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Mori K, Naganuma T, Kihara A. Role of 2-hydroxy acyl-CoA lyase HACL2 in odd-chain fatty acid production via α-oxidation in vivo. Mol Biol Cell 2023; 34:ar85. [PMID: 37285239 PMCID: PMC10398889 DOI: 10.1091/mbc.e23-02-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
Although most fatty acids (FAs) are even chain, certain tissues, including brain, contain relatively large quantities of odd-chain FAs in their sphingolipids. One of the pathways producing odd-chain FAs is the α-oxidation of 2-hydroxy (2-OH) FAs, where 2-OH acyl-CoA lyases (HACL1 and HACL2) catalyze the key cleavage reaction. However, the contribution of each HACL to odd-chain FA production in vivo remains unknown. Here, we found that HACL2 and HACL1 play major roles in the α-oxidation of 2-OH FAs (especially very-long-chain types) and 3-methyl FAs (other α-oxidation substrates), respectively, using ectopic expression systems of human HACL2 and HACL1 in yeast and analyzing Hacl1 and/or Hacl2 knockout (KO) CHO-K1 cells. We then generated Hacl2 KO mice and measured the quantities of odd-chain and 2-OH lipids (free FAs and sphingolipids [ceramides, sphingomyelins, and monohexosylceramides]) in 17 tissues. We observed fewer odd-chain lipids and more 2-OH lipids in many tissues of Hacl2 KO mice than in wild-type mice, and of these differences the reductions were most prominent for odd-chain monohexosylceramides in the brain and ceramides in the stomach. These results indicate that HACL2-involved α-oxidation of 2-OH FAs is mainly responsible for odd-chain FA production in the brain and stomach.
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Affiliation(s)
- Keisuke Mori
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tatsuro Naganuma
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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2
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Kirsche M, Prabhu G, Sherman R, Ni B, Battle A, Aganezov S, Schatz MC. Jasmine and Iris: population-scale structural variant comparison and analysis. Nat Methods 2023; 20:408-417. [PMID: 36658279 PMCID: PMC10006329 DOI: 10.1038/s41592-022-01753-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/15/2022] [Indexed: 01/21/2023]
Abstract
The availability of long reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine and Iris ( https://github.com/mkirsche/Jasmine/ ), for fast and accurate SV refinement, comparison and population analysis. Using an SV proximity graph, Jasmine outperforms six widely used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than fivefold, and reveals a set of high-confidence de novo SVs confirmed by multiple technologies. We also present a unified callset of 122,813 SVs and 82,379 indels from 31 samples of diverse ancestry sequenced with long reads. We genotype these variants in 1,317 samples from the 1000 Genomes Project and the Genotype-Tissue Expression project with DNA and RNA-sequencing data and assess their widespread impact on gene expression, including within medically relevant genes.
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Affiliation(s)
- Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Gautam Prabhu
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Rachel Sherman
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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3
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Kocherlakota S, Swinkels D, Van Veldhoven PP, Baes M. Mouse Models to Study Peroxisomal Functions and Disorders: Overview, Caveats, and Recommendations. Methods Mol Biol 2023; 2643:469-500. [PMID: 36952207 DOI: 10.1007/978-1-0716-3048-8_34] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
During the last three decades many mouse lines were created or identified that are deficient in one or more peroxisomal functions. Different methodologies were applied to obtain global, hypomorph, cell type selective, inducible, and knockin mice. Whereas some models closely mimic pathologies in patients, others strongly deviate or no human counterpart has been reported. Often, mice, apparently endowed with a stronger transcriptional adaptation, have to be challenged with dietary additions or restrictions in order to trigger phenotypic changes. Depending on the inactivated peroxisomal protein, several approaches can be taken to validate the loss-of-function. Here, an overview is given of the available mouse models and their most important characteristics.
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Affiliation(s)
- Sai Kocherlakota
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniëlle Swinkels
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Paul P Van Veldhoven
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium.
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4
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Abstract
Peroxisomes are subcellular organelles that play a central role in human physiology by catalyzing a range of unique metabolic functions. The importance of peroxisomes for human health is exemplified by the existence of a group of usually severe diseases caused by an impairment in one or more peroxisomal functions. Among others these include the Zellweger spectrum disorders, X-linked adrenoleukodystrophy, and Refsum disease. To fulfill their role in metabolism, peroxisomes require continued interaction with other subcellular organelles including lipid droplets, lysosomes, the endoplasmic reticulum, and mitochondria. In recent years it has become clear that the metabolic alliance between peroxisomes and other organelles requires the active participation of tethering proteins to bring the organelles physically closer together, thereby achieving efficient transfer of metabolites. This review intends to describe the current state of knowledge about the metabolic role of peroxisomes in humans, with particular emphasis on the metabolic partnership between peroxisomes and other organelles and the consequences of genetic defects in these processes. We also describe the biogenesis of peroxisomes and the consequences of the multiple genetic defects therein. In addition, we discuss the functional role of peroxisomes in different organs and tissues and include relevant information derived from model systems, notably peroxisomal mouse models. Finally, we pay particular attention to a hitherto underrated role of peroxisomes in viral infections.
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Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
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5
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Wang X, Rao J, Tan Z, Xun T, Zhao J, Yang X. Inflammatory signaling on cytochrome P450-mediated drug metabolism in hepatocytes. Front Pharmacol 2022; 13:1043836. [PMID: 36353494 PMCID: PMC9637984 DOI: 10.3389/fphar.2022.1043836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/11/2022] [Indexed: 12/11/2023] Open
Abstract
Cytochrome P450 (CYP450) enzymes are membrane-bound blood proteins that are vital to drug detoxification, cell metabolism, and homeostasis. CYP450s belonging to CYP families 1-3 are responsible for nearly 80% of oxidative metabolism and complete elimination of approximately 50% of all common clinical drugs in humans liver hepatocytes. CYP450s can affect the body's response to drugs by altering the reaction, safety, bioavailability, and toxicity. They can also regulate metabolic organs and the body's local action sites to produce drug resistance through altered drug metabolism. Genetic polymorphisms in the CYP gene alone do not explain ethnic and individual differences in drug efficacy in the context of complex diseases. The purpose of this review is to summarize the impact of new inflammatory-response signaling pathways on the activity and expression of CYP drug-metabolizing enzymes. Included is a summary of recent studies that have identified drugs with the potential to regulate drug-metabolizing enzyme activity. Our goal is to inspire the development of clinical drug treatment processes that consider the impact of the inflammatory environment on drug treatment, as well as provide research targets for those studying drug metabolism.
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Affiliation(s)
- Xiaokang Wang
- Department of Pharmacy, Shenzhen Longhua District Central Hospital, Shenzhen, China
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jiaoyu Rao
- Department of Pharmacy, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Zhiyi Tan
- Guangzhou Customs Technology Center, Guangzhou, China
| | - Tianrong Xun
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jingqian Zhao
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xixiao Yang
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
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6
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Chen CT, Shao Z, Fu Z. Dysfunctional peroxisomal lipid metabolisms and their ocular manifestations. Front Cell Dev Biol 2022; 10:982564. [PMID: 36187472 PMCID: PMC9524157 DOI: 10.3389/fcell.2022.982564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Retina is rich in lipids and dyslipidemia causes retinal dysfunction and eye diseases. In retina, lipids are not only important membrane component in cells and organelles but also fuel substrates for energy production. However, our current knowledge of lipid processing in the retina are very limited. Peroxisomes play a critical role in lipid homeostasis and genetic disorders with peroxisomal dysfunction have different types of ocular complications. In this review, we focus on the role of peroxisomes in lipid metabolism, including degradation and detoxification of very-long-chain fatty acids, branched-chain fatty acids, dicarboxylic acids, reactive oxygen/nitrogen species, glyoxylate, and amino acids, as well as biosynthesis of docosahexaenoic acid, plasmalogen and bile acids. We also discuss the potential contributions of peroxisomal pathways to eye health and summarize the reported cases of ocular symptoms in patients with peroxisomal disorders, corresponding to each disrupted peroxisomal pathway. We also review the cross-talk between peroxisomes and other organelles such as lysosomes, endoplasmic reticulum and mitochondria.
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Affiliation(s)
- Chuck T. Chen
- Department of Nutritional Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Zhuo Shao
- Post-Graduate Medical Education, University of Toronto, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, the Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- The Genetics Program, North York General Hospital, University of Toronto, Toronto, ON, Canada
| | - Zhongjie Fu
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- *Correspondence: Zhongjie Fu,
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Beteta-Göbel R, Miralles M, Fernández-Díaz J, Rodríguez-Lorca R, Torres M, Fernández-García P, Escribá PV, Lladó V. HCA (2-Hydroxy-Docosahexaenoic Acid) Induces Apoptosis and Endoplasmic Reticulum Stress in Pancreatic Cancer Cells. Int J Mol Sci 2022; 23:9902. [PMID: 36077299 PMCID: PMC9456069 DOI: 10.3390/ijms23179902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 12/09/2022] Open
Abstract
Pancreatic cancer has a high mortality rate due to its aggressive nature and high metastatic rate. When coupled to the difficulties in detecting this type of tumor early and the lack of effective treatments, this cancer is currently one of the most important clinical challenges in the field of oncology. Melitherapy is an innovative therapeutic approach that is based on modifying the composition and structure of cell membranes to treat different diseases, including cancers. In this context, 2-hydroxycervonic acid (HCA) is a melitherapeutic agent developed to combat pancreatic cancer cells, provoking the programmed cell death by apoptosis of these cells by inducing ER stress and triggering the production of ROS species. The efficacy of HCA was demonstrated in vivo, alone and in combination with gemcitabine, using a MIA PaCa-2 cell xenograft model of pancreatic cancer in which no apparent toxicity was evident. HCA is metabolized by α-oxidation to C21:5n-3 (heneicosapentaenoic acid), which in turn also showed anti-proliferative effect in these cells. Given the unmet clinical needs associated with pancreatic cancer, the data presented here suggest that the use of HCA merits further study as a potential therapy for this condition.
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Affiliation(s)
- Roberto Beteta-Göbel
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- R&D Department, Laminar Pharmaceuticals, C/Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Marc Miralles
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- R&D Department, Laminar Pharmaceuticals, C/Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Javier Fernández-Díaz
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- R&D Department, Laminar Pharmaceuticals, C/Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Raquel Rodríguez-Lorca
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- R&D Department, Laminar Pharmaceuticals, C/Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Manuel Torres
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Paula Fernández-García
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- R&D Department, Laminar Pharmaceuticals, C/Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Pablo V. Escribá
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Victoria Lladó
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- R&D Department, Laminar Pharmaceuticals, C/Isaac Newton, 07121 Palma de Mallorca, Spain
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8
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Zhu W, Zhang Z, Gui W, Shen Z, Chen Y, Yin X, Liang L, Li L. Identification of the Key Pathways and Genes in Hypoxia Pulmonary Arterial Hypertension Following Intrauterine Growth Retardation. Front Mol Biosci 2022; 9:789736. [PMID: 35433826 PMCID: PMC9008831 DOI: 10.3389/fmolb.2022.789736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/08/2022] [Indexed: 11/30/2022] Open
Abstract
High-throughput sequencing and weighted gene co-expression network analysis (WGCNA) were used to identify susceptibility modules and genes in liver tissue for the hypoxic pulmonary arterial hypertension (PAH) animal model following intrauterine growth retardation (IUGR). A total of 5,000 genes were clustered into eight co-expression modules via WGCNA. Module blue was mostly significantly correlated with the IUGR–hypoxia group. Gene Ontology analysis showed that genes in the module blue were mainly enriched in the fatty acid metabolic process, lipid modification, and fatty acid catabolic process. The Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the genes in module blue were mainly associated with fatty acid metabolism, PPAR signaling pathway, and biosynthesis of unsaturated fatty acids. In addition, the maximal clique centrality method was used to identify the hub genes in the subnetworks, and the obtained results were verified using real-time quantitative PCR. Finally, we identified that four genes including Cyp2f4, Lipc, Acadl, and Hacl1 were significantly associated with IUGR-hypoxia. Our study identified a module and several key genes that acted as essential components in the etiology of the long-term metabolic consequences in hypoxia PAH following IUGR.
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Affiliation(s)
- Weifen Zhu
- Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ziming Zhang
- Department of Neonatology, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Weiwei Gui
- Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zheng Shen
- Department of Central Laboratory, Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yixin Chen
- Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xueyao Yin
- Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Liang
- Department of Pediatrics, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lin Li
- Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Lin Li,
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9
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Blankestijn M, Bloks VW, Struik D, Huijkman N, Kloosterhuis N, Wolters JC, Wanders RJA, Vaz FM, Islinger M, Kuipers F, van de Sluis B, Groen AK, Verkade HJ, Jonker JW. Mice with a deficiency in Peroxisomal Membrane Protein 4 (PXMP4) display mild changes in hepatic lipid metabolism. Sci Rep 2022; 12:2512. [PMID: 35169201 DOI: 10.1038/s41598-022-06479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/31/2022] [Indexed: 11/08/2022] Open
Abstract
Peroxisomes play an important role in the metabolism of a variety of biomolecules, including lipids and bile acids. Peroxisomal Membrane Protein 4 (PXMP4) is a ubiquitously expressed peroxisomal membrane protein that is transcriptionally regulated by peroxisome proliferator-activated receptor α (PPARα), but its function is still unknown. To investigate the physiological function of PXMP4, we generated a Pxmp4 knockout (Pxmp4-/-) mouse model using CRISPR/Cas9-mediated gene editing. Peroxisome function was studied under standard chow-fed conditions and after stimulation of peroxisomal activity using the PPARα ligand fenofibrate or by using phytol, a metabolite of chlorophyll that undergoes peroxisomal oxidation. Pxmp4-/- mice were viable, fertile, and displayed no changes in peroxisome numbers or morphology under standard conditions. Also, no differences were observed in the plasma levels of products from major peroxisomal pathways, including very long-chain fatty acids (VLCFAs), bile acids (BAs), and BA intermediates di- and trihydroxycholestanoic acid. Although elevated levels of the phytol metabolites phytanic and pristanic acid in Pxmp4-/- mice pointed towards an impairment in peroxisomal α-oxidation capacity, treatment of Pxmp4-/- mice with a phytol-enriched diet did not further increase phytanic/pristanic acid levels. Finally, lipidomic analysis revealed that loss of Pxmp4 decreased hepatic levels of the alkyldiacylglycerol class of neutral ether lipids, particularly those containing polyunsaturated fatty acids. Together, our data show that while PXMP4 is not critical for overall peroxisome function under the conditions tested, it may have a role in the metabolism of (ether)lipids.
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10
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Khalil Y, Carrino S, Lin F, Ferlin A, Lad HV, Mazzacuva F, Falcone S, Rivers N, Banks G, Concas D, Aguilar C, Haynes AR, Blease A, Nicol T, Al-Shawi R, Heywood W, Potter P, Mills K, Gale DP, Clayton PT. Tissue Proteome of 2-Hydroxyacyl-CoA Lyase Deficient Mice Reveals Peroxisome Proliferation and Activation of ω-Oxidation. Int J Mol Sci 2022; 23:ijms23020987. [PMID: 35055171 PMCID: PMC8781152 DOI: 10.3390/ijms23020987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Peroxisomal fatty acid α-oxidation is an essential pathway for the degradation of β-carbon methylated fatty acids such as phytanic acid. One enzyme in this pathway is 2-hydroxyacyl CoA lyase (HACL1), which is responsible for the cleavage of 2-hydroxyphytanoyl-CoA into pristanal and formyl-CoA. Hacl1 deficient mice do not present with a severe phenotype, unlike mice deficient in other α-oxidation enzymes such as phytanoyl-CoA hydroxylase deficiency (Refsum disease) in which neuropathy and ataxia are present. Tissues from wild-type and Hacl1−/− mice fed a high phytol diet were obtained for proteomic and lipidomic analysis. There was no phenotype observed in these mice. Liver, brain, and kidney tissues underwent trypsin digestion for untargeted proteomic liquid chromatography-mass spectrometry analysis, while liver tissues also underwent fatty acid hydrolysis, extraction, and derivatisation for fatty acid gas chromatography-mass spectrometry analysis. The liver fatty acid profile demonstrated an accumulation of phytanic and 2-hydroxyphytanic acid in the Hacl1−/− liver and significant decrease in heptadecanoic acid. The liver proteome showed a significant decrease in the abundance of Hacl1 and a significant increase in the abundance of proteins involved in PPAR signalling, peroxisome proliferation, and omega oxidation, particularly Cyp4a10 and Cyp4a14. In addition, the pathway associated with arachidonic acid metabolism was affected; Cyp2c55 was upregulated and Cyp4f14 and Cyp2b9 were downregulated. The kidney proteome revealed fewer significantly upregulated peroxisomal proteins and the brain proteome was not significantly different in Hacl1−/− mice. This study demonstrates the powerful insight brought by proteomic and metabolomic profiling of Hacl1−/− mice in better understanding disease mechanism in fatty acid α-oxidation disorders.
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Affiliation(s)
- Youssef Khalil
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
| | - Sara Carrino
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Fujun Lin
- Department of Renal Medicine, University College London, London NW3 2PF, UK; (F.L.); (A.F.); (D.P.G.)
- Department of Nephrology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200082, China
| | - Anna Ferlin
- Department of Renal Medicine, University College London, London NW3 2PF, UK; (F.L.); (A.F.); (D.P.G.)
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, London SW3 6NP, UK
| | - Heena V. Lad
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Francesca Mazzacuva
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
- Department of Bioscience, University of East London, London E15 4LZ, UK
| | - Sara Falcone
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Natalie Rivers
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Gareth Banks
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Danilo Concas
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Carlos Aguilar
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Andrew R. Haynes
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Andy Blease
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Thomas Nicol
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Raya Al-Shawi
- Genetics Unit and Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London NW3 2PF, UK;
| | - Wendy Heywood
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
| | - Paul Potter
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Kevin Mills
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
| | - Daniel P. Gale
- Department of Renal Medicine, University College London, London NW3 2PF, UK; (F.L.); (A.F.); (D.P.G.)
| | - Peter T. Clayton
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
- Correspondence:
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Yao J, Yan J, Wu J, Yu J, He B, Chen X, Chen Z. Predicting Target Genes of San-Huang-Chai-Zhu Formula in Treating ANIT-Induced Acute Intrahepatic Cholestasis Rat Model via Bioinformatics Analysis Combined with Experimental Validation. Evid Based Complement Alternat Med 2021; 2021:5320445. [PMID: 34512777 DOI: 10.1155/2021/5320445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022]
Abstract
Background San-Huang-Chai-Zhu formula (SHCZF) has been used to improve cholestasis for many years. This study aims to predict the possible gene targets of SHCZF in treating acute intrahepatic cholestasis (AIC) in rats. Materials and Methods Eighteen SD rats were randomly assigned to the normal group, ANIT group, and ANIT + SHCZF group. Alpha-naphthylisothiocyanate (ANIT) was used to induce AIC. Serum biochemical indexes were detected in each group. After treatment, the livers were collected and used to extract RNA. The library was constructed by TruSeq RNA, sequenced by Illumina, and analyzed by various bioinformatics methods. qRT-PCR was used to verify the target genes related to the efficacy of SHCZF. Results Serum ALT, AST, ALP, and TBIL were significantly higher in the ANIT group than in the normal group. Serum ALT and AST levels in the ANIT + SHCZF group were substantially lower than those in the ANIT group. A total of 354 intersected genes were screened by expression level correlation and PCA analysis, GO and KEGG pathway enrichment analysis, and WGCNA and STEM analysis. Then, 4 overlapping genes were found by pathway/BP/gene network construction. SHCZF reversed the downregulation of expression of CYP4A1 and HACL1 and the upregulation of expression of DBI and F11R induced by ANIT. In addition, the qRT-PCR result showed that mRNA expression of CYP4A1, HACL1, and F11R genes in the liver was consistent with the prediction result of bioinformatics analysis. Conclusion CYP4A1, HACL1, and F11R are genes related to the occurrence of ANIT-induced AIC in rats and may be considered as targets of SHCZF for the treatment of AIC.
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Van Veldhoven PP, de Schryver E, Young SG, Zwijsen A, Fransen M, Espeel M, Baes M, Van Ael E. Slc25a17 Gene Trapped Mice: PMP34 Plays a Role in the Peroxisomal Degradation of Phytanic and Pristanic Acid. Front Cell Dev Biol 2020; 8:144. [PMID: 32266253 PMCID: PMC7106852 DOI: 10.3389/fcell.2020.00144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/20/2020] [Indexed: 12/04/2022] Open
Abstract
Mice lacking PMP34, a peroxisomal membrane transporter encoded by Slc25a17, did not manifest any obvious phenotype on a Swiss Webster genetic background, even with various treatments designed to unmask impaired peroxisomal functioning. Peroxisomal α- and β-oxidation rates in PMP34 deficient fibroblasts or liver slices were not or only modestly affected and in bile, no abnormal bile acid intermediates were detected. Peroxisomal content of cofactors like CoA, ATP, NAD+, thiamine-pyrophosphate and pyridoxal-phosphate, based on direct or indirect data, appeared normal as were tissue plasmalogen and very long chain fatty acid levels. However, upon dietary phytol administration, the knockout mice displayed hepatomegaly, liver inflammation, and an induction of peroxisomal enzymes. This phenotype was partially mediated by PPARα. Hepatic triacylglycerols and cholesterylesters were elevated and both phytanic acid and pristanic acid accumulated in the liver lipids, in females to higher extent than in males. In addition, pristanic acid degradation products were detected, as wells as the CoA-esters of all these branched fatty acids. Hence, PMP34 is important for the degradation of phytanic/pristanic acid and/or export of their metabolites. Whether this is caused by a shortage of peroxisomal CoA affecting the intraperoxisomal formation of pristanoyl-CoA (and perhaps of phytanoyl-CoA), or the SCPx-catalyzed thiolytic cleavage during pristanic acid β-oxidation, could not be proven in this model, but the phytol-derived acyl-CoA profile is compatible with the latter possibility. On the other hand, the normal functioning of other peroxisomal pathways, and especially bile acid formation, seems to exclude severe transport problems or a shortage of CoA, and other cofactors like FAD, NAD(P)+, TPP. Based on our findings, PMP34 deficiency in humans is unlikely to be a life threatening condition but could cause elevated phytanic/pristanic acid levels in older adults.
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Affiliation(s)
| | - Evelyn de Schryver
- LIPIT, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stephen G. Young
- Departments of Medicine and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - An Zwijsen
- Laboratory of Developmental Signaling, Department Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Marc Fransen
- LIPIT, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Marc Espeel
- Department of Anatomy, Embryology, Histology and Medical Physics, Ghent University, Ghent, Belgium
| | - Myriam Baes
- Laboratory of Cell Metabolism, Faculty of Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Elke Van Ael
- LIPIT, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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Dhir S, Tarasenko M, Napoli E, Giulivi C. Neurological, Psychiatric, and Biochemical Aspects of Thiamine Deficiency in Children and Adults. Front Psychiatry 2019; 10:207. [PMID: 31019473 PMCID: PMC6459027 DOI: 10.3389/fpsyt.2019.00207] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/22/2019] [Indexed: 01/19/2023] Open
Abstract
Thiamine (vitamin B1) is an essential nutrient that serves as a cofactor for a number of enzymes, mostly with mitochondrial localization. Some thiamine-dependent enzymes are involved in energy metabolism and biosynthesis of nucleic acids whereas others are part of the antioxidant machinery. The brain is highly vulnerable to thiamine deficiency due to its heavy reliance on mitochondrial ATP production. This is more evident during rapid growth (i.e., perinatal periods and children) in which thiamine deficiency is commonly associated with either malnutrition or genetic defects. Thiamine deficiency contributes to a number of conditions spanning from mild neurological and psychiatric symptoms (confusion, reduced memory, and sleep disturbances) to severe encephalopathy, ataxia, congestive heart failure, muscle atrophy, and even death. This review discusses the current knowledge on thiamine deficiency and associated morbidity of neurological and psychiatric disorders, with special emphasis on the pediatric population, as well as the putative beneficial effect of thiamine supplementation in autism spectrum disorder (ASD) and other neurological conditions.
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Affiliation(s)
- Shibani Dhir
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Maya Tarasenko
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California, Davis, Davis, CA, United States
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Islam MT, Ali ES, Uddin SJ, Shaw S, Islam MA, Ahmed MI, Chandra Shill M, Karmakar UK, Yarla NS, Khan IN, Billah MM, Pieczynska MD, Zengin G, Malainer C, Nicoletti F, Gulei D, Berindan-Neagoe I, Apostolov A, Banach M, Yeung AW, El-Demerdash A, Xiao J, Dey P, Yele S, Jóźwik A, Strzałkowska N, Marchewka J, Rengasamy KR, Horbańczuk J, Kamal MA, Mubarak MS, Mishra SK, Shilpi JA, Atanasov AG. Phytol: A review of biomedical activities. Food Chem Toxicol 2018; 121:82-94. [PMID: 30130593 DOI: 10.1016/j.fct.2018.08.032] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/14/2018] [Accepted: 08/18/2018] [Indexed: 02/08/2023]
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Shinde AB, Baboota RK, Denis S, Loizides-Mangold U, Peeters A, Espeel M, Malheiro AR, Riezman H, Vinckier S, Vaz FM, Brites P, Ferdinandusse S, Van Veldhoven PP, Baes M. Mitochondrial disruption in peroxisome deficient cells is hepatocyte selective but is not mediated by common hepatic peroxisomal metabolites. Mitochondrion 2018; 39:51-59. [DOI: 10.1016/j.mito.2017.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/25/2017] [Indexed: 01/06/2023]
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Jenkins B, de Schryver E, Van Veldhoven PP, Koulman A. Peroxisomal 2-Hydroxyacyl-CoA Lyase Is Involved in Endogenous Biosynthesis of Heptadecanoic Acid. Molecules 2017; 22:molecules22101718. [PMID: 29027957 PMCID: PMC6151664 DOI: 10.3390/molecules22101718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 12/18/2022] Open
Abstract
Circulating heptadecanoic acid (C17:0) is reported to be a pathology risk/prognosis biomarker and a dietary biomarker. This pathology relationship has been shown to be reliably predictive even when independent of dietary contributions, suggesting that the endogenous biosynthesis of C17:0 is related to the pathological aetiology. Little is known about C17:0 biosynthesis, which tissues contribute to the circulating levels, and how C17:0 is related to pathology. Hacl1+/− mice were mated to obtain Hacl1−/− and Hacl1+/+ control mice. At 14 weeks, they were anesthetized for tissue collection and fatty acid analysis. Compared to Hacl1+/+, C15:0 was not significantly affected in any Hacl1−/− tissues. However, the Hacl1−/− plasma and liver C17:0 levels were significantly lower: ~26% and ~22%, respectively. No significant differences were seen in the different adipose tissues. To conclude, Hacl1 plays a significant role in the liver and plasma levels of C17:0, providing evidence it can be endogenously biosynthesized via alpha-oxidation. The strong inverse association of C17:0 with pathology raises the question whether there is a direct link between α-oxidation and these diseases. Currently, there is no clear evidence, warranting further research into the role of α-oxidation in relation to metabolic diseases.
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Affiliation(s)
- Benjamin Jenkins
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Pathology building Level 4, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
- Medical Research Council Elsie Widdowson Laboratory, Fulbourn Road, Cambridge CB1 9NL, UK.
| | - Evelyn de Schryver
- Laboratory of Lipid Biochemistry and Protein Interactions (LIPIT), Campus Gasthuisberg-KU Leuven, Herestraat Box 601, B-3000 Leuven, Belgium.
| | - Paul P. Van Veldhoven
- Laboratory of Lipid Biochemistry and Protein Interactions (LIPIT), Campus Gasthuisberg-KU Leuven, Herestraat Box 601, B-3000 Leuven, Belgium.
| | - Albert Koulman
- NIHR BRC Core Metabolomics and Lipidomics Laboratory, University of Cambridge, Pathology building Level 4, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
- Medical Research Council Elsie Widdowson Laboratory, Fulbourn Road, Cambridge CB1 9NL, UK.
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