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M M, Chhatar S, Dey S, Panda TR, Chakraborty S, Ray P, Patra C, Patra M. Analysis of Antiangiogenic Potential and Cell Death Mechanism of a Kinetically Inert Platinum Antitumor Agent. ACS Med Chem Lett 2024; 15:1482-1490. [PMID: 39291013 PMCID: PMC11403735 DOI: 10.1021/acsmedchemlett.4c00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 09/19/2024] Open
Abstract
Cancer is a multifaceted disease involving various pathological processes, including uncontrolled proliferation, development of resistance, angiogenesis, metastasis, etc. Therefore, chemotherapeutic agents capable of simultaneously inhibiting proliferation, circumventing chemoresistance, and inhibiting angiogenesis can address multiple aspects of cancer progression. We recently identified a highly promising kinetically inert platinum antitumor agent, namely, Pt-1, that can circumvent cisplatin resistance and showed negligible nephrotoxicity. In this study, we explored the antiangiogenic potential and elucidated the detailed mechanism of cell death through which it exerts its antitumor activity. Pt-1 strongly inhibited angiogenesis in a zebrafish in vivo model at its therapeutically relevant nontoxic dose. Further, Pt-1 exerted antitumor activity through necroptosis- and paraptosis-mediated cell death. Taken together, the combination of antitumor activity with antiangiogenic property in Pt-1 makes it a highly promising antitumor candidate.
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Affiliation(s)
- Manikandan M
- Medicinal Chemistry and Cell Biology Laboratory, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, Maharashtra 400005, India
| | - Sushanta Chhatar
- Medicinal Chemistry and Cell Biology Laboratory, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, Maharashtra 400005, India
| | - Saurabh Dey
- Department of Developmental Biology, Agharkar Research Institute, G G Agarkar Road, Pune, 411004 Maharashtra, India
| | - Tushar Ranjan Panda
- Medicinal Chemistry and Cell Biology Laboratory, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, Maharashtra 400005, India
| | - Sourav Chakraborty
- Imaging Cell Signaling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi Bhabha National Institute, second floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Pritha Ray
- Imaging Cell Signaling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Sector 22, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi Bhabha National Institute, second floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Chinmoy Patra
- Department of Developmental Biology, Agharkar Research Institute, G G Agarkar Road, Pune, 411004 Maharashtra, India
| | - Malay Patra
- Medicinal Chemistry and Cell Biology Laboratory, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, Maharashtra 400005, India
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2
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Zhu F, Xia L, Wen J, Zhang L. Recent Advances in the Biosynthesis of Mid- and Long-Chain Dicarboxylic Acids Using Terminally Oxidizing Unconventional Yeasts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19566-19580. [PMID: 39207200 DOI: 10.1021/acs.jafc.4c05028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
As high-performance monomers for the manufacture of polyamide materials, mid- and long-chain dicarboxylic acids (DCAi, i ≥ 6) have received extensive attention from researchers. Biosynthesis is gradually replacing chemical synthesis due to its outstanding advantages in the industrial production of mid- and long-chain dicarboxylic acids, which is mostly achieved by using the strong terminal oxidation ability of nonmodel microorganisms such as Candida tropicalis to oxidize hydrophobic substrates such as alkanes. Here, we first summarize the metabolic pathways of oxidative alkane conversion into dicarboxylic acid by terminally oxidizing unconventional yeasts and the corresponding metabolic engineering strategies. Then, we summarize the research progress on new dicarboxylic acid production processes. Finally, the future development directions in the biosynthesis of mid- and long-chain dicarboxylic acids are prospected from synthetic biology and bioprocess engineering, which can also provide a reference for the synthesis of other biobased chemicals and biomaterials.
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Affiliation(s)
- Fuzhou Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Li Xia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
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3
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Oft HC, Simon DW, Sun D. New insights into metabolism dysregulation after TBI. J Neuroinflammation 2024; 21:184. [PMID: 39075578 PMCID: PMC11288120 DOI: 10.1186/s12974-024-03177-6] [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: 05/01/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
Traumatic brain injury (TBI) remains a leading cause of death and disability that places a great physical, social, and financial burden on individuals and the health system. In this review, we summarize new research into the metabolic changes described in clinical TBI trials, some of which have already shown promise for informing injury classification and staging. We focus our discussion on derangements in glucose metabolism, cell respiration/mitochondrial function and changes to ketone and lipid metabolism/oxidation to emphasize potentially novel biomarkers for clinical outcome prediction and intervention and offer new insights into possible underlying mechanisms from preclinical research of TBI pathology. Finally, we discuss nutrition supplementation studies that aim to harness the gut/microbiome-brain connection and manipulate systemic/cellular metabolism to improve post-TBI recovery. Taken together, this narrative review summarizes published TBI-associated changes in glucose and lipid metabolism, highlighting potential metabolite biomarkers for clinical use, the cellular processes linking these markers to TBI pathology as well as the limitations and future considerations for TBI "omics" work.
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Affiliation(s)
- Helena C Oft
- Department of Neurology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, 15213, USA
- Pittsburgh Institute for Neurodegenerative Disorders, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Dennis W Simon
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dandan Sun
- Department of Neurology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, 15213, USA.
- Pittsburgh Institute for Neurodegenerative Disorders, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
- Geriatric Research, Educational and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA, 15213, USA.
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Mishra JS, Zhao H, Zheng J, Kumar S. Sex-Specific Dysregulation of Placental Lipid Metabolism in Preeclampsia. OBSTETRICS AND GYNECOLOGY RESEARCH 2024; 7:49-58. [PMID: 39131546 PMCID: PMC11315440 DOI: 10.26502/ogr0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Background Preeclampsia (PE) is a hypertensive disorder of pregnancy associated with adverse maternal and fetal outcomes. While placental dysfunction is implicated in PE pathogenesis, the impact of PE on placental lipid metabolism and its potential sexual dimorphism remains poorly understood. Methods We conducted a comprehensive analysis of term placentas from PE and normotensive pregnancies with male and female fetuses. Lipid profiles were quantified using mass spectrometry, and mRNA expression of genes involved in fatty acid oxidation, esterification, and transport was assessed using qPCR. Results Placentas from PE pregnancies exhibited elevated lipid levels, with male placentas showing a more pronounced increase in triacylglycerols, cholesteryl esters, and free cholesterol compared to female placentas. Gene expression analysis revealed sexually dimorphic alterations, with male PE placentas exhibiting upregulation of genes involved in fatty acid uptake, oxidation, and esterification, while female PE placentas showed a more complex response with both upregulation and downregulation of certain genes. Notably, peroxisomal fatty acid oxidation was upregulated in male PE placentas but suppressed in female PE placentas. Conclusions Our findings reveal sexually dimorphic alterations in placental lipid metabolism in PE, suggesting that male placentas may be more vulnerable to lipotoxicity. These insights may have implications for understanding the pathogenesis of PE and developing sex-specific interventions to improve maternal and fetal outcomes.
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Affiliation(s)
- Jay S Mishra
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Hanjie Zhao
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jing Zheng
- Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Sathish Kumar
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
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Robison ZL, Ren Q, Zhang Z. How to Survive without Water: A Short Lesson on the Desiccation Tolerance of Budding Yeast. Int J Mol Sci 2024; 25:7514. [PMID: 39062766 PMCID: PMC11277543 DOI: 10.3390/ijms25147514] [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: 06/21/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Water is essential to all life on earth. It is a major component that makes up living organisms and plays a vital role in multiple biological processes. It provides a medium for chemical and enzymatic reactions in the cell and is a major player in osmoregulation and the maintenance of cell turgidity. Despite this, many organisms, called anhydrobiotes, are capable of surviving under extremely dehydrated conditions. Less is known about how anhydrobiotes adapt and survive under desiccation stress. Studies have shown that morphological and physiological changes occur in anhydrobiotes in response to desiccation stress. Certain disaccharides and proteins, including heat shock proteins, intrinsically disordered proteins, and hydrophilins, play important roles in the desiccation tolerance of anhydrobiotes. In this review, we summarize the recent findings of desiccation tolerance in the budding yeast Saccharomyces cerevisiae. We also propose that the yeast under desiccation could be used as a model to study neurodegenerative disorders.
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Affiliation(s)
| | | | - Zhaojie Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA; (Z.L.R.); (Q.R.)
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Kaczara P, Czyzynska-Cichon I, Kus E, Kurpinska A, Olkowicz M, Wojnar-Lason K, Pacia MZ, Lytvynenko O, Baes M, Chlopicki S. Liver sinusoidal endothelial cells rely on oxidative phosphorylation but avoid processing long-chain fatty acids in their mitochondria. Cell Mol Biol Lett 2024; 29:67. [PMID: 38724891 PMCID: PMC11084093 DOI: 10.1186/s11658-024-00584-8] [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: 12/20/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND It is generally accepted that endothelial cells (ECs), primarily rely on glycolysis for ATP production, despite having functional mitochondria. However, it is also known that ECs are heterogeneous, and their phenotypic features depend on the vascular bed. Emerging evidence suggests that liver sinusoidal ECs (LSECs), located in the metabolically rich environment of the liver, show high metabolic plasticity. However, the substrate preference for energy metabolism in LSECs remains unclear. METHODS Investigations were conducted in primary murine LSECs in vitro using the Seahorse XF technique for functional bioenergetic assays, untargeted mass spectrometry-based proteomics to analyse the LSEC proteome involved in energy metabolism pathways, liquid chromatography-tandem mass spectrometry-based analysis of acyl-carnitine species and Raman spectroscopy imaging to track intracellular palmitic acid. RESULTS This study comprehensively characterized the energy metabolism of LSECs, which were found to depend on oxidative phosphorylation, efficiently fuelled by glucose-derived pyruvate, short- and medium-chain fatty acids and glutamine. Furthermore, despite its high availability, palmitic acid was not directly oxidized in LSEC mitochondria, as evidenced by the acylcarnitine profile and etomoxir's lack of effect on oxygen consumption. However, together with L-carnitine, palmitic acid supported mitochondrial respiration, which is compatible with the chain-shortening role of peroxisomal β-oxidation of long-chain fatty acids before further degradation and energy generation in mitochondria. CONCLUSIONS LSECs show a unique bioenergetic profile of highly metabolically plastic ECs adapted to the liver environment. The functional reliance of LSECs on oxidative phosphorylation, which is not a typical feature of ECs, remains to be determined.
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Affiliation(s)
- Patrycja Kaczara
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland.
| | - Izabela Czyzynska-Cichon
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Edyta Kus
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Anna Kurpinska
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Mariola Olkowicz
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Kamila Wojnar-Lason
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
- Jagiellonian University Medical College, Department of Pharmacology, Grzegorzecka 16, 31-531, Krakow, Poland
| | - Marta Z Pacia
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Olena Lytvynenko
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
| | - Myriam Baes
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Cell Metabolism, 3000, Leuven, Belgium
| | - Stefan Chlopicki
- Jagiellonian University, Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzynskiego 14, 30-348, Krakow, Poland
- Jagiellonian University Medical College, Department of Pharmacology, Grzegorzecka 16, 31-531, Krakow, Poland
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Bajdzienko J, Bremm A. Mammalian pexophagy at a glance. J Cell Sci 2024; 137:jcs259775. [PMID: 38752931 PMCID: PMC11166455 DOI: 10.1242/jcs.259775] [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] [Indexed: 05/21/2024] Open
Abstract
Peroxisomes are highly plastic organelles that are involved in several metabolic processes, including fatty acid oxidation, ether lipid synthesis and redox homeostasis. Their abundance and activity are dynamically regulated in response to nutrient availability and cellular stress. Damaged or superfluous peroxisomes are removed mainly by pexophagy, the selective autophagy of peroxisomes induced by ubiquitylation of peroxisomal membrane proteins or ubiquitin-independent processes. Dysregulated pexophagy impairs peroxisome homeostasis and has been linked to the development of various human diseases. Despite many recent insights into mammalian pexophagy, our understanding of this process is still limited compared to our understanding of pexophagy in yeast. In this Cell Science at a Glance article and the accompanying poster, we summarize current knowledge on the control of mammalian pexophagy and highlight which aspects require further attention. We also discuss the role of ubiquitylation in pexophagy and describe the ubiquitin machinery involved in regulating signals for the recruitment of phagophores to peroxisomes.
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Affiliation(s)
- Justyna Bajdzienko
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Anja Bremm
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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8
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Ognean ML, Mutică IB, Vișa GA, Șofariu CR, Matei C, Neamțu B, Cucerea M, Galiș R, Cocișiu GA, Mătăcuță-Bogdan IO. D-Bifunctional Protein Deficiency Diagnosis-A Challenge in Low Resource Settings: Case Report and Review of the Literature. Int J Mol Sci 2024; 25:4924. [PMID: 38732138 PMCID: PMC11084724 DOI: 10.3390/ijms25094924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
D-bifunctional protein deficiency (D-BPD) is a rare, autosomal recessive peroxisomal disorder that affects the breakdown of long-chain fatty acids. Patients with D-BPD typically present during the neonatal period with hypotonia, seizures, and facial dysmorphism, followed by severe developmental delay and early mortality. While some patients have survived past two years of age, the detectable enzyme activity in these rare cases was likely a contributing factor. We report a D-BPD case and comment on challenges faced in diagnosis based on a narrative literature review. An overview of Romania's first patient diagnosed with D-BPD is provided, including clinical presentation, imaging, biochemical, molecular data, and clinical course. Establishing a diagnosis can be challenging, as the clinical picture is often incomplete or similar to many other conditions. Our patient was diagnosed with type I D-BPD based on whole-exome sequencing (WES) results revealing a pathogenic frameshift variant of the HSD17B4 gene, c788del, p(Pro263GInfs*2), previously identified in another D-BPD patient. WES also identified a variant of the SUOX gene with unclear significance. We advocate for using molecular diagnosis in critically ill newborns and infants to improve care, reduce healthcare costs, and allow for familial counseling.
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Affiliation(s)
- Maria Livia Ognean
- Faculty of Medicine, Lucian Blaga University, 550025 Sibiu, Romania; (M.L.O.); (C.M.); (B.N.); (I.O.M.-B.)
- Neonatology Department, Clinical County Emergency Hospital, 550245 Sibiu, Romania
| | - Ioana Bianca Mutică
- Neonatology Department, Clinical County Emergency Hospital, 550245 Sibiu, Romania
| | - Gabriela Adriana Vișa
- Research and Telemedicine Center in Pediatric Neurology, Pediatric Clinical Hospital Sibiu, 550169 Sibiu, Romania; (G.A.V.); (C.R.Ș.)
| | - Ciprian Radu Șofariu
- Research and Telemedicine Center in Pediatric Neurology, Pediatric Clinical Hospital Sibiu, 550169 Sibiu, Romania; (G.A.V.); (C.R.Ș.)
- Pediatric Clinical Hospital Sibiu, 550169 Sibiu, Romania
| | - Claudiu Matei
- Faculty of Medicine, Lucian Blaga University, 550025 Sibiu, Romania; (M.L.O.); (C.M.); (B.N.); (I.O.M.-B.)
| | - Bogdan Neamțu
- Faculty of Medicine, Lucian Blaga University, 550025 Sibiu, Romania; (M.L.O.); (C.M.); (B.N.); (I.O.M.-B.)
- Research and Telemedicine Center in Pediatric Neurology, Pediatric Clinical Hospital Sibiu, 550169 Sibiu, Romania; (G.A.V.); (C.R.Ș.)
- Department of Computer Science and Electrical Engineering, Faculty of Engineering, Lucian Blaga University Sibiu, 550025 Sibiu, Romania
| | - Manuela Cucerea
- Department of Neonatology, George Emil Palade University of Medicine, Pharmacy, Science, and Technology, 540142 Targu Mures, Romania;
| | - Radu Galiș
- Department of Neonatology, Clinical County Emergency Hospital Bihor, 410167 Oradea, Romania;
- Department of Neonatology, Poznan University Medical Sciences, 60-512 Poznan, Poland
| | | | - Ioana Octavia Mătăcuță-Bogdan
- Faculty of Medicine, Lucian Blaga University, 550025 Sibiu, Romania; (M.L.O.); (C.M.); (B.N.); (I.O.M.-B.)
- Pediatric Clinical Hospital Sibiu, 550169 Sibiu, Romania
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9
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Whitfield-Cargile CM, Chung HC, Coleman MC, Cohen ND, Chamoun-Emanuelli AM, Ivanov I, Goldsby JS, Davidson LA, Gaynanova I, Ni Y, Chapkin RS. Integrated analysis of gut metabolome, microbiome, and exfoliome data in an equine model of intestinal injury. MICROBIOME 2024; 12:74. [PMID: 38622632 PMCID: PMC11017594 DOI: 10.1186/s40168-024-01785-1] [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: 09/13/2023] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND The equine gastrointestinal (GI) microbiome has been described in the context of various diseases. The observed changes, however, have not been linked to host function and therefore it remains unclear how specific changes in the microbiome alter cellular and molecular pathways within the GI tract. Further, non-invasive techniques to examine the host gene expression profile of the GI mucosa have been described in horses but not evaluated in response to interventions. Therefore, the objectives of our study were to (1) profile gene expression and metabolomic changes in an equine model of non-steroidal anti-inflammatory drug (NSAID)-induced intestinal inflammation and (2) apply computational data integration methods to examine host-microbiota interactions. METHODS Twenty horses were randomly assigned to 1 of 2 groups (n = 10): control (placebo paste) or NSAID (phenylbutazone 4.4 mg/kg orally once daily for 9 days). Fecal samples were collected on days 0 and 10 and analyzed with respect to microbiota (16S rDNA gene sequencing), metabolomic (untargeted metabolites), and host exfoliated cell transcriptomic (exfoliome) changes. Data were analyzed and integrated using a variety of computational techniques, and underlying regulatory mechanisms were inferred from features that were commonly identified by all computational approaches. RESULTS Phenylbutazone induced alterations in the microbiota, metabolome, and host transcriptome. Data integration identified correlation of specific bacterial genera with expression of several genes and metabolites that were linked to oxidative stress. Concomitant microbiota and metabolite changes resulted in the initiation of endoplasmic reticulum stress and unfolded protein response within the intestinal mucosa. CONCLUSIONS Results of integrative analysis identified an important role for oxidative stress, and subsequent cell signaling responses, in a large animal model of GI inflammation. The computational approaches for combining non-invasive platforms for unbiased assessment of host GI responses (e.g., exfoliomics) with metabolomic and microbiota changes have broad application for the field of gastroenterology. Video Abstract.
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Affiliation(s)
- C M Whitfield-Cargile
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA.
| | - H C Chung
- Department of Statistics, College of Arts & Sciences, Texas A&M University, College Station, TX, USA
- Mathematics & Statistics Department, College of Science, University of North Carolina Charlotte, Charlotte, NC, USA
| | - M C Coleman
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - N D Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - A M Chamoun-Emanuelli
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - I Ivanov
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - J S Goldsby
- Program in Integrative Nutrition & Complex Diseases, College of Agriculture & Life Sciences, Texas A&M University, College Station, TX, USA
| | - L A Davidson
- Program in Integrative Nutrition & Complex Diseases, College of Agriculture & Life Sciences, Texas A&M University, College Station, TX, USA
| | - I Gaynanova
- Department of Statistics, College of Arts & Sciences, Texas A&M University, College Station, TX, USA
| | - Y Ni
- Department of Statistics, College of Arts & Sciences, Texas A&M University, College Station, TX, USA
| | - R S Chapkin
- Program in Integrative Nutrition & Complex Diseases, College of Agriculture & Life Sciences, Texas A&M University, College Station, TX, USA
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Wang-Heaton H, Wingard MC, Dalal S, Shook PL, Connelly BA, Johnson P, Nichols PL, Singh M, Singh K. ATM deficiency differentially affects expression of proteins related to fatty acid oxidation and oxidative stress in a sex-specific manner in response to Western-type diet prior to and following myocardial infarction. Life Sci 2024; 342:122541. [PMID: 38428572 PMCID: PMC10949412 DOI: 10.1016/j.lfs.2024.122541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
AIMS Published work has shown that ataxia-telangiectasia mutated kinase (ATM) deficiency is associated with cardioprotective effects in Western-type diet (WD)-fed female mice. This study assessed the expression of proteins related to fatty acid oxidation (FAO) and oxidative stress in WD-fed male and female mouse hearts, and investigated if sex-specific cardioprotective effects in WD-fed female ATM-deficient mice are maintained following myocardial infarction (MI). MAIN METHODS Wild-type (WT) and ATM-deficient (hKO) mice (both sexes) were placed on WD for 14 weeks. Myocardial tissue from a subset of mice was used for western blot analyses, while another subset of WD-fed mice underwent MI. Heart function was analyzed by echocardiography prior to and 1 day post-MI. KEY FINDINGS CPT1B (mitochondrial FAO enzyme) expression was lower in male hKO-WD, while it was higher in female hKO-WD vs WT-WD. WD-mediated decrease in ACOX1 (peroxisomal FAO enzyme) expression was only observed in male WT-WD. PMP70 (transports fatty acyl-CoA across peroxisomal membrane) expression was lower in male hKO-WD vs WT-WD. Catalase (antioxidant enzyme) expression was higher, while Nox4 (pro-oxidant enzyme) expression was lower in female hKO-WD vs WT-WD. Heart function was better in female hKO-WD vs WT-WD. However, post-MI heart function was not significantly different among all MI groups. Post-MI, CPT1B and catalase expression was higher in male hKO-WD-MI vs WT-WD-MI, while Nox4 expression was higher in female hKO-WD-MI vs WT-WD-MI. SIGNIFICANCE Increased mitochondrial FAO and decreased oxidative stress contribute towards ATM deficiency-mediated cardioprotective effects in WD-fed female mice which are abolished post-MI with increased Nox4 expression.
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Affiliation(s)
- Hui Wang-Heaton
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Mary C Wingard
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Suman Dalal
- Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, TN, USA; Center of Excellence in Inflammation, Infectious Disease and Immunity, East Tennessee State University, Johnson City, TN, USA
| | - Paige L Shook
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Barbara A Connelly
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Patrick Johnson
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Phillip L Nichols
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Mahipal Singh
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Krishna Singh
- Department of Biomedical Sciences, James H Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA; Center of Excellence in Inflammation, Infectious Disease and Immunity, East Tennessee State University, Johnson City, TN, USA; Center for Cardiovascular Risk Research, East Tennessee State University, Johnson City, TN, USA; James H Quillen Veterans Affairs Medical Center, Mountain Home, TN, USA.
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11
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Gu S, Zhu F, Zhang L, Wen J. Mid-Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5555-5573. [PMID: 38442481 DOI: 10.1021/acs.jafc.4c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Mid-to-long-chain dicarboxylic acids (DCAi, i ≥ 6) are organic compounds in which two carboxylic acid functional groups are present at the terminal position of the carbon chain. These acids find important applications as structural components and intermediates across various industrial sectors, including organic compound synthesis, food production, pharmaceutical development, and agricultural manufacturing. However, conventional petroleum-based DCA production methods cause environmental pollution, making sustainable development challenging. Hence, the demand for eco-friendly processes and renewable raw materials for DCA production is rising. Owing to advances in systems metabolic engineering, new tools from systems biology, synthetic biology, and evolutionary engineering can now be used for the sustainable production of energy-dense biofuels. Here, we explore systems metabolic engineering strategies for DCA synthesis in various chassis via the conversion of different raw materials into mid-to-long-chain DCAs. Subsequently, we discuss the future challenges in this field and propose synthetic biology approaches for the efficient production and successful commercialization of these acids.
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Affiliation(s)
- Shanna Gu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Fuzhou Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
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12
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Manoharan RR, Prasad A, Pospíšil P, Kzhyshkowska J. ROS signaling in innate immunity via oxidative protein modifications. Front Immunol 2024; 15:1359600. [PMID: 38515749 PMCID: PMC10954773 DOI: 10.3389/fimmu.2024.1359600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
The innate immune response represents the first-line of defense against invading pathogens. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) have been implicated in various aspects of innate immune function, which involves respiratory bursts and inflammasome activation. These reactive species widely distributed within the cellular environment are short-lived intermediates that play a vital role in cellular signaling and proliferation and are likely to depend on their subcellular site of formation. NADPH oxidase complex of phagocytes is known to generate superoxide anion radical (O2 •-) that functions as a precursor for antimicrobial hydrogen peroxide (H2O2) production, and H2O2 is utilized by myeloperoxidase (MPO) to generate hypochlorous acid (HOCl) that mediates pathogen killing. H2O2 modulates the expression of redox-responsive transcriptional factors, namely NF-kB, NRF2, and HIF-1, thereby mediating redox-based epigenetic modification. Survival and function of immune cells are under redox control and depend on intracellular and extracellular levels of ROS/RNS. The current review focuses on redox factors involved in the activation of immune response and the role of ROS in oxidative modification of proteins in macrophage polarization and neutrophil function.
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Affiliation(s)
| | - Ankush Prasad
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Pavel Pospíšil
- Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and Immunology, Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
- Laboratory of Translational Cellular and Molecular Biomedicine, National Research Tomsk State University, Tomsk, Russia
- Laboratory of Genetic Technologies, Siberian State Medical University, Tomsk, Russia
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13
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Kalidasan V, Suresh D, Zulkifle N, Hwei YS, Kok Hoong L, Rajasuriar R, Theva Das K. Investigating D-Amino Acid Oxidase Expression and Interaction Network Analyses in Pathways Associated With Cellular Stress: Implications in the Biology of Aging. Bioinform Biol Insights 2024; 18:11779322241234772. [PMID: 38425413 PMCID: PMC10903195 DOI: 10.1177/11779322241234772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
D-amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids by oxidative deamination, producing hydrogen peroxide (H2O2) as a by-product. The generation of intracellular H2O2 may alter the redox-homeostasis mechanism of cells and increase the oxidative stress levels in tissues, associated with the pathogenesis of age-related diseases and organ decline. This study investigates the effect of DAO knockdown using clustered regularly interspaced short palindromic repeats (CRISPR) through an in silico approach on its protein-protein interactions (PPIs) and their potential roles in the process of aging. The target sequence and guide RNA of DAO were designed using the CCTop database, PPI analysis using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, Reactome biological pathway, protein docking using GalaxyTongDock database, and structure analysis. The translated target sequence of DAO lies between amino acids 43 to 50. The 10 proteins that were predicted to interact with DAO are involved in peroxisome pathways such as acyl-coenzyme A oxidase 1 (ACOX1), alanine-glyoxylate and serine-pyruvate aminotransferase (AGXT), catalase (CAT), carnitine O-acetyltransferase (CRAT), glyceronephosphate O-acyltransferase (GNPAT), hydroxyacid oxidase 1 (HAO1), hydroxyacid oxidase 2 (HAO2), trans-L-3-hydroxyproline dehydratase (L3HYPDH), polyamine oxidase (PAOX), and pipecolic acid and sarcosine oxidase (PIPOX). In summary, DAO mutation would most likely reduce activity with its interacting proteins that generate H2O2. However, DAO mutation may result in peroxisomal disorders, and thus, alternative techniques should be considered for an in vivo approach.
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Affiliation(s)
- V Kalidasan
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
| | - Darshinie Suresh
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Nurulisa Zulkifle
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
| | - Yap Siew Hwei
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Leong Kok Hoong
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Reena Rajasuriar
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- Centre of Excellence for Research in AIDS (CERiA), Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kumitaa Theva Das
- Department of Biomedical Sciences, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Malaysia
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14
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Zheng D, Li F, Wang S, Liu PS, Xie X. High-content image screening to identify chemical modulators for peroxisome and ferroptosis. Cell Mol Biol Lett 2024; 29:26. [PMID: 38368371 PMCID: PMC10874541 DOI: 10.1186/s11658-024-00544-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND The peroxisome is a dynamic organelle with variety in number, size, shape, and activity in different cell types and physiological states. Recent studies have implicated peroxisomal homeostasis in ferroptosis susceptibility. Here, we developed a U-2OS cell line with a fluorescent peroxisomal tag and screened a target-selective chemical library through high-content imaging analysis. METHODS U-2OS cells stably expressing the mOrange2-Peroxisomes2 tag were generated to screen a target-selective inhibitor library. The nuclear DNA was counterstained with Hoechst 33342 for cell cycle analysis. Cellular images were recorded and quantitatively analyzed through a high-content imaging platform. The effect of selected compounds on ferroptosis induction was analyzed in combination with ferroptosis inducers (RSL3 and erastin). Flow cytometry analysis was conducted to assess the level of reactive oxygen species (ROS) and cell death events. RESULTS Through the quantification of DNA content and peroxisomal signals in single cells, we demonstrated that peroxisomal abundance was closely linked with cell cycle progression and that peroxisomal biogenesis mainly occurred in the G1/S phase. We further identified compounds that positively and negatively regulated peroxisomal abundance without significantly affecting the cell cycle distribution. Some compounds promoted peroxisomal signals by inducing oxidative stress, while others regulated peroxisomal abundance independent of redox status. Importantly, compounds with peroxisome-enhancing activity potentiated ferroptosis induction. CONCLUSIONS Our findings pinpoint novel cellular targets that might be involved in peroxisome homeostasis and indicate that compounds promoting peroxisomal abundance could be jointly applied with ferroptosis inducers to potentiate anticancer effect.
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Affiliation(s)
- Daheng Zheng
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing City, Zhejiang, China
| | - Fei Li
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing City, Zhejiang, China
| | - Shanshan Wang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangdong, China
| | - Pu-Ste Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Xin Xie
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing City, Zhejiang, China.
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15
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Plessner M, Thiele L, Hofhuis J, Thoms S. Tissue-specific roles of peroxisomes revealed by expression meta-analysis. Biol Direct 2024; 19:14. [PMID: 38365851 PMCID: PMC10873952 DOI: 10.1186/s13062-024-00458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Peroxisomes are primarily studied in the brain, kidney, and liver due to the conspicuous tissue-specific pathology of peroxisomal biogenesis disorders. In contrast, little is known about the role of peroxisomes in other tissues such as the heart. In this meta-analysis, we explore mitochondrial and peroxisomal gene expression on RNA and protein levels in the brain, heart, kidney, and liver, focusing on lipid metabolism. Further, we evaluate a potential developmental and heart region-dependent specificity of our gene set. We find marginal expression of the enzymes for peroxisomal fatty acid oxidation in cardiac tissue in comparison to the liver or cardiac mitochondrial β-oxidation. However, the expression of peroxisome biogenesis proteins in the heart is similar to other tissues despite low levels of peroxisomal fatty acid oxidation. Strikingly, peroxisomal targeting signal type 2-containing factors and plasmalogen biosynthesis appear to play a fundamental role in explaining the essential protective and supporting functions of cardiac peroxisomes.
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Affiliation(s)
- Matthias Plessner
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Leonie Thiele
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Julia Hofhuis
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sven Thoms
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany.
- Department of Child and Adolescent Health, University Medical Center, Göttingen, Germany.
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16
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Sun S, Zhao G, Jia M, Jiang Q, Li S, Wang H, Li W, Wang Y, Bian X, Zhao YG, Huang X, Yang G, Cai H, Pastor-Pareja JC, Ge L, Zhang C, Hu J. Stay in touch with the endoplasmic reticulum. SCIENCE CHINA. LIFE SCIENCES 2024; 67:230-257. [PMID: 38212460 DOI: 10.1007/s11427-023-2443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024]
Abstract
The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.
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Affiliation(s)
- Sha Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gan Zhao
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjing Li
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yan G Zhao
- Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ge Yang
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jose C Pastor-Pareja
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Neurosciences, Consejo Superior de Investigaciones Cientfflcas-Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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17
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Landowski M, Gogoi P, Ikeda S, Ikeda A. Roles of transmembrane protein 135 in mitochondrial and peroxisomal functions - implications for age-related retinal disease. FRONTIERS IN OPHTHALMOLOGY 2024; 4:1355379. [PMID: 38576540 PMCID: PMC10993500 DOI: 10.3389/fopht.2024.1355379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Aging is the most significant risk factor for age-related diseases in general, which is true for age-related diseases in the eye including age-related macular degeneration (AMD). Therefore, in order to identify potential therapeutic targets for these diseases, it is crucial to understand the normal aging process and how its mis-regulation could cause age-related diseases at the molecular level. Recently, abnormal lipid metabolism has emerged as one major aspect of age-related symptoms in the retina. Animal models provide excellent means to identify and study factors that regulate lipid metabolism in relation to age-related symptoms. Central to this review is the role of transmembrane protein 135 (TMEM135) in the retina. TMEM135 was identified through the characterization of a mutant mouse strain exhibiting accelerated retinal aging and positional cloning of the responsible mutation within the gene, indicating the crucial role of TMEM135 in regulating the normal aging process in the retina. Over the past decade, the molecular functions of TMEM135 have been explored in various models and tissues, providing insights into the regulation of metabolism, particularly lipid metabolism, through its action in multiple organelles. Studies indicated that TMEM135 is a significant regulator of peroxisomes, mitochondria, and their interaction. Here, we provide an overview of the molecular functions of TMEM135 which is crucial for regulating mitochondria, peroxisomes, and lipids. The review also discusses the age-dependent phenotypes in mice with TMEM135 perturbations, emphasizing the importance of a balanced TMEM135 function for the health of the retina and other tissues including the heart, liver, and adipose tissue. Finally, we explore the potential roles of TMEM135 in human age-related retinal diseases, connecting its functions to the pathobiology of AMD.
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Affiliation(s)
- Michael Landowski
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Purnima Gogoi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Sakae Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
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18
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Osiewacz HD. The impact of biomembranes and their dynamics on organismic aging: insights from a fungal aging model. FRONTIERS IN AGING 2024; 5:1356697. [PMID: 38327611 PMCID: PMC10847301 DOI: 10.3389/fragi.2024.1356697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Biomembranes fulfill several essential functions. They delimitate cells and control the exchange of compounds between cells and the environment. They generate specialized cellular reaction spaces, house functional units such as the respiratory chain (RC), and are involved in content trafficking. Biomembranes are dynamic and able to adjust their properties to changing conditions and requirements. An example is the inner mitochondrial membrane (IMM), which houses the RC involved in the formation of adenosine triphosphate (ATP) and the superoxide anion as a reactive oxygen species (ROS). The IMM forms a characteristic ultrastructure that can adapt to changing physiological situations. In the fungal aging model Podospora anserina, characteristic age-related changes of the mitochondrial ultrastructure occur. More recently, the impact of membranes on aging was extended to membranes involved in autophagy, an important pathway involved in cellular quality control (QC). Moreover, the effect of oleic acid on the lifespan was linked to basic biochemical processes and the function of membranes, providing perspectives for the elucidation of the mechanistic effects of this nutritional component, which positively affects human health and aging.
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Affiliation(s)
- Heinz D. Osiewacz
- Institute for Molecular Biosciences, Faculty of Biosciences, Goethe University, Frankfurt, Germany
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19
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Rashan EH, Bartlett AK, Khana DB, Zhang J, Jain R, Smith AJ, Baker ZN, Cook T, Caldwell A, Chevalier AR, Pfleger BF, Yuan P, Amador-Noguez D, Simcox JA, Pagliarini DJ. ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574893. [PMID: 38260250 PMCID: PMC10802472 DOI: 10.1101/2024.01.09.574893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Fatty acid β-oxidation (FAO) is a central catabolic pathway with broad implications for organismal health. However, various fatty acids are largely incompatible with standard FAO machinery until they are modified by other enzymes. Included among these are the 4-hydroxy acids (4-HAs)-fatty acids hydroxylated at the 4 (γ) position-which can be provided from dietary intake, lipid peroxidation, and certain drugs of abuse. Here, we reveal that two atypical and poorly characterized acyl-CoA dehydrogenases (ACADs), ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains N-terminal to their ACAD domains that phosphorylate the 4-OH position as a requisite step in the conversion of 4-hydroxyacyl-CoAs into 2-enoyl-CoAs-conventional FAO intermediates. Our ACAD11 cryo-EM structure and molecular modeling reveal a unique binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma while comparable 3- and 5-hydroxy acids remain unchanged. Collectively, this work defines ACAD10 and ACAD11 as the primary gatekeepers of mammalian 4-HA catabolism and sets the stage for broader investigations into the ramifications of aberrant 4-HA metabolism in human health and disease.
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Affiliation(s)
- Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Abigail K. Bartlett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Daven B. Khana
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jingying Zhang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Raghav Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew J. Smith
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Zakery N. Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Taylor Cook
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Alana Caldwell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Autumn R. Chevalier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Daniel Amador-Noguez
- Department of Microbiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith A. Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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20
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Kashyap I, Deb R, Battineni A, Nagotu S. Acyl CoA oxidase: from its expression, structure, folding, and import to its role in human health and disease. Mol Genet Genomics 2023; 298:1247-1260. [PMID: 37555868 DOI: 10.1007/s00438-023-02059-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/24/2023] [Indexed: 08/10/2023]
Abstract
β-oxidation of fatty acids is an important metabolic pathway and is a shared function between mitochondria and peroxisomes in mammalian cells. On the other hand, peroxisomes are the sole site for the degradation of fatty acids in yeast. The first reaction of this pathway is catalyzed by the enzyme acyl CoA oxidase housed in the matrix of peroxisomes. Studies in various model organisms have reported the conserved function of the protein in fatty acid oxidation. The importance of this enzyme is highlighted by the lethal conditions caused in humans due to its altered function. In this review, we discuss various aspects ranging from gene expression, structure, folding, and import of the protein in both yeast and human cells. Further, we highlight recent findings on the role of the protein in human health and aging, and discuss the identified mutations in the protein associated with debilitating conditions in patients.
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Affiliation(s)
- Isha Kashyap
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Rachayeeta Deb
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Abhigna Battineni
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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21
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Bingham PM, Zachar Z. Toward a Unifying Hypothesis for Redesigned Lipid Catabolism as a Clinical Target in Advanced, Treatment-Resistant Carcinomas. Int J Mol Sci 2023; 24:14365. [PMID: 37762668 PMCID: PMC10531647 DOI: 10.3390/ijms241814365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
We review extensive progress from the cancer metabolism community in understanding the specific properties of lipid metabolism as it is redesigned in advanced carcinomas. This redesigned lipid metabolism allows affected carcinomas to make enhanced catabolic use of lipids in ways that are regulated by oxygen availability and is implicated as a primary source of resistance to diverse treatment approaches. This oxygen control permits lipid catabolism to be an effective energy/reducing potential source under the relatively hypoxic conditions of the carcinoma microenvironment and to do so without intolerable redox side effects. The resulting robust access to energy and reduced potential apparently allow carcinoma cells to better survive and recover from therapeutic trauma. We surveyed the essential features of this advanced carcinoma-specific lipid catabolism in the context of treatment resistance and explored a provisional unifying hypothesis. This hypothesis is robustly supported by substantial preclinical and clinical evidence. This approach identifies plausible routes to the clinical targeting of many or most sources of carcinoma treatment resistance, including the application of existing FDA-approved agents.
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Affiliation(s)
- Paul M. Bingham
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;
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22
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Smith G, Sweeney ST, O’Kane CJ, Prokop A. How neurons maintain their axons long-term: an integrated view of axon biology and pathology. Front Neurosci 2023; 17:1236815. [PMID: 37564364 PMCID: PMC10410161 DOI: 10.3389/fnins.2023.1236815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
Axons are processes of neurons, up to a metre long, that form the essential biological cables wiring nervous systems. They must survive, often far away from their cell bodies and up to a century in humans. This requires self-sufficient cell biology including structural proteins, organelles, and membrane trafficking, metabolic, signalling, translational, chaperone, and degradation machinery-all maintaining the homeostasis of energy, lipids, proteins, and signalling networks including reactive oxygen species and calcium. Axon maintenance also involves specialised cytoskeleton including the cortical actin-spectrin corset, and bundles of microtubules that provide the highways for motor-driven transport of components and organelles for virtually all the above-mentioned processes. Here, we aim to provide a conceptual overview of key aspects of axon biology and physiology, and the homeostatic networks they form. This homeostasis can be derailed, causing axonopathies through processes of ageing, trauma, poisoning, inflammation or genetic mutations. To illustrate which malfunctions of organelles or cell biological processes can lead to axonopathies, we focus on axonopathy-linked subcellular defects caused by genetic mutations. Based on these descriptions and backed up by our comprehensive data mining of genes linked to neural disorders, we describe the 'dependency cycle of local axon homeostasis' as an integrative model to explain why very different causes can trigger very similar axonopathies, providing new ideas that can drive the quest for strategies able to battle these devastating diseases.
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Affiliation(s)
- Gaynor Smith
- Cardiff University, School of Medicine, College of Biomedical and Life Sciences, Cardiff, United Kingdom
| | - Sean T. Sweeney
- Department of Biology, University of York and York Biomedical Research Institute, York, United Kingdom
| | - Cahir J. O’Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Prokop
- Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, The University of Manchester, Manchester, United Kingdom
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23
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de Mello NP, Fecher C, Pastor AM, Perocchi F, Misgeld T. Ex vivo immunocapture and functional characterization of cell-type-specific mitochondria using MitoTag mice. Nat Protoc 2023:10.1038/s41596-023-00831-w. [PMID: 37328604 DOI: 10.1038/s41596-023-00831-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Mitochondria are key bioenergetic organelles involved in many biosynthetic and signaling pathways. However, their differential contribution to specific functions of cells within complex tissues is difficult to dissect with current methods. The present protocol addresses this need by enabling the ex vivo immunocapture of cell-type-specific mitochondria directly from their tissue context through a MitoTag reporter mouse. While other available methods were developed for bulk mitochondria isolation or more abundant cell-type-specific mitochondria, this protocol was optimized for the selective isolation of functional mitochondria from medium-to-low-abundant cell types in a heterogeneous tissue, such as the central nervous system. The protocol has three major parts: First, mitochondria of a cell type of interest are tagged via an outer mitochondrial membrane eGFP by crossing MitoTag mice to a cell-type-specific Cre-driver line or by delivery of viral vectors for Cre expression. Second, homogenates are prepared from relevant tissues by nitrogen cavitation, from which tagged organelles are immunocaptured using magnetic microbeads. Third, immunocaptured mitochondria are used for downstream assays, e.g., to probe respiratory capacity or calcium handling, revealing cell-type-specific mitochondrial diversity in molecular composition and function. The MitoTag approach enables the identification of marker proteins to label cell-type-specific organelle populations in situ, elucidates cell-type-enriched mitochondrial metabolic and signaling pathways, and reveals functional mitochondrial diversity between adjacent cell types in complex tissues, such as the brain. Apart from establishing the mouse colony (6-8 weeks without import), the immunocapture protocol takes 2 h and functional assays require 1-2 h.
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Affiliation(s)
- Natalia Prudente de Mello
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians Universität München, Munich, Germany
| | - Caroline Fecher
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians Universität München, Munich, Germany
- Department of Cell Biology & Physiology, School of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Adrian Marti Pastor
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany
| | - Fabiana Perocchi
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
- German Center for Neurodegenerative Diseases, Munich, Germany.
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24
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Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539585. [PMID: 37205355 PMCID: PMC10187285 DOI: 10.1101/2023.05.06.539585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mammalian organs exhibit distinct physiology, disease susceptibility and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA-seq data demonstrated sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors demonstrated androgen receptor (AR) mediated regulation of gene activity in PT cells as the regulatory mechanism. Interestingly, caloric restriction feminizes the male kidney. Single-nuclear multiomic analysis identified putative cis-regulatory regions and cooperating factors mediating PT responses to AR activity in the mouse kidney. In the human kidney, a limited set of genes showed conserved sex-linked regulation while analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. These findings raise interesting questions on the evolution, physiological significance, and disease and metabolic linkage, of sexually dimorphic gene activity.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Seung Yub Han
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Megan Rommelfanger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center at Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Lead Contact
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25
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Kuna RS, Kumar A, Wessendorf-Rodriguez KA, Galvez H, Green CR, McGregor GH, Cordes T, Shaw RJ, Svensson RU, Metallo CM. Inter-organelle cross-talk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress. SCIENCE ADVANCES 2023; 9:eadf0138. [PMID: 37134162 PMCID: PMC10156121 DOI: 10.1126/sciadv.adf0138] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023]
Abstract
Proliferating cells rely on acetyl-CoA to support membrane biogenesis and acetylation. Several organelle-specific pathways are available for provision of acetyl-CoA as nutrient availability fluctuates, so understanding how cells maintain acetyl-CoA homeostasis under such stresses is critically important. To this end, we applied 13C isotope tracing cell lines deficient in these mitochondrial [ATP-citrate lyase (ACLY)]-, cytosolic [acetyl-CoA synthetase (ACSS2)]-, and peroxisomal [peroxisomal biogenesis factor 5 (PEX5)]-dependent pathways. ACLY knockout in multiple cell lines reduced fatty acid synthesis and increased reliance on extracellular lipids or acetate. Knockout of both ACLY and ACSS2 (DKO) severely stunted but did not entirely block proliferation, suggesting that alternate pathways can support acetyl-CoA homeostasis. Metabolic tracing and PEX5 knockout studies link peroxisomal oxidation of exogenous lipids as a major source of acetyl-CoA for lipogenesis and histone acetylation in cells lacking ACLY, highlighting a role for inter-organelle cross-talk in supporting cell survival in response to nutrient fluctuations.
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Affiliation(s)
- Ramya S. Kuna
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Avi Kumar
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karl A. Wessendorf-Rodriguez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hector Galvez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Courtney R. Green
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace H. McGregor
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thekla Cordes
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Reuben J. Shaw
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Christian M. Metallo
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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26
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Bravo-Sagua R, Lopez-Crisosto C, Criollo A, Inagi R, Lavandero S. Organelle Communication: Joined in Sickness and in Health. Physiology (Bethesda) 2023; 38:0. [PMID: 36856309 DOI: 10.1152/physiol.00024.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Organelles are membrane-lined structures that compartmentalize subcellular biochemical functions. Therefore, interorganelle communication is crucial for cellular responses that require the coordination of such functions. Multiple principles govern interorganelle interactions, which arise from the complex nature of organelles: position, multilingualism, continuity, heterogeneity, proximity, and bidirectionality, among others. Given their importance, alterations in organelle communication have been linked to many diseases. Among the different types of contacts, endoplasmic reticulum mitochondria interactions are the best known; however, mounting evidence indicates that other organelles also have something to say in the pathophysiological conversation.
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Affiliation(s)
- Roberto Bravo-Sagua
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Pharmaceutical and Chemical Sciences and Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Laboratory of Obesity and Metabolism (OMEGA), Institute of Nutrition and Food Technology (INTA), Universidad de Chile, Santiago, Chile.,Interuniversity Center for Healthy Aging (CIES), Consortium of Universities of the State of Chile (CUECH), Santiago, Chile
| | - Camila Lopez-Crisosto
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Pharmaceutical and Chemical Sciences and Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Alfredo Criollo
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Pharmaceutical and Chemical Sciences and Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Cellular and Molecular Biology Laboratory, Institute in Dentistry Sciences, Dentistry Faculty, Universidad de Chile, Santiago, Chile
| | - Reiko Inagi
- Division of Chronic Kidney Disease Pathophysiology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Faculty of Pharmaceutical and Chemical Sciences and Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Department of Internal Medicine, Cardiology Division, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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27
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Chen L, Chou CL, Yang CR, Knepper MA. Multiomics Analyses Reveal Sex Differences in Mouse Renal Proximal Subsegments. J Am Soc Nephrol 2023; 34:829-845. [PMID: 36758122 PMCID: PMC10125651 DOI: 10.1681/asn.0000000000000089] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
SIGNIFICANCE STATEMENT Sex-dependent differences in kidney function are recognized but the underlying molecular mechanisms are largely unexplored. Advances in genomics and proteomic technologies now allow extensive characterization of differences between the same cell types of males and females. Multiomics integrating RNA-seq, ATAC-seq, and proteomics data to investigate differences in gene expression, chromatin accessibility, and protein expression in proximal tubules of male and female mice identified many sex-biased genes and proteins associated with kidney functions, including metabolic and transport processes. Sex differences may also arise from variations of the interaction between transcription factors and accessible chromatin regions. A comprehensive web resource is provided to advance understanding of sex differences in cells of the proximal tubule. BACKGROUND Sex differences have been increasingly recognized as important in kidney physiology and pathophysiology, but limited resources are available for comprehensive interrogation of sex differences. METHODS RNA-seq and ATAC-seq of microdissected mouse proximal tubules and protein mass spectrometry of homogenized perfused mouse kidneys reveal differences in proximal tubule cells of males and females. RESULTS The transcriptomic data indicated that the major differences in the proximal tubules between the sexes were in the S2/S3 segments, and most of the sex-biased transcripts mapped to autosomes rather than to the sex chromosomes. Many of the transcripts exhibiting sex-biased expression are involved in monocarboxylic acid metabolic processes, organic anion transport, and organic acid transport. The ATAC-seq method on microdissected tubules captured chromatin accessibility. Many of the more than 7000 differentially accessible DNA regions identified were in distal regions. Motif analyses revealed a lack of direct involvement of estrogen receptors or the androgen receptor (absence of canonical hormone response elements), suggesting an indirect regulatory role of sex hormones. Instead, analyses identified several transcription factors (TFs) ( Tead1 , Nfia/b , and Pou3f3 ) whose interplay with proximal tubule-specific TFs ( e.g. , Hnf1b , Hnf4a ) may contribute to sex differences. Finally, the whole-kidney proteome was correlated with the transcriptome, and many sex-biased proteins ( e.g. , Cyp2e1, Acsm2/3) were identified. CONCLUSIONS Sex-dependent cis-regulatory elements interact with TFs in ways that lead to sex-biased gene expression in proximal tubule cells. These data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/MRECA/PT/ .
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Affiliation(s)
- Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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28
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Aleksic M, Golic I, Jankovic A, Cvoro A, Korac A. ACOX-driven peroxisomal heterogeneity and functional compartmentalization in brown adipocytes of hypothyroid rats. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230109. [PMID: 37153362 PMCID: PMC10154930 DOI: 10.1098/rsos.230109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023]
Abstract
We previously demonstrated that hypothyroidism increases peroxisomal biogenesis in rat brown adipose tissue (BAT). We also showed heterogeneity in peroxisomal origin and their unique structural association with mitochondria and/or lipid bodies to carry out β-oxidation, contributing thus to BAT thermogenesis. Distinctive heterogeneity creates structural compartmentalization within peroxisomal population, raising the question of whether it is followed by their functional compartmentalization regarding localization/colocalization of two main acyl-CoA oxidase (ACOX) isoforms, ACOX1 and ACOX3. ACOX is the first and rate-limiting enzyme of peroxisomal β-oxidation, and, to date, their protein expression patterns in BAT have not been fully defined. Therefore, we used methimazole-induced hypothyroidism to study ACOX1 and ACOX3 protein expression and their tissue immunolocalization. Additionally, we analysed their specific peroxisomal localization and colocalization in parallel with peroxisomal structural compartmentalization in brown adipocytes. Hypothyroidism caused a linear increase in ACOX1 expression, while a temporary decrease in ACOX3 levels is only recovered to the control level at day 21. Peroxisomal ACOX1 and ACOX3 localization and colocalization patterns entirely mirrored heterogeneous peroxisomal biogenesis pathways and structural compartmentalization, e.g. associations with mitochondria and/or lipid bodies. Hence, different ACOX isoforms localization/colocalization creates distinct functional heterogeneity of peroxisomes and drives their functional compartmentalization in rat brown adipocytes.
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Affiliation(s)
- Marija Aleksic
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
| | - Igor Golic
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
| | - Aleksandra Jankovic
- Institute for Biological Research 'Sinisa Stankovic'—National Institute of Republic of Serbia, University of Belgrade, Belgrade 11000, Serbia
| | - Aleksandra Cvoro
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
| | - Aleksandra Korac
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
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29
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Phung NV, Rong F, Xia WY, Fan Y, Li XY, Wang SA, Li FL. Nervonic acid and its sphingolipids: Biological functions and potential food applications. Crit Rev Food Sci Nutr 2023; 64:8766-8785. [PMID: 37114919 DOI: 10.1080/10408398.2023.2203753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Nervonic acid, a 24-carbon fatty acid with only one double bond at the 9th carbon (C24:1n-9), is abundant in the human brain, liver, and kidney. It not only functions in free form but also serves as a critical component of sphingolipids which participate in many biological processes such as cell membrane formation, apoptosis, and neurotransmission. Recent studies show that nervonic acid supplementation is not only beneficial to human health but also can improve the many medical conditions such as neurological diseases, cancers, diabetes, obesity, and their complications. Nervonic acid and its sphingomyelins serve as a special material for myelination in infants and remyelination patients with multiple sclerosis. Besides, the administration of nervonic acid is reported to reduce motor disorder in mice with Parkinson's disease and limit weight gain. Perturbations of nervonic acid and its sphingolipids might lead to the pathogenesis of many diseases and understanding these mechanisms is critical for investigating potential therapeutic approaches for such diseases. However, available studies about this aspect are limited. In this review, relevant findings about functional mechanisms of nervonic acid have been comprehensively and systematically described, focusing on four interconnected functions: cellular structure, signaling, anti-inflammation, lipid mobilization, and their related diseases.
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Affiliation(s)
- Nghi Van Phung
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Fei Rong
- Department of Anesthesiology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Wan Yue Xia
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yong Fan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Xian Yu Li
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Shi An Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
| | - Fu Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- Shandong Energy Institute, Qingdao, China
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30
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Wang Z, Brannick E, Abasht B. Integrative transcriptomic and metabolomic analysis reveals alterations in energy metabolism and mitochondrial functionality in broiler chickens with wooden breast. Sci Rep 2023; 13:4747. [PMID: 36959331 PMCID: PMC10036619 DOI: 10.1038/s41598-023-31429-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/11/2023] [Indexed: 03/25/2023] Open
Abstract
This integrative study of transcriptomics and metabolomics aimed to improve our understanding of Wooden Breast myopathy (WB). Breast muscle samples from 8 WB affected and 8 unaffected male broiler chickens of 47 days of age were harvested for metabolite profiling. Among these 16 samples, 5 affected and 6 unaffected also underwent gene expression profiling. The Joint Pathway Analysis was applied on 119 metabolites and 3444 genes exhibiting differential abundance or expression between WB affected and unaffected chickens. Mitochondrial dysfunctions in WB was suggested by higher levels of monoacylglycerols and down-regulated genes involved in lipid production, fatty acid beta oxidation, and oxidative phosphorylation. Lower levels of carnosine and anserine, along with down-regulated carnosine synthase 1 suggested decreased carnosine synthesis and hence impaired antioxidant capacity in WB. Additionally, Weighted Gene Co-expression Network Analysis results indicated that abundance of inosine monophosphate, significantly lower in WB muscle, was correlated with mRNA expression levels of numerous genes related to focal adhesion, extracellular matrix and intercellular signaling, implying its function in connecting and possibly regulating multiple key biological pathways. Overall, this study showed not only the consistency between transcript and metabolite profiles, but also the potential in gaining further insights from analyzing multi-omics data.
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Affiliation(s)
- Ziqing Wang
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
| | - Erin Brannick
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
| | - Behnam Abasht
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA.
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31
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Rodencal J, Dixon SJ. A tale of two lipids: Lipid unsaturation commands ferroptosis sensitivity. Proteomics 2023; 23:e2100308. [PMID: 36398995 DOI: 10.1002/pmic.202100308] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022]
Abstract
Membrane lipids play important roles in the regulation of cell fate, including the execution of ferroptosis. Ferroptosis is a non-apoptotic cell death mechanism defined by iron-dependent membrane lipid peroxidation. Phospholipids containing polyunsaturated fatty acids (PUFAs) are highly vulnerable to peroxidation and are essential for ferroptosis execution. By contrast, the incorporation of less oxidizable monounsaturated fatty acids (MUFAs) in membrane phospholipids protects cells from ferroptosis. The enzymes and pathways that govern PUFA and MUFA metabolism therefore play a critical role in determining cellular sensitivity to ferroptosis. Here, we review three lipid metabolic processes-fatty acid biosynthesis, ether lipid biosynthesis, and phospholipid remodeling-that can govern ferroptosis sensitivity by regulating the balance of PUFAs and MUFAs in membrane phospholipids.
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Affiliation(s)
- Jason Rodencal
- Department of Biology, Stanford University, Stanford, California, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, California, USA
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32
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Pradhan SS, Rao KR, Manjunath M, Saiswaroop R, Patnana DP, Phalguna KS, Choudhary B, Sivaramakrishnan V. Vitamin B 6, B 12 and folate modulate deregulated pathways and protein aggregation in yeast model of Huntington disease. 3 Biotech 2023; 13:96. [PMID: 36852176 PMCID: PMC9958225 DOI: 10.1007/s13205-023-03525-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Huntington's disease (HD) is an incurable and progressive neurodegenerative disease affecting the basal ganglia of the brain. HD is caused due to expansion of the polyglutamine tract in the protein Huntingtin resulting in aggregates. The increased PolyQ length results in aggregation of protein Huntingtin leading to neuronal cell death. Vitamin B6, B12 and folate are deficient in many neurodegenerative diseases. We performed an integrated analysis of transcriptomic, metabolomic and cofactor-protein network of vitamin B6, B12 and folate was performed. Our results show considerable overlap of pathways modulated by Vitamin B6, B12 and folate with those obtained from transcriptomic and metabolomic data of HD patients and model systems. Further, in yeast model of HD we showed treatment of B6, B12 or folate either alone or in combination showed impaired aggregate formation. Transcriptomic analysis of yeast model treated with B6, B12 and folate showed upregulation of pathways like ubiquitin mediated proteolysis, autophagy, peroxisome, fatty acid, lipid and nitrogen metabolism. Metabolomic analysis of yeast model shows deregulation of pathways like aminoacyl-tRNA biosynthesis, metabolism of various amino acids, nitrogen metabolism and glutathione metabolism. Integrated transcriptomic and metabolomic analysis of yeast model showed concordance in the pathways obtained. Knockout of Peroxisomal (PXP1 and PEX7) and Autophagy (ATG5) genes in yeast increased aggregates which is mitigated by vitamin B6, B12 and folate treatment. Taken together our results show a role for Vitamin B6, B12 and folate mediated modulation of pathways important for preventing protein aggregation with potential implications for HD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03525-y.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - K. Raksha Rao
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - R. Saiswaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Durga Prasad Patnana
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Kanikaram Sai Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
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Deb R, Nagotu S. The nexus between peroxisome abundance and chronological ageing in Saccharomyces cerevisiae. Biogerontology 2023; 24:81-97. [PMID: 36209442 DOI: 10.1007/s10522-022-09992-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/23/2022] [Indexed: 01/20/2023]
Abstract
Ageing is characterized by changes in several cellular processes, with dysregulation of peroxisome function being one of them. Interestingly, the most conserved function of peroxisomes, ROS homeostasis, is strongly associated with ageing and age-associated pathologies. Previous studies have identified a role for peroxisomes in the regulation of chronological lifespan in yeast. In this study, we report the effect of altered peroxisome number on the chronological lifespan of yeast in two different growth media conditions. Three mutants, pex11, pex25 and pex27, defective in peroxisome fission, have been thoroughly investigated for the chronological lifespan. Reduced chronological lifespan of all the mutants was observed in peroxisome-inducing growth conditions. Furthermore, the combined deletion pex11pex25 exhibited the most prominent reduction in lifespan. Interestingly altered peroxisomal phenotype upon ageing was observed in all the cells. Increased ROS accumulation and reduced catalase activity was exhibited by chronologically aged mutant cells. Interestingly, mutants with reduced number of peroxisomes concomitantly also exhibited an accumulation of free fatty acids and increased number of lipid droplets. Taken together, our results reveal a previously unrealized effect of fission proteins in the chronological lifespan of yeast.
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Affiliation(s)
- Rachayeeta Deb
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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Pruss KM, Chen H, Liu Y, Van Treuren W, Higginbottom SK, Jarman JB, Fischer CR, Mak J, Wong B, Cowan TM, Fischbach MA, Sonnenburg JL, Dodd D. Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid. Nat Commun 2023; 14:512. [PMID: 36720857 PMCID: PMC9889317 DOI: 10.1038/s41467-023-36138-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 01/17/2023] [Indexed: 02/01/2023] Open
Abstract
The human gut microbiota produces dozens of small molecules that circulate in blood, accumulate to comparable levels as pharmaceutical drugs, and influence host physiology. Despite the importance of these metabolites to human health and disease, the origin of most microbially-produced molecules and their fate in the host remains largely unknown. Here, we uncover a host-microbe co-metabolic pathway for generation of hippuric acid, one of the most abundant organic acids in mammalian urine. Combining stable isotope tracing with bacterial and host genetics, we demonstrate reduction of phenylalanine to phenylpropionic acid by gut bacteria; the host re-oxidizes phenylpropionic acid involving medium-chain acyl-CoA dehydrogenase (MCAD). Generation of germ-free male and female MCAD-/- mice enabled gnotobiotic colonization combined with untargeted metabolomics to identify additional microbial metabolites processed by MCAD in host circulation. Our findings uncover a host-microbe pathway for the abundant, non-toxic phenylalanine metabolite hippurate and identify β-oxidation via MCAD as a novel mechanism by which mammals metabolize microbiota-derived metabolites.
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Affiliation(s)
- Kali M Pruss
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haoqing Chen
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA
| | - Yuanyuan Liu
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - John B Jarman
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA
| | - Curt R Fischer
- ChEM-H, Stanford University, Stanford, CA, USA
- Octant Bio, Emeryville, CA, USA
| | | | | | - Tina M Cowan
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA
| | - Michael A Fischbach
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford, CA, USA
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology Stanford University School of Medicine, Stanford, CA, USA.
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Huguenard CJC, Cseresznye A, Darcey T, Nkiliza A, Evans JE, Hazen SL, Mullan M, Crawford F, Abdullah L. Age and APOE affect L-carnitine system metabolites in the brain in the APOE-TR model. Front Aging Neurosci 2023; 14:1059017. [PMID: 36688151 PMCID: PMC9853982 DOI: 10.3389/fnagi.2022.1059017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
With age the apolipoprotein E (APOE) E4 allele (involved in lipid homeostasis) is associated with perturbation of bioenergetics pathways in Alzheimer's disease (AD). We therefore hypothesized that in aging mice APOE genotype would affect the L-carnitine system (central to lipid bioenergetics), in the brain and in the periphery. Using liquid chromatography-mass spectrometry, levels of L-carnitine and associated metabolites: γ-butyrobetaine (GBB), crotonobetaine, as well as acylcarnitines, were evaluated at 10-, 25-, and 50-weeks, in the brain and the periphery, in a targeted replacement mouse model of human APOE (APOE-TR). Aged APOE-TR mice were also orally administered 125 mg/kg of L-carnitine daily for 7 days followed by evaluation of brain, liver, and plasma L-carnitine system metabolites. Compared to E4-TR, an age-dependent increase among E2- and E3-TR mice was detected for medium- and long-chain acylcarnitines (MCA and LCA, respectively) within the cerebrovasculature and brain parenchyma. While following L-carnitine oral challenge, E4-TR mice had higher increases in the L-carnitine metabolites, GBB and crotonobetaine in the brain and a reduction of plasma to brain total acylcarnitine ratios compared to other genotypes. These studies suggest that with aging, the presence of the E4 allele may contribute to alterations in the L-carnitine bioenergetic system and to the generation of L-carnitine metabolites that could have detrimental effects on the vascular system. Collectively the E4 allele and aging may therefore contribute to AD pathogenesis through aging-related lipid bioenergetics as well as cerebrovascular dysfunctions.
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Affiliation(s)
- Claire J. C. Huguenard
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
- School of Life, Health and Chemical Sciences, Open University, Milton Keynes, United Kingdom
| | - Adam Cseresznye
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
| | - Teresa Darcey
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
| | - Aurore Nkiliza
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
- James A. Haley VA Hospital, Tampa, FL, United States
| | - James E. Evans
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
| | - Stanley L. Hazen
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Michael Mullan
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
- School of Life, Health and Chemical Sciences, Open University, Milton Keynes, United Kingdom
| | - Fiona Crawford
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
- School of Life, Health and Chemical Sciences, Open University, Milton Keynes, United Kingdom
- James A. Haley VA Hospital, Tampa, FL, United States
| | - Laila Abdullah
- Department of Metabolomics, Roskamp Institute, Sarasota, FL, United States
- School of Life, Health and Chemical Sciences, Open University, Milton Keynes, United Kingdom
- James A. Haley VA Hospital, Tampa, FL, United States
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Westrick NM, Park SC, Keller NP, Smith DL, Kabbage M. A broadly conserved fungal alcohol oxidase (AOX) facilitates fungal invasion of plants. MOLECULAR PLANT PATHOLOGY 2023; 24:28-43. [PMID: 36251755 PMCID: PMC9742500 DOI: 10.1111/mpp.13274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Alcohol oxidases (AOXs) are ecologically important enzymes that facilitate a number of plant-fungal interactions. Within Ascomycota they are primarily associated with methylotrophy, as a peroxisomal AOX catalysing the conversion of methanol to formaldehyde in methylotrophic yeast. In this study we demonstrate that AOX orthologues are phylogenetically conserved proteins that are common in the genomes of nonmethylotrophic, plant-associating fungi. Additionally, AOX orthologues are highly expressed during infection in a range of diverse pathosystems. To study the role of AOX in plant colonization, AOX knockout mutants were generated in the broad host range pathogen Sclerotinia sclerotiorum. Disease assays in soybean showed that these mutants had a significant virulence defect as evidenced by markedly reduced stem lesions and mortality rates. Chemical genomics suggested that SsAOX may function as an aromatic AOX, and growth assays demonstrated that ΔSsAOX is incapable of properly utilizing plant extract as a nutrient source. Profiling of known aromatic alcohols pointed towards the monolignol coniferyl alcohol (CA) as a possible substrate for SsAOX. As CA and other monolignols are ubiquitous among land plants, the presence of highly conserved AOX orthologues throughout Ascomycota implies that this is a broadly conserved protein used by ascomycete fungi during plant colonization.
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Affiliation(s)
- Nathaniel M. Westrick
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- United States Department of Agriculture–Agricultural Research ServiceMadisonWisconsinUSA
| | - Sung Chul Park
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Nancy P. Keller
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Damon L. Smith
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Mehdi Kabbage
- Department of Plant PathologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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Wanders RJA, Baes M, Ribeiro D, Ferdinandusse S, Waterham HR. The physiological functions of human peroxisomes. Physiol Rev 2023; 103:957-1024. [PMID: 35951481 DOI: 10.1152/physrev.00051.2021] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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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Bhandari S, Hong K, Miyawaki-Kuwakado A, Tomimatsu K, Kim YI, Nam IK, Sagerström CG, Nakamura M, Choe SK. nudt7 gene depletion causes transcriptomic change in early development of zebrafish. J Biochem 2022; 173:53-63. [PMID: 36270274 DOI: 10.1093/jb/mvac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/23/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
The Nudt family has been identified as enzymes performing Coenzyme A to 3'5'-ADP + 4'-phospho pantetheine catalysis. The members of this family have been shown to be particularly involved in lipid metabolism, while their involvement in gene regulation through regulating transcription or mRNA metabolism has also been suggested. Here, we focused on peroxisomal NUDT7, possessing enzymatic activity similar to that of its paralog, peroxisomal NUDT19, which is involved in mRNA degradation. No reports have been published about the Nudt family in zebrafish. Our transcriptomic data showed that the Nudt family members are highly expressed around zygotic gene activation (ZGA) in developing zebrafish embryos. Therefore, we confirmed the computational prediction that the products of the nudt7 gene in zebrafish were localized in the peroxisome and highly expressed in early embryogenesis. The depletion of nudt7 genes by the CRISPR/Cas9 system did not affect development; however, it decreased the rate of transcription in ZGA. In addition, H3K27ac ChIP-seq analysis demonstrated that this decrease in transcription was correlated with the genome-wide decrease of H3K27ac level. This study suggests that peroxisomal Nudt7 functions in regulating transcription in ZGA via formation of the H3K27ac domain in active chromatin.
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Key Words
- ChIP-seq.Abbreviations: (ChIP-seq), chromatin immunoprecipitation sequencing; (CRISPR), clustered regularly interspaced short palindromic repeats; (DEG), differentially expressed genes; (DHA), docosahexaenoic acid; (EGFP), enhanced green fluorescence protein; (ERK), extracellular-signal-regulated kinase; (FDR), false discovery rate; (GO), gene ontology; (H3K27ac), histone 3 acetylated at lysine 27; (hpf), hours post-fertilization; (IGV), Integrative Genome Viewer; (KO), knockout; (Nudt), Nudix; (PCA), principal component analysis; (Pex), peroxin; (PTS1), peroxisomal localization signal sequence 1; (TSS), transcription start site; (WT), wild-type; (ZGA), zygotic gene activation
- Nudt family
- RNA-seq
- zebrafish
- zygotic gene activation
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Affiliation(s)
- Sushil Bhandari
- Department of Medicine, Graduate School, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - KwangHeum Hong
- Department of Medicine, Graduate School, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - Atsuko Miyawaki-Kuwakado
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 8128582 Japan
| | - Kosuke Tomimatsu
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 8128582 Japan
| | - Yong-Il Kim
- Department of Medicine, Graduate School, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - In-Koo Nam
- Institute of Brain Science, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - Charles G Sagerström
- Department of Pediatrics, University of Colorado Medical School, 13001 East 17th Place, Campus Box C290, Aurora, CO 80045, USA
| | - Mako Nakamura
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-Ku, Fukuoka, 8190395 Japan
| | - Seong-Kyu Choe
- Department of Microbiology, Wonkwang University School of Medicine, 460 Iksadae-ro, Iksan, 54538 South Korea
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Anteghini M, Haja A, Martins dos Santos VA, Schomaker L, Saccenti E. OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection. Comput Struct Biotechnol J 2022; 21:128-133. [PMID: 36544474 PMCID: PMC9747352 DOI: 10.1016/j.csbj.2022.11.058] [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: 07/20/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
We present the OrganelX e-Science Web Server that provides a user-friendly implementation of the In-Pero and In-Mito classifiers for sub-peroxisomal and sub-mitochondrial localization of peroxisomal and mitochondrial proteins and the Is-PTS1 algorithm for detecting and validating potential peroxisomal proteins carrying a PTS1 signal sequence. The OrganelX e-Science Web Server is available at https://organelx.hpc.rug.nl/fasta/.
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Affiliation(s)
- Marco Anteghini
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Asmaa Haja
- Bernoulli Institute, University of Groningen, Groningen, The Netherlands
| | - Vitor A.P. Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Bioprocess Engineering, Wageningen University & Research, Wageningen, The Netherlands
| | - Lambert Schomaker
- Bernoulli Institute, University of Groningen, Groningen, The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
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Liang D, Batross J, Fiedler N, Prapamontol T, Suttiwan P, Panuwet P, Naksen W, Baumert BO, Yakimavets V, Tan Y, D'Souza P, Mangklabruks A, Sittiwang S, Kaewthit K, Kohsuwan K, Promkam N, Pingwong S, Ryan PB, Barr DB. Metabolome-wide association study of the relationship between chlorpyrifos exposure and first trimester serum metabolite levels in pregnant Thai farmworkers. ENVIRONMENTAL RESEARCH 2022; 215:114319. [PMID: 36108722 PMCID: PMC9909724 DOI: 10.1016/j.envres.2022.114319] [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: 06/23/2022] [Revised: 09/03/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Organophosphate (OP) insecticides, including chlorpyrifos, have been linked with numerous harmful health effects on maternal and child health. Limited data are available on the biological mechanisms and endogenous pathways underlying the toxicity of chlorpyrifos exposures on pregnancy and birth outcomes. In this study, we measured a urinary chlorpyrifos metabolite and used high-resolution metabolomics (HRM) to identify biological perturbations associated with chlorpyrifos exposure among pregnant women in Thailand, who are disparately exposed to high levels of OP insecticides. METHODS This study included 50 participants from the Study of Asian Women and their Offspring's Development and Environmental Exposures (SAWASDEE). We used liquid chromatography-high resolution mass spectrometry to conduct metabolic profiling on first trimester serum samples collected from participants to evaluate metabolic perturbations in relation to chlorpyrifos exposures. We measured 3,5,6-trichloro-2-pyridinol (TCPy), a specific metabolite of chlorpyrifos and chlorpyrifos-methyl, in first trimester urine samples to assess the levels of exposures. Following an untargeted metabolome-wide association study workflow, we used generalized linear models, pathway enrichment analyses, and chemical annotation to identify significant metabolites and pathways associated with urinary TCPy levels. RESULTS In the 50 SAWASDEE participants, the median urinary TCPy level was 4.36 μg TCPy/g creatinine. In total, 691 unique metabolic features were found significantly associated with TCPy levels (p < 0.05) after controlling for confounding factors. Pathway analysis of metabolic features associated with TCPy indicated perturbations in 24 metabolic pathways, most closely linked to the production of reactive oxygen species and cellular damage. These pathways include tryptophan metabolism, fatty acid oxidation and peroxisome metabolism, cytochromes P450 metabolism, glutathione metabolism, and vitamin B3 metabolism. We confirmed the chemical identities of 25 metabolites associated with TCPy levels, including glutathione, cystine, arachidic acid, itaconate, and nicotinamide adenine dinucleotide. DISCUSSION The metabolic perturbations associated with TCPy levels were related to oxidative stress, cellular damage and repair, and systemic inflammation, which could ultimately contribute to health outcomes, including neurodevelopmental deficits in the child. These findings support the future development of sensitive biomarkers to investigate the metabolic underpinnings related to pesticide exposure during pregnancy and to understand its link to adverse outcomes in children.
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Affiliation(s)
- Donghai Liang
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA.
| | - Jonathan Batross
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA
| | - Nancy Fiedler
- Rutgers University, Environmental and Occupational Health Science Institute, Piscataway, NJ, USA
| | - Tippawan Prapamontol
- Chiang Mai University, Research Institute for Health Sciences, Chiang Mai, Thailand
| | - Panrapee Suttiwan
- Chulalongkorn University, Faculty of Psychology, LIFE Di Center, Bangkok, Thailand
| | - Parinya Panuwet
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA
| | - Warangkana Naksen
- Chiang Mai University, Faculty of Public Health, Chiang Mai, Thailand
| | - Brittney O Baumert
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA; Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Volha Yakimavets
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA
| | - Youran Tan
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA
| | - Priya D'Souza
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA
| | - Ampica Mangklabruks
- Chiang Mai University, Research Institute for Health Sciences, Chiang Mai, Thailand
| | - Supattra Sittiwang
- Chulalongkorn University, Faculty of Psychology, LIFE Di Center, Bangkok, Thailand
| | | | - Kanyapak Kohsuwan
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Thailand
| | - Nattawadee Promkam
- Chiang Mai University, Research Institute for Health Sciences, Chiang Mai, Thailand
| | - Sureewan Pingwong
- Chiang Mai University, Research Institute for Health Sciences, Chiang Mai, Thailand
| | - P Barry Ryan
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA
| | - Dana Boyd Barr
- Emory University, Rollins School of Public Health, Gangarosa Department of Environmental Health, Atlanta, GA, USA.
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Martin WP, Nair M, Chuah YH, Malmodin D, Pedersen A, Abrahamsson S, Hutter M, Abdelaal M, Elliott JA, Fearon N, Eckhardt H, Godson C, Brennan EP, Fändriks L, le Roux CW, Docherty NG. Dietary restriction and medical therapy drives PPARα-regulated improvements in early diabetic kidney disease in male rats. Clin Sci (Lond) 2022; 136:1485-1511. [PMID: 36259366 PMCID: PMC7613831 DOI: 10.1042/cs20220205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022]
Abstract
The attenuation of diabetic kidney disease (DKD) by metabolic surgery is enhanced by pharmacotherapy promoting renal fatty acid oxidation (FAO). Using the Zucker Diabetic Fatty and Zucker Diabetic Sprague Dawley rat models of DKD, we conducted studies to determine if these effects could be replicated with a non-invasive bariatric mimetic intervention. Metabolic control and renal injury were compared in rats undergoing a dietary restriction plus medical therapy protocol (DMT; fenofibrate, liraglutide, metformin, ramipril, and rosuvastatin) and ad libitum-fed controls. The global renal cortical transcriptome and urinary 1H-NMR metabolomic profiles were also compared. Kidney cell type-specific and medication-specific transcriptomic responses were explored through in silico deconvolution. Transcriptomic and metabolomic correlates of improvements in kidney structure were defined using a molecular morphometric approach. The DMT protocol led to ∼20% weight loss, normalized metabolic parameters and was associated with reductions in indices of glomerular and proximal tubular injury. The transcriptomic response to DMT was dominated by changes in fenofibrate- and peroxisome proliferator-activated receptor-α (PPARα)-governed peroxisomal and mitochondrial FAO transcripts localizing to the proximal tubule. DMT induced urinary excretion of PPARα-regulated metabolites involved in nicotinamide metabolism and reversed DKD-associated changes in the urinary excretion of tricarboxylic acid (TCA) cycle intermediates. FAO transcripts and urinary nicotinamide and TCA cycle metabolites were moderately to strongly correlated with improvements in glomerular and proximal tubular injury. Weight loss plus pharmacological PPARα agonism is a promising means of attenuating DKD.
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Affiliation(s)
- William P. Martin
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Meera Nair
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Yeong H.D. Chuah
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Daniel Malmodin
- Swedish NMR Centre, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Anders Pedersen
- Swedish NMR Centre, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Sanna Abrahamsson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Michaela Hutter
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Mahmoud Abdelaal
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Jessie A. Elliott
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Naomi Fearon
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Hans Eckhardt
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Catherine Godson
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Eoin P. Brennan
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Lars Fändriks
- Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Carel W. le Roux
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Diabetes Research Group, Ulster University, Coleraine BT52 1SA, UK
| | - Neil G. Docherty
- Diabetes Complications Research Centre, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
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42
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Ma Y, Wang M, Guo S, Li T, Liu X, Zhao L. The serum acylcarnitines profile in epileptic children treated with valproic acid and the protective roles of peroxisome proliferator-activated receptor a activation in valproic acid-induced liver injury. Front Pharmacol 2022; 13:1048728. [PMID: 36425583 PMCID: PMC9681037 DOI: 10.3389/fphar.2022.1048728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/25/2022] [Indexed: 09/04/2023] Open
Abstract
Valproic acid (VPA) is widely used as a major drug in the treatment of epilepsy. Despite the undisputed pharmacological importance and effectiveness of VPA, its potential hepatotoxicity is still a major concern. Being a simple fatty acid, the hepatotoxicity induced by VPA has long been considered to be due primarily to its interference with fatty acid β-oxidation (β-FAO). The aim of this study was to investigate the biomarkers for VPA-induced abnormal liver function in epileptic children and to determine potential mechanisms of its liver injury. Targeted metabolomics analysis of acylcarnitines (ACs) was performed in children's serum. Metabolomic analysis revealed that VPA -induced abnormal liver function resulted in the accumulation of serum long-chain acylcarnitines (LCACs), and the reduced expression of β-FAO relevant genes (Carnitine palmitoyltrans-ferase (CPT)1, CPT2 and Long-chain acyl-CoA dehydrogenase (LCAD)), indicating the disruption of β-FAO. As direct peroxisome proliferator-activated receptor a (PPARα)- regulated genes, CPT1A, CPT2 and LCAD were up-regulated after treatment with PPARα agonist, fenofibrate (Feno), indicating the improvement of β-FAO. Feno significantly ameliorated the accumulation of various lipids in the plasma of VPA-induced hepatotoxic mice by activating PPARα, significantly reduced the plasma ACs concentration, and attenuated VPA-induced hepatic steatosis. Enhanced oxidative stress and induced by VPA exposure were significantly recovered using Feno treatment. In conclusion, this study indicates VPA-induced β-FAO disruption might lead to liver injury, and a significant Feno protective effect against VPA -induced hepatotoxicity through reversing fatty acid metabolism.
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Affiliation(s)
| | | | | | | | | | - Limei Zhao
- Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, China
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43
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Fujiki Y, Okumoto K, Honsho M, Abe Y. Molecular insights into peroxisome homeostasis and peroxisome biogenesis disorders. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119330. [PMID: 35917894 DOI: 10.1016/j.bbamcr.2022.119330] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes are single-membrane organelles essential for cell metabolism including the β-oxidation of fatty acids, synthesis of etherlipid plasmalogens, and redox homeostasis. Investigations into peroxisome biogenesis and the human peroxisome biogenesis disorders (PBDs) have identified 14 PEX genes encoding peroxins involved in peroxisome biogenesis and the mutation of PEX genes is responsible for the PBDs. Many recent findings have further advanced our understanding of the biology, physiology, and consequences of a functional deficit of peroxisomes. In this Review, we discuss cell defense mechanisms that counteract oxidative stress by 1) a proapoptotic Bcl-2 factor BAK-mediated release to the cytosol of H2O2-degrading catalase from peroxisomes and 2) peroxisomal import suppression of catalase by Ser232-phosphorylation of Pex14, a docking protein for the Pex5-PTS1 complex. With respect to peroxisome division, the important issue of how the energy-rich GTP is produced and supplied for the division process was recently addressed by the discovery of a nucleoside diphosphate kinase-like protein, termed DYNAMO1 in a lower eukaryote, which has a mammalian homologue NME3. In regard to the mechanisms underlying the pathogenesis of PBDs, a new PBD model mouse defective in Pex14 manifests a dysregulated brain-derived neurotrophic factor (BDNF)-TrkB pathway, an important signaling pathway for cerebellar morphogenesis. Communications between peroxisomes and other organelles are also addressed.
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Affiliation(s)
- Yukio Fujiki
- Medical Institute of Bioregulation, Institute of Rheological Functions of Food, Collaboration Program, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan.
| | - Kanji Okumoto
- Department of Biology and Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Masanori Honsho
- Medical Institute of Bioregulation, Institute of Rheological Functions of Food, Collaboration Program, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan
| | - Yuichi Abe
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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44
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Deori NM, Nagotu S. Peroxisome biogenesis and inter-organelle communication: an indispensable role for Pex11 and Pex30 family proteins in yeast. Curr Genet 2022; 68:537-550. [PMID: 36242632 DOI: 10.1007/s00294-022-01254-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022]
Abstract
Peroxisomes are highly dynamic organelles present in most eukaryotic cells. They also play an important role in human health and the optimum functioning of cells. An extensive repertoire of proteins is associated with the biogenesis and function of these organelles. Two protein families that are involved in regulating peroxisome number in a cell directly or indirectly are Pex11 and Pex30. Interestingly, these proteins are also reported to regulate the contact sites between peroxisomes and other cell organelles such as mitochondria, endoplasmic reticulum and lipid droplets. In this manuscript, we review our current knowledge of the role of these proteins in peroxisome biogenesis in various yeast species. Further, we also discuss in detail the role of these protein families in the regulation of inter-organelle contacts in yeast.
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Affiliation(s)
- Nayan Moni Deori
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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45
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Clifford MN, King LJ, Kerimi A, Pereira-Caro MG, Williamson G. Metabolism of phenolics in coffee and plant-based foods by canonical pathways: an assessment of the role of fatty acid β-oxidation to generate biologically-active and -inactive intermediates. Crit Rev Food Sci Nutr 2022; 64:3326-3383. [PMID: 36226718 DOI: 10.1080/10408398.2022.2131730] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
ω-Phenyl-alkenoic acids are abundant in coffee, fruits, and vegetables. Along with ω-phenyl-alkanoic acids, they are produced from numerous dietary (poly)phenols and aromatic amino acids in vivo. This review addresses how phenyl-ring substitution and flux modulates their gut microbiota and endogenous β-oxidation. 3',5'-Dihydroxy-derivatives (from alkyl-resorcinols, flavanols, proanthocyanidins), and 4'-hydroxy-phenolic acids (from tyrosine, p-coumaric acid, naringenin) are β-oxidation substrates yielding benzoic acids. In contrast, 3',4',5'-tri-substituted-derivatives, 3',4'-dihydroxy-derivatives and 3'-methoxy-4'-hydroxy-derivatives (from coffee, tea, cereals, many fruits and vegetables) are poor β-oxidation substrates with metabolism diverted via gut microbiota dehydroxylation, phenylvalerolactone formation and phase-2 conjugation, possibly a strategy to conserve limited pools of coenzyme A. 4'-Methoxy-derivatives (citrus fruits) or 3',4'-dimethoxy-derivatives (coffee) are susceptible to hepatic "reverse" hydrogenation suggesting incompatibility with enoyl-CoA-hydratase. Gut microbiota-produced 3'-hydroxy-4'-methoxy-derivatives (citrus fruits) and 3'-hydroxy-derivatives (numerous (poly)phenols) are excreted as the phenyl-hydracrylic acid β-oxidation intermediate suggesting incompatibility with hydroxy-acyl-CoA dehydrogenase, albeit with considerable inter-individual variation. Further investigation is required to explain inter-individual variation, factors determining the amino acid to which C6-C3 and C6-C1 metabolites are conjugated, the precise role(s) of l-carnitine, whether glycine might be limiting, and whether phenolic acid-modulation of β-oxidation explains how phenolic acids affect key metabolic conditions, such as fatty liver, carbohydrate metabolism and insulin resistance.
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Affiliation(s)
- Michael N Clifford
- School of Bioscience and Medicine, University of Surrey, Guildford, UK
- Department of Nutrition, Dietetics and Food, Monash University, Clayton, Australia
| | - Laurence J King
- School of Bioscience and Medicine, University of Surrey, Guildford, UK
| | - Asimina Kerimi
- Department of Nutrition, Dietetics and Food, Monash University, Clayton, Australia
| | - Maria Gema Pereira-Caro
- Department of Food Science and Health, Instituto Andaluz de Investigacion y Formacion Agraria Pesquera Alimentaria y de la Produccion Ecologica, Sevilla, Spain
| | - Gary Williamson
- Department of Nutrition, Dietetics and Food, Monash University, Clayton, Australia
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46
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Granados JC, Falah K, Koo I, Morgan EW, Perdew GH, Patterson AD, Jamshidi N, Nigam SK. AHR is a master regulator of diverse pathways in endogenous metabolism. Sci Rep 2022; 12:16625. [PMID: 36198709 PMCID: PMC9534852 DOI: 10.1038/s41598-022-20572-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a transcription factor with roles in detoxification, development, immune response, chronic kidney disease and other syndromes. It regulates the expression of drug transporters and drug metabolizing enzymes in a proposed Remote Sensing and Signaling Network involved in inter-organ communication via metabolites and signaling molecules. Here, we use integrated omics approaches to analyze its contributions to metabolism across multiple scales from the organ to the organelle. Global metabolomics analysis of Ahr-/- mice revealed the role of AHR in the regulation of 290 metabolites involved in many biochemical pathways affecting fatty acids, bile acids, gut microbiome products, antioxidants, choline derivatives, and uremic toxins. Chemoinformatics analysis suggest that AHR plays a role in determining the hydrophobicity of metabolites and perhaps their transporter-mediated movement into and out of tissues. Of known AHR ligands, indolepropionate was the only significantly altered molecule, and it activated AHR in both human and murine cells. To gain a deeper biological understanding of AHR, we employed genome scale metabolic reconstruction to integrate knockout transcriptomics and metabolomics data, which indicated a role for AHR in regulation of organic acids and redox state. Together, the results indicate a central role of AHR in metabolism and signaling between multiple organs and across multiple scales.
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Affiliation(s)
- Jeffry C Granados
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kian Falah
- Departments of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ethan W Morgan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, 16801, USA
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Neema Jamshidi
- Department of Radiological Sciences, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sanjay K Nigam
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine (Nephrology), University of California San Diego, La Jolla, CA, 92093, USA.
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47
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Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
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Affiliation(s)
| | | | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
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48
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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] [Abstract] [Key Words] [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
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49
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Takashima S, Fujita H, Toyoshi K, Ohba A, Hirata Y, Shimozawa N, Oh-Hashi K. Hypomorphic mutation of PEX3 with peroxisomal mosaicism reveals the oscillating nature of peroxisome biogenesis coupled with differential metabolic activities. Mol Genet Metab 2022; 137:68-80. [PMID: 35932552 DOI: 10.1016/j.ymgme.2022.07.008] [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: 04/20/2022] [Revised: 06/18/2022] [Accepted: 07/16/2022] [Indexed: 10/17/2022]
Abstract
Impaired peroxisome assembly caused by mutations in PEX genes results in a human congenital metabolic disease called Zellweger spectrum disorder (ZSD), which impacts the development and physiological function of multiple organs. In this study, we revealed a long-standing problem of heterogeneous peroxisome distribution among cell population, so called "peroxisomal mosaicism", which appears in patients with mild form of ZSD. We mutated PEX3 gene in HEK293 cells and obtained a mutant clone with peroxisomal mosaicism. We found that peroxisomal mosaicism can be reproducibly arise from a single cell, even if the cell has many or no peroxisomes. Using time-lapse imaging and a long-term culture experiment, we revealed that peroxisome biogenesis oscillates over a span of days; this was also confirmed in the patient's fibroblasts. During the oscillation, the metabolic activity of peroxisomes was maintained in the cells with many peroxisomes while depleted in the cells without peroxisomes. Our results indicate that ZSD patients with peroxisomal mosaicism have a cell population whose number and metabolic activities of peroxisomes can be recovered. This finding opens the way to develop novel treatment strategy for ZSD patients with peroxisomal mosaicism, who currently have very limited treatment options.
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Affiliation(s)
- Shigeo Takashima
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan; Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.
| | - Haruka Fujita
- Graduate School of Natural Science and Technology, Gifu University, Gifu, Japan; Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Kayoko Toyoshi
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Akiko Ohba
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Yoko Hirata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan; Graduate School of Natural Science and Technology, Gifu University, Gifu, Japan; Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Nobuyuki Shimozawa
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan; Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Kentaro Oh-Hashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan; Graduate School of Natural Science and Technology, Gifu University, Gifu, Japan; Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan.
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50
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Takeshita Y, Honda M, Harada K, Kita Y, Takata N, Tsujiguchi H, Tanaka T, Goto H, Nakano Y, Iida N, Arai K, Yamashita T, Mizukoshi E, Nakamura H, Kaneko S, Takamura T. Comparison of Tofogliflozin and Glimepiride Effects on Nonalcoholic Fatty Liver Disease in Participants With Type 2 Diabetes: A Randomized, 48-Week, Open-Label, Active-Controlled Trial. Diabetes Care 2022; 45:2064-2075. [PMID: 35894933 PMCID: PMC9472500 DOI: 10.2337/dc21-2049] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/21/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Nonalcoholic fatty liver disease (NAFLD) is a liver phenotype of type 2 diabetes and obesity. Currently, the efficacy of sodium-glucose cotransporter 2 (SGLT2) inhibitors and sulfonylureas in liver pathology and hepatic gene expression profiles for type 2 diabetes with NAFLD are unknown. RESEARCH DESIGN AND METHODS We conducted a 48 week, randomized, open-label, parallel-group trial involving participants with biopsy-confirmed NAFLD. A total of 40 participants were randomly assigned to receive once daily 20 mg tofogliflozin or 0.5 mg glimepiride. The primary outcome was the percentage of participants with at least an improvement in all individual scores for histological categories of steatosis, hepatocellular ballooning, lobular inflammation, and fibrosis by at least 1 point. The secondary end points were the changes in liver enzymes, metabolic markers, and hepatic gene expression profiles. RESULTS Fibrosis scores improved in the tofogliflozin group (60%, P = 0.001), whereas the change from baseline did not differ significantly between the groups (P = 0.172). The histological variables of steatosis (65%, P = 0.001), hepatocellular ballooning (55%, P = 0.002), and lobular inflammation (50%, P = 0.003) were improved in the tofogliflozin group, whereas only hepatocellular ballooning was improved in the glimepiride group (25%, P = 0.025). Hepatic gene expression profiling revealed histology-associated signatures in energy metabolism, inflammation, and fibrosis that were reversed with tofogliflozin. CONCLUSIONS Tofogliflozin and, to a lesser degree, glimepiride led to liver histological and metabolic improvement in participants with type 2 diabetes and NAFLD, with no significant difference between the agents. The hepatic expression of the genes involved in energy metabolism, inflammation, and fibrosis was well correlated with liver histological changes and rescued by tofogliflozin. We need further confirmation through long-term larger-scale clinical trials of SGLT2 inhibitors.
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Affiliation(s)
- Yumie Takeshita
- Department of Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masao Honda
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University Kanazawa, Ishikawa, Japan
| | - Kenichi Harada
- Department of Human Pathology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yuki Kita
- Department of Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Noboru Takata
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University Kanazawa, Ishikawa, Japan
| | - Hiromasa Tsujiguchi
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takeo Tanaka
- Department of Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hisanori Goto
- Department of Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yujiro Nakano
- Department of Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Noriho Iida
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University Kanazawa, Ishikawa, Japan
| | - Kuniaki Arai
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University Kanazawa, Ishikawa, Japan
| | - Tatsuya Yamashita
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University Kanazawa, Ishikawa, Japan
| | - Eishiro Mizukoshi
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University Kanazawa, Ishikawa, Japan
| | - Hiroyuki Nakamura
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University Kanazawa, Ishikawa, Japan
| | - Toshinari Takamura
- Department of Endocrinology and Metabolism, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
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