1
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Beaufort N, Ingendahl L, Merdanovic M, Schmidt A, Podlesainski D, Richter T, Neumann T, Kuszner M, Vetter IR, Stege P, Burston SG, Filipovic A, Ruiz-Blanco YB, Bravo-Rodriguez K, Mieres-Perez J, Beuck C, Uebel S, Zobawa M, Schillinger J, Malik R, Todorov-Völgyi K, Rey J, Roberti A, Hagemeier B, Wefers B, Müller SA, Wurst W, Sanchez-Garcia E, Zimmermann A, Hu XY, Clausen T, Huber R, Lichtenthaler SF, Schmuck C, Giese M, Kaiser M, Ehrmann M, Dichgans M. Rational correction of pathogenic conformational defects in HTRA1. Nat Commun 2024; 15:5944. [PMID: 39013852 PMCID: PMC11252331 DOI: 10.1038/s41467-024-49982-8] [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: 01/21/2021] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Abstract
Loss-of-function mutations in the homotrimeric serine protease HTRA1 cause cerebral vasculopathy. Here, we establish independent approaches to achieve the functional correction of trimer assembly defects. Focusing on the prototypical R274Q mutation, we identify an HTRA1 variant that promotes trimer formation thus restoring enzymatic activity in vitro. Genetic experiments in Htra1R274Q mice further demonstrate that expression of this protein-based corrector in trans is sufficient to stabilize HtrA1-R274Q and restore the proteomic signature of the brain vasculature. An alternative approach employs supramolecular chemical ligands that shift the monomer-trimer equilibrium towards proteolytically active trimers. Moreover, we identify a peptidic ligand that activates HTRA1 monomers. Our findings open perspectives for tailored protein repair strategies.
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Affiliation(s)
- Nathalie Beaufort
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Linda Ingendahl
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Melisa Merdanovic
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Andree Schmidt
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), LMU Munich, Munich, Germany
| | - David Podlesainski
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Tim Richter
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Thorben Neumann
- Organic Chemistry, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Michael Kuszner
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Ingrid R Vetter
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Patricia Stege
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Steven G Burston
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol, UK
| | - Anto Filipovic
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Kenny Bravo-Rodriguez
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Joel Mieres-Perez
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Department of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, Germany
| | - Christine Beuck
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Stephan Uebel
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Monika Zobawa
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Jasmin Schillinger
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Katalin Todorov-Völgyi
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Juliana Rey
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Annabell Roberti
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Birte Hagemeier
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Developmental Genetics (IDG), Helmholtz Zentrum München, Neuherberg, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Developmental Genetics (IDG), Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Technische Universität München-Weihenstephan, Freising, Germany
| | - Elsa Sanchez-Garcia
- Department of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, Germany
| | - Alexander Zimmermann
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Xiao-Yu Hu
- College of Material Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Robert Huber
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carsten Schmuck
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Michael Giese
- Organic Chemistry, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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2
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Glennie L, Solà MC, Xunclà M, Español GA, Garcia-Arumí E, Tizzano EF, Wood NT, Macartney TJ, Lasa-Aranzasti A, Sapkota GP. A novel FAM83G variant from palmoplantar keratoderma patient disrupts WNT signalling via loss of FAM83G-CK1α interaction. Open Biol 2024; 14:240075. [PMID: 39043225 PMCID: PMC11265864 DOI: 10.1098/rsob.240075] [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: 03/22/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Palmoplantar keratoderma (PPK) is a multi-faceted skin disorder characterized by the thickening of the epidermis and abrasions on the palms and soles of the feet. Among the genetic causes, biallelic pathogenic variants in the FAM83G gene have been associated with PPK in dogs and humans. Here, a novel homozygous variant (c.794G>C, p.Arg265Pro) in the FAM83G gene, identified by whole exome sequencing in a 60-year-old female patient with PPK, is reported. The patient exhibited alterations in the skin of both hands and feet, dystrophic nails, thin, curly and sparse hair, long upper eyelid eyelashes, and poor dental enamel. FAM83G activates WNT signalling through association with ser/thr protein kinase CK1α. When expressed in FAM83G-/- DLD1 colorectal cancer cells, the FAM83GR265P variant displayed poor stability, a loss of interaction with CK1α and attenuated WNT signalling response. These defects persisted in skin fibroblast cells derived from the patient. Our findings imply that the loss of FAM83G-CK1α interaction and subsequent attenuation of WNT signalling underlie the pathogenesis of PPK caused by the FAM83GR265P variant.
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Affiliation(s)
- Lorraine Glennie
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, UK
| | - Marta Codina Solà
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Mar Xunclà
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | | | - Elena Garcia-Arumí
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Eduardo Fidel Tizzano
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Nicola T. Wood
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, UK
| | - Thomas J. Macartney
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, UK
| | - Amaia Lasa-Aranzasti
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Gopal P. Sapkota
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, UK
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3
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Liu Y, Wang D, Luan Y, Tao B, Li Q, Feng Q, Zhou H, Mu J, Yu J. The application of organoids in colorectal diseases. Front Pharmacol 2024; 15:1412489. [PMID: 38983913 PMCID: PMC11231380 DOI: 10.3389/fphar.2024.1412489] [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: 04/05/2024] [Accepted: 06/07/2024] [Indexed: 07/11/2024] Open
Abstract
Intestinal organoids are a three-dimensional cell culture model derived from colon or pluripotent stem cells. Intestinal organoids constructed in vitro strongly mimic the colon epithelium in cell composition, tissue architecture, and specific functions, replicating the colon epithelium in an in vitro culture environment. As an emerging biomedical technology, organoid technology has unique advantages over traditional two-dimensional culture in preserving parental gene expression and mutation, cell function, and biological characteristics. It has shown great potential in the research and treatment of colorectal diseases. Organoid technology has been widely applied in research on colorectal topics, including intestinal tumors, inflammatory bowel disease, infectious diarrhea, and intestinal injury regeneration. This review focuses on the application of organoid technology in colorectal diseases, including the basic principles and preparation methods of organoids, and explores the pathogenesis of and personalized treatment plans for various colorectal diseases to provide a valuable reference for organoid technology development and application.
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Affiliation(s)
- Yanxin Liu
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Yanhong Luan
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Boqiang Tao
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Qirong Li
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Hengzong Zhou
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Jianfeng Mu
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Jinhai Yu
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
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4
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Nummela P, Zafar S, Veikkolainen E, Ukkola I, Cinella V, Ayo A, Asghar MY, Välimäki N, Törnquist K, Karhu A, Laakkonen P, Aaltonen LA, Ristimäki A. GNAS mutation inhibits growth and induces phosphodiesterase 4D expression in colorectal cancer cell lines. Int J Cancer 2024; 154:1987-1998. [PMID: 38319157 DOI: 10.1002/ijc.34865] [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: 05/17/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024]
Abstract
Approximately 5% of colorectal cancers (CRCs) have a gain-of-function mutation in the GNAS gene, which leads to the activation of cAMP-dependent signaling pathways and associates with poor prognosis. We investigated the effect of an activating GNAS mutation in CRC cell lines on gene expression and cell proliferation in vitro, and tumor growth in vivo. GNAS-mutated (GNASmt) HCT116 cells showed stimulated synthesis of cAMP as compared to parental (Par) cells. The most upregulated gene in the GNASmt cells was cAMP-hydrolyzing phosphodiesterase 4D (PDE4D) as detected by RNA sequencing. To further validate our finding, we analyzed PDE4D expression in a set of human CRC tumors (n = 35) and demonstrated overexpression in GNAS mutant CRC tumors as compared to GNAS wild-type tumors. The GNASmt HCT116 cells proliferated more slowly than the Par cells. PDE4 inhibitor Ro 20-1724 and PDE4D subtype selective inhibitor GEBR-7b further suppressed the proliferation of GNASmt cells without an effect on Par cells. The growth inhibitory effect of these inhibitors was also seen in the intrinsically GNAS-mutated SK-CO-1 CRC cell line having high levels of cAMP synthesis and PDE4D expression. In vivo, GNASmt HCT116 cells formed smaller tumors than the Par cells in nude mice. In conclusion, our findings demonstrate that GNAS mutation results in the growth suppression of CRC cells. Moreover, the GNAS mutation-induced overexpression of PDE4D provides a potential avenue to impede the proliferation of CRC cells through the use of PDE4 inhibitors.
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Affiliation(s)
- Pirjo Nummela
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sadia Zafar
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Erika Veikkolainen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Iiris Ukkola
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Vincenzo Cinella
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Abiodun Ayo
- Translational Cancer Medicine Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Muhammad Yasir Asghar
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, HiLife, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Niko Välimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Kid Törnquist
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Auli Karhu
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Pirjo Laakkonen
- Translational Cancer Medicine Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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5
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Wang D, Madunić K, Mayboroda OA, Lageveen-Kammeijer GSM, Wuhrer M. (Sialyl)Lewis Antigen Expression on Glycosphingolipids, N-, and O-Glycans in Colorectal Cancer Cell Lines is Linked to a Colon-Like Differentiation Program. Mol Cell Proteomics 2024; 23:100776. [PMID: 38670309 PMCID: PMC11128521 DOI: 10.1016/j.mcpro.2024.100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/03/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024] Open
Abstract
Alterations in the glycomic profile are a hallmark of cancer, including colorectal cancer (CRC). While, the glycosylation of glycoproteins and glycolipids has been widely studied for CRC cell lines and tissues, a comprehensive overview of CRC glycomics is still lacking due to the usage of different samples and analytical methods. In this study, we compared glycosylation features of N-, O-glycans, and glycosphingolipid glycans for a set of 22 CRC cell lines, all measured by porous graphitized carbon nano-liquid chromatography-tandem mass spectrometry. An overall, high abundance of (sialyl)Lewis antigens for colon-like cell lines was found, while undifferentiated cell lines showed high expression of H blood group antigens and α2-3/6 sialylation. Moreover, significant associations of glycosylation features were found between the three classes of glycans, such as (sialyl)Lewis and H blood group antigens. Integration of the datasets with transcriptomics data revealed positive correlations between (sialyl)Lewis antigens, the corresponding glycosyltransferase FUT3 and transcription factors CDX1, ETS, HNF1/4A, MECOM, and MYB. This indicates a possible role of these transcription factors in the upregulation of (sialyl)Lewis antigens, particularly on glycosphingolipid glycans, via FUT3/4 expression in colon-like cell lines. In conclusion, our study provides insights into the possible regulation of glycans in CRC and can serve as a guide for the development of diagnostic and therapeutic biomarkers.
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Affiliation(s)
- Di Wang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Katarina Madunić
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Guinevere S M Lageveen-Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Division of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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6
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Coman IS, Vital RC, Coman VE, Burleanu C, Liţescu M, Florea CG, Cristian DA, Gorecki GP, Radu PA, Pleşea IE, Erchid A, Grigorean VT. Emergency and Elective Colorectal Cancer-Relationship between Clinical Factors, Tumor Topography and Surgical Strategies: A Cohort Study. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:898. [PMID: 38929515 PMCID: PMC11205460 DOI: 10.3390/medicina60060898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Background and Objectives: The purpose of the study was to analyze the relationships among several clinical factors and also the tumor topography and surgical strategies used in patients with colorectal cancer. Materials and Methods: We designed an analytical, observational, retrospective study that included patients admitted to our emergency surgical department and diagnosed with colorectal cancer. The study group inclusion criteria were: patients admitted during 2020-2022; patients diagnosed with colorectal cancer (including the ileocecal valve); patients who benefited from a surgical procedure, either emergency or elective. Results: In our study group, consisting of 153 patients, we accounted for 56.9% male patients and 43.1% female patients. The most common clinical manifestations were pain (73.2% of the study group), followed by abdominal distension (69.3% of the study group) and absence of intestinal transit (38.6% of the study group). A total of 69 patients had emergency surgery (45.1%), while 84 patients (54.9%) benefited from elective surgery. The most frequent topography of the tumor was the sigmoid colon, with 19.60% of the patients, followed by the colorectal junction, with 15.68% of the patients, and superior rectum and inferior rectum, with 11.11% of the patients in each subcategory. The most frequent type of procedure was right hemicolectomy (21.6% of the study group), followed by rectosigmoid resection (20.9% of the study group). The surgical procedure was finished by performing an anastomosis in 49% of the patients, and an ostomy in 43.1% of the patients, while for 7.8% of the patients, a tumoral biopsy was performed. Conclusions: Colorectal cancer remains one of the most frequent cancers in the world, with a heavy burden that involves high mortality, alterations in the quality of life of patients and their families, and also the financial costs of the medical systems.
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Affiliation(s)
- Ionuţ Simion Coman
- 10th Clinical Department—General Surgery, Discipline of General Surgery—“Bagdasar-Arseni” Clinical Emergency Hospital, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania; (I.S.C.); (V.E.C.); (V.T.G.)
- General Surgery Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania; (R.C.V.); (C.B.); (C.G.F.); (A.E.)
| | - Raluca Cristina Vital
- General Surgery Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania; (R.C.V.); (C.B.); (C.G.F.); (A.E.)
| | - Violeta Elena Coman
- 10th Clinical Department—General Surgery, Discipline of General Surgery—“Bagdasar-Arseni” Clinical Emergency Hospital, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania; (I.S.C.); (V.E.C.); (V.T.G.)
- General Surgery Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania; (R.C.V.); (C.B.); (C.G.F.); (A.E.)
| | - Cosmin Burleanu
- General Surgery Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania; (R.C.V.); (C.B.); (C.G.F.); (A.E.)
| | - Mircea Liţescu
- 2nd Department of Surgery and General Anesthesia, Discipline of Surgery and General Anesthesia—“Sf. Ioan” Clinical Emergency Hospital, Faculty of Dental Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania
- General Surgery Department, “Sf. Ioan” Clinical Emergency Hospital, 13 Vitan-Bârzeşti Road, 042122 Bucharest, Romania
| | - Costin George Florea
- General Surgery Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania; (R.C.V.); (C.B.); (C.G.F.); (A.E.)
| | - Daniel Alin Cristian
- 10th Clinical Department—General Surgery, Discipline of General Surgery—“Colţea” Clinical Hospital, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania;
- General Surgery Department, “Colţea” Clinical Hospital, 1 Ion C. Brătianu Boulevard, 030167 Bucharest, Romania
| | - Gabriel-Petre Gorecki
- Faculty of Medicine, “Titu Maiorescu” University, 67A Gheorghe Petraşcu Street, 031593 Bucharest, Romania;
- Department of Anesthesia and Intensive Care, CF2 Clinical Hospital, 63 Mărăşti Boulevard, 011464 Bucharest, Romania
| | - Petru Adrian Radu
- 10th Clinical Department—General Surgery, Discipline of General Surgery—“Dr. Carol Davila” Clinical Nephrology Hospital, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania;
- General Surgery Department, “Dr. Carol Davila” Clinical Nephrology Hospital, 4 Griviţei Road, 010731 Bucharest, Romania
| | - Iancu Emil Pleşea
- Pathology Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania;
| | - Anwar Erchid
- General Surgery Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania; (R.C.V.); (C.B.); (C.G.F.); (A.E.)
| | - Valentin Titus Grigorean
- 10th Clinical Department—General Surgery, Discipline of General Surgery—“Bagdasar-Arseni” Clinical Emergency Hospital, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 37 Dionisie Lupu Street, 020021 Bucharest, Romania; (I.S.C.); (V.E.C.); (V.T.G.)
- General Surgery Department, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni Road, 041915 Bucharest, Romania; (R.C.V.); (C.B.); (C.G.F.); (A.E.)
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7
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Routila E, Mahran R, Salminen S, Irjala H, Haapio E, Kytö E, Ventelä S, Petterson K, Routila J, Gidwani K, Leivo J. Identification of stemness-related glycosylation changes in head and neck squamous cell carcinoma. BMC Cancer 2024; 24:443. [PMID: 38600440 PMCID: PMC11005150 DOI: 10.1186/s12885-024-12161-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/21/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Altered glycosylation is a hallmark of cancer associated with therapy resistance and tumor behavior. In this study, we investigated the glycosylation profile of stemness-related proteins OCT4, CIP2A, MET, and LIMA1 in HNSCC tumors. METHODS Tumor, adjacent normal tissue, and blood samples of 25 patients were collected together with clinical details. After tissue processing, lectin-based glycovariant screens were performed. RESULTS Strong correlation between glycosylation profiles of all four stemness-related proteins was observed in tumor tissue, whereas glycosylation in tumor tissue, adjacent normal tissue, and serum was differential. CONCLUSIONS A mannose- and galactose-rich glycosylation niche associated with stemness-related proteins was identified.
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Affiliation(s)
- E Routila
- Department of Life Technologies, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland.
- InFLAMES Research Flagship, University of Turku, 20014, Turku, Finland.
- FICAN West Cancer Centre, Turku, Finland.
| | - R Mahran
- Department of Life Technologies, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
- FICAN West Cancer Centre, Turku, Finland
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - S Salminen
- Department of Life Technologies, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
- FICAN West Cancer Centre, Turku, Finland
| | - H Irjala
- Department for Otorhinolaryngology- Head and Neck surgery, University of Turku and Turku University Hospital, Savitehtaankatu 5, 20520, Turku, Finland
| | - E Haapio
- Department for Otorhinolaryngology- Head and Neck surgery, University of Turku and Turku University Hospital, Savitehtaankatu 5, 20520, Turku, Finland
| | - E Kytö
- Department for Otorhinolaryngology- Head and Neck surgery, University of Turku and Turku University Hospital, Savitehtaankatu 5, 20520, Turku, Finland
| | - S Ventelä
- FICAN West Cancer Centre, Turku, Finland
- Department for Otorhinolaryngology- Head and Neck surgery, University of Turku and Turku University Hospital, Savitehtaankatu 5, 20520, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland
| | - K Petterson
- Department of Life Technologies, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - J Routila
- FICAN West Cancer Centre, Turku, Finland
- Department for Otorhinolaryngology- Head and Neck surgery, University of Turku and Turku University Hospital, Savitehtaankatu 5, 20520, Turku, Finland
| | - K Gidwani
- Department of Life Technologies, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - J Leivo
- Department of Life Technologies, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014, Turku, Finland
- FICAN West Cancer Centre, Turku, Finland
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8
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You S, Xu J, Guo Y, Guo X, Zhang Y, Zhang N, Sun G, Sun Y. E3 ubiquitin ligase WWP2 as a promising therapeutic target for diverse human diseases. Mol Aspects Med 2024; 96:101257. [PMID: 38430667 DOI: 10.1016/j.mam.2024.101257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
Mammalian E3 ubiquitin ligases have emerged in recent years as critical regulators of cellular homeostasis due to their roles in targeting substrate proteins for ubiquitination and triggering subsequent downstream signals. In this review, we describe the multiple roles of WWP2, an E3 ubiquitin ligase with unique and important functions in regulating a wide range of biological processes, including DNA repair, gene expression, signal transduction, and cell-fate decisions. As such, WWP2 has evolved to play a key role in normal physiology and diseases, such as tumorigenesis, skeletal development and diseases, immune regulation, cardiovascular disease, and others. We attempt to provide an overview of the biochemical, physiological, and pathophysiological roles of WWP2, as well as open questions for future research, particularly in the context of putative therapeutic opportunities.
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Affiliation(s)
- Shilong You
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jiaqi Xu
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yushan Guo
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaofan Guo
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ying Zhang
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning, China.
| | - Naijin Zhang
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning, China; NHC Key Laboratory of Advanced Reproductive Medicine and Fertility, National Health Commission, China Medical University, Shenyang, Liaoning, China.
| | - Guozhe Sun
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Yingxian Sun
- Department of Cardiology, First Hospital of China Medical University, Shenyang, Liaoning, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning, China.
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9
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Ayass MA, Tripathi T, Griko N, Okyay T, Ramankutty Nair R, Zhang J, Zhu K, Melendez K, Pashkov V, Abi-Mosleh L. Dual Checkpoint Aptamer Immunotherapy: Unveiling Tailored Cancer Treatment Targeting CTLA-4 and NKG2A. Cancers (Basel) 2024; 16:1041. [PMID: 38473398 DOI: 10.3390/cancers16051041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/13/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Recent strides in immunotherapy have illuminated the crucial role of CTLA-4 and PD-1/PD-L1 pathways in contemporary oncology, presenting both promises and challenges in response rates and adverse effects. This study employs a computational biology tool (in silico approach) to craft aptamers capable of binding to dual receptors, namely, inhibitory CTLA4 and NKG2A, thereby unleashing both T and NK cells and enhancing CD8+ T and NK cell functions for tumor cell lysis. Computational analysis highlighted AYA22T-R2-13 with HADDOCK scores of -78.2 ± 10.2 (with CTLA4), -60.0 ± 4.2 (with NKG2A), and -77.5 ± 5.6 (with CD94/NKG2A). Confirmation of aptamer binding to targeted proteins was attained via ELISA and flow cytometry methods. In vitro biological functionality was assessed using lactate dehydrogenase (LDH) cytotoxicity assay. Direct and competitive assays using ELISA and flow cytometry demonstrated the selective binding of AYA22T-R2-13 to CTLA4 and NKG2A proteins, as well as to the cell surface receptors of IL-2-stimulated T cells and NK cells. This binding was inhibited in the presence of competition from CTLA4 or NKG2A proteins. Remarkably, the blockade of CTLA4 or NKG2A by AYA22T-R2-13 augmented human CD8 T cell- and NK cell-mediated tumor cell lysis in vitro. Our findings highlight the precise binding specificity of AYA22T-R2-13 for CTLA4-B7-1/B7-2 (CD80/CD86) or CD94/NKG2A-HLA-E interactions, positioning it as a valuable tool for immune checkpoint blockade aptamer research in murine tumor models. These in vitro studies establish a promising foundation for further enhancing binding capacity and establishing efficacy and safety in animal models. Consequently, our results underscore the potential of AYA22T-R2-13 in cancer immunotherapy, offering high specificity, low toxicity, and the potential for cost-effective production.
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Affiliation(s)
| | | | - Natalya Griko
- Ayass Bioscience LLC, 8501 Wade Blvd, Bld 9, Frisco, TX 75034, USA
| | - Tutku Okyay
- Ayass Bioscience LLC, 8501 Wade Blvd, Bld 9, Frisco, TX 75034, USA
| | | | - Jin Zhang
- Ayass Bioscience LLC, 8501 Wade Blvd, Bld 9, Frisco, TX 75034, USA
| | - Kevin Zhu
- Ayass Bioscience LLC, 8501 Wade Blvd, Bld 9, Frisco, TX 75034, USA
| | - Kristen Melendez
- Ayass Bioscience LLC, 8501 Wade Blvd, Bld 9, Frisco, TX 75034, USA
| | - Victor Pashkov
- Ayass Bioscience LLC, 8501 Wade Blvd, Bld 9, Frisco, TX 75034, USA
| | - Lina Abi-Mosleh
- Ayass Bioscience LLC, 8501 Wade Blvd, Bld 9, Frisco, TX 75034, USA
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10
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Chen D, Ermine K, Wang YJ, Chen X, Lu X, Wang P, Beer-Stolz D, Yu J, Zhang L. PUMA/RIP3 Mediates Chemotherapy Response via Necroptosis and Local Immune Activation in Colorectal Cancer. Mol Cancer Ther 2024; 23:354-367. [PMID: 37992761 DOI: 10.1158/1535-7163.mct-23-0162] [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: 03/19/2023] [Revised: 10/02/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023]
Abstract
Induction of programmed cell death (PCD) is a key cytotoxic effect of anticancer therapies. PCD is not confined to caspase-dependent apoptosis, but includes necroptosis, a regulated form of necrotic cell death controlled by receptor-interacting protein (RIP) kinases 1 and 3, and mixed lineage kinase domain-like (MLKL) pseudokinase. Necroptosis functions as a defense mechanism against oncogenic mutations and pathogens and can be induced by a variety of anticancer agents. However, the functional role and regulatory mechanisms of necroptosis in anticancer therapy are poorly understood. In this study, we found that RIP3-dependent but RIP1-independent necroptosis is engaged by 5-fluorouracil (5-FU) and other widely used antimetabolite drugs, and functions as a major mode of cell death in a subset of colorectal cancer cells that express RIP3. We identified a novel 5-FU-induced necroptosis pathway involving p53-mediated induction of the BH3-only Bcl-2 family protein, p53 upregulated modulator of apoptosis (PUMA), which promotes cytosolic release of mitochondrial DNA and stimulates its sensor z-DNA-binding protein 1 (ZBP1) to activate RIP3. PUMA/RIP3-dependent necroptosis mediates the in vitro and in vivo antitumor effects of 5-FU and promotes a robust antitumor immune response. Our findings provide a rationale for stimulating necroptosis to enhance tumor cell killing and antitumor immune response leading to improved colorectal cancer treatments.
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Affiliation(s)
- Dongshi Chen
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, Keck School of Medicine of University of Southern California (USC), Los Angeles, California
| | - Kaylee Ermine
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yi-Jun Wang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Xiaojun Chen
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Xinyan Lu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, Keck School of Medicine of University of Southern California (USC), Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
| | - Peng Wang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Donna Beer-Stolz
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jian Yu
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, Keck School of Medicine of University of Southern California (USC), Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lin Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, Keck School of Medicine of University of Southern California (USC), Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
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11
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Jenkins LJ, Luk IY, Chionh F, Tan T, Needham K, Ayton J, Reehorst CM, Vukelic N, Sieber OM, Mouradov D, Gibbs P, Williams DS, Tebbutt NC, Desai J, Hollande F, Dhillon AS, Lee EF, Merino D, Fairlie WD, Mariadason JM. BCL-X L inhibitors enhance the apoptotic efficacy of BRAF inhibitors in BRAF V600E colorectal cancer. Cell Death Dis 2024; 15:183. [PMID: 38429301 PMCID: PMC10907349 DOI: 10.1038/s41419-024-06478-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 03/03/2024]
Abstract
Metastatic BRAFV600E colorectal cancer (CRC) carries an extremely poor prognosis and is in urgent need of effective new treatments. While the BRAFV600E inhibitor encorafenib in combination with the EGFR inhibitor cetuximab (Enc+Cet) was recently approved for this indication, overall survival is only increased by 3.6 months and objective responses are observed in only 20% of patients. We have found that a limitation of Enc+Cet treatment is the failure to efficiently induce apoptosis in BRAFV600E CRCs, despite inducing expression of the pro-apoptotic protein BIM and repressing expression of the pro-survival protein MCL-1. Here, we show that BRAFV600E CRCs express high basal levels of the pro-survival proteins MCL-1 and BCL-XL, and that combining encorafenib with a BCL-XL inhibitor significantly enhances apoptosis in BRAFV600E CRC cell lines. This effect was partially dependent on the induction of BIM, as BIM deletion markedly attenuated BRAF plus BCL-XL inhibitor-induced apoptosis. As thrombocytopenia is an established on-target toxicity of BCL-XL inhibition, we also examined the effect of combining encorafenib with the BCL-XL -targeting PROTAC DT2216, and the novel BCL-2/BCL-XL inhibitor dendrimer conjugate AZD0466. Combining encorafenib with DT2216 significantly increased apoptosis induction in vitro, while combining encorafenib with AZD0466 was well tolerated in mice and further reduced growth of BRAFV600E CRC xenografts compared to either agent alone. Collectively, these findings demonstrate that combined BRAF and BCL-XL inhibition significantly enhances apoptosis in pre-clinical models of BRAFV600E CRC and is a combination regimen worthy of clinical investigation to improve outcomes for these patients.
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Affiliation(s)
- Laura J Jenkins
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Ian Y Luk
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Fiona Chionh
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Tao Tan
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kristen Needham
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Jamieson Ayton
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Camilla M Reehorst
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Natalia Vukelic
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
| | - Oliver M Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Surgery, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Dmitri Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - David S Williams
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Pathology, Austin Health, Melbourne, VIC, Australia
| | - Niall C Tebbutt
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- Department of Surgery, The University of Melbourne, Melbourne, VIC, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Australia
| | - Jayesh Desai
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Frédéric Hollande
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Amardeep S Dhillon
- The institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, Australia
| | - Erinna F Lee
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Delphine Merino
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - W Douglas Fairlie
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - John M Mariadason
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia.
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12
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Vincenzi M, Mercurio FA, Autiero I, Leone M. Cancer-Related Mutations in the Sam Domains of EphA2 Receptor and Ship2 Lipid Phosphatase: A Computational Study. Molecules 2024; 29:1024. [PMID: 38474536 DOI: 10.3390/molecules29051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The lipid phosphatase Ship2 interacts with the EphA2 receptor by forming a heterotypic Sam (sterile alpha motif)-Sam complex. Ship2 works as a negative regulator of receptor endocytosis and consequent degradation, and anti-oncogenic effects in cancer cells should be induced by hindering its association with EphA2. Herein, a computational approach is presented to investigate the relationship between Ship2-Sam/EphA2-Sam interaction and cancer onset and further progression. A search was first conducted through the COSMIC (Catalogue of Somatic Mutations in Cancer) database to identify cancer-related missense mutations positioned inside or close to the EphA2-Sam and Ship2-Sam reciprocal binding interfaces. Next, potential differences in the chemical-physical properties of mutant and wild-type Sam domains were evaluated by bioinformatics tools based on analyses of primary sequences. Three-dimensional (3D) structural models of mutated EphA2-Sam and Ship2-Sam domains were built as well and deeply analysed with diverse computational instruments, including molecular dynamics, to classify potentially stabilizing and destabilizing mutations. In the end, the influence of mutations on the EphA2-Sam/Ship2-Sam interaction was studied through docking techniques. This in silico approach contributes to understanding, at the molecular level, the mutation/cancer relationship by predicting if amino acid substitutions could modulate EphA2 receptor endocytosis.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
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13
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Cheng F, Li P, Xu S, Zhang C, Liang H, Ding Z. A pair of primary colorectal cancer-derived and corresponding synchronous liver metastasis-derived organoid cell lines. Aging (Albany NY) 2024; 16:4396-4422. [PMID: 38407980 PMCID: PMC10968669 DOI: 10.18632/aging.205595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024]
Abstract
Proper preclinical models for the research of colorectal cancer (CRC) and CRC liver metastases (CLM) are a clear and unmet need. Patient-derived organoids have recently emerged as a robust preclinical model, but are not available to all scientific researchers. Here, we present paired 3D organoid cell lines of CWH22 (CRC-derived) and CLM22 (CLM-derived) with sound background information and the short tandem repeats are identical to those of the normal tissue. Morphological and immunohistochemical staining, along with whole-exome sequencing (WES), confirmed that the organoids exhibited the same differentiation, molecular expression, and mutation status as the corresponding tumor tissue. Both organoids possessed mutated APC/KRAS/SMAD4/CDKN1B/KMT2C genes and wild-type TP53 and PIK3CA; stably secreted the tumor markers CEA and CA19-9, and possessed sound proliferation rates in vitro, as well as subcutaneous tumorigenicity and liver metastatic abilities in vivo. IC50 assays confirmed that both cell lines were sensitive to 5-fluorouracil, oxaliplatin, SN-38, and sotorasib. WES and karyotype analyses revealed the genomic instability status as chromosome instability. The corresponding adherent cultured CWH22-2D/CLM22-2D cells were established and compared with commonly used CRC cell lines from the ATCC. Both organoids are publicly available to all researchers and will be useful tools for specific human CRC/CLM studies both in vitro and in vivo.
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Affiliation(s)
- Fangling Cheng
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, China
| | - Pengcheng Li
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, China
| | - Sanpeng Xu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chao Zhang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huifang Liang
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, China
| | - Zeyang Ding
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, China
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14
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Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
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Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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15
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Pathira Kankanamge L, Mora A, Ondrechen MJ, Beuning PJ. Biochemical Activity of 17 Cancer-Associated Variants of DNA Polymerase Kappa Predicted by Electrostatic Properties. Chem Res Toxicol 2023; 36:1789-1803. [PMID: 37883788 PMCID: PMC10664756 DOI: 10.1021/acs.chemrestox.3c00233] [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: 08/06/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
DNA damage and repair have been widely studied in relation to cancer and therapeutics. Y-family DNA polymerases can bypass DNA lesions, which may result from external or internal DNA damaging agents, including some chemotherapy agents. Overexpression of the Y-family polymerase human pol kappa can result in tumorigenesis and drug resistance in cancer. This report describes the use of computational tools to predict the effects of single nucleotide polymorphism variants on pol kappa activity. Partial Order Optimum Likelihood (POOL), a machine learning method that uses input features from Theoretical Microscopic Titration Curve Shapes (THEMATICS), was used to identify amino acid residues most likely involved in catalytic activity. The μ4 value, a metric obtained from POOL and THEMATICS that serves as a measure of the degree of coupling between one ionizable amino acid and its neighbors, was then used to identify which protein mutations are likely to impact the biochemical activity. Bioinformatic tools SIFT, PolyPhen-2, and FATHMM predicted most of these variants to be deleterious to function. Along with computational and bioinformatic predictions, we characterized the catalytic activity and stability of 17 cancer-associated DNA pol kappa variants. We identified pol kappa variants R48I, H105Y, G147D, G154E, V177L, R298C, E362V, and R470C as having lower activity relative to wild-type pol kappa; the pol kappa variants T102A, H142Y, R175Q, E210K, Y221C, N330D, N338S, K353T, and L383F were identified as being similar in catalytic efficiency to WT pol kappa. We observed that POOL predictions can be used to predict which variants have decreased activity. Predictions from bioinformatic tools like SIFT, PolyPhen-2, and FATHMM are based on sequence comparisons and therefore are complementary to POOL but are less capable of predicting biochemical activity. These bioinformatic and computational tools can be used to identify SNP variants with deleterious effects and altered biochemical activity from a large data set.
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Affiliation(s)
- Lakindu
S. Pathira Kankanamge
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Alexandra Mora
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Mary Jo Ondrechen
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
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16
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Molica C, Gili A, Nardelli C, Pierini T, Arniani S, Beacci D, Mavridou E, Mandarano M, Corinaldesi R, Metro G, Gorello P, Giovenali P, Cenci N, Castrioto C, Lupattelli M, Roila F, Mecucci C, La Starza R. Optimizing the risk stratification of astrocytic tumors by applying the cIMPACT-NOW Update 3 signature: real-word single center experience. Sci Rep 2023; 13:20101. [PMID: 37973912 PMCID: PMC10654668 DOI: 10.1038/s41598-023-46701-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Our work reports implementation of a useful genetic diagnosis for the clinical managment of patients with astrocytic tumors. We investigated 313 prospectively recruited diffuse astrocytic tumours by applying the cIMPACT-NOW Update 3 signature. The cIMPACT-NOW Update 3 (cIMPACT-NOW 3) markers, i.e., alterations of TERT promoter, EGFR, and/or chromosome 7 and 10, characterized 96.4% of IDHwt cases. Interestingly, it was also found in 48,5% of IDHmut cases. According to the genomic profile, four genetic subgroups could be distinguished: (1) IDwt/cIMPACT-NOW 3 (n = 270); (2) IDHwt/cIMPACT-NOW 3 negative (= 10); (3) IDHmut/cIMPACT-NOW 3 (n = 16); and 4) IDHmut/cIMPACT-NOW 3 negative (n = 17). Multivariate analysis confirmed that IDH1/2 mutations confer a favorable prognosis (IDHwt, HR 2.91 95% CI 1.39-6.06), and validated the prognostic value of the cIMPACT-NOW 3 signature (cIMPACT-NOW 3, HR 2.15 95% CI 1.15-4.03). To accurately identify relevant prognostic categories, overcoming the limitations of histopathology and immunohistochemistry, molecular-cytogenetic analyses must be fully integrated into the diagnostic work-up of astrocytic tumors.
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Affiliation(s)
- Carmen Molica
- Medical Oncology, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Alessio Gili
- Public Health Section, Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Carlotta Nardelli
- Molecular Medicine Laboratory, Centro di Ricerche Emato-Oncologiche (C.R.E.O.), S. Maria Della Misericordia Hospital, University of Perugia, Piazzale Menghini 9, 06132, Perugia, Italy
| | - Tiziana Pierini
- Molecular Medicine Laboratory, Centro di Ricerche Emato-Oncologiche (C.R.E.O.), S. Maria Della Misericordia Hospital, University of Perugia, Piazzale Menghini 9, 06132, Perugia, Italy
| | - Silvia Arniani
- Molecular Medicine Laboratory, Centro di Ricerche Emato-Oncologiche (C.R.E.O.), S. Maria Della Misericordia Hospital, University of Perugia, Piazzale Menghini 9, 06132, Perugia, Italy
| | - Donatella Beacci
- Molecular Medicine Laboratory, Centro di Ricerche Emato-Oncologiche (C.R.E.O.), S. Maria Della Misericordia Hospital, University of Perugia, Piazzale Menghini 9, 06132, Perugia, Italy
| | - Elena Mavridou
- Molecular Medicine Laboratory, Centro di Ricerche Emato-Oncologiche (C.R.E.O.), S. Maria Della Misericordia Hospital, University of Perugia, Piazzale Menghini 9, 06132, Perugia, Italy
| | - Martina Mandarano
- Diagnostic Cytology and Histology Unit, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Rodolfo Corinaldesi
- Division of Neurosurgery, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Giulio Metro
- Medical Oncology, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Paolo Gorello
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06100, Perugia, Italy
| | - Paolo Giovenali
- Diagnostic Cytology and Histology Unit, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Nunzia Cenci
- Division of Neurosurgery, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Corrado Castrioto
- Division of Neurosurgery, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Marco Lupattelli
- Division of Radiotherapy, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Fausto Roila
- Medical Oncology, S. Maria Della Misericordia Hospital, Piazzale Giorgio Menghini 8/9, 06132, Perugia, Italy
| | - Cristina Mecucci
- Molecular Medicine Laboratory, Centro di Ricerche Emato-Oncologiche (C.R.E.O.), S. Maria Della Misericordia Hospital, University of Perugia, Piazzale Menghini 9, 06132, Perugia, Italy
| | - Roberta La Starza
- Molecular Medicine Laboratory, Centro di Ricerche Emato-Oncologiche (C.R.E.O.), S. Maria Della Misericordia Hospital, University of Perugia, Piazzale Menghini 9, 06132, Perugia, Italy.
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17
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Blachman A, Birocco AM, Curcio S, Camperi SA, Gianvincenzo PD, Rodriguez JA, Barredo-Vacchelli GR, Cenci G, Sosnik A, Moya S, Calabrese GC. Dermatan Sulfate/Chitosan Nanoparticles Loaded with an Anti-Inflammatory Peptide Increase the Response of Human Colorectal Cancer Cells to 5-Fluorouracil. Macromol Biosci 2023; 23:e2300193. [PMID: 37469233 DOI: 10.1002/mabi.202300193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/24/2023] [Accepted: 07/18/2023] [Indexed: 07/21/2023]
Abstract
The gold standard drug for colorectal cancer (CRC) treatment, 5-Fluorouracil (5-FU), induces pharmacological tolerance in long-term management. The transcriptional factor nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) plays a key role in 5-FU resistance. The aim of this work is to study the capability of polyelectrolytes complex nanoparticles of dermatan sulfate (DS) and chitosan (CS), loaded with the anti-inflammatory tripeptide IRW, to sensitize colorectal cancer cells to 5-FU. Fluorescence and flow cytometry studies confirmed the recognition by the nanoformulation, of the cluster of differentiation 44 (CD44) receptor, involved in the initiation and progression of colorectal tumors. Dynamic light scattering (DLS) and flow cytometry reinforced the importance of DS and CD44 receptor in the interaction, as the addition of DS or anti-CD44 antibody blocked the binding. Moreover, the nanoformulation also interacts with 3D colon cancer cultures, namely colonospheres, enriched in cancer stem cells (CSC), subpopulation responsible for drug resistance and metastasis. To evaluate the consequences of this interaction, the subcellular distribution of the transcriptional factor NFκB, is determined by immunofluorescence analysis. Internalization and the intracellular release of IRW inhibited nuclear translocation of NFκB and increased cellular sensitivity to 5-FU. Altogether, the nanoformulation could provide a selective delivery platform for IRW distribution to colorectal tumors, being an innovative strategy toward overcoming 5-FU resistance in CRC therapy.
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Affiliation(s)
- Agustín Blachman
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Ciencias Biológicas. Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), UBA- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, C1113AAD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Ariadna María Birocco
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Ciencias Biológicas. Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), UBA- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, C1113AAD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Sofía Curcio
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Ciencias Biológicas. Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), UBA- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, C1113AAD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Junín 956, C1113AAD, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Silvia Andrea Camperi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Junín 956, C1113AAD, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Paolo Di Gianvincenzo
- Soft Matter Nanotechnology, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 182 C, Donostia, San Sebastián, 20014, Spain
| | - Jésica Ayelén Rodriguez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Junín 956, C1113AAD, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Gabriela Romina Barredo-Vacchelli
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Nanobiotecnología (NANOBIOTEC), Junín 956, C1113AAD, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Gloria Cenci
- Soft Matter Nanotechnology, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 182 C, Donostia, San Sebastián, 20014, Spain
| | - Alejandro Sosnik
- Laboratory of Pharmaceutical Nanomaterials Science, Department of Materials Science and Engineering Technion-Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | - Sergio Moya
- Soft Matter Nanotechnology, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 182 C, Donostia, San Sebastián, 20014, Spain
| | - Graciela Cristina Calabrese
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Ciencias Biológicas. Instituto de Química y Fisicoquímica Biológicas "Prof. Alejandro C. Paladini" (IQUIFIB), UBA- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Junín 956, C1113AAD Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
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18
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Xie M, Zhang L, Han L, Huang L, Huang Y, Yang M, Zhang N. The ASH1L-AS1-ASH1L axis controls NME1-mediated activation of the RAS signaling in gastric cancer. Oncogene 2023; 42:3435-3445. [PMID: 37805663 DOI: 10.1038/s41388-023-02855-8] [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: 04/03/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023]
Abstract
Gastric cancer (GC) is one of the most leading cause of malignancies. However, the molecular mechanisms underlying stomach carcinogenesis remain incompletely understood. Dysregulated genetic and epigenetic alternations significantly contribute to GC development. Here, we report that ASH1L and its antisense lncRNA ASH1L-AS1, which are transcribed from the most significant GC-risk signal at 1q22, act as novel oncogenes. The high levels of ASH1L or lncRNA ASH1L-AS1 expression in GC specimens are associated with worse prognosis of patients. In line with this, ASH1L and ASH1L-AS1 are functionally important in promoting GC disease progression. LncRNA ASH1L-AS1 up-regulates ASH1L transcription, increases histone methyltransferase ASH1L expression and elevates genome-wide H3K4me3 modification levels in GC cells. Furthermore, ASH1L-AS1 directly interacts with transcription factor NME1 protein to form the ASH1L-AS1-NME1 ribonucleoprotein, which transcriptionally promotes expression of ASH1L, ASH1L-AS1, KRAS and RAF1, and activates the RAS signaling pathway in GC cells. Taken together, our data demonstrated that the ASH1L-AS1-ASH1L regulatory axis controls histone modification reprogram and activation of the RAS signaling in cancers. Thus, ASH1L-AS1 might be a novel targets of GC therapeutics and diagnosis in the clinic.
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Affiliation(s)
- Mengyu Xie
- Departemnt of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Long Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Linyu Han
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Linying Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Yizhou Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Nasha Zhang
- Departemnt of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
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19
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Di Donato M, Di Zazzo E, Salvati A, Sorrentino C, Giurato G, Fiore D, Proto MC, Rienzo M, Casamassimi A, Gazzerro P, Bifulco M, Castoria G, Weisz A, Nassa G, Abbondanza C. RIZ2 at the crossroad of the EGF/EGFR signaling in colorectal cancer. J Transl Med 2023; 21:736. [PMID: 37853459 PMCID: PMC10585774 DOI: 10.1186/s12967-023-04621-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most deadly and fourth most diagnosed cancer worldwide. Despite the progress in early diagnosis and advanced therapeutic options, CRC shows a poor prognosis with a 5 year survival rate of ~ 45%. PRDM2/RIZ, a member of PR/SET domain family (PRDM), expresses two main molecular variants, the PR-plus isoform (RIZ1) and the PR-minus (RIZ2). The imbalance in their expression levels in favor of RIZ2 is observed in many cancer types. The full length RIZ1 has been extensively investigated in several cancers where it acts as a tumor suppressor, whereas few studies have explored the RIZ2 oncogenic properties. PRDM2 is often target of frameshift mutations and aberrant DNA methylation in CRC. However, little is known about its role in CRC. METHODS We combined in-silico investigation of The Cancer Genome Atlas (TCGA) CRC datasets, cellular and molecular assays, transcriptome sequencing and functional annotation analysis to assess the role of RIZ2 in human CRC. RESULTS Our in-silico analysis on TCGA datasets confirmed that PRDM2 gene is frequently mutated and transcriptionally deregulated in CRC and revealed that a RIZ2 increase is highly correlated with a significant RIZ1 downregulation. Then, we assayed several CRC cell lines by qRT-PCR analysis for the main PRDM2 transcripts and selected DLD1 cell line, which showed the lowest RIZ2 levels. Therefore, we overexpressed RIZ2 in these cells to mimic TCGA datasets analysis results and consequently to assess the PRDM2/RIZ2 role in CRC. Data from RNA-seq disclosed that RIZ2 overexpression induced profound changes in CRC cell transcriptome via EGF pathway deregulation, suggesting that RIZ2 is involved in the EGF autocrine regulation of DLD1 cell behavior. Noteworthy, the forced RIZ2 expression increased cell viability, growth, colony formation, migration and organoid formation. These effects could be mediated by the release of high EGF levels by RIZ2 overexpressing DLD1 cells. CONCLUSIONS Our findings add novel insights on the putative RIZ2 tumor-promoting functions in CRC, although additional efforts are warranted to define the underlying molecular mechanism.
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Affiliation(s)
- Marzia Di Donato
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Di Zazzo
- Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
| | - Carmela Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | | | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
| | | | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Gabriella Castoria
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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20
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Sundel MH, Sampaio Moura N, Cheng K, Chatain O, Hu S, Drachenberg CB, Xie G, Raufman JP. Selective Activation of M 1 Muscarinic Receptors Attenuates Human Colon Cancer Cell Proliferation. Cancers (Basel) 2023; 15:4766. [PMID: 37835460 PMCID: PMC10571583 DOI: 10.3390/cancers15194766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
M3 muscarinic receptor (M3R) activation stimulates colon cancer cell proliferation, migration, and invasion; M3R expression is augmented in colon cancer and ablating M3R expression in mice attenuates colon neoplasia. Several lines of investigation suggest that in contrast to these pro-neoplastic effects of M3R, M1R plays an opposite role, protecting colon epithelial cells against neoplastic transformation. To pursue these intriguing findings, we examined the relative expression of M1R versus M3R in progressive stages of colon neoplasia and the effect of treating colon cancer cells with selective M1R agonists. We detected divergent expression of M1R and M3R in progressive colon neoplasia, from aberrant crypt foci to adenomas, primary colon cancers, and colon cancer metastases. Treating three human colon cancer cell lines with two selective M1R agonists, we found that in contrast to the effects of M3R activation, selective activation of M1R reversibly inhibited cell proliferation. Moreover, these effects were diminished by pre-incubating cells with a selective M1R inhibitor. Mechanistic insights were gained using selective chemical inhibitors of post-muscarinic receptor signaling molecules and immunoblotting to demonstrate M1R-dependent changes in the activation (phosphorylation) of key downstream kinases, EGFR, ERK1/2, and p38 MAPK. We did not detect a role for drug toxicity, cellular senescence, or apoptosis in mediating M1R agonist-induced attenuated cell proliferation. Lastly, adding M1R-selective agonists to colon cancer cells augmented the anti-proliferative effects of conventional chemotherapeutic agents. Collectively, these results suggest that selective M1R agonism for advanced colon cancer, alone or in combination with conventional chemotherapy, is a therapeutic strategy worth exploring.
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Affiliation(s)
- Margaret H. Sundel
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Natalia Sampaio Moura
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (K.C.); (O.C.); (S.H.); (G.X.)
| | - Kunrong Cheng
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (K.C.); (O.C.); (S.H.); (G.X.)
| | - Oscar Chatain
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (K.C.); (O.C.); (S.H.); (G.X.)
| | - Shien Hu
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (K.C.); (O.C.); (S.H.); (G.X.)
| | - Cinthia B. Drachenberg
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Guofeng Xie
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (K.C.); (O.C.); (S.H.); (G.X.)
- VA Maryland Healthcare System, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jean-Pierre Raufman
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (K.C.); (O.C.); (S.H.); (G.X.)
- VA Maryland Healthcare System, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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21
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Todorova VK, Byrum SD, Mackintosh SG, Jamshidi-Parsian A, Gies AJ, Washam CL, Jenkins SV, Spiva T, Bowman E, Reyna NS, Griffin RJ, Makhoul I. Exosomal MicroRNA and Protein Profiles of Hepatitis B Virus-Related Hepatocellular Carcinoma Cells. Int J Mol Sci 2023; 24:13098. [PMID: 37685904 PMCID: PMC10487651 DOI: 10.3390/ijms241713098] [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: 07/18/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Infection with hepatitis B virus (HBV) is a main risk factor for hepatocellular carcinoma (HCC). Extracellular vesicles, such as exosomes, play an important role in tumor development and metastasis, including regulation of HBV-related HCC. In this study, we have characterized exosome microRNA and proteins released in vitro from hepatitis B virus (HBV)-related HCC cell lines SNU-423 and SNU-182 and immortalized normal hepatocyte cell lines (THLE2 and THLE3) using microRNA sequencing and mass spectrometry. Bioinformatics, including functional enrichment and network analysis, combined with survival analysis using data related to HCC in The Cancer Genome Atlas (TCGA) database, were applied to examine the prognostic significance of the results. More than 40 microRNAs and 200 proteins were significantly dysregulated (p < 0.05) in the exosomes released from HCC cells in comparison with the normal liver cells. The functional analysis of the differentially expressed exosomal miRNAs (i.e., mir-483, mir-133a, mir-34a, mir-155, mir-183, mir-182), their predicted targets, and exosomal differentially expressed proteins (i.e., POSTN, STAM, EXOC8, SNX9, COL1A2, IDH1, FN1) showed correlation with pathways associated with HBV, virus activity and invasion, exosome formation and adhesion, and exogenous protein binding. The results from this study may help in our understanding of the role of HBV infection in the development of HCC and in the development of new targets for treatment or non-invasive predictive biomarkers of HCC.
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Affiliation(s)
- Valentina K. Todorova
- Department of Internal Medicine/Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Allen J. Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Charity L. Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Samir V. Jenkins
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Timothy Spiva
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Emily Bowman
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Nathan S. Reyna
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Robert J. Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Issam Makhoul
- Department of Internal Medicine/Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
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Rotermund A, Staege MS, Brandt S, Luetzkendorf J, Lucas H, Mueller LP, Mueller T. Luciferase Expressing Preclinical Model Systems Representing the Different Molecular Subtypes of Colorectal Cancer. Cancers (Basel) 2023; 15:4122. [PMID: 37627150 PMCID: PMC10452405 DOI: 10.3390/cancers15164122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease. More insight into the biological diversity of CRC is needed to improve therapeutic outcomes. Established CRC cell lines are frequently used and were shown to be representative models of the main subtypes of CRC at the genomic and transcriptomic level. In the present work, we established stable, luciferase expressing derivatives from 10 well-established CRC cell lines, generated spheroids and subcutaneous xenograft tumors in nude mice, and performed comparative characterization of these model systems. Transcriptomic analyses revealed the close relation of cell lines with their derived spheroids and xenograft tumors. The preclinical model systems clustered with patient tumor samples when compared to normal tissue thereby confirming that cell-line-based tumor models retain specific characteristics of primary tumors. Xenografts showed different differentiation patterns and bioluminescence imaging revealed metastatic spread to the lungs. In addition, the models were classified according to the CMS classification system, with further sub-classification according to the recently identified two intrinsic epithelial tumor cell states of CRC, iCMS2 and iCMS3. The combined data showed that regarding primary tumor characteristics, 3D-spheroid cultures resemble xenografts more closely than 2D-cultured cells do. Furthermore, we set up a bioluminescence-based spheroid cytotoxicity assay in order to be able to perform dose-response relationship studies in analogy to typical monolayer assays. Applying the established assay, we studied the efficacy of oxaliplatin. Seven of the ten used cell lines showed a significant reduction in the response to oxaliplatin in the 3D-spheroid model compared to the 2D-monolayer model. Therapy studies in selected xenograft models confirmed the response or lack of response to oxaliplatin treatment. Analyses of differentially expressed genes in these models identified CAV1 as a possible marker of oxaliplatin resistance. In conclusion, we established a combined 2D/3D, in vitro/in vivo model system representing the heterogeneity of CRC, which can be used in preclinical research applications.
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Affiliation(s)
- Arne Rotermund
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
| | - Sarah Brandt
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Jana Luetzkendorf
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Henrike Lucas
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
| | - Lutz P. Mueller
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
| | - Thomas Mueller
- Department of Internal Medicine IV, Hematology and Oncology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (A.R.); (S.B.); (J.L.); (L.P.M.)
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Wu X, Li Z, Wang ZQ, Xu X. The neurological and non-neurological roles of the primary microcephaly-associated protein ASPM. Front Neurosci 2023; 17:1242448. [PMID: 37599996 PMCID: PMC10436222 DOI: 10.3389/fnins.2023.1242448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Primary microcephaly (MCPH), is a neurological disorder characterized by small brain size that results in numerous developmental problems, including intellectual disability, motor and speech delays, and seizures. Hitherto, over 30 MCPH causing genes (MCPHs) have been identified. Among these MCPHs, MCPH5, which encodes abnormal spindle-like microcephaly-associated protein (ASPM), is the most frequently mutated gene. ASPM regulates mitotic events, cell proliferation, replication stress response, DNA repair, and tumorigenesis. Moreover, using a data mining approach, we have confirmed that high levels of expression of ASPM correlate with poor prognosis in several types of tumors. Here, we summarize the neurological and non-neurological functions of ASPM and provide insight into its implications for the diagnosis and treatment of MCPH and cancer.
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Affiliation(s)
- Xingxuan Wu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Zheng Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhao-Qi Wang
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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24
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Aquino A, Bianchi N, Terrazzan A, Franzese O. Protein Kinase C at the Crossroad of Mutations, Cancer, Targeted Therapy and Immune Response. BIOLOGY 2023; 12:1047. [PMID: 37626933 PMCID: PMC10451643 DOI: 10.3390/biology12081047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023]
Abstract
The frequent PKC dysregulations observed in many tumors have made these enzymes natural targets for anticancer applications. Nevertheless, this considerable interest in the development of PKC modulators has not led to the expected therapeutic benefits, likely due to the complex biological activities regulated by PKC isoenzymes, often playing ambiguous and protective functions, further driven by the occurrence of mutations. The structure, regulation and functions of PKCs have been extensively covered in other publications. Herein, we focused on PKC alterations mostly associated with complete functional loss. We also addressed the modest yet encouraging results obtained targeting PKC in selected malignancies and the more frequent negative clinical outcomes. The reported observations advocate the need for more selective molecules and a better understanding of the involved pathways. Furthermore, we underlined the most relevant immune mechanisms controlled by PKC isoforms potentially impacting the immune checkpoint inhibitor blockade-mediated immune recovery. We believe that a comprehensive examination of the molecular features of the tumor microenvironment might improve clinical outcomes by tailoring PKC modulation. This approach can be further supported by the identification of potential response biomarkers, which may indicate patients who may benefit from the manipulation of distinctive PKC isoforms.
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Affiliation(s)
- Angelo Aquino
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.T.)
| | - Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (N.B.); (A.T.)
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Ornella Franzese
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
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25
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Franz C, Wuehrl M, Hartmann S, Klupp F, Schmidt T, Schneider M. Long non-coding RNAs CCAT1 and CCAT2 in colorectal liver metastases are tumor-suppressive via MYC interaction and might predict patient outcomes. PLoS One 2023; 18:e0286486. [PMID: 37347737 PMCID: PMC10287004 DOI: 10.1371/journal.pone.0286486] [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: 01/30/2023] [Accepted: 05/17/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Liver metastases severely reduce the long term survival of colorectal cancer patients. Long non-coding RNAs (lncRNAs) CCAT1 and CCAT2 have previously been found to be associated with impaired patient outcomes in primary colorectal cancer. We aimed to elucidate the role of CCAT1 and CCAT2 in colorectal liver metastases. METHODS Total RNA was isolated from 97 human tissue samples of colorectal liver metastases and adjacent normal liver tissue. Gene expression analysis was performed by RT-qPCR and Multiplex ELISA and correlated with patient characteristics and survival. Gene expression, cancer cell migration, invasion, and proliferation were studied after siRNA-mediated knockdown of CCAT1, CCAT2, and MYC in metastatic colorectal cancer cell lines Colo205 and HROC277Met2. RESULTS Elevated expression levels of lncRNAs CCAT1 and CCAT2, and their common target MYC in colorectal liver metastases were associated with prolonged progression-free survival after liver resection. High expression of CCAT1 was likewise associated with prolonged overall survival. Knockdown of CCAT1, CCAT2, and MYC resulted in increased migratory and invasive potential in metastatic colorectal cancer cell lines. Gene expression analysis revealed alterations in constituents of Wnt signaling following knockdown. CONCLUSION Our findings demonstrate tumor-suppressive functions of lncRNAs CCAT1 and CCAT2 in colorectal liver metastases. They suppress Wnt signaling directly and indirectly through target gene MYC and might prevent further metastatic spread from colorectal liver metastases.
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Affiliation(s)
- Clemens Franz
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Michael Wuehrl
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Sibylle Hartmann
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Fee Klupp
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Thomas Schmidt
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Martin Schneider
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
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26
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He JH, Cao C, Ding Y, Yi Y, Lv YQ, Wang C, Chang Y. A nomogram model for predicting distant metastasis of newly diagnosed colorectal cancer based on clinical features. Front Oncol 2023; 13:1186298. [PMID: 37397373 PMCID: PMC10311479 DOI: 10.3389/fonc.2023.1186298] [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: 03/16/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
Objective Colorectal cancer is one of the most common primary malignancies and the third most common cause of cancer death in both men and women in the United States. Among people diagnosed with initial colorectal cancer, 22% had metastatic colorectal cancer, while the 5-year survival rate was less than 20%. The purpose of this study is to develop a nomogram for predicting distant metastasis in newly diagnosed colorectal cancer patients and to identify high-risk groups. Methods We retrospectively reviewed the data of patients who were diagnosed with colorectal cancer at Zhong nan Hospital of Wuhan University and People's Hospital of Gansu Province between January 2016 and December 2021. Risk predictors for distant metastasis from colorectal patients were determined by the univariate and multivariate logistic regression analyses. Nomograms were developed to predict the probabilities of distant metastatic sites of colorectal cancer patients and evaluated by calibration curves, receiver operating characteristic curves, and decision curve analysis (DCA). Results A total of 327 cases were included in this study: 224 colorectal cancer patients from Zhong nan Hospital of Wuhan University were incorporated into the training set, and 103 colorectal cancer patients from Gansu Provincial People's Hospital were incorporated into the testing set. By univariate logistic regression analysis, platelet (PLT) level (p = 0.009), carcinoembryonic antigen (CEA) level (p = 0.032), histological grade (p < 0.001), colorectal cancer tumor markers (p < 0.001), N stage (p < 0.001), and tumor site (p = 0.005) were associated with distant metastasis in colorectal cancer patients. Multivariate logistic regression analysis showed that N stage (p < 0.001), histological grade (p = 0.026), and colorectal cancer markers (p < 0.001) were independent predictors of distant metastasis in patients initially diagnosed with colorectal cancer. The above six risk factors were used to predict distant metastasis of newly diagnosed colorectal cancer. The C-indexes for the prediction of the nomogram were 0.902 (95% confidence interval (CI), 0.857-0.948). Conclusion The nomogram showed excellent accuracy in predicting distant metastatic sites, and clinical utility may facilitate clinical decision-making.
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Affiliation(s)
- Jiang-Hua He
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Cong Cao
- Department of Colorectal Surgery, Gansu Provincial People’s Hospital, Gansu, China
| | - Yang Ding
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yun Yi
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu-Qing Lv
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chun Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
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27
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Palmieri M, Catimel B, Mouradov D, Sakthianandeswaren A, Kapp E, Ang CS, Williamson NA, Nowell CJ, Christie M, Desai J, Gibbs P, Burgess AW, Sieber OM. PI3K-alpha translocation mediates nuclear PtdIns(3,4,5)P 3 effector signaling in colorectal cancer. Mol Cell Proteomics 2023; 22:100529. [PMID: 36931626 PMCID: PMC10130476 DOI: 10.1016/j.mcpro.2023.100529] [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: 05/12/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The canonical view of phosphatidylinositol 3-kinase alpha (PI3Kα) signaling describes PtdIns(3,4,5)P3 generation and activation of downstream effectors at the plasma membrane or at microtubule-bound endosomes. Here, we show that colorectal cancer (CRC) cell lines exhibit a diverse plasma membrane-nuclear distribution of PI3Kα, controlling corresponding levels of subcellular PtdIns(3,4,5)P3 pools. PI3Kα nuclear translocation was mediated by the importin β-dependent nuclear import pathway. By PtdIns(3,4,5)P3 affinity capture mass spectrometry done in the presence of SDS on CRC cell lines with PI3Kα nuclear localization, we identified 867 potential nuclear PtdIns(3,4,5)P3 effector proteins. Nuclear PtdIns(3,4,5)P3 interactome proteins were characterized by non-canonical PtdIns(3,4,5)P3 binding domains and showed overrepresentation for nuclear membrane, nucleolus and nuclear speckles. The nuclear PtdIns(3,4,5)P3 interactome was enriched for proteins related to RNA metabolism, with splicing reporter assays and SC-35 foci staining suggesting a role of EGF-stimulated nuclear PI3Kα signaling in modulating pre-mRNA splicing. In patient tumors, nuclear p110α staining was associated with lower T stage and mucinous histology. These results indicate that PI3Kα translocation mediates nuclear PtdIns(3,4,5)P3 effector signaling in human CRC, modulating signaling responses.
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Affiliation(s)
- Michelle Palmieri
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Bruno Catimel
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Dmitri Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Anuratha Sakthianandeswaren
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Eugene Kapp
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cameron J Nowell
- Monash Institute for Pharmaceutical Science, Parkville, Victoria, 3052, Australia
| | - Michael Christie
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Pathology, Royal Melbourne Hospital, Parkville, Victoria, 3050, Australia
| | - Jayesh Desai
- Division of Cancer Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, 3050, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Medical Oncology, Western Health, Footscray, Victoria, 3011, Australia
| | - Antony W Burgess
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria, 3050, Australia
| | - Oliver M Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, Victoria, 3050, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia.
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Glutamine Starvation Affects Cell Cycle, Oxidative Homeostasis and Metabolism in Colorectal Cancer Cells. Antioxidants (Basel) 2023; 12:antiox12030683. [PMID: 36978930 PMCID: PMC10045305 DOI: 10.3390/antiox12030683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Cancer cells adjust their metabolism to meet energy demands. In particular, glutamine addiction represents a distinctive feature of several types of tumors, including colorectal cancer. In this study, four colorectal cancer cell lines (Caco-2, HCT116, HT29 and SW480) were cultured with or without glutamine. The growth and proliferation rate, colony-forming capacity, apoptosis, cell cycle, redox homeostasis and metabolomic analysis were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide test (MTT), flow cytometry, high-performance liquid chromatography and gas chromatography/mass spectrometry techniques. The results show that glutamine represents an important metabolite for cell growth and that its deprivation reduces the proliferation of colorectal cancer cells. Glutamine depletion induces cell death and cell cycle arrest in the GO/G1 phase by modulating energy metabolism, the amino acid content and antioxidant defenses. Moreover, the combined glutamine starvation with the glycolysis inhibitor 2-deoxy-D-glucose exerted a stronger cytotoxic effect. This study offers a strong rationale for targeting glutamine metabolism alone or in combination with glucose metabolism to achieve a therapeutic benefit in the treatment of colon cancer.
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In-Depth Analysis of the N-Glycome of Colorectal Cancer Cell Lines. Int J Mol Sci 2023; 24:ijms24054842. [PMID: 36902272 PMCID: PMC10003090 DOI: 10.3390/ijms24054842] [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: 02/03/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer deaths worldwide. A well-known hallmark of cancer is altered glycosylation. Analyzing the N-glycosylation of CRC cell lines may provide potential therapeutic or diagnostic targets. In this study, an in-depth N-glycomic analysis of 25 CRC cell lines was conducted using porous graphitized carbon nano-liquid chromatography coupled to electrospray ionization mass spectrometry. This method allows for the separation of isomers and performs structural characterization, revealing profound N-glycomic diversity among the studied CRC cell lines with the elucidation of a number of 139 N-glycans. A high degree of similarity between the two N-glycan datasets measured on the two different platforms (porous graphitized carbon nano-liquid chromatography electrospray ionization tandem mass spectrometry (PGC-nano-LC-ESI-MS) and matrix-assisted laser desorption/ionization time of flight-mass spectrometry (MALDI-TOF-MS)) was discovered. Furthermore, we studied the associations between glycosylation features, glycosyltransferases (GTs), and transcription factors (TFs). While no significant correlations between the glycosylation features and GTs were found, the association between TF CDX1 and (s)Le antigen expression and relevant GTs FUT3/6 suggests that CDX1 contributes to the expression of the (s)Le antigen through the regulation of FUT3/6. Our study provides a comprehensive characterization of the N-glycome of CRC cell lines, which may contribute to the future discovery of novel glyco-biomarkers of CRC.
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Dotsenko V, Sioofy-Khojine AB, Hyöty H, Viiri K. Human intestinal organoid models for celiac disease research. Methods Cell Biol 2023; 179:173-193. [PMID: 37625874 DOI: 10.1016/bs.mcb.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Celiac disease pathogenesis, in addition to immune cell component, encompasses pathogenic events also in the duodenal epithelium. In celiac disease patients, exposure to dietary gluten induces drastic changes in epithelial differentiation and elicit cellular response to inflammatory cytokines. The autoantigen in celiac disease, transglutaminase 2 (TG2) enzyme, has been also suggested to play its pathogenic gliadin deamidation event in the intestinal epithelium. Therefore in vitro epithelial cell-line models have been exploited in the past to study these pathogenic mechanisms, but they are hampered by their simplistic nature lacking proper cell-type composition and intestinal environ. Moreover, these cell models harbor many cancer-related mutations in tumor suppressor genes making them unsuitable for studying cell differentiation. Intestinal organoids provide a near-native epithelial cell model to study pathogenic agents and mechanisms related to celiac disease. Here we describe protocols to initiate and maintain celiac patient-derived organoid cultures and how to grow them in alternative ways allowing their exploitation in different kind of experiments.
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Affiliation(s)
- Valeriia Dotsenko
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland
| | | | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland
| | - Keijo Viiri
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere University Hospital, Tampere, Finland.
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31
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Lechuga S, Braga-Neto MB, Naydenov NG, Rieder F, Ivanov AI. Understanding disruption of the gut barrier during inflammation: Should we abandon traditional epithelial cell lines and switch to intestinal organoids? Front Immunol 2023; 14:1108289. [PMID: 36875103 PMCID: PMC9983034 DOI: 10.3389/fimmu.2023.1108289] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
Disruption of the intestinal epithelial barrier is a hallmark of mucosal inflammation. It increases exposure of the immune system to luminal microbes, triggering a perpetuating inflammatory response. For several decades, the inflammatory stimuli-induced breakdown of the human gut barrier was studied in vitro by using colon cancer derived epithelial cell lines. While providing a wealth of important data, these cell lines do not completely mimic the morphology and function of normal human intestinal epithelial cells (IEC) due to cancer-related chromosomal abnormalities and oncogenic mutations. The development of human intestinal organoids provided a physiologically-relevant experimental platform to study homeostatic regulation and disease-dependent dysfunctions of the intestinal epithelial barrier. There is need to align and integrate the emerging data obtained with intestinal organoids and classical studies that utilized colon cancer cell lines. This review discusses the utilization of human intestinal organoids to dissect the roles and mechanisms of gut barrier disruption during mucosal inflammation. We summarize available data generated with two major types of organoids derived from either intestinal crypts or induced pluripotent stem cells and compare them to the results of earlier studies with conventional cell lines. We identify research areas where the complementary use of colon cancer-derived cell lines and organoids advance our understanding of epithelial barrier dysfunctions in the inflamed gut and identify unique questions that could be addressed only by using the intestinal organoid platforms.
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Affiliation(s)
- Susana Lechuga
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Manuel B. Braga-Neto
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Nayden G. Naydenov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
| | - Andrei I. Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States
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32
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Zhu J, Peng Z, Tian X, Wu T, Sun A, Yang W, Lin Q. Activation of E3 ubiquitin ligase WWP2 by non-receptor tyrosine kinase ACK1. IUBMB Life 2023. [PMID: 36773333 DOI: 10.1002/iub.2705] [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: 12/03/2022] [Accepted: 01/19/2023] [Indexed: 02/13/2023]
Abstract
WW domain containing E3 ubiquitin protein ligase 2 (WWP2) is a member of the NEDD4 E3 ubiquitin ligase family. WWP2 ligase activity is regulated by the 2, 3-linker auto-inhibition. Tyrosine phosphorylation of the 2, 3-linker was identified as an activating means for releasing the auto-inhibition of WWP2. However, the tyrosine kinase (TK) for the phosphorylation and activation remains unknown. In this report, we have found that non-receptor TK ACK1 binds to the WW3 domain of WWP2 and phosphorylates WWP2. ACK1 phosphorylates WWP2 at the 2, 3-linker and partially activates the ubiquitination ligase activity. Unexpectedly, tyrosine phosphorylation of the 2, 3-linker seems not a major mode for activation of WWP2, as ACK1 causes much higher activation of the 2, 3-linker tyrosine phosphorylation defective mutants of WWP2 than that of wild-type WWP2. Furthermore, epidermal growth factor (EGF) stimulates tyrosine phosphorylation of WWP2 and this EGF-stimulated phosphorylation of WWP2 is mediated by ACK1. Finally, knockdown of WWP2 by shWWP2 inhibits the EGF-dependent cell proliferation of lung cancer A549 cells, suggesting that WWP2 may function in the EGFR signaling in lung cancer progression. Taken together, our findings have revealed a novel mechanism underlying activation of WWP2.
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Affiliation(s)
- Jun Zhu
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ziluo Peng
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xianyan Tian
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tiantian Wu
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Aiqin Sun
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wannian Yang
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qiong Lin
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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33
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Fröhlich J, Rose K, Hecht A. Transcriptional activity mediated by β-CATENIN and TCF/LEF family members is completely dispensable for survival and propagation of multiple human colorectal cancer cell lines. Sci Rep 2023; 13:287. [PMID: 36609428 PMCID: PMC9822887 DOI: 10.1038/s41598-022-27261-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 12/29/2022] [Indexed: 01/08/2023] Open
Abstract
Unrestrained transcriptional activity of β-CATENIN and its binding partner TCF7L2 frequently underlies colorectal tumor initiation and is considered an obligatory oncogenic driver throughout intestinal carcinogenesis. Yet, the TCF7L2 gene carries inactivating mutations in about 10% of colorectal tumors and is non-essential in colorectal cancer (CRC) cell lines. To determine whether CRC cells acquire TCF7L2-independence through cancer-specific compensation by other T-cell factor (TCF)/lymphoid enhancer-binding factor (LEF) family members, or rather lose addiction to β-CATENIN/TCF7L2-driven gene expression altogether, we generated multiple CRC cell lines entirely negative for TCF/LEF or β-CATENIN expression. Survival of these cells and the ability to propagate them demonstrate their complete β-CATENIN- and TCF/LEF-independence. Nonetheless, one β-CATENIN-deficient cell line eventually became senescent, and absence of TCF/LEF proteins and β-CATENIN consistently impaired CRC cell proliferation, reminiscent of mitogenic effects of WNT/β-CATENIN signaling in the healthy intestine. Despite this common phenotype, β-CATENIN-deficient cells exhibited highly cell-line-specific gene expression changes with little overlap between β-CATENIN- and TCF7L2-dependent transcriptomes. Apparently, β-CATENIN and TCF7L2 independently control sizeable fractions of their target genes. The observed divergence of β-CATENIN and TCF7L2 transcriptional programs, and the finding that neither β-CATENIN nor TCF/LEF activity is strictly required for CRC cell survival has important implications when evaluating these factors as potential drug targets.
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Affiliation(s)
- Janna Fröhlich
- grid.5963.9Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Katja Rose
- grid.5963.9Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
| | - Andreas Hecht
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany. .,Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.
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34
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Khawaja H, Briggs R, Latimer CH, Rassel M, Griffin D, Hanson L, Bardelli A, Di Nicolantonio F, McDade SS, Scott CJ, Lambe S, Maurya M, Lindner AU, Prehn JH, Sousa J, Winnington C, LaBonte MJ, Ross S, Van Schaeybroeck S. Bcl-xL Is a Key Mediator of Apoptosis Following KRASG12C Inhibition in KRASG12C-mutant Colorectal Cancer. Mol Cancer Ther 2023; 22:135-149. [PMID: 36279564 PMCID: PMC9808374 DOI: 10.1158/1535-7163.mct-22-0301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/26/2022] [Accepted: 10/13/2022] [Indexed: 01/04/2023]
Abstract
Novel covalent inhibitors of KRASG12C have shown limited response rates in patients with KRASG12C-mutant (MT) colorectal cancer. Thus, novel KRASG12C inhibitor combination strategies that can achieve deep and durable responses are needed. Small-molecule KRASG12C inhibitors AZ'1569 and AZ'8037 were used. To identify novel candidate combination strategies for AZ'1569, we performed RNA sequencing, siRNA, and high-throughput drug screening. Top hits were validated in a panel of KRASG12CMT colorectal cancer cells and in vivo. AZ'1569-resistant colorectal cancer cells were generated and characterized. We found that response to AZ'1569 was heterogeneous across the KRASG12CMT models. AZ'1569 was ineffective at inducing apoptosis when used as a single agent or combined with chemotherapy or agents targeting the EGFR/KRAS/AKT axis. Using a systems biology approach, we identified the antiapoptotic BH3-family member BCL2L1/Bcl-xL as a top hit mediating resistance to AZ'1569. Further analyses identified acute increases in the proapoptotic protein BIM following AZ'1569 treatment. ABT-263 (navitoclax), a pharmacologic Bcl-2 family inhibitor that blocks the ability of Bcl-xL to bind and inhibit BIM, led to dramatic and universal apoptosis when combined with AZ'1569. Furthermore, this combination also resulted in dramatically attenuated tumor growth in KRASG12CMT xenografts. Finally, AZ'1569-resistant cells showed amplification of KRASG12C, EphA2/c-MET activation, increased proinflammatory chemokine profile and cross-resistance to several targeted agents. Importantly, KRAS amplification and AZ'1569 resistance were reversible upon drug withdrawal, arguing strongly for the use of drug holidays in the case of KRAS amplification. Taken together, combinatorial targeting of Bcl-xL and KRASG12C is highly effective, suggesting a novel therapeutic strategy for patients with KRASG12CMT colorectal cancer.
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Affiliation(s)
- Hajrah Khawaja
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Rebecca Briggs
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Cheryl H. Latimer
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Mustasin Rassel
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Daryl Griffin
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | | | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Frederica Di Nicolantonio
- Department of Oncology, University of Torino, Candiolo, Torino, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Simon S. McDade
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Christopher J. Scott
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Shauna Lambe
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Manisha Maurya
- Precision Medicine Centre of Excellence, Health Sciences Building, Queen's University Belfast, Belfast, United Kingdom
| | - Andreas U. Lindner
- Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Jochen H.M. Prehn
- Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Jose Sousa
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom.,Personal Health Data Science Group, Sano. Centre for Computational Personalised Medicine, Krakow, Poland
| | - Chris Winnington
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | - Melissa J. LaBonte
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom
| | | | - Sandra Van Schaeybroeck
- Drug Resistance Group, Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Belfast, United Kingdom.,Corresponding Author: Sandra Van Schaeybroeck, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Lisburn Road 97, Belfast BT9 7AE, United Kingdom. Phone: 4428-9097-2954; Fax: 4428-9097-2776; E-mail:
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35
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Pharmacological Mechanism of Pingxiao Formula against Colorectal Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:7884740. [PMID: 36582768 PMCID: PMC9794442 DOI: 10.1155/2022/7884740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is the most common cancer worldwide and develops due to a broad range of causative factors. Pingxiao (PX) formula and Xihuang (XH) formula are two commonly used drugs to treat CRC, especially as an alternative therapy for those patients who could not suffer surgery, chemotherapy, or immunotherapy, namely, elder or advanced CRC patients. However, the pertinent pharmacological mechanisms are still elusive. The investigation was designed to explain the pharmacological mechanisms of the PX formula. A murine model of CRC was established by injecting CT26.WT cells into the caecum of 4-week-old male Balb/c mice, following PX or XH treatment for 30 days. Network pharmacology analysis combined with weighted gene coexpression network analysis (WGCNA) predicted the pharmacological mechanisms and therapeutic value. High-throughput 16S rRNA sequencing determined the alterations in the gut microbiota communities. Western blotting, immunofluorescence, and flow cytometry examined the influence of PX on the tumor microenvironment (TME). Injection of CT26.WT-induced CRC in Balb/c mice was markedly attenuated by PX treatment. Compared with XH administration, PX exhibited a stronger antitumor effect, such as smaller tumor volume, lower interleukin 17 (IL-17), IL-6 and tumor necrosis factor-alpha (TNFα) serum levels, and higher interferon-gamma (IFN-γ) concentration. Network pharmacology analysis demonstrated that both PX and XH targets were enriched in cancers and inflammatory responses. RNA sequencing confirmed that PX treatment induced cancer cell apoptosis and inhibited inflammatory reactions within the tumor. Moreover, the PX formula considerably restored homeostasis of the gut microbiota, which was not observed in the XH group. PX targets, those associated with the survival probability of CRC patients, correlated with macrophage (Mφ) infiltration, which presented an independent risk factor for the CRC outcome. PX treatment promoted the transition of alternatively activated Mφs (M2 Mφs) to classically activated Mφs (M1 Mφs). Moreover, the peritoneal Mφs from the PX group inhibited the migration of CW26.WT cells, as evidenced by the wound healing experiment and transwell assay, which was consistent with the decreased expression of the vascular endothelial growth factor (VEGF). Furthermore, the coculturing system confirmed that PX-treated Mφs suppressed colorectal tumor-derived organoid proliferation. PX formula exhibits a potential antitumor effect against CRC by suppressing the colonization of pathological microorganisms, reshaping Mφ effector functions and hence inhibiting cancer cell proliferation.
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36
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Sanders LM, Chandra R, Zebarjadi N, Beale HC, Lyle AG, Rodriguez A, Kephart ET, Pfeil J, Cheney A, Learned K, Currie R, Gitlin L, Vengerov D, Haussler D, Salama SR, Vaske OM. Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors. Commun Biol 2022; 5:1367. [PMID: 36513728 PMCID: PMC9747808 DOI: 10.1038/s42003-022-04075-4] [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: 06/17/2020] [Accepted: 10/06/2022] [Indexed: 12/15/2022] Open
Abstract
Cancer cell lines have been widely used for decades to study biological processes driving cancer development, and to identify biomarkers of response to therapeutic agents. Advances in genomic sequencing have made possible large-scale genomic characterizations of collections of cancer cell lines and primary tumors, such as the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA). These studies allow for the first time a comprehensive evaluation of the comparability of cancer cell lines and primary tumors on the genomic and proteomic level. Here we employ bulk mRNA and micro-RNA sequencing data from thousands of samples in CCLE and TCGA, and proteomic data from partner studies in the MD Anderson Cell Line Project (MCLP) and The Cancer Proteome Atlas (TCPA), to characterize the extent to which cancer cell lines recapitulate tumors. We identify dysregulation of a long non-coding RNA and microRNA regulatory network in cancer cell lines, associated with differential expression between cell lines and primary tumors in four key cancer driver pathways: KRAS signaling, NFKB signaling, IL2/STAT5 signaling and TP53 signaling. Our results emphasize the necessity for careful interpretation of cancer cell line experiments, particularly with respect to therapeutic treatments targeting these important cancer pathways.
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Affiliation(s)
- Lauren M. Sanders
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Rahul Chandra
- grid.34477.330000000122986657Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA USA
| | - Navid Zebarjadi
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - Holly C. Beale
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - A. Geoffrey Lyle
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - Analiz Rodriguez
- grid.241054.60000 0004 4687 1637Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Ellen Towle Kephart
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Jacob Pfeil
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Allison Cheney
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
| | - Katrina Learned
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Rob Currie
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Leonid Gitlin
- grid.266102.10000 0001 2297 6811Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California USA
| | - David Vengerov
- grid.419799.b0000 0004 4662 4679Oracle Labs, Oracle Corporation, Pleasanton, CA USA
| | - David Haussler
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA
| | - Sofie R. Salama
- grid.205975.c0000 0001 0740 6917Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA USA
| | - Olena M. Vaske
- grid.205975.c0000 0001 0740 6917UC Santa Cruz Genomics Institute, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Department of Molecular, Cell and Developmental Biology, UC Santa Cruz, Santa Cruz, CA USA
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37
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The chromatin remodeler CHD6 promotes colorectal cancer development by regulating TMEM65-mediated mitochondrial dynamics via EGF and Wnt signaling. Cell Discov 2022; 8:130. [PMID: 36473865 PMCID: PMC9727023 DOI: 10.1038/s41421-022-00478-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/28/2022] [Indexed: 12/12/2022] Open
Abstract
Chromodomain helicase DNA binding protein (CHD) family plays critical roles in regulating gene transcription. The family is linked to cancer disease, but the family member's role in tumorigenesis remains largely unknown. Here, we report that CHD6 is highly expressed in colorectal cancer (CRC). CHD6 knockdown inhibited cancer cell proliferation, migration, invasion, and tumorigenesis. Consistently, Villin-specific Chd6 knockout in mice attenuates cancer formation in AOM/DSS model. We found that aberrant EGF signals promoted the stability of CHD6 by diminishing ubiquitin-mediated degradation. EGF signal inhibits GSK3β activity, which in turn prevents phosphodegron formation of CHD6, thereby hindering E3 ligase FBXW7-mediated CHD6 ubiquitination and degradation. CHD6's chromatin remodeler activity engages in binding Wnt signaling transcription factor TCF4 to facilitate the transcriptional expression of TMEM65, a mitochondrial inner membrane protein involved in ATP production and mitochondrial dynamics. In addition, Wnt signaling is also an upstream regulator of CHD6. CHD6 promoter contains TCF4 and β-catenin binding site, and CHD6 can be transcriptionally activated by Wnt ligand to facilitate TMEM65 transcription. Thus CHD6-TMEM65 axis can be regulated by both EGF and Wnt signaling pathways through two different mechanisms. We further illustrate that CHD6-TMEM65 axis is deregulated in cancer and that co-administration of Wnt inhibitor LGK974 and the anti-EGFR monoclonal antibody cetuximab largely restricted the growth of patient-derived xenografts of CRC. Targeting CHD6-TMEM65 axis may be effective for cancer intervention.
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38
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Desai N, Morris JS, Baladandayuthapani V. NetCellMatch: Multiscale Network-Based Matching of Cancer Cell Lines to Patients Using Graphical Wavelets. Chem Biodivers 2022; 19:e202200746. [PMID: 36279370 PMCID: PMC10066864 DOI: 10.1002/cbdv.202200746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/21/2022] [Indexed: 12/27/2022]
Abstract
Cancer cell lines serve as model in vitro systems for investigating therapeutic interventions. Recent advances in high-throughput genomic profiling have enabled the systematic comparison between cell lines and patient tumor samples. The highly interconnected nature of biological data, however, presents a challenge when mapping patient tumors to cell lines. Standard clustering methods can be particularly susceptible to the high level of noise present in these datasets and only output clusters at one unknown scale of the data. In light of these challenges, we present NetCellMatch, a robust framework for network-based matching of cell lines to patient tumors. NetCellMatch first constructs a global network across all cell line-patient samples using their genomic similarity. Then, a multi-scale community detection algorithm integrates information across topologically meaningful (clustering) scales to obtain Network-Based Matching Scores (NBMS). NBMS are measures of cluster robustness which map patient tumors to cell lines. We use NBMS to determine representative "avatar" cell lines for subgroups of patients. We apply NetCellMatch to reverse-phase protein array data obtained from The Cancer Genome Atlas for patients and the MD Anderson Cell Line Project for cell lines. Along with avatar cell line identification, we evaluate connectivity patterns for breast, lung, and colon cancer and explore the proteomic profiles of avatars and their corresponding top matching patients. Our results demonstrate our framework's ability to identify both patient-cell line matches and potential proteomic drivers of similarity. Our methods are general and can be easily adapted to other'omic datasets.
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Affiliation(s)
- Neel Desai
- Division of Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeffrey S Morris
- Division of Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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39
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Zhao D, Zhang M, Huang S, Liu Q, Zhu S, Li Y, Jiang W, Kiss DL, Cao Q, Zhang L, Chen K. CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells. Nucleic Acids Res 2022; 50:12186-12201. [PMID: 36408932 PMCID: PMC9757051 DOI: 10.1093/nar/gkac1090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/19/2022] [Indexed: 11/22/2022] Open
Abstract
Despite being a member of the chromodomain helicase DNA-binding protein family, little is known about the exact role of CHD6 in chromatin remodeling or cancer disease. Here we show that CHD6 binds to chromatin to promote broad nucleosome eviction for transcriptional activation of many cancer pathways. By integrating multiple patient cohorts for bioinformatics analysis of over a thousand prostate cancer datasets, we found CHD6 expression elevated in prostate cancer and associated with poor prognosis. Further comprehensive experiments demonstrated that CHD6 regulates oncogenicity of prostate cancer cells and tumor development in a murine xenograft model. ChIP-Seq for CHD6, along with MNase-Seq and RNA-Seq, revealed that CHD6 binds on chromatin to evict nucleosomes from promoters and gene bodies for transcriptional activation of oncogenic pathways. These results demonstrated a key function of CHD6 in evicting nucleosomes from chromatin for transcriptional activation of prostate cancer pathways.
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Affiliation(s)
- Dongyu Zhao
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Min Zhang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Shaodong Huang
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qi Liu
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sen Zhu
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yanqiang Li
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Weihua Jiang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Daniel L Kiss
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qi Cao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kaifu Chen
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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40
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Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
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Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
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41
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Won Y, Choi E. Mouse models of Kras activation in gastric cancer. Exp Mol Med 2022; 54:1793-1798. [PMID: 36369466 PMCID: PMC9723172 DOI: 10.1038/s12276-022-00882-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Gastric cancer has one of the highest incidence rates and is one of the leading causes of cancer-related mortality worldwide. Sequential steps within the carcinogenic process are observed in gastric cancer as well as in pancreatic cancer and colorectal cancer. Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most well-known oncogene and can be constitutively activated by somatic mutations in the gene locus. For over 2 decades, the functions of Kras activation in gastrointestinal (GI) cancers have been studied to elucidate its oncogenic roles during the carcinogenic process. Different approaches have been utilized to generate distinct in vivo models of GI cancer, and a number of mouse models have been established using Kras-inducible systems. In this review, we summarize the genetically engineered mouse models in which Kras is activated with cell-type and/or tissue-type specificity that are utilized for studying carcinogenic processes in gastric cancer as well as pancreatic cancer and colorectal cancer. We also provide a brief description of histological phenotypes and characteristics of those mouse models and the current limitations in the gastric cancer field to be investigated further.
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Affiliation(s)
- Yoonkyung Won
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Eunyoung Choi
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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42
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Fragoso MF, Fernandez GJ, Vanderveer L, Cooper HS, Slifker M, Clapper ML. Dysregulation of miR-1-3p: An Early Event in Colitis-Associated Dysplasia. Int J Mol Sci 2022; 23:13024. [PMID: 36361810 PMCID: PMC9657954 DOI: 10.3390/ijms232113024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023] Open
Abstract
Detection of colorectal dysplasia during surveillance colonoscopy remains the best method of determining risk for colitis-associated colorectal cancer (CAC). miRNAs (miRs) show great promise as tissue-specific biomarkers of neoplasia. The goal of this study was to explore the miR expression profile of precancerous dysplastic lesions in the AOM/DSS mouse model and identify early molecular changes associated with CAC. Epithelial cells were laser-microdissected from the colonic mucosa (inflamed versus dysplastic) of mice with AOM/DSS-induced colitis. A miR signature that can distinguish inflamed non-neoplastic mucosa from dysplasia was identified. Bioinformatic analyses led to the discovery of associated miR gene targets and enriched pathways and supported the construction of a network interaction map. miR-1a-3p was one of the miRs with the highest number of predicted targets, including Cdk6. Interestingly, miR-1a-3p and Cdk6 were down- and up-regulated in dysplastic lesions, respectively. Transfection of HCT116 and RKO cells with miR-1a-3p mimics induced apoptosis and cell cycle arrest in G1, suggesting its biological function. A slight reduction in the level of CDK6 transcripts was also observed in cells transfected with miR-1. These data provide novel insight into the early molecular alterations that accompany the development of CAC and identify a miR signature that represents a promising biomarker for the early detection of colitis-associated dysplasia.
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Affiliation(s)
- Mariana F. Fragoso
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Geysson J. Fernandez
- Group Biología y Control de Enfermedades Infecciosas, Universidad de Antioquia–UdeA, Medellín 050010, Colombia
| | - Lisa Vanderveer
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Harry S. Cooper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Michael Slifker
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Margie L. Clapper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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43
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Augustine T, John P, Friedman T, Jiffry J, Guzik H, Mannan R, Gupta R, Delano C, Mariadason JM, Zang X, Maitra R, Goel S. Potentiating effect of reovirus on immune checkpoint inhibition in microsatellite stable colorectal cancer. Front Oncol 2022; 12:1018767. [PMID: 36387154 PMCID: PMC9642964 DOI: 10.3389/fonc.2022.1018767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/28/2022] [Indexed: 09/27/2023] Open
Abstract
The majority of colorectal cancers (CRCs) are microsatellite stable (MSS) and resistant to immunotherapy. The current study explores the possibility of using oncolytic reovirus to sensitize MSS CRC to immune checkpoint inhibition. While reovirus reduced metabolic activity among KRAS Mut cells, microarray/computational analysis revealed microsatellite status-oriented activation of immune-response pathways. Reovirus plus anti-PD-1 treatment increased cell death among MSS cells ex vivo. Reduced tumorigenicity and proliferative index, and increased apoptosis were evident among CT26 [MSS, KRAS Mut], but not in MC38 [microsatellite unstable/MSI, KRAS Wt] syngeneic mouse models under combinatorial treatment. PD-L1-PD-1 signaling axis were differentially altered among CT26/MC38 models. Combinatorial treatment activated the innate immune system, pattern recognition receptors, and antigen presentation markers. Furthermore, we observed the reduction of immunosuppressive macrophages and expansion of effector T cell subsets, as well as reduction in T cell exhaustion. The current investigation sheds light on the immunological mechanisms of the reovirus-anti-PD-1 combination to reduce the growth of MSS CRC.
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Affiliation(s)
- Titto Augustine
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Peter John
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Tyler Friedman
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Neuroscience, Florida State University, Tallahassee, FL, United States
| | - Jeeshan Jiffry
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Hillary Guzik
- Analytical Imaging Facility, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Rifat Mannan
- Department of Pathology, City of Hope, Duarte, CA, United States
| | - Riya Gupta
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Computer Science, Columbia University, New York, NY, United States
| | - Catherine Delano
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - John M. Mariadason
- Gastrointestinal Cancers Program and Oncogenic Transcription Laboratory, Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, VIC, Australia
| | - Xingxing Zang
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Urology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Radhashree Maitra
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY, United States
- Department of Biology, Yeshiva University, New York, NY, United States
| | - Sanjay Goel
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY, United States
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44
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Schamschula E, Kinzel M, Wernstedt A, Oberhuber K, Gottschling H, Schnaiter S, Friedrichs N, Merkelbach-Bruse S, Zschocke J, Gallon R, Wimmer K. Teenage-Onset Colorectal Cancers in a Digenic Cancer Predisposition Syndrome Provide Clues for the Interaction between Mismatch Repair and Polymerase δ Proofreading Deficiency in Tumorigenesis. Biomolecules 2022; 12:biom12101350. [PMID: 36291559 PMCID: PMC9599501 DOI: 10.3390/biom12101350] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) in adolescents and young adults (AYA) is very rare. Known predisposition syndromes include Lynch syndrome (LS) due to highly penetrant MLH1 and MSH2 alleles, familial adenomatous polyposis (FAP), constitutional mismatch-repair deficiency (CMMRD), and polymerase proofreading-associated polyposis (PPAP). Yet, 60% of AYA-CRC cases remain unexplained. In two teenage siblings with multiple adenomas and CRC, we identified a maternally inherited heterozygous PMS2 exon 12 deletion, NM_000535.7:c.2007-786_2174+493del1447, and a paternally inherited POLD1 variant, NP_002682.2:p.Asp316Asn. Comprehensive molecular tumor analysis revealed ultra-mutation (>100 Mut/Mb) and a large contribution of COSMIC signature SBS20 in both siblings’ CRCs, confirming their predisposition to AYA-CRC results from a high propensity for somatic MMR deficiency (MMRd) compounded by a constitutional Pol δ proofreading defect. COSMIC signature SBS20 as well as SBS26 in the index patient’s CRC were associated with an early mutation burst, suggesting MMRd was an early event in tumorigenesis. The somatic second hits in PMS2 were through loss of heterozygosity (LOH) in both tumors, suggesting PPd-independent acquisition of MMRd. Taken together, these patients represent the first cases of cancer predisposition due to heterozygous variants in PMS2 and POLD1. Analysis of their CRCs supports that POLD1-mutated tumors acquire hypermutation only with concurrent MMRd.
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Affiliation(s)
- Esther Schamschula
- Institute of Human Genetics, Medizinische Universität Innsbruck, 6020 Innsbruck, Austria
| | - Miriam Kinzel
- Medicover Humangenetik—Berlin-Lichtenberg, 10315 Berlin, Germany
| | - Annekatrin Wernstedt
- Institute of Human Genetics, Medizinische Universität Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Oberhuber
- Institute of Human Genetics, Medizinische Universität Innsbruck, 6020 Innsbruck, Austria
| | - Hendrik Gottschling
- Institute of Human Genetics, Medizinische Universität Innsbruck, 6020 Innsbruck, Austria
| | - Simon Schnaiter
- Institute of Human Genetics, Medizinische Universität Innsbruck, 6020 Innsbruck, Austria
| | | | | | - Johannes Zschocke
- Institute of Human Genetics, Medizinische Universität Innsbruck, 6020 Innsbruck, Austria
| | - Richard Gallon
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Katharina Wimmer
- Institute of Human Genetics, Medizinische Universität Innsbruck, 6020 Innsbruck, Austria
- Correspondence:
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45
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Shen Y, Xiang Y, Huang X, Zhang Y, Yue Z. Pharmacogenomic Cluster Analysis of Lung Cancer Cell Lines Provides Insights into Preclinical Model Selection in NSCLC. Interdiscip Sci 2022; 14:712-721. [PMID: 35476185 DOI: 10.1007/s12539-022-00517-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Human lung cell lines are utilized widely for investigating tumor biology, experimental therapy, anticancer drug screening and biomarkers identification. However, the consistency of drug responses of these established cell lines and non-small cell lung cancer (NSCLC) is uncertain. In this study, we assessed the drug response consistency between lung cell lines and NSCLC tumors in The Cancer Genome Atlas by hierarchical clustering using copy number variations in driver genes, and profiled the molecular patterns and correlations in cell lines. We found that some frequently used cell lines of NSCLC subtypes were not clustered with their matched subtypes of tumor. Mutation profiles in the oxidative stress response and squamous differentiation pathway in lung cell lines were in concordance with lung squamous cell carcinoma. Furthermore, lung cell lines and tumors in the same sub-cluster had very similar responses to certain drugs but some were inconsistent, suggesting that clustering through copy number variation data could capture part of the suitability of lung cell lines. The analysis of these results could aid investigators in evaluating drug response models and eventually enabling personalized treatment recommendations for individual patients with NSCLC.
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Affiliation(s)
- Yueyue Shen
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Ying Xiang
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Xiaolong Huang
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Youhua Zhang
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhenyu Yue
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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46
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Sialana F, Roumeliotis TI, Bouguenina H, Chan Wah Hak L, Wang H, Caldwell J, Collins I, Chopra R, Choudhary JS. SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics. J Proteome Res 2022; 21:1842-1856. [PMID: 35848491 PMCID: PMC9361352 DOI: 10.1021/acs.jproteome.2c00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations, enabling proteogenomic associations and elucidation of pharmacological mechanisms of action. Although isobaric labeling has increased the throughput of proteomic analysis, the commonly used sample preparation workflows often require time-consuming steps and costly consumables, limiting their suitability for large scale studies. Here, we present a simplified and cost-effective one-pot reaction workflow in a 96-well plate format (SimPLIT) that minimizes processing steps and demonstrates improved reproducibility compared to alternative approaches. The workflow is based on a sodium deoxycholate lysis buffer and a single detergent cleanup step after peptide labeling, followed by quick off-line fractionation and MS2 analysis. We showcase the applicability of the workflow in a panel of colorectal cancer cell lines and by performing target discovery for a set of molecular glue degraders in different cell lines, in a 96-sample assay. Using this workflow, we report frequently dysregulated proteins in colorectal cancer cells and uncover cell-dependent protein degradation profiles of seven cereblon E3 ligase modulators (CRL4CRBN). Overall, SimPLIT is a robust method that can be easily implemented in any proteomics laboratory for medium-to-large scale TMT-based studies for deep profiling of cell lines.
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Affiliation(s)
- Fernando
J. Sialana
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Theodoros I. Roumeliotis
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
| | - Habib Bouguenina
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Laura Chan Wah Hak
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Hannah Wang
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - John Caldwell
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Ian Collins
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rajesh Chopra
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
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47
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Design, Synthesis, and Biological Evaluation of N14-Amino Acid-Substituted Tetrandrine Derivatives as Potential Antitumor Agents against Human Colorectal Cancer. Molecules 2022; 27:molecules27134040. [PMID: 35807286 PMCID: PMC9268013 DOI: 10.3390/molecules27134040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
As a typical dibenzylisoquinoline alkaloid, tetrandrine (TET) is clinically used for the treatment of silicosis, inflammatory pulmonary, and cardiovascular diseases in China. Recent investigations have demonstrated the outstanding anticancer activity of this structure, but its poor aqueous solubility severely restricts its further development. Herein, a series of its 14-N-amino acid-substituted derivatives with improved anticancer effects and aqueous solubility were designed and synthesized. Among them, compound 16 displayed the best antiproliferative activity against human colorectal cancer (HCT-15) cells, with an IC50 value of 0.57 μM. Compared with TET, 16 was markedly improved in terms of aqueous solubility (by 5-fold). Compound 16 significantly suppressed the colony formation, migration, and invasion of HCT-15 cells in a concentration-dependent manner, with it being more potent in this respect than TET. Additionally, compound 16 markedly impaired the morphology and motility of HCT-15 cells and induced the death of colorectal cancer cells in double-staining and flow cytometry assays. Western blot results revealed that 16 could induce the autophagy of HCT-15 cells by significantly decreasing the content of p62/SQSTM1 and enhancing the Beclin-1 level and the ratio of LC3-II to LC3-I. Further study showed that 16 effectively inhibited the proliferation, migration, and tube formation of umbilical vein endothelial cells, manifesting in a potent anti-angiogenesis effect. Overall, these results revealed the potential of 16 as a promising candidate for further preclinical studies.
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48
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Fang L, Ford-Roshon D, Russo M, O'Brien C, Xiong X, Gurjao C, Grandclaudon M, Raghavan S, Corsello SM, Carr SA, Udeshi ND, Berstler J, Sicinska E, Ng K, Giannakis M. RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition. Nat Commun 2022; 13:3181. [PMID: 35676246 PMCID: PMC9177965 DOI: 10.1038/s41467-022-30794-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 05/18/2022] [Indexed: 12/11/2022] Open
Abstract
The RNF43_p.G659fs mutation occurs frequently in colorectal cancer, but its function remains poorly understood and there are no specific therapies directed against this alteration. In this study, we find that RNF43_p.G659fs promotes cell growth independent of Wnt signaling. We perform a drug repurposing library screen and discover that cells with RNF43_p.G659 mutations are selectively killed by inhibition of PI3K signaling. PI3K/mTOR inhibitors yield promising antitumor activity in RNF43659mut isogenic cell lines and xenograft models, as well as in patient-derived organoids harboring RNF43_p.G659fs mutations. We find that RNF43659mut binds p85 leading to increased PI3K signaling through p85 ubiquitination and degradation. Additionally, RNA-sequencing of RNF43659mut isogenic cells reveals decreased interferon response gene expression, that is reversed by PI3K/mTOR inhibition, suggesting that RNF43659mut may alter tumor immunity. Our findings suggest a therapeutic application for PI3K/mTOR inhibitors in treating RNF43_p.G659fs mutant cancers.
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Affiliation(s)
- Lishan Fang
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Research Center, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Dane Ford-Roshon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Max Russo
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Casey O'Brien
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Carino Gurjao
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maximilien Grandclaudon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Srivatsan Raghavan
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven M Corsello
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Ewa Sicinska
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kimmie Ng
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Marios Giannakis
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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49
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Wagner C, Hois V, Taschler U, Schupp M, Lass A. KIAA1363-A Multifunctional Enzyme in Xenobiotic Detoxification and Lipid Ester Hydrolysis. Metabolites 2022; 12:516. [PMID: 35736449 PMCID: PMC9229287 DOI: 10.3390/metabo12060516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/04/2022] Open
Abstract
KIAA1363, annotated as neutral cholesterol ester hydrolase 1 (NCEH1), is a member of the arylacetamide deacetylase (AADAC) protein family. The name-giving enzyme, AADAC, is known to hydrolyze amide and ester bonds of a number of xenobiotic substances, as well as clinical drugs and of endogenous lipid substrates such as diglycerides, respectively. Similarly, KIAA1363, annotated as the first AADAC-like protein, exhibits enzymatic activities for a diverse substrate range including the xenobiotic insecticide chlorpyrifos oxon and endogenous substrates, acetyl monoalkylglycerol ether, cholesterol ester, and retinyl ester. Two independent knockout mouse models have been generated and characterized. However, apart from reduced acetyl monoalkylglycerol ether and cholesterol ester hydrolase activity in specific tissues and cell types, no gross-phenotype has been reported. This raises the question of its physiological role and whether it functions as drug detoxifying enzyme and/or as hydrolase/lipase of endogenous substrates. This review delineates the current knowledge about the structure, function and of the physiological role of KIAA1363, as evident from the phenotypical changes inflicted by pharmacological inhibition or by silencing as well as knockout of KIAA1363 gene expression in cells, as well as mouse models, respectively.
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Affiliation(s)
- Carina Wagner
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; (C.W.); (U.T.)
| | - Victoria Hois
- Division of Endocrinology and Diabetology, Medical University of Graz, 8036 Graz, Austria;
| | - Ulrike Taschler
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; (C.W.); (U.T.)
| | - Michael Schupp
- Cardiovascular Metabolic Renal (CMR)—Research Center, Institute of Pharmacology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
| | - Achim Lass
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; (C.W.); (U.T.)
- BioTechMed-Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, 8010 Graz, Austria
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50
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Wang D, Madunić K, Zhang T, Mayboroda OA, Lageveen-Kammeijer GSM, Wuhrer M. High Diversity of Glycosphingolipid Glycans of Colorectal Cancer Cell Lines Reflects the Cellular Differentiation Phenotype. Mol Cell Proteomics 2022; 21:100239. [PMID: 35489554 PMCID: PMC9157004 DOI: 10.1016/j.mcpro.2022.100239] [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: 02/21/2022] [Revised: 04/04/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC)–associated changes of protein glycosylation have been widely studied. In contrast, the expression of glycosphingolipid (GSL) patterns in CRC has, hitherto, remained largely unexplored. Even though GSLs are major carriers of cell surface carbohydrates, they are understudied due to their complexity and analytical challenges. In this study, we provide an in-depth analysis of GSL glycans of 22 CRC cell lines using porous graphitized carbon nano–liquid chromatography coupled with electrospray ionization–mass spectrometry. Our data revealed that the GSL expression varies among different cell line classifications, with undifferentiated cell lines showing high expression of blood group A, B, and H antigens while for colon-like cell lines the most prominent GSL glycans contained (sialyl)-LewisA/X and LewisB/Y antigens. Moreover, the GSL expression correlated with relevant glycosyltransferases that are involved in their biosynthesis as well as with transcription factors (TFs) implicated in colon differentiation. Additionally, correlations between certain glycosyltransferases and TFs at mRNA expression level were found, such as FUT3, which correlated with CDX1, ETS2, HNF1A, HNF4A, MECOM, and MYB. These TFs are upregulated in colon-like cell lines pointing to their potential role in regulating fucosylation during colon differentiation. In conclusion, our study reveals novel layers of potential GSL glycans regulation relevant for future research in colon differentiation and CRC. Undifferentiated cell lines showed high expression of blood group A, B, and H antigens. Colon-like cell lines are high in GSLs carrying (sialyl)-LewisA/X and LewisB/Y antigens. (Sialyl)-LewisA/X and LewisB/Y antigens associated with expression of FUT3 and CDX1. I-branching was elevated in undifferentiated cells.
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Affiliation(s)
- Di Wang
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | - Katarina Madunić
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | - Tao Zhang
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | - Oleg A Mayboroda
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands
| | | | - Manfred Wuhrer
- Leiden University Medical Center, Center for Proteomics and Metabolomics, RC Leiden, The Netherlands.
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