bicêtre, France
| | - F Habarou
- Metabolic Biochemistry Department, Hôpital Necker Enfants Malades, Assistance Publique - Hôpitaux de Paris, 75015 Paris, France
| | - C Ottolenghi
- Metabolic Biochemistry Department, Hôpital Necker Enfants Malades, Assistance Publique - Hôpitaux de Paris, 75015 Paris, France
| | - P Thérond
- Biochemistry Department, Hôpital de Bicêtre, Hôpitaux universitaires Paris-Sud, Assistance Publique - Hôpitaux de Paris, 94270 Le Kremlin Bicêtre, France
| | - C Bouton
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - M P Golinelli-Cohen
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - A Boutron
- Biochemistry Department, Hôpital de Bicêtre, Hôpitaux universitaires Paris-Sud, Assistance Publique - Hôpitaux de Paris, 94270 Le Kremlin Bicêtre, France.
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Habarou F, Hamel Y, Haack TB, Feichtinger RG, Lebigot E, Marquardt I, Busiah K, Laroche C, Madrange M, Grisel C, Pontoizeau C, Eisermann M, Boutron A, Chrétien D, Chadefaux-Vekemans B, Barouki R, Bole-Feysot C, Nitschke P, Goudin N, Boddaert N, Nemazanyy I, Delahodde A, Kölker S, Rodenburg RJ, Korenke GC, Meitinger T, Strom TM, Prokisch H, Rotig A, Ottolenghi C, Mayr JA, de Lonlay P. Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy. Am J Hum Genet 2017; 101:283-290. [PMID: 28757203 DOI: 10.1016/j.ajhg.2017.07.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/05/2017] [Indexed: 11/25/2022] Open
Abstract
Lipoate serves as a cofactor for the glycine cleavage system (GCS) and four 2-oxoacid dehydrogenases functioning in energy metabolism (α-oxoglutarate dehydrogenase [α-KGDHc] and pyruvate dehydrogenase [PDHc]), or amino acid metabolism (branched-chain oxoacid dehydrogenase, 2-oxoadipate dehydrogenase). Mitochondrial lipoate synthesis involves three enzymatic steps catalyzed sequentially by lipoyl(octanoyl) transferase 2 (LIPT2), lipoic acid synthetase (LIAS), and lipoyltransferase 1 (LIPT1). Mutations in LIAS have been associated with nonketotic hyperglycinemia-like early-onset convulsions and encephalopathy combined with a defect in mitochondrial energy metabolism. LIPT1 deficiency spares GCS deficiency and has been associated with a biochemical signature of combined 2-oxoacid dehydrogenase deficiency leading to early death or Leigh-like encephalopathy. We report on the identification of biallelic LIPT2 mutations in three affected individuals from two families with severe neonatal encephalopathy. Brain MRI showed major cortical atrophy with white matter abnormalities and cysts. Plasma glycine was mildly increased. Affected individuals' fibroblasts showed reduced oxygen consumption rates, PDHc, α-KGDHc activities, leucine catabolic flux, and decreased protein lipoylation. A normalization of lipoylation was observed after expression of wild-type LIPT2, arguing for LIPT2 requirement in intramitochondrial lipoate synthesis. Lipoic acid supplementation did not improve clinical condition nor activities of PDHc, α-KGDHc, or leucine metabolism in fibroblasts and was ineffective in yeast deleted for the orthologous LIP2.
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Bernardinelli E, Costa R, Scantamburlo G, To J, Morabito R, Nofziger C, Doerrier C, Krumschnabel G, Paulmichl M, Dossena S. Mis-targeting of the mitochondrial protein LIPT2 leads to apoptotic cell death. PLoS One 2017; 12:e0179591. [PMID: 28628643 PMCID: PMC5476274 DOI: 10.1371/journal.pone.0179591] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/01/2017] [Indexed: 11/27/2022] Open
Abstract
Lipoyl(Octanoyl) Transferase 2 (LIPT2) is a protein involved in the post-translational modification of key energy metabolism enzymes in humans. Defects of lipoic acid synthesis and transfer start to emerge as causes of fatal or severe early-onset disease. We show that the first 31 amino acids of the N-terminus of LIPT2 represent a mitochondrial targeting sequence and inhibition of the transit of LIPT2 to the mitochondrion results in apoptotic cell death associated with activation of the apoptotic volume decrease (AVD) current in normotonic conditions, as well as over-activation of the swelling-activated chloride current (IClswell), mitochondrial membrane potential collapse, caspase-3 cleavage and nuclear DNA fragmentation. The findings presented here may help elucidate the molecular mechanisms underlying derangements of lipoic acid biosynthesis.
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Affiliation(s)
- Emanuele Bernardinelli
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Roberta Costa
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Giada Scantamburlo
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rossana Morabito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Charity Nofziger
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | | | | | - Markus Paulmichl
- Center for Health and Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
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Heimer G, Kerätär J, Riley L, Balasubramaniam S, Eyal E, Pietikäinen L, Hiltunen JK, Marek-Yagel D, Hamada J, Gregory A, Rogers C, Hogarth P, Nance MA, Shalva N, Veber A, Tzadok M, Nissenkorn A, Tonduti D, Renaldo F, Kraoua I, Panteghini C, Valletta L, Garavaglia B, Cowley MJ, Gayevskiy V, Roscioli T, Silberstein JM, Hoffmann C, Raas-Rothschild A, Tiranti V, Anikster Y, Christodoulou J, Kastaniotis AJ, Ben-Zeev B, Hayflick SJ, Bamshad M, Leal S, Nickerson D, Anderson P, Annable M, Blue E, Buckingham K, Chin J, Chong J, Cornejo R, Davis C, Frazar C, He Z, Jarvik G, Jimenez G, Johanson E, Kolar T, Krauter S, Luksic D, Marvin C, McGee S, McGoldrick D, Patterson K, Perez M, Phillips S, Pijoan J, Robertson P, Santos-Cortez R, Shankar A, Slattery K, Shively K, Siegel D, Smith J, Tackett M, Wang G, Wegener M, Weiss J, Wernick R, Wheeler M, Yi Q. MECR Mutations Cause Childhood-Onset Dystonia and Optic Atrophy, a Mitochondrial Fatty Acid Synthesis Disorder. Am J Hum Genet 2016; 99:1229-1244. [PMID: 27817865 DOI: 10.1016/j.ajhg.2016.09.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/26/2016] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial fatty acid synthesis (mtFAS) is an evolutionarily conserved pathway essential for the function of the respiratory chain and several mitochondrial enzyme complexes. We report here a unique neurometabolic human disorder caused by defective mtFAS. Seven individuals from five unrelated families presented with childhood-onset dystonia, optic atrophy, and basal ganglia signal abnormalities on MRI. All affected individuals were found to harbor recessive mutations in MECR encoding the mitochondrial trans-2-enoyl-coenzyme A-reductase involved in human mtFAS. All six mutations are extremely rare in the general population, segregate with the disease in the families, and are predicted to be deleterious. The nonsense c.855T>G (p.Tyr285∗), c.247_250del (p.Asn83Hisfs∗4), and splice site c.830+2_830+3insT mutations lead to C-terminal truncation variants of MECR. The missense c.695G>A (p.Gly232Glu), c.854A>G (p.Tyr285Cys), and c.772C>T (p.Arg258Trp) mutations involve conserved amino acid residues, are located within the cofactor binding domain, and are predicted by structural analysis to have a destabilizing effect. Yeast modeling and complementation studies validated the pathogenicity of the MECR mutations. Fibroblast cell lines from affected individuals displayed reduced levels of both MECR and lipoylated proteins as well as defective respiration. These results suggest that mutations in MECR cause a distinct human disorder of the mtFAS pathway. The observation of decreased lipoylation raises the possibility of a potential therapeutic strategy.
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Batllori M, Molero-Luis M, Casado M, Sierra C, Artuch R, Ormazabal A. Biochemical Analyses of Cerebrospinal Fluid for the Diagnosis of Neurometabolic Conditions. What Can We Expect? Semin Pediatr Neurol 2016; 23:273-284. [PMID: 28284389 DOI: 10.1016/j.spen.2016.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this article, we review the state-of-the-art analysis of different biomarkers in the cerebrospinal fluid for the diagnosis of genetically conditioned, rare, neurometabolic diseases, including glucose transport defects, neurotransmitter (dopamine, serotonin, and gamma-aminobutyric acid) and pterin deficiencies, and vitamin defects (folate, vitamin B6, and thiamine) that affect the brain. The analysis of several key metabolites are detailed, which thus highlights the preanalytical and analytical factors that should be cautiously controlled to avoid misdiagnosis; moreover, these factors may facilitate an adequate interpretation of the biochemical profiles in the context of severe neuropediatric disorders. Secondary disturbances in these biomarkers, which are associated with other genetic or environmental conditions, are also detailed. Importantly, the early biochemical identification of biochemical disturbances in the cerebrospinal fluid may improve the clinical outcomes of a remarkable number of patients, who may exhibit good neurologic outcomes using the available therapies for these disorders.
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Affiliation(s)
- Marta Batllori
- Clinical Biochemistry Department, Centre for Biomedical Research on Rare Disease (CIBERER-ISCIII), Pediatric Research Institute, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Marta Molero-Luis
- Clinical Biochemistry Department, Centre for Biomedical Research on Rare Disease (CIBERER-ISCIII), Pediatric Research Institute, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Mercedes Casado
- Clinical Biochemistry Department, Centre for Biomedical Research on Rare Disease (CIBERER-ISCIII), Pediatric Research Institute, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Cristina Sierra
- Clinical Biochemistry Department, Centre for Biomedical Research on Rare Disease (CIBERER-ISCIII), Pediatric Research Institute, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Centre for Biomedical Research on Rare Disease (CIBERER-ISCIII), Pediatric Research Institute, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Aida Ormazabal
- Clinical Biochemistry Department, Centre for Biomedical Research on Rare Disease (CIBERER-ISCIII), Pediatric Research Institute, Hospital Sant Joan de Déu, Barcelona, Spain.
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Tort F, Ferrer-Cortes X, Ribes A. Differential diagnosis of lipoic acid synthesis defects. J Inherit Metab Dis 2016; 39:781-793. [PMID: 27586888 DOI: 10.1007/s10545-016-9975-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 01/16/2023]
Abstract
Lipoic acid (LA) is an essential cofactor required for the activity of five multienzymatic complexes that play a central role in the mitochondrial energy metabolism: four 2-oxoacid dehydrogenase complexes [pyruvate dehydrogenase (PDH), branched-chain ketoacid dehydrogenase (BCKDH), 2-ketoglutarate dehydrogenase (2-KGDH), and 2-oxoadipate dehydrogenase (2-OADH)] and the glycine cleavage system (GCS). LA is synthesized in a complex multistep process that requires appropriate function of the mitochondrial fatty acid synthesis (mtFASII) and the biogenesis of iron-sulphur (Fe-S) clusters. Defects in the biosynthesis of LA have been reported to be associated with multiple and severe defects of the mitochondrial energy metabolism. In recent years, disease-causing mutations in genes encoding for proteins involved in LA metabolism have been reported: NFU1, BOLA3, IBA57, LIAS, GLRX5, LIPT1, ISCA2, and LIPT2. These studies represented important progress in understanding the pathophysiology and molecular bases underlying these disorders. Here we review current knowledge regarding involvement of LA synthesis defects in human diseases with special emphasis on the diagnostic strategies for these disorders. The clinical and biochemical characteristics of patients with LA synthesis defects are discussed and a workup for the differential diagnosis proposed.
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Affiliation(s)
- Frederic Tort
- Secció d'Errors Congènits del Metabolisme -IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Edifici Helios III, planta baixa, C/Mejía Lequerica s/n, 08028, Barcelona, Spain.
| | - Xènia Ferrer-Cortes
- Secció d'Errors Congènits del Metabolisme -IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Edifici Helios III, planta baixa, C/Mejía Lequerica s/n, 08028, Barcelona, Spain
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme -IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic, IDIBAPS, CIBERER, Edifici Helios III, planta baixa, C/Mejía Lequerica s/n, 08028, Barcelona, Spain
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Kastaniotis AJ, Autio KJ, Kerätär JM, Monteuuis G, Mäkelä AM, Nair RR, Pietikäinen LP, Shvetsova A, Chen Z, Hiltunen JK. Mitochondrial fatty acid synthesis, fatty acids and mitochondrial physiology. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:39-48. [PMID: 27553474 DOI: 10.1016/j.bbalip.2016.08.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/20/2016] [Accepted: 08/17/2016] [Indexed: 02/07/2023]
Abstract
Mitochondria and fatty acids are tightly connected to a multiplicity of cellular processes that go far beyond mitochondrial fatty acid metabolism. In line with this view, there is hardly any common metabolic disorder that is not associated with disturbed mitochondrial lipid handling. Among other aspects of mitochondrial lipid metabolism, apparently all eukaryotes are capable of carrying out de novo fatty acid synthesis (FAS) in this cellular compartment in an acyl carrier protein (ACP)-dependent manner. The dual localization of FAS in eukaryotic cells raises the questions why eukaryotes have maintained the FAS in mitochondria in addition to the "classic" cytoplasmic FAS and what the products are that cannot be substituted by delivery of fatty acids of extramitochondrial origin. The current evidence indicates that mitochondrial FAS is essential for cellular respiration and mitochondrial biogenesis. Although both β-oxidation and FAS utilize thioester chemistry, CoA acts as acyl-group carrier in the breakdown pathway whereas ACP assumes this role in the synthetic direction. This arrangement metabolically separates these two pathways running towards opposite directions and prevents futile cycling. A role of this pathway in mitochondrial metabolic sensing has recently been proposed. This article is part of a Special Issue entitled: Lipids of Mitochondria edited by Guenther Daum.
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Affiliation(s)
- Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Juha M Kerätär
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anne M Mäkelä
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Remya R Nair
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Laura P Pietikäinen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure and Materials and Institute of Theoretical Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland; State Key Laboratory of Supramolecular Structure and Materials and Institute of Theoretical Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China.
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