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Kim S, Kim E, Park M, Kim SH, Kim BG, Na S, Sadongo VW, Wijesinghe WCB, Eom YG, Yoon G, Jeong H, Hwang E, Lee C, Myung K, Kim CU, Choi JM, Min SK, Kwon TH, Min D. Hidden route of protein damage through oxygen-confined photooxidation. Nat Commun 2024; 15:10873. [PMID: 39738007 DOI: 10.1038/s41467-024-55168-z] [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: 05/16/2024] [Accepted: 12/04/2024] [Indexed: 01/01/2025] Open
Abstract
Oxidative modifications can disrupt protein folds and functions, and are strongly associated with human aging and diseases. Conventional oxidation pathways typically involve the free diffusion of reactive oxygen species (ROS), which primarily attack the protein surface. Yet, it remains unclear whether and how internal protein folds capable of trapping oxygen (O2) contribute to oxidative damage. Here, we report a hidden pathway of protein damage, which we refer to as O2-confined photooxidation. In this process, O2 is captured in protein cavities and subsequently converted into multiple ROS, primarily mediated by tryptophan residues under blue light irradiation. The generated ROS then attack the protein interior through constrained diffusion, causing protein damage. The effects of this photooxidative reaction appear to be extensive, impacting a wide range of cellular proteins, as supported by whole-cell proteomic analysis. This photooxidative mechanism may represent a latent oxidation pathway in human tissues directly exposed to visible light, such as skin and eyes.
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Affiliation(s)
- Seoyoon Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Eojin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Mingyu Park
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Seong Ho Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Seungjin Na
- Digital Omics Research Center, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Victor W Sadongo
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan, 46241, Republic of Korea
| | - Gwangsu Yoon
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Hannah Jeong
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Eunhye Hwang
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Chaiheon Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan, 46241, Republic of Korea
- Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Seung Kyu Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
| | - Tae-Hyuk Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- X-Dynamic Research Center, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
- X-Dynamic Research Center, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
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Piki E, Dini A, Rantanen F, Bentz F, Paavolainen L, Barker H, Raivola J, Hirasawa A, Kallioniemi O, Murumägi A, Ungureanu D. Molecular and functional profiling of primary normal ovarian cells defines insights into cancer development and drug responses. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200903. [PMID: 39634630 PMCID: PMC11616607 DOI: 10.1016/j.omton.2024.200903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 10/11/2024] [Accepted: 11/01/2024] [Indexed: 12/07/2024]
Abstract
Patients with ovarian cancer, especially the high-grade serous ovarian cancer (HGSOC) subtype, face poor prognosis due to late diagnosis and treatment resistance. Owing to the high heterogeneity of HGSOC, identifying the origin of the disease and optimal treatments is difficult. Here, we characterized two primary immortalized human ovarian cell lines, human ovarian surface epithelium (HOSE)1C and HOSE2C, comparing their molecular profiling with representative HGSOC cells. We identified molecular features associated with normal and malignant phenotype of ovarian cells by applying single-cell transcriptomics, high-content image-based cell painting, and high-throughput drug testing. Our findings reveal distinct transcriptomic and morphological profiles for the two HOSEs, with a stromal phenotype. Moreover, their responses to the tumor microenvironment differ, exemplified by STAT1 and GREM1 upregulation in HOSE1C and HOSE2C, respectively. We identified selective activation of ERK/MEK targeted inhibitors in cancer cells compared to HOSEs. This study offers insights into the normal and malignant ovarian cells, shedding light on cancer development and drug responses.
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Affiliation(s)
- Emilia Piki
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Alice Dini
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Frida Rantanen
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Franziska Bentz
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Harlan Barker
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
- Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Juuli Raivola
- Applied Tumor Genomics, Research Program Unit, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
- Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Daniela Ungureanu
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
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Magaña-Ávila G, Carbajal-Contreras H, Amnekar R, Dite T, Téllez-Sutterlin M, García-Ávila K, Marquina-Castillo B, Lopez-Saavedra A, Vazquez N, Rojas-Ortega E, Delpire E, Ellison DH, Alessi DR, Gamba G, Castañeda-Bueno M. NRBP1 and TSC22D proteins impact distal convoluted tubule physiology through modulation of the WNK pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.12.628222. [PMID: 39764004 PMCID: PMC11702584 DOI: 10.1101/2024.12.12.628222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
Abstract
The With No lysine (WNK) kinases regulate processes such as cell volume and epithelial ion transport through the modulation of Cation Chloride Cotransporters such as the NaCl cotransporter, NCC, present in the distal convoluted tubule (DCT) of the kidney. Recently, the interaction of WNKs with Nuclear Receptor Binding Protein 1 (NRBP1) and Transforming Growth Factor β-Stimulated Clone 22 Domain (TSC22D) proteins was reported. Here we explored the effect of NRBP1 and TSC22Ds on WNK signaling in vitro and in the DCT. TSC22D1.1, TSC22D2, and NRBP1 are localized in DCT WNK bodies, which are cytoplasmic biomolecular condensates associated with WNK activation. In HEK293 cells, long TSC22D isoforms and NRBP1 increase WNK4 activity. DCT-specific NRBP1 knockout mice have reduced NCC phosphorylation and activate a compensatory response. Thus, NRBP1 and long TSC22D proteins are positive modulators of WNK signaling and modulate Na + reabsorption in the kidney. NRBP1 and TSC22Ds likely influence WNK signaling in other tissues, impacting various physiological processes. Teaser The pseudokinase NRBP1 and its associated TSC22D proteins modulate WNK kinases to regulate sodium reabsorption in the kidney.
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Yay F, Ayan D. Bioinformatic analysis of neuropeptide related genes in patients diagnosed with invasive breast carcinoma. Comput Biol Med 2024; 183:109304. [PMID: 39437604 DOI: 10.1016/j.compbiomed.2024.109304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/28/2024] [Accepted: 10/18/2024] [Indexed: 10/25/2024]
Abstract
PURPOSE Neuropeptide receptors are expressed in many malignancies. Effectors involved in the action mechanisms of HCRTR1, HCRTR2, NPY4R (PPYR1) may be related to breast cancer (BC). Genes encoding these receptors and PPY and PTPN11 genes were aimed to examine via bioinformatics tools in the BRCA cohort. To our knowledge, this is the first study in which these receptor genes and PP, which have not found much research in BC, are examined together with PTPN11 and analyzed comprehensively in large patient cohorts from public databases. METHODS cBioPortal was used for gene alteration analyses, GeneMania for association analyses with other genes, Kaplan-Meier Plotter for Overall Survival (OS) and Relapse Free Survival (RFS) analyses, UALCAN for methylation analyses, TIMER2.0 for expression analyses, The Human Protein Atlas database for expression validations, TIMER for immune infiltration analyses, WEKA 3.8.6 for diagnostic classification performances of the genes based on Random Forest Classifier and Enrichr-KG for Gene Ontology (GO) Biological Process (BP) and KEGG analysis. RESULTS 19 (1.9 %) nucleotide changes were found in 996 cases. Missense mutation is most common. Decreased expression levels of the HCRTR1 gene were associated with shorter OS and RFS, but decreased expression levels of the PTPN11 gene were associated with longer OS and RFS. Decreased expression levels NPY4R (PPYR1) gene were associated with shorter RFS. Increased expression levels of HCRTR2 and PPY genes were associated with longer RFS. HCRTR1 and NPY4R (PPYR1) genes were statistically hypermethylated; conversely HCRTR2 and PPY genes were hypomethylated. There was no significant change in PTPN11 gene promoter methylation level. HCRTR1, NPY4R (PPYR1) and PTPN11 gene expressions were downregulated; conversely, HCRTR2 and PPY gene expressions upregulated. Weak correlations were observed between NPY4R (PPYR1) gene expression and CD4+ T Cell, Neutrophil, Dendritic Cell and between PTPN11 gene expression and CD8+ T Cell, Macrophage, Neutrophil, Dendritic Cell infiltrations. Area under the receiver operating characteristics curve values of the 10-fold cross-validation and by splitting the dataset in a ratio of 80:20 models were 0.930 and 0.963 respectively. HCRTR2 and HCRTR1 belong to regulation of cytosolic calcium ion concentration, cellular calcium ion homeostasis GO BPs. CONCLUSION In BC patients, increases in HCRTR2 and PPY gene expressions could be considered as positive prognostic factors. Decreases in HCRTR1 and NPY4R (PPYR1) gene expressions could be considered as negative prognostic factors. Decreased expression of PTPN11 gene may have a positive prognostic factor. Changes in existing genes are likely to be both a biomarker and therapeutic target for BC. However, experimental and clinical studies are needed to elucidate the mechanisms underlying these neuropeptide receptors in terms of breast carcinogenesis.
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Affiliation(s)
- Fatih Yay
- Nigde Omer Halisdemir University Training and Research Hospital, Clinical Biochemistry Laboratory, Nigde, Turkey.
| | - Durmus Ayan
- Nigde Omer Halisdemir University Training and Research Hospital, Clinical Biochemistry Laboratory, Nigde, Turkey; Nigde Omer Halisdemir University, Faculty of Medicine, Medical Biochemistry, Nigde, Turkey.
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Heseltine SJ, Billenness GJ, Martin HL, Tiede C, Tang AAS, Foy E, Reddy G, Gibson N, Johnson M, Webb ME, McPherson MJ, Tomlinson DC. Generating and validating renewable affimer protein binding reagents targeting SH2 domains. Sci Rep 2024; 14:28322. [PMID: 39550397 PMCID: PMC11569188 DOI: 10.1038/s41598-024-79357-4] [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: 02/15/2024] [Accepted: 11/08/2024] [Indexed: 11/18/2024] Open
Abstract
Despite SH2 domains, being pivotal in protein interactions linked to various diseases like cancer, we lack specific research tools for intracellular assays. Understanding SH2-mediated interactions and creating effective inhibitors requires tools which target individual protein domains. Affimer reagents exhibit promise, yet their potential against the extensive SH2 domain family remains largely unexplored. Our study aimed to bridge this gap by identifying Affimer reagents that selectively bind to 22 out of 41 SH2 domains. These reagents enabled a medium-throughput screening approach resembling siRNA studies, shedding light on their functionality. Notably, select Affimers demonstrated the ability to curtail the nuclear translocation of pERK, with Grb2 being a prominent target. Further analyses revealed that these Grb2-specific Affimer reagents displayed competitive inhibition with impressive metrics: IC50s ranging from 270.9 nM to 1.22 µM, together with low nanomolar binding affinities. Moreover, they exhibited the ability to pull down endogenous Grb2 from cell lysates, illustrating their efficacy in binding the Grb2 SH2 domain. This comprehensive assessment underscores the potential of Affimer reagents as domain-specific inhibitors. Their viability for medium/high-throughput phenotypic screening presents a promising avenue via which to identify and characterize potential drug targets within the SH2 domain family.
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Affiliation(s)
- Sophie J Heseltine
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | | | - Heather L Martin
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Anna A S Tang
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Eleanor Foy
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Grace Reddy
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Naomi Gibson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | | | - Michael E Webb
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- School of Chemistry, University of Leeds, Leeds, UK
| | - Michael J McPherson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Darren C Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK.
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Tannir R, Chan L, Grzywa TM, Arevalo O, Neeser A, Kahn S, Cozzone A, Olenick L, Mason NJ, Ma L. Enhanced lentiviral gene delivery to mammalian cells via paired cell surface and viral envelope engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.08.622723. [PMID: 39605559 PMCID: PMC11601255 DOI: 10.1101/2024.11.08.622723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Lentiviral vectors that facilitate gene delivery to desired cell types have been widely used in routine laboratory research and therapeutic cell engineering. However, the lack of proper entry receptors on many cell types often results in poor gene delivery. Here, we present a simple paired virus-cell engineering approach that promotes lentiviral gene delivery into mammalian cells. Lentiviruses are dual-pseudotyped with VSV-G and a chimeric envelope protein specifically recognizing a small molecule fluorescein (αFITC-Env), and target cells are transiently labelled with FITC to create surrogate receptors for lentivirus attachment. The synthetic interaction between FITC-labeled cells and FITC-binding LVs enables efficient LV docking, viral entry and stable transgene expression in a range of mammalian cell lines and primary T cells. We showed that this approach enabled efficient delivery of a CD19-targeted chimeric antigen receptor (CAR) into naïve human T cells that are naturally refractory to conventional VSV-G LVs, which upon activation rapidly eradicated CD19 + leukemic cells. This paired cell surface and virus envelope engineering approach may serve as a universal method for engineering synthetic virus-cell interactions to improve lentiviral gene delivery to mammalian cells.
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7
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Wang Y, Muraleetharan A, Langiu M, Gregory KJ, Hellyer SD. SCA44- and SCAR13-associated GRM1 mutations affect metabotropic glutamate receptor 1 function through distinct mechanisms. Br J Pharmacol 2024; 181:4514-4530. [PMID: 39030902 DOI: 10.1111/bph.16510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/09/2024] [Accepted: 06/18/2024] [Indexed: 07/22/2024] Open
Abstract
BACKGROUND AND PURPOSE Metabotropic glutamate receptor 1 (mGlu1) is a promising therapeutic target for neurodegenerative CNS disorders including spinocerebellar ataxias (SCAs). Clinical reports have identified naturally-occurring mGlu1 mutations in rare SCA subtypes and linked symptoms to mGlu1 mutations. However, how mutations alter mGlu1 function remains unknown, as does amenability of receptor function to pharmacological rescue. Here, we explored SCA-associated mutation effects on mGlu1 cell surface expression, canonical signal transduction and allosteric ligand pharmacology. EXPERIMENTAL APPROACH Orthosteric agonists, positive allosteric modulators (PAMs) and negative allosteric modulators (NAMs) were assessed at two functional endpoints (iCa2+ mobilisation and inositol 1-phosphate [IP1] accumulation) in FlpIn Trex HEK293A cell lines expressing five mutant mGlu1 subtypes. Key pharmacological parameters including ligand potency, affinity and cooperativity were derived using operational models of agonism and allostery. KEY RESULTS mGlu1 mutants exhibited differential impacts on mGlu1 expression, with a C-terminus truncation significantly reducing surface expression. Mutations differentially influenced orthosteric ligand affinity, efficacy and functional cooperativity between allosteric and orthosteric ligands. Loss-of-function mutations L454F and N885del reduced orthosteric affinity and efficacy, respectively. A gain-of-function Y792C mutant mGlu1 displayed enhanced constitutive activity in IP1 assays, which manifested as reduced orthosteric agonist activity. The mGlu1 PAMs restored glutamate potency in iCa2+ mobilisation for loss-of-function mutations and mGlu1 NAMs displayed enhanced inverse agonist activity at Y792C relative to wild-type mGlu1. CONCLUSION AND IMPLICATIONS Collectively, these data highlight distinct mechanisms by which mGlu1 mutations affect receptor function and show allosteric modulators may present a therapeutic strategy to restore aberrant mGlu1 function in rare SCA subtypes.
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Affiliation(s)
- Yuyang Wang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Ashwin Muraleetharan
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Monica Langiu
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Karen J Gregory
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Shane D Hellyer
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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Dini A, Barker H, Piki E, Sharma S, Raivola J, Murumägi A, Ungureanu D. A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery. Nat Chem Biol 2024:10.1038/s41589-024-01761-8. [PMID: 39482470 DOI: 10.1038/s41589-024-01761-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/22/2024] [Indexed: 11/03/2024]
Abstract
The gene-regulatory dynamics governing drug responses in cancer are yet to be fully understood. Here, we report a pipeline capable of producing high-throughput pharmacotranscriptomic profiling through live-cell barcoding using antibody-oligonucleotide conjugates. This pipeline combines drug screening with 96-plex single-cell RNA sequencing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of phosphatidylinositol 3-OH kinase (PI3K), protein kinase B (AKT) and mammalian target of rapamycin (mTOR) inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this was mediated by the upregulation of caveolin 1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of agents targeting PI3K-AKT-mTOR and EGFR for HGSOC with CAV1 and EGFR expression. Using this workflow could enable the personalized testing of patient-derived tumor samples at single-cell resolution.
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Affiliation(s)
- Alice Dini
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Harlan Barker
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Emilia Piki
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Subodh Sharma
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Juuli Raivola
- Applied Tumor Genomics, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Daniela Ungureanu
- Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
- Applied Tumor Genomics, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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Oesinghaus L, Castillo-Hair S, Ludwig N, Keller A, Seelig G. Quantitative design of cell type-specific mRNA stability from microRNA expression data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.28.620728. [PMID: 39554011 PMCID: PMC11565874 DOI: 10.1101/2024.10.28.620728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Limiting expression to target cell types is a longstanding goal in gene therapy, which could be met by sensing endogenous microRNA. However, an unclear association between microRNA expression and activity currently hampers such an approach. Here, we probe this relationship by measuring the stability of synthetic microRNA-responsive 3'UTRs across 10 cell lines in a library format. By systematically addressing biases in microRNA expression data and confounding factors such as microRNA crosstalk, we demonstrate that a straightforward model can quantitatively predict reporter stability purely from expression data. We use this model to design constructs with previously unattainable response patterns across our cell lines. The rules we derive for microRNA expression data selection and processing should apply to microRNA- responsive devices for any environment with available expression data.
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10
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Reeves AE, Vilen Z, Fuentecilla TR, Parker CG, Huang ML. Charting the Dynamic Trophoblast Plasma Membrane Identifies LYN As a Functional Regulator of Syncytialization. ACS Chem Biol 2024; 19:2220-2231. [PMID: 39289808 DOI: 10.1021/acschembio.4c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The differentiation of placental cytotrophoblasts (CTBs) into the syncytiotrophoblast (STB) layer results in a significant remodeling of the plasma membrane proteome. Here, we use a peroxidase-catalyzed proximity labeling strategy to map the dynamic plasma membrane proteomes of CTBs and STBs. Coupled with mass-spectrometry-based proteomics, we identify hundreds of plasma membrane proteins and observe relative changes in protein abundance throughout differentiation, including the upregulation of the plasma-membrane-localized nonreceptor tyrosine kinase LYN. We show that both siRNA-mediated knockdown and small molecule inhibition of LYN kinase function impairs CTB fusion and reduces the expression of syncytialization markers, presenting a function for LYN outside of its canonical role in immunological signaling. Our results demonstrate the use of the proximity labeling platform to discover functional regulators within the plasma membrane and provide new avenues to regulate trophoblast differentiation.
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Affiliation(s)
- Abigail E Reeves
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Zak Vilen
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Trinity R Fuentecilla
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Christopher G Parker
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
| | - Mia L Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States
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11
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Saranya KR, Vimina ER. DRN-CDR: A cancer drug response prediction model using multi-omics and drug features. Comput Biol Chem 2024; 112:108175. [PMID: 39191166 DOI: 10.1016/j.compbiolchem.2024.108175] [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: 02/20/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Cancer drug response (CDR) prediction is an important area of research that aims to personalize cancer therapy, optimizing treatment plans for maximum effectiveness while minimizing potential negative effects. Despite the advancements in Deep learning techniques, the effective integration of multi-omics data for drug response prediction remains challenging. In this paper, a regression method using Deep ResNet for CDR (DRN-CDR) prediction is proposed. We aim to explore the potential of considering sole cancer genes in drug response prediction. Here the multi-omics data such as gene expressions, mutation data, and methylation data along with the molecular structural information of drugs were integrated to predict the IC50 values of drugs. Drug features are extracted by employing a Uniform Graph Convolution Network, while Cell line features are extracted using a combination of Convolutional Neural Network and Fully Connected Networks. These features are then concatenated and fed into a deep ResNet for the prediction of IC50 values between Drug - Cell line pairs. The proposed method yielded higher Pearson's correlation coefficient (rp) of 0.7938 with lowest Root Mean Squared Error (RMSE) value of 0.92 when compared with similar methods of tCNNS, MOLI, DeepCDR, TGSA, NIHGCN, DeepTTA, GraTransDRP and TSGCNN. Further, when the model is extended to a classification problem to categorize drugs as sensitive or resistant, we achieved AUC and AUPR measures of 0.7623 and 0.7691, respectively. The drugs such as Tivozanib, SNX-2112, CGP-60474, PHA-665752, Foretinib etc., exhibited low median IC50 values and were found to be effective anti-cancer drugs. The case studies with different TCGA cancer types also revealed the effectiveness of SNX-2112, CGP-60474, Foretinib, Cisplatin, Vinblastine etc. This consistent pattern strongly suggests the effectiveness of the model in predicting CDR.
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Affiliation(s)
- K R Saranya
- Department of Computer Science and IT, School of Computing, Amrita Vishwa Vidyapeetham, Kochi Campus, India
| | - E R Vimina
- Department of Computer Science and IT, School of Computing, Amrita Vishwa Vidyapeetham, Kochi Campus, India.
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12
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Osmani H, Sharma I, Moonah S. Generating Cytokines and Growth Factors for Functional Activity: Feasibility of Method Using MIF Protein. Methods Protoc 2024; 7:72. [PMID: 39311373 PMCID: PMC11417903 DOI: 10.3390/mps7050072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/26/2024] Open
Abstract
Cytokines and growth factors are signaling molecules that regulate a variety of biological processes. Understanding their role is essential for basic research and clinical utilization. Thus, cytokines and growth factors are widely used throughout research labs in a significant number of applications. Additionally, genetic polymorphisms result in variant forms of cytokines and growth factors, which can alter their function. Becoming more common, researchers will need to generate these important proteins and their variants themselves in functional forms for activity studies. The expression systems used to generate these proteins can have a major impact on their function. In some instances, post-translational modifications are needed to produce a functionally active protein, which can only be conducted using eukaryotic expression systems. Ideally, for functional relevance, a human expression system should be used for human-related research and applications. Most human cell-based expression systems primarily use HEK (Human Embryonic Kidney) cells; however, relying on just one cell type can lead to several issues, considering the variety of proteins derived from various cell sources. Here, we provide a protocol to effectively and efficiently generate functional recombinant proteins, taking into consideration the diverse range of proteins from different cell types throughout the human body.
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Affiliation(s)
- Hiba Osmani
- Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
| | - Ishrya Sharma
- Department of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Shannon Moonah
- Department of Medicine, University of Florida, Gainesville, FL 32608, USA;
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13
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Blahetek G, Mayer C, Zuber J, Lenter M, Strobel B. Suppression of toxic transgene expression by optimized artificial miRNAs increases AAV vector yields in HEK-293 cells. Mol Ther Methods Clin Dev 2024; 32:101280. [PMID: 39015407 PMCID: PMC11250862 DOI: 10.1016/j.omtm.2024.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/07/2024] [Indexed: 07/18/2024]
Abstract
Adeno-associated virus (AAV) vectors have become the leading platform for gene delivery in both preclinical research and therapeutic applications, making the production of high-titer AAV preparations essential. To date, most AAV-based studies use constitutive promoters (e.g., CMV, CAG), which are also active in human embryonic kidney (HEK)-293 producer cells, thus leading to the expression of the transgene already during production. Depending on the transgene's function, this might negatively impact producer cell performance and result in decreased AAV vector yields. Here, we evaluated a panel of diverse microRNA (miRNA)-based shRNA designs to identify a highly potent artificial miRNA for the transient suppression of transgenes during AAV production. Our results demonstrate that insertion of miRNA target sites into the 3' UTR of the transgene and simultaneous expression of the corresponding miRNA from the 3' UTR of conventional AAV production plasmids (rep/cap, pHelper) enabled efficient silencing of toxic transgene expression, thereby increasing AAV vector yields up to 240-fold. This strategy not only allows to maintain the traditional triple-transfection protocol, but also represents a universally applicable approach to suppress toxic transgenes, thereby boosting vector yields with so far unprecedented efficiency.
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Affiliation(s)
- Gina Blahetek
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Christine Mayer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Martin Lenter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Benjamin Strobel
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
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14
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Williams JK, Ngo JM, Murugupandiyan A, Croall DE, Hartzell HC, Schekman R. Calpains Orchestrate Secretion of Annexin-containing Microvesicles during Membrane Repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611512. [PMID: 39282443 PMCID: PMC11398502 DOI: 10.1101/2024.09.05.611512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Microvesicles (MVs) are membrane-enclosed, plasma membrane-derived particles released by cells from all branches of life. MVs have utility as disease biomarkers and may participate in intercellular communication; however, physiological processes that induce their secretion are not known. Here, we isolate and characterize annexin-containing MVs and show that these vesicles are secreted in response to the calcium influx caused by membrane damage. The annexins in these vesicles are cleaved by calpains. After plasma membrane injury, cytoplasmic calcium-bound annexins are rapidly recruited to the plasma membrane and form a scab-like structure at the lesion. In a second phase, recruited annexins are cleaved by calpains-1/2, disabling membrane scabbing. Cleavage promotes annexin secretion within MVs. Our data supports a new model of plasma membrane repair, where calpains relax annexin-membrane aggregates in the lesion repair scab, allowing secretion of damaged membrane and annexins as MVs. We anticipate that cells experiencing plasma membrane damage, including muscle and metastatic cancer cells, secrete these MVs at elevated levels.
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Affiliation(s)
- Justin Krish Williams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jordan Matthew Ngo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Abinayaa Murugupandiyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Dorothy E. Croall
- Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, United States
| | - H Criss Hartzell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, United States
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
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15
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Kotliar IB, Bendes A, Dahl L, Chen Y, Saarinen M, Ceraudo E, Dodig-Crnković T, Uhlén M, Svenningsson P, Schwenk JM, Sakmar TP. Multiplexed mapping of the interactome of GPCRs with receptor activity-modifying proteins. SCIENCE ADVANCES 2024; 10:eado9959. [PMID: 39083597 PMCID: PMC11290489 DOI: 10.1126/sciadv.ado9959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Receptor activity-modifying proteins (RAMPs) form complexes with G protein-coupled receptors (GPCRs) and may regulate their cellular trafficking and pharmacology. RAMP interactions have been identified for about 50 GPCRs, but only a few GPCR-RAMP complexes have been studied in detail. To elucidate a comprehensive GPCR-RAMP interactome, we created a library of 215 dual epitope-tagged (DuET) GPCRs representing all GPCR subfamilies and coexpressed each GPCR with each of the three RAMPs. Screening the GPCR-RAMP pairs with customized multiplexed suspension bead array (SBA) immunoassays, we identified 122 GPCRs that showed strong evidence for interaction with at least one RAMP. We screened for interactions in three cell lines and found 23 endogenously expressed GPCRs that formed complexes with RAMPs. Mapping the GPCR-RAMP interactome expands the current system-wide functional characterization of RAMP-interacting GPCRs to inform the design of selective therapeutics targeting GPCR-RAMP complexes.
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Affiliation(s)
- Ilana B. Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Leo Dahl
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Yuanhuang Chen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Marcus Saarinen
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
| | - Tea Dodig-Crnković
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Basal and Clinical Neuroscience, King’s College London, London, UK
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
- Department of Neurobiology, Care Sciences and Society, Section for Neurogeriatrics, Karolinska Institutet, Solna, Sweden
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16
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Li X, Liu D, Wu Z, Xu Y. Diffuse tumors: Molecular determinants shared by different cancer types. Comput Biol Med 2024; 178:108703. [PMID: 38850961 DOI: 10.1016/j.compbiomed.2024.108703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/02/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Most cancer types have both diffuse and non-diffuse subtypes, which have rather distinct morphologies, namely scattered tiny tumors vs. one solid tumor, and different levels of aggressiveness. However, the causes for forming such distinct subtypes remain largely unknown. Using the diffuse and non-diffuse gastric cancers (GCs) as the illustrative example, we present a computational study based on the transcriptomic data from the TCGA and GEO databases, to address the following questions: (i) What are the key molecular determinants that give rise to the distinct morphologies between diffuse and non-diffuse cancers? (ii) What are the main reasons for diffuse cancers to be generally more aggressive than non-diffuse ones of the same cancer type? (iii) What are the reasons for their distinct immunoactivities? And (iv) why do diffuse cancers on average tend to take place in younger patients? The study is conducted using the framework we have previously developed for elucidation of general drivers cancer formation and development. Our main discoveries are: (a) the level of (poly-) sialic acids deployed on the surface of cancer cells is a significant factor contributing to questions (i) and (ii); (b) poly-sialic acids synthesized by ST8SIA4 are the key to question (iii); and (c) the circulating growth factors specifically needed by the diffuse subtype dictate the answer to question (iv). All these predictions are substantiated by published experimental studies. Our further analyses on breast, prostate, lung, liver, and thyroid cancers reveal that these discoveries generally apply to the diffuse subtypes of these cancer types, hence indicating the generality of our discoveries.
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Affiliation(s)
- Xuan Li
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China; School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Dingyun Liu
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Zhipeng Wu
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Ying Xu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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17
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Lin YC, Sun DP, Hsieh TH, Chen CH. Targeting CK1δ and CK1ε as a New Therapeutic Approach for Clear Cell Renal Cell Carcinoma. Pharmacology 2024; 109:330-340. [PMID: 38955142 DOI: 10.1159/000540182] [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: 02/16/2024] [Accepted: 06/30/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Kidney cancer ranks as the ninth most common cancer in men and the fourteenth in women globally, with renal cell carcinoma (RCC) being the most prevalent type. Despite advances in therapeutic strategies targeting angiogenesis and immune checkpoints, the absence of reliable markers for patient selection and limited duration of disease control underline the need for innovative approaches. CK1δ and CK1ε are highly conserved serine/threonine kinases involved in cell cycle regulation, apoptosis, and circadian rhythm. While CK1δ dysregulation is reportedly associated with breast and bladder cancer progression, their role in RCC remains elusive. This study aimed to investigate the feasibility of CK1δ/ε as new therapeutic targets for RCC patients. METHODS The relationship between CK1δ/ε and RCC progression was evaluated by the analysis of microarray dataset and TCGA database. The anticancer activity of CK1δ/ε inhibitor was examined by MTT/SRB assay, and apoptotic cell death was analyzed by flow cytometry and Western blotting. RESULTS Our data demonstrate that the gene expression of CSNK1D and CSNK1E is significantly higher in clear cell RCC (ccRCC) tissues compared to normal kidney samples, which is correlated with lower survival rates in ccRCC patients. SR3029, a selective inhibitor targeting CK1δ/ε, significantly suppresses the viability and proliferation of ccRCC cell lines regardless of the status of VHL deficiency. Importantly, the inhibitor promotes the population of subG1 cells and induces apoptosis, and ectopically expression of CK1δ partially rescued SR3029-induced apoptosis in ccRCC cells. CONCLUSION These findings underscore the crucial role of CK1δ and CK1ε in ccRCC progression, suggesting CK1δ/ε inhibitors as new therapeutic options for ccRCC patients.
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Affiliation(s)
- Yu-Chen Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ding-Ping Sun
- Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
- Department of Food Science and Technology, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Tsung-Han Hsieh
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Chun-Han Chen
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
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18
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Wang Y, Ji B, Zhang L, Wang J, He J, Ding B, Ren M. Identification of metastasis-related genes for predicting prostate cancer diagnosis, metastasis and immunotherapy drug candidates using machine learning approaches. Biol Direct 2024; 19:50. [PMID: 38918844 PMCID: PMC11197330 DOI: 10.1186/s13062-024-00494-x] [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: 05/15/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the second leading cause of tumor-related mortality in men. Metastasis from advanced tumors is the primary cause of death among patients. Identifying novel and effective biomarkers is essential for understanding the mechanisms of metastasis in PCa patients and developing successful interventions. METHODS Using the GSE8511 and GSE27616 data sets, 21 metastasis-related genes were identified through the weighted gene co-expression network analysis (WGCNA) method. Subsequent functional analysis of these genes was conducted on the gene set cancer analysis (GSCA) website. Cluster analysis was utilized to explore the relationship between these genes, immune infiltration in PCa, and the efficacy of targeted drug IC50 scores. Machine learning algorithms were then employed to construct diagnostic and prognostic models, assessing their predictive accuracy. Additionally, multivariate COX regression analysis highlighted the significant role of POLD1 and examined its association with DNA methylation. Finally, molecular docking and immunohistochemistry experiments were carried out to assess the binding affinity of POLD1 to PCa drugs and its impact on PCa prognosis. RESULTS The study identified 21 metastasis-related genes using the WGCNA method, which were found to be associated with DNA damage, hormone AR activation, and inhibition of the RTK pathway. Cluster analysis confirmed a significant correlation between these genes and PCa metastasis, particularly in the context of immunotherapy and targeted therapy drugs. A diagnostic model combining multiple machine learning algorithms showed strong predictive capabilities for PCa diagnosis, while a transfer model using the LASSO algorithm also yielded promising results. POLD1 emerged as a key prognostic gene among the metastatic genes, showing associations with DNA methylation. Molecular docking experiments supported its high affinity with PCa-targeted drugs. Immunohistochemistry experiments further validated that increased POLD1 expression is linked to poor prognosis in PCa patients. CONCLUSIONS The developed diagnostic and metastasis models provide substantial value for patients with prostate cancer. The discovery of POLD1 as a novel biomarker related to prostate cancer metastasis offers a promising avenue for enhancing treatment of prostate cancer metastasis.
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Affiliation(s)
- YaXuan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Bo Ji
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Lu Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Jinfeng Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - JiaXin He
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - BeiChen Ding
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
| | - MingHua Ren
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
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19
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Jandova J, Wondrak GT. Melanotransferrin (MELTF, MFI2, CD228) Expression Attenuates Malignant Melanoma Progression in the A375-Luc2 Murine Metastasis Model and Human Patients. J Invest Dermatol 2024:S0022-202X(24)01864-5. [PMID: 38909843 DOI: 10.1016/j.jid.2024.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024]
Affiliation(s)
- Jana Jandova
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, The University of Arizona, Tucson, Arizona, USA
| | - Georg T Wondrak
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, The University of Arizona, Tucson, Arizona, USA.
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20
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Koufaris C, Demetriadou C, Nicolaidou V, Kirmizis A. Bioinformatic Analysis Reveals the Association of Human N-Terminal Acetyltransferase Complexes with Distinct Transcriptional and Post-Transcriptional Processes. Biochem Genet 2024:10.1007/s10528-024-10860-z. [PMID: 38864963 DOI: 10.1007/s10528-024-10860-z] [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: 04/22/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024]
Abstract
N-terminal acetyltransferases (NAT) are the protein complexes that deposit the abundant N-terminal acetylation (Nt-Ac) on eukaryotic proteins, with seven human complexes currently identified. Despite the increasing recognition of their biological and clinical importance, NAT regulation remains elusive. In this study, we performed a bioinformatic investigation to identify transcriptional and post-transcriptional processes that could be involved in the regulation of human NAT complexes. First, co-expression analysis of independent transcriptomic datasets revealed divergent pathway associations for human NAT, which are potentially connected to their distinct cellular functions. One interesting connection uncovered was the coordinated regulation of the NatA and proteasomal genes in cancer and immune cells, confirmed by analysis of multiple datasets and in isolated primary T cells. Another distinctive association was of NAA40 (NatD) with DNA replication, in cancer and non-cancer settings. The link between NAA40 transcription and DNA replication is potentially mediated through E2F1, which we have experimentally shown to bind the promoter of this NAT. Second, the coupled examination of transcriptomic and proteomic datasets revealed a much greater intra-complex concordance of NAT subunits at the protein compared to the transcript level, indicating the predominance of post-transcriptional processes for achieving their coordination. In agreement with this concept, we also found that the effects of somatic copy number alterations affecting NAT genes are attenuated post-transcriptionally. In conclusion, this study provides novel insights into the regulation of human NAT complexes.
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Affiliation(s)
- C Koufaris
- Epigenetics and Gene Regulation Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - C Demetriadou
- Epigenetics and Gene Regulation Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - V Nicolaidou
- Department of Life Sciences, University of Nicosia, Nicosia, Cyprus
| | - A Kirmizis
- Epigenetics and Gene Regulation Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus.
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21
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Ramsey KM, Barrick D. Unraveling paralog-specific Notch signaling through thermodynamics of ternary complex formation and transcriptional activation of chimeric receptors. Protein Sci 2024; 33:e4947. [PMID: 38511488 PMCID: PMC10962485 DOI: 10.1002/pro.4947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Notch signaling in humans is mediated by four paralogous receptors that share conserved architectures and possess overlapping, yet non-redundant functions. The receptors share a canonical activation pathway wherein upon extracellular ligand binding, the Notch intracellular domain (NICD) is cleaved from the membrane and translocates to the nucleus where its N-terminal RBP-j-associated molecule (RAM) region and ankyrin repeat (ANK) domain bind transcription factor CSL and recruit co-activator Mastermind-like-1 (MAML1) to activate transcription. However, different paralogs can lead to distinct outcomes. To better understand paralog-specific differences in Notch signaling, we performed a thermodynamic analysis of the Notch transcriptional activation complexes for all four Notch paralogs using isothermal titration calorimetry. Using chimeric constructs, we find that the RAM region is the primary determinant of stability of binary RAMANK:CSL complexes, and that the ANK regions are largely the determinants of MAML1 binding to pre-formed RAMANK:CSL complexes. Free energies of these binding reactions (ΔGRA and ΔGMAML) vary among the four Notch paralogs, although variations for Notch2, 3, and 4 offset in the free energy of the ternary complex (ΔGTC, where ΔGTC = ΔGRA + ΔGMAML). To probe how these affinity differences affect Notch signaling, we performed transcriptional activation assays with the paralogous and chimeric NICDs, and analyzed the results with an independent multiplicative model that quantifies contributions of the paralogous RAM, ANK, and C-terminal regions (CTR) to activation. This analysis shows that transcription activation correlates with ΔGTC, but that activation is further modified by CTR identity in a paralog-specific way.
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Affiliation(s)
- Kristen M. Ramsey
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Doug Barrick
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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22
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Verma S, Giagnocavo SD, Curtin MC, Arumugam M, Osburn-Staker SM, Wang G, Atkinson A, Nix DA, Lum DH, Cox JE, Hilgendorf KI. Zinc Alpha-2-Glycoprotein (ZAG/AZGP1) secreted by triple-negative breast cancer promotes tumor microenvironment fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583349. [PMID: 38496643 PMCID: PMC10942361 DOI: 10.1101/2024.03.04.583349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Obesity is a predisposition factor for breast cancer, suggesting a localized, reciprocal interaction between breast cancer cells and the surrounding mammary white adipose tissue. To investigate how breast cancer cells alter the composition and function of adipose tissue, we screened the secretomes of ten human breast cancer cell lines for the ability to modulate the differentiation of adipocyte stem and progenitor cells (ASPC). The screen identified a key adipogenic modulator, Zinc Alpha-2-Glycoprotein (ZAG/AZGP1), secreted by triple-negative breast cancer (TNBC) cells. TNBC-secreted ZAG inhibits adipogenesis and instead induces the expression of fibrotic genes. Accordingly, depletion of ZAG in TNBC cells attenuates fibrosis in white adipose tissue and inhibits tumor growth. Further, high expression of ZAG in TNBC patients, but not other clinical subtypes of breast cancer, is linked to poor prognosis. Our findings suggest a role of TNBC-secreted ZAG in promoting the transdifferentiation of ASPCs into cancer-associated fibroblasts to support tumorigenesis.
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Affiliation(s)
- Surbhi Verma
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Meghan C Curtin
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Menusha Arumugam
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sandra M Osburn-Staker
- Metabolomics, Proteomics and Mass Spectrometry Core, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Guoying Wang
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Aaron Atkinson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - David A Nix
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - David H Lum
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Metabolomics, Proteomics and Mass Spectrometry Core, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Keren I Hilgendorf
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Lead contact:
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23
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Kotliar IB, Bendes A, Dahl L, Chen Y, Saarinen M, Ceraudo E, Dodig-Crnković T, Uhle’n M, Svenningsson P, Schwenk JM, Sakmar TP. Expanding the GPCR-RAMP interactome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568247. [PMID: 38045268 PMCID: PMC10690247 DOI: 10.1101/2023.11.22.568247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Receptor activity-modifying proteins (RAMPs) can form complexes with G protein-coupled receptors (GPCRs) and regulate their cellular trafficking and pharmacology. RAMP interactions have been identified for about 50 GPCRs, but only a few GPCR-RAMP complexes have been studied in detail. To elucidate a complete interactome between GPCRs and the three RAMPs, we developed a customized library of 215 Dual Epitope-Tagged (DuET) GPCRs representing all GPCR subfamilies. Using a multiplexed suspension bead array (SBA) assay, we identified 122 GPCRs that showed strong evidence for interaction with at least one RAMP. We screened for native interactions in three cell lines and found 23 GPCRs that formed complexes with RAMPs. Mapping the GPCR-RAMP interactome expands the current system-wide functional characterization of RAMP-interacting GPCRs to inform the design of selective GPCR-targeted therapeutics.
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Affiliation(s)
- Ilana B. Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Leo Dahl
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Yuanhuang Chen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065, USA
| | - Marcus Saarinen
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
| | - Tea Dodig-Crnković
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Mathias Uhle’n
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Basal and Clinical Neuroscience, King’s College London, London, UK
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
- Department of Neurobiology, Care Sciences and Society, Section for Neurogeriatrics, Karolinska Institutet; Solna, 171 64, Sweden
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24
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Pouliou M, Koutsi MA, Champezou L, Giannopoulou AI, Vatsellas G, Piperi C, Agelopoulos M. MYCN Amplifications and Metabolic Rewiring in Neuroblastoma. Cancers (Basel) 2023; 15:4803. [PMID: 37835497 PMCID: PMC10571721 DOI: 10.3390/cancers15194803] [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: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Cancer is a disease caused by (epi)genomic and gene expression abnormalities and characterized by metabolic phenotypes that are substantially different from the normal phenotypes of the tissues of origin. Metabolic reprogramming is one of the key features of tumors, including those established in the human nervous system. In this work, we emphasize a well-known cancerous genomic alteration: the amplification of MYCN and its downstream effects in neuroblastoma phenotype evolution. Herein, we extend our previous computational biology investigations by conducting an integrative workflow applied to published genomics datasets and comprehensively assess the impact of MYCN amplification in the upregulation of metabolism-related transcription factor (TF)-encoding genes in neuroblastoma cells. The results obtained first emphasized overexpressed TFs, and subsequently those committed in metabolic cellular processes, as validated by gene ontology analyses (GOs) and literature curation. Several genes encoding for those TFs were investigated at the mechanistic and regulatory levels by conducting further omics-based computational biology assessments applied on published ChIP-seq datasets retrieved from MYCN-amplified- and MYCN-enforced-overexpression within in vivo systems of study. Hence, we approached the mechanistic interrelationship between amplified MYCN and overexpression of metabolism-related TFs in neuroblastoma and showed that many are direct targets of MYCN in an amplification-inducible fashion. These results illuminate how MYCN executes its regulatory underpinnings on metabolic processes in neuroblastoma.
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Affiliation(s)
- Marialena Pouliou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Marianna A. Koutsi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Lydia Champezou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Angeliki-Ioanna Giannopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527 Athens, Greece;
| | - Giannis Vatsellas
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527 Athens, Greece;
| | - Marios Agelopoulos
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
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