1
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Yuan Y, Chen L. Transporters in vitamin uptake and cellular metabolism: impacts on health and disease. LIFE METABOLISM 2025; 4:loaf008. [PMID: 40444179 PMCID: PMC12121362 DOI: 10.1093/lifemeta/loaf008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 02/20/2025] [Accepted: 03/01/2025] [Indexed: 06/02/2025]
Abstract
Vitamins are vital nutrients essential for metabolism, functioning as coenzymes, antioxidants, and regulators of gene expression. Their absorption and metabolism rely on specialized transport proteins that ensure bioavailability and cellular utilization. Water-soluble vitamins, including B-complex and vitamin C, are transported by solute carrier (SLC) family proteins and ATP-binding cassette (ABC) transporters for efficient uptake and cellular distribution. Fat-soluble vitamins (A, D, E, and K) rely on lipid-mediated pathways through proteins like scavenger receptor class B type I (SR-BI), CD36, and Niemann-Pick C1-like 1 (NPC1L1), integrating their absorption with lipid metabolism. Defective vitamin transporters are associated with diverse metabolic disorders, including neurological, hematological, and mitochondrial diseases. Advances in structural and functional studies of vitamin transporters highlight their tissue-specific roles and regulatory mechanisms, shedding light on their impact on health and disease. This review emphasizes the significance of vitamin transporters and their potential as therapeutic targets for deficiencies and related chronic conditions.
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Affiliation(s)
- Yaxuan Yuan
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Metabolic Dysregulation & Prevention and Treatment of Esophageal Cancer, Innovation Center of Basic Research for Metabolic-Associated Fatty Liver Disease, Ministry of Education of China, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical sciences, Zhengzhou University, Zhengzhou, Henan, China, 450001
| | - Ligong Chen
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Metabolic Dysregulation & Prevention and Treatment of Esophageal Cancer, Innovation Center of Basic Research for Metabolic-Associated Fatty Liver Disease, Ministry of Education of China, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical sciences, Zhengzhou University, Zhengzhou, Henan, China, 450001
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2
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Aba N, Ducos C, Morel E, El Fayech C, Fresneau B, de Vathaire F, Le Teuff G, Haddy N. Influence of genetic biomarkers on cardiac diseases in childhood cancer survivors: a systematic review. THE PHARMACOGENOMICS JOURNAL 2025; 25:15. [PMID: 40413218 PMCID: PMC12103300 DOI: 10.1038/s41397-025-00369-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/21/2025] [Accepted: 04/02/2025] [Indexed: 05/27/2025]
Abstract
Childhood cancer survivors (CCS) often suffer from cardiac disease (CD) after treatment that included anthracycline and radiotherapy involving the heart. However, the variability in CD occurrence cannot be explained solely by these treatments, suggesting the existence of genetic predisposition. We conducted a systematic review searching on Medline-PubMed and Scopus, to identify studies reporting associations between genetic factors and CD in CCS. We included studies published up to 11 April 2023, with no lower limit, and assessed the quality of genetic associations by the Q-genie tool. As a result, 20 studies were included (15 case-control and five cohorts), revealing several genes and variants associated with cardiomyopathy, among which, SLC28A3-rs7853758, RARG-rs2229774, P2RX7-rs208294 and P2RX7-rs3751143 variants gave the most consistent findings. This review highlights the necessity to establish a set of clinically useful genes and variants to identify patients most at risk of developing cardiomyopathy, and to implement monitoring and prevention strategies.
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Affiliation(s)
- Naïla Aba
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France.
- CESP, INSERM U 1018, Cancer and Radiation team, Gustave Roussy, Villejuif, France.
| | - Claire Ducos
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France
- CESP, INSERM U 1018, Cancer and Radiation team, Gustave Roussy, Villejuif, France
| | - Eric Morel
- Inserm, U769, Univ. Paris-Sud 11, IFR141, Labex Lermit, Châtenay-Malabry, France
| | - Chiraz El Fayech
- CESP, INSERM U 1018, Cancer and Radiation team, Gustave Roussy, Villejuif, France
- Department of Childhood and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Brice Fresneau
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France
- CESP, INSERM U 1018, Cancer and Radiation team, Gustave Roussy, Villejuif, France
- Department of Childhood and Adolescent Oncology, Gustave Roussy, Villejuif, France
- Department of Research, Gustave Roussy, Villejuif, France
| | - Florent de Vathaire
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France
- CESP, INSERM U 1018, Cancer and Radiation team, Gustave Roussy, Villejuif, France
- Department of Research, Gustave Roussy, Villejuif, France
| | - Gwénaël Le Teuff
- Bureau de Biostatistique et d'Epidémiologie, Gustave Roussy, Villejuif, France
- Université Paris-Saclay, CESP, INSERM U1018 Oncostat, labeled Ligue Contre le Cancer, Villejuif, France
| | - Nadia Haddy
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France
- CESP, INSERM U 1018, Cancer and Radiation team, Gustave Roussy, Villejuif, France
- Department of Research, Gustave Roussy, Villejuif, France
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3
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Chen SJ, Wu CL, Lin LY, Horng JL. Evaluating N-acetylcysteine for mitigating cisplatin-induced oxidative stress and ionocyte damage in a zebrafish model. Toxicol Appl Pharmacol 2025; 501:117401. [PMID: 40398509 DOI: 10.1016/j.taap.2025.117401] [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: 03/22/2025] [Revised: 05/17/2025] [Accepted: 05/17/2025] [Indexed: 05/23/2025]
Abstract
In this study, we examined the protective effects of N-acetylcysteine (NAC) against cisplatin-induced toxicity in zebrafish embryos. Cisplatin (cis-diamminedichloroplatinum II), a widely used anticancer drug, is associated with significant cytotoxic effects toward non-target tissues, including renal and ototoxic damage. Using zebrafish embryos exposed to cisplatin, we evaluated survival rates, hatching rates, ionocyte densities, oxidative stress, and platinum accumulation. NAC co-treatment significantly enhanced survival and hatching rates, preserved ionocyte density, mitigated oxidative stress, and reduced platinum accumulation. These findings highlight ionocytes as an effective model for assessing non-renal toxicity due to their high metabolic activity and mitochondrial abundance. The results suggest that NAC might serve as a co-therapeutic agent to alleviate cisplatin-induced toxicity during chemotherapy.
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Affiliation(s)
- Szu-Jung Chen
- Department of Radiation Oncology, Taoyuan General Hospital, Taoyuan, Taiwan
| | - Ciao-Ling Wu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Li-Yih Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jiun-Lin Horng
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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4
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Kotlyar M, Guo Z, Rao AVS, Peng H, Wang J, Ma Z, Schiene-Fischer C, Fischer G, Liu JO. Identification of Rapaglutin E as an Isoform-Specific Inhibitor of Glucose Transporter 1. ACS Chem Biol 2025; 20:1004-1009. [PMID: 40226990 DOI: 10.1021/acschembio.5c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2025]
Abstract
Natural products rapamycin and FK506 are macrocyclic compounds with therapeutic benefits whose unique scaffold inspired the generation and exploration of hybrid macrocycle rapafucins. From this library, a potent inhibitor of the facilitative glucose transporter (GLUT), rapaglutin A (RgA), was previously identified. RgA is a pan-GLUT inhibitor of Class I isoforms GLUT1, GLUT3, and GLUT4. Herein, we report the discovery of rapaglutin E (RgE). Unlike RgA, RgE is highly specific for GLUT1. Further characterization revealed that RgE and RgA likely bound to distinct sites on GLUT1 despite their shared FKBP-binding domain, suggesting that the distinct effector domains of RgE and RgA play key roles in the recognition of GLUTs.
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Affiliation(s)
- Marnie Kotlyar
- Chemistry Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Zufeng Guo
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - A V Subba Rao
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Hanjing Peng
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Jingxin Wang
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Zhongnan Ma
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Gunter Fischer
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jun O Liu
- Chemistry Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland 21218, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Departments of Pharmacology and Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
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5
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Wen H, Dai F, Wang H, Lin Y, Xu Z, Lyu Z. Identification and validation of SLC16A8 as a prognostic biomarker in clear cell renal cell carcinoma: a six-gene solute carrier signature. Exp Cell Res 2025; 448:114567. [PMID: 40268265 DOI: 10.1016/j.yexcr.2025.114567] [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: 01/15/2025] [Revised: 04/10/2025] [Accepted: 04/20/2025] [Indexed: 04/25/2025]
Abstract
Solute carrier (SLC) proteins are essential for nutrient transport, influencing tumor metabolism and growth while preserving cellular homeostasis. Despite the critical biological functions of these transporters, their applicability as therapeutic targets in clear cell renal cell carcinoma (ccRCC) remains largely unexplored. In the current study, we analyzed transcriptomic data and discovered 77 differentially expressed SLC genes in ccRCC, with 24 demonstrating predictive potential. Using Lasso regression, we developed a prognostic signature comprising six key genes: SLC2A3, SLC11A1, SLC14A1, SLC16A8, SLC22A6, and SLC28A1. This signature demonstrated strong diagnostic performance and served as an independent predictor of patient survival. Further analysis integrating clinical variables and risk scores enabled the construction of nomograms, which exhibited high predictive accuracy for patient outcomes. Immune profiling revealed distinct infiltration patterns between risk groups: high-risk patients showed elevated levels of memory B cells, activated CD4+ T cells, regulatory T cells (Tregs), M0 macrophages, and neutrophils. In contrast, their low-risk counterparts showed M1 macrophages, resting dendritic cells, and resting mast cells. Validation experiments confirmed that SLC16A8 was significantly overexpressed in ccRCC tissues compared to normal samples, correlating with poor prognosis. Functional studies demonstrated that SLC16A8 knockdown impaired tumor progression in vitro. Consistent with these findings, in vivo experiments demonstrated reduced tumor growth upon SLC16A8 knockdown. Mechanistically, decreased SLC16A8 attenuated PI3K/AKT signaling, suggesting a potential regulatory pathway in ccRCC progression. In summary, we established a six-gene SLC signature with significant prognostic value in ccRCC. Among these genes, SLC16A8 emerged as a promising biomarker and therapeutic target, warranting further investigation.
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Affiliation(s)
- Hantao Wen
- Institute of Precision Medicine, Peking University Shenzhen Hospital, PKU-Shenzhen Clinical Institute of Shantou University Medical College, Shenzhen, China, 518036
| | - Fang Dai
- Department of Urology, PKU-Shenzhen Clinical Institute of Anhui Medical University, Shenzhen, China, 518036
| | - Huming Wang
- Department of Urology, PKU-Shenzhen Clinical Institute of Anhui Medical University, Shenzhen, China, 518036
| | - Yu Lin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, PKU-Shenzhen Clinical Institute of Shantou University Medical College, Shenzhen, China, 518036
| | - Zihan Xu
- Institute of Precision Medicine, Peking University Shenzhen Hospital, PKU-Shenzhen Clinical Institute of Shantou University Medical College, Shenzhen, China, 518036
| | - Zhaojie Lyu
- Institute of Precision Medicine, Peking University Shenzhen Hospital, PKU-Shenzhen Clinical Institute of Shantou University Medical College, Shenzhen, China, 518036; Department of Urology, PKU-Shenzhen Clinical Institute of Anhui Medical University, Shenzhen, China, 518036.
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6
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Wiedmer T, Teoh ST, Christodoulaki E, Wolf G, Tian C, Sedlyarov V, Jarret A, Leippe P, Frommelt F, Ingles-Prieto A, Lindinger S, Barbosa BMG, Onstein S, Klimek C, Garcia J, Serrano I, Reil D, Santacruz D, Piotrowski M, Noell S, Bueschl C, Li H, Chi G, Mereiter S, Oliveira T, Penninger JM, Sauer DB, Steppan CM, Viollet C, Klavins K, Hannich JT, Goldmann U, Superti-Furga G. Metabolic mapping of the human solute carrier superfamily. Mol Syst Biol 2025:10.1038/s44320-025-00106-4. [PMID: 40355754 DOI: 10.1038/s44320-025-00106-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 05/15/2025] Open
Abstract
Solute carrier (SLC) transporters govern most of the chemical exchange across cellular membranes and are integral to metabolic regulation, which in turn is linked to cellular function and identity. Despite their key role, individual functions of the SLC superfamily members were not evaluated systematically. We determined the metabolic and transcriptional profiles upon SLC overexpression in knock-out or wild-type isogenic cell backgrounds for 378 SLCs and 441 SLCs, respectively. Targeted metabolomics provided a fingerprint of 189 intracellular metabolites, while transcriptomics offered insights into cellular programs modulated by SLC expression. Beyond the metabolic profiles of 102 SLCs directly related to their known substrates, we identified putative substrates or metabolic pathway connections for 71 SLCs without previously annotated bona fide substrates, including SLC45A4 as a new polyamine transporter. By comparing the molecular profiles, we identified functionally related SLC groups, including some with distinct impacts on osmolyte balancing and glycosylation. The assessment of functionally related human genes presented here may serve as a blueprint for other systematic studies and supports future investigations into the functional roles of SLCs.
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Affiliation(s)
- Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Shao Thing Teoh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Eirini Christodoulaki
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Chengzhe Tian
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Abigail Jarret
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Philipp Leippe
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Barbara M G Barbosa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Svenja Onstein
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Christoph Klimek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Julio Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Daniela Reil
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Diana Santacruz
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach, Germany
| | - Mary Piotrowski
- Pfizer Worldwide Research and Development, Groton, CT, 06340, USA
| | - Stephen Noell
- Pfizer Worldwide Research and Development, Groton, CT, 06340, USA
| | - Christoph Bueschl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Huanyu Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stefan Mereiter
- Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030, Vienna, Austria
| | - Tiago Oliveira
- Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030, Vienna, Austria
| | - Josef M Penninger
- Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030, Vienna, Austria
- Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, V6T 1Z3, Vancouver, Canada
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claire M Steppan
- Pfizer Worldwide Research and Development, Groton, CT, 06340, USA
| | - Coralie Viollet
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400, Biberach, Germany
| | - Kristaps Klavins
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria.
- Fondazione Ri.MED, Palermo, Italy.
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7
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Goldmann U, Wiedmer T, Garofoli A, Sedlyarov V, Bichler M, Haladik B, Wolf G, Christodoulaki E, Ingles-Prieto A, Ferrada E, Frommelt F, Teoh ST, Leippe P, Onea G, Pfeifer M, Kohlbrenner M, Chang L, Selzer P, Reinhardt J, Digles D, Ecker GF, Osthushenrich T, MacNamara A, Malarstig A, Hepworth D, Superti-Furga G. Data- and knowledge-derived functional landscape of human solute carriers. Mol Syst Biol 2025:10.1038/s44320-025-00108-2. [PMID: 40355757 DOI: 10.1038/s44320-025-00108-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 03/28/2025] [Accepted: 04/11/2025] [Indexed: 05/15/2025] Open
Abstract
The human solute carrier (SLC) superfamily of ~460 membrane transporters remains the largest understudied protein family despite its therapeutic potential. To advance SLC research, we developed a comprehensive knowledgebase that integrates systematic multi-omics data sets with selected curated information from public sources. We annotated SLC substrates through literature curation, compiled SLC disease associations using data mining techniques, and determined the subcellular localization of SLCs by combining annotations from public databases with an immunofluorescence imaging approach. This SLC-centric knowledge is made accessible to the scientific community via a web portal featuring interactive dashboards and visualization tools. Utilizing this systematically collected and curated resource, we computationally derived an integrated functional landscape for the entire human SLC superfamily. We identified clusters with distinct properties and established functional distances between transporters. Based on all available data sets and their integration, we assigned biochemical/biological functions to each SLC, making this study one of the largest systematic annotations of human gene function and a potential blueprint for future research endeavors.
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Affiliation(s)
- Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Garofoli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuel Bichler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ben Haladik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eirini Christodoulaki
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Evandro Ferrada
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Shao Thing Teoh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Leippe
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gabriel Onea
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Daniela Digles
- University of Vienna, Department of Pharmaceutical Sciences, Vienna, Austria
| | - Gerhard F Ecker
- University of Vienna, Department of Pharmaceutical Sciences, Vienna, Austria
| | | | | | | | | | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
- Fondazione Ri.MED, Palermo, Italy.
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8
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Frommelt F, Ladurner R, Goldmann U, Wolf G, Ingles-Prieto A, Lineiro-Retes E, Gelová Z, Hopp AK, Christodoulaki E, Teoh ST, Leippe P, Santini BL, Rebsamen M, Lindinger S, Serrano I, Onstein S, Klimek C, Barbosa B, Pantielieieva A, Dvorak V, Hannich TJ, Schoenbett J, Sansig G, Mocking TAM, Ooms JF, IJzerman AP, Heitman LH, Sykacek P, Reinhardt J, Müller AC, Wiedmer T, Superti-Furga G. The solute carrier superfamily interactome. Mol Syst Biol 2025:10.1038/s44320-025-00109-1. [PMID: 40355756 DOI: 10.1038/s44320-025-00109-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 03/28/2025] [Accepted: 04/11/2025] [Indexed: 05/15/2025] Open
Abstract
Solute carrier (SLC) transporters form a protein superfamily that enables transmembrane transport of diverse substrates including nutrients, ions and drugs. There are about 450 different SLCs, residing in a variety of subcellular membranes. Loss-of-function of an unusually high proportion of SLC transporters is genetically associated with a plethora of human diseases, making SLCs a rapidly emerging but challenging drug target class. Knowledge of their protein environment may elucidate the molecular basis for their functional integration with metabolic and cellular pathways and help conceive pharmacological interventions based on modulating proteostatic regulation. We aimed at obtaining a global survey of the SLC-protein interaction landscape and mapped the protein-protein interactions of 396 SLCs by interaction proteomics. We employed a functional assessment based on RNA interference of interactors in combination with measurement of protein stability and localization. As an example, we detail the role of a SLC16A6 phospho-degron and the contributions of PDZ-domain proteins LIN7C and MPP1 to the trafficking of SLC43A2. Overall, our work offers a resource for SLC-protein interactions for the scientific community.
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Affiliation(s)
- Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Rene Ladurner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Eva Lineiro-Retes
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Zuzana Gelová
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Ann-Katrin Hopp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Eirini Christodoulaki
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Shao Thing Teoh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Philipp Leippe
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Brianda L Santini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Svenja Onstein
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Christoph Klimek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Barbara Barbosa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Anastasiia Pantielieieva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Thomas J Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Julian Schoenbett
- Novartis Pharma AG, Novartis Biomedical Research NBR/DSc, CH-4002, Basel, Switzerland
| | - Gilles Sansig
- Novartis Pharma AG, Novartis Biomedical Research NBR/DSc, CH-4002, Basel, Switzerland
| | - Tamara A M Mocking
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jasper F Ooms
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Peter Sykacek
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Juergen Reinhardt
- Novartis Pharma AG, Novartis Biomedical Research NBR/DSc, CH-4002, Basel, Switzerland
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria.
- Fondazione Ri.MED, Palermo, Italy.
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9
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Saner N, Uzun C, Akarlar BA, Özkan SN, Geiszler DJ, Öztürk E, Tunçbağ N, Özlü N. Proximity labeling and SILAC based proteomic approach identifies proteins at the interface of homotypic and heterotypic cancer cell interactions. Mol Cell Proteomics 2025:100986. [PMID: 40334745 DOI: 10.1016/j.mcpro.2025.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 04/13/2025] [Accepted: 05/03/2025] [Indexed: 05/09/2025] Open
Abstract
Cell-cell interactions are critical for the growth of organisms and maintaining homeostasis. In the tumor microenvironment, these interactions promote cancer progression. Given their importance in healthy and diseased conditions, we have developed a method to analyze the cell-to-cell interactome. Our approach uses enzyme-catalyzed proximity labeling and SILAC-based proteomics to identify the proteins involved in cancer cell interactions. By targeting HRP to the outer leaflet of the plasma membrane in bait cells, we were able to label the neighboring prey cells and distinguish between the proteomes of bait and prey cells using SILAC labeling in a co-culture system. We mapped both the homotypic and heterotypic interactomes of epithelial and mesenchymal breast cancer cells. The enrichment of cell surface and extracellular proteins confirms the specificity of our methodology. We further verified selected hits from different cell-cell interactomes in co-cultures using microscopy. This method revealed prominent signaling pathways orchestrating homotypic and heterotypic interactions of epithelial and mesenchymal cells. It also highlights the importance of exosomes in these interactions. Our methodology can be applied to any type of cell-cell interaction in 2D co-culture or 3D tumor models.
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Affiliation(s)
- Nazan Saner
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Türkiye.
| | - Ceren Uzun
- Department of Chemical and Biological Engineering, Koç University, İstanbul, Türkiye
| | - Büşra Aytül Akarlar
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Türkiye
| | - Sena Nur Özkan
- Koç University, Research Center for Translational Medicine (KUTTAM), Koç University, İstanbul, Türkiye
| | - Daniel Jon Geiszler
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Türkiye
| | - Ece Öztürk
- Koç University, Research Center for Translational Medicine (KUTTAM), Koç University, İstanbul, Türkiye; Department of Medical Biology, School of Medicine, Koç University, İstanbul, Türkiye
| | - Nurcan Tunçbağ
- Department of Chemical and Biological Engineering, Koç University, İstanbul, Türkiye
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Türkiye; Koç University, Research Center for Translational Medicine (KUTTAM), Koç University, İstanbul, Türkiye.
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10
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Malik M, Le VT, Ou YY. NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential. J Proteome Res 2025; 24:2324-2335. [PMID: 40193588 PMCID: PMC12053934 DOI: 10.1021/acs.jproteome.4c00884] [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: 10/15/2024] [Revised: 01/01/2025] [Accepted: 03/19/2025] [Indexed: 04/09/2025]
Abstract
Sodium transporters maintain cellular homeostasis by transporting ions, minerals, and nutrients across the membrane, and Na+/K+ ATPases facilitate the cotransport of solutes in neurons, muscle cells, and epithelial cells. Sodium transporters are important for many physiological processes, and their dysfunction leads to diseases such as hypertension, diabetes, neurological disorders, and cancer. The NA_mCNN computational method highlights the functional diversity and significance of sodium transporters in membrane proteins using protein language model embeddings (PLMs) and multiple-window scanning deep learning models. This work investigates PLMs that include Tape, ProtTrans, ESM-1b-1280, and ESM-2-128 to achieve more accuracy in sodium transporter classification. Five-fold cross-validation and independent testing demonstrate ProtTrans embedding robustness. In cross-validation, ProtTrans achieved an AUC of 0.9939, a sensitivity of 0.9829, and a specificity of 0.9889, demonstrating its ability to distinguish positive and negative samples. In independent testing, ProtTrans maintained a sensitivity of 0.9765, a specificity of 0.9991, and an AUC of 0.9975, which indicates its high level of discrimination. This study advances the understanding of sodium transporter diversity and function, as well as their role in human pathophysiology. Our goal is to use deep learning techniques and protein language models for identifying sodium transporters to accelerate identification and develop new therapeutic interventions.
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Affiliation(s)
- Muhammad
Shahid Malik
- Department
of Computer Science and Engineering, Yuan
Ze University, Chung-Li 32003, Taiwan
- Department
of Computer Sciences, Karakoram International
University, Gilgit-Baltistan 15100, Pakistan
| | - Van The Le
- Department
of Computer Science and Engineering, Yuan
Ze University, Chung-Li 32003, Taiwan
| | - Yu-Yen Ou
- Department
of Computer Science and Engineering, Yuan
Ze University, Chung-Li 32003, Taiwan
- Graduate
Program in Biomedical Informatics, Yuan
Ze University, Chung-Li 32003, Taiwan
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11
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Yan H, He Q, Gao Y, He X, Luo H, Shao L, Dong J, Li F. SLC4A7 suppresses lung adenocarcinoma oncogenesis by reducing lactate transport and protein lactylation. Int J Oncol 2025; 66:33. [PMID: 40084702 PMCID: PMC12002671 DOI: 10.3892/ijo.2025.5739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 10/21/2024] [Indexed: 03/16/2025] Open
Abstract
Lactate and protein lactylation serve a key role in tumor pathogenesis. Solute carrier 4A7 (SLC4A7), a key transporter, participates in cellular acid homeostasis. However, its impact on lactate transport and protein lactylation in solid tumors, particularly lung adenocarcinoma (LUAD), remains largely unexplored. In the present study, lactylome analysis, Transwell and wound healing assay, animal experiments were conducted to validate functional regulation mediated by SLC4A7 in LUAD. SLC4A7 inhibited tumor progression, including metastasis, invasion and proliferation. Mechanistically, SLC4A7 decreased both intracellular and extracellular lactate accumulation and inhibited overall protein lactylation, as confirmed by lactylome analysis. Analyzing the lactylome revealed that SLC4A7 suppressed lysine lactylation of numerous genes like HSP90AA1 and pathways such as focal adhesion associated with carcinogenesis. Additionally, low expression levels of SLC4A7 in LUAD cancer stem cells were validated using tumor tissue samples from patients with LUAD. Moreover, the inhibitory role of SLC4A7 in regulating tumor stemness was verified. Collectively, the present results uncovered the inhibitory effect exerted by SLC4A7 on tumor progression via its regulation of lactate transport, protein lactylation and stemness properties. Targeting SLC4A7 may hold promise as a novel therapeutic strategy for LUAD.
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Affiliation(s)
- Haojie Yan
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, P.R. China
- Post-doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, Guangdong 518020, P.R. China
| | - Qian He
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, P.R. China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, Guangdong 518020, P.R. China
- School of Food and Drug, Shenzhen Polytechnic University, Shenzhen, Guangdong 518055, P.R. China
| | - Yubiao Gao
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, P.R. China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, Guangdong 518020, P.R. China
| | - Xiaomei He
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, P.R. China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, Guangdong 518020, P.R. China
| | - Haitao Luo
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, P.R. China
- Post-doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, Guangdong 518020, P.R. China
| | - Lijuan Shao
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, P.R. China
- Post-doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, Guangdong 518020, P.R. China
| | - Jun Dong
- Post-doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Furong Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 518020, P.R. China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, Shenzhen, Guangdong 518020, P.R. China
- Institute of Health Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P.R. China
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12
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Wu Y, Li Z, Xi P, Wang Y, Guo H, Yin H, Zhu L. The ammonia-Slc4a11 axis in T cells alleviates LPS-induced mastitis. Front Immunol 2025; 16:1537483. [PMID: 40370468 PMCID: PMC12075193 DOI: 10.3389/fimmu.2025.1537483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2024] [Accepted: 04/10/2025] [Indexed: 05/16/2025] Open
Abstract
Background Mastitis is an inflammatory condition of the mammary gland, commonly observed in lactating and non-puerperal women, posing significant health and economic challenges. Lipopolysaccharide (LPS), a component of the outer membrane of Gram-negative bacteria, is a major inducer of mastitis. Ammonia, a key molecule in nitrogen metabolism, has been implicated in inflammatory pathways, yet its specific role in mastitis remains unclear. This study aims to investigate the mechanism by which ammonia influences the development of mastitis, particularly its effects on T cell activity and inflammatory factor expression. Methods qRT-PCR and ELISA were performed to measure the levels of IL-6, TNF, and IL-1β in the breast tissue of mice with LPS-induced mastitis, with or without ammonia treatment. HE staining was used to evaluate the degree of inflammation in the mammary tissue. FACS analysis was employed to assess the percentage, viability, and proliferation of immune cells in the breast tissue. CRISPR-Cas9 technology was used to knockout the SLC4A11 gene in T cells. Results Ammonia treatment significantly alleviated LPS-induced mastitis by reducing inflammation and inflammatory factor levels. It also decreased the percentage of CD4+ and CD8+ T cells, inhibited T cell viability and proliferation, and reduced pro-inflammatory cytokine expression (TNF and IFN-γ). Knockdown of the ammonia transporter Slc4a11 in T cells exacerbated mastitis, suggesting that Slc4a11 regulates T cell activity and inflammation during the progression of mastitis. Conclusion In summary, these findings highlight the critical role of ammonia and its transporter Slc4a11 in LPS-induced mastitis, providing potential therapeutic targets for future interventions.
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Affiliation(s)
- Yuqing Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Zhi Li
- Department of Breast and Thyroid Surgery, Huai’an First People’s Hospital, Nanjing Medical University, Huai’an, China
| | - Peiwen Xi
- Health Management Center, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Yaman Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Haowei Guo
- Department of Breast Surgery, Women’s Hospital of Nanjing Medical University (Nanjing Women and Children’s Healthcare Hospital), Nanjing, China
| | - Hong Yin
- Department of Breast Surgery, Women’s Hospital of Nanjing Medical University (Nanjing Women and Children’s Healthcare Hospital), Nanjing, China
| | - Lei Zhu
- Department of Breast Surgery, Women’s Hospital of Nanjing Medical University (Nanjing Women and Children’s Healthcare Hospital), Nanjing, China
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13
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Mori MP, Lozoya OA, Brooks AM, Bortner CD, Nadalutti CA, Ryback B, Rickard BP, Overchuk M, Rizvi I, Rogasevskaia T, Huang KT, Hasan P, Hajnóczky G, Santos JH. Mitochondrial membrane hyperpolarization modulates nuclear DNA methylation and gene expression through phospholipid remodeling. Nat Commun 2025; 16:4029. [PMID: 40301431 PMCID: PMC12041266 DOI: 10.1038/s41467-025-59427-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 04/23/2025] [Indexed: 05/01/2025] Open
Abstract
Maintenance of the mitochondrial inner membrane potential (ΔΨm) is critical for many aspects of mitochondrial function. While ΔΨm loss and its consequences are well studied, little is known about the effects of mitochondrial hyperpolarization. In this study, we used cells deleted of ATP5IF1 (IF1), a natural inhibitor of the hydrolytic activity of the ATP synthase, as a genetic model of increased resting ΔΨm. We found that the nuclear DNA hypermethylates when the ΔΨm is chronically high, regulating the transcription of mitochondrial, carbohydrate and lipid genes. These effects can be reversed by decreasing the ΔΨm and recapitulated in wild-type (WT) cells exposed to environmental chemicals that cause hyperpolarization. Surprisingly, phospholipid changes, but not redox or metabolic alterations, linked the ΔΨm to the epigenome. Sorted hyperpolarized WT and ovarian cancer cells naturally depleted of IF1 also showed phospholipid remodeling, indicating this as an adaptation to mitochondrial hyperpolarization. These data provide a new framework for how mitochondria can impact epigenetics and cellular biology to influence health outcomes, including through chemical exposures and in disease states.
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Affiliation(s)
- Mateus Prates Mori
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Durham, NC, USA
| | - Oswaldo A Lozoya
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Durham, NC, USA
| | - Ashley M Brooks
- Biostatistics and Computational Biology Branch, Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Durham, NC, USA
| | - Carl D Bortner
- Flow Cytometry Center, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Durham, NC, USA
| | - Cristina A Nadalutti
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Durham, NC, USA
| | - Birgitta Ryback
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Brittany P Rickard
- Curriculum in Toxicology & Environmental Medicine, University of North Carolina (UNC), Chapel Hill, NC, USA
| | - Marta Overchuk
- Department of Biomedical Engineering, North Carolina State University, Raleigh, NC, USA
| | - Imran Rizvi
- Department of Biomedical Engineering, North Carolina State University, Raleigh, NC, USA
- Lineberger Comprehensive Cancer Center, UNC, Chapel Hill, NC, USA
| | | | - Kai Ting Huang
- MitoCare Center, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Prottoy Hasan
- MitoCare Center, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - György Hajnóczky
- MitoCare Center, Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Janine H Santos
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Durham, NC, USA.
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14
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Schmidt M, Binder H, Schneider MR. The metabolic underpinnings of sebaceous lipogenesis. Commun Biol 2025; 8:670. [PMID: 40289206 PMCID: PMC12034822 DOI: 10.1038/s42003-025-08105-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Accepted: 04/17/2025] [Indexed: 04/30/2025] Open
Abstract
Sebaceous glands synthesize and secrete sebum, a mélange of lipids and other cellular products that safeguards the mammalian integument. Differentiating sebocytes delaminate from the basal membrane and dislodge towards the gland's middle, where they eventually undergo a poorly understood death mode in which the whole cell becomes a secretion product (holocrine secretion). Supported by recent transcriptomics data, this review examines the idea that peripheral sebocytes have a remarkable ability to draw nutrients from the blood and become committed to unrestrainedly invest all available resources into synthetic processes for accomplishing sebum synthesis, thereby exploiting core metabolic fluxes as glycogen turnover, glutamine-directed anaplerosis, the pentose phosphate pathway and de novo lipogenesis. Finally, we propose that metabolic-driven processes are an important mechanistic component of holocrine secretion. A deeper understanding of these metabolic adaptations could indicate novel strategies for modulating sebum synthesis, a key pathogenic factor in acne and other skin diseases.
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Affiliation(s)
- Maria Schmidt
- Interdisciplinary Institute for Bioinformatics (IZBI), University of Leipzig, Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Institute for Bioinformatics (IZBI), University of Leipzig, Leipzig, Germany
- Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Marlon R Schneider
- Institute of Veterinary Physiology, Veterinary Faculty, University of Leipzig, Leipzig, Germany.
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15
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De la Cruz-Cano E, González-Díaz JÁ, Olivares-Corichi IM, Ayala-Sumuano JT, Díaz-Gandarilla JA, Torres-Sauret Q, Larios-Serrato V, Vilchis-Reyes MÁ, López-Victorio CJ, González-Garrido JA, García-Sánchez JR. Identifying Genes Associated with the Anticancer Activity of a Fluorinated Chalcone in Triple-Negative Breast Cancer Cells Using Bioinformatics Tools. Int J Mol Sci 2025; 26:3662. [PMID: 40332279 PMCID: PMC12027753 DOI: 10.3390/ijms26083662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 04/04/2025] [Accepted: 04/08/2025] [Indexed: 05/08/2025] Open
Abstract
Fluorinated chalcones are molecules reported to possess potent anticancer properties against triple-negative breast cancer (TNBC) cells. However, their molecular mechanisms have not yet been fully explored. Using bioinformatics tools, we analyzed the transcriptomes of MDA-MB-231 cells treated with either a novel fluorinated chalcone (compound 3) or a control in order to identify differentially expressed (DE) genes associated with its anticancer activity and determine the biological processes in which these genes are involved. A fluorinated chalcone was synthesized using the Claisen-Schmidt method. The transcriptome of MDA-MB-231 cells was then analyzed on an Illumina NextSeq500, and DE genes with significant changes in expression were identified using the DESeq2 v1.38.0 bioinformatics tool under the strict detection criteria of |log2FC| ≥ 2 and adjusted p < 0.05. We identified 504 DE genes, which were enriched in terms related to "regulation of cell death", "cation transport", "response to topologically incorrect proteins", and "response to unfolded proteins". Surprisingly, these genes were involved in "the HSF1-dependent transactivation pathway" and "the attenuation phase pathway". This bioinformatics-based study suggests that the tested fluorinated chalcone could influence HSF-1 silencing in addition to promoting the up-regulation of several genes involved in stress-induced apoptosis. Therefore, the tested compound could have enormous potential as a novel approach for TNBC treatment.
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Affiliation(s)
- Eduardo De la Cruz-Cano
- Laboratorio de Bioquímica y Biología Molecular, División Académica de Ciencias Básicas, Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco (CICTAT), Universidad Juárez Autónoma de Tabasco, Cunduacán C.P. 86690, Mexico; (E.D.l.C.-C.); (J.Á.G.-D.); (Q.T.-S.); (M.Á.V.-R.); (J.A.G.-G.)
| | - José Ángel González-Díaz
- Laboratorio de Bioquímica y Biología Molecular, División Académica de Ciencias Básicas, Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco (CICTAT), Universidad Juárez Autónoma de Tabasco, Cunduacán C.P. 86690, Mexico; (E.D.l.C.-C.); (J.Á.G.-D.); (Q.T.-S.); (M.Á.V.-R.); (J.A.G.-G.)
| | - Ivonne María Olivares-Corichi
- Laboratorio de Oncología Molecular y Estrés Oxidativo, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México C.P. 11340, Mexico;
| | | | - José Alfredo Díaz-Gandarilla
- Laboratorio de Análisis Clínicos, División Académica Multidisciplinaria de Comalcalco, Universidad Juárez Autónoma de Tabasco, Comalcalco C.P. 86650, Mexico;
| | - Quirino Torres-Sauret
- Laboratorio de Bioquímica y Biología Molecular, División Académica de Ciencias Básicas, Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco (CICTAT), Universidad Juárez Autónoma de Tabasco, Cunduacán C.P. 86690, Mexico; (E.D.l.C.-C.); (J.Á.G.-D.); (Q.T.-S.); (M.Á.V.-R.); (J.A.G.-G.)
| | - Violeta Larios-Serrato
- Laboratorio de Biotecnología Genómica y Bioinformática, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México C.P. 11340, Mexico;
| | - Miguel Ángel Vilchis-Reyes
- Laboratorio de Bioquímica y Biología Molecular, División Académica de Ciencias Básicas, Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco (CICTAT), Universidad Juárez Autónoma de Tabasco, Cunduacán C.P. 86690, Mexico; (E.D.l.C.-C.); (J.Á.G.-D.); (Q.T.-S.); (M.Á.V.-R.); (J.A.G.-G.)
| | - Carlos Javier López-Victorio
- Laboratorio de Bioquímica y Biología Molecular, División Académica de Ciencias Básicas, Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco (CICTAT), Universidad Juárez Autónoma de Tabasco, Cunduacán C.P. 86690, Mexico; (E.D.l.C.-C.); (J.Á.G.-D.); (Q.T.-S.); (M.Á.V.-R.); (J.A.G.-G.)
| | - José Arnold González-Garrido
- Laboratorio de Bioquímica y Biología Molecular, División Académica de Ciencias Básicas, Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco (CICTAT), Universidad Juárez Autónoma de Tabasco, Cunduacán C.P. 86690, Mexico; (E.D.l.C.-C.); (J.Á.G.-D.); (Q.T.-S.); (M.Á.V.-R.); (J.A.G.-G.)
| | - José Rubén García-Sánchez
- Laboratorio de Oncología Molecular y Estrés Oxidativo, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México C.P. 11340, Mexico;
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16
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Zehetner L, Széliová D, Kraus B, Hernandez Bort JA, Zanghellini J. Multi-omics driven genome-scale metabolic modeling improves viral vector yield in HEK293. Metab Eng 2025; 91:103-118. [PMID: 40220853 DOI: 10.1016/j.ymben.2025.03.011] [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: 10/10/2024] [Revised: 02/06/2025] [Accepted: 03/19/2025] [Indexed: 04/14/2025]
Abstract
HEK293 cells are a versatile cell line extensively used in the production of recombinant proteins and viral vectors, notably Adeno-associated virus (AAV) (Bulcha et al., 2021). Despite their high transfection efficiency and adaptability to various culture conditions, challenges remain in achieving sufficient yields of active viral particles. This study presents a comprehensive multi-omics analysis of two HEK293 strains under good manufacturing practice conditions, focusing on the metabolic and cellular responses during AAV production. The investigation included lipidomic, exometabolomic, and transcriptomic profiling across different conditions and time points. Genome-scale metabolic models (GSMMs) were reconstructed for these strains to elucidate metabolic shifts and identify potential bottlenecks in AAV production. Notably, the study revealed significant differences between a High-producing (HP) and a Low-producing (LP) HEK293 strains, highlighting pseudohypoxia in the LP strain. Key findings include the identification of hypoxia-inducible factor 1-alpha (HIF-1α) as a critical regulator in the LP strain, linking pseudohypoxia to poor AAV productivity. Inhibition of HIF-1α resulted in immediate cessation of cell growth and a 2.5-fold increase in viral capsid production, albeit with a decreased number of viral genomes, impacting the full-to-empty particle ratio. This trade-off is significant because it highlights a key challenge in AAV production: achieving a balance between capsid assembly and genome packaging to optimize the yield of functional viral vectors. Overall this suggests that while HIF-1α inhibition enhances capsid assembly, it simultaneously hampers nucleotide synthesis via the pentose phosphate pathway (PPP), necessary for nucleotide synthesis, and therefore for AAV genome replication.
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Affiliation(s)
- L Zehetner
- Department for Analytical Chemistry, University of Vienna, Vienna, 1090, Austria; Doctoral School of Chemistry, University of Vienna, Vienna, 1090, Austria.
| | - D Széliová
- Department for Analytical Chemistry, University of Vienna, Vienna, 1090, Austria.
| | - B Kraus
- Institute of Molecular Biotechnology, Institut für Molekulare Biotechnologie GmbH, Vienna, 1030, Austria
| | - J A Hernandez Bort
- Department of Applied Life Sciences, Bioengineering, University of Applied Sciences Campus Vienna, Vienna, 1100, Austria.
| | - J Zanghellini
- Department for Analytical Chemistry, University of Vienna, Vienna, 1090, Austria.
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17
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Liebing A, Rabe P, Krumbholz P, Zieschang C, Bischof F, Schulz A, Billig S, Birkemeyer C, Pillaiyar T, Garcia‐Marcos M, Kraft R, Stäubert C. Succinate receptor 1 signaling mutually depends on subcellular localization and cellular metabolism. FEBS J 2025; 292:2017-2050. [PMID: 39838520 PMCID: PMC12001207 DOI: 10.1111/febs.17407] [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: 08/21/2024] [Revised: 11/08/2024] [Accepted: 01/09/2025] [Indexed: 01/23/2025]
Abstract
Succinate is a pivotal tricarboxylic acid cycle metabolite but also specifically activates the Gi- and Gq-coupled succinate receptor 1 (SUCNR1). Contradictory roles of succinate and succinate-SUCNR1 signaling include reports about its anti- or pro-inflammatory effects. The link between cellular metabolism and localization-dependent SUCNR1 signaling qualifies as a potential cause for the reported conflicts. To systematically address this connection, we used a diverse set of methods, including several bioluminescence resonance energy transfer-based biosensors, dynamic mass redistribution measurements, second messenger and kinase phosphorylation assays, calcium imaging, and metabolic analyses. Different cellular metabolic states were mimicked using glucose (Glc) or glutamine (Gln) as available energy substrates to provoke differential endogenous succinate (SUC) production. We show that SUCNR1 signaling, localization, and metabolism are mutually dependent, with SUCNR1 showing distinct spatial and energy substrate-dependent Gi and Gq protein activation. We found that Gln-consumption associated with a higher rate of oxidative phosphorylation causes increased extracellular SUC concentrations, accompanied by a higher rate of SUCNR1 internalization, reduced miniGq protein recruitment to the plasma membrane, and lower Ca2+ signals. In Glc, under basal conditions, SUCNR1 causes stronger Gq than Gi protein activation, while the opposite is true upon stimulation with an agonist. In addition, SUCNR1 specifically interacts with miniG proteins in endosomal compartments. In THP-1 cells, polarized to M2-like macrophages, endogenous SUCNR1-mediated Gi signaling stimulates glycolysis, while Gq signaling inhibits the glycolytic rate. Our results suggest that the metabolic context determines spatially dependent SUCNR1 signaling, which in turn modulates cellular energy homeostasis and mediates adaptations to changes in SUC concentrations.
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Affiliation(s)
| | - Philipp Rabe
- Rudolf Schönheimer Institute of Biochemistry, Medical FacultyLeipzig UniversityGermany
| | - Petra Krumbholz
- Rudolf Schönheimer Institute of Biochemistry, Medical FacultyLeipzig UniversityGermany
| | - Christian Zieschang
- Rudolf Schönheimer Institute of Biochemistry, Medical FacultyLeipzig UniversityGermany
| | - Franziska Bischof
- Rudolf Schönheimer Institute of Biochemistry, Medical FacultyLeipzig UniversityGermany
| | - Angela Schulz
- Rudolf Schönheimer Institute of Biochemistry, Medical FacultyLeipzig UniversityGermany
| | - Susan Billig
- Research Group of Mass Spectrometry, Institute of Analytical ChemistryLeipzig UniversityGermany
| | - Claudia Birkemeyer
- Research Group of Mass Spectrometry, Institute of Analytical ChemistryLeipzig UniversityGermany
- German Center for Integrative Biodiversity Research (iDiv) Halle‐Leipzig‐JenaGermany
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug DiscoveryEberhard Karls University TübingenGermany
| | - Mikel Garcia‐Marcos
- Department of Biochemistry & Cell Biology, Chobanian & Avedisian School of MedicineBoston UniversityMAUSA
- Department of BiologyBoston University College of Arts & SciencesMAUSA
| | - Robert Kraft
- Carl Ludwig Institute for Physiology, Medical FacultyLeipzig UniversityGermany
| | - Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Medical FacultyLeipzig UniversityGermany
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18
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Zhou C, Yang MJ, Shi P, Li ZQ, Li YR, Guo YJ, Zhang T, Song H. Ascorbic acid transporter MmSLC23A2 functions to inhibit apoptosis via ROS scavenging in hard clam (Mercenaria mercenaria) under acute hypo-salinity stress. Int J Biol Macromol 2025; 302:139483. [PMID: 39756741 DOI: 10.1016/j.ijbiomac.2025.139483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Revised: 12/19/2024] [Accepted: 01/02/2025] [Indexed: 01/07/2025]
Abstract
Solute carrier family 23 (SLC23) mediates cellular uptake of ascorbic acid, a crucial antioxidant protecting organisms against oxidative stress. Despite advances in understanding SLC23 in mammals, its physiological roles in bivalves remain poorly understood. Notably, euryhaline bivalves exhibit a significant expansion and positive selection of SLC23, highlighting the need for deeper investigation. Here, we identified 25 MmSLC23 in the hard clam genome. These genes predominantly cluster on chromosomes 3 and 14, with tandem duplications driving their expansion. All MmSLC23 localize to the plasma membrane, containing 9-14 transmembrane domains. Syntenic conservation of SLC23 was limited across order Venerida, with most expanded members being lineage-specific paralogs. Transcriptome analysis and fluorescence in situ hybridization revealed that MmSLC23 exhibited divergent expression patterns under acute and chronic salinity stress. Notably, RNA interference of MmSLC23A2 led to a significant reduction in intracellular ascorbic acid levels. Under acute hypo-salinity stress, increased ROS levels and elevated apoptosis rate were observed in MmSLC23A2 knockdown clams, as assessed by flow cytometry and transmission electron microscopy. These findings underscore the crucial role of SLC23 in mitigating oxidative damage and preventing premature apoptosis under acute salinity stress, offering new insights into the molecular mechanisms underlying the remarkable salinity adaptability of euryhaline bivalves.
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Affiliation(s)
- Cong Zhou
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Mei-Jie Yang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Pu Shi
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo-Qing Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Ren Li
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, China
| | - Yong-Jun Guo
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, China
| | - Tao Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Hao Song
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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19
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Fonseca PADS, Suarez-Vega A, Esteban-Blanco C, Marina H, Pelayo R, Gutiérrez-Gil B, Arranz JJ. Integration of epigenomic and genomic data to predict residual feed intake and the feed conversion ratio in dairy sheep via machine learning algorithms. BMC Genomics 2025; 26:313. [PMID: 40165084 PMCID: PMC11956460 DOI: 10.1186/s12864-025-11520-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 03/24/2025] [Indexed: 04/02/2025] Open
Abstract
BACKGROUND Feed efficiency (FE) is an essential trait in livestock species because of the constant demand to increase the productivity and sustainability of livestock production systems. A better understanding of the biological mechanisms associated with FEs might help improve the estimation and selection of superior animals. In this work, differentially methylated regions (DMRs) were identified via genome-wide bisulfite sequencing (GWBS) by comparing the DNA methylation profiles of milk somatic cells from dairy ewes that were divergent in terms of residual feed intake. The DMRs were identified by comparing divergent groups for residual feed intake (RFI), the feed conversion ratio (FCR), and the consensus between both metrics (Cons). Additionally, the predictive performance of these DMRs and genetic variants mapped within these regions was evaluated via three machine learning (ML) models (xgboost, random forest (RF), and multilayer feedforward artificial neural network (deeplearning)). The average performance of each model was based on the root mean squared error (RMSE) and squared Spearman correlation (rho2). Finally, the best model for each scenario was selected on the basis of the highest ratio between rho2 and RMSE. RESULTS In total, 12,257, 9,328, and 6,723 genes were annotated for DMRs detected in the RFI, FCR, and Cons groups, respectively. These genes are associated with important pathways for regulating FE in dairy sheep, such as protein digestion and absorption, hormone synthesis and secretion, control of energy availability, cellular signaling, and feed behavior pathways. With respect to the ML predictions, the smallest mean RMSE (0.17) was obtained using RF, which was used to predict RFI. The highest mean rho2 (0.20) was obtained when the RFI was predicted via the mean methylation within the DMRs identified, the consensus groups were compared, and the genetic variants mapped within these DMRs were included. The best overall models were obtained for the prediction of RFI using the DMRs obtained in the comparison of RFI groups (RMSE = 0.10, rho2 = 0.86) using xgboost and the DMRs plus the genetic variants identified via the Cons groups (RMSE = 0.07, rho2 = 0.62) using RF. CONCLUSIONS The results provide new insights into the biological mechanisms associated with FE and the control of these processes through epigenetic mechanisms. Additionally, the potential use of epigenetic information as a biomarker for the prediction of FE can be suggested based on the obtained results.
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Affiliation(s)
| | - Aroa Suarez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, Leon, 24007, Spain
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, Leon, 24007, Spain
| | - Héctor Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, Leon, 24007, Spain
| | - Rocío Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, Leon, 24007, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, Leon, 24007, Spain
| | - Juan-José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, Leon, 24007, Spain.
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20
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Zhang C, Yang X, Xue Y, Li H, Zeng C, Chen M. The Role of Solute Carrier Family Transporters in Hepatic Steatosis and Hepatic Fibrosis. J Clin Transl Hepatol 2025; 13:233-252. [PMID: 40078199 PMCID: PMC11894391 DOI: 10.14218/jcth.2024.00348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 12/19/2024] [Accepted: 12/31/2024] [Indexed: 03/14/2025] Open
Abstract
Solute carrier (SLC) family transporters are crucial transmembrane proteins responsible for transporting various molecules, including amino acids, electrolytes, fatty acids, and nucleotides. To date, more than fifty SLC transporter subfamilies have been identified, many of which are linked to the progression of hepatic steatosis and fibrosis. These conditions are often caused by factors such as non-alcoholic fatty liver disease and non-alcoholic steatohepatitis, which are major contributors to the global liver disease burden. The activity of SLC members regulates the transport of substrates across biological membranes, playing key roles in lipid synthesis and metabolism, mitochondrial function, and ferroptosis. These processes, in turn, influence the function of hepatocytes, hepatic stellate cells, and macrophages, thereby contributing to the development of hepatic steatosis and fibrosis. Additionally, some SLC transporters are involved in drug transport, acting as critical regulators of drug-induced hepatic steatosis. Beyond substrate transport, certain SLC members also exhibit additional functions. Given the pivotal role of the SLC family in hepatic steatosis and fibrosis, this review aimed to summarize the molecular mechanisms through which SLC transporters influence these conditions.
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Affiliation(s)
| | | | - Yi Xue
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Huan Li
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Chuanfei Zeng
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Mingkai Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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21
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Srivastava P, Bhoumik S, Yadawa AK, Kesherwani R, Rizvi SI. Coenzyme Q 10 supplementation affects cellular ionic balance: relevance to aging. Z NATURFORSCH C 2025; 80:95-102. [PMID: 38963236 DOI: 10.1515/znc-2024-0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 06/20/2024] [Indexed: 07/05/2024]
Abstract
Aging results into disruptive physiological functioning and cellular processes that affect the composition and structure of the plasma membrane. The plasma membrane is the major regulator of ionic homeostasis that regulates the functioning of membrane transporters and exchangers. Coenzyme Q10 is a lipid-soluble antioxidant molecule that declines during aging and age-associated diseases. The present study aims to explore the role of Coenzyme Q10 supplementation to rats during aging on membrane transporters and redox biomarkers. The study was conducted on young and old male Wistar rats supplemented with 20 mg/kg b.w. of Coenzyme Q10 per day. After a period of 28 days, rats were sacrificed and erythrocyte membrane was isolated. The result exhibits significant decline in biomarkers of oxidative stress in old control rats when compared with young control. The effect of Coenzyme Q10 supplementation was more pronounced in old rats. The functioning of membrane transporters and Na+/H+ exchanger showed potential return to normal levels in the Coenzyme Q10 treated rats. Overall, the results demonstrate that Coenzyme Q10 plays an important role in maintaining redox balance in cells which interconnects with membrane integrity. Thus, Coenzyme Q10 supplementation may play an important role in protecting age related alterations in erythrocyte membrane physiology.
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Affiliation(s)
- Parisha Srivastava
- Department of Biochemistry, 314956 University of Allahabad , Allahabad, Uttar Pradesh 211002, India
| | - Sukanya Bhoumik
- Department of Biochemistry, 314956 University of Allahabad , Allahabad, Uttar Pradesh 211002, India
| | - Arun K Yadawa
- Department of Biochemistry, 314956 University of Allahabad , Allahabad, Uttar Pradesh 211002, India
| | - Rashmi Kesherwani
- Department of Biochemistry, 314956 University of Allahabad , Allahabad, Uttar Pradesh 211002, India
| | - Syed Ibrahim Rizvi
- Department of Biochemistry, 314956 University of Allahabad , Allahabad, Uttar Pradesh 211002, India
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22
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Van Goor A, Pasternak A, Walker KE, Chick S, Harding JCS, Lunney JK. Altered structural and transporter-related gene expression patterns in the placenta play a role in fetal demise during Porcine reproductive and respiratory syndrome virus infection. BMC Genomics 2025; 26:279. [PMID: 40119254 PMCID: PMC11927291 DOI: 10.1186/s12864-025-11397-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 02/21/2025] [Indexed: 03/24/2025] Open
Abstract
BACKGROUND Porcine reproductive and respiratory syndrome virus (PRRSV) can be transmitted across the maternal-fetal-interface from an infected gilt to her fetuses. Although fetal infection status and disease outcomes vary, the mechanisms are not completely understood. The objective was to assess targeted placental structural and transporter-related gene expression patterns. At day 85 of gestation pregnant pigs were challenged with PRRSV, and at 12 days post maternal infection sows and fetuses were sacrificed, and the placental tissue was collected. Grouping of fetuses was by preservation status and PRRS viral load (VL): control (CTRL, n = 14), viable and low VL fetus (VIA_LVF, n = 15), viable and high VL fetus (VIA_HVF, n = 21), meconium mild and low VL fetus (MECm_LVF, n = 14), meconium mild and high VL fetus (MECm_HVF, n = 14), and meconium severe and high VL fetus (MECs_HVF, n = 13). NanoString was used to evaluate the expression of 86 genes: actin cytoskeleton signaling, arachidonic acid pathway, integrin signaling, intercellular junctions, transporters, and VEGF signaling. Statistical analyses were performed using Limma with P ≤ 0.05 considered significant. RESULTS We identified 1, 7, 0, 29, and 39 differentially expressed genes in VIA_LVF, VIA_HVF, MECm_LVF, MECm_HVF, and MECs_HVF, respectively, contrasted to CTRL. Placental transporter genes were significantly impacted (i.e., downregulation of SLC1A3, SLC1A5, SLC2A1, SLC2A3, SLC2A5, SLC2A10, SLC2A12, SLC7A4, SLC16A5, SLC16A10, and SLC27A6; and upregulation of SLC2A2, SLC16A3, and SLC27A4), compared to CTRL. Actin cytoskeleton signaling (ARHGEF6 and ARHGEF7), arachidonic acid (PTGES3 and PTGIS), integrin signaling (FN1 and ITGB6), intercellular junctions (CDH3 and CDH11), and VEGF signaling (MAPK3 and HPSE) gene groupings were significantly impacted, compared to CTRL. CONCLUSION Data reported here indicate that fetal PRRSV infection levels rather than fetal demise is necessary for transcriptional dysregulation of the fetal placenta, with a tendency towards more downregulation in the target gene sets among susceptible fetuses. These results generally support that in susceptible fetuses there is altered solute transportation, placental structural integrity, and reduced angiogenesis. The data described here is associated with fetal PRRS resistance/resilience and susceptibility.
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Affiliation(s)
- Angelica Van Goor
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD, USA
- Division of Animal Systems, Institute of Food Production and Sustainability, NIFA, USDA, Kansas City, MO, USA
| | - Alex Pasternak
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Kristen E Walker
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD, USA
| | - Shannon Chick
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD, USA
| | - John C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD, USA.
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23
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Zebene ED, Pucci B, Lombardi R, Medhin HT, Seife E, Di Gennaro E, Budillon A, Woldemichael GB. Serum-Based Proteomic Approach to Identify Clinical Biomarkers of Radiation Exposure. Cancers (Basel) 2025; 17:1010. [PMID: 40149344 PMCID: PMC11940482 DOI: 10.3390/cancers17061010] [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: 12/30/2024] [Revised: 02/25/2025] [Accepted: 03/13/2025] [Indexed: 03/29/2025] Open
Abstract
BACKGROUND Ionizing radiation (IR) exposure poses a significant health risk due to its widespread use in medical diagnostics and therapeutic applications, necessitating rapid and effective biomarkers for assessment. OBJECTIVE The aim of this study is to identify the serum proteomic signature of IR exposure in patients undergoing radiotherapy (RT). METHODS Blood samples were obtained from eighteen patients with head and neck cancer (HNC) and five patients with rectal cancer before and immediately after they underwent curative intensity-modulated radiotherapy (IMRT). The comprehensive serum proteome was analyzed in individual samples using nanoHPLC-MS/MS. RESULTS Forty radiation-modulated proteins (RMPs), 24 upregulated and 16 downregulated, with a fold change ≥1.5 and p-value < 0.05 were identified. About 40% of the RMPs are involved in acute phase response, DNA repair, and inflammation; the key RMPs were ADCY1, HGF, MCEMP1, CHD4, RECQL5, MSH6, and ZNF224. Conclusions: This study identifies a panel of serum proteins that may reflect the radiation response, providing a valuable molecular fingerprint of IR exposure and paving the way for the development of sensitive and specific biomarkers for early detection and clinical management of IR-related injuries.
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Affiliation(s)
- Emeshaw Damtew Zebene
- Nuclear Medicine Unit, Department of Internal Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia; (E.D.Z.); (H.T.M.)
- Department of Microbial Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia;
| | - Biagio Pucci
- Experimental Pharmacology Unit, Laboratory of Naples and Mercogliano (AV), Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy; (B.P.); (E.D.G.)
| | - Rita Lombardi
- Experimental Animal Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Hagos Tesfay Medhin
- Nuclear Medicine Unit, Department of Internal Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia; (E.D.Z.); (H.T.M.)
| | - Edom Seife
- Radiotherapy Center, College of Health Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia;
| | - Elena Di Gennaro
- Experimental Pharmacology Unit, Laboratory of Naples and Mercogliano (AV), Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy; (B.P.); (E.D.G.)
| | - Alfredo Budillon
- Scientific Directorate, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy;
| | - Gurja Belay Woldemichael
- Department of Microbial Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia;
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24
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Qi C, Cao B, Gong Z, Zhang W, Yang P, Qin H, Zhao Y, Chen Y. SLC35C2 promotes stemness and progression in hepatocellular carcinoma by activating lipogenesis. Cell Signal 2025; 127:111589. [PMID: 39765278 DOI: 10.1016/j.cellsig.2025.111589] [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: 10/18/2024] [Revised: 12/23/2024] [Accepted: 01/03/2025] [Indexed: 01/13/2025]
Abstract
Metabolic reprogramming plays a critical role in tumorigenesis and progression, including hepatocellular carcinoma (HCC). The Solute Carriers (SLCs) family is responsible for the transport of a range of nutrients and has been linked to various cancers. Cancer stem cells (CSC) are a contributing factor to the recurrence and metastasis of HCC. However, the regulatory genes that govern this process remain unclear. The present study identified SLC35C2 as a crucial factor in maintaining the stem-cell characteristics of HCC cells through CRISPR-dCas9 screening. Further investigation demonstrated that SLC35C2 was significantly elevated in HCC tissues and correlated with a poor prognosis in HCC patients. It is an independent prognostic factor for HCC patients. The knockdown and overexpression of SLC35C2 inhibited or promoted stemness in HCC cell. Both in vitro and in vivo studies demonstrated that SLC35C2 promoted the proliferation, migration, invasion and metastasis in HCC cells. Through RNA-seq and lipidomics analysis, it was found that SLC35C2 regulated lipid reprogramming, particularly triglyceride synthesis. Mechanistically, SLC35C2 stimulated lipogenesis through the up-regulation of SREBP1, ACC, FAS, and SCD-1, thereby increasing lipid accumulation in HCC cells. SLC35C2 interacted with ACSL4, which plays a critical role in lipogenesis, and to protect it from degradation. Inhibition of ACSL4 with PRGL493 can reverse the lipogenesis, stemness and proliferation induced by SLC35C2 overexpression. In conclusion, our study demonstrates the pivotal role of SLC35C2 in stemness and malignant progression in HCC by promoting lipogenesis. These findings suggest that SLC35C2 is a prognostic marker and promising therapeutic target for HCC treatment.
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Affiliation(s)
- Chunhui Qi
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China; Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, Guangdong Province, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Bin Cao
- Department of Cardiology, The 7th People's Hospital of Zhengzhou, Zhengzhou, Henan Province 450016, China
| | - Zhiwen Gong
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Weiyu Zhang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Pengfei Yang
- Department of Pathology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Haorui Qin
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Yan Zhao
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China.
| | - Yingchun Chen
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China.
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25
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Nandigrami P, Goldman ID, Fiser A. Mechanistic insights into mutation in the proton-coupled folate transporter (SLC46A1) causing hereditary folate malabsorption. J Biol Chem 2025; 301:108280. [PMID: 39924111 PMCID: PMC11929075 DOI: 10.1016/j.jbc.2025.108280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 01/17/2025] [Accepted: 01/31/2025] [Indexed: 02/11/2025] Open
Abstract
Hereditary folate malabsorption (HFM) is a rare, autosomal recessive disorder characterized by impaired intestinal absorption and impaired transport of folates across the choroid plexus into cerebral spinal fluid due to inactivating mutations in the human proton-coupled folate transporter (hPCFT) gene, which encodes the proton-coupled folate transporter (PCFT) SLC46A1. Understanding the structural impact of these mutations is crucial for elucidating the mechanistic basis for PCFT function and the pathophysiology of HFM. Recently, the cryo-electron microscopic structural characterization of the Gallus gallus PCFT was obtained, which shares significant sequence identity with hPCFT. We conducted molecular dynamics simulations of hPCFT based on this structure, to explore structural changes induced by functionally defective disease-causing and other mutant proteins and mutations that restore function. Simulations revealed that the mutually mechanistic basis for the loss of function is partial loss of structural integrity of hPCFT primarily manifested in an enlarged and distorted pore accompanied by loss of long-range contacts, less stable, fluctuating inner helices with reduced solvent accessibility, and a marked loss of ordered secondary structures. These changes are reversed by the introduction of compensatory mutations. These findings provide novel insights into the structural and functional consequences of PCFT mutations associated with HFM and provide correlations with kinetic and biochemical properties of the mutant proteins.
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Affiliation(s)
- Prithviraj Nandigrami
- Departments of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - I David Goldman
- Departments of Medicine, Oncology and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andras Fiser
- Departments of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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26
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Jin S, Wu J, Wang C, He Y, Tang Y, Huang L, Zhou H, Liu D, Wu Z, Feng Y, Chen H, He X, Yang G, Peng C, Qiu J, Li T, Yin Y, He L. Aspartate Metabolism-Driven Gut Microbiota Dynamics and RIP-Dependent Mitochondrial Function Counteract Oxidative Stress. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2404697. [PMID: 39874197 PMCID: PMC11923965 DOI: 10.1002/advs.202404697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 12/18/2024] [Indexed: 01/30/2025]
Abstract
Aspartate (Asp) metabolism-mediated antioxidant functions have important implications for neonatal growth and intestinal health; however, the antioxidant mechanisms through which Asp regulates the gut microbiota and influences RIP activation remain elusive. This study reports that chronic oxidative stress disrupts gut microbiota and metabolite balance and that such imbalance is intricately tied to the perturbation of Asp metabolism. Under normal conditions, in vivo and in vitro studies reveal that exogenous Asp improves intestinal health by regulating epithelial cell proliferation, nutrient uptake, and apoptosis. During oxidative stress, Asp reduces Megasphaera abundance while increasing Ruminococcaceae. This reversal effect depends on the enhanced production of the antioxidant eicosapentaenoic acid mediated through Asp metabolism and microbiota. Mechanistically, the application of exogenous Asp orchestrates the antioxidant responses in enterocytes via the modulation of the RIP3-MLKL and RIP1-Nrf2-NF-κB pathways to eliminate excessive reactive oxygen species and maintain mitochondrial functionality and cellular survival. These results demonstrate that Asp signaling alleviates oxidative stress by dynamically modulating the gut microbiota and RIP-dependent mitochondrial function, providing a potential therapeutic strategy for oxidative stress disease treatment.
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Affiliation(s)
- Shunshun Jin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan international joint laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangsha410081China
- Department of Animal ScienceUniversity of ManitobaWinnipegManitobaR3T2N2Canada
| | - Jian Wu
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Chenyu Wang
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan international joint laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangsha410081China
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Yiwen He
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan international joint laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangsha410081China
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Yulong Tang
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Le Huang
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Hui Zhou
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan international joint laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangsha410081China
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Di Liu
- Heilongjiang Academy of Agricultural SciencesHarbin150086China
| | - Ziping Wu
- Agricultural and Food EconomicsQueen's University BelfastNorthern IrelandBT95PXUK
| | - Yanzhong Feng
- Heilongjiang Academy of Agricultural SciencesHarbin150086China
| | - Heshu Chen
- Heilongjiang Academy of Agricultural SciencesHarbin150086China
| | - Xinmiao He
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan international joint laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangsha410081China
- Heilongjiang Academy of Agricultural SciencesHarbin150086China
| | - Guan Yang
- Department of Infectious Diseases and Public HealthCity University of Hong KongKowloonHong Kong SAR999077China
| | - Can Peng
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infections DiseaseKey Laboratory for Zoonosis Research of the Ministry of EducationCollege of Veterinary MedicineJilin UniversityChangchun130025China
| | - Tiejun Li
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
| | - Yulong Yin
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
- Yuelushan LaboratoryNo. 246 Hongqi Road, Furong DistrictChangsha410128China
| | - Liuqin He
- Hunan Provincial Key Laboratory of Animal Intestinal Function and RegulationHunan international joint laboratory of Animal Intestinal Ecology and HealthLaboratory of Animal Nutrition and Human HealthCollege of Life SciencesHunan Normal UniversityChangsha410081China
- Key Laboratory of Agro‐ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesHunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic ProcessChangsha410125China
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27
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Fung TS, Ryu KW, Thompson CB. Arginine: at the crossroads of nitrogen metabolism. EMBO J 2025; 44:1275-1293. [PMID: 39920310 PMCID: PMC11876448 DOI: 10.1038/s44318-025-00379-3] [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: 09/24/2024] [Revised: 12/06/2024] [Accepted: 12/10/2024] [Indexed: 02/09/2025] Open
Abstract
L-arginine is the most nitrogen-rich amino acid, acting as a key precursor for the synthesis of nitrogen-containing metabolites and an essential intermediate in the clearance of excess nitrogen. Arginine's side chain possesses a guanidino group which has unique biochemical properties, and plays a primary role in nitrogen excretion (urea), cellular signaling (nitric oxide) and energy buffering (phosphocreatine). The post-translational modification of protein-incorporated arginine by guanidino-group methylation also contributes to epigenetic gene control. Most human cells do not synthesize sufficient arginine to meet demand and are dependent on exogenous arginine. Thus, dietary arginine plays an important role in maintaining health, particularly upon physiologic stress. How cells adapt to changes in extracellular arginine availability is unclear, mostly because nearly all tissue culture media are supplemented with supraphysiologic levels of arginine. Evidence is emerging that arginine-deficiency can influence disease progression. Here, we review new insights into the importance of arginine as a metabolite, emphasizing the central role of mitochondria in arginine synthesis/catabolism and the recent discovery that arginine can act as a signaling molecule regulating gene expression and organelle dynamics.
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Affiliation(s)
- Tak Shun Fung
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Keun Woo Ryu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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28
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Vieira AB, Cavanaugh SM, Ciambarella BT, Machado MV. Sodium-glucose co-transporter 2 inhibitors: a pleiotropic drug in humans with promising results in cats. Front Vet Sci 2025; 12:1480977. [PMID: 40093620 PMCID: PMC11906673 DOI: 10.3389/fvets.2025.1480977] [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: 08/14/2024] [Accepted: 02/10/2025] [Indexed: 03/19/2025] Open
Abstract
Diabetes mellitus is a common metabolic disease in humans and cats. Cats share several features of human type-2 diabetes and can be considered an animal model for this disease. In the last decade, sodium-glucose transporter 2 inhibitors (SGLT2i) have been used successfully as a class of hypoglycemic drug that inhibits the reabsorption of glucose from the renal proximal tubules, consequently managing hyperglycemia through glycosuria. Furthermore, SGLT2i have been shown to have cardiac, renal, and other protective effects in diabetic humans acting as a pleiotropic drug. Currently, at least six SGLT2i are approved by the Food and Drug Administration (FDA) for use in humans with type-2 diabetes, and recently, two drugs were approved for use in diabetic cats. This narrative review focuses on the use of SGLT2i to treat diabetes mellitus in humans and cats. We summarize the human data that support the use of SGLT2i in controlling type-2 diabetes and protecting against cardiovascular and renal damage. We also review the available literature regarding other benefits of these drugs in humans as well as the effects of SGLT2i in cats. Adverse effects related to the use of these hypoglycemic drugs are also discussed.
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Affiliation(s)
- Aline B. Vieira
- Biomedical Sciences Department, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Sarah M. Cavanaugh
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Bianca T. Ciambarella
- Laboratory of Ultrastructure and Tissue Biology, Anatomy Department, Biology Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcus V. Machado
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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29
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Wolf G, Craigon C, Teoh ST, Essletzbichler P, Onstein S, Cassidy D, Uijttewaal ECH, Dvorak V, Cao Y, Bensimon A, Elling U, Ciulli A, Superti-Furga G. The efflux pump ABCC1/MRP1 constitutively restricts PROTAC sensitivity in cancer cells. Cell Chem Biol 2025; 32:291-306.e6. [PMID: 39755121 DOI: 10.1016/j.chembiol.2024.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 09/24/2024] [Accepted: 11/27/2024] [Indexed: 01/06/2025]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce selective protein degradation by linking an E3 ubiquitin ligase enzyme to a target protein. This approach allows scope for targeting "undruggable" proteins, and several PROTACs have reached the stage of clinical candidates. However, the roles of cellular transmembrane transporters in PROTAC uptake and efflux remain underexplored. Here, we utilized transporter-focused genetic screens to identify the ATP-binding cassette transporter ABCC1/MRP1 as a key PROTAC resistance factor. Unlike the previously identified inducible PROTAC exporter ABCB1/MDR1, ABCC1 is highly expressed among cancers of various origins and constitutively restricts PROTAC bioavailability. Moreover, in a genome-wide PROTAC resistance screen, we identified candidates involved in processes such as ubiquitination, mTOR signaling, and apoptosis as genetic factors involved in PROTAC resistance. In summary, our findings reveal ABCC1 as a crucial constitutively active efflux pump limiting PROTAC efficacy in various cancer cells, offering insights for overcoming drug resistance.
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Affiliation(s)
- Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Conner Craigon
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Shao Thing Teoh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Patrick Essletzbichler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Svenja Onstein
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Diane Cassidy
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Esther C H Uijttewaal
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Yuting Cao
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Ariel Bensimon
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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30
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Zhou B, Sui R, Yu L, Qi D, Fu S, Luo Y, Qi H, Li X, Zhao K, Liu S, Tian F. Transcriptomics and proteomics provide insights into the adaptative strategies of Tibetan naked carps (Gymnocypris przewalskii) to saline-alkaline variations. BMC Genomics 2025; 26:162. [PMID: 39972273 PMCID: PMC11837439 DOI: 10.1186/s12864-025-11336-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 02/07/2025] [Indexed: 02/21/2025] Open
Abstract
Gymnocypris przewalskii is an exclusively cyprinid fish that inhabits Lake Qinghai, which is characterized by high salinity and alkalinity. To elucidate the molecular basis of the adaptation of G. przewalskii to a wide range of salinity‒alkalinity conditions, we performed morphological, biochemical, transcriptomic and proteomic analyses of the major osmoregulatory organs of the gills and kidney. Morphological examination revealed that mitochondria-rich cells were replaced by mucus cells in the gills during the transition of G. przewalskii from freshwater to lake water. In the kidney, the tight junction formed dense structure in the renal tubules under lake water condition compared with the loose structure in freshwater. The results of the biochemical assays revealed an increased content of total amino acids, indicating their potential roles as osmolytes and energy supplies in freshwater. The decreased urea concentration suggested that urea synthesis might not be involved in the detoxicity of ammonia. The transcriptomic and proteomic data revealed that genes involved in ion absorption and ammonia excretion were activated in freshwater and that genes involved in cell junction and glutamine synthesis were induced in lake water, which was consistent with the morphological and biochemical observations. Together with the higher levels of glutamine and glutamate, we proposed that G. przewalskii alleviated the toxic effect of ammonia direct excretion through gills under freshwater and the activation of the conversion of glutamate to glutamine under high saline-alkaline condition. Our results revealed different expression profiles of genes involved in metabolic pathways, including the upregulation of genes involved in energy production in freshwater and the induction of genes involved in the synthesis of acetylneuramic acid and sphingolipid in soda lake water. In conclusion, the appearance of mitochondria-rich cells and increased energy production might contribute to ion absorption in G. przewalskii to maintain ion and solute homeostasis in freshwater. The existence of mucus cells and dense junctions, which are associated with increased gene expression, might be related to the adaptation of G. przewalskii to high salinity-alkalinity.
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Affiliation(s)
- Bingzheng Zhou
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810006, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruichen Sui
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luxian Yu
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, The Rescue Center of Qinghai Lake Naked Carp, Xining, 810006, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810006, China
| | - Shengyun Fu
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, The Rescue Center of Qinghai Lake Naked Carp, Xining, 810006, China
| | - Ying Luo
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, The Rescue Center of Qinghai Lake Naked Carp, Xining, 810006, China
| | - Hongfang Qi
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, The Rescue Center of Qinghai Lake Naked Carp, Xining, 810006, China
| | - Xiaohuan Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810006, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, China
| | - Sijia Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, China.
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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31
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Fu Y, Chen J, Zhu X, Ding M, Wang H, Fu S. Roles and therapeutic potential of the SLC family in prostate cancer-literature review. BMC Urol 2025; 25:32. [PMID: 39966814 PMCID: PMC11837367 DOI: 10.1186/s12894-025-01714-w] [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: 10/01/2024] [Accepted: 02/10/2025] [Indexed: 02/20/2025] Open
Abstract
Prostate cancer (PCa) is one of the most common malignancies in men worldwide. Despite advances in treatment, many patients develop resistance to conventional therapies. Solute carrier (SLC) proteins, as transmembrane transporters, have recently emerged as potential therapeutic targets due to their role in tumor metabolism and progression. This review summarizes the key roles of six SLC proteins in PCa, including their involvement in metabolic reprogramming, regulation of signaling pathways, and effects on the tumor microenvironment. Although targeting of SLC family members in prostate cancer remains an underexplored area, the growing body of evidence suggests that it holds potential for future development.
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Affiliation(s)
- Yuanzhi Fu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, 650101, Yunnan, China
- Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Junhao Chen
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, 650101, Yunnan, China
| | - Xingcheng Zhu
- Department of Clinical Laboratory, The Second People's Hospital of Qujing City Qujing, Yunnan, China
| | - Mingxia Ding
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, 650101, Yunnan, China
| | - Haifeng Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, 650101, Yunnan, China.
| | - Shi Fu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Wuhua District, Kunming, 650101, Yunnan, China.
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32
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Alqarni SS, Khan NU. Integrating alternative therapies in overcoming chemotherapy resistance in tumors. Mol Biol Rep 2025; 52:239. [PMID: 39961936 DOI: 10.1007/s11033-025-10361-1] [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: 10/08/2024] [Accepted: 02/11/2025] [Indexed: 05/09/2025]
Abstract
Chemotherapy-resistant tumors present a significant challenge in oncology, often leading to treatment failures owing to mechanisms such as genetic mutations, drug efflux, altered metabolism, and adaptations within the tumor microenvironment. These factors limit the effectiveness of treatment and contribute to tumor resistance. This review highlights the role of alternative therapies aimed at overcoming resistance mechanisms. Several alternative strategies with high efficacy rate against tumor resistance are being explored, including targeted therapies (58-64%), immunotherapy (80%), hormone therapy (22-61%), and emerging approaches such as herbal therapies (90%), probiotics (34-90%), metabolic therapies (> 50%), epigenetic therapies (51-89%), microbiome-based therapies (50%), gene therapy (67-80%), photodynamic therapy/hypothermia (86-99%), and nanotechnology (50-67%). Integrating these alternative strategies with conventional treatments has the potent-al to augment the therapeutic efficacy and patient outcomes. Despite this progress, limitations in cancer therapeutics include the lack of predictive biomarkers, resistance mechanisms, and tumor heterogeneity, all of which contribute to treatment failure and relapse. To address these limitations, advancements in molecular diagnostics, as well as early detection through liquid biopsies, and the use of biomarkers to monitor resistance and guide treatment are crucial. Additionally, expanding clinical trials is essential to validate new therapies and improve patient outcomes.
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Affiliation(s)
- Sana S Alqarni
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, 11421, Riyadh, Saudi Arabia
| | - Najeeb Ullah Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, 25130, Pakistan.
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33
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Zhang Y, Newstead S, Sarkies P. Predicting substrates for orphan solute carrier proteins using multi-omics datasets. BMC Genomics 2025; 26:130. [PMID: 39930358 PMCID: PMC11812203 DOI: 10.1186/s12864-025-11330-5] [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: 07/09/2024] [Accepted: 02/05/2025] [Indexed: 02/13/2025] Open
Abstract
Solute carriers (SLC) are integral membrane proteins responsible for transporting a wide variety of metabolites, signaling molecules and drugs across cellular membranes. Despite key roles in metabolism, signaling and pharmacology, around one third of SLC proteins are 'orphans' whose substrates are unknown. Experimental determination of SLC substrates is technically challenging, given the wide range of possible physiological candidates. Here, we develop a predictive algorithm to identify correlations between SLC expression levels and intracellular metabolite concentrations by leveraging existing cancer multi-omics datasets. Our predictions recovered known SLC-substrate pairs with high sensitivity and specificity compared to simulated random pairs. CRISPR-Cas9 dependency screen data and metabolic pathway adjacency data further improved the performance of our algorithm. In parallel, we combined drug sensitivity data with SLC expression profiles to predict new SLC-drug interactions. Together, we provide a novel bioinformatic pipeline to predict new substrate predictions for SLCs, offering new opportunities to de-orphanise SLCs with important implications for understanding their roles in health and disease.
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Affiliation(s)
- Y Zhang
- Department of Biochemistry, University of Oxford, Oxford, OX13QU, UK
| | - S Newstead
- Department of Biochemistry, University of Oxford, Oxford, OX13QU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - P Sarkies
- Department of Biochemistry, University of Oxford, Oxford, OX13QU, UK.
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34
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Li D, Zheng P, Huang S. SLC12A9 is an immunological and prognostic biomarker for glioma. Gene 2025; 937:149136. [PMID: 39622394 DOI: 10.1016/j.gene.2024.149136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 11/20/2024] [Accepted: 11/27/2024] [Indexed: 12/07/2024]
Abstract
BACKGROUND Glioma is one of the most common malignant brain tumors. It has a high rate of progression and a poor prognosis, and effective biomarkers still need to be identified. The solute carrier family 12 (SLC12) family has been reported to be involved in various physiological and pathological processes, but their functional roles in glioma remain unclear. METHODS Using public datasets, we studied the mutation and expression level of SLC12 family genes in glioma and identified the significantly differentially expressed member solute carrier family 12 member 9 (SLC12A9). We further predicted the prognostic role of SLC12A9 in glioma by using the Kaplan-Meier method and Cox regression analysis. Then, we performed biological functional enrichment analysis. We focused on the relationships between SLC12A9 expression and immune infiltration in glioma. Meanwhile, we conducted in vitro experiments to evaluate the effect of SLC12A9 expression on glioma cells. RESULTS Among the members of the SLC12 family, SLC12A9 had the highest mutation rate in glioma, with gene amplification as the major mutation type, and its expression was significantly upregulated in glioma. Higher SLC12A9 expression was significantly associated with older age, higher grade, wild-type isocitrate dehydrogenase (IDH), and a worse prognosis. The functional enrichment analysis indicated that SLC12A9 is mainly related to ion channel annotation. Gene set enrichment analysis (GSEA) revealed that SLC12A9 was mainly related to the DNA replication pathway. Furthermore, we found that SLC12A9 correlated with tumor-infiltrating immune cells and immune checkpoints. Thus, SLC12A9 may be involved in regulating the immune response of glioma. Finally, our in vitro experiments revealed that silencing SLC12A9 dramatically inhibited glioma cell growth and migration. CONCLUSIONS We showed that SLC12A9 may be a new predictive biomarker for glioma diagnosis, prognosis, and immunotherapy response, offering helpful guidelines to advance glioma treatment.
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Affiliation(s)
- Danting Li
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China; School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Peilin Zheng
- Department of General Practice, People's Hospital of Longhua, Shenzhen 518109, Guangdong, China.
| | - Shoujun Huang
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
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35
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Rana AK, Bhatt B, Gusain C, Biswal SN, Das D, Kumar M. Neuroimmunometabolism: how metabolism orchestrates immune response in healthy and diseased brain. Am J Physiol Endocrinol Metab 2025; 328:E217-E229. [PMID: 39787332 DOI: 10.1152/ajpendo.00331.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 10/18/2024] [Accepted: 12/30/2024] [Indexed: 01/12/2025]
Abstract
Neuroimmunometabolism describes how neuroimmune cells, such as microglia, adapt their intracellular metabolic pathways to alter their immune functions in the central nervous system (CNS). Emerging evidence indicates that neurons also orchestrate the microglia-mediated immune response through neuro-immune cross talk, perhaps through metabolic signaling. However, little is known about how the brain's metabolic microenvironment and microglial intracellular metabolism orchestrate the neuroimmune response in healthy and diseased brains. This review addresses the balance of immunometabolic substrates in healthy and diseased brains, their metabolism by brain-resident microglia, and the potential impact of metabolic dysregulation of these substrates on the neuroimmune response and pathophysiology of psychiatric disorders. This review also suggests metabolic reprogramming of microglia as a preventive strategy for the management of neuroinflammation-related brain disorders, including psychiatric diseases.
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Affiliation(s)
- Anil Kumar Rana
- Food & Nutrition Biotechnology Division, National Agri-Food and Biomanufacturing Institute (BRIC-NABI), S.A.S Nagar, Punjab, India
| | - Babita Bhatt
- Food & Nutrition Biotechnology Division, National Agri-Food and Biomanufacturing Institute (BRIC-NABI), S.A.S Nagar, Punjab, India
| | - Chitralekha Gusain
- Food & Nutrition Biotechnology Division, National Agri-Food and Biomanufacturing Institute (BRIC-NABI), S.A.S Nagar, Punjab, India
| | - Surya Narayan Biswal
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Debashree Das
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States
| | - Mohit Kumar
- Food & Nutrition Biotechnology Division, National Agri-Food and Biomanufacturing Institute (BRIC-NABI), S.A.S Nagar, Punjab, India
- Regional Centre for Biotechnology (BRIC-RCB), Faridabad, Haryana, India
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Singh A, Shadangi S, Gupta PK, Rana S. Type 2 Diabetes Mellitus: A Comprehensive Review of Pathophysiology, Comorbidities, and Emerging Therapies. Compr Physiol 2025; 15:e70003. [PMID: 39980164 DOI: 10.1002/cph4.70003] [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: 12/19/2024] [Revised: 02/03/2025] [Accepted: 02/07/2025] [Indexed: 02/22/2025]
Abstract
Humans are perhaps evolutionarily engineered to get deeply addicted to sugar, as it not only provides energy but also helps in storing fats, which helps in survival during starvation. Additionally, sugars (glucose and fructose) stimulate the feel-good factor, as they trigger the secretion of serotonin and dopamine in the brain, associated with the reward sensation, uplifting the mood in general. However, when consumed in excess, it contributes to energy imbalance, weight gain, and obesity, leading to the onset of a complex metabolic disorder, generally referred to as diabetes. Type 2 diabetes mellitus (T2DM) is one of the most prevalent forms of diabetes, nearly affecting all age groups. T2DM is clinically diagnosed with a cardinal sign of chronic hyperglycemia (excessive sugar in the blood). Chronic hyperglycemia, coupled with dysfunctions of pancreatic β-cells, insulin resistance, and immune inflammation, further exacerbate the pathology of T2DM. Uncontrolled T2DM, a major public health concern, also contributes significantly toward the onset and progression of several micro- and macrovascular diseases, such as diabetic retinopathy, nephropathy, neuropathy, atherosclerosis, and cardiovascular diseases, including cancer. The current review discusses the epidemiology, causative factors, pathophysiology, and associated comorbidities, including the existing and emerging therapies related to T2DM. It also provides a future roadmap for alternative drug discovery for the management of T2DM.
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Affiliation(s)
- Aditi Singh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Sucharita Shadangi
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Pulkit Kr Gupta
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
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Ferdigg A, Hopp AK, Wolf G, Superti-Furga G. Membrane transporters modulating the toxicity of arsenic, cadmium, and mercury in human cells. Life Sci Alliance 2025; 8:e202402866. [PMID: 39578074 PMCID: PMC11584324 DOI: 10.26508/lsa.202402866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 11/07/2024] [Accepted: 11/08/2024] [Indexed: 11/24/2024] Open
Abstract
Non-essential metals are extremely toxic to living organisms, posing significant health risks, particularly in developing nations where they are a major contributor to illness and death. Although their toxicity is widely acknowledged, the mechanisms by which they are regulated within human cells remain incompletely understood. Specifically, the role of membrane transporters in mediating heavy metal toxicity is not well comprehended. Our study demonstrates how specific transporters can modulate the toxicity of cadmium, mercury, and the metalloid arsenic in human cells. Using CRISPR/Cas9 loss-of-function screens, we found that the multidrug resistance protein MRP1/ABCC1 provided protection against toxicity induced by arsenic and mercury. In addition, we found that SLC39A14 and SLC30A1 increased cellular sensitivity to cadmium. Using a reporter cell line to monitor cellular metal accumulation and performing a cDNA gain-of-function screen, we were able to clarify the function of SLC30A1 in controlling cadmium toxicity through the modulation of intracellular zinc levels. This transporter-wide approach provides new insights into the complex roles of membrane transporters in influencing the toxicity of arsenic, cadmium, and mercury in human cell lines.
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Affiliation(s)
- Andrè Ferdigg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ann-Katrin Hopp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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Chaudhari BY, Pradhan AG, Joshi RS. Metabolic gatekeepers: Dynamic roles of sugar transporters in insect metabolism and physiology. INSECT MOLECULAR BIOLOGY 2025; 34:1-18. [PMID: 39394882 DOI: 10.1111/imb.12963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/25/2024] [Indexed: 10/14/2024]
Abstract
Sugars play multiple critical roles in insects, serving as energy sources, carbon skeletons, osmolytes and signalling molecules. The transport of sugars from source to sink via membrane proteins is essential for the uptake, distribution and utilization of sugars across various tissues. Sugar supply and distribution are crucial for insect development, flight, diapause and reproduction. Insect sugar transporters (STs) share significant structural and functional similarities with those in mammals and other higher eukaryotes. However, they exhibit unique characteristics, including differential regulation, substrate selectivity and kinetics. Here, we have discussed structural diversity, evolutionary trends, expression dynamics, mechanisms of action and functional significance of insect STs. The sequence and structural diversity of insect STs, highlighted by the analysis of conserved domains and evolutionary patterns, underpins their functional differentiation and divergence. The review emphasizes the importance of STs in insect metabolism, physiology and stress tolerance. It also discusses how variations in transporter regulation, expression, selectivity and activity contribute to functional differences. Furthermore, we have underlined the potential and necessity of studying these mechanisms and roles to gain a deeper understanding of insect glycobiology. Understanding the regulation and function of sugar transporters is vital for comprehending insect metabolism and physiological potential. This review provides valuable insights into the diverse functionalities of insect STs and their significant roles in metabolism and physiology.
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Affiliation(s)
- Bhagyashri Y Chaudhari
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya G Pradhan
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
| | - Rakesh S Joshi
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Delpire E. Chloride-Dependent Cation Transport via SLC12 Carriers at Atomic Resolution. Annu Rev Physiol 2025; 87:397-419. [PMID: 39928503 DOI: 10.1146/annurev-physiol-022624-020130] [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] [Indexed: 02/12/2025]
Abstract
The SLC12 family of genes encodes electroneutral Cl--dependent cation transporters (i.e., Na-Cl, K-Cl, Na-K-2Cl cotransporters), which play significant roles in maintaining cell and body homeostasis. Recent resolution of their structures at the atomic level provides a new understanding how these transporters operate in health and disease and how they are targeted for therapeutic intervention. Overall, the SLC12 transporter cryo-EM structures confirm some key features established by traditional biochemical and molecular methods, such as the presence of 12 transmembrane domains and the formation of a functional dimer. Study of these structures also uncovers previously unknown features, such as the presence of strategic salt bridges that explain why transporters are stabilized in specific conformations. The cryo-EM structures show similarities with other transport protein structures, especially regarding the position of the cations. The structures also pose challenging questions regarding the number of ions bound and the strict electroneutrality that is conventional understanding.
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Affiliation(s)
- Eric Delpire
- Department of Anesthesiology and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA;
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40
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Zeinolabedini A, Zarredar H, Zafari V, Soleimani Z, Sabbagh-Jadid H, Raeisi M. SLC16A13 Downregulation Contributes to Apoptosis Induction in A549 Lung Cancer Cell Line. Asian Pac J Cancer Prev 2025; 26:525-532. [PMID: 40022697 PMCID: PMC12118009 DOI: 10.31557/apjcp.2025.26.2.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Accepted: 02/13/2025] [Indexed: 03/03/2025] Open
Abstract
BACKGROUND Lung cancer, a lethal type of malignancy in the world, has different pathological subcategories, among which NSCLC is the most common form. The complex pathogenesis of this disease has caused its treatment in advanced stages to be accompanied by many problems. Recently, the genes involved in metabolism, especially those coding for membrane transporter proteins (the solute carrier) have received attention in cancer studies. The Solute Carrier Family 16 Member 1 (SLC16A) is membrane transporters the role of which in the promotion of cancer has been revealed in recent years. This study aimed to examine the effect of SLC16A13 low expression in A549 lung cancer cells, focusing on its role in key cellular processes such as viability, proliferation, and apoptosis. By targeting SLC16A13, a critical member of the solute carrier family implicated in cancer metabolism, the study search for to uncover molecular mechanisms that could inform novel therapeutic strategies for non-small cell lung cancer. METHODS At first, the A549 lung cancer cell line was cultured in a standard medium, and then specific synthetic SLC16A13 sh-RNA was transfected into the A549 cell line to suppress the expression of this membrane transporter. We used MTT and flow cytometry tests to investigate the effect of reducing the expression of SLC16A13 on the process of cell viability and apoptosis. Also, the change of gene expression was analyzed by Real-Time PCR. RESULTS In the present study, the reduction of SLC16A13 gene expression caused an increase in the apoptosis rate and reduced cell viability in lung cancer cells. Also, SLC16A13 suppression may induce apoptosis pathway by upregulating Bax, Caspase-3, and Caspase-9 expression while downregulation Bcl-2 expression. Besides, it was shown that SLC16A13 downregulation couldn't affect E-cadherin expression. CONCLUSION SLC16A13 may a promising target to increase cell death in lung cancer cells by inducing apoptosis pathways.
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Affiliation(s)
- Aysan Zeinolabedini
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Habib Zarredar
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Venus Zafari
- Department of basic oncology of health institute of Ege University, Izmir, Turkey.
| | - Zahra Soleimani
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hamed Sabbagh-Jadid
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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41
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Trinh LT, Finnel RR, Osipovich AB, Musselman JR, Sampson LL, Wright CVE, Magnuson MA. Positive autoregulation of Sox17 is necessary for gallbladder and extrahepatic bile duct formation. Development 2025; 152:dev203033. [PMID: 39745200 PMCID: PMC11829758 DOI: 10.1242/dev.203033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 12/17/2024] [Indexed: 01/18/2025]
Abstract
Expression of SRY-box transcription factor 17 (Sox17) in the endodermal region caudal to the hepatic diverticulum during late gastrulation is necessary for hepato-pancreato-biliary system formation. Analysis of an allelic series of promoter-proximal mutations near the transcription start site (TSS) 2 of Sox17 in mouse has revealed that gallbladder (GB) and extrahepatic bile duct (EHBD) development is exquisitely sensitive to Sox17 expression levels. Deletion of a SOX17-binding cis-regulatory element in the TSS2 promoter impairs GB and EHBD development by reducing outgrowth of the nascent biliary bud. These findings reveal the existence of a SOX17-dependent autoregulatory loop that drives Sox17 expression above a critical threshold concentration necessary for GB and EHBD development to occur, and that minor impairments in Sox17 gene expression are sufficient to impair the expression of SOX17-regulated genes in the nascent GB and EHBD system, impairing or preventing development.
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Affiliation(s)
- Linh T. Trinh
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Ryan R. Finnel
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Anna B. Osipovich
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Leesa L. Sampson
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher V. E. Wright
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark A. Magnuson
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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Du J, Shen M, Chen J, Yan H, Xu Z, Yang X, Yang B, Luo P, Ding K, Hu Y, He Q. The impact of solute carrier proteins on disrupting substance regulation in metabolic disorders: insights and clinical applications. Front Pharmacol 2025; 15:1510080. [PMID: 39850557 PMCID: PMC11754210 DOI: 10.3389/fphar.2024.1510080] [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: 10/12/2024] [Accepted: 12/20/2024] [Indexed: 01/25/2025] Open
Abstract
Carbohydrates, lipids, bile acids, various inorganic salt ions and organic acids are the main nutrients or indispensable components of the human body. Dysregulation in the processes of absorption, transport, metabolism, and excretion of these metabolites can lead to the onset of severe metabolic disorders, such as type 2 diabetes, non-alcoholic fatty liver disease, gout and hyperbilirubinemia. As the second largest membrane receptor supergroup, several major families in the solute carrier (SLC) supergroup have been found to play key roles in the transport of substances such as carbohydrates, lipids, urate, bile acids, monocarboxylates and zinc ions. Based on common metabolic dysregulation and related metabolic substances, we explored the relationship between several major families of SLC supergroup and metabolic diseases, providing examples of drugs targeting SLC proteins that have been approved or are currently in clinical/preclinical research as well as SLC-related diagnostic techniques that are in clinical use or under investigation. By highlighting these connections, we aim to provide insights that may contribute to the development of improved treatment strategies and targeted therapies for metabolic disorders.
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Affiliation(s)
- Jiangxia Du
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Minhui Shen
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiajia Chen
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Yan
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhifei Xu
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaochun Yang
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bo Yang
- Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Peihua Luo
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Pharmaceutical and Translational Toxicology, Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang, China
| | - Kefeng Ding
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuhuai Hu
- Yuhong Pharmaceutical Technology Co., Ltd., Hangzhou, Zhejiang, China
| | - Qiaojun He
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Department of Pharmaceutical and Translational Toxicology, Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang, China
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Yan R, Chen T. SLC35A2 is a novel prognostic biomarker and promotes cell proliferation and metastasis via Wnt/β-catenin/EMT signaling pathway in breast cancer. Sci Rep 2025; 15:130. [PMID: 39748019 PMCID: PMC11695858 DOI: 10.1038/s41598-024-84584-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 12/24/2024] [Indexed: 01/04/2025] Open
Abstract
Although it is a leading cause of cancer-related mortality among women globally, breast cancer (BC) has drawn increased attention owing to its poor prognosis and the challenges associated with limited treatment options. SLC35A2 was shown to be dysregulated in a number of tumor types according to multiple investigations. However, its function in BC was rarely reported. This study aims to investigate the expression of SLC35A2 in BC and its impact on the functionality and prognosis of BC cells. We collected 11 pairs of BC tissues and normal specimens, obtaining clinical information from 1,118 BC patients through RNA sequencing analysis. Different BC cell lines were used in experiments, and the roles of SLC35A2 in cell proliferation, invasion, and migration was assessed through gene silencing and functional assays. Additionally, a prognostic model, including SLC35A2 expression levels, age, T-stage, M-stage, N-stage, and clinical stage, was constructed, and its predictive performance in overall survival was validated using time-dependent receiver operating characteristic curves. High SLC35A2 expression was correlated positively with patient age and T-stage. Kaplan-Meier survival curves and Cox regression analysis confirmed the independent and significant prognostic value of SLC35A2 in overall survival. Functional experiments demonstrated that SLC35A2 silencing inhibited the proliferation, migration, and invasion of BC cells, affecting their metastatic potential through modulation of the Wnt/β-catenin/EMT signaling pathway. In conclusion, our study reveals the crucial role of SLC35A2 in BC, providing a novel biomarker for clinical management and valuable insights into the underlying mechanisms of BC pathogenesis.
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Affiliation(s)
- Rushu Yan
- Department of Surgery, Medical School Shenzhen University, Shenzhen, China
| | - Tianwen Chen
- Department of Breast Surgery, Huazhong University of Science and Technology Union Medical College Shenzhen Hospital, No. 89 Taoyuan Road, Shenzhen, China.
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Kavakli E, Gul N, Begentas OC, Kiris E. Astrocytes in Primary Familial Brain Calcification (PFBC): Emphasis on the Importance of Induced Pluripotent Stem Cell-Derived Human Astrocyte Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2025; 1479:19-38. [PMID: 39841380 DOI: 10.1007/5584_2024_840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2025]
Abstract
Primary familial brain calcification (PFBC) is a rare, progressive central nervous system (CNS) disorder without a cure, and the current treatment methodologies primarily aim to relieve neurological and psychiatric symptoms of the patients. The disease is characterized by abnormal bilateral calcifications in the brain, however, our mechanistic understanding of the biology of the disease is still limited. Determining the roles of the specific cell types and molecular mechanisms involved in the pathophysiological processes of the disease is of great importance for the development of novel and effective treatment methodologies. There is a growing interest in the involvement of astrocytes in PFBC, as recent studies have suggested that astrocytes play a central role in the disease and that functional defects in these cells are critical for the development and progression of the disease. This review aims to discuss recent findings on the roles of astrocytes in PFBC pathophysiology, with a focus on known expression and roles of PFBC genes in astrocytes. Additionally, we discuss the importance of human astrocytes for PFBC disease modeling, and astrocytes as a potential therapeutic target in PFBC. Utilization of species-specific and physiologically relevant PFBC model systems can open new avenues for basic research, drug development, and regenerative medicine.
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Affiliation(s)
- Ebru Kavakli
- Department of Biological Sciences, Middle East Technical University, Ankara, Türkiye
| | - Nazli Gul
- Department of Biological Sciences, Middle East Technical University, Ankara, Türkiye
| | - Onur Can Begentas
- Department of Biological Sciences, Middle East Technical University, Ankara, Türkiye
| | - Erkan Kiris
- Department of Biological Sciences, Middle East Technical University, Ankara, Türkiye.
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Joly A, Schott A, Phadke I, Gonzalez-Menendez P, Kinet S, Taylor N. Beyond ATP: Metabolite Networks as Regulators of Physiological and Pathological Erythroid Differentiation. Physiology (Bethesda) 2025; 40:0. [PMID: 39226028 DOI: 10.1152/physiol.00035.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/28/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024] Open
Abstract
Hematopoietic stem cells (HSCs) possess the capacity for self-renewal and the sustained production of all mature blood cell lineages. It has been well established that a metabolic rewiring controls the switch of HSCs from a self-renewal state to a more differentiated state, but it is only recently that we have appreciated the importance of metabolic pathways in regulating the commitment of progenitors to distinct hematopoietic lineages. In the context of erythroid differentiation, an extensive network of metabolites, including amino acids, sugars, nucleotides, fatty acids, vitamins, and iron, is required for red blood cell (RBC) maturation. In this review, we highlight the multifaceted roles via which metabolites regulate physiological erythropoiesis as well as the effects of metabolic perturbations on erythroid lineage commitment and differentiation. Of note, the erythroid differentiation process is associated with an exceptional breadth of solute carrier (SLC) metabolite transporter upregulation. Finally, we discuss how recent research, revealing the critical impact of metabolic reprogramming in diseases of disordered and ineffective erythropoiesis, has created opportunities for the development of novel metabolic-centered therapeutic strategies.
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Affiliation(s)
- Axel Joly
- Université de Montpellier, CNRS, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
| | - Arthur Schott
- Université de Montpellier, CNRS, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
| | - Ira Phadke
- Université de Montpellier, CNRS, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Pediatric Oncology Branch, CCR, NCI, National Institutes of Health, Bethesda, Maryland, United States
| | - Pedro Gonzalez-Menendez
- Departamento de Morfologia y Biologia Celular, Instituto Universitario de Oncologia del Principado de Asturias (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Sandrina Kinet
- Université de Montpellier, CNRS, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
| | - Naomi Taylor
- Université de Montpellier, CNRS, Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- Pediatric Oncology Branch, CCR, NCI, National Institutes of Health, Bethesda, Maryland, United States
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Calame DG, Wong JH, Panda P, Nguyen DT, Leong NCP, Sangermano R, Patankar SG, Abdel-Hamid MS, AlAbdi L, Safwat S, Flannery KP, Dardas Z, Fatih JM, Murali C, Kannan V, Lotze TE, Herman I, Ammouri F, Rezich B, Efthymiou S, Alavi S, Murphy D, Firoozfar Z, Nasab ME, Bahreini A, Ghasemi M, Haridy NA, Goldouzi HR, Eghbal F, Karimiani EG, Begtrup A, Elloumi H, Srinivasan VM, Gowda VK, Du H, Jhangiani SN, Coban-Akdemir Z, Marafi D, Rodan L, Isikay S, Rosenfeld JA, Ramanathan S, Staton M, Oberg KC, Clark RD, Wenman C, Loughlin S, Saad R, Ashraf T, Male A, Tadros S, Boostani R, Abdel-Salam GMH, Zaki M, Mardi A, Hashemi-Gorji F, Abdalla E, Manzini MC, Pehlivan D, Posey JE, Gibbs RA, Houlden H, Alkuraya FS, Bujakowska K, Maroofian R, Lupski JR, Nguyen LN. Biallelic variation in the choline and ethanolamine transporter FLVCR1 underlies a severe developmental disorder spectrum. Genet Med 2025; 27:101273. [PMID: 39306721 DOI: 10.1016/j.gim.2024.101273] [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: 03/21/2024] [Revised: 09/13/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024] Open
Abstract
PURPOSE FLVCR1 encodes a solute carrier protein implicated in heme, choline, and ethanolamine transport. Although Flvcr1-/- mice exhibit skeletal malformations and defective erythropoiesis reminiscent of Diamond-Blackfan anemia (DBA), biallelic FLVCR1 variants in humans have previously only been linked to childhood or adult-onset ataxia, sensory neuropathy, and retinitis pigmentosa. METHODS We identified individuals with undiagnosed neurodevelopmental disorders and biallelic FLVCR1 variants through international data sharing and characterized the functional consequences of their FLVCR1 variants. RESULTS We ascertained 30 patients from 23 unrelated families with biallelic FLVCR1 variants and characterized a novel FLVCR1-related phenotype: severe developmental disorders with profound developmental delay, microcephaly (z-score -2.5 to -10.5), brain malformations, epilepsy, spasticity, and premature death. Brain malformations ranged from mild brain volume reduction to hydranencephaly. Severely affected patients share traits, including macrocytic anemia and skeletal malformations, with Flvcr1-/- mice and DBA. FLVCR1 variants significantly reduce choline and ethanolamine transport and/or disrupt mRNA splicing. CONCLUSION These data demonstrate a broad FLVCR1-related phenotypic spectrum ranging from severe multiorgan developmental disorders resembling DBA to adult-onset neurodegeneration. Our study expands our understanding of Mendelian choline and ethanolamine disorders and illustrates the importance of anticipating a wide phenotypic spectrum for known disease genes and incorporating model organism data into genome analysis to maximize genetic testing yield.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.
| | - Jovi Huixin Wong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Puravi Panda
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dat Tuan Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nancy C P Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Riccardo Sangermano
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Sohil G Patankar
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Lama AlAbdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sylvia Safwat
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt; Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, New Brunswick, NJ
| | - Kyle P Flannery
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, New Brunswick, NJ
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Chaya Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Varun Kannan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Timothy E Lotze
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Boys Town National Research Hospital, Boys Town, NE
| | - Farah Ammouri
- Boys Town National Research Hospital, Boys Town, NE; The University of Kansas Health System, Westwood, KS
| | - Brianna Rezich
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Shahryar Alavi
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | | | - Mahya Ebrahimi Nasab
- Meybod Genetic Research Center, Yazd, Iran; Yazd Welfare Organization, Yazd, Iran
| | - Amir Bahreini
- KaryoGen, Isfahan, Iran; Department of Human Genetics, University of Pittsburgh, PA
| | - Majid Ghasemi
- Department of Neurology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nourelhoda A Haridy
- Department of Neurology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Hamid Reza Goldouzi
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Eghbal
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, London, United Kingdom
| | | | | | | | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Lance Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Sedat Isikay
- Gaziantep Islam Science and Technology University, Medical Faculty, Department of Pediatric Neurology, Gaziantep, Turkey
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics Laboratories, Houston, TX
| | - Subhadra Ramanathan
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA
| | - Michael Staton
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA
| | - Kerby C Oberg
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA
| | - Robin D Clark
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA
| | - Catharina Wenman
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Sam Loughlin
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Ramy Saad
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Tazeen Ashraf
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Alison Male
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Shereen Tadros
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom; Genetics and Genomic Medicine Department, University College London, United Kingdom
| | - Reza Boostani
- Department of Neurology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Maha Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ali Mardi
- Center for Comprehensive Genetic Services, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebtesam Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - M Chiara Manzini
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, New Brunswick, NJ
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Kinga Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - James R Lupski
- Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX.
| | - Long N Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore; Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Grosche A, Grosche J, Verkhratsky A. Physiology and pathophysiology of the retinal neuroglia. HANDBOOK OF CLINICAL NEUROLOGY 2025; 210:239-265. [PMID: 40148047 DOI: 10.1016/b978-0-443-19102-2.00017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2025]
Abstract
Neuroglia of the retina are represented by Müller glia, parenchymal astrocytes, microglia and oligodendrocytes mainly associated with the optic nerve. Müller glia are the most numerous glia, endowed with multiple homeostatic functions and indispensable for the retinal morphofunctional organization. Müller cells integrate retinal neurons into individual functional units (known as retinal columns) and act as a living light guide, transmitting photons to photoreceptors. In pathology, retinal neuroglia undergo complex changes, which include upregulation of neuroprotection, reactive gliosis, and functional asthenia. The balance between all these changes defines the progression and outcome of retinal disorders.
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Affiliation(s)
- Antje Grosche
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, München, Germany.
| | | | - Alexei Verkhratsky
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom; Department of Neurosciences, University of the Basque Country UPV/EHU and CIBERNED, Leioa, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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48
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Verkhratsky A, Semyanov A. Physiology of neuroglia of the central nervous system. HANDBOOK OF CLINICAL NEUROLOGY 2025; 209:69-91. [PMID: 40122632 DOI: 10.1016/b978-0-443-19104-6.00005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
Abstract
Neuroglia of the central nervous system (CNS) are a diverse and highly heterogeneous population of cells of ectodermal, neuroepithelial origin (macroglia, that includes astroglia and oligodendroglia) and mesodermal, myeloid origin (microglia). Neuroglia are primary homeostatic cells of the CNS, responsible for the support, defense, and protection of the nervous tissue. The extended class of astroglia (which includes numerous parenchymal astrocytes, such as protoplasmic, fibrous, velate, marginal, etc., radial astrocytes such as Bergmann glia, Muller glia, etc., and ependymoglia lining the walls of brain ventricles and central canal of the spinal cord) is primarily responsible for overall homeostasis of the nervous tissue. Astroglial cells control homeostasis of ions, neurotransmitters, hormones, metabolites, and are responsible for neuroprotection and defense of the CNS. Oligodendroglia provide for myelination of axons, hence supporting and sustaining CNS connectome. Microglia are tissue macrophages adapted to the CNS environment which contribute to the host of physiologic functions including regulation of synaptic connectivity through synaptic pruning, regulation of neurogenesis, and even modifying neuronal excitability. Neuroglial cells express numerous receptors, transporters, and channels that allow neuroglia to perceive and follow neuronal activity. Activation of these receptors triggers intracellular ionic signals that govern various homeostatic cascades underlying glial supportive and defensive capabilities. Ionic signaling therefore represents the substrate of glial excitability.
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Affiliation(s)
- Alexei Verkhratsky
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom; Department of Neurosciences, University of the Basque Country UPV/EHU and CIBERNED, Leioa, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Alexey Semyanov
- Department of Physiology, Jiaxing University College of Medicine, Jiaxing, Zhejiang, China
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He L, Xu Y, Lin J, Lin SL, Cui Y. Increased SLC7A3 Expression Inhibits Tumor Cell Proliferation and Predicts a Favorable Prognosis in Breast Cancer. Recent Pat Anticancer Drug Discov 2025; 20:55-70. [PMID: 38204267 PMCID: PMC11826905 DOI: 10.2174/0115748928279007231130070056] [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: 08/25/2023] [Revised: 10/22/2023] [Accepted: 10/31/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Arginine plays significant and contrasting roles in breast cancer growth and survival. However, the factors governing arginine balance remain poorly characterized. OBJECTIVE We aimed to identify the molecule that governs arginine metabolism in breast cancer and to elucidate its significance. METHODS We analyzed the correlation between the expression of solute carrier family 7 member 3 (SLC7A3), the major arginine transporter, and breast cancer survival in various databases, including GEPIA, UALCAN, Metascape, String, Oncomine, KM-plotter, CBioPortal and PrognoScan databases. Additionally, we validated our findings through bioinformatic analyses and experimental investigations, including colony formation, wound healing, transwell, and mammosphere formation assays. RESULTS Our analysis revealed a significant reduction in SLC7A3 expression in all breast cancer subtypes compared to adjacent breast tissues. Kaplan-Meier survival analyses demonstrated that high SLC7A3 expression was positively associated with decreased nodal metastasis (HR=0.70, 95% CI [0.55, 0.89]), ER positivity (HR=0.79, 95% CI [0.65, 0.95]), and HER2 negativity (HR=0.69, 95% CI [0.58, 0.82]), and increased recurrence-free survival. Moreover, low SLC7A3 expression predicted poor prognosis in breast cancer patients for overall survival. Additionally, the knockdown of SLC7A3 in MCF-7 and MDA-MB-231 cells resulted in increased cell proliferation and invasion in vitro. CONCLUSION Our findings indicate a downregulation of SLC7A3 expression in breast cancer tissues compared to adjacent breast tissues. High SLC7A3 expression could serve as a prognostic indicator for favorable outcomes in breast cancer patients due to its inhibitory effects on breast cancer cell proliferation and invasion.
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Affiliation(s)
- Lifang He
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515000, China
- Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515000, China
| | - Yue Xu
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515000, China
| | - Jiediao Lin
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515000, China
| | - Stanley Li Lin
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515000, China
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong Province, 515000, China
| | - Yukun Cui
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515000, China
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50
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Swapna GVT, Dube N, Roth MJ, Montelione GT. Modeling Alternative Conformational States of Pseudo-Symmetric Solute Carrier Transporters using Methods from Deep Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603529. [PMID: 39071413 PMCID: PMC11275918 DOI: 10.1101/2024.07.15.603529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The Solute Carrier (SLC) superfamily of integral membrane proteins function to transport a wide array of small molecules across plasma and organelle membranes. SLC proteins also function as important drug transporters and as viral receptors. Despite being classified as a single superfamily, SLC proteins do not share a single common fold classification; however, most belong to multi-pass transmembrane helical protein fold families. SLC proteins populate different conformational states during the solute transport process, including outward-open, intermediate (occluded), and inward-open conformational states. For some SLC fold families this structural "flipping" corresponds to swapping between conformations of their N-terminal and C-terminal symmetry-related sub-structures. Conventional AlphaFold2, AlphaFold3, or Evolutionary Scale Modeling methods typically generate models for only one of these multiple conformational states of SLC proteins. Several modifications of these AI-based protocols for modeling multiple conformational states of proteins have been described recently. These methods are often impacted by "memorization" of one of the alternative conformational states, and do not always provide both the inward and outward facing conformations of SLC proteins. Here we describe a combined ESM - template-based-modeling process, based on a previously described template-based modeling method that relies on the internal pseudo-symmetry of many SLC proteins, to consistently model alternate conformational states of SLC proteins. We further demonstrate how the resulting multi-state models can be validated experimentally by comparison with sequence-based evolutionary co-variance data (ECs) that encode information about contacts present in the various conformational states adopted by the protein. This simple, rapid, and robust approach for modeling conformational landscapes of pseudo-symmetric SLC proteins is demonstrated for several integral membrane protein transporters, including SLC35F2 the receptor of a feline leukemia virus envelope protein required for viral entry into eukaryotic cells.
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Affiliation(s)
- G V T Swapna
- Dept. of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway NJ 08854 USA
| | - Namita Dube
- Dept. of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
| | - Monica J Roth
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway NJ 08854 USA
| | - Gaetano T Montelione
- Dept. of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180 USA
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