1
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Chidley C, Darnell AM, Gaudio BL, Lien EC, Barbeau AM, Vander Heiden MG, Sorger PK. A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments. Nat Cell Biol 2024; 26:825-838. [PMID: 38605144 PMCID: PMC11098743 DOI: 10.1038/s41556-024-01402-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Blocking the import of nutrients essential for cancer cell proliferation represents a therapeutic opportunity, but it is unclear which transporters to target. Here we report a CRISPR interference/activation screening platform to systematically interrogate the contribution of nutrient transporters to support cancer cell proliferation in environments ranging from standard culture media to tumours. We applied this platform to identify the transporters of amino acids in leukaemia cells and found that amino acid transport involves high bidirectional flux dependent on the microenvironment composition. While investigating the role of transporters in cystine starved cells, we uncovered a role for serotonin uptake in preventing ferroptosis. Finally, we identified transporters essential for cell proliferation in subcutaneous tumours and found that levels of glucose and amino acids can restrain proliferation in that environment. This study establishes a framework for systematically identifying critical cellular nutrient transporters, characterizing their function and exploring how the tumour microenvironment impacts cancer metabolism.
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Affiliation(s)
- Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin L Gaudio
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Evan C Lien
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna M Barbeau
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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2
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Song K, Zhang L, Fu X, Li L, Zhu G, Wu M, Zhang W, He J, Zhu S, Dang Y, Liu JY, Chen C, Guo Z. A rapid and simple non-radioactive assay for measuring uptake by solute carrier transporters. Front Pharmacol 2024; 15:1355507. [PMID: 38720778 PMCID: PMC11076738 DOI: 10.3389/fphar.2024.1355507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024] Open
Abstract
Introduction: Solute carrier (SLC) transport proteins play a crucial role in maintaining cellular nutrient and metabolite homeostasis and are implicated in various human diseases, making them potential targets for therapeutic interventions. However, the study of SLCs has been limited due to the lack of suitable tools, particularly cell-based substrate uptake assays, necessary for understanding their biological functions and for drug discovery purposes. Methods: In this study, a cell-based uptake assay was developed using a stable isotope-labeled compound as the substrate for SLCs, with detection facilitated by liquid chromatography-tandem mass spectrometry (LC-MS/MS). This assay aimed to address the limitations of existing assays, such as reliance on hazardous radiolabeled substrates and limited availability of fluorescent biosensors. Results: The developed assay was successfully applied to detect substrate uptakes by two specific SLCs: L-type amino acid transporter 1 (LAT1) and sodium taurocholate co-transporting polypeptide (NTCP). Importantly, the assay demonstrated comparable results to the radioactive method, indicating its reliability and accuracy. Furthermore, the assay was utilized to screen for novel inhibitors of NTCP, leading to the identification of a potential NTCP inhibitor compound. Discussion: The findings highlight the utility of the developed cell-based uptake assay as a rapid, simple, and environmentally friendly tool for investigating SLCs' biological roles and for drug discovery purposes. This assay offers a safer alternative to traditional methods and has the potential to contribute significantly to advancing our understanding of SLC function and identifying therapeutic agents targeting SLC-mediated pathways.
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Affiliation(s)
- Kunling Song
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Longbin Zhang
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Xian Fu
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Anesthesiology, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Linfeng Li
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Gaolin Zhu
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Mingjun Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Wei Zhang
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jia He
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Sanyong Zhu
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yongjun Dang
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Jun-Yan Liu
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Anesthesiology, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Chang Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Zufeng Guo
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention (Ministry of Education), Institute of Life Sciences and Department of Breast and Thyroid Surgery, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
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3
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Møller-Hansen I, Sáez-Sáez J, van der Hoek SA, Dyekjær JD, Christensen HB, Wright Muelas M, O’Hagan S, Kell DB, Borodina I. Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds. Front Microbiol 2024; 15:1376653. [PMID: 38680917 PMCID: PMC11045925 DOI: 10.3389/fmicb.2024.1376653] [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: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).
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Affiliation(s)
- Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Jane D. Dyekjær
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Hanne B. Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Steve O’Hagan
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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Galetin A, Brouwer KLR, Tweedie D, Yoshida K, Sjöstedt N, Aleksunes L, Chu X, Evers R, Hafey MJ, Lai Y, Matsson P, Riselli A, Shen H, Sparreboom A, Varma MVS, Yang J, Yang X, Yee SW, Zamek-Gliszczynski MJ, Zhang L, Giacomini KM. Membrane transporters in drug development and as determinants of precision medicine. Nat Rev Drug Discov 2024; 23:255-280. [PMID: 38267543 DOI: 10.1038/s41573-023-00877-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The effect of membrane transporters on drug disposition, efficacy and safety is now well recognized. Since the initial publication from the International Transporter Consortium, significant progress has been made in understanding the roles and functions of transporters, as well as in the development of tools and models to assess and predict transporter-mediated activity, toxicity and drug-drug interactions (DDIs). Notable advances include an increased understanding of the effects of intrinsic and extrinsic factors on transporter activity, the application of physiologically based pharmacokinetic modelling in predicting transporter-mediated drug disposition, the identification of endogenous biomarkers to assess transporter-mediated DDIs and the determination of the cryogenic electron microscopy structures of SLC and ABC transporters. This article provides an overview of these key developments, highlighting unanswered questions, regulatory considerations and future directions.
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Affiliation(s)
- Aleksandra Galetin
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, The University of Manchester, Manchester, UK.
| | - Kim L R Brouwer
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Kenta Yoshida
- Clinical Pharmacology, Genentech Research and Early Development, South San Francisco, CA, USA
| | - Noora Sjöstedt
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Lauren Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA
| | - Xiaoyan Chu
- Department of Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, Merck & Co., Inc., Rahway, NJ, USA
| | - Raymond Evers
- Preclinical Sciences and Translational Safety, Johnson & Johnson, Janssen Pharmaceuticals, Spring House, PA, USA
| | - Michael J Hafey
- Department of Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, Merck & Co., Inc., Rahway, NJ, USA
| | - Yurong Lai
- Drug Metabolism, Gilead Sciences Inc., Foster City, CA, USA
| | - Pär Matsson
- Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Andrew Riselli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Hong Shen
- Department of Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb Research and Development, Princeton, NJ, USA
| | - Alex Sparreboom
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Manthena V S Varma
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design, Worldwide R&D, Pfizer Inc, Groton, CT, USA
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Xinning Yang
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Lei Zhang
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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5
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Yang X, Tao Y, Xu Y, Cai W, Shao Q. SLC35A2 expression drives breast cancer progression via ERK pathway activation. FEBS J 2024; 291:1483-1505. [PMID: 38143314 DOI: 10.1111/febs.17044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023]
Abstract
Alterations in glycosylation are associated with breast tumor formation and progression. Nevertheless, the specific functions and mechanisms of the human major UDP-galactose transporter-encoding gene solute carrier family 35 member A2 (SLC35A2) in breast invasive carcinoma (BRCA) have not been fully determined. Here, we report that SLC35A2 promotes BRCA progression by activating extracellular signal regulated kinase (ERK). SLC35A2 expression and prognosis-predictive significance in pan-cancer were evaluated using public databases. The upstream non-coding RNAs (ncRNAs) of SLC35A2 were analyzed, and their expression and regulations were validated in breast tissues and cell lines by a quantitative PCR and dual-luciferase assays. We used bioinformatic tools to assess the link between SLC35A2 expression and immune infiltration and performed immunohistochemistry for validation. Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine, transwell, flow cytometer and western blotting were used to assess the proliferation, motility, cell cycle and apoptosis of BRCA cells in vitro. The xenograft models were constructed to assess the effect of SLC35A2 on BRCA tumor growth in vivo. The results indicated that SLC35A2 expression was upregulated and linked to an unfavorable prognosis in BRCA. The most likely upstream ncRNA-associated pathway of SLC35A2 in BRCA was the AC074117.1/hsa-let-7b-5p axis. SLC35A2 expression had positive correlations with the presence of Th2 cells, regulatory T cells and immune checkpoints. Knockdown of SLC35A2 could reduce BRCA cell proliferation, motility, and cause G2/M arrest and cell apoptosis via ERK signaling. Moreover, ERK activation can rescue the inhibitory effects of knockdown SLC35A2 in BRCA. In conclusion, AC074117.1/hsa-let-7b-5p axis-mediated high expression of SLC35A2 acts as a tumor promoter in BRCA via ERK signaling, which provides a potential target for BRCA treatment.
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Affiliation(s)
- Xiaochen Yang
- Department of Thyroid and Breast Surgery, Affiliated Kunshan Hospital of Jiangsu University, China
| | - Yukai Tao
- Clinical Research & Lab Center, Affiliated Kunshan Hospital of Jiangsu University, China
| | - Yan Xu
- Department of Thyroid and Breast Surgery, Affiliated Kunshan Hospital of Jiangsu University, China
| | - Weili Cai
- Institute of Medical Genetics and Reproductive Immunity, The Digestive and Reproductive System Cancers Precise Prevention Engineering Research Center of Jiangsu Province, Jiangsu College of Nursing, Huai'an, China
| | - Qixiang Shao
- Clinical Research & Lab Center, Affiliated Kunshan Hospital of Jiangsu University, China
- Institute of Medical Genetics and Reproductive Immunity, The Digestive and Reproductive System Cancers Precise Prevention Engineering Research Center of Jiangsu Province, Jiangsu College of Nursing, Huai'an, China
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6
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Meng Q, Xie Y, Sun K, He L, Wu H, Zhang Q, Liang T. ALYREF-JunD-SLC7A5 axis promotes pancreatic ductal adenocarcinoma progression through epitranscriptome-metabolism reprogramming and immune evasion. Cell Death Discov 2024; 10:97. [PMID: 38402198 PMCID: PMC10894212 DOI: 10.1038/s41420-024-01862-2] [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: 11/03/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a kind of tumor lacking nutrients due to its poor vascularity and desmoplasia. Recent studies have shown that cancer cells might achieve growth advantage through epitranscriptome reprogramming. However, the role of m5C in PDAC was not fully understood. We found that Aly/REF export factor (ALYREF), a reader of m5C modification, was overexpressed in PDAC, and associated with bad prognosis. In addition, the ALYREF expression was negatively related to CD8+ T cells infiltration in clinical samples. ALYREF knockdown decreased tumor growth in vivo partly dependent of immunity. ALYREF silencing decreased SLC7A5 expression and subsequently inactivated mTORC1 pathway, resulting in decreased tumor proliferation. Mechanically, ALYREF specifically recognized m5C sites in JunD mRNA, maintained the stabilization of JunD mRNA and subsequently upregulated transcription of SLC7A5. Since SLC7A5 was a key transporter of large neutral amino acids (LNAAs), overexpression of SLC7A5 on tumor cells depleted amino acid in microenvironment and restricted CD8+ T cells function. Moreover, ALYREF-JunD-SLC7A5 axis was overexpressed and negatively related with survival through TMA assays. In conclusion, this research revealed the relationship between m5C modification, amino acid transportation and immune microenvironment. ALYREF might be a novel target for PDAC metabolic vulnerability and immune surveillance.
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Affiliation(s)
- Qingbo Meng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Joint International Research Laboratory of Pancreatic Diseases, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuting Xie
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Joint International Research Laboratory of Pancreatic Diseases, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kang Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Joint International Research Laboratory of Pancreatic Diseases, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lihong He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Joint International Research Laboratory of Pancreatic Diseases, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongkun Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Joint International Research Laboratory of Pancreatic Diseases, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Joint International Research Laboratory of Pancreatic Diseases, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- MOE Joint International Research Laboratory of Pancreatic Diseases, Zhejiang University, Hangzhou, Zhejiang, China.
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7
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Ni MM, Yang JF, Miao J, Xu J. Association between genetic variants of transmembrane transporters and susceptibility to anthracycline-induced cardiotoxicity: Current understanding and existing evidence. Clin Genet 2024; 105:115-129. [PMID: 37961936 DOI: 10.1111/cge.14452] [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: 08/28/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
Anthracyclines remain the cornerstone of numerous chemotherapeutic protocols, with beneficial effects against haematological malignancies and solid tumours. Unfortunately, the clinical usefulness of anthracyclines is compromised by the development of cardiotoxic side effects, leading to dose limitations or treatment discontinuation. There is no absolute linear correlation between the incidence of cardiotoxicity and the threshold dose, suggesting that genetic factors may modify the association between anthracyclines and cardiotoxicity risk. And the majority of single nucleotide polymorphisms (SNPs) associated with anthracycline pharmacogenomics were identified in the ATP-binding cassette (ABC) and solute carrier (SLC) transporters, generating increasing interest in the pharmacogenetic implications of their genetic variations for anthracycline-induced cardiotoxicity (AIC). This review focuses on the influence of SLC and ABC polymorphisms on AIC and highlights the prospects and clinical significance of pharmacogenetics for individualised preventive approaches.
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Affiliation(s)
- Ming-Ming Ni
- Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ju-Fei Yang
- Department of Pharmacy, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jing Miao
- Department of Pharmacy, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
- Research Center for Clinical Pharmacy, Zhejiang University, Hangzhou, China
| | - Jin Xu
- Department of Pharmacy, Children's Hospital of Nanjing Medical University, Nanjing, China
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8
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Fessart D, Robert J. [Mechanisms of cancer drug resistance]. Bull Cancer 2024; 111:37-50. [PMID: 37679207 DOI: 10.1016/j.bulcan.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 09/09/2023]
Abstract
Despite decades of research into the molecular mechanisms of cancer and the development of new treatments, drug resistance persists as a major problem. This is in part due to the heterogeneity of cancer, including the diversity of tumor cell lineage and cell plasticity, the spectrum of somatic mutations, the complexity of microenvironments, and immunosuppressive characteristic, then necessitating the use of many different therapeutic approaches. We summarize here the biological causes of resistance, thus offering new perspectives for tackle drug resistance.
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Affiliation(s)
- Delphine Fessart
- ARTiSt lab, Université de Bordeaux, Inserm U1312 BRIC, 33000 Bordeaux, France.
| | - Jacques Robert
- ARTiSt lab, Université de Bordeaux, Inserm U1312 BRIC, 33000 Bordeaux, France
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9
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Shen X, Wang G, He H, Shang P, Yan B, Wang X, Shen W. SLC38A5 promotes glutamine metabolism and inhibits cisplatin chemosensitivity in breast cancer. Breast Cancer 2024; 31:96-104. [PMID: 37914960 DOI: 10.1007/s12282-023-01516-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/15/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Solute carrier family 38 member 5 (SLC38A5), as an amino acid transporter, play a vital role in cellular biological processes. In this study, we analyzed the function of SLC38A5 and its potential mechanism in breast cancer (BC) progression. METHODS The expression of SLC38A5 in cancer and adjacent-normal tissues was analyzed by qRT-PCR and Western blot, and its correlation with patient prognosis was analyzed. The immunohistochemical staining of cancer tissues and adjacent-normal tissues was performed on SLC38A5-positive specimens. BC mice were successfully applied to examine the role of SLC38A5 on tumor proliferation using the CCK-8 assay. In BC cells and mouse tumor tissues, SLC38A5 and PCNA expression were determined by Western blotting. RESULTS The study found that SLC38A5 was highly expressed in BC patients and associated with a poor survival. SLC38A5 silencing inhibited BC cell viability and glutamine uptake. In addition, SLC38A5 overexpression promoted BC cell viability via the glutamine metabolism. SLC38A5 inhibited cisplatin chemosensitivity in BC cells. Importantly, SLC38A5 silencing inhibited tumor growth in vivo. CONCLUSION Our findings suggest that SLC38A5 enhances BC cell viability by glutamine metabolism, inhibits the chemical sensitivity of cisplatin in BC cells, and promotes tumor growth, emphasizing the clinical relevance of SLC38A5 in BC management as a novel potential therapeutic target.
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Affiliation(s)
- Xiaowei Shen
- Department of General Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, QingPu District Central Hospital Shanghai, No. 1158, Gong Yuan Dong Road, Shanghai, 201700, China.
| | - Ganggang Wang
- Department of Hepatobiliary Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Hua He
- Department of General Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, QingPu District Central Hospital Shanghai, No. 1158, Gong Yuan Dong Road, Shanghai, 201700, China
| | - Ping Shang
- Department of General Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, QingPu District Central Hospital Shanghai, No. 1158, Gong Yuan Dong Road, Shanghai, 201700, China
| | - Bin Yan
- Department of General Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, QingPu District Central Hospital Shanghai, No. 1158, Gong Yuan Dong Road, Shanghai, 201700, China
| | - Xiaoliang Wang
- Department of General Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, QingPu District Central Hospital Shanghai, No. 1158, Gong Yuan Dong Road, Shanghai, 201700, China
- Department of Hepatobiliary Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Weixing Shen
- Department of General Surgery, QingPu Branch of Zhongshan Hospital Affiliated to Fudan University, QingPu District Central Hospital Shanghai, No. 1158, Gong Yuan Dong Road, Shanghai, 201700, China
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10
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Li Y, Tan M, Sun S, Stea E, Pang B. Targeted CRISPR activation and knockout screenings identify novel doxorubicin transporters. Cell Oncol (Dordr) 2023; 46:1807-1820. [PMID: 37523060 DOI: 10.1007/s13402-023-00847-0] [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] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
PURPOSE Tissue-specific drug uptake has not been well studied, compared to the deeper understanding of drug resistance mediated by the cellular efflux system such as MDR1 proteins. It has been suggested that many drugs need active or defined transporters to pass the cell membrane. In contrast to efflux components induced after anti-cancer drugs reach the intracellular compartment, drug importers are required for initial drug responses. Furthermore, tissue-specific uptake of anti-cancer drugs may directly impact the side effects of many drugs when they accumulate in healthy tissues. Therefore, linking anti-cancer drugs to their respective drug import transporters would directly help to predict drug responses, whilst minimizing side effects. METHODS To identify drug transporters of the commonly used anti-cancer drug doxorubicin, we performed focused CRISPR activation and knockout genetic screens targeting all potential membrane-associated transporters and proteins. We monitored the direct uptake of doxorubicin by fluorescence-activated cell sorting (FACS) as the screening readout for identifying transporters/proteins directly involved in doxorubicin uptake. RESULTS Integrating the data from these comprehensive CRISPR screenings, we confirmed previously indicated doxorubicin exporters such as ABCB1 and ABCG2 genes, and identified novel doxorubicin importer gene SLC2A3 (GLUT3). Upregulation of SLC2A3 led to higher doxorubicin uptake and better cell killing, indicating SLC2A3 could be a new marker to predict doxorubicin drug response and minimize side effects for the personalized application of this conventional chemotherapeutic drug. CONCLUSIONS Our study provides a comprehensive way for identifying drug transporters, as exemplified by the commonly used anti-cancer drug doxorubicin. The newly identified importers may have direct clinical implications for the personalized application of doxorubicin in treating distinct tumors. Our results also highlight the necessity of combining both CRISPR knockout and CRISPR activation genetic screens to identify drug transporters.
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Affiliation(s)
- Yufeng Li
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Minkang Tan
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Shengnan Sun
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Elena Stea
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Baoxu Pang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands.
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11
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Alam S, Doherty E, Ortega-Prieto P, Arizanova J, Fets L. Membrane transporters in cell physiology, cancer metabolism and drug response. Dis Model Mech 2023; 16:dmm050404. [PMID: 38037877 PMCID: PMC10695176 DOI: 10.1242/dmm.050404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
By controlling the passage of small molecules across lipid bilayers, membrane transporters influence not only the uptake and efflux of nutrients, but also the metabolic state of the cell. With more than 450 members, the Solute Carriers (SLCs) are the largest transporter super-family, clustering into families with different substrate specificities and regulatory properties. Cells of different types are, therefore, able to tailor their transporter expression signatures depending on their metabolic requirements, and the physiological importance of these proteins is illustrated by their mis-regulation in a number of disease states. In cancer, transporter expression is heterogeneous, and the SLC family has been shown to facilitate the accumulation of biomass, influence redox homeostasis, and also mediate metabolic crosstalk with other cell types within the tumour microenvironment. This Review explores the roles of membrane transporters in physiological and malignant settings, and how these roles can affect drug response, through either indirect modulation of sensitivity or the direct transport of small-molecule therapeutic compounds into cells.
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Affiliation(s)
- Sara Alam
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Emily Doherty
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Paula Ortega-Prieto
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Julia Arizanova
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Louise Fets
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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12
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Wang Y, Chen L, Chen J, Bai Z, Cao L. Comprehensive analysis of transcriptome data and experimental identification show that solute carrier 35 member A2 (SLC35A2) is a prognostic marker of colorectal cancer. Aging (Albany NY) 2023; 15:11554-11570. [PMID: 37889544 PMCID: PMC10637800 DOI: 10.18632/aging.205145] [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: 02/03/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is a solid tumor with high morbidity and mortality rates. Accumulating evidence shows that the soluble carrier family 35 member A2 (SLC35A2), a nucleotide sugar transporter, plays a key role in the pathogenesis of various tumors. However, its expression and function in CRC has not been fully elucidated. METHODS The prognosis-related gene SLC35A2 was obtained using differential analysis, prognosis correlation analysis, and LASSO regression screening. Its expression levels in CRC tissues were analyzed, and so was the relationship of this expression with clinical characteristics of patients. Subsequently, the expression levels were correlated with clinicopathological parameters using immunohistochemical analysis. Analysis based on GO/KEGG databases was used to reveal the potential mechanisms of SLC35A2. Next, we explored the relationship between SLC35A2 and immune cells in CRC tissues. A nomogram was created to help understand the prognosis of CRC patients. Finally, western blotting and qRT-PCR reaction were used to verify the expression of SLC35A2 in CRC cell lines. RESULTS SLC35A2 expression was upregulated and related to tumor pathological stage and lymph node metastasis, indicating that SLC35A2 is an independent prognostic factor and a potential diagnostic marker for CRC. We verified by IHC, WB and PCR that the expression of SLC35A2 was up-regulated in colorectal cancer tissues and cell lines, and its high expression was related to the tumor pathological stage of CRC clinical samples. CONCLUSIONS Our study found that SLC35A2 can be used as a biomarker for the diagnosis and prognosis of CRC, providing motivation for further study.
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Affiliation(s)
- Yue Wang
- Department of Pathology, School of Basic Medical Science, Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Liang Chen
- First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, People’s Republic of China
| | - Jing Chen
- Department of Pathology, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, Anhui, People’s Republic of China
| | - Zhenzhen Bai
- Department of Pathology, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, Anhui, People’s Republic of China
| | - Liyu Cao
- Department of Pathology, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, Anhui, People’s Republic of China
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Nies AT, König J, Leuthold P, Damme K, Winter S, Haag M, Masuda S, Kruck S, Daniel H, Spanier B, Fromm MF, Bedke J, Inui KI, Schwab M, Schaeffeler E. Novel drug transporter substrates identification: An innovative approach based on metabolomic profiling, in silico ligand screening and biological validation. Pharmacol Res 2023; 196:106941. [PMID: 37775020 DOI: 10.1016/j.phrs.2023.106941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Solute carrier (SLC) transport proteins are fundamental for the translocation of endogenous compounds and drugs across membranes, thus playing a critical role in disease susceptibility and drug response. Because only a limited number of transporter substrates are currently known, the function of a large number of SLC transporters is elusive. Here, we describe the proof-of-concept of a novel strategy to identify SLC transporter substrates exemplarily for the proton-coupled peptide transporter (PEPT) 2 (SLC15A2) and multidrug and toxin extrusion (MATE) 1 transporter (SLC47A1), which are important renal transporters of drug reabsorption and excretion, respectively. By combining metabolomic profiling of mice with genetically-disrupted transporters, in silico ligand screening and in vitro transport studies for experimental validation, we identified nucleobases and nucleoside-derived anticancer and antiviral agents (flucytosine, cytarabine, gemcitabine, capecitabine) as novel drug substrates of the MATE1 transporter. Our data confirms the successful applicability of this new approach for the identification of transporter substrates in general, which may prove particularly relevant in drug research.
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Affiliation(s)
- Anne T Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Germany
| | - Jörg König
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Patrick Leuthold
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
| | - Katja Damme
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
| | - Satohiro Masuda
- Department of Clinical Pharmacology & Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan; Department of Clinical Pharmaceutics, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Japan
| | - Stephan Kruck
- Department of Urology, University Hospital Tuebingen, Germany
| | - Hannelore Daniel
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Britta Spanier
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Martin F Fromm
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jens Bedke
- Department of Urology, University Hospital Tuebingen, Germany
| | | | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Germany; Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Germany.
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Germany
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Schlessinger A, Zatorski N, Hutchinson K, Colas C. Targeting SLC transporters: small molecules as modulators and therapeutic opportunities. Trends Biochem Sci 2023; 48:801-814. [PMID: 37355450 PMCID: PMC10525040 DOI: 10.1016/j.tibs.2023.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023]
Abstract
Solute carrier (SLCs) transporters mediate the transport of a broad range of solutes across biological membranes. Dysregulation of SLCs has been associated with various pathologies, including metabolic and neurological disorders, as well as cancer and rare diseases. SLCs are therefore emerging as key targets for therapeutic intervention with several recently approved drugs targeting these proteins. Unlocking this large and complex group of proteins is essential to identifying unknown SLC targets and developing next-generation SLC therapeutics. Recent progress in experimental and computational techniques has significantly advanced SLC research, including drug discovery. Here, we review emerging topics in therapeutic discovery of SLCs, focusing on state-of-the-art approaches in structural, chemical, and computational biology, and discuss current challenges in transporter drug discovery.
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Affiliation(s)
- Avner Schlessinger
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Nicole Zatorski
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claire Colas
- University of Vienna, Department of Pharmaceutical Chemistry, Vienna, Austria.
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15
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Sun X, Yuan Z, Zhang L, Ren M, Yang J, Xu Y, Hao J. Comprehensive Analysis of SLC35A2 in Pan-Cancer and Validation of Its Role in Breast Cancer. J Inflamm Res 2023; 16:3381-3398. [PMID: 37593196 PMCID: PMC10427759 DOI: 10.2147/jir.s419994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023] Open
Abstract
Purpose Elucidation of the oncogenic role of SLC35A2 in human tumors and the potential function and clinical significance in breast cancer. Methods Pan-cancer analysis was performed via various bioinformatics tools to explain the pathogenic role of SLC35A2. A prognostic nomogram was also developed based on the SLC35A2 expression and clinicopathological characteristics in breast cancer patients. In addition, the role of SLC35A2 was validated in breast cancer by in vivo and in vitro experiments. Results SLC35A2 expression is increased in 27 tumor types, and its high expression is substantially correlated with poor prognosis in patients with a variety of cancers. Receiver operating characteristic (ROC) curves showed that SLC35A2 expression levels could accurately distinguish most tumor tissues from normal tissues. High SLC35A2 expression was linked to increased immune infiltration in myeloid-derived suppressor cells (MDSC), as well as immune checkpoints, ferroptosis-related genes, tumor mutational burden (TMB), and microsatellite instability (MSI). SLC35A2 may be involved in tumorigenesis by regulating the glycosylation process. Furthermore, multivariate Cox analysis showed that SLC35A2 was an independent prognostic factor for breast cancer. And the nomogram model had good predictive accuracy for the prognosis of breast cancer patients. Meanwhile, cellular experiments demonstrated that knockdown of SLC35A2 could significantly inhibit the proliferation, migration and invasion of breast cancer cells, while increasing the protein level of E-cadherin and decreasing N-cadherin. A nude mouse xenograft model showed that inhibition of SLA35A2 expression could significantly inhibit tumor growth. Conclusion SLC35A2 has good diagnostic and prognostic values in multiple cancers and is closely related to tumor immune infiltration. In addition, SLA35A2 as an oncogene in breast cancer may be involved in the progression of epithelial mesenchymal transition (EMT).
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Affiliation(s)
- Xiaonan Sun
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Zhichao Yuan
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Lu Zhang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Min Ren
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Jing Yang
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Yidan Xu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
| | - Jiqing Hao
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People’s Republic of China
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16
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Taurino G, Chiu M, Bianchi MG, Griffini E, Bussolati O. The SLC38A5/SNAT5 amino acid transporter: from pathophysiology to pro-cancer roles in the tumor microenvironment. Am J Physiol Cell Physiol 2023; 325:C550-C562. [PMID: 37458433 DOI: 10.1152/ajpcell.00169.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
SLC38A5/SNAT5 is a system N transporter that can mediate net inward or outward transmembrane fluxes of neutral amino acids coupled with Na+ (symport) and H+ (antiport). Its preferential substrates are not only amino acids with side chains containing amide (glutamine and asparagine) or imidazole (histidine) groups, but also serine, glycine, and alanine are transported by the carrier. Expressed in the pancreas, intestinal tract, brain, liver, bone marrow, and placenta, it is regulated at mRNA and protein levels by mTORC1 and WNT/β-catenin pathways, and it is sensitive to pH, nutritional stress, inflammation, and hypoxia. SNAT5 expression has been found to be altered in pathological conditions such as chronic inflammatory diseases, gestational complications, chronic metabolic acidosis, and malnutrition. Growing experimental evidence shows that SNAT5 is overexpressed in several types of cancer cells. Moreover, recently published results indicate that SNAT5 expression in stromal cells can support the metabolic exchanges occurring in the tumor microenvironment of asparagine-auxotroph tumors. We review the functional role of the SNAT5 transporter in pathophysiology and propose that, due to its peculiar operational and regulatory features, SNAT5 may play important pro-cancer roles when expressed either in neoplastic or in stromal cells of glutamine-auxotroph tumors.NEW & NOTEWORTHY The transporter SLC38A5/SNAT5 provides net influx or efflux of glutamine, asparagine, and serine. These amino acids are of particular metabolic relevance in several conditions. Changes in transporter expression or activity have been described in selected types of human cancers, where SNAT5 can mediate amino acid exchanges between tumor and stromal cells, thus providing a potential therapeutic target. This is the first review that recapitulates the characteristics and roles of the transporter in physiology and pathology.
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Affiliation(s)
- Giuseppe Taurino
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Massimiliano G Bianchi
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
| | - Erika Griffini
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
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Kagan AB, Garrison DA, Anders NM, Webster J, Baker SD, Yegnasubramanian S, Rudek MA. DNA methyltransferase inhibitor exposure-response: Challenges and opportunities. Clin Transl Sci 2023; 16:1309-1322. [PMID: 37345219 PMCID: PMC10432879 DOI: 10.1111/cts.13548] [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: 02/22/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Although DNA methyltransferase inhibitors (DNMTis), such as azacitidine and decitabine, are used extensively in the treatment of myelodysplastic syndromes and acute myeloid leukemia, there remain unanswered questions about DNMTi's mechanism of action and predictors of clinical response. Because patients often remain on single-agent DNMTis or DNMTi-containing regimens for several months before knowing whether clinical benefit can be achieved, the development and clinical validation of response-predictive biomarkers represents an important unmet need in oncology. In this review, we will summarize the clinical studies that led to the approval of azacitidine and decitabine, as well as the real-world experience with these drugs. We will then focus on biomarker development for DNMTis-specifically, efforts at determining exposure-response relationships and challenges that remain impacting the broader clinical translation of these methods. We will highlight recent progress in liquid-chromatography tandem mass spectrometry technology that has allowed for the simultaneous measurement of decitabine genomic incorporation and global DNA methylation, which has significant potential as a mechanism-of-action based biomarker in patients on DNMTis. Last, we will cover important research questions that need to be addressed in order to optimize this potential biomarker for clinical use.
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Affiliation(s)
- Amanda B. Kagan
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Dominique A. Garrison
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Nicole M. Anders
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Jonathan A. Webster
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Sharyn D. Baker
- Division of Pharmaceutics and Pharmacology, College of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Srinivasan Yegnasubramanian
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Michelle A. Rudek
- Department of Oncology, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Medicine, School of MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins UniversityBaltimoreMarylandUSA
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Huang Z, Yang H, Lao J, Deng W. Solute carrier family 35 member A2 (SLC35A2) is a prognostic biomarker and correlated with immune infiltration in stomach adenocarcinoma. PLoS One 2023; 18:e0287303. [PMID: 37467193 DOI: 10.1371/journal.pone.0287303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/03/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Solute carrier family 35 member A2 (SLC35A2) located on the X chromosome is considered involved in the UDP-galactose transport from cytosol to Golgi apparatus and endoplasmic reticulum. It has been reported that the SLC35A2 expression is associated with carcinogenesis in recent studies, however, its specific roles in cancer progression have not been exhaustively elucidated. Herein, a system analysis was conducted to evaluate the role of SLC35A2 in prognostic, and immunology in stomach adenocarcinoma (STAD). METHODS The TIMER, GEPIA, UALCAN, Kaplan-Meier Plotter were employed to explore the SLC35A2 expression pattern and prognostic value in STAD. Genomic alterations were searched through the MEXPRESS and cBioPortal platforms. The LinkedOmics, GEPIA and Metascape databases were employed to explore the biological processes. The TIMER and TISIDB websites were utilized to investigate the relationships between SLC35A2 expression and immune cell infiltration. The associations between SLC35A2 expression and tumor mutational burden (TMB), microsatellite instability (MSI) in pan-cancer were explored using the SangerBox database. RESULTS Compared to the normal gastric mucosa, SLC35A2 expression was significantly increased in STAD tissues, accompanied by the robust relationships with tumor grade, histological subtypes, TP53 mutation status, TMB and prognosis. SLC35A2 and its co-expression genes played the primarily roles in purine metabolism and purinosome, including the asparagine N-linked glycosylation, protein processing in endoplasmic reticulum, regulation of transcription involved in G1/S transition of mitotic cell cycle, with the potential to participate in the regulation of VEGFA-VEGFR2 signaling pathway. Concurrently, SLC35A2 expression was correlated with macrophages and CD4+T lymphocytes infiltration in STAD. CONCLUSIONS Our study has proposed that SLC35A2 correlated with immune cell infiltration could serve as a prognostic biomarker in STAD.
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Affiliation(s)
- Zigao Huang
- Department of Gastrointestinal Surgery, The First People's Hospital of Qinzhou, Qinzhou, Guangxi Zhuang Autonomous Region, China
| | - Hong Yang
- Department of Vascular Surgery, The First People's Hospital of Qinzhou, Qinzhou, Guangxi Zhuang Autonomous Region, China
| | - Jingmao Lao
- Department of Gastrointestinal Surgery, The First People's Hospital of Qinzhou, Qinzhou, Guangxi Zhuang Autonomous Region, China
| | - Wei Deng
- Department of Gastrointestinal Surgery, The First People's Hospital of Qinzhou, Qinzhou, Guangxi Zhuang Autonomous Region, China
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Dvorak V, Superti-Furga G. Structural and functional annotation of solute carrier transporters: implication for drug discovery. Expert Opin Drug Discov 2023; 18:1099-1115. [PMID: 37563933 DOI: 10.1080/17460441.2023.2244760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
INTRODUCTION Solute carriers (SLCs) represent the largest group of membrane transporters in the human genome. They play a central role in controlling the compartmentalization of metabolism and most of this superfamily is linked to human disease. Despite being in general considered druggable and attractive therapeutic targets, many SLCs remain poorly annotated, both functionally and structurally. AREAS COVERED The aim of this review is to provide an overview of functional and structural parameters of SLCs that play important roles in their druggability. To do this, the authors provide an overview of experimentally solved structures of human SLCs, with emphasis on structures solved in complex with chemical modulators. From the functional annotations, the authors focus on SLC localization and SLC substrate annotations. EXPERT OPINION Recent progress in the structural and functional annotations allows to refine the SLC druggability index. Particularly the increasing number of experimentally solved structures of SLCs provides insights into mode-of-action of a significant number of chemical modulators of SLCs.
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Affiliation(s)
- Vojtech Dvorak
- 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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20
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Liu H, Che H, Zhang M, Lv J, Pu C, Wu J, Zhang Y, Gu Y. Developing CuS for Predicting Aggressiveness and Prognosis in Lung Adenocarcinoma. Genes (Basel) 2023; 14:genes14051055. [PMID: 37239416 DOI: 10.3390/genes14051055] [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: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Cuproptosis is a newfound cell death form that depends on copper (Cu) ionophores to transport Cu into cancer cells. Studies on the relationship have covered most common cancer types and analyzed the links between cuproptosis-related genes (CRGs) and various aspects of tumor characteristics. In this study, we evaluated the role of cuproptosis in lung adenocarcinoma (LUAD) and constructed the cuproptosis-related score (CuS) to predict aggressiveness and prognosis in LUAD, so as to achieve precise treatment for patients. CuS had a better predictive performance than cuproptosis genes, possibly due to the synergy of SLC family genes, and patients with a high CuS had a poor prognosis. Functional enrichment analysis revealed the correlation between CuS and immune and mitochondrial pathways in multiple datasets. Furthermore, we predicted six potential drugs targeting high-CuS patients, including AZD3759, which is a targeted drug for LUAD. In conclusion, cuproptosis is involved in LUAD aggressiveness, and CuS can accurately predict the prognosis of patients. These findings provide a basis for precise treatment of patients with high CuS in LUAD.
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Affiliation(s)
- Honghao Liu
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Haijun Che
- College of Pharmacy, Chengdu Airport Campus, Southwest Minzu University, Chengdu 610041, China
| | - Mengyan Zhang
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Jinyue Lv
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Chengjie Pu
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Jiawei Wu
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- College of Pathology, Qiqihar Medical University, Qiqihar 161042, China
| | - Yue Gu
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
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21
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Cacic D, Hervig T, Reikvam H. Platelets for advanced drug delivery in cancer. Expert Opin Drug Deliv 2023; 20:673-688. [PMID: 37212640 DOI: 10.1080/17425247.2023.2217378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
INTRODUCTION Cancer-related drug expenses are rising with the increasing cancer incidence and cost may represent a severe challenge for drug access for patients with cancer. Consequently, strategies for increasing therapeutic efficacy of already available drugs may be essential for the future health-care system. AREAS COVERED In this review, we have investigated the potential for the use of platelets as drug-delivery systems. We searched PubMed and Google Scholar to identify relevant papers written in English and published up to January 2023. Papers were included at the authors' discretion to reflect an overview of state of the art. EXPERT OPINION It is known that cancer cells interact with platelets to gain functional advantages including immune evasion and metastasis development. This platelet-cancer interaction has been the inspiration for numerous platelet-based drug delivery systems using either drug-loaded or drug-bound platelets, or platelet membrane-containing hybrid vesicles combining platelet membranes with synthetic nanocarriers. Compared to treatment with free drug or synthetic drug vectors, these strategies may improve pharmacokinetics and selective cancer cell targeting. There are multiple studies showing improved therapeutic efficacy using animal models, however, no platelet-based drug delivery systems have been tested in humans, meaning the clinical relevance of this technology remains uncertain.
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Affiliation(s)
- Daniel Cacic
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Tor Hervig
- Irish Blood Transfusion Service, Dublin, Ireland
| | - Håkon Reikvam
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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22
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Bo L, Wang Y, Li Y, Wurpel JND, Huang Z, Chen ZS. The Battlefield of Chemotherapy in Pediatric Cancers. Cancers (Basel) 2023; 15:cancers15071963. [PMID: 37046624 PMCID: PMC10093214 DOI: 10.3390/cancers15071963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/12/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
The survival rate for pediatric cancers has remarkably improved in recent years. Conventional chemotherapy plays a crucial role in treating pediatric cancers, especially in low- and middle-income countries where access to advanced treatments may be limited. The Food and Drug Administration (FDA) approved chemotherapy drugs that can be used in children have expanded, but patients still face numerous side effects from the treatment. In addition, multidrug resistance (MDR) continues to pose a major challenge in improving the survival rates for a significant number of patients. This review focuses on the severe side effects of pediatric chemotherapy, including doxorubicin-induced cardiotoxicity (DIC) and vincristine-induced peripheral neuropathy (VIPN). We also delve into the mechanisms of MDR in chemotherapy to the improve survival and reduce the toxicity of treatment. Additionally, the review focuses on various drug transporters found in common types of pediatric tumors, which could offer different therapeutic options.
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Affiliation(s)
- Letao Bo
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - Youyou Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - Yidong Li
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - John N. D. Wurpel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
| | - Zoufang Huang
- Ganzhou Key Laboratory of Hematology, Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
- Correspondence: (Z.H.); (Z.-S.C.); Tel.: +86-138-797-27439 (Z.H.); +1-718-990-1432 (Z.-S.C.); Fax: +1-718-990-1877 (Z.-S.C.)
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY 11439, USA
- Institute for Biotechnology, St. John’s University, Queens, NY 11439, USA
- Correspondence: (Z.H.); (Z.-S.C.); Tel.: +86-138-797-27439 (Z.H.); +1-718-990-1432 (Z.-S.C.); Fax: +1-718-990-1877 (Z.-S.C.)
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23
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Truong JK, Li J, Li Q, Pachura K, Rao A, Gumber S, Fuchs CD, Feranchak AP, Karpen SJ, Trauner M, Dawson PA. Active enterohepatic cycling is not required for the choleretic actions of 24-norUrsodeoxycholic acid in mice. JCI Insight 2023; 8:e149360. [PMID: 36787187 PMCID: PMC10070106 DOI: 10.1172/jci.insight.149360] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
The pronounced choleretic properties of 24-norUrsodeoxycholic acid (norUDCA) to induce bicarbonate-rich bile secretion have been attributed to its ability to undergo cholehepatic shunting. The goal of this study was to identify the mechanisms underlying the choleretic actions of norUDCA and the role of the bile acid transporters. Here, we show that the apical sodium-dependent bile acid transporter (ASBT), organic solute transporter-α (OSTα), and organic anion transporting polypeptide 1a/1b (OATP1a/1b) transporters are dispensable for the norUDCA stimulation of bile flow and biliary bicarbonate secretion. Chloride channels in biliary epithelial cells provide the driving force for biliary secretion. In mouse large cholangiocytes, norUDCA potently stimulated chloride currents that were blocked by siRNA silencing and pharmacological inhibition of calcium-activated chloride channel transmembrane member 16A (TMEM16A) but unaffected by ASBT inhibition. In agreement, blocking intestinal bile acid reabsorption by coadministration of an ASBT inhibitor or bile acid sequestrant did not impact norUDCA stimulation of bile flow in WT mice. The results indicate that these major bile acid transporters are not directly involved in the absorption, cholehepatic shunting, or choleretic actions of norUDCA. Additionally, the findings support further investigation of the therapeutic synergy between norUDCA and ASBT inhibitors or bile acid sequestrants for cholestatic liver disease.
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Affiliation(s)
- Jennifer K. Truong
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Jianing Li
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Qin Li
- Department of Pediatrics, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kimberly Pachura
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Anuradha Rao
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Sanjeev Gumber
- Division of Pathology and Laboratory Medicine, Yerkes National Research Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Claudia Daniela Fuchs
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andrew P. Feranchak
- Department of Pediatrics, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Saul J. Karpen
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Paul A. Dawson
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
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24
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Bongers BJ, Sijben HJ, Hartog PBR, Tarnovskiy A, IJzerman AP, Heitman LH, van Westen GJP. Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. J Chem Inf Model 2023; 63:1745-1755. [PMID: 36926886 PMCID: PMC10052348 DOI: 10.1021/acs.jcim.2c01645] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Solute carriers (SLCs) are relatively underexplored compared to other prominent protein families such as kinases and G protein-coupled receptors. However, proteins from the SLC family play an essential role in various diseases. One such SLC is the high-affinity norepinephrine transporter (NET/SLC6A2). In contrast to most other SLCs, the NET has been relatively well studied. However, the chemical space of known ligands has a low chemical diversity, making it challenging to identify chemically novel ligands. Here, a computational screening pipeline was developed to find new NET inhibitors. The approach increases the chemical space to model for NETs using the chemical space of related proteins that were selected utilizing similarity networks. Prior proteochemometric models added data from related proteins, but here we use a data-driven approach to select the optimal proteins to add to the modeled data set. After optimizing the data set, the proteochemometric model was optimized using stepwise feature selection. The final model was created using a two-step approach combining several proteochemometric machine learning models through stacking. This model was applied to the extensive virtual compound database of Enamine, from which the top predicted 22,000 of the 600 million virtual compounds were clustered to end up with 46 chemically diverse candidates. A subselection of 32 candidates was synthesized and subsequently tested using an impedance-based assay. There were five hit compounds identified (hit rate 16%) with sub-micromolar inhibitory potencies toward NET, which are promising for follow-up experimental research. This study demonstrates a data-driven approach to diversify known chemical space to identify novel ligands and is to our knowledge the first to select this set based on the sequence similarity of related targets.
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Affiliation(s)
- Brandon J Bongers
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Huub J Sijben
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Peter B R Hartog
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | | | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands.,Oncode Institute, Jaarbeursplein 6, Utrecht 3521 AL, The Netherlands
| | - Gerard J P van Westen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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25
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Yan C, Hu X, Liu X, Zhao J, Le Z, Feng J, Zhou M, Ma X, Zheng Q, Sun J. Upregulation of SLC12A3 and SLC12A9 Mediated by the HCP5/miR-140-5p Axis Confers Aggressiveness and Unfavorable Prognosis in Uveal Melanoma. J Transl Med 2023; 103:100022. [PMID: 36925204 DOI: 10.1016/j.labinv.2022.100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/09/2022] [Accepted: 10/21/2022] [Indexed: 01/11/2023] Open
Abstract
Perturbation of solute carriers (SLCs) has been implicated in metabolic disorders and cancer, highlighting the potential for drug discovery and therapeutic opportunities. However, there is relatively little exploration of the clinical relevance and potential molecular mechanisms underlying the role of the SLC12 family in uveal melanoma (UVM). Here, we performed an integrative multiomics analysis of the SLC12 family in multicenter UVM datasets and found that high expression of SLC12A3 and SLC12A9 was associated with unfavorable prognosis. Moreover, SLC12A3 and SLC12A9 were highly expressed in UVM in vivo. We experimentally characterized the roles of these proteins in tumorigenesis in vitro and explored their association with the prognosis of UVM. Lastly, we identified the HCP5-miR-140-5p axis as a potential noncoding RNA pathway upstream of SLC12A3 and SLC12A9, which was associated with immunomodulation and may represent a novel predictor for clinical prognosis and responsiveness to checkpoint blockade immunotherapy. These findings may facilitate a better understanding of the SLCome and guide future rationalized development of SLC-targeted therapy and drug discovery for UVM.
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Affiliation(s)
- Congcong Yan
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xiaojuan Hu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Liu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jingting Zhao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Zhenmin Le
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jiayao Feng
- The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, Ningbo, China
| | - Meng Zhou
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China; Institute of PSI Genomics, Wenzhou, China
| | - Xiaoyin Ma
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China.
| | - Qingxiang Zheng
- The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, Ningbo, China.
| | - Jie Sun
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China.
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26
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Nwosu ZC, Song MG, di Magliano MP, Lyssiotis CA, Kim SE. Nutrient transporters: connecting cancer metabolism to therapeutic opportunities. Oncogene 2023; 42:711-724. [PMID: 36739364 PMCID: PMC10266237 DOI: 10.1038/s41388-023-02593-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/08/2023] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Cancer cells rely on certain extracellular nutrients to sustain their metabolism and growth. Solute carrier (SLC) transporters enable cells to acquire extracellular nutrients or shuttle intracellular nutrients across organelles. However, the function of many SLC transporters in cancer is unknown. Determining the key SLC transporters promoting cancer growth could reveal important therapeutic opportunities. Here we summarize recent findings and knowledge gaps on SLC transporters in cancer. We highlight existing inhibitors for studying these transporters, clinical trials on treating cancer by blocking transporters, and compensatory transporters used by cancer cells to evade treatment. We propose targeting transporters simultaneously or in combination with targeted therapy or immunotherapy as alternative strategies for effective cancer therapy.
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Affiliation(s)
- Zeribe Chike Nwosu
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Mun Gu Song
- Department of Biosystems and Biomedical Sciences, College of Health Sciences, Korea University, Seoul, 02841, Republic of Korea
- Department of Integrated Biomedical and Life Sciences, College of Health Sciences, Korea University, Seoul, 02841, Republic of Korea
| | | | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Sung Eun Kim
- Department of Biosystems and Biomedical Sciences, College of Health Sciences, Korea University, Seoul, 02841, Republic of Korea.
- Department of Integrated Biomedical and Life Sciences, College of Health Sciences, Korea University, Seoul, 02841, Republic of Korea.
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27
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Prognostic 7-SLC-Gene Signature Identified via Weighted Gene Co-Expression Network Analysis for Patients with Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2023; 2023:4364654. [PMID: 36844876 PMCID: PMC9957622 DOI: 10.1155/2023/4364654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 11/24/2022] [Indexed: 02/19/2023]
Abstract
Background Solute carrier (SLC) proteins play an important role in tumor metabolism. But SLC-associated genes' prognostic significance in hepatocellular carcinoma (HCC) remained elusive. We identified SLC-related factors and developed an SLC-related classifier to predict and improve HCC prognosis and treatment. Methods From the TCGA database, corresponding clinical data and mRNA expression profiles of 371 HCC patients were acquired, and those of 231 tumor samples were derived from the ICGC database. Genes associated with clinical features were filtered using weighted gene correlation network analysis (WGCNA). Next, univariate LASSO Cox regression studies developed SLC risk profiles, with the ICGC cohort data being used in validation. Result Univariate Cox regression analysis revealed that 31 SLC genes (P < 0.05) were related to HCC prognosis. 7 (SLC22A25, SLC2A2, SLC41A3, SLC44A1, SLC48A1, SLC4A2, and SLC9A3R1) of these genes were applied in developing a SLC gene prognosis model. Samples were classified into the low-andhigh-risk groups by the prognostic signature, with those in the high-risk group showing a significantly worse prognosis (P < 0.001 in the TCGA cohort and P=0.0068 in the ICGC cohort). ROC analysis validated the signature's prediction power. In addition, functional analyses showed enrichment of immune-related pathways and different immune status between the two risk groups. Conclusion The 7-SLC-gene prognostic signature established in this study helped predict the prognosis, and was also correlated with the tumor immune status and infiltration of different immune cells in the tumor microenvironment. The current findings may provide important clinical indications for proposing a novel combination therapy consists of targeted anti-SLC therapy and immunotherapy for HCC patients.
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28
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LIU CHIENLIANG, CHENG SHIHPING, HUANG WENCHIEN, CHEN MINGJEN, LIN CHIHSIN, CHEN SHANNA, CHANG YUANCHING. Aberrant Expression of Solute Carrier Family 35 Member A2 Correlates With Tumor Progression in Breast Cancer. In Vivo 2023; 37:262-269. [PMID: 36593004 PMCID: PMC9843756 DOI: 10.21873/invivo.13076] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND/AIM A recent study suggested that solute carrier family 35 member A2 (SLC35A2) is related to poor prognosis in patients with breast cancer. SLC35A2 transports uridine diphosphate-galactose from the cytosol to the lumen of the endoplasmic reticulum and Golgi. MATERIALS AND METHODS Immunohistochemical expression of SLC35A2 was evaluated using tissue microarrays. Cell growth, migration, and invasion of breast cancer cells were examined following loss- and gain-of-expression of SLC35A2. RESULTS Normal breast tissue exhibited SLC35A2 immunoreactivity in the nucleus. A progressive increase in cytoplasmic expression from in situ carcinoma to invasive carcinoma was observed. There was a correlation between cytoplasmic SLC35A2 expression and breast cancer stage (p<0.001). MDA-MB-468 and MCF-7 cells transfected with SLC35A2 shRNA had unchanged cell viability but significantly reduced cell migration and invasion. In contrast, MDA-MB-231 and HCC1806 cells transfected with the SLC35A2 expression vector showed increased migration. CONCLUSION Breast cancer progression is accompanied by differential expression patterns of SLC35A2. The migratory or invasive capacity of breast cancer cells is associated with SLC35A2 expression.
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Affiliation(s)
- CHIEN-LIANG LIU
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan, R.O.C
| | - SHIH-PING CHENG
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan, R.O.C.,Institute of Biomedical Sciences, Mackay Medical College, New Taipei, Taiwan, R.O.C
| | - WEN-CHIEN HUANG
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan, R.O.C
| | - MING-JEN CHEN
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan, R.O.C.,Institute of Biomedical Sciences, Mackay Medical College, New Taipei, Taiwan, R.O.C
| | - CHI-HSIN LIN
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan, R.O.C.,Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan, Taiwan, R.O.C
| | - SHAN-NA CHEN
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan, R.O.C
| | - YUAN-CHING CHANG
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan, R.O.C
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29
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Liu X, Liu Y, Qiang L, Ren Y, Lin Y, Li H, Chen Q, Gao S, Yang X, Zhang C, Fan M, Zheng P, Li S, Wang J. Multifunctional 3D-printed bioceramic scaffolds: Recent strategies for osteosarcoma treatment. J Tissue Eng 2023; 14:20417314231170371. [PMID: 37205149 PMCID: PMC10186582 DOI: 10.1177/20417314231170371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/31/2023] [Indexed: 05/21/2023] Open
Abstract
Osteosarcoma is the most prevalent bone malignant tumor in children and teenagers. The bone defect, recurrence, and metastasis after surgery severely affect the life quality of patients. Clinically, bone grafts are implanted. Primary bioceramic scaffolds show a monomodal osteogenesis function. With the advances in three-dimensional printing technology and materials science, while maintaining the osteogenesis ability, scaffolds become more patient-specific and obtain additional anti-tumor ability with functional agents being loaded. Anti-tumor therapies include photothermal, magnetothermal, old and novel chemo-, gas, and photodynamic therapy. These strategies kill tumors through novel mechanisms to treat refractory osteosarcoma due to drug resistance, and some have shown the potential to reverse drug resistance and inhibit metastasis. Therefore, multifunctional three-dimensional printed bioceramic scaffolds hold excellent promise for osteosarcoma treatments. To better understand, we review the background of osteosarcoma, primary 3D-printed bioceramic scaffolds, and different therapies and have a prospect for the future.
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Affiliation(s)
- Xingran Liu
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Yihao Liu
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Lei Qiang
- Southwest Jiaotong University, Chengdu,
China
| | - Ya Ren
- Southwest Jiaotong University, Chengdu,
China
| | - Yixuan Lin
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Li
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Qiuhan Chen
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Shuxin Gao
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Xue Yang
- Southwest Jiaotong University, Chengdu,
China
| | - Changru Zhang
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
| | - Minjie Fan
- Department of Orthopaedic Surgery,
Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Zheng
- Department of Orthopaedic Surgery,
Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Shuai Li
- Department of Orthopedics, The First
Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinwu Wang
- Shanghai Key Laboratory of Orthopedic
Implant, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of
Medicine, Shanghai, China
- Southwest Jiaotong University, Chengdu,
China
- Shanghai Jiao Tong University,
Shanghai, China
- Weifang Medical University School of
Rehabilitation Medicine, Weifang, Shandong Province, China
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Zhang W, Lyu P, Andreev D, Jia Y, Zhang F, Bozec A. Hypoxia-immune-related microenvironment prognostic signature for osteosarcoma. Front Cell Dev Biol 2022; 10:974851. [PMID: 36578780 PMCID: PMC9791087 DOI: 10.3389/fcell.2022.974851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Increasing evidences have shown that hypoxia and the immune microenvironment play vital roles in the development of osteosarcoma. However, reliable gene signatures based on the combination of hypoxia and the immune status for prognostic prediction of osteosarcoma have so far not been identified. Methods: The individual hypoxia and immune status of osteosarcoma patients were identified with transcriptomic profiles of a training cohort from the TARGET database using ssGSEA and ESTIMATE algorithms, respectively. Lasso regression and stepwise Cox regression were performed to develop a hypoxia-immune-based gene signature. An independent cohort from the GEO database was used for external validation. Finally, a nomogram was constructed based on the gene signature and clinical features to improve the risk stratification and to quantify the risk assessment for individual patients. Results: Hypoxia and the immune status were significantly associated with the prognosis of osteosarcoma patients. Seven hypoxia- and immune-related genes (BNIP3, SLC38A5, SLC5A3, CKMT2, S100A3, CXCL11 and PGM1) were identified to be involved in our prognostic signature. In the training cohort, the prognostic signature discriminated high-risk patients with osteosarcoma. The hypoxia-immune-based gene signature proved to be a stable and predictive method as determined in different datasets and subgroups of patients. Furthermore, a nomogram based on the prognostic signature was generated to optimize the risk stratification and to quantify the risk assessment. Similar results were validated in an independent GEO cohort, confirming the stability and reliability of the prognostic signature. Conclusion: The hypoxia-immune-based prognostic signature might contribute to the optimization of risk stratification for survival and personalized management of osteosarcoma patients.
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Guo Y, Zhao W, Li N, Dai S, Wu H, Wu Z, Zeng S. Integration analysis of metabolome and transcriptome reveals the effect of exogenous supplementation with mixtures of vitamins ADE, zinc, and selenium on follicular growth and granulosa cells molecular metabolism in donkeys (Equus asinus). Front Vet Sci 2022; 9:993426. [DOI: 10.3389/fvets.2022.993426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Vitamins and microelements play essential roles in mammalian ovarian physiology, including follicle development, ovulation, and synthesis and secretion of hormones and growth factors. However, it is nevertheless elusive to what extent exogenous supplementation with mixtures of vitamins ADE, zinc (Zn), and selenium (Se) affects follicular growth and granulosa cells (GCs) molecular function. We herein investigated their effect on follicular growth and GCs physiological function. We showed that follicular growth and ovulation time was accelerated and shortened with the increases of vitamins ADE, Zn, and Se doses by continually monitoring and recording (one estrus cycle of about 21 days) with an ultrasound scanner. Integrated omics analysis showed that there was a sophisticated network relationship, correlation expression, and enrichment pathways of the genes and metabolites highly related to organic acids and their derivatives and lipid-like molecules. Quantitative real-time PCR (qPCR) results showed that vitamin D receptor (VDR), transient receptor potential cation channel subfamily m member 6 (TRPM6), transient receptor potential cation channel subfamily v member 6 (TRPV6), solute carrier family 5 member 1 (SLC5A1), arachidonate 5-lipoxygenase (ALOX5), steroidogenic acute regulatory protein (STAR), prostaglandin-endoperoxide synthase 2 (PTGS2), and insulin like growth factor 1 (IGF-1) had a strong correlation between the transcriptome data. Combined multi-omics analysis revealed that the protein digestion and absorption, ABC transporters, biosynthesis of amino acids, aminoacyl-tRNA biosynthesis, mineral absorption, alanine, aspartate and glutamate metabolism, glycine, serine and threonine metabolism, arginine biosynthesis, and ovarian steroidogenesis were significantly enriched. We focused on the gene-metabolite interactions in ovarian steroidogenesis, founding that insulin receptor (INSR), phospholipase a2 group IVA (PLA2G4A), adenylate cyclase 6 (ADCY6), cytochrome p450 family 1 subfamily b member 1 (CYP1B1), protein kinase camp-activated catalytic subunit beta (PRKACB), cytochrome p450 family 17 subfamily a member 1 (CYP17A1), and phospholipase a2 group IVF (PLA2G4F) were negatively correlated with β-estradiol (E2), progesterone (P4), and testosterone (T) (P < 0.05). while ALOX5 was a positive correlation with E2, P4, and T (P < 0.05); cytochrome p450 family 19 subfamily a member 1 (CYP19A1) was a negative correlation with cholesterol (P < 0.01). In mineral absorption, our findings further demonstrated that there was a positive correlation between solute carrier family 26 member 6 (SLC26A6), SLC5A1, and solute carrier family 6 member 19 (SLC6A19) with Glycine and L-methionine. Solute carrier family 40 member 1 (SLC40A1) was a negative correlation with Glycine and L-methionine (P < 0.01). TRPV6 and ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1) were positively associated with Glycine (P < 0.05); while ATPase Na+/K+ transporting subunit beta 3 (ATP1B3) and cytochrome b reductase 1 (CYBRD1) were negatively related to L-methionine (P < 0.05). These outcomes suggested that the vitamins ADE, Zn, and Se of mixtures play an important role in the synthesis and secretion of steroid hormones and mineral absorption metabolism pathway through effects on the expression of the key genes and metabolites in GCs. Meanwhile, these also are required for physiological function and metabolism of GCs. Collectively, our outcomes shed new light on the underlying mechanisms of their effect on follicular growth and GCs molecular physiological function, helping explore valuable biomarkers.
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Nies AT, Schaeffeler E, Schwab M. Hepatic solute carrier transporters and drug therapy: Regulation of expression and impact of genetic variation. Pharmacol Ther 2022; 238:108268. [DOI: 10.1016/j.pharmthera.2022.108268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/25/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022]
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Cordova RA, Misra J, Amin PH, Klunk AJ, Damayanti NP, Carlson KR, Elmendorf AJ, Kim HG, Mirek ET, Elzey BD, Miller MJ, Dong XC, Cheng L, Anthony TG, Pili R, Wek RC, Staschke KA. GCN2 eIF2 kinase promotes prostate cancer by maintaining amino acid homeostasis. eLife 2022; 11:e81083. [PMID: 36107759 PMCID: PMC9578714 DOI: 10.7554/elife.81083] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/14/2022] [Indexed: 12/15/2022] Open
Abstract
A stress adaptation pathway termed the integrated stress response has been suggested to be active in many cancers including prostate cancer (PCa). Here, we demonstrate that the eIF2 kinase GCN2 is required for sustained growth in androgen-sensitive and castration-resistant models of PCa both in vitro and in vivo, and is active in PCa patient samples. Using RNA-seq transcriptome analysis and a CRISPR-based phenotypic screen, GCN2 was shown to regulate expression of over 60 solute-carrier (SLC) genes, including those involved in amino acid transport and loss of GCN2 function reduces amino acid import and levels. Addition of essential amino acids or expression of 4F2 (SLC3A2) partially restored growth following loss of GCN2, suggesting that GCN2 targeting of SLC transporters is required for amino acid homeostasis needed to sustain tumor growth. A small molecule inhibitor of GCN2 showed robust in vivo efficacy in androgen-sensitive and castration-resistant mouse models of PCa, supporting its therapeutic potential for the treatment of PCa.
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Affiliation(s)
- Ricardo A Cordova
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
- Indiana University Melvin and Bren Simon Comprehensive Cancer CenterIndianapolisUnited States
| | - Jagannath Misra
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
| | - Parth H Amin
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
| | - Anglea J Klunk
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
| | - Nur P Damayanti
- Indiana University Melvin and Bren Simon Comprehensive Cancer CenterIndianapolisUnited States
- Department of Neurological Surgery, Indiana University School of MedicineIndianapolisUnited States
| | - Kenneth R Carlson
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
| | - Andrew J Elmendorf
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
| | - Hyeong-Geug Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
| | - Emily T Mirek
- Department of Nutritional Sciences, Rutgers UniversityNew BrunswickUnited States
| | - Bennet D Elzey
- Department of Comparative Pathology, Purdue UniversityWest LafayetteUnited States
- Department of Urology, Indiana University School of MedicineIndianapolisUnited States
| | - Marcus J Miller
- Department of Medical and Molecular Genetics, Indiana University School of MedicineIndianapolisUnited States
| | - X Charlie Dong
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
| | - Liang Cheng
- Indiana University Melvin and Bren Simon Comprehensive Cancer CenterIndianapolisUnited States
- Department of Urology, Indiana University School of MedicineIndianapolisUnited States
- Department of Pathology and Laboratory Medicine, Indiana University School of MedicineIndianapolisUnited States
| | - Tracy G Anthony
- Department of Nutritional Sciences, Rutgers UniversityNew BrunswickUnited States
| | - Roberto Pili
- Jacobs School of Medicine and Biomedical Sciences, University at BuffaloBuffaloUnited States
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
- Indiana University Melvin and Bren Simon Comprehensive Cancer CenterIndianapolisUnited States
| | - Kirk A Staschke
- Department of Biochemistry and Molecular Biology, Indiana University School of MedicineIndianapolisUnited States
- Indiana University Melvin and Bren Simon Comprehensive Cancer CenterIndianapolisUnited States
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Wright NJ, Fedor JG, Zhang H, Jeong P, Suo Y, Yoo J, Hong J, Im W, Lee SY. Methotrexate recognition by the human reduced folate carrier SLC19A1. Nature 2022; 609:1056-1062. [PMID: 36071163 DOI: 10.1038/s41586-022-05168-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/01/2022] [Indexed: 02/01/2023]
Abstract
Folates are essential nutrients with important roles as cofactors in one-carbon transfer reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of amino acids during cell division1,2. Mammals lack de novo folate synthesis pathways and thus rely on folate uptake from the extracellular milieu3. The human reduced folate carrier (hRFC, also known as SLC19A1) is the major importer of folates into the cell1,3, as well as chemotherapeutic agents such as methotrexate4-6. As an anion exchanger, RFC couples the import of folates and antifolates to anion export across the cell membrane and it is a major determinant in methotrexate (antifolate) sensitivity, as genetic variants and its depletion result in drug resistance4-8. Despite its importance, the molecular basis of substrate specificity by hRFC remains unclear. Here we present cryo-electron microscopy structures of hRFC in the apo state and captured in complex with methotrexate. Combined with molecular dynamics simulations and functional experiments, our study uncovers key determinants of hRFC transport selectivity among folates and antifolate drugs while shedding light on important features of anion recognition by hRFC.
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Affiliation(s)
- Nicholas J Wright
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Justin G Fedor
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Han Zhang
- Departments of Biological Sciences, Chemistry and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | | | - Yang Suo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Jiho Yoo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.,College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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Identification and validation of a novel prognostic model of inflammation-related gene signature of lung adenocarcinoma. Sci Rep 2022; 12:14729. [PMID: 36042374 PMCID: PMC9427773 DOI: 10.1038/s41598-022-19105-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Previous literatures have suggested the importance of inflammatory response during lung adenocarcinoma (LUAD) development. This study aimed at exploring the inflammation-related genes and developing a prognostic signature for predicting the prognosis of LUAD. Survival‑associated inflammation-related genes were identified by univariate Cox regression analysis in the dataset of The Cancer Genome Atlas (TCGA). The least absolute shrinkage and selection operator (LASSO) penalized Cox regression model was used to derive a risk signature which is significantly negatively correlated with OS and divide samples into high-, medium- and low-risk group. Univariate and multivariate Cox analyses suggested that the level of risk group was an independent prognostic factor of the overall survival (OS). Time-dependent receiver operating characteristic (ROC) curve indicated the AUC of 1-, 3- and 5-years of the risk signature was 0.715, 0.719, 0.699 respectively. A prognostic nomogram was constructed by integrating risk group and clinical features. The independent dataset GSE30219 of Gene Expression Omnibus (GEO) was used for verification. We further explored the differences among risk groups in Gene set enrichment analysis (GSEA), tumor mutation and tumor microenvironment. Furthermore, Single Sample Gene Set Enrichment Analysis (ssGSEA) and the results of Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) suggested the status of immune cell infiltration was highly associated with risk groups. We demonstrated the prediction effect of CTLA-4 and PD-1/PD-L1 inhibitors in the low-risk group was better than that in the high-risk group using two methods of immune score include immunophenoscore from The Cancer Immunome Atlas (TCIA) and TIDE score from Tumor Immune Dysfunction and Exclusion (TIDE). In addition, partial targeted drugs and chemotherapy drugs for lung cancer had higher drug sensitivity in the high-risk group. Our findings provide a foundation for future research targeting inflammation-related genes to predictive prognosis and some reference significance for the selection of immunotherapy and drug regimen for lung adenocarcinoma.
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Xu S, Hao Z, Li Y, Zhou Y, Shao R, Chen R, Zheng M, Xu Y, Wang H. Biochemical toxicity and transcriptome aberration induced by dinotefuran in Bombyx mori. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119562. [PMID: 35659910 DOI: 10.1016/j.envpol.2022.119562] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/20/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Dinotefuran is a third-generation neonicotinoid pesticide and is increasingly used in agricultural production, which has adverse effects on nontarget organisms. However, the research on the impact of dinotefuran on nontarget organisms is still limited. Here the toxic effects of dinotefuran on an important economic species and a model lepidopteran insect, Bombyx mori, were investigated. Exposure to different doses of dinotefuran caused physiological disorders or death. Cytochrome P450, glutathione S-transferase, carboxylesterase, and UDP glycosyl-transferase activities were induced in the fat body at early stages after dinotefuran exposure. By contrast, only glutathione S-transferase activity was increased in the midgut. To overcome the lack of sensitivity of the biological assays at the individual organism level, RNA sequencing was performed to measure differential expressions of mRNA from silkworm larvae after dinotefuran exposure. Differential gene expression profiling revealed that various detoxification enzyme genes were significantly increased after dinotefuran exposure, which was consistent with the upregulation of the detoxifying enzyme. The global transcriptional pattern showed that the physiological responses induced by dinotefuran toxicity involved multiple cellular processes, including energy metabolism, oxidative stress, detoxification, and other fundamental physiological processes. Many metabolism processes, such as carbon metabolism, fatty acid biosynthesis, pyruvate metabolism, and the citrate cycle, were partially repressed in the midgut or fat body. Furthermore, dinotefuran significantly activated the MAPK/CREB, CncC/Keap1, PI3K/Akt, and Toll/IMD pathways. The links between physiological, biochemical toxicity and comparative transcriptomic analysis facilitated the systematic understanding of the integrated biological toxicity of dinotefuran. This study provides a holistic view of the toxicity and detoxification metabolism of dinotefuran in silkworm and other organisms.
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Affiliation(s)
- Shiliang Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhihua Hao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghui Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanyan Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ruixi Shao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meidan Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yusong Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huabing Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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Vinceti A, Perron U, Trastulla L, Iorio F. Reduced gene templates for supervised analysis of scale-limited CRISPR-Cas9 fitness screens. Cell Rep 2022; 40:111145. [PMID: 35905712 DOI: 10.1016/j.celrep.2022.111145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/26/2022] [Accepted: 07/07/2022] [Indexed: 12/21/2022] Open
Abstract
Pooled genome-wide CRISPR-Cas9 screens are furthering our mechanistic understanding of human biology and have allowed us to identify new oncology therapeutic targets. Scale-limited CRISPR-Cas9 screens-typically employing guide RNA libraries targeting subsets of functionally related genes, biological pathways, or portions of the druggable genome-constitute an optimal setting for investigating narrow hypotheses and are easier to execute on complex models, such as organoids and in vivo models. Different supervised methods are used for computational analysis of genome-wide CRISPR-Cas9 screens; most are not well suited for scale-limited screens, as they require large sets of positive/negative control genes (gene templates) to be included among the screened ones. Here, we develop a computational framework identifying optimal subsets of known essential and nonessential genes (at different subsampling percentages) that can be used as templates for supervised analyses of scale-limited CRISPR-Cas9 screens, while having a reduced impact on the size of the employed library.
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Affiliation(s)
- Alessandro Vinceti
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Umberto Perron
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Lucia Trastulla
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Francesco Iorio
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy; Cancer Dependency Map Analytics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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Dong S, Li S, Wang X, Liang S, Zhang W, Li L, Xu Q, Shi B, Cheng Z, Zhang X, Zhong M, Zhang G, Hu S. CD147 Mediates 5-Fluorouracil Resistance in Colorectal Cancer by Reprogramming Glycolipid Metabolism. Front Oncol 2022; 12:813852. [PMID: 35898887 PMCID: PMC9309564 DOI: 10.3389/fonc.2022.813852] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Chemoresistance against 5-fluorouracil (5-FU) is a major issue for colorectal cancer (CRC) patients. Increasing evidence for the roles of CD147 in glycolipid metabolic reprogramming and chemoresistance of tumor cells has emerged in recent years. However, whether CD147 contributes to 5-FU resistance in CRC and the role of abnormal glycolipid metabolism in this process remain poorly understood. We analyzed CD147 expression in primary tumor samples of CRC patients and found that upregulated CD147 correlated with decreased 5-FU chemosensitivity and an unfavorable prognosis of CRC patients. Moreover, in vivo and in vitro experiments confirmed that CD147 regulates glycolipid metabolism through two separate pathways. Mechanistically, CD147 upregulates HIF-1α-mediated glycolysis by activating the PI3K/AKT/mTOR pathway and CD147 also attenuates PPARα-mediated fatty acid oxidation by activation of the MAPK pathway. Most importantly, we found that CD147 confers 5-FU resistance in CRC via these glycolipid metabolic signatures. Our results demonstrated that CD147 is a potential 5-FU resistance biomarker for CRC patients and a candidate therapeutic target to restore 5-FU sensitivity of 5-FU-resistant CRC by remodeling glycolipid metabolism.
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Affiliation(s)
- Shuohui Dong
- Department of General Surgery, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Songhan Li
- Department of General Surgery, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoyan Wang
- Department of Neonatology, Weifang Yidu Central Hospital, Weifang, China
| | - Shuo Liang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial Ear-nose-throat (ENT) Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenjie Zhang
- Department of General Surgery, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Linchuan Li
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Qian Xu
- Department of General Surgery, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bowen Shi
- Department of General Surgery, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhiqiang Cheng
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiang Zhang
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Mingwei Zhong
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Guangyong Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Sanyuan Hu
- Department of General Surgery, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: SanYuan Hu,
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Wang S, Yang W, Shi W, Chen F, Shen F, Zhang M, Su Q, Shi C, Yu Q, Chen T. Investigations on the Changes of Serum Proteins in Rabbits after Trimeresurus stejnegeri Venom Injection via Mass Spectrometry-Based Proteomics. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:9239662. [PMID: 35783526 PMCID: PMC9249469 DOI: 10.1155/2022/9239662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Purpose There are few studies on protein phosphorylation in the process of snake poisoning. The purpose of this study was to investigate the toxic mechanism of Trimeresurus stejnegeri at the protein level by determining the differential expression of phosphorylated proteins in rabbits after poisoning using proteomics. Methods The Trimeresurus stejnegeri venom model in rabbits was established by intramuscular injection of 20 mg/kg venom. The serum was collected and the differential expression of phosphorylated proteins in the serum was determined by the iTRAQ technology, TiO2 enriched phosphorylated peptides, and the mass spectrometry analysis. The functional analysis was conducted using ClueGO software and the related mechanism was evaluated by the network analysis of biological interaction. The expression level of related proteins was determined by the Western blotting assay. Results Compared to the control group, 77 differentially expressed proteins were observed in the model group. These proteins were closely associated with the complement and agglomerate cascade signaling pathways, the HIF signaling pathway, the pentose phosphate pathway, and the cholesterol metabolism signaling pathway. According to the results of network analysis, TF and SCL16A1 were determined as the core proteins, which were identified by the Western blotting assay. Conclusion The present study provided valuable phosphorylation signal transduction resources for investigating the toxic mechanism and the therapies for Trimeresurus stejnegeri poisoning.
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Affiliation(s)
- Shijun Wang
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Weilian Yang
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Wanling Shi
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Fuwei Chen
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Fanghua Shen
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Meiji Zhang
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Qiuxiang Su
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Chao Shi
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Qinyao Yu
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
| | - Tao Chen
- Surgery of Traditional Chinese Medicine, People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine, Fuzhou 350004, Fujian, China
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Denecke S, Bảo Lương HN, Koidou V, Kalogeridi M, Socratous R, Howe S, Vogelsang K, Nauen R, Batterham P, Geibel S, Vontas J. Characterization of a novel pesticide transporter and P-glycoprotein orthologues in Drosophila melanogaster. Proc Biol Sci 2022; 289:20220625. [PMID: 35582794 PMCID: PMC9114944 DOI: 10.1098/rspb.2022.0625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Pesticides remain one of the most effective ways of controlling agricultural and public health insects, but much is still unknown regarding how these compounds reach their targets. Specifically, the role of ABC transporters in pesticide absorption and excretion is poorly understood, especially compared to the detailed knowledge about mammalian systems. Here, we present a comprehensive characterization of pesticide transporters in the model insect Drosophila melanogaster. An RNAi screen was performed, which knocked down individual ABCs in specific epithelial tissues and examined the subsequent changes in sensitivity to the pesticides spinosad and fipronil. This implicated a novel ABC drug transporter, CG4562, in spinosad transport, but also highlighted the P-glycoprotein orthologue Mdr65 as the most impactful ABC in terms of chemoprotection. Further characterization of the P-glycoprotein family was performed via transgenic overexpression and immunolocalization, finding that Mdr49 and Mdr50 play enigmatic roles in pesticide toxicology perhaps determined by their different subcellular localizations within the midgut. Lastly, transgenic Drosophila lines expressing P-glycoprotein from the major malaria vector Anopheles gambiae were used to establish a system for in vivo characterization of this transporter in non-model insects. This study provides the basis for establishing Drosophila as a model for toxicology research on drug transporters.
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Affiliation(s)
- Shane Denecke
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 100N. Plastira Street, 700 13 Heraklion Crete, Greece
| | - Hằng Ngọc Bảo Lương
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 100N. Plastira Street, 700 13 Heraklion Crete, Greece
| | - Venetia Koidou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 100N. Plastira Street, 700 13 Heraklion Crete, Greece,Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece
| | - Maria Kalogeridi
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece
| | - Rafaella Socratous
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Greece
| | - Steven Howe
- School of BioSciences, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kathrin Vogelsang
- Bayer AG, CropScience Division, R&D Pest Control, D-40789 Monheim, Germany
| | - Ralf Nauen
- Bayer AG, CropScience Division, R&D Pest Control, D-40789 Monheim, Germany
| | - Philip Batterham
- School of BioSciences, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sven Geibel
- Bayer AG, CropScience Division, R&D Pest Control, D-40789 Monheim, Germany
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 100N. Plastira Street, 700 13 Heraklion Crete, Greece,Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Greece
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Giacomini KM, Yee SW, Koleske ML, Zou L, Matsson P, Chen EC, Kroetz DL, Miller MA, Gozalpour E, Chu X. New and Emerging Research on Solute Carrier and ATP Binding Cassette Transporters in Drug Discovery and Development: Outlook from the International Transporter Consortium. Clin Pharmacol Ther 2022; 112:540-561. [PMID: 35488474 PMCID: PMC9398938 DOI: 10.1002/cpt.2627] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023]
Abstract
Enabled by a plethora of new technologies, research in membrane transporters has exploded in the past decade. The goal of this state‐of‐the‐art article is to describe recent advances in research on membrane transporters that are particularly relevant to drug discovery and development. This review covers advances in basic, translational, and clinical research that has led to an increased understanding of membrane transporters at all levels. At the basic level, we describe the available crystal structures of membrane transporters in both the solute carrier (SLC) and ATP binding cassette superfamilies, which has been enabled by the development of cryogenic electron microscopy methods. Next, we describe new research on lysosomal and mitochondrial transporters as well as recently deorphaned transporters in the SLC superfamily. The translational section includes a summary of proteomic research, which has led to a quantitative understanding of transporter levels in various cell types and tissues and new methods to modulate transporter function, such as allosteric modulators and targeted protein degraders of transporters. The section ends with a review of the effect of the gut microbiome on modulation of transporter function followed by a presentation of 3D cell cultures, which may enable in vivo predictions of transporter function. In the clinical section, we describe new genomic and pharmacogenomic research, highlighting important polymorphisms in transporters that are clinically relevant to many drugs. Finally, we describe new clinical tools, which are becoming increasingly available to enable precision medicine, with the application of tissue‐derived small extracellular vesicles and real‐world biomarkers.
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Affiliation(s)
- Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sook W Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Ling Zou
- Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California, USA
| | - Pär Matsson
- Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Eugene C Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California, USA
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elnaz Gozalpour
- Drug Safety and Metabolism, IMED Biotech Unit, Safety and ADME Translational Sciences Department, AstraZeneca R&D, Cambridge, UK
| | - Xiaoyan Chu
- Department of ADME and Discovery Toxicology, Merck & Co. Inc, Kenilworth, New Jersey, USA
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42
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A Chemogenomic Toolkit to Evaluate the "Ins and Outs" of Yeast Plasma Membrane Transporters. mBio 2022; 13:e0095522. [PMID: 35467415 PMCID: PMC9239070 DOI: 10.1128/mbio.00955-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Over the years, there has been a lot of emphasis on the development of high-throughput platforms that help identify transporters of drugs and xenobiotics. However, major hinderances in these approaches include substrate promiscuity and functional redundancy of membrane transporters. To tackle such issues, Almeida and colleagues (L. D. Almeida, A. S. F. Silva, D. C. Mota, A. A. Vasconcelos, et al., mBio 12(6):e03221-21, 2021) elegantly used the power of yeast genetics and created a double gene deletion library for 122 nonessential plasma membrane transporters that facilitates high-throughput identification of drug/xenobiotic transporters. While examining a library of cytotoxic compounds, the authors identified a strong correlation between the chemical structure of azoles and possible import/export routes. Interestingly, the authors also identified the myo-inositol transporter Itr1 to be responsible for import of triazole and imidazole antifungal compounds and proposed a role for the ABC transporter Pdr5 in carbendazim uptake.
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43
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Tyner JW, Haderk F, Kumaraswamy A, Baughn LB, Van Ness B, Liu S, Marathe H, Alumkal JJ, Bivona TG, Chan KS, Druker BJ, Hutson AD, Nelson PS, Sawyers CL, Willey CD. Understanding Drug Sensitivity and Tackling Resistance in Cancer. Cancer Res 2022; 82:1448-1460. [PMID: 35195258 PMCID: PMC9018544 DOI: 10.1158/0008-5472.can-21-3695] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/21/2022] [Accepted: 02/15/2022] [Indexed: 11/16/2022]
Abstract
Decades of research into the molecular mechanisms of cancer and the development of novel therapeutics have yielded a number of remarkable successes. However, our ability to broadly assign effective, rationally targeted therapies in a personalized manner remains elusive for many patients, and drug resistance persists as a major problem. This is in part due to the well-documented heterogeneity of cancer, including the diversity of tumor cell lineages and cell states, the spectrum of somatic mutations, the complexity of microenvironments, and immune-suppressive features and immune repertoires, which collectively require numerous different therapeutic approaches. Here, we describe a framework to understand the types and biological causes of resistance, providing translational opportunities to tackle drug resistance by rational therapeutic strategies.
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Affiliation(s)
- Jeffrey W. Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | | | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Brian Van Ness
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Himangi Marathe
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Joshi J. Alumkal
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Trever G. Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | - Keith Syson Chan
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Alan D. Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Peter S. Nelson
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Charles L. Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, New York
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Christopher D. Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
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44
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Holbrook-Smith D, Durot S, Sauer U. High-throughput metabolomics predicts drug-target relationships for eukaryotic proteins. Mol Syst Biol 2022; 18:e10767. [PMID: 35194925 PMCID: PMC8864444 DOI: 10.15252/msb.202110767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 01/22/2023] Open
Abstract
Chemical probes are important tools for understanding biological systems. However, because of the huge combinatorial space of targets and potential compounds, traditional chemical screens cannot be applied systematically to find probes for all possible druggable targets. Here, we demonstrate a novel concept for overcoming this challenge by leveraging high‐throughput metabolomics and overexpression to predict drug–target interactions. The metabolome profiles of yeast treated with 1,280 compounds from a chemical library were collected and compared with those of inducible yeast membrane protein overexpression strains. By matching metabolome profiles, we predicted which small molecules targeted which signaling systems and recovered known interactions. Drug–target predictions were generated across the 86 genes studied, including for difficult to study membrane proteins. A subset of those predictions were tested and validated, including the novel targeting of GPR1 signaling by ibuprofen. These results demonstrate the feasibility of predicting drug–target relationships for eukaryotic proteins using high‐throughput metabolomics.
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Affiliation(s)
| | - Stephan Durot
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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45
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Meng Y, Li Y, Fang D, Huang Y. Identification of solute carrier family genes related to the prognosis and tumor-infiltrating immune cells of pancreatic ductal adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:57. [PMID: 35282128 PMCID: PMC8848431 DOI: 10.21037/atm-21-6341] [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: 11/08/2021] [Accepted: 12/23/2021] [Indexed: 12/24/2022]
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) has persisted as one of the worst prognostic tumors with a 5-year survival rate of lower than 6%. Although many studies have investigated PDAC, new biomarkers are required to ensure early diagnosis and predict the prognosis of PDAC. Methods In this study, we used bioinformatics methods to evaluate differences in the expression of solute carrier (SLC) family genes in tumors and non-tumors. A Kaplan-Meier analysis, least absolute shrinkage and selection operator (LASSO) analysis, and multivariate Cox proportional hazards regression analysis were used to evaluate the relationship between SLC genes and prognosis using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. The prognostic signature was constructed depending on the risk score to assess the impact of multiple genes on the prognosis, receiver operating characteristic (ROC) curves and forest plot was constructed to assess the ability to predict the prognosis and effects of clinical variables in both high- and low-risk groups. Tumor-infiltrating immune cells were evaluated using Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) in both high- and low-risk groups. Results In 32 SLC genes, 9 were significantly associated with the OS after LASSO analysis. SLC19A3 (P=0.007), SLC25A39 (P=0.027), SLC39A11 (P=0.043) were significantly associated with prognosis and included into the prognostic model. CIBERSORT demonstrated that memory B cells (P=0.004), naive B cells (P=0.007), CD8 T cells (P=0.003), activated memory CD4 T cells (P=0.004), and activated NK cells (P=0.019) were significantly higher in the low-risk group. Gene set enrichment analysis (GSEA) showed that potential molecular mechanisms enriched in MYC and p53 signaling pathways. Conclusions SLC19A3, SLC25A35, and SLC39A11 were significantly relative to the prognosis of PDAC and changed the tumor microenvironment, as well as the MYC and p53 signaling pathways. The SLC19A3 gene may represent a new tumor suppressor in PDAC.
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Affiliation(s)
- Yuhua Meng
- Department of Glandular Surgery, the People's Hospital of Baise, Baise, China
| | - Yanting Li
- Department of Glandular Surgery, the People's Hospital of Baise, Baise, China
| | - Dalang Fang
- Department of Breast and Thyroid Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yuanlu Huang
- Department of Glandular Surgery, the People's Hospital of Baise, Baise, China
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46
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Yeast Double Transporter Gene Deletion Library for Identification of Xenobiotic Carriers in Low or High Throughput. mBio 2021; 12:e0322121. [PMID: 34903049 PMCID: PMC8669479 DOI: 10.1128/mbio.03221-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The routes of uptake and efflux should be considered when developing new drugs so that they can effectively address their intracellular targets. As a general rule, drugs appear to enter cells via protein carriers that normally carry nutrients or metabolites. A previously developed pipeline that searched for drug transporters using Saccharomyces cerevisiae mutants carrying single-gene deletions identified import routes for most compounds tested. However, due to the redundancy of transporter functions, we propose that this methodology can be improved by utilizing double mutant strains in both low- and high-throughput screens. We constructed a library of over 14,000 strains harboring double deletions of genes encoding 122 nonessential plasma membrane transporters and performed low- and high-throughput screens identifying possible drug import routes for 23 compounds. In addition, the high-throughput assay enabled the identification of putative efflux routes for 21 compounds. Focusing on azole antifungals, we were able to identify the involvement of the myo-inositol transporter, Itr1p, in the uptake of these molecules and to confirm the role of Pdr5p in their export.
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47
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Pennemann FL, Mussabekova A, Urban C, Stukalov A, Andersen LL, Grass V, Lavacca TM, Holze C, Oubraham L, Benamrouche Y, Girardi E, Boulos RE, Hartmann R, Superti-Furga G, Habjan M, Imler JL, Meignin C, Pichlmair A. Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. Nat Commun 2021; 12:7009. [PMID: 34853303 PMCID: PMC8636641 DOI: 10.1038/s41467-021-27192-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, -2 and -3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.
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Affiliation(s)
- Friederike L Pennemann
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Assel Mussabekova
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Christian Urban
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Alexey Stukalov
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Line Lykke Andersen
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Vincent Grass
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Teresa Maria Lavacca
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Cathleen Holze
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Lila Oubraham
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Yasmine Benamrouche
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Enrico Girardi
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Rasha E Boulos
- Computer Science and Mathematics Department, School of Arts and Science, Lebanese American University, Byblos, Lebanon
| | - Rune Hartmann
- Aarhus University, Department of Molecular Biology and Genetics - Structural Biology, Aarhus, Denmark
| | - Giulio Superti-Furga
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Carine Meignin
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany.
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany.
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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Ta HDK, Minh Xuan DT, Tang WC, Anuraga G, Ni YC, Pan SR, Wu YF, Fitriani F, Putri Hermanto EM, Athoillah M, Andriani V, Ajiningrum PS, Wang CY, Lee KH. Novel Insights into the Prognosis and Immunological Value of the SLC35A (Solute Carrier 35A) Family Genes in Human Breast Cancer. Biomedicines 2021; 9:1804. [PMID: 34944621 PMCID: PMC8698499 DOI: 10.3390/biomedicines9121804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
According to statistics 2020, female breast cancer (BRCA) became the most commonly diagnosed malignancy worldwide. Prognosis of BRCA patients is still poor, especially in population with advanced or metastatic. Particular functions of each members of the solute carrier 35A (SLC35A) gene family in human BRCA are still unknown regardless of awareness that they play critical roles in tumorigenesis and progression. Using integrated bioinformatics analyses to identify therapeutic targets for specific cancers based on transcriptomics, proteomics, and high-throughput sequencing, we obtained new information and a better understanding of potential underlying molecular mechanisms. Leveraging BRCA dataset that belongs to The Cancer Genome Atlas (TCGA), which were employed to clarify SLC35A gene expression levels. Then we used a bioinformatics approach to investigate biological processes connected to SLC35A family genes in BRCA development. Beside that, the Kaplan-Meier estimator was leveraged to explore predictive values of SLC35A family genes in BCRA patients. Among individuals of this family gene, expression levels of SLC35A2 were substantially related to poor prognostic values, result from a hazard ratio of 1.3 (with 95 percent confidence interval (95% CI: 1.18-1.44), the p for trend (ptrend) is 3.1 × 10-7). Furthermore, a functional enrichment analysis showed that SLC35A2 was correlated with hypoxia-inducible factor 1A (HIF1A), heat shock protein (HSP), E2 transcription factor (E2F), DNA damage, and cell cycle-related signaling. Infiltration levels observed in specific types of immune cell, especially the cluster of differentiation found on macrophages and neutrophils, were positively linked with SLC35A2 expression in multiple BRCA subclasses (luminal A, luminal B, basal, and human epidermal growth factor receptor 2). Collectively, SLC35A2 expression was associated with a lower recurrence-free survival rate, suggesting that it could be used as a biomarker in treating BRCA.
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Affiliation(s)
- Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Wan-Chun Tang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Yi-Chun Ni
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Syu-Ruei Pan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Yung-Fu Wu
- National Defense Medical Center, School of Medicine, Department of Medical Research, Tri-Service General Hospital, Taipei 11490, Taiwan;
| | - Fenny Fitriani
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Elvira Mustikawati Putri Hermanto
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Muhammad Athoillah
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Vivin Andriani
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (V.A.); (P.S.A.)
| | - Purity Sabila Ajiningrum
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (V.A.); (P.S.A.)
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Kuen-Haur Lee
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei 11031, Taiwan
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Qiu Y, Li H, Xie J, Qiao X, Wu J. Identification of ABCC5 Among ATP-Binding Cassette Transporter Family as a New Biomarker for Hepatocellular Carcinoma Based on Bioinformatics Analysis. Int J Gen Med 2021; 14:7235-7246. [PMID: 34737618 PMCID: PMC8560065 DOI: 10.2147/ijgm.s333904] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
Purpose Liver cancer is the fifth most common type of cancer worldwide, and the ATP-binding cassette (ABC) transporter family has been widely accepted as a cause of multidrug resistance. This study was conducted to explore the potential value and mechanisms of the ABC transporter gene family in the liver hepatocellular carcinoma (LIHC). Materials and Methods Data were collected from different public databases. UALCAN, ONCOMINE, and GEPIA were used to retrieve a selection of differently expressed and pathological stage-related genes among the ABC family. Principal component analysis (PCA) was utilized for grouping, and its prognostic value was evaluated by univariate and multivariate Cox analyses. The co-expression pattern was constructed with UALCAN, and the functional analyses were carried out with DAVID. The correlation between the biomarker and immune infiltration, genetic alteration frequency, and drug sensitivity were explored with TIMER, cBioPortal, GDSC and CTRP, respectively. Finally, tSNE algorithm was used to explore the distribution of ABCC5 expressed cells. Results Among the ABC transporter family members, ABCC5 was differently expressed and strongly related to the pathological stage of LIHC. PCA divided patients of LIHC into two groups, and Cox analyses demonstrated that ABCC5 was an independent risk factor of LIHC. Functional analyses indicated that the genes were enriched in the pathways of transmembrane transporter, ATPase activity, and bile secretion. ABCC5 is also associated with immune infiltration of cells like macrophages, neutrophils, and dendritic cells. The genetic alteration frequency of ABCC5 confirmed its potential value in LIHC. In addition, several drugs were explored and found to be relevant to LIHC. The t-SNE showed that expression of ABCC5 was most concentrated in macrophages, followed by hepatocytes. Conclusion ABCC5 may facilitate LIHC progression through different mechanisms and be a potential biomarker and target for diagnosis, prognosis, and therapy of LIHC.
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Affiliation(s)
- Yuting Qiu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Centre for Digestive Diseases, Beijing, 100050, People's Republic of China
| | - Haobo Li
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100029, People's Republic of China
| | - Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, People's Republic of China
| | - Xinwei Qiao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Centre for Digestive Diseases, Beijing, 100050, People's Republic of China
| | - Jing Wu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Centre for Digestive Diseases, Beijing, 100050, People's Republic of China
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Salcedo-Sora JE, Robison ATR, Zaengle-Barone J, Franz KJ, Kell DB. Membrane Transporters Involved in the Antimicrobial Activities of Pyrithione in Escherichia coli. Molecules 2021; 26:molecules26195826. [PMID: 34641370 PMCID: PMC8510280 DOI: 10.3390/molecules26195826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 02/06/2023] Open
Abstract
Pyrithione (2-mercaptopyridine-N-oxide) is a metal binding modified pyridine, the antibacterial activity of which was described over 60 years ago. The formulation of zinc-pyrithione is commonly used in the topical treatment of certain dermatological conditions. However, the characterisation of the cellular uptake of pyrithione has not been elucidated, although an unsubstantiated assumption has persisted that pyrithione and/or its metal complexes undergo a passive diffusion through cell membranes. Here, we have profiled specific membrane transporters from an unbiased interrogation of 532 E. coli strains of knockouts of genes encoding membrane proteins from the Keio collection. Two membrane transporters, FepC and MetQ, seemed involved in the uptake of pyrithione and its cognate metal complexes with copper, iron, and zinc. Additionally, the phenotypes displayed by CopA and ZntA knockouts suggested that these two metal effluxers drive the extrusion from the bacterial cell of potentially toxic levels of copper, and perhaps zinc, which hyperaccumulate as a function of pyrithione. The involvement of these distinct membrane transporters contributes to the understanding of the mechanisms of action of pyrithione specifically and highlights, more generally, the important role that membrane transporters play in facilitating the uptake of drugs, including metal-drug compounds.
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Affiliation(s)
- Jesus Enrique Salcedo-Sora
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
- Correspondence: (J.E.S.-S.); (K.J.F.); (D.B.K.)
| | - Amy T. R. Robison
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA; (A.T.R.R.); (J.Z.-B.)
| | - Jacqueline Zaengle-Barone
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA; (A.T.R.R.); (J.Z.-B.)
| | - Katherine J. Franz
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA; (A.T.R.R.); (J.Z.-B.)
- Correspondence: (J.E.S.-S.); (K.J.F.); (D.B.K.)
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Correspondence: (J.E.S.-S.); (K.J.F.); (D.B.K.)
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