1
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Shiota M, Ushijima M, Tsukahara S, Nagakawa S, Okada T, Tanegashima T, Kobayashi S, Matsumoto T, Eto M. Oxidative stress in peroxisomes induced by androgen receptor inhibition through peroxisome proliferator-activated receptor promotes enzalutamide resistance in prostate cancer. Free Radic Biol Med 2024; 221:81-88. [PMID: 38762061 DOI: 10.1016/j.freeradbiomed.2024.05.030] [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: 05/02/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
Androgen receptor (AR)-targeting therapy induces oxidative stress in prostate cancer. However, the mechanism of oxidative stress induction by AR-targeting therapy remains unclear. This study investigated the mechanism of oxidative stress induction by AR-targeting therapy, with the aim to develop novel therapeutics targeting oxidative stress induced by AR-targeting therapy. Intracellular reactive oxygen species (ROS) was examined by fluorescence microscopy and flow cytometry analysis. The effects of silencing gene expression and small molecule inhibitors on gene expression and cytotoxic effects were examined by quantitative real-time PCR and cell proliferation assay. ROS induced by androgen depletion co-localized with peroxisomes in prostate cancer cells. Among peroxisome-related genes, PPARA was commonly induced by AR inhibition and involved in ROS production via PKC signaling. Inhibition of PPARα by specific siRNA and a small molecule inhibitor suppressed cell proliferation and increased cellular sensitivity to the antiandrogen enzalutamide in prostate cancer cells. This study revealed a novel pathway by which AR inhibition induced intracellular ROS mainly in peroxisomes through PPARα activation in prostate cancer. This pathway is a promising target for the development of novel therapeutics for prostate cancer in combination with AR-targeting therapy such as antiandrogen enzalutamide.
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Affiliation(s)
- Masaki Shiota
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Miho Ushijima
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shigehiro Tsukahara
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shohei Nagakawa
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tatsunori Okada
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tokiyoshi Tanegashima
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Satoshi Kobayashi
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takashi Matsumoto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
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2
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Naimy S, Sølberg JBK, Kuczek DE, Løvendorf MB, Bzorek M, Litman T, Mund A, Rahbek Gjerdrum LM, Clark RA, Mann M, Dyring-Andersen B. Comparative Quantitative Proteomic Analysis of Melanoma Subtypes, Nevus-Associated Melanoma, and Corresponding Nevi. J Invest Dermatol 2024; 144:1608-1621.e4. [PMID: 38185415 DOI: 10.1016/j.jid.2023.12.011] [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: 07/04/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
A substantial part of cutaneous malignant melanomas develops from benign nevi. However, the precise molecular events driving the transformation from benign to malignant melanoma are not well-understood. We used laser microdissection and mass spectrometry to analyze the proteomes of melanoma subtypes, including superficial spreading melanomas (n = 17), nodular melanomas (n = 17), and acral melanomas (n = 15). Furthermore, we compared the proteomes of nevi cells with those of melanoma cells within the same specimens (nevus-associated melanoma (n = 14)). In total, we quantified 7935 proteins. Despite the genomic and clinical differences of the melanoma subtypes, our analysis revealed relatively similar proteomes, except for the upregulation of proteins involved in immune activation in nodular melanomas versus acral melanomas. Examining nevus-associated melanoma versus nevi, we found 1725 differentially expressed proteins (false discovery rate < 0.05). Among these proteins were 140 that overlapped with cancer hallmarks, tumor suppressors, and regulators of metabolism and cell cycle. Pathway analysis indicated aberrant activation of the phosphoinositide 3-kinase-protein kinase B-mTOR pathways and the Hippo-YAP pathway. Using a classifier, we identified six proteins capable of distinguishing melanoma from nevi samples. Our study represents a comprehensive comparative analysis of the proteome in melanoma subtypes and associated nevi, offering insights into the biological behavior of these distinct entities.
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Affiliation(s)
- Soraya Naimy
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Julie B K Sølberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark
| | - Dorota E Kuczek
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Bengtson Løvendorf
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark; Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Bzorek
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Litman
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Mund
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Beatrice Dyring-Andersen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark; Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Lin P, Lu Y, Zheng J, Lin Y, Zhao X, Cui L. Strategic disruption of cancer's powerhouse: precise nanomedicine targeting of mitochondrial metabolism. J Nanobiotechnology 2024; 22:318. [PMID: 38849914 PMCID: PMC11162068 DOI: 10.1186/s12951-024-02585-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024] Open
Abstract
Mitochondria occupy a central role in the biology of most eukaryotic cells, functioning as the hub of oxidative metabolism where sugars, fats, and amino acids are ultimately oxidized to release energy. This crucial function fuels a variety of cellular activities. Disruption in mitochondrial metabolism is a common feature in many diseases, including cancer, neurodegenerative conditions and cardiovascular diseases. Targeting tumor cell mitochondrial metabolism with multifunctional nanosystems emerges as a promising strategy for enhancing therapeutic efficacy against cancer. This review comprehensively outlines the pathways of mitochondrial metabolism, emphasizing their critical roles in cellular energy production and metabolic regulation. The associations between aberrant mitochondrial metabolism and the initiation and progression of cancer are highlighted, illustrating how these metabolic disruptions contribute to oncogenesis and tumor sustainability. More importantly, innovative strategies employing nanomedicines to precisely target mitochondrial metabolic pathways in cancer therapy are fully explored. Furthermore, key challenges and future directions in this field are identified and discussed. Collectively, this review provides a comprehensive understanding of the current state and future potential of nanomedicine in targeting mitochondrial metabolism, offering insights for developing more effective cancer therapies.
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Affiliation(s)
- Pei Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Ye Lu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yunfan Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Xinyuan Zhao
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
| | - Li Cui
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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4
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Passi G, Lieberman S, Zahdeh F, Murik O, Renbaum P, Beeri R, Linial M, May D, Levy-Lahad E, Schneidman-Duhovny D. Discovering predisposing genes for hereditary breast cancer using deep learning. Brief Bioinform 2024; 25:bbae346. [PMID: 39038933 PMCID: PMC11262808 DOI: 10.1093/bib/bbae346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/18/2024] [Accepted: 07/04/2024] [Indexed: 07/24/2024] Open
Abstract
Breast cancer (BC) is the most common malignancy affecting Western women today. It is estimated that as many as 10% of BC cases can be attributed to germline variants. However, the genetic basis of the majority of familial BC cases has yet to be identified. Discovering predisposing genes contributing to familial BC is challenging due to their presumed rarity, low penetrance, and complex biological mechanisms. Here, we focused on an analysis of rare missense variants in a cohort of 12 families of Middle Eastern origins characterized by a high incidence of BC cases. We devised a novel, high-throughput, variant analysis pipeline adapted for family studies, which aims to analyze variants at the protein level by employing state-of-the-art machine learning models and three-dimensional protein structural analysis. Using our pipeline, we analyzed 1218 rare missense variants that are shared between affected family members and classified 80 genes as candidate pathogenic. Among these genes, we found significant functional enrichment in peroxisomal and mitochondrial biological pathways which segregated across seven families in the study and covered diverse ethnic groups. We present multiple evidence that peroxisomal and mitochondrial pathways play an important, yet underappreciated, role in both germline BC predisposition and BC survival.
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Affiliation(s)
- Gal Passi
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sari Lieberman
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem PO Box 12271 Jerusalem 9112102, Israel
| | - Fouad Zahdeh
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Omer Murik
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Paul Renbaum
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Rachel Beeri
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Dalit May
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
- Clalit Health Services, Jerusalem, Israel
| | - Ephrat Levy-Lahad
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem PO Box 12271 Jerusalem 9112102, Israel
| | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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5
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Garcia MR, Andrade PB, Lefranc F, Gomes NGM. Marine-Derived Leads as Anticancer Candidates by Disrupting Hypoxic Signaling through Hypoxia-Inducible Factors Inhibition. Mar Drugs 2024; 22:143. [PMID: 38667760 PMCID: PMC11051506 DOI: 10.3390/md22040143] [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: 03/06/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The inadequate vascularization seen in fast-growing solid tumors gives rise to hypoxic areas, fostering specific changes in gene expression that bolster tumor cell survival and metastasis, ultimately leading to unfavorable clinical prognoses across different cancer types. Hypoxia-inducible factors (HIF-1 and HIF-2) emerge as druggable pivotal players orchestrating tumor metastasis and angiogenesis, thus positioning them as prime targets for cancer treatment. A range of HIF inhibitors, notably natural compounds originating from marine organisms, exhibit encouraging anticancer properties, underscoring their significance as promising therapeutic options. Bioprospection of the marine environment is now a well-settled approach to the discovery and development of anticancer agents that might have their medicinal chemistry developed into clinical candidates. However, despite the massive increase in the number of marine natural products classified as 'anticancer leads,' most of which correspond to general cytotoxic agents, and only a few have been characterized regarding their molecular targets and mechanisms of action. The current review presents a critical analysis of inhibitors of HIF-1 and HIF-2 and hypoxia-selective compounds that have been sourced from marine organisms and that might act as new chemotherapeutic candidates or serve as templates for the development of structurally similar derivatives with improved anticancer efficacy.
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Affiliation(s)
- Maria Rita Garcia
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (M.R.G.); (P.B.A.)
- 1H-TOXRUN-Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Paula B. Andrade
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (M.R.G.); (P.B.A.)
| | - Florence Lefranc
- Department of Neurosurgery, Hôpital Universitaire de Bruxelles (H.U.B), CUB Hôpital Erasme, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium;
| | - Nelson G. M. Gomes
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (M.R.G.); (P.B.A.)
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6
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Carroll C, Manaprasertsak A, Boffelli Castro A, van den Bos H, Spierings DC, Wardenaar R, Bukkuri A, Engström N, Baratchart E, Yang M, Biloglav A, Cornwallis CK, Johansson B, Hagerling C, Arsenian-Henriksson M, Paulsson K, Amend SR, Mohlin S, Foijer F, McIntyre A, Pienta KJ, Hammarlund EU. Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation. CANCER RESEARCH COMMUNICATIONS 2024; 4:691-705. [PMID: 38385626 PMCID: PMC10919208 DOI: 10.1158/2767-9764.crc-23-0396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/27/2023] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Therapeutic resistance and recurrence remain core challenges in cancer therapy. How therapy resistance arises is currently not fully understood with tumors surviving via multiple alternative routes. Here, we demonstrate that a subset of cancer cells survives therapeutic stress by entering a transient state characterized by whole-genome doubling. At the onset of the polyploidization program, we identified an upregulation of key transcriptional regulators, including the early stress-response protein AP-1 and normoxic stabilization of HIF2α. We found altered chromatin accessibility, ablated expression of retinoblastoma protein (RB1), and enrichment of AP-1 motif accessibility. We demonstrate that AP-1 and HIF2α regulate a therapy resilient and survivor phenotype in cancer cells. Consistent with this, genetic or pharmacologic targeting of AP-1 and HIF2α reduced the number of surviving cells following chemotherapy treatment. The role of AP-1 and HIF2α in stress response by polyploidy suggests a novel avenue for tackling chemotherapy-induced resistance in cancer. SIGNIFICANCE In response to cisplatin treatment, some surviving cancer cells undergo whole-genome duplications without mitosis, which represents a mechanism of drug resistance. This study presents mechanistic data to implicate AP-1 and HIF2α signaling in the formation of this surviving cell phenotype. The results open a new avenue for targeting drug-resistant cells.
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Affiliation(s)
- Christopher Carroll
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
| | - Auraya Manaprasertsak
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
| | - Arthur Boffelli Castro
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Anuraag Bukkuri
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
| | - Niklas Engström
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
| | - Etienne Baratchart
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
| | - Minjun Yang
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Catharina Hagerling
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
| | - Marie Arsenian-Henriksson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sarah R. Amend
- Cancer Ecology Center, the Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sofie Mohlin
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
- Division of Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Alan McIntyre
- Hypoxia and Acidosis Group, Nottingham Breast Cancer Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Kenneth J. Pienta
- Cancer Ecology Center, the Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emma U. Hammarlund
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- Lund Stem Cell Center (SCC), Lund University, Lund, Sweden
- Lund University Cancer Center (LUCC), Lund University, Lund, Sweden
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7
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Mah CY, Nguyen ADT, Niijima T, Helm M, Dehairs J, Ryan FJ, Ryan N, Quek LE, Hoy AJ, Don AS, Mills IG, Swinnen JV, Lynn DJ, Nassar ZD, Butler LM. Peroxisomal β-oxidation enzyme, DECR2, regulates lipid metabolism and promotes treatment resistance in advanced prostate cancer. Br J Cancer 2024; 130:741-754. [PMID: 38216720 PMCID: PMC10912652 DOI: 10.1038/s41416-023-02557-8] [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: 12/12/2022] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Peroxisomes are central metabolic organelles that have key roles in fatty acid homoeostasis. As prostate cancer (PCa) is particularly reliant on fatty acid metabolism, we explored the contribution of peroxisomal β-oxidation (perFAO) to PCa viability and therapy response. METHODS Bioinformatic analysis was performed on clinical transcriptomic datasets to identify the perFAO enzyme, 2,4-dienoyl CoA reductase 2 (DECR2) as a target gene of interest. Impact of DECR2 and perFAO inhibition via thioridazine was examined in vitro, in vivo, and in clinical prostate tumours cultured ex vivo. Transcriptomic and lipidomic profiling was used to determine the functional consequences of DECR2 inhibition in PCa. RESULTS DECR2 is upregulated in clinical PCa, most notably in metastatic castrate-resistant PCa (CRPC). Depletion of DECR2 significantly suppressed proliferation, migration, and 3D growth of a range of CRPC and therapy-resistant PCa cell lines, and inhibited LNCaP tumour growth and proliferation in vivo. DECR2 influences cell cycle progression and lipid metabolism to support tumour cell proliferation. Further, co-targeting of perFAO and standard-of-care androgen receptor inhibition enhanced suppression of PCa cell proliferation. CONCLUSION Our findings support a focus on perFAO, specifically DECR2, as a promising therapeutic target for CRPC and as a novel strategy to overcome lethal treatment resistance.
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Affiliation(s)
- Chui Yan Mah
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - An Dieu Trang Nguyen
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Takuto Niijima
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
| | - Madison Helm
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Jonas Dehairs
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven, Leuven, Belgium
| | - Feargal J Ryan
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Natalie Ryan
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Lake-Ee Quek
- School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Andrew J Hoy
- School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Anthony S Don
- School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Ian G Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Johannes V Swinnen
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven, Leuven, Belgium
| | - David J Lynn
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Zeyad D Nassar
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia.
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
| | - Lisa M Butler
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia.
- Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
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8
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Rahane D, Dhingra T, Chalavady G, Datta A, Ghosh B, Rana N, Borah A, Saraf S, Bhattacharya P. Hypoxia and its effect on the cellular system. Cell Biochem Funct 2024; 42:e3940. [PMID: 38379257 DOI: 10.1002/cbf.3940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 02/22/2024]
Abstract
Eukaryotic cells utilize oxygen for different functions of cell organelles owing to cellular survival. A balanced oxygen homeostasis is an essential requirement to maintain the regulation of normal cellular systems. Any changes in the oxygen level are stressful and can alter the expression of different homeostasis regulatory genes and proteins. Lack of oxygen or hypoxia results in oxidative stress and formation of hypoxia inducible factors (HIF) and reactive oxygen species (ROS). Substantial cellular damages due to hypoxia have been reported to play a major role in various pathological conditions. There are different studies which demonstrated that the functions of cellular system are disrupted by hypoxia. Currently, study on cellular effects following hypoxia is an important field of research as it not only helps to decipher different signaling pathway modulation, but also helps to explore novel therapeutic strategies. On the basis of the beneficial effect of hypoxia preconditioning of cellular organelles, many therapeutic investigations are ongoing as a promising disease management strategy in near future. Hence, the present review discusses about the effects of hypoxia on different cellular organelles, mechanisms and their involvement in the progression of different diseases.
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Affiliation(s)
- Dipali Rahane
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
| | - Tannu Dhingra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
| | - Guruswami Chalavady
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
| | - Aishika Datta
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
| | - Bijoyani Ghosh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
| | - Nikita Rana
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
| | - Anupom Borah
- Cellular and Molecular Neurobiology Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, Assam, India
| | - Shailendra Saraf
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
| | - Pallab Bhattacharya
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat, India
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9
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Bacci M, Lorito N, Smiriglia A, Subbiani A, Bonechi F, Comito G, Morriset L, El Botty R, Benelli M, López-Velazco JI, Caffarel MM, Urruticoechea A, Sflomos G, Malorni L, Corsini M, Ippolito L, Giannoni E, Meattini I, Matafora V, Havas K, Bachi A, Chiarugi P, Marangoni E, Morandi A. Acetyl-CoA carboxylase 1 controls a lipid droplet-peroxisome axis and is a vulnerability of endocrine-resistant ER + breast cancer. Sci Transl Med 2024; 16:eadf9874. [PMID: 38416843 DOI: 10.1126/scitranslmed.adf9874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/30/2024] [Indexed: 03/01/2024]
Abstract
Targeting aromatase deprives ER+ breast cancers of estrogens and is an effective therapeutic approach for these tumors. However, drug resistance is an unmet clinical need. Lipidomic analysis of long-term estrogen-deprived (LTED) ER+ breast cancer cells, a model of aromatase inhibitor resistance, revealed enhanced intracellular lipid storage. Functional metabolic analysis showed that lipid droplets together with peroxisomes, which we showed to be enriched and active in the LTED cells, controlled redox homeostasis and conferred metabolic adaptability to the resistant tumors. This reprogramming was controlled by acetyl-CoA-carboxylase-1 (ACC1), whose targeting selectively impaired LTED survival. However, the addition of branched- and very long-chain fatty acids reverted ACC1 inhibition, a process that was mediated by peroxisome function and redox homeostasis. The therapeutic relevance of these findings was validated in aromatase inhibitor-treated patient-derived samples. Last, targeting ACC1 reduced tumor growth of resistant patient-derived xenografts, thus identifying a targetable hub to combat the acquisition of estrogen independence in ER+ breast cancers.
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Affiliation(s)
- Marina Bacci
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Nicla Lorito
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Alfredo Smiriglia
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Angela Subbiani
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Francesca Bonechi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Giuseppina Comito
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Ludivine Morriset
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 rue d'Ulm, 75005 Paris, France
| | - Rania El Botty
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 rue d'Ulm, 75005 Paris, France
| | - Matteo Benelli
- Department of Medical Oncology, Azienda USL Toscana Centro, Hospital of Prato, Via Suor Niccolina Infermiera 20, 59100 Prato, Italy
| | - Joanna I López-Velazco
- Biodonostia Health Research Institute, Paseo Dr Begiristain s/n, 20014 San Sebastian, Spain
| | - Maria M Caffarel
- Biodonostia Health Research Institute, Paseo Dr Begiristain s/n, 20014 San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Ander Urruticoechea
- Biodonostia Health Research Institute, Paseo Dr Begiristain s/n, 20014 San Sebastian, Spain
- Gipuzkoa Cancer Unit, OSI Donostialdea-Onkologikoa Foundation, Paseo Dr Begiristain 121, 20014 San Sebastian, Spain
| | - George Sflomos
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Luca Malorni
- Department of Medical Oncology, Azienda USL Toscana Centro, Hospital of Prato, Via Suor Niccolina Infermiera 20, 59100 Prato, Italy
| | - Michela Corsini
- Department of Molecular and Translational Medicine, University of Brescia, Via Branze 39, 25123 Brescia, Italy
| | - Luigi Ippolito
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Elisa Giannoni
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Icro Meattini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
- Radiation Oncology Unit, Oncology Department, Azienda Ospedaliero Universitaria Careggi, Largo Brambilla 3, 50134 Florence, Italy
| | - Vittoria Matafora
- IFOM ETS-AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Kristina Havas
- IFOM ETS-AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Angela Bachi
- IFOM ETS-AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Paola Chiarugi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Elisabetta Marangoni
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 rue d'Ulm, 75005 Paris, France
| | - Andrea Morandi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
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10
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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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11
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Indari O, Ghosh S, Bal AS, James A, Garg M, Mishra A, Karmodiya K, Jha HC. Awakening the sleeping giant: Epstein-Barr virus reactivation by biological agents. Pathog Dis 2024; 82:ftae002. [PMID: 38281067 PMCID: PMC10901609 DOI: 10.1093/femspd/ftae002] [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: 03/27/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 01/29/2024] Open
Abstract
Epstein-Barr virus (EBV) may cause harm in immunocompromised conditions or on stress stimuli. Various chemical agents have been utilized to induce the lytic cycle in EBV-infected cells. However, apart from chemical agents and external stress stimuli, certain infectious agents may reactivate the EBV. In addition, the acute infection of other pathogens may provide suitable conditions for EBV to thrive more and planting the roots for EBV-associated pathologies. Various bacteria such as periodontal pathogens like Aggregatibacter, Helicobacter pylori, etc. have shown to induce EBV reactivation either by triggering host cells directly or indirectly. Viruses such as Human simplex virus-1 (HSV) induce EBV reactivation by HSV US3 kinase while other viruses such as HIV, hepatitis virus, and even novel SARS-CoV-2 have also been reported to cause EBV reactivation. The eukaryotic pathogens such as Plasmodium falciparum and Aspergillus flavus can also reactivate EBV either by surface protein interaction or as an impact of aflatoxin, respectively. To highlight the underexplored niche of EBV reactivation by biological agents, we have comprehensively presented the related information in this review. This may help to shedding the light on the research gaps as well as to unveil yet unexplored mechanisms of EBV reactivation.
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Affiliation(s)
- Omkar Indari
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Simrol, Indore 453552, India
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Subhrojyoti Ghosh
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Simrol, Indore 453552, India
| | - Adhiraj Singh Bal
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Simrol, Indore 453552, India
| | - Ajay James
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Simrol, Indore 453552, India
| | - Mehek Garg
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Simrol, Indore 453552, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Krishanpal Karmodiya
- Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune 411008, India
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Simrol, Indore 453552, India
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12
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Niknafs S, Meijer MMY, Khaskheli AA, Roura E. In ovo delivery of oregano essential oil activated xenobiotic detoxification and lipid metabolism at hatch in broiler chickens. Poult Sci 2024; 103:103321. [PMID: 38100943 PMCID: PMC10762474 DOI: 10.1016/j.psj.2023.103321] [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: 09/01/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
In ovo interventions are used to improve embryonic development and robustness of chicks. The objective of this study was to identify the optimal dose for in ovo delivery of oregano essential oil (OEO), and to investigate metabolic impacts. Broiler chickens Ross 308 fertile eggs were injected with 7 levels of OEO (0, 5, 10, 20, 30, 40, and 50 µL) into the amniotic fluid at embryonic d 17.5 (E17.5) (n = 48). Chick quality was measured by navel score (P < 0.05) and/or hatchability rates (P < 0.01) were significantly decreased at doses at or above 10 or 20 µL/egg, respectively, indicating potential toxicity. However, no effects were observed at the 5 µL/egg, suggesting that compensatory mechanisms were effective to maintain homeostasis in the developing embryo. To pursue a better understanding of these mechanisms, transcriptomic analyses of the jejunum were performed comparing the control injected with saline and the group injected with 5 µL of OEO. The transcriptomic analyses identified that 167 genes were upregulated and 90 were downregulated in the 5 µL OEO compared to the control group injected with saline (P < 0.01). Functional analyses of the differentially expressed genes (DEG) showed that metabolic pathways related to the epoxygenase cytochrome P450 pathway associated with xenobiotic catabolic processes were significantly upregulated (P < 0.05). In addition, long-chain fatty acid metabolism associated with ATP binding transporters was also upregulated in the OEO treated group (P < 0.05). The results indicated that low doses of OEO in ovo have the potential to increase lipid metabolism in late stages (E17.5) of embryonic development. In conclusion, in ovo delivery of 5 µL OEO did not show any negative impact on hatchability and chick quality. OEO elevated expression of key enzymes and receptors involved in detoxification pathways and lipid metabolism in the jejunum of hatchling broiler chicks.
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Affiliation(s)
- Shahram Niknafs
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Qld 4072, Australia
| | - Mila M Y Meijer
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Qld 4072, Australia
| | - Asad A Khaskheli
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Qld 4072, Australia
| | - Eugeni Roura
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Qld 4072, Australia.
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13
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Pilz JF, Klein M, Neumann-Haefelin E, Ganner A. VHL-dependence of EHHADH Expression in a Human Renal Cell Carcinoma Cell Line. J Kidney Cancer VHL 2024; 11:12-18. [PMID: 38304003 PMCID: PMC10834178 DOI: 10.15586/jkcvhl.v11i1.322] [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: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024] Open
Abstract
The von Hippel-Lindau tumor suppressor gene (VHL) is mutated in up to 90% of clear cell renal cell carcinoma (ccRCC) cases, thus playing a key role in ccRCC pathogenesis. ccRCC can be classified as a metabolic disease in which alterations in fatty acid metabolism facilitate cancer cell proliferation. Enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) is an enzyme involved in peroxisomal fatty acid degradation. It is primarily expressed in renal proximal tubule cells, presumably the origin of ccRCC. Although EHHADH is still a relatively unexplored gene, it is known to be differentially expressed in several tumors. In this study, analysis of several databases revealed that EHHADH expression is downregulated in ccRCC samples compared to healthy kidney samples. Moreover, cell culture experiments were performed to investigate the relationship between EHHADH and VHL at the gene and protein level. qPCR and Western blot analyses using the human ccRCC cell line RCC4 revealed that EHHADH is expressed in a VHL-dependent manner. RCC4 cells reconstituted with VHL show significantly higher EHHADH mRNA and protein levels than VHL-deficient RCC4 control cells. These results indicate that the downregulation of EHHADH in ccRCC reported may be due to the loss of VHL function. This study is the first to molecularly characterize EHHADH, a key enzyme in peroxisomal ß-oxidation, in relation to VHL, suggesting a potential pathogenic interaction that is worthy of further investigation.
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Affiliation(s)
- Julia Felicitas Pilz
- Renal Division, Department of Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marinella Klein
- Renal Division, Department of Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Athina Ganner
- Renal Division, Department of Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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14
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Chen L, Yan J, Shi H, Zhang Z, Zhao Y, Zhao Y, Wang Y, Ou J. Intervention mechanism of marine-based chito-oligosaccharide on acute liver injury induced by AFB 1 in rats. BIORESOUR BIOPROCESS 2024; 11:13. [PMID: 38647922 PMCID: PMC10992386 DOI: 10.1186/s40643-023-00708-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/22/2023] [Indexed: 04/25/2024] Open
Abstract
Aflatoxin B1 (AFB1) is extremely hepatotoxic, a causative agent of liver cancer, and can cause symptoms of acute or chronic liver damage. Chito-oligosaccharides (COS), obtained from the degradation of chitosan derived from shrimp and crab shells, is a natural antioxidant substance and its antitumor properties have been widely studied, but less research has been done on the prevention of AFB1-induced acute liver injury. In this study, rats were acutely exposed to 1 mg/kg BW AFB1 and simultaneously gavaged with different doses of COS for 8 days. The results showed that COS attenuated the hepatic histopathological changes and reduced serum biochemical indices (ALT, AST, ALP, and TBIL) in rats. It significantly inhibited MDA content and promoted SOD and GSH-Px activity production. Moreover, it also improved hepatocyte apoptosis. Furthermore, AFB1-vs-HCOS differential genes were enriched with 622 GO entries, and 380 were Biological Processes, 170 were Molecular Functions, 72 were Cellular Components. Differentially expressed genes (DEGs) analyzed by KEGG enrichment were more enriched in pathways, such as metabolism, PPAR signaling pathway, and peroxisome. Q-PCR technique verified that Lama5, Egr1, Cyp2b1, and Gadd45g in DEGs were associated with oxidative stress damage and apoptosis. In conclusion, COS intervention reduces the effect of AFB1 on hepatic genes and thus reduces the changes in hepatic gene function.
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Affiliation(s)
- Lin Chen
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiahui Yan
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Huijun Shi
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhaohuan Zhang
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, 201306, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China
| | - YueLiang Zhao
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Zhao
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, 201306, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China
| | - Yuan Wang
- Engineering Research Center of Modern Preparation Technology of TCM, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Jie Ou
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai, 201306, China.
- Laboratory of Quality and Safety Risk Assessment for Aquatic Product on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China.
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15
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Zhang T, Liu J, Wang M, Liu X, Qu J, Zhang H. Prognosis stratification and response to treatment in breast cancer based on one-carbon metabolism-related signature. Front Oncol 2024; 13:1288909. [PMID: 38239641 PMCID: PMC10794736 DOI: 10.3389/fonc.2023.1288909] [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: 09/05/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction Breast cancer (BC) is the most common malignant tumor in the female population. Despite staging and treatment consensus guidelines, significant heterogeneity exists in BC patients' prognosis and treatment efficacy. Alterations in one-carbon (1C) metabolism are critical for tumor growth, but the value of the role of 1C metabolism in BC has not been fully investigated. Methods To investigate the prognostic value of 1C metabolism-related genes in BC, 72 1C metabolism-related genes from GSE20685 dataset were used to construct a risk-score model via univariate Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) regression algorithm, which was validated on three external datasets. Based on the risk score, all BC patients were categorized into high-risk and low-risk groups. The predictive ability of the model in the four datasets was verified by plotting Kaplan-Meier curve and receiver operating characteristic (ROC) curve. The candidate genes were then analyzed in relation to gene mutations, gene enrichment pathways, immune infiltration, immunotherapy, and drug sensitivity. Results We identified a 7-gene 1C metabolism-related signature for prognosis and structured a prognostic model. ROC analysis demonstrated that the model accurately predicted the 2-, 3-, and 5-year overall survival rate of BC patients in the four cohorts. Kaplan-Meier analysis revealed that survival time of high-risk patients was markedly shorter than that of low-risk patients (p < 0.05). Meanwhile, high-risk patients had a higher tumor mutational burden (TMB), enrichment of tumor-associated pathways such as the IL-17 signaling pathway, lower levels of T follicular helper (Tfh) and B cells naive infiltration, and poorer response to immunotherapy. Furthermore, a strong correlation was found between MAT2B and CHKB and immune checkpoints. Discussion These findings offer new insights into the effect of 1C metabolism in the onset, progression, and therapy of BC and can be used to assess BC patients' prognosis, study immune infiltration, and develop potentially more effective clinical treatment options.
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Affiliation(s)
| | | | | | | | - Jia Qu
- Department of Ultrasound, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huawei Zhang
- Department of Ultrasound, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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16
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Zuo A, Zhou Y, Chen Y, Liu S, Lu Y, Li Y, Cao S, Liu Z. Physiological and Transcriptome Analysis Reveal the Regulation Mechanism Underlying the Muscle Quality Effect of Dietary Schisandra chinensis in Triploid Crucian Carp (Carassius auratus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1191-1207. [PMID: 38079085 DOI: 10.1007/s10126-023-10270-z] [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: 09/22/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Schisandra chinensis (sc) is generally demonstrated to improve antioxidant and immune functions in mammal. The present study through physiological and transcriptome analysis revealed alterations in muscle metabolisms of triploid crucian carp (Carassius auratus) cultured at different concentrations of S. chinensis diets (sc0, sc0.125%, sc0.25%, sc0.5%, sc1%, sc2%) after 8 weeks. The serum antioxidant enzyme activities analysis showed that dietary S. chinensis could reduce oxidative stress and increase organismic antioxidant capacity. Meanwhile, the detected results of muscle components presented that the amino acids and two flavor nucleotides of GMP and IMP significantly elevated while muscle crude lipid significantly reduced in S. chinensis feeding groups. In addition, springiness, chewiness, and fiber density in S. chinensis feeding groups muscle were significantly upregulated while muscle fiber diameter and area showed an opposite trend. By comparative transcriptome analysis of the muscles, functional enrichments of differentially expressed genes showed that multiple terms were related to purine metabolism, glycerolipid metabolism, regulation of actin cytoskeleton, and peroxisome. Finally, some key hub genes such as egln, gst, ggct, su1b, pi3kr4, myh9, lpl, gcdh, mylk, and col4a were identified by weighted gene co-expression network analysis. Taken together, our findings facilitate the understanding of the molecular basis underlying the muscle quality effect of dietary S. chinensis in triploid crucian carp, which provides valuable insights into the nutritional strategies of the aquaculture industry.
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Affiliation(s)
- Anli Zuo
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yonghua Zhou
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China
| | - Yuxian Chen
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China
| | - Sipu Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China
| | - Yuyao Lu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China
| | - Yingjie Li
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China
| | - Shenping Cao
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China
| | - Zhen Liu
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Chemical Engineering, Changsha University, Changsha, 410022, China.
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17
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Sun B, Zhou R, Zhu G, Xie X, Chai A, Li L, Fan T, Li B, Shi Y. Transcriptome Analysis Reveals the Involvement of Mitophagy and Peroxisome in the Resistance to QoIs in Corynespora cassiicola. Microorganisms 2023; 11:2849. [PMID: 38137993 PMCID: PMC10745780 DOI: 10.3390/microorganisms11122849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/08/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Quinone outside inhibitor fungicides (QoIs) are crucial fungicides for controlling plant diseases, but resistance, mainly caused by G143A, has been widely reported with the high and widespread use of QoIs. However, two phenotypes of Corynespora casiicola (RI and RII) with the same G143A showed significantly different resistance to QoIs in our previous study, which did not match the reported mechanisms. Therefore, transcriptome analysis of RI and RII strains after trifloxystrobin treatment was used to explore the new resistance mechanism in this study. The results show that 332 differentially expressed genes (DEGs) were significantly up-regulated and 448 DEGs were significantly down-regulated. The results of GO and KEGG enrichment showed that DEGs were most enriched in ribosomes, while also having enrichment in peroxide, endocytosis, the lysosome, autophagy, and mitophagy. In particular, mitophagy and peroxisome have been reported in medicine as the main mechanisms of reactive oxygen species (ROS) scavenging, while the lysosome and endocytosis are an important organelle and physiological process, respectively, that assist mitophagy. The oxidative stress experiments showed that the oxidative stress resistance of the RII strains was significantly higher than that of the RI strains: specifically, it was more than 1.8-fold higher at a concentration of 0.12% H2O2. This indicates that there is indeed a significant difference in the scavenging capacity of ROS between the two phenotypic strains. Therefore, we suggest that QoIs' action caused a high production of ROS, and that scavenging mechanisms such as mitophagy and peroxisomes functioned in RII strains to prevent oxidative stress, whereas RI strains were less capable of resisting oxidative stress, resulting in different resistance to QoIs. In this study, it was first revealed that mitophagy and peroxisome mechanisms available for ROS scavenging are involved in the resistance of pathogens to fungicides.
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Affiliation(s)
| | | | | | | | | | | | | | - Baoju Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (B.S.); (R.Z.)
| | - Yanxia Shi
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (B.S.); (R.Z.)
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Ma X, Deng Z, Li Z, Ma T, Li G, Zhang C, Zhang W, Chang J. Leveraging a disulfidptosis/ferroptosis-based signature to predict the prognosis of lung adenocarcinoma. Cancer Cell Int 2023; 23:267. [PMID: 37946181 PMCID: PMC10634118 DOI: 10.1186/s12935-023-03125-z] [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: 07/20/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Disulfidptosis and Ferroptosis are two novel forms of cell death. Although their mechanisms differ, research has shown that there is a relationship between the two. Investigating the connection between these two forms of cell death can further deepen our understanding of the development and progression of cancer, and provide better prediction models for accurate prognosis. METHODS In this study, RNA sequencing (RNA-seq) data, clinical data, single nucleotide polymorphism (SNP) data, and single-cell sequencing data were obtained from public databases. We used weighted gene co-expression network analysis (WGCNA) and unsupervised clustering to identify new Disulfidptosis/Ferroptosis-Related Genes (DFRG), and constructed a LASSO COX prognosis model that was externally validated. To further explore this novel signature, pathway and function analysis was performed, and differences in gene mutation frequency between high- and low-risk groups were studied. Importantly, we also conducted research on immune checkpoint, immune cell infiltration levels and immune resistance indicators, in addition to analyzing real clinical immunotherapy data. RESULTS We have identified four optimal disulfidptosis/ferroptosis-related genes (ODFRGs) that are differentially expressed and associated with the prognosis of Lung Adenocarcinoma (LUAD). These genes include GMPR, MCFD2, MRPL13, and SALL2. Based on these ODFRGs, we constructed a robust prognostic model in this study, and the high-risk group showed significantly lower overall survival (OS) compared to the low-risk group. Furthermore, this model can also predict the immunotherapy outcomes of LUAD patients to some extent.
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Affiliation(s)
- Xiaoqing Ma
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Zilin Deng
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Zhen Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Ting Ma
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Guiqing Li
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Cuijia Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
- Shandong First Medical University, Jinan, Shandong, China
| | - Wentao Zhang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
- Shandong First Medical University, Jinan, Shandong, China.
| | - Jin Chang
- Department of Radiation Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China.
- Shandong First Medical University, Jinan, Shandong, China.
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19
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George S, Serpe L. Exploring the redox potential induced by low-intensity focused ultrasound on tumor masses. Life Sci 2023; 332:122040. [PMID: 37633418 DOI: 10.1016/j.lfs.2023.122040] [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: 06/23/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
Cancer is still a major health problem worldwide despite huge efforts being spent on its biomedical research. Beyond the mainstream therapeutic interventions (i.e., surgery, chemotherapy, immunotherapy and radiotherapy), further significant progresses in anticancer therapy could rely on the development of novel treatment paradigms. To this end, one emerging approach consists in the use of non-thermal low-intensity focused ultrasound (LIFU) for conditioning cancer molecules and/or cancer-targeted compounds, thereby leading to cancer cell death with least side-effects. Cellular redox homeostasis manifested as the generation of reactive oxygen species (ROS) during energy metabolism as well as the antioxidant capacity is interwoven to the composition, size and anatomical location of the tumor masses. The higher content of "oxide free radicals" in cancers makes them vulnerable to disruption of redox homeostasis than in the healthy cells and therefore, one of the best options for preferentially eradicating them is increasing their oxidative stress, excessively. A little is known about the modulation of cellular redox homeostasis by LIFU, and so it will be of great interest and utility to understand the effects of LIFU on the energy metabolism of cancer cells. This review is intended to improve our knowledge on the effect of LIFU on cancer cells with particular reference to its redox metabolism for ultrasound-based therapies. Thereby, it could pave the way for exploring novel methodologies and designing combined anti-cancer therapies, especially, for faster and safer eradication of drug resistant and metastasizing solid tumors.
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Affiliation(s)
- Sajan George
- School of Bio Sciences & Technology, Vellore Institute of Technology, TN 632 014, India; Laser Research Centre, University of Johannesburg, Doornfontein 2028, South Africa.
| | - Loredana Serpe
- Department of Drug Science & Technology, University of Turin, Turin 10125, Italy
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20
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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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21
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Tai R, Leng J, Li W, Wu Y, Yang J. Construction of the metabolic reprogramming-associated gene signature for clear cell renal cell carcinoma prognosis prediction. BMC Urol 2023; 23:147. [PMID: 37715154 PMCID: PMC10503121 DOI: 10.1186/s12894-023-01317-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 09/04/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Metabolism reprogramming is a hallmark that associates tumor growth, metastasis, progressive, and poor prognosis. However, the metabolism-related molecular patterns and mechanism in clear cell renal cell carcinoma (ccRCC) remain unclear. Herein, the purpose of this study was to identify metabolism-related molecular pattern and to investigate the characteristics and prognostic values of the metabolism-related clustering. METHODS We comprehensively analyzed the differentially expressed genes (DEGs), and metabolism-related genes (MAGs) in ccRCC based on the TCGA database. Consensus clustering was used to construct a metabolism-related molecular pattern. Then, the biological function, molecular characteristics, Estimate/immune/stomal scores, immune cell infiltration, response to immunotherapy, and chemotherapy were analyzed. We also identified the DEGs between subclusters and constructed a poor signature and risk model based on LASSO regression cox analysis and univariable and multivariable cox regression analyses. Then, a predictive nomogram was constructed and validated by calibration curves. RESULTS A total of 1942 DEGs (1004 upregulated and 838 downregulated) between ccRCC tumor and normal samples were identified, and 254 MRGs were screened out from those DEGs. Then, 526 ccRCC patients were divided into two subclusters. The 7 metabolism-related pathways enriched in cluster 2. And cluster 2 with high Estimate/immune/stomal scores and poor survival. While, cluster 1 with higher immune cell infiltrating, expression of the immune checkpoint, IFN, HLA, immune activation-related genes, response to anti-CTLA4 treatment, and chemotherapy. Moreover, we identified 295 DEGs between two metabolism-related subclusters and constructed a 15-gene signature and 9 risk factors. Then, a risk score was calculated and the patients into high- and low-risk groups in TCGA-KIRC and E-MTAB-1980 datasets. And the prediction viability of the risk score was validated by ROC curves. Finally, the clinicopathological characteristics (age and stage), risk score, and molecular clustering, were identified as independent prognostic variables, and were used to construct a nomogram for 1-, 3-, 5-year overall survival predicting. The calibration curves were used to verify the performance of the predicted ability of the nomogram. CONCLUSION Our finding identified two metabolism-related molecular subclusters for ccRCC, which facilitates the estimation of response to immunotherapy and chemotherapy, and prognosis after treatment.
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Affiliation(s)
- Rongfen Tai
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Jinjun Leng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Wei Li
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Yuerong Wu
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China
| | - Junfeng Yang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
- Department of Urology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, 650032, China.
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22
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Krauze AV, Sierk M, Nguyen T, Chen Q, Yan C, Hu Y, Jiang W, Tasci E, Zgela TC, Sproull M, Mackey M, Shankavaram U, Meerzaman D, Camphausen K. Glioblastoma survival is associated with distinct proteomic alteration signatures post chemoirradiation in a large-scale proteomic panel. Front Oncol 2023; 13:1127645. [PMID: 37637066 PMCID: PMC10448824 DOI: 10.3389/fonc.2023.1127645] [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: 12/19/2022] [Accepted: 06/20/2023] [Indexed: 08/29/2023] Open
Abstract
Background Glioblastomas (GBM) are rapidly progressive, nearly uniformly fatal brain tumors. Proteomic analysis represents an opportunity for noninvasive GBM classification and biological understanding of treatment response. Purpose We analyzed differential proteomic expression pre vs. post completion of concurrent chemoirradiation (CRT) in patient serum samples to explore proteomic alterations and classify GBM by integrating clinical and proteomic parameters. Materials and methods 82 patients with GBM were clinically annotated and serum samples obtained pre- and post-CRT. Serum samples were then screened using the aptamer-based SOMAScan® proteomic assay. Significant traits from uni- and multivariate Cox models for overall survival (OS) were designated independent prognostic factors and principal component analysis (PCA) was carried out. Differential expression of protein signals was calculated using paired t-tests, with KOBAS used to identify associated KEGG pathways. GSEA pre-ranked analysis was employed on the overall list of differentially expressed proteins (DEPs) against the MSigDB Hallmark, GO Biological Process, and Reactome databases with weighted gene correlation network analysis (WGCNA) and Enrichr used to validate pathway hits internally. Results 3 clinical clusters of patients with differential survival were identified. 389 significantly DEPs pre vs. post-treatment were identified, including 284 upregulated and 105 downregulated, representing several pathways relevant to cancer metabolism and progression. The lowest survival group (median OS 13.2 months) was associated with DEPs affiliated with proliferative pathways and exhibiting distinct oppositional response including with respect to radiation therapy related pathways, as compared to better-performing groups (intermediate, median OS 22.4 months; highest, median OS 28.7 months). Opposite signaling patterns across multiple analyses in several pathways (notably fatty acid metabolism, NOTCH, TNFα via NF-κB, Myc target V1 signaling, UV response, unfolded protein response, peroxisome, and interferon response) were distinct between clinical survival groups and supported by WGCNA. 23 proteins were statistically signficant for OS with 5 (NETO2, CST7, SEMA6D, CBLN4, NPS) supported by KM. Conclusion Distinct proteomic alterations with hallmarks of cancer, including progression, resistance, stemness, and invasion, were identified in serum samples obtained from GBM patients pre vs. post CRT and corresponded with clinical survival. The proteome can potentially be employed for glioma classification and biological interrogation of cancer pathways.
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Affiliation(s)
- Andra Valentina Krauze
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Michael Sierk
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Trinh Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Qingrong Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Chunhua Yan
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Ying Hu
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - William Jiang
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Erdal Tasci
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Theresa Cooley Zgela
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Mary Sproull
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Megan Mackey
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Uma Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, NIH, Rockville, MD, United States
| | - Kevin Camphausen
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
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Abstract
Peroxisomes are involved in a multitude of metabolic and catabolic pathways, as well as the innate immune system. Their dysfunction is linked to severe peroxisome-specific diseases, as well as cancer and neurodegenerative diseases. To ensure the ability of peroxisomes to fulfill their many roles in the organism, more than 100 different proteins are post-translationally imported into the peroxisomal membrane and matrix, and their functionality must be closely monitored. In this Review, we briefly discuss the import of peroxisomal membrane proteins, and we emphasize an updated view of both classical and alternative peroxisomal matrix protein import pathways. We highlight different quality control pathways that ensure the degradation of dysfunctional peroxisomal proteins. Finally, we compare peroxisomal matrix protein import with other systems that transport folded proteins across membranes, in particular the twin-arginine translocation (Tat) system and the nuclear pore.
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Affiliation(s)
- Markus Rudowitz
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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24
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Pedrosa AG, Reglinski K, Lismont C, Kors S, Costello J, Rodrigues TA, Marques M, Linka N, Argyriou C, Weinhofer I, Kocherlakota S, Riccio V, Ferreira V, Di Cara F, Ferreira AR, Francisco T, Azevedo JE, Ribeiro D. Peroxisomes : novel findings and future directions. Histochem Cell Biol 2023; 159:379-387. [PMID: 37160800 PMCID: PMC10170047 DOI: 10.1007/s00418-023-02201-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 05/11/2023]
Affiliation(s)
- Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Katharina Reglinski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
- Leibniz-Institute of Photonic Technologies, Albert-Einstein Strasse 9, 07745, Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Max-Wien-Platz 1, 07743, Jena, Germany
- University Hospital Jena, Bachstraße 18, Jena, Germany
| | - Celien Lismont
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Suzan Kors
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Joseph Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Mariana Marques
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Nicole Linka
- Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | | | - Isabelle Weinhofer
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | | | - Victoria Riccio
- Cell Biology Department, Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Vanessa Ferreira
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Francesca Di Cara
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Nova Scotia Health Authority IWK, Halifax, NS, Canada
| | - Ana Rita Ferreira
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
| | - Daniela Ribeiro
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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25
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Erukainure OL, Oyenihi OR, Amaku JF, Chukwuma CI, Nde AL, Salau VF, Matsabisa MG. Cannabis sativa L. modulates altered metabolic pathways involved in key metabolisms in human breast cancer (MCF-7) cells: A metabolomics study. Heliyon 2023; 9:e16156. [PMID: 37215911 PMCID: PMC10196869 DOI: 10.1016/j.heliyon.2023.e16156] [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: 01/24/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
The present study investigated the ability of Cannabis sativa leaves infusion (CSI) to modulate major metabolisms implicated in cancer cells survival, as well as to induce cell death in human breast cancer (MCF-7) cells. MCF-7 cell lines were treated with CSI for 48 h, doxorubicin served as the standard anticancer drug, while untreated MCF-7 cells served as the control. CSI caused 21.2% inhibition of cell growth at the highest dose. Liquid chromatography-mass spectroscopy (LC-MS) profiling of the control cells revealed the presence of carbohydrate, vitamins, oxidative, lipids, nucleotides, and amino acids metabolites. Treatment with CSI caused a 91% depletion of these metabolites, while concomitantly generating selenomethionine, l-cystine, deoxyadenosine triphosphate, cyclic AMP, selenocystathionine, inosine triphosphate, adenosine phosphosulfate, 5'-methylthioadenosine, uric acid, malonic semialdehyde, 2-methylguanosine, ganglioside GD2 and malonic acid. Metabolomics analysis via pathway enrichment of the metabolites revealed the activation of key metabolic pathways relevant to glucose, lipid, amino acid, vitamin, and nucleotide metabolisms. CSI caused a total inactivation of glucose, vitamin, and nucleotide metabolisms, while inactivating key lipid and amino acid metabolic pathways linked to cancer cell survival. Flow cytometry analysis revealed an induction of apoptosis and necrosis in MCF-7 cells treated with CSI. High-performance liquid chromatography (HPLC) analysis of CSI revealed the presence of cannabidiol, rutin, cinnamic acid, and ferulic. These results portray the antiproliferative potentials of CSI as an alternative therapy for the treatment and management of breast cancer as depicted by its modulation of glucose, lipid, amino acid, vitamin, and nucleotide metabolisms, while concomitantly inducing cell death in MCF-7 cells.
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Affiliation(s)
- Ochuko L. Erukainure
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Omolola R. Oyenihi
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - James F. Amaku
- Department of Chemistry, Michael Okpara University of Agriculture, Umudike, Abia State, Nigeria
| | - Chika I. Chukwuma
- Center for Quality of Health and Living, Faculty of Health Sciences, Central University of Technology, Bloemfontein 9301, South Africa
| | - Adeline Lum Nde
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Veronica F. Salau
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Motlalepula G. Matsabisa
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
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Shang K, Ma N, Che J, Li H, Hu J, Sun H, Cao B. SLC27A2 mediates FAO in colorectal cancer through nongenic crosstalk regulation of the PPARs pathway. BMC Cancer 2023; 23:335. [PMID: 37041476 PMCID: PMC10091540 DOI: 10.1186/s12885-023-10816-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/06/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Peroxisome proliferator activated receptors (PPARs) are a nuclear hormone receptors superfamily that is closely related to fatty acid (FA) metabolism and tumor progression. Solute carrier family 27 member 2 (SLC27A2) is important for FA transportation and metabolism and is related to cancer progression. This study aims to explore the mechanisms of how PPARs and SLC27A2 regulate FA metabolism in colorectal cancer (CRC) and find new strategies for CRC treatment. METHODS Biological information analysis was applied to detect the expression and the correlation of PPARs and SLC27A2 in CRC. The protein-protein interaction (PPI) interaction networks were explored by using the STRING database. Uptake experiments and immunofluorescence staining were used to analyse the function and number of peroxisomes and colocalization of FA with peroxisomes, respectively. Western blotting and qRT‒PCR were performed to explore the mechanisms. RESULTS SLC27A2 was overexpressed in CRC. PPARs had different expression levels, and PPARG was significantly highly expressed in CRC. SLC27A2 was correlated with PPARs in CRC. Both SLC27A2 and PPARs were closely related to fatty acid oxidation (FAO)‒related genes. SLC27A2 affected the activity of ATP Binding Cassette Subfamily D Member 3 (ABCD3), also named PMP70, the most abundant peroxisomal membrane protein. We found that the ratios of p-Erk/Erk and p-GSK3β/GSK3β were elevated through nongenic crosstalk regulation of the PPARs pathway. CONCLUSIONS SLC27A2 mediates FA uptake and beta-oxidation through nongenic crosstalk regulation of the PPARs pathway in CRC. Targeting SLC27A2/FATP2 or PPARs may provide new insights for antitumour strategies.
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Affiliation(s)
- Kun Shang
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xi-Cheng District, Beijing, 100050, China
| | - Nina Ma
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xi-Cheng District, Beijing, 100050, China
| | - Juanjuan Che
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xi-Cheng District, Beijing, 100050, China
| | - Huihui Li
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xi-Cheng District, Beijing, 100050, China
| | - Jiexuan Hu
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xi-Cheng District, Beijing, 100050, China
| | - Haolin Sun
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xi-Cheng District, Beijing, 100050, China
| | - Bangwei Cao
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xi-Cheng District, Beijing, 100050, China.
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Chen Y, Liu S, Papageorgiou LG, Theofilatos K, Tsoka S. Optimisation Models for Pathway Activity Inference in Cancer. Cancers (Basel) 2023; 15:1787. [PMID: 36980673 PMCID: PMC10046797 DOI: 10.3390/cancers15061787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND With advances in high-throughput technologies, there has been an enormous increase in data related to profiling the activity of molecules in disease. While such data provide more comprehensive information on cellular actions, their large volume and complexity pose difficulty in accurate classification of disease phenotypes. Therefore, novel modelling methods that can improve accuracy while offering interpretable means of analysis are required. Biological pathways can be used to incorporate a priori knowledge of biological interactions to decrease data dimensionality and increase the biological interpretability of machine learning models. METHODOLOGY A mathematical optimisation model is proposed for pathway activity inference towards precise disease phenotype prediction and is applied to RNA-Seq datasets. The model is based on mixed-integer linear programming (MILP) mathematical optimisation principles and infers pathway activity as the linear combination of pathway member gene expression, multiplying expression values with model-determined gene weights that are optimised to maximise discrimination of phenotype classes and minimise incorrect sample allocation. RESULTS The model is evaluated on the transcriptome of breast and colorectal cancer, and exhibits solution results of good optimality as well as good prediction performance on related cancer subtypes. Two baseline pathway activity inference methods and three advanced methods are used for comparison. Sample prediction accuracy, robustness against noise expression data, and survival analysis suggest competitive prediction performance of our model while providing interpretability and insight on key pathways and genes. Overall, our work demonstrates that the flexible nature of mathematical programming lends itself well to developing efficient computational strategies for pathway activity inference and disease subtype prediction.
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Affiliation(s)
- Yongnan Chen
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, London WC2B 4BG, UK
| | - Songsong Liu
- School of Management, Harbin Institute of Technology, Harbin 150001, China
| | - Lazaros G Papageorgiou
- The Sargent Centre for Process Systems Engineering, Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Konstantinos Theofilatos
- King's College London British Heart Foundation Centre, School of Cardiovascular and Metabolic Medicine and Sciences, London SE1 7EH, UK
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, London WC2B 4BG, UK
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O’Sullivan É, Keogh A, Henderson B, Finn SP, Gray SG, Gately K. Treatment Strategies for KRAS-Mutated Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:1635. [PMID: 36980522 PMCID: PMC10046549 DOI: 10.3390/cancers15061635] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Activating mutations in KRAS are highly prevalent in solid tumours and are frequently found in 35% of lung, 45% of colorectal, and up to 90% of pancreatic cancers. Mutated KRAS is a prognostic factor for disease-free survival (DFS) and overall survival (OS) in NSCLC and is associated with a more aggressive clinical phenotype, highlighting the need for KRAS-targeted therapy. Once considered undruggable due to its smooth shallow surface, a breakthrough showed that the activated G12C-mutated KRAS isozyme can be directly inhibited via a newly identified switch II pocket. This discovery led to the development of a new class of selective small-molecule inhibitors against the KRAS G12C isoform. Sotorasib and adagrasib are approved in locally advanced or metastatic NSCLC patients who have received at least one prior systemic therapy. Currently, there are at least twelve KRAS G12C inhibitors being tested in clinical trials, either as a single agent or in combination. In this study, KRAS mutation prevalence, subtypes, rates of occurrence in treatment-resistant invasive mucinous adenocarcinomas (IMAs), and novel drug delivery options are reviewed. Additionally, the current status of KRAS inhibitors, multiple resistance mechanisms that limit efficacy, and their use in combination treatment strategies and novel multitargeted approaches in NSCLC are discussed.
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Affiliation(s)
- Éabha O’Sullivan
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
| | - Anna Keogh
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
| | - Brian Henderson
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
| | - Stephen P. Finn
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
| | - Kathy Gately
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
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Lin Z, Fan W, Sui X, Wang J, Zhao J. Necroptosis-Related LncRNA Signatures for Prognostic Prediction in Uterine Corpora Endometrial Cancer. Reprod Sci 2023; 30:576-589. [PMID: 35854199 PMCID: PMC9988759 DOI: 10.1007/s43032-022-01023-9] [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: 01/28/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
Necroptosis is one of the common modes of apoptosis, and it has an intrinsic association with cancer prognosis. However, the role of the necroptosis-related long non-coding RNA LncRNA (NRLncRNAs) in uterine corpora endometrial cancer (UCEC) has not yet been fully elucidated at present. Therefore, the present study is designed to investigate the potential prognostic value of necroptosis-related LncRNAs in UCEC. In the present study, the expression profiles and clinical data of UCEC patients were downloaded from TCGA database to identify the differentially expressed NRLncRNAs associated with overall survival. A LncRNA risk model was constructed via Cox regression analysis, and its prognostic value was evaluated. We have also further evaluated the relationships between the LncRNA features and the related cellular function, related pathways, immune status, and immune checkpoints m6A-related genes. Seven signatures, including PCAT19, CDKN2B-AS1, LINC01936, LINC02178, BMPR1B-DT, LINC00237, and TRPM2-AS, were established to assess the overall survival (OS) of the UCEC in the present study. Survival analysis and ROC curves indicated that the correlated signature has good predictable performance. The normogram could accurately predict the overall survival of the patients with an excellent clinical practical value. Enrichment analysis of gene sets indicated that risk signals were enriched in several immune-related pathways. In addition, the risk characteristics were significantly correlated with immune cells, immune function, immune cell infiltration, immune checkpoints, and some m6A-related genes. This study has identified seven necroptosis-related LncRNA signatures for the first time, providing a valuable basis for a more accurate prognostic prediction of UCEC.
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Affiliation(s)
- Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Weisen Fan
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Xiaohui Sui
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Juntao Wang
- Department of Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China.
| | - Junde Zhao
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China.
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Di Cara F, Savary S, Kovacs WJ, Kim P, Rachubinski RA. The peroxisome: an up-and-coming organelle in immunometabolism. Trends Cell Biol 2023; 33:70-86. [PMID: 35788297 DOI: 10.1016/j.tcb.2022.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 12/27/2022]
Abstract
Peroxisomes are essential metabolic organelles, well known for their roles in the metabolism of complex lipids and reactive ionic species. In the past 10 years, peroxisomes have also been cast as central regulators of immunity. Lipid metabolites of peroxisomes, such as polyunsaturated fatty acids (PUFAs), are precursors for important immune mediators, including leukotrienes (LTs) and resolvins. Peroxisomal redox metabolism modulates cellular immune signaling such as nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation. Additionally, peroxisomal β-oxidation and ether lipid synthesis control the development and aspects of the activation of both innate and adaptive immune cells. Finally, peroxisome number and metabolic activity have been linked to inflammatory diseases. These discoveries have opened avenues of investigation aimed at targeting peroxisomes for therapeutic intervention in immune disorders, inflammation, and cancer.
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Affiliation(s)
- Francesca Di Cara
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada.
| | - Stéphane Savary
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France
| | - Werner J Kovacs
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology in Zurich (ETH Zürich), Zurich, Switzerland
| | - Peter Kim
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
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31
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Li R, Tong R, Zhang Z, Deng M, Wang T, Hou G. Single-cell sequencing analysis and transcriptome analysis constructed the macrophage related gene-related signature in lung adenocarcinoma and verified by an independent cohort. Genomics 2022; 114:110520. [PMID: 36372305 DOI: 10.1016/j.ygeno.2022.110520] [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: 08/10/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Recent studies have emphasized the close relationship between macrophages and tumor immunity, and the prognosis of lung adenocarcinoma (LUAD) patients is intimately linked to this. Nonetheless, the prognostic signature and classification of different immune patterns in LUAD patients based on the macrophages is largely unexplored. METHODS Two sc-RNAseq datasets of LUAD patients were collected and reprocessed. The differentially expressed genes (DEGs) related to macrophages between LUAD tissues and normal lung tissues were then identified. Based upon the above genes, three distinct immune patterns in the TCGA-LUAD cohort were identified. The ssGSEA and CIBERSORT were applied for immune profiling and characterization of different subtypes. A four-gene prognostic signature for LUAD patients was established based on the DEGs between the subtypes using stepwise multi-Cox regression. TCGA-LUAD cohort was used as training set. Five GEO-LUAD datasets and an independent cohort containing 112 LUAD samples were used for validation. TIDE (tumor immune dysfunction and exclusion) and drug sensitivity analyses were also performed. RESULTS Macrophage-related differentially expressed genes were found out using the publicly available scRNA-seq data of LUAD. Three different immune patterns which were proved to have distinct immune infiltration characteristics in the TCGA-LUAD cohort were recognized based on the above macrophage-related genes. Thereafter, 174 DEGs among the above three different immune patterns were figured out; on the basis of this, a four-gene prognostic signature was constructed. This signature distinguished the prognosis of LUAD patients well in various GSE datasets as well as our independent cohort. Further analyses revealed that patients which had a higher risk score also accompanied with a lower immune infiltration level and a worse response to several immunotherapy biomarkers. CONCLUSION This study highlighted that macrophage were significantly associated with TME diversity and complexity. The four-gene prognostic signature could be used for predicting outcomes and immune landscapes for patients with LUAD.
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Affiliation(s)
- Ruixia Li
- Department of Pulmonary and Critical Care Medicine, First Hospital of China Medical University, Shenyang 110001, China
| | - Run Tong
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; National Center for Respiratory Medicine, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Zhe Zhang
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang 110001, China
| | - Mingming Deng
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100029, China; National Center for Respiratory Medicine, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Tao Wang
- Department of Pathology, Shenyang KingMed Center for Clinical Laboratory Co., Ltd., Shenyang 110001, China
| | - Gang Hou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; National Center for Respiratory Medicine, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; National Clinical Research Center for Respiratory Diseases, Beijing 100029, China.
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Gatalica Z, Stafford P, Vranic S. Alpha-methylacyl-CoA racemase (AMACR) protein is upregulated in early proliferative lesions of the breast irrespective of apocrine differentiation. Hum Pathol 2022; 129:40-46. [PMID: 35998819 DOI: 10.1016/j.humpath.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022]
Abstract
Alpha-methylacyl-CoA racemase (AMACR/P504S) is a mitochondrial and peroxisomal enzyme involved in the branched-chain fatty acid and bile acid metabolism. AMACR is a useful diagnostic biomarker for prostate carcinomas and several other malignancies. Its expression in apocrine breast lesions had been previously reported, but its role in breast cancer progression has not been fully investigated. One hundred fifty breast samples (80 with invasive carcinomas) were studied. The expression of AMACR protein was analyzed using the immunohistochemical method (IHC). Lesions were considered positive if AMACR was detected in ≥10% of the cells at any intensity comprising a histologically defined normal epithelial structure or a pathologic lesion. In addition, AMACR mRNA relative expression was calculated from the whole-transcript RNA-Seq performed on >20,000 diverse tumor samples using a 20,000+ hybrid-capture NGS assay with the transcript capture panel based on the Agilent SureSelect Human All ExonV7. Expression of AMACR protein was restricted to epithelia. It was uncommon in the normal breast (7/81 samples, 9%). Increasing AMACR expression was observed with proliferative epithelial lesions (18% of usual ductal hyperplasias/adenosis, 70% of atypical lesions and 72% of DCIS/LCIS). Invasive ductal carcinomas NST and invasive lobular carcinomas expressed AMACR in 64% and 46%, respectively. The highest AMACR expression was observed in luminal B and HER2-positive breast carcinomas (86-100%). Triple-negative breast carcinomas exhibited AMACR in 50% of the cases. Apocrine lesions showed strong, nearly uniform overexpression of AMACR (100% of metaplasias, hyperplasias and in situ carcinomas and 88% of invasive apocrine carcinomas were positive). RNA-Seq analysis also confirmed AMACR expression in breast carcinomas, although its median value was substantially lower with a lower standard deviation than in prostate carcinomas. Over-expression of AMACR characterizes various proliferative, preinvasive and invasive breast lesions and is not specific to the apocrine morphology. It points to altered lipid metabolism (branched fatty acids) as one of the general characteristics of breast carcinogenesis, like several other malignancies. Its early detection may represent a potential target for cancer progression intervention.
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Affiliation(s)
- Zoran Gatalica
- Department of Pathology, University of Oklahoma College of Medicine, Oklahoma City, OK 73104, United States
| | | | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, 2713, Qatar.
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Kim YH, Jo DS, Park NY, Bae JE, Kim JB, Lee HJ, Kim SH, Kim SH, Lee S, Son M, Park K, Jeong K, Yeom E, Cho DH. Inhibition of BRD4 Promotes Pexophagy by Increasing ROS and ATM Activation. Cells 2022; 11:cells11182839. [PMID: 36139416 PMCID: PMC9497081 DOI: 10.3390/cells11182839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
Although autophagy regulates the quality and quantity of cellular compartments, the regulatory mechanisms underlying peroxisomal autophagy (pexophagy) remain largely unknown. In this study, we identified several BRD4 inhibitors, including molibresib, a novel pexophagy inducer, via chemical library screening. Treatment with molibresib promotes loss of peroxisomes selectively, but not mitochondria, ER, or Golgi apparatus in HeLa cells. Consistently, depletion of BRD4 expression also induced pexophagy in RPE cells. In addition, the inhibition of BRD4 by molibresib increased autophagic degradation of peroxisome ATG7-dependency. We further found that molibresib produced reactive oxygen species (ROS), which potentiates ATM activation. Inhibition of ROS or ATM suppressed the loss of peroxisomes in molibresib-treated cells. Taken together, our data suggest that inhibition of BRD4 promotes pexophagy by increasing ROS and ATM activation.
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Affiliation(s)
- Yong Hwan Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Doo Sin Jo
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Na Yeon Park
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Ji-Eun Bae
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
| | - Joon Bum Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Ha Jung Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - So Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Seong Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Sunwoo Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Mikyung Son
- Orgasis Corp., Suwon 16229, Gyeonggi-do, Korea
| | - Kyuhee Park
- Bio-Center, Gyeonggido Business & Science Accelerator, Suwon 16229, Gyeonggi-do, Korea
| | - Kwiwan Jeong
- Bio-Center, Gyeonggido Business & Science Accelerator, Suwon 16229, Gyeonggi-do, Korea
| | - Eunbyul Yeom
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Dong-Hyung Cho
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
- Orgasis Corp., Suwon 16229, Gyeonggi-do, Korea
- Correspondence: ; Tel.: +82-53-950-5382
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Yifrach E, Holbrook-Smith D, Bürgi J, Othman A, Eisenstein M, van Roermund CW, Visser W, Tirosh A, Rudowitz M, Bibi C, Galor S, Weill U, Fadel A, Peleg Y, Erdmann R, Waterham HR, Wanders RJA, Wilmanns M, Zamboni N, Schuldiner M, Zalckvar E. Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions. Mol Syst Biol 2022; 18:e11186. [PMID: 36164978 PMCID: PMC9513677 DOI: 10.15252/msb.202211186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Seventy years following the discovery of peroxisomes, their complete proteome, the peroxi‐ome, remains undefined. Uncovering the peroxi‐ome is crucial for understanding peroxisomal activities and cellular metabolism. We used high‐content microscopy to uncover peroxisomal proteins in the model eukaryote – Saccharomyces cerevisiae. This strategy enabled us to expand the known peroxi‐ome by ~40% and paved the way for performing systematic, whole‐organellar proteome assays. By characterizing the sub‐organellar localization and protein targeting dependencies into the organelle, we unveiled non‐canonical targeting routes. Metabolomic analysis of the peroxi‐ome revealed the role of several newly identified resident enzymes. Importantly, we found a regulatory role of peroxisomes during gluconeogenesis, which is fundamental for understanding cellular metabolism. With the current recognition that peroxisomes play a crucial part in organismal physiology, our approach lays the foundation for deep characterization of peroxisome function in health and disease.
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Affiliation(s)
- Eden Yifrach
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Jérôme Bürgi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Alaa Othman
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Miriam Eisenstein
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Carlo Wt van Roermund
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Wouter Visser
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Asa Tirosh
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot, Israel
| | - Markus Rudowitz
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Chen Bibi
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Shahar Galor
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Uri Weill
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Peleg
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Maya Schuldiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
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35
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Rabow Z, Laubach K, Kong X, Shen T, Mohibi S, Zhang J, Fiehn O, Chen X. p73α1, an Isoform of the p73 Tumor Suppressor, Modulates Lipid Metabolism and Cancer Cell Growth via Stearoyl-CoA Desaturase-1. Cells 2022; 11:2516. [PMID: 36010592 PMCID: PMC9406568 DOI: 10.3390/cells11162516] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 01/26/2023] Open
Abstract
Altered lipid metabolism is a hallmark of cancer. p73, a p53 family member, regulates cellular processes and is expressed as multiple isoforms. However, the role of p73 in regulating lipid metabolism is not well-characterized. Previously, we found that loss of p73 exon 12 (E12) leads to an isoform switch from p73α to p73α1, the latter of which has strong tumor suppressive activity. In this study, comprehensive untargeted metabolomics was performed to determine whether p73α1 alters lipid metabolism in non-small cell lung carcinoma cells. RNA-seq and molecular biology approaches were combined to identify lipid metabolism genes altered upon loss of E12 and identify a direct target of p73α1. We found that loss of E12 leads to decreased levels of phosphatidylcholines, and this was due to decreased expression of genes involved in phosphatidylcholine synthesis. Additionally, we found that E12-knockout cells had increased levels of phosphatidylcholines containing saturated fatty acids (FAs) and decreased levels of phosphatidylcholines containing monounsaturated fatty acids (MUFAs). We then found that p73α1 inhibits cancer cell viability through direct transcriptional suppression of Stearoyl-CoA Desaturase-1 (SCD1), which converts saturated FAs to MUFAs. Finally, we showed that p73α1-mediated suppression of SCD1 leads to increased ratios of saturated FAs to MUFAs.
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Affiliation(s)
- Zachary Rabow
- West Coast Metabolomics Center, University of California, Davis, CA 95616, USA
| | - Kyra Laubach
- Comparative Oncology Laboratory, Schools of Medicine and Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Xiangmudong Kong
- Comparative Oncology Laboratory, Schools of Medicine and Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Tong Shen
- West Coast Metabolomics Center, University of California, Davis, CA 95616, USA
| | - Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Medicine and Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Medicine and Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, CA 95616, USA
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Medicine and Veterinary Medicine, University of California, Davis, CA 95616, USA
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Dai L, Wang X, Bai T, Liu J, Chen B, Li T, Yang W. Identification of a novel cellular senescence-related signature for the prediction of prognosis and immunotherapy response in colon cancer. Front Genet 2022; 13:961554. [PMID: 35991564 PMCID: PMC9386482 DOI: 10.3389/fgene.2022.961554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
The study was conducted to construct a cellular senescence-related risk score signature to predict prognosis and immunotherapy response in colon cancer. Colon cancer data were acquired from the Gene Expression Omnibus and The Cancer Genome Atlas databases. And cellular senescence-related genes were obtained from the CellAge database. The colon cancer data were classified into different clusters based on cellular senescence-related gene expression. Next, prognostic differential genes among clusters were identified with survival analysis. A cellular senescence-related risk score signature was developed by performing the LASSO regression analysis. Finally, PCA analysis, t-SNE analysis, Kaplan-Meier survival analysis, ROC analysis, univariate Cox regression analysis, multivariate Cox regression analysis, C-index analysis, meta-analysis, immune infiltration analysis, and IPS score analysis were used to evaluate the significance of the risk signature for predicting prognosis and immunotherapy response in colon cancer. The colon cancer data were classified into three clusters. The patients in cluster A and cluster B had longer survival. A cellular senescence-related risk score signature was developed. Patients in the low-risk score group showed a better prognosis. The risk score signature could predict colon cancer patients’ prognosis independently of other clinical characteristics. The risk score signature predicted the prognosis of colon cancer patients more accurately than other signatures. Patients in the low-risk score group showed a better response to immunotherapy. The opposite was true for the high-risk score group. In conclusion, the cellular senescence-related risk score signature could be used for the prediction of prognosis and immunotherapy response in colon cancer.
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Whyte SS, Karns R, Min K, Cho J, Lee S, Lake C, Bondoc A, Yoon J, Shin S. Integrated analysis using ToppMiR uncovers altered miRNA- mRNA regulatory networks in pediatric hepatocellular carcinoma-A pilot study. Cancer Rep (Hoboken) 2022; 6:e1685. [PMID: 35859536 PMCID: PMC9875636 DOI: 10.1002/cnr2.1685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pediatric hepatocellular carcinoma (HCC) is a group of liver cancers whose mechanisms behind their pathogenesis and progression are poorly understood. AIM We aimed to identify alterations in the expression of miRNAs and their putative target mRNAs in not only tumor tissues of patients with pediatric HCC but also in corresponding non-tumorous background livers by using liver tissues without underlying liver disease as a control. METHODS AND RESULTS We performed a small-scale miRNA and mRNA profiling of pediatric HCC (consisting of fibrolamellar carcinoma [FLC] and non-FLC HCC) and paired liver tissues to identify miRNAs whose expression levels differed significantly from control livers without underlying liver disease. ToppMiR was used to prioritize both miRNAs and their putative target mRNAs in a gene-annotation network, and the mRNA profile was used to refine the prioritization. Our analysis generated prioritized lists of miRNAs and mRNAs from the following three sets of analyses: (a) pediatric HCC versus control; (b) FLC versus control; and (c) corresponding non-tumorous background liver tissues from the same patients with pediatric HCC versus control. No liver disease liver tissues were used as the control group for all analyses. Many miRNAs whose expressions were deregulated in pediatric HCC were consistent with their roles in adult HCC and/or other non-hepatic cancers. Our gene ontology analysis of target mRNAs revealed enrichment of biological processes related to the sustenance and propagation of cancer and significant downregulation of metabolic processes. CONCLUSION Our pilot study indicates that alterations in miRNA-mRNA networks were detected in not only tumor tissues but also corresponding non-tumorous liver tissues from patients with pediatric HCC, suggesting multi-faceted roles of miRNAs in disease progression. Our results may lead to novel hypotheses for future large-scale studies.
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Affiliation(s)
- Senyo S. Whyte
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology & NutritionCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Kyung‐Won Min
- Department of BiologyGangneung‐Wonju National UniversityGangneungRepublic of Korea
| | - Jung‐Hyun Cho
- Department of Biochemistry and Molecular BiologyMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Sanghoon Lee
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Charissa Lake
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
| | - Alexander Bondoc
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA,Department of SurgeryUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
| | - Je‐Hyun Yoon
- Department of Biochemistry and Molecular BiologyMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Soona Shin
- Division of Pediatric General and Thoracic SurgeryCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA,Department of SurgeryUniversity of Cincinnati College of MedicineCincinnatiOhioUSA
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Sahoo DK, Borcherding DC, Chandra L, Jergens AE, Atherly T, Bourgois-Mochel A, Ellinwood NM, Snella E, Severin AJ, Martin M, Allenspach K, Mochel JP. Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor. Cancers (Basel) 2022; 14:3525. [PMID: 35884586 PMCID: PMC9322748 DOI: 10.3390/cancers14143525] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 12/14/2022] Open
Abstract
Lipopolysaccharide (LPS) is associated with chronic intestinal inflammation and promotes intestinal cancer progression in the gut. While the interplay between LPS and intestinal immune cells has been well-characterized, little is known about LPS and the intestinal epithelium interactions. In this study, we explored the differential effects of LPS on proliferation and the transcriptome in 3D enteroids/colonoids obtained from dogs with naturally occurring gastrointestinal (GI) diseases including inflammatory bowel disease (IBD) and intestinal mast cell tumor. The study objective was to analyze the LPS-induced modulation of signaling pathways involving the intestinal epithelia and contributing to colorectal cancer development in the context of an inflammatory (IBD) or a tumor microenvironment. While LPS incubation resulted in a pro-cancer gene expression pattern and stimulated proliferation of IBD enteroids and colonoids, downregulation of several cancer-associated genes such as Gpatch4, SLC7A1, ATP13A2, and TEX45 was also observed in tumor enteroids. Genes participating in porphyrin metabolism (CP), nucleocytoplasmic transport (EEF1A1), arachidonic acid, and glutathione metabolism (GPX1) exhibited a similar pattern of altered expression between IBD enteroids and IBD colonoids following LPS stimulation. In contrast, genes involved in anion transport, transcription and translation, apoptotic processes, and regulation of adaptive immune responses showed the opposite expression patterns between IBD enteroids and colonoids following LPS treatment. In brief, the crosstalk between LPS/TLR4 signal transduction pathway and several metabolic pathways such as primary bile acid biosynthesis and secretion, peroxisome, renin-angiotensin system, glutathione metabolism, and arachidonic acid pathways may be important in driving chronic intestinal inflammation and intestinal carcinogenesis.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
- SMART Pharmacology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Dana C. Borcherding
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Lawrance Chandra
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Albert E. Jergens
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Todd Atherly
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Agnes Bourgois-Mochel
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - N. Matthew Ellinwood
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (N.M.E.); (E.S.)
| | - Elizabeth Snella
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA; (N.M.E.); (E.S.)
| | - Andrew J. Severin
- Office of Biotechnology’s Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA;
| | | | - Karin Allenspach
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.C.B.); (L.C.); (A.E.J.); (T.A.); (A.B.-M.); (K.A.)
| | - Jonathan P. Mochel
- SMART Pharmacology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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Signature for Prostate Cancer Based on Autophagy-Related Genes and a Nomogram for Quantitative Risk Stratification. DISEASE MARKERS 2022; 2022:7598942. [PMID: 35860692 PMCID: PMC9293571 DOI: 10.1155/2022/7598942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022]
Abstract
Background. Prostate cancer (PCa) ranks as the most common malignancy and the second leading cause of cancer-related death among males worldwide. The essential role of autophagy in the progression of PCa and treatment resistance has been preliminarily revealed. However, comprehensive molecular elucidations of the correlation between PCa and autophagy are rare. Method. We obtained transcription information and corresponding clinicopathological profiles of PCa patients from TCGA, MSKCC, and GEO datasets. LAASO analysis was employed to select gene signatures and estimate the autophagy score for each patient. Correlations between the signature and prognosis of PCa were investigated by K-M and multivariate Cox regression analyses. A nomogram was established on the basis of the above results. Further validations relied on ROC, calibration analysis, decision curve analysis, and external cohorts. Variable activated signaling pathways were revealed using GSVA algorithms, and the genetic alteration landscape was elucidated via the oncodrive module from the “maftools” R package. In addition, we also examined the therapeutic role of the signature based on phenotype data from GDSC 2016. Result. Six autophagy-related genes were eventually selected to establish the signature, including ULK1, CAPN10, FKBP5, UBE2T, NLRC4, and BNIP3L. We used these genes and corresponding coefficients to calculate an autophagy score (AutS) for each patient in this study. A high AutS group and a low AutS group were divided on the mean AutS of the patients. Longer overall survival, higher Gleason score and PSA, and better response to ADT were observed in patients with high AutS. Meanwhile, we found that high AutS PCa was related to more proliferation-associated signaling activation and higher genetic mutation frequencies, manifesting a poor prognosis. A nomogram was constructed based on GS, T stage, PSA, and AutS as covariates. Its discriminative efficacy and clinical value were validated using robust statistical methods. Finally, we tested its prognostic value through two external cohorts and six published signatures. Conclusion. The autophagy-related gene signature is a highly discriminative model for risk stratification and drug therapy in PCa, and a nomogram incorporating AutS might be a promising tool for precision medicine.
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Chen AS, Liu H, Wu Y, Luo S, Patz EF, Glass C, Su L, Du M, Christiani DC, Wei Q. Genetic variants in DDO and PEX5L in peroxisome-related pathways predict non-small cell lung cancer survival. Mol Carcinog 2022; 61:619-628. [PMID: 35502931 DOI: 10.1002/mc.23400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 01/14/2023]
Abstract
Peroxisomes play a role in lipid metabolism and regulation of reactive oxygen species, but its role in development and progression of non-small cell lung cancer (NSCLC) is not well understood. Here, we investigated the associations between 9708 single-nucleotide polymorphisms (SNPs) in 113 genes in the peroxisome-related pathways and survival of NSCLC patients from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) and the Harvard Lung Cancer Susceptibility (HLCS) study. In 1185 NSCLC patients from the PLCO trial, we found that 213 SNPs were significantly associated with NSCLC overall survival (OS) (p ≤ 0.05, Bayesian false discovery probability [BFDP] ≤ 0.80), of which eight SNPs were validated in the HLCS data set. In a multivariate Cox proportional hazards regression model, two independent SNPs (rs9384742 DDO and rs9825224 PEX5L) were significantly associated with NSCLC survival (hazards ratios [HR] of 1.17 with 95% CI [confidence interval] of 1.06-1.28 and 0.86 with 95% CI of 0.77-0.96, respectively). Patients with one or two protective genotypes had a significantly higher OS (HR: 0.787 [95% CI: 0.620-0.998] and 0.691 [95% CI: 0.543-0.879], respectively). Further expression quantitative trait loci analysis using whole blood and lung tissue showed that the minor allele of rs9384742 DDO was significantly associated with decreased messenger RNA (mRNA) expression levels and that DDO expression was also decreased in NSCLC tumor tissue. Additionally, high PEX5L expression levels were significantly associated with lower survival of NSCLC. Our data suggest that variants in these peroxisome-related genes may influence gene regulation and are potential predictors of NSCLC OS, once validated by additional studies.
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Affiliation(s)
- Allan S Chen
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yufeng Wu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Edward F Patz
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Departments of Radiology, Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Carolyn Glass
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Li Su
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mulong Du
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
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41
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Wang N, Gu Y, Li L, Chi J, Liu X, Xiong Y, Zhong C. Development and Validation of a Prognostic Classifier Based on Lipid Metabolism-Related Genes for Breast Cancer. J Inflamm Res 2022; 15:3477-3499. [PMID: 35726216 PMCID: PMC9206459 DOI: 10.2147/jir.s357144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
Background The changes of lipid metabolism have been implicated in the development of many tumors, but its role in breast invasive carcinoma (BRCA) remains to be fully established. Here, we attempted to ascertain the prognostic value of lipid metabolism-related genes in BRCA. Methods We obtained RNA expression data and clinical information for BRCA and normal samples from public databases and downloaded a lipid metabolism-related gene set. Ingenuity Pathway Analysis (IPA) was applied to identify the potential pathways and functions of Differentially Expressed Genes (DEGs) related to lipid metabolism. Subsequently, univariate and multivariate Cox regression analyses were utilized to construct the prognostic gene signature. Functional enrichment analysis of prognostic genes was achieved by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Kaplan-Meier analysis, Receiver Operating Characteristic (ROC) curves, clinical follow-up results were employed to assess the prognostic potency. Potential compounds targeting prognostic genes were screened by Connectivity Map (CMap) database and a prognostic gene-drug interaction network was constructed using Comparative Toxicogenomics Database (CTD). Furthermore, we separately validated the selected marker genes in BRCA samples and human breast cancer cell lines (MCF-7, MDA-MB-231). Results IPA and functional enrichment analysis demonstrated that the 162 lipid metabolism-related DEGs we obtained were involved in many lipid metabolism and BRCA pathological signatures. The prognostic classifier we constructed comprising SDC1 and SORBS1 can serve as an independent prognostic marker for BRCA. CMap filtered 37 potential compounds against prognostic genes, of which 16 compounds could target both two prognostic genes were identified by CTD. The functions of the two prognostic genes in breast cancer cells were verified by cell function experiments. Conclusion Within this study, we identified a novel prognostic classifier based on two lipid metabolism-related genes: SDC1 and SORBS1. This result highlighted a new perspective on the metabolic exploration of BRCA.
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Affiliation(s)
- Nan Wang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Yuanting Gu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Lin Li
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Jiangrui Chi
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Xinwei Liu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Youyi Xiong
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Chaochao Zhong
- Department of Plastic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
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Zalckvar E, Schuldiner M. Beyond rare disorders: A new era for peroxisomal pathophysiology. Mol Cell 2022; 82:2228-2235. [PMID: 35714584 DOI: 10.1016/j.molcel.2022.05.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 12/17/2022]
Abstract
Metabolism is emerging as a central influencer of multiple disease states in humans. Peroxisomes are central metabolic organelles whose decreased function gives rise to severe peroxisomal diseases. Recently, it is becoming clear that, beyond such rare inborn errors, the deterioration of peroxisomal functions contributes to multiple and prevalent diseases such as cancer, viral infection, diabetes, and neurodegeneration. Despite the clear importance of peroxisomes in common pathophysiological processes, research on the mechanisms underlying their contributions is still sparse. Here, we highlight the timeliness of focusing on peroxisomes in current research on central, abundant, and society-impacting human pathologies. As peroxisomes are now coming into the spotlight, it is clear that intensive research into these important organelles will enable a better understanding of their contribution to human health, serving as the basis to develop new diagnostic and therapeutic approaches to prevent and treat human diseases.
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Affiliation(s)
- Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Shen J, Chen A, Cai Z, Chen Z, Cao R, Liu Z, Li Y, Hao J. Exhausted local lactate accumulation via injectable nanozyme-functionalized hydrogel microsphere for inflammation relief and tissue regeneration. Bioact Mater 2022; 12:153-168. [PMID: 35310385 PMCID: PMC8897073 DOI: 10.1016/j.bioactmat.2021.10.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/11/2021] [Accepted: 10/10/2021] [Indexed: 12/15/2022] Open
Abstract
Local lactate accumulation greatly hinders tissue repair and regeneration under ischemic condition. Herein, an injectable microsphere (MS@MCL) for local lactate exhaustion was constructed by grafting manganese dioxide (MnO2) -lactate oxidase (LOX) composite nanozyme on microfluidic hyaluronic acid methacrylate (HAMA) microspheres via chemical bonds, achieving a long-term oxygen-promoted lactate exhaustion effect and a long half-life in vivo. The uniform and porous microspheres synthesized by microfluidic technology is beneficial to in situ injection therapy and improving encapsulation efficiency. Furthermore, chemical grafting into HAMA microspheres through amide reactions promoted local enzymatic concentration and activity enhancement. It was showed that the MS@MCL eliminated oxidative and inflammatory stress and promoted extracellular matrix metabolism and cell survival when co-cultured with nucleus pulposus cells (NPCs) in vitro. In the rat degenerative intervertebral disc model caused by lactate injection, MS@MCL showed a long-term therapeutic effect in reducing intervertebral height narrowing and preventing extracellular matrix (ECM) degradation as well as inflammatory damage in vivo. Altogether, this study confirms that this nanozyme-functionalized injectable MS@MCL effectively improves the regenerative and reparative effect in ischemic tissues by disposing of enriched lactate in local microenvironment. Exhausted local lactate accumulation via injectable hydrogel microsphere. Long-acting microfluidic hyaluronic acid microspheres. Manganese dioxide-lactate oxidase composited nanozyme via covalent bond. Promoted sustained release of nanozyme and maintained enzymatic activity.
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Affiliation(s)
- Jieliang Shen
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Chongqing, 40042, PR China
| | - Ao Chen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, PR China
| | - Zhengwei Cai
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, PR China
| | - Zhijie Chen
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, PR China
| | - Ruichao Cao
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Chongqing, 40042, PR China
| | - Zongchao Liu
- Department of Orthopaedics, Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, No.182 Chunhui Road, Sichuan, 646699, PR China
- Corresponding author.
| | - Yuling Li
- Department of Orthopaedics, Affiliated Hospital of North Sichuan Medical College, No.63 Wenhua Road, Nanchong, Sichuan, 637000, PR China
- Corresponding author.
| | - Jie Hao
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Chongqing, 40042, PR China
- Corresponding author.
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Space- and Time-Resolved Metabolomics of a High-Grade Serous Ovarian Cancer Mouse Model. Cancers (Basel) 2022; 14:cancers14092262. [PMID: 35565391 PMCID: PMC9104348 DOI: 10.3390/cancers14092262] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/10/2022] Open
Abstract
The dismally low survival rate of ovarian cancer patients diagnosed with high-grade serous carcinoma (HGSC) emphasizes the lack of effective screening strategies. One major obstacle is the limited knowledge of the underlying mechanisms of HGSC pathogenesis at very early stages. Here, we present the first 10-month time-resolved serum metabolic profile of a triple mutant (TKO) HGSC mouse model, along with the spatial lipidome profile of its entire reproductive system. A high-coverage liquid chromatography mass spectrometry-based metabolomics approach was applied to longitudinally collected serum samples from both TKO (n = 15) and TKO control mice (n = 15), tracking metabolome and lipidome changes from premalignant stages to tumor initiation, early stages, and advanced stages until mouse death. Time-resolved analysis showed specific temporal trends for 17 lipid classes, amino acids, and TCA cycle metabolites, associated with HGSC progression. Spatial lipid distributions within the reproductive system were also mapped via ultrahigh-resolution matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and compared with serum lipid profiles for various lipid classes. Altogether, our results show that the remodeling of lipid and fatty acid metabolism, amino acid biosynthesis, TCA cycle and ovarian steroidogenesis are critical components of HGSC onset and development. These metabolic alterations are accompanied by changes in energy metabolism, mitochondrial and peroxisomal function, redox homeostasis, and inflammatory response, collectively supporting tumorigenesis.
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Zhou Y, Li X, Guan A, Zhou H, Zhu Y, Wang R, Li R. EPHX2 Inhibits Colon Cancer Progression by Promoting Fatty Acid Degradation. Front Oncol 2022; 12:870721. [PMID: 35433439 PMCID: PMC9005964 DOI: 10.3389/fonc.2022.870721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022] Open
Abstract
Tumor cells use metabolic reprogramming to keep up with the need for bioenergy, biosynthesis, and oxidation balance needed for rapid tumor division. This phenomenon is considered a marker of tumors, including colon cancer (CRC). As an important pathway of cellular energy metabolism, fatty acid metabolism plays an important role in cellular energy supply and oxidation balance, but presently, our understanding of the exact role of fatty acid metabolism in CRC is limited. Currently, no lipid metabolism therapy is available for the treatment of CRC. The establishment of a lipidmetabolism model regulated by oncogenes/tumor suppressor genes and associated with the clinical characteristics of CRC is necessary to further understand the mechanism of fatty acid metabolism in CRC. In this study, through multi-data combined with bioinformatic analysis and basic experiments, we introduced a tumor suppressor gene, EPHX2, which is rarely reported in CRC, and confirmed that its inhibitory effect on CRC is related to fatty acid degradation.
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Affiliation(s)
- Yiran Zhou
- Department of General Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Yan'an Hospital of Kunming City, Kunming, China.,Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, China
| | - Xiao Li
- Department of General Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Yan'an Hospital of Kunming City, Kunming, China.,Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, China
| | - Aoran Guan
- Department of General Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Yan'an Hospital of Kunming City, Kunming, China.,Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, China
| | - Haodong Zhou
- Department of General Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Yan'an Hospital of Kunming City, Kunming, China.,Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, China
| | - Yankun Zhu
- Department of General Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Yan'an Hospital of Kunming City, Kunming, China.,Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, China
| | - Ruotian Wang
- Department of General Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Yan'an Hospital of Kunming City, Kunming, China.,Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, China
| | - Ruhong Li
- Department of General Surgery, Yan'an Hospital Affiliated to Kunming Medical University, Yan'an Hospital of Kunming City, Kunming, China.,Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Kunming, China
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46
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Gregorio JD, Petricca S, Iorio R, Toniato E, Flati V. MITOCHONDRIAL AND METABOLIC ALTERATIONS IN CANCER CELLS. Eur J Cell Biol 2022; 101:151225. [DOI: 10.1016/j.ejcb.2022.151225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 02/07/2023] Open
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47
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Zhao Z, Zhao Z, Wang J, Zhang H, Xi Z, Xia Q. ABCC6 Knockdown Fuels Cell Proliferation by Regulating PPARα in Hepatocellular Carcinoma. Front Oncol 2022; 12:840287. [PMID: 35280774 PMCID: PMC8907651 DOI: 10.3389/fonc.2022.840287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/28/2022] [Indexed: 11/18/2022] Open
Abstract
The ATP binding cassette (ABC) transporter family is ubiquitous in eukaryotes, specifically in vertebrates, and plays a crucial role in energy homeostasis, cell signaling, and drug resistance. Accumulating evidence indicates that some ABC transporters contribute to cancer cell proliferation and tumor progression; however, relatively little is known about the behavior of the ABC transporter family in hepatocellular carcinoma (HCC). By analyzing two public transcriptomic databases, we evaluated the effect of genes in the ABC transporter family on HCC prognostic prediction; ABCC6 was selected for further study. Notably, ABCC6 was found to be downregulated in HCC tissues and correlated with favorable outcomes in patients with HCC. Moreover, ABCC6 knockdown not only significantly promoted cell proliferation in vitro and in vivo, but also inhibited cell cycle arrest and cell apoptosis. Transcriptome analysis revealed that ABCC6 depletion enhanced the “mitotic cell cycle” and “DNA replication” pathways, and suppressed the “PPAR signaling pathway”. Further investigation demonstrated that PPARα, one of the key regulators in peroxisome metabolism, is located downstream of ABCC6. In summary, our study provides profound insights into the behavior of ABC transporter family genes in various HCC cohorts, identifies ABCC6 as a biomarker for early-stage HCC diagnosis, and offers experimental basis for further investigations of targeting ABCC6 in the treatment of patients with HCC.
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Affiliation(s)
- Zhicong Zhao
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Zhenjun Zhao
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianye Wang
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Surgery, School of Medicine, Technical University of Munich, Munich, Germany
| | - He Zhang
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Surgery, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Zhifeng Xi
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China.,Shanghai Institute of Transplantation, Shanghai, China
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48
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Ferreira AR, Marques M, Ramos B, Kagan JC, Ribeiro D. Emerging roles of peroxisomes in viral infections. Trends Cell Biol 2021; 32:124-139. [PMID: 34696946 DOI: 10.1016/j.tcb.2021.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023]
Abstract
Peroxisomes, essential subcellular organelles that fulfill important functions in lipid and reactive oxygen species metabolism, have recently emerged as key players during viral infections. Their importance for the establishment of the cellular antiviral response has been highlighted by numerous reports of specific evasion of peroxisome-dependent signaling by different viruses. Recent data demonstrate that peroxisomes also assume important proviral functions. Here, we review and discuss the recent advances in the study of the diverse roles of peroxisomes during viral infections, from animal to plant viruses, and from basic to translational perspectives. We further discuss the future development of this emerging area and propose that peroxisome-related mechanisms represent a promising target for the development of novel antiviral strategies.
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Affiliation(s)
- Ana Rita Ferreira
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mariana Marques
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Bruno Ramos
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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Meyer MT, Watermann C, Dreyer T, Wagner S, Wittekindt C, Klussmann JP, Ergün S, Baumgart-Vogt E, Karnati S. Differential Expression of Peroxisomal Proteins in Distinct Types of Parotid Gland Tumors. Int J Mol Sci 2021; 22:7872. [PMID: 34360635 PMCID: PMC8345988 DOI: 10.3390/ijms22157872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
Salivary gland cancers are rare but aggressive tumors that have poor prognosis and lack effective cure. Of those, parotid tumors constitute the majority. Functioning as metabolic machinery contributing to cellular redox balance, peroxisomes have emerged as crucial players in tumorigenesis. Studies on murine and human cells have examined the role of peroxisomes in carcinogenesis with conflicting results. These studies either examined the consequences of altered peroxisomal proliferators or compared their expression in healthy and neoplastic tissues. None, however, examined such differences exclusively in human parotid tissue or extended comparison to peroxisomal proteins and their associated gene expressions. Therefore, we examined differences in peroxisomal dynamics in parotid tumors of different morphologies. Using immunofluorescence and quantitative PCR, we compared the expression levels of key peroxisomal enzymes and proliferators in healthy and neoplastic parotid tissue samples. Three parotid tumor subtypes were examined: pleomorphic adenoma, mucoepidermoid carcinoma and acinic cell carcinoma. We observed higher expression of peroxisomal matrix proteins in neoplastic samples with exceptional down regulation of certain enzymes; however, the degree of expression varied between tumor subtypes. Our findings confirm previous experimental results on other organ tissues and suggest peroxisomes as possible therapeutic targets or markers in all or certain subtypes of parotid neoplasms.
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Affiliation(s)
- Malin Tordis Meyer
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Christoph Watermann
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Thomas Dreyer
- Institute of Pathology, Justus Liebig University, Langhansstrasse 10, D-35392 Gießen, Germany;
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Claus Wittekindt
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Jens Peter Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Süleyman Ergün
- Institute for Anatomy and Cell Biology, Julius-Maximilians-University Würzburg, Koellikerstrasse 6, D-97070 Würzburg, Germany;
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology II, Medical Cell Biology, Justus Liebig University, D-35385 Gießen, Germany;
| | - Srikanth Karnati
- Institute for Anatomy and Cell Biology, Julius-Maximilians-University Würzburg, Koellikerstrasse 6, D-97070 Würzburg, Germany;
- Institute for Anatomy and Cell Biology II, Medical Cell Biology, Justus Liebig University, D-35385 Gießen, Germany;
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50
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Peroxisomal ABC Transporters: An Update. Int J Mol Sci 2021; 22:ijms22116093. [PMID: 34198763 PMCID: PMC8201181 DOI: 10.3390/ijms22116093] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
ATP-binding cassette (ABC) transporters constitute one of the largest superfamilies of conserved proteins from bacteria to mammals. In humans, three members of this family are expressed in the peroxisomal membrane and belong to the subfamily D: ABCD1 (ALDP), ABCD2 (ALDRP), and ABCD3 (PMP70). These half-transporters must dimerize to form a functional transporter, but they are thought to exist primarily as tetramers. They possess overlapping but specific substrate specificity, allowing the transport of various lipids into the peroxisomal matrix. The defects of ABCD1 and ABCD3 are responsible for two genetic disorders called X-linked adrenoleukodystrophy and congenital bile acid synthesis defect 5, respectively. In addition to their role in peroxisome metabolism, it has recently been proposed that peroxisomal ABC transporters participate in cell signaling and cell control, particularly in cancer. This review presents an overview of the knowledge on the structure, function, and mechanisms involving these proteins and their link to pathologies. We summarize the different in vitro and in vivo models existing across the species to study peroxisomal ABC transporters and the consequences of their defects. Finally, an overview of the known and possible interactome involving these proteins, which reveal putative and unexpected new functions, is shown and discussed.
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