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Nair MG, Mavatkar AD, Naidu CM, V. P. S, C. E. A, Rajarajan S, Sahoo S, Mohan G, Jaikumar VS, Ramesh RS, B. S. S, Jolly MK, Maliekal TT, Prabhu JS. Elucidating the Role of MicroRNA-18a in Propelling a Hybrid Epithelial-Mesenchymal Phenotype and Driving Malignant Progression in ER-Negative Breast Cancer. Cells 2024; 13:821. [PMID: 38786043 PMCID: PMC11119613 DOI: 10.3390/cells13100821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Epigenetic alterations that lead to differential expression of microRNAs (miRNAs/miR) are known to regulate tumour cell states, epithelial-mesenchymal transition (EMT) and the progression to metastasis in breast cancer. This study explores the key contribution of miRNA-18a in mediating a hybrid E/M cell state that is pivotal to the malignant transformation and tumour progression in the aggressive ER-negative subtype of breast cancer. The expression status and associated effects of miR-18a were evaluated in patient-derived breast tumour samples in combination with gene expression data from public datasets, and further validated in in vitro and in vivo breast cancer model systems. The clinical relevance of the study findings was corroborated against human breast tumour specimens (n = 446 patients). The down-regulated expression of miR-18a observed in ER-negative tumours was found to drive the enrichment of hybrid epithelial/mesenchymal (E/M) cells with luminal attributes, enhanced traits of migration, stemness, drug-resistance and immunosuppression. Further analysis of the miR-18a targets highlighted possible hypoxia-inducible factor 1-alpha (HIF-1α)-mediated signalling in these tumours. This is a foremost report that validates the dual role of miR-18a in breast cancer that is subtype-specific based on hormone receptor expression. The study also features a novel association of low miR-18a levels and subsequent enrichment of hybrid E/M cells, increased migration and stemness in a subgroup of ER-negative tumours that may be attributed to HIF-1α mediated signalling. The results highlight the possibility of stratifying the ER-negative disease into clinically relevant groups by analysing miRNA signatures.
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Affiliation(s)
- Madhumathy G. Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Apoorva D. Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Chandrakala M. Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Snijesh V. P.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Anupama C. E.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Savitha Rajarajan
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science (Bangalore), Bengaluru 560012, Karnataka, India
| | - Gayathri Mohan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Vishnu Sunil Jaikumar
- Animal Research Facility, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Rakesh S. Ramesh
- Department of Surgical Oncology, St. John’s Medical College and Hospital, Bangalore 560034, Karnataka, India
| | - Srinath B. S.
- Department of Surgical Oncology, Sri Shankara Cancer Hospital and Research Centre, Bangalore 560004, Karnataka, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science (Bangalore), Bengaluru 560012, Karnataka, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Jyothi S. Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
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Zhou Q, Pichlmeier S, Denz AM, Schreiner N, Straub T, Benitz S, Wolff J, Fahr L, Del Socorro Escobar Lopez M, Kleeff J, Mayerle J, Mahajan UM, Regel I. Altered histone acetylation patterns in pancreatic cancer cell lines induce subtype‑specific transcriptomic and phenotypical changes. Int J Oncol 2024; 64:26. [PMID: 38240084 PMCID: PMC10807649 DOI: 10.3892/ijo.2024.5614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at advanced tumor stages with chemotherapy as the only treatment option. Transcriptomic analysis has defined a classical and basal‑like PDAC subtype, which are regulated by epigenetic modification. The present study aimed to determine if drug‑induced epigenetic reprogramming of pancreatic cancer cells affects PDAC subtype identity and chemosensitivity. Classical and basal‑like PDAC cell lines PaTu‑S, Capan‑1, Capan‑2, Colo357, PaTu‑T, PANC‑1 and MIAPaCa‑2, were treated for a short (up to 96 h) and long (up to 30 weeks) period with histone acetyltransferase (HAT) and histone deacetylase (HDAC) inhibitors. The cells were analyzed using gene expression approaches, immunoblot analysis, and various cell assays to assess cell characteristics, such as proliferation, colony formation, cell migration and sensitivity to chemotherapeutic drugs. Classical and basal‑like PDAC cell lines showed pronounced epigenetic regulation of subtype‑specific genes through acetylation of lysine 27 on Histone H3 (H3K27ac). Moreover, classical cell lines revealed a significantly decreased expression of HDAC2 and increased total levels of H3K27ac in comparison with the basal‑like cell lines. Following HAT inhibitor treatment, classical cell lines exhibited a loss of epithelial marker gene expression, decreased chemotherapy response gene score and increased cell migration in vitro, indicating a tumor‑promoting phenotype. HDAC inhibitor treatment, however, exerted minimal reprogramming effects in both subtypes. Epigenetic reprogramming of classical and basal‑like tumor cells did not have a major impact on gemcitabine response, although the gemcitabine transporter gene SLC29A1 (solute carrier family 29 member 1) was epigenetically regulated.
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Affiliation(s)
- Quan Zhou
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
| | - Svenja Pichlmeier
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
- Department of Diagnostic and Interventional Radiology, University Hospital Würzburg, D-97080 Würzburg, Germany
| | - Anna Maria Denz
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
| | - Nicole Schreiner
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
| | - Tobias Straub
- Bioinformatic Unit, Biomedical Center, Faculty of Medicine, LMU Munich, D-82152 Planegg-Martinsried, Germany
| | - Simone Benitz
- Department of Surgery, Henry Ford Health System, Detroit, MI 48208, USA
| | - Julia Wolff
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
| | - Lisa Fahr
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
| | | | - Jörg Kleeff
- Department of Surgery, Martin-Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
| | | | - Ivonne Regel
- Department of Medicine II, University Hospital, LMU Munich, D-81377 Munich, Germany
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3
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Patrignani P, Tacconelli S, Contursi A, Piazuelo E, Bruno A, Nobili S, Mazzei M, Milillo C, Hofling U, Hijos-Mallada G, Sostres C, Lanas A. Optimizing aspirin dose for colorectal cancer patients through deep phenotyping using novel biomarkers of drug action. Front Pharmacol 2024; 15:1362217. [PMID: 38495101 PMCID: PMC10941341 DOI: 10.3389/fphar.2024.1362217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/15/2024] [Indexed: 03/19/2024] Open
Abstract
Background: Low-dose aspirin's mechanism of action for preventing colorectal cancer (CRC) is still debated, and the optimal dose remains uncertain. We aimed to optimize the aspirin dose for cancer prevention in CRC patients through deep phenotyping using innovative biomarkers for aspirin's action. Methods: We conducted a Phase II, open-label clinical trial in 34 CRC patients of both sexes randomized to receive enteric-coated aspirin 100 mg/d, 100 mg/BID, or 300 mg/d for 3 ± 1 weeks. Biomarkers were evaluated in blood, urine, and colorectal biopsies at baseline and after dosing with aspirin. Novel biomarkers of aspirin action were assessed in platelets and colorectal tissues using liquid chromatography-mass spectrometry to quantify the extent of cyclooxygenase (COX)-1 and COX-2 acetylation at Serine 529 and Serine 516, respectively. Results: All aspirin doses caused comparable % acetylation of platelet COX-1 at Serine 529 associated with similar profound inhibition of platelet-dependent thromboxane (TX)A2 generation ex vivo (serum TXB2) and in vivo (urinary TXM). TXB2 was significantly reduced in CRC tissue by aspirin 300 mg/d and 100 mg/BID, associated with comparable % acetylation of COX-1. Differently, 100 mg/day showed a lower % acetylation of COX-1 in CRC tissue and no significant reduction of TXB2. Prostaglandin (PG)E2 biosynthesis in colorectal tumors and in vivo (urinary PGEM) remained unaffected by any dose of aspirin associated with the variable and low extent of COX-2 acetylation at Serine 516 in tumor tissue. Increased expression of tumor-promoting genes like VIM (vimentin) and TWIST1 (Twist Family BHLH Transcription Factor 1) vs. baseline was detected with 100 mg/d of aspirin but not with the other two higher doses. Conclusion: In CRC patients, aspirin 300 mg/d or 100 mg/BID had comparable antiplatelet effects to aspirin 100 mg/d, indicating similar inhibition of the platelet's contribution to cancer. However, aspirin 300 mg/d and 100 mg/BID can have additional anticancer effects by inhibiting cancerous tissue's TXA2 biosynthesis associated with a restraining impact on tumor-promoting gene expression. EUDRACT number: 2018-002101-65. Clinical Trial Registration: ClinicalTrials.gov, identifier NCT03957902.
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Affiliation(s)
- Paola Patrignani
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, “G. d’Annunzio” University Medical School, Chieti, Italy
| | - Stefania Tacconelli
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, “G. d’Annunzio” University Medical School, Chieti, Italy
| | - Annalisa Contursi
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, “G. d’Annunzio” University Medical School, Chieti, Italy
| | - Elena Piazuelo
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - Annalisa Bruno
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, “G. d’Annunzio” University Medical School, Chieti, Italy
| | - Stefania Nobili
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, “G. d’Annunzio” University Medical School, Chieti, Italy
| | - Matteo Mazzei
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, “G. d’Annunzio” University Medical School, Chieti, Italy
| | - Cristina Milillo
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Psychological Sciences, Health, and Territory, “G. d’Annunzio” University, Chieti, Italy
| | - Ulrika Hofling
- Systems Pharmacology and Translational Therapeutics Laboratory, at the Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Science, “G. d’Annunzio” University Medical School, Chieti, Italy
| | - Gonzalo Hijos-Mallada
- University Hospital LB, Aragon Health Research Institute (IISAragon), CIBERehd, University of Zaragoza, Zaragoza, Spain
| | - Carlos Sostres
- University Hospital LB, Aragon Health Research Institute (IISAragon), CIBERehd, University of Zaragoza, Zaragoza, Spain
| | - Angel Lanas
- University Hospital LB, Aragon Health Research Institute (IISAragon), CIBERehd, University of Zaragoza, Zaragoza, Spain
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Benitz S, Steep A, Nasser M, Preall J, Mahajan UM, McQuithey H, Loveless I, Davis ET, Wen HJ, Long DW, Metzler T, Zwernik S, Louw M, Rempinski D, Salas-Escabillas D, Brender S, Song L, Huang L, Zhang Z, Steele NG, Regel I, Bednar F, Crawford HC. ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.13.571566. [PMID: 38168289 PMCID: PMC10760092 DOI: 10.1101/2023.12.13.571566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Cellular plasticity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) starting from the conversion of normal cells into precancerous lesions to the progression of carcinoma subtypes associated with aggressiveness and therapeutic response. We discovered that normal acinar cell differentiation, maintained by the transcription factor Pdx1, suppresses a broad gastric cell identity that is maintained in metaplasia, neoplasia, and the classical subtype of PDAC in mouse and human. We have identified the receptor tyrosine kinase Ror2 as marker of a gastric metaplasia (SPEM)-like identity in the pancreas. Ablation of Ror2 in a mouse model of pancreatic tumorigenesis promoted a switch to a gastric pit cell identity that largely persisted through progression to the classical subtype of PDAC. In both human and mouse pancreatic cancer, ROR2 activity continued to antagonize the gastric pit cell identity, strongly promoting an epithelial to mesenchymal transition, conferring resistance to KRAS inhibition, and vulnerability to AKT inhibition.
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Affiliation(s)
- Simone Benitz
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Alec Steep
- Center of Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | - Malak Nasser
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Jonathan Preall
- Cold Spring Harbor Laboratory Cancer Center, Cold Spring Harbor, New York, USA
| | - Ujjwal M Mahajan
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Holly McQuithey
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Ian Loveless
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Erick T Davis
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Hui-Ju Wen
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Daniel W Long
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Thomas Metzler
- Comparative Experimental Pathology (CEP), Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Samuel Zwernik
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Michaela Louw
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Donald Rempinski
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | | | - Sydney Brender
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Linghao Song
- Center of Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | - Ling Huang
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Zhenyu Zhang
- Center of Translational Data Science, University of Chicago, Chicago, Illinois, USA
| | - Nina G Steele
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
- Department of Pathology, Wayne State University, Detroit, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, Lansing, Michigan, USA
- Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Ivonne Regel
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Filip Bednar
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Howard C Crawford
- Department of Surgery, Henry Ford Health System, Detroit, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, Lansing, Michigan, USA
- Department of Oncology, Wayne State University, Detroit, Michigan, USA
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5
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Pilcher L, Solomon L, Dragon JA, Gupta D, Spees JL. The Neural Progenitor Cell-Associated Transcription Factor FoxG1 Regulates Cardiac Epicardial Cell Proliferation. Stem Cells Int 2024; 2024:8601360. [PMID: 38239823 PMCID: PMC10796189 DOI: 10.1155/2024/8601360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/10/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024] Open
Abstract
The epicardium is a layer of mesothelial cells that covers the surface of the heart. During development, epicardial cells undergo epithelial-to-mesenchymal transition (EMT) to form multipotent precursors that migrate into the heart and contribute to the coronary vasculature by differentiating into adventitial fibroblasts, smooth muscle cells, and endothelial cells. Epicardial cells also provide paracrine signals to cardiac myocytes that are required for appropriate heart growth. In adult hearts, a similar process of epicardial cell EMT, migration, and differentiation occurs after myocardial infarction (MI, heart attack). Pathological cardiac hypertrophy is associated with fibrosis, negative remodeling, and reduced cardiac function. In contrast, aerobic exercises such as swimming and running promote physiological (i.e., beneficial) hypertrophy, which is associated with angiogenesis and improved cardiac function. As epicardial cell function(s) during physiological hypertrophy are poorly understood, we analyzed and compared the native epicardial cells isolated directly from the hearts of running-exercised mice and age-matched, nonrunning littermates. To obtain epicardial cells, we enzymatically digested the surfaces of whole hearts and performed magnetic-activated cell sorting (MACS) with antibodies against CD104 (integrin β4). By cDNA microarray assays, we identified genes with increased transcription in epicardial cells after running exercise; these included FoxG1, a transcription factor that controls neural progenitor cell proliferation during brain development and Snord116, a small noncoding RNA that coordinates expression of genes with epigenetic, circadian, and metabolic functions. In cultured epicardial cells, shRNA-mediated FoxG1 knockdown significantly decreased cell proliferation, as well as Snord116 expression. Our results demonstrate that FoxG1 regulates epicardial proliferation, and suggest it may affect cardiac remodeling.
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Affiliation(s)
- Lucy Pilcher
- Department of Medicine, Cardiovascular Research Institute, University of Vermont, Colchester, VT 05446, USA
- Cellular and Molecular Biomedical Sciences Program, University of Vermont, Burlington, VT 05401, USA
| | - Lara Solomon
- Department of Medicine, Cardiovascular Research Institute, University of Vermont, Colchester, VT 05446, USA
- Cellular and Molecular Biomedical Sciences Program, University of Vermont, Burlington, VT 05401, USA
| | - Julie A. Dragon
- Vermont Integrative Genomics Resource, University of Vermont Larner College of Medicine, Burlington, VT 05405, USA
| | - Dhananjay Gupta
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA
| | - Jeffrey L. Spees
- Department of Medicine, Cardiovascular Research Institute, University of Vermont, Colchester, VT 05446, USA
- Cellular and Molecular Biomedical Sciences Program, University of Vermont, Burlington, VT 05401, USA
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Tangsiri M, Hheidari A, Liaghat M, Razlansari M, Ebrahimi N, Akbari A, Varnosfaderani SMN, Maleki-Sheikhabadi F, Norouzi A, Bakhtiyari M, Zalpoor H, Nabi-Afjadi M, Rahdar A. Promising applications of nanotechnology in inhibiting chemo-resistance in solid tumors by targeting epithelial-mesenchymal transition (EMT). Biomed Pharmacother 2024; 170:115973. [PMID: 38064969 DOI: 10.1016/j.biopha.2023.115973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024] Open
Abstract
The resistance of cancer cells to chemotherapy, also known as chemo-resistance, poses a significant obstacle to cancer treatment and can ultimately result in patient mortality. Epithelial-mesenchymal transition (EMT) is one of the many factors and processes responsible for chemo-resistance. Studies have shown that targeting EMT can help overcome chemo-resistance, and nanotechnology and nanomedicine have emerged as promising approaches to achieve this goal. This article discusses the potential of nanotechnology in inhibiting EMT and proposes a viable strategy to combat chemo-resistance in various solid tumors, including breast cancer, lung cancer, pancreatic cancer, glioblastoma, ovarian cancer, gastric cancer, and hepatocellular carcinoma. While nanotechnology has shown promising results in targeting EMT, further research is necessary to explore its full potential in overcoming chemo-resistance and discovering more effective methods in the future.
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Affiliation(s)
- Mona Tangsiri
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Hheidari
- Department of Mechanical Engineering, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Mahsa Liaghat
- Department of Medical Laboratory sciences, Faculty of Medical Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran; Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Mahtab Razlansari
- Faculty of Mathematics and Natural Sciences, Tübingen University, Tübingen 72076, Germany
| | - Narges Ebrahimi
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Abdullatif Akbari
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran; Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Fahimeh Maleki-Sheikhabadi
- Department of Hematology and Blood Banking, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Norouzi
- Dental Research Center, Faculty of Dentistry, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maryam Bakhtiyari
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran; Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hamidreza Zalpoor
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran; Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol 98613-35856, Iran.
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Katuwal NB, Kang MS, Ghosh M, Hong SD, Jeong YG, Park SM, Kim SG, Sohn J, Kim TH, Moon YW. Targeting PEG10 as a novel therapeutic approach to overcome CDK4/6 inhibitor resistance in breast cancer. J Exp Clin Cancer Res 2023; 42:325. [PMID: 38017459 PMCID: PMC10683152 DOI: 10.1186/s13046-023-02903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Breast cancer is the global leading cancer burden in women and the hormone receptor-positive (HR+) subtype is a major part of breast cancer. Though cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors are highly effective therapy for HR+ subtype, acquired resistance is inevitable in most cases. Herein, we investigated the paternally expressed gene 10 (PEG10)-associated mechanism of acquired resistance to CDK4/6 inhibitors. METHODS Palbociclib-resistant cells were generated by exposing human HR+ breast cancer cell lines to palbociclib for 7-9 months. In vitro mechanistic study and in vivo xenograft assay were performed. For clinical relevance, public mRNA microarray data sets of early breast cancer were analyzed and PEG10 immunohistochemical staining was performed using pre-CDK4/6 inhibitor tumor samples. RESULTS We observed that PEG10 was significantly upregulated in palbociclib-resistant cells. Ectopic overexpression of PEG10 in parental cells caused CDK4/6 inhibitor resistance and enhanced epithelial-mesenchymal transition (EMT). On the contrary, PEG10-targeting siRNA or antisense oligonucleotides (ASOs) combined with palbociclib synergistically inhibited proliferation of palbociclib-resistant cells and growth of palbociclib-resistant xenograft in mice and suppressed EMT as well. The mechanistic study confirmed that high PEG10 expression suppressed p21, a natural CDK inhibitor, and SIAH1, a post-translational degrader of ZEB1, augmenting CDK4/6 inhibitor resistance. Then PEG10 siRNA combined with palbociclib suppressed cell cycle progression and EMT via activating p21 and SIAH1, respectively. Consequently, combined PEG10 inhibition and palbociclib overcame CDK4/6 inhibitor resistance. Furthermore, high PEG10 expression was significantly associated with a shorter recurrence-free survival (RFS) based on public mRNA expression data. In pre-CDK4/6 inhibitor treatment tissues, PEG10 positivity by IHC also showed a trend toward a shorter progression-free survival (PFS) with CDK4/6 inhibitor. These results support clinical relevance of PEG10 as a therapeutic target. CONCLUSIONS We demonstrated a novel PEG10-associated mechanism of CDK4/6 inhibitor resistance. We propose PEG10 as a promising therapeutic target for overcoming PEG10-associated resistance to CDK4/6 inhibitors.
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Affiliation(s)
- Nar Bahadur Katuwal
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam-Si, 13488, Republic of Korea
| | - Min Sil Kang
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam-Si, 13488, Republic of Korea
| | - Mithun Ghosh
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam-Si, 13488, Republic of Korea
| | - Sa Deok Hong
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam-Si, 13488, Republic of Korea
| | - Yeong Gyu Jeong
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam-Si, 13488, Republic of Korea
| | - Seong Min Park
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam-Si, 13488, Republic of Korea
| | - Seul-Gi Kim
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, 59 Yatap-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13496, Republic of Korea
| | - Joohyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei, University College of Medicine, Seoul, 03080, Korea
| | - Tae Hoen Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam-Si, 13496, Republic of Korea
| | - Yong Wha Moon
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, 59 Yatap-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13496, Republic of Korea.
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8
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Freke GM, Martins T, Davies RJ, Beyer T, Seda M, Peskett E, Haq N, Prasai A, Otto G, Jeyabalan Srikaran J, Hernandez V, Diwan GD, Russell RB, Ueffing M, Huranova M, Boldt K, Beales PL, Jenkins D. De-Suppression of Mesenchymal Cell Identities and Variable Phenotypic Outcomes Associated with Knockout of Bbs1. Cells 2023; 12:2662. [PMID: 37998397 PMCID: PMC10670506 DOI: 10.3390/cells12222662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue-specific, as well as gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane-trafficking and intraflagellar transport (IFT) adaptor protein complex formed by eight BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis, we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations in Bbs1, as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach, we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically defined clones. Our results suggest that BBS1 is required for the suppression of mesenchymal cell identities as the IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, as well as BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively, this work suggests that the dynamic stability of the BBSome is essential for the suppression of mesenchymal cell identities as epithelial cells differentiate.
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Affiliation(s)
- Grace Mercedes Freke
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tiago Martins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Rosalind Jane Davies
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tina Beyer
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Marian Seda
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Emma Peskett
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Naila Haq
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Avishek Prasai
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Georg Otto
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Jeshmi Jeyabalan Srikaran
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Victor Hernandez
- Life Sciences Department, CHMLS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK;
| | - Gaurav D. Diwan
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Robert B. Russell
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Karsten Boldt
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Philip L. Beales
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Dagan Jenkins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
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9
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AbdelHafez FF, Klausen C, Zhu H, Yi Y, Leung PCK. Growth differentiation factor myostatin regulates epithelial-mesenchymal transition genes and enhances invasion by increasing serine protease inhibitors E1 and E2 in human trophoblast cells. FASEB J 2023; 37:e23204. [PMID: 37738042 DOI: 10.1096/fj.202300740r] [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: 04/14/2023] [Revised: 06/21/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]
Abstract
Placental insufficiency disorders, including preeclampsia and intrauterine growth restriction, are major obstetric complications that can have devastating effects on both the mother and the fetus. These syndromes have underlying poor placental trophoblast cell invasion into uterine tissues. Placental invasion is controlled by many hormones and growth factors. Myostatin (MSTN) is a transforming growth factor-β superfamily member recognized for its important role in muscle growth control. MSTN has also been shown to be secreted and functioning in the placenta, and its serum and/or placental levels were found to be upregulated in preeclampsia and intrauterine growth restriction. Considering that the mechanistic role of MSTN in placentation remains poorly understood, we hypothesized that MSTN uses ALK4/5-SMAD2/3/4 signaling to increase human trophoblast invasion through a group of epithelial-mesenchymal transition genes including SERPINE2, PAI-1, and SOX4. mRNA sequencing of control and MSTN-treated primary human trophoblast cells (n = 5) yielded a total of 610 differentially expressed genes (false discovery rate <0.05) of which 380 genes were upregulated and 230 were downregulated. These differentially expressed genes were highly enriched in epithelial-mesenchymal transition genes, and a subset including SERPINE2, PAI-1, and SOX4 was investigated for its role in MSTN-induced trophoblast cell invasion. We found that MSTN induced upregulation of SERPINE2 via ALK4/5-SMAD2/3/4 signaling; however, SMAD2 was not involved in MSTN-induced PAI-1 upregulation. SOX4 was involved in MSTN-induced upregulation of SERPINE2, but not PAI-1. Collectively, this study discovers novel molecular mechanisms of MSTN-induced human trophoblast cell invasion and provides insight into the functional consequences of its dysregulation in placental insufficiency disorders.
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Affiliation(s)
- Faten F AbdelHafez
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Obstetrics and Gynecology, Assiut School of Medicine, Assiut, Egypt
| | - Christian Klausen
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hua Zhu
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuyin Yi
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter C K Leung
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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10
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Yang Y, Ma B, Djamshidi M, Zhang Q, Sarkar A, Chanda A, Tran U, Soh J, Sandall C, Chen HM, MacDonald JA, Bonni S, Sensen CW, Zheng J, Riabowol K. ING1 inhibits Twist1 expression to block EMT and is antagonized by the HDAC inhibitor vorinostat. Eur J Cell Biol 2023; 102:151341. [PMID: 37459799 DOI: 10.1016/j.ejcb.2023.151341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 09/22/2023] Open
Abstract
ING1 is a chromatin targeting subunit of the Sin3a histone deacetylase (HDAC) complex that alters chromatin structure to subsequently regulate gene expression. We find that ING1 knockdown increases expression of Twist1, Zeb 1&2, Snai1, Bmi1 and TSHZ1 drivers of EMT, promoting EMT and cell motility. ING1 expression had the opposite effect, promoting epithelial cell morphology and inhibiting basal and TGF-β-induced motility in 3D organoid cultures. ING1 binds the Twist1 promoter and Twist1 was largely responsible for the ability of ING1 to reduce cell migration. Consistent with ING1 inhibiting Twist1 expression in vivo, an inverse relationship between ING1 and Twist1 levels was seen in breast cancer samples from The Cancer Genome Atlas (TCGA). The HDAC inhibitor vorinostat is approved for treatment of multiple myeloma and cutaneous T cell lymphoma and is in clinical trials for solid tumours as adjuvant therapy. One molecular target of vorinostat is INhibitor of Growth 2 (ING2), that together with ING1 serve as targeting subunits of the Sin3a HDAC complex. Treatment with sublethal (LD25-LD50) levels of vorinostat promoted breast cancer cell migration several-fold, which increased further upon ING1 knockout. These observations indicate that correct targeting of the Sin3a HDAC complex, and HDAC activity in general decreases luminal and basal breast cancer cell motility, suggesting that use of HDAC inhibitors as adjuvant therapies in breast cancers that are prone to metastasize may not be optimal and requires further investigation.
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Affiliation(s)
- Yang Yang
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, PR China
| | - Biao Ma
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, PR China
| | - Mahbod Djamshidi
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Qingrun Zhang
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Anusi Sarkar
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Ayan Chanda
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Uyen Tran
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Jung Soh
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Christina Sandall
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Huey-Miin Chen
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Justin A MacDonald
- Libin Cardiovascular Institute of Alberta, Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Shirin Bonni
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada
| | | | - Jianhua Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, PR China
| | - Karl Riabowol
- Arnie Charbonneau Cancer Institute, Departments of Biochemistry and Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, Canada.
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11
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Sample RA, Nogueira MF, Mitra RD, Puram SV. Epigenetic regulation of hybrid epithelial-mesenchymal cell states in cancer. Oncogene 2023; 42:2237-2248. [PMID: 37344626 PMCID: PMC10578205 DOI: 10.1038/s41388-023-02749-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/09/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a process by which cells lose their epithelial characteristics and gain mesenchymal phenotypes. In cancer, EMT is thought to drive tumor invasion and metastasis. Recent efforts to understand EMT biology have uncovered that cells undergoing EMT attain a spectrum of intermediate "hybrid E/M" states, which exist along an epithelial-mesenchymal continuum. Here, we summarize recent studies characterizing the epigenetic drivers of hybrid E/M states. We focus on the histone-modification writers, erasers, and readers that assist or oppose the canonical hybrid E/M transcription factors that modulate hybrid E/M state transitions. We also examine the role of chromatin remodelers and DNA methylation in hybrid E/M states. Finally, we highlight the challenges of targeting hybrid E/M pharmacologically, and we propose future directions that might reveal the specific and targetable mechanisms by which hybrid E/M drives metastasis in patients.
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Affiliation(s)
- Reilly A Sample
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Marina F Nogueira
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Sidharth V Puram
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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12
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Zhou J, Zhang XC, Xue S, Dai M, Wang Y, Peng X, Chen J, Wang X, Shen Y, Qin H, Chen B, Zheng Y, Gao X, Xie Z, Ding J, Jiang H, Wu YL, Geng M, Ai J. SYK-mediated epithelial cell state is associated with response to c-Met inhibitors in c-Met-overexpressing lung cancer. Signal Transduct Target Ther 2023; 8:185. [PMID: 37183231 PMCID: PMC10183461 DOI: 10.1038/s41392-023-01403-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/19/2023] [Accepted: 03/05/2023] [Indexed: 05/16/2023] Open
Abstract
Genomic MET amplification and exon 14 skipping are currently clinically recognized biomarkers for stratifying subsets of non-small cell lung cancer (NSCLC) patients according to the predicted response to c-Met inhibitors (c-Metis), yet the overall clinical benefit of this strategy is quite limited. Notably, c-Met protein overexpression, which occurs in approximately 20-25% of NSCLC patients, has not yet been clearly defined as a clinically useful biomarker. An optimized strategy for accurately classifying patients with c-Met overexpression for decision-making regarding c-Meti treatment is lacking. Herein, we found that SYK regulates the plasticity of cells in an epithelial state and is associated with their sensitivity to c-Metis both in vitro and in vivo in PDX models with c-Met overexpression regardless of MET gene status. Furthermore, TGF-β1 treatment resulted in SYK transcriptional downregulation, increased Sp1-mediated transcription of FRA1, and restored the mesenchymal state, which conferred resistance to c-Metis. Clinically, a subpopulation of NSCLC patients with c-Met overexpression coupled with SYK overexpression exhibited a high response rate of 73.3% and longer progression-free survival with c-Meti treatment than other patients. SYK negativity coupled with TGF-β1 positivity conferred de novo and acquired resistance. In summary, SYK regulates cell plasticity toward a therapy-sensitive epithelial cell state. Furthermore, our findings showed that SYK overexpression can aid in precisely stratifying NSCLC patients with c-Met overexpression regardless of MET alterations and expand the population predicted to benefit from c-Met-targeted therapy.
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Affiliation(s)
- Ji Zhou
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xu-Chao Zhang
- Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, 510080, China
| | - Shan Xue
- Department of Respiratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Mengdi Dai
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yueliang Wang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xia Peng
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jianjiao Chen
- Department of Neurobiology, Brain Institute, University of Pittsburgh, Pittsburgh, 15213, USA
| | - Xinyi Wang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yanyan Shen
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hui Qin
- Department of Respiratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Bi Chen
- Department of Respiratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Yu Zheng
- Department of Respiratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiwen Gao
- Department of Respiratory Medicine, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Zuoquan Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jian Ding
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, P. R. China
| | - Handong Jiang
- Department of Respiratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Yi-Long Wu
- Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, 510080, China.
| | - Meiyu Geng
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, P. R. China.
| | - Jing Ai
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, P. R. China.
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13
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Bingham MA, Neijman K, Yang CR, Aponte A, Mak A, Kikuchi H, Jung HJ, Poll BG, Raghuram V, Park E, Chou CL, Chen L, Leipziger J, Knepper MA, Dona M. Circadian gene expression in mouse renal proximal tubule. Am J Physiol Renal Physiol 2023; 324:F301-F314. [PMID: 36727945 PMCID: PMC9988533 DOI: 10.1152/ajprenal.00231.2022] [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: 08/30/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Circadian variability in kidney function is well recognized but is often ignored as a potential confounding variable in physiological experiments. Here, we have created a data resource consisting of expression levels for mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. Small-sample RNA sequencing was applied to microdissected S1 proximal convoluted tubules and S2 proximal straight tubules. After stringent filtering, the data were analyzed using JTK-Cycle to detect periodicity. The data set is provided as a user-friendly webpage at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox2/. In proximal convoluted tubules, 234 transcripts varied in a circadian manner (4.0% of the total). In proximal straight tubules, 334 transcripts varied in a circadian manner (5.3%). Transcripts previously known to be associated with corticosteroid action and with increased flow were found to be overrepresented among circadian transcripts peaking during the "dark" portion of the day [zeitgeber time (ZT)14-22], corresponding to peak levels of corticosterone and glomerular filtration rate in mice. To ask whether there is a time-of-day dependence of protein abundances in the kidney, we carried out LC-MS/MS-based proteomics in whole mouse kidneys at ZT12 and ZT0. The full data set (n = 6,546 proteins) is available at https://esbl.nhlbi.nih.gov/Databases/Circadian-Proteome/. Overall, 293 proteins were differentially expressed between ZT12 and ZT0 (197 proteins greater at ZT12 and 96 proteins greater at ZT0). Among the regulated proteins, only nine proteins were found to be periodic in the RNA-sequencing analysis, suggesting a high level of posttranscriptional regulation of protein abundances.NEW & NOTEWORTHY Circadian variation in gene expression can be an important determinant in the regulation of kidney function. The authors used RNA-sequencing transcriptomics and LC-MS/MS-based proteomics to identify gene products expressed in a periodic manner. The data were used to construct user-friendly web resources.
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Affiliation(s)
- Molly A Bingham
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Kim Neijman
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Chin-Rang Yang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Angel Aponte
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Angela Mak
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hiroaki Kikuchi
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hyun Jun Jung
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Brian G Poll
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Viswanathan Raghuram
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Euijung Park
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Chung-Lin Chou
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Lihe Chen
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Jens Leipziger
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - Mark A Knepper
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Margo Dona
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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14
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Choi J, Choi JH, Lee HW, Seo D, Lkhagvasuren G, Kim JW, Seo SB, Lee K, Lee KH. KPNA3 promotes epithelial-mesenchymal transition by regulating TGF-β and AKT signaling pathways in MDA-MB-231, a triple-negative breast cancer cell line. BMB Rep 2023; 56:120-125. [PMID: 36593106 PMCID: PMC9978358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Indexed: 01/04/2023] Open
Abstract
Karyopherin-α3 (KPNA3), a karyopherin- α isoform, is intimately associated with metastatic progression via epithelial-mesenchymal transition (EMT). However, the molecular mechanism underlying how KPNA3 acts as an EMT inducer remains to be elucidated. In this report, we identified that KPNA3 was significantly upregulated in cancer cells, particularly in triple-negative breast cancer, and its knockdown resulted in the suppression of cell proliferation and metastasis. The comprehensive transcriptome analysis from KPNA3 knockdown cells indicated that KPNA3 is involved in the regulation of numerous EMTrelated genes, including the downregulation of GATA3 and E-cadherin and the up-regulation of HAS2. Moreover, it was found that KPNA3 EMT-mediated metastasis can be achieved by TGF-β or AKT signaling pathways; this suggests that the novel independent signaling pathways KPNA3-TGF-β-GATA3-HAS2/E-cadherin and KPNA3-AKT-HAS2/E-cadherin are involved in the EMT-mediated progress of TNBC MDA-MB-231 cells. These findings provide new insights into the divergent EMT inducibility of KPNA3 according to cell and cancer type. [BMB Reports 2023; 56(2): 120-125].
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Affiliation(s)
- Jaesung Choi
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea
| | - Jee-Hye Choi
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea
| | - Ho Woon Lee
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea
| | - Dongbeom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea
| | - Gavaachimed Lkhagvasuren
- Department of Science of Cultural Heritage, Graduate School, Chung-Ang University, Seoul 06974, Korea
| | - Jung-Woong Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea
| | - Sang-Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea
| | - Kangseok Lee
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea
| | - Kwang-Ho Lee
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Korea, Seoul 06974, Korea,Department of Science of Cultural Heritage, Graduate School, Chung-Ang University, Seoul 06974, Korea,Corresponding author. Tel: +82-2-820-5213; Fax: +82-2-825-5206; E-mail:
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15
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Nygaard V, Ree AH, Dagenborg VJ, Børresen-Dale AL, Edwin B, Fretland ÅA, Grzyb K, Haugen MH, Mælandsmo GM, Flatmark K. A PRRX1 Signature Identifies TIM-3 and VISTA as Potential Immune Checkpoint Targets in a Subgroup of Microsatellite Stable Colorectal Cancer Liver Metastases. CANCER RESEARCH COMMUNICATIONS 2023; 3:235-244. [PMID: 36968142 PMCID: PMC10035516 DOI: 10.1158/2767-9764.crc-22-0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/21/2022] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
Disease recurrence and drug resistance are major challenges in the clinical management of patients with colorectal cancer liver metastases (CLM), and because tumors are generally microsatellite stable (MSS), responses to immune therapies are poor. The mesenchymal phenotype is overrepresented in treatment-resistant cancers and is associated with an immunosuppressed microenvironment. The aim of this work was to molecularly identify and characterize a mesenchymal subgroup of MSS CLM to identify novel therapeutic approaches. We here generated a mesenchymal gene expression signature by analysis of resection specimens from 38 patients with CLM using ranked expression level of the epithelial-to-mesenchymal transition-related transcription factor PRRX1. Downstream pathway analysis based on the resulting gene signature was performed and independent, publicly available datasets were used to validate the findings. A subgroup comprising 16% of the analyzed CLM samples were classified as mesenchymal, or belonging to the PRRX1 high group. Analysis of the PRRX1 signature genes revealed a distinct immunosuppressive phenotype with high expression of immune checkpoints HAVCR2/TIM-3 and VISTA, in addition to the M2 macrophage marker CD163. The findings were convincingly validated in datasets from three external CLM cohorts. Upregulation of immune checkpoints HAVCR2/TIM-3 and VISTA in the PRRX1 high subgroup is a novel finding, and suggests immune evasion beyond the PD-1/PD-L1 axis, which may contribute to poor response to PD-1/PD-L1-directed immune therapy in MSS colorectal cancer. Importantly, these checkpoints represent potential novel opportunities for immune-based therapy approaches in a subset of MSS CLM. Significance CLM is an important cause of colorectal cancer mortality where the majority of patients have yet to benefit from immunotherapies. In this study of gene expression profiling analyses, we uncovered novel immune checkpoint targets in a subgroup of patients with MSS CLMs harboring a mesenchymal phenotype.
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Affiliation(s)
- Vigdis Nygaard
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anne Hansen Ree
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Vegar Johansen Dagenborg
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Bjørn Edwin
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway
- The Intervention Center, Oslo University Hospital, Oslo, Norway
| | - Åsmund Avdem Fretland
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Oslo, Norway
- The Intervention Center, Oslo University Hospital, Oslo, Norway
| | - Krzysztof Grzyb
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Mads H. Haugen
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Gunhild M. Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
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16
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Pettitt GA, Hurst CD, Khan Z, McPherson HR, Dunning MC, Alder O, Platt FM, Black EVI, Burns JE, Knowles MA. Development of resistance to FGFR inhibition in urothelial carcinoma via multiple pathways in vitro. J Pathol 2023; 259:220-232. [PMID: 36385700 PMCID: PMC10107504 DOI: 10.1002/path.6034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/14/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Alterations of fibroblast growth factor receptors (FGFRs) are common in bladder and other cancers and result in disrupted signalling via several pathways. Therapeutics that target FGFRs have now entered the clinic, but, in common with many cancer therapies, resistance develops in most cases. To model this, we derived resistant sublines of two FGFR-driven bladder cancer cell lines by long-term culture with the FGFR inhibitor PD173074 and explored mechanisms using expression profiling and whole-exome sequencing. We identified several resistance-associated molecular profiles. These included HRAS mutation in one case and reversible mechanisms resembling a drug-tolerant persister phenotype in others. Upregulated IGF1R expression in one resistant derivative was associated with sensitivity to linsitinib and a profile with upregulation of a YAP/TAZ signature to sensitivity to the YAP inhibitor CA3 in another. However, upregulation of other potential therapeutic targets was not indicative of sensitivity. Overall, the heterogeneity in resistance mechanisms and commonality of the persister state present a considerable challenge for personalised therapy. Nevertheless, the reversibility of resistance may indicate a benefit from treatment interruptions or retreatment following disease relapse in some patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Geoffrey A Pettitt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Zubeda Khan
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Helen R McPherson
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Matthew C Dunning
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Olivia Alder
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Fiona M Platt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Emma VI Black
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Julie E Burns
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
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17
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Antón-García P, Haghighi EB, Rose K, Vladimirov G, Boerries M, Hecht A. TGFβ1-Induced EMT in the MCF10A Mammary Epithelial Cell Line Model Is Executed Independently of SNAIL1 and ZEB1 but Relies on JUNB-Coordinated Transcriptional Regulation. Cancers (Basel) 2023; 15:558. [PMID: 36672507 PMCID: PMC9856774 DOI: 10.3390/cancers15020558] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) fosters cancer cell invasion and metastasis, the main cause of cancer-related mortality. Growing evidence that SNAIL and ZEB transcription factors, typically portrayed as master regulators of EMT, may be dispensable for this process, led us to re-investigate its mechanistic underpinnings. For this, we used an unbiased computational approach that integrated time-resolved analyses of chromatin structure and differential gene expression, to predict transcriptional regulators of TGFβ1-inducible EMT in the MCF10A mammary epithelial cell line model. Bioinformatic analyses indicated comparatively minor contributions of SNAIL proteins and ZEB1 to TGFβ1-induced EMT, whereas the AP-1 subunit JUNB was anticipated to have a much larger impact. CRISPR/Cas9-mediated loss-of-function studies confirmed that TGFβ1-induced EMT proceeded independently of SNAIL proteins and ZEB1. In contrast, JUNB was necessary and sufficient for EMT in MCF10A cells, but not in A549 lung cancer cells, indicating cell-type-specificity of JUNB EMT-regulatory capacity. Nonetheless, the JUNB-dependence of EMT-associated transcriptional reprogramming in MCF10A cells allowed to define a gene expression signature which was regulated by TGFβ1 in diverse cellular backgrounds, showed positively correlated expression with TGFβ signaling in multiple cancer transcriptomes, and was predictive of patient survival in several cancer types. Altogether, our findings provide novel mechanistic insights into the context-dependent control of TGFβ1-driven EMT and thereby may lead to improved diagnostic and therapeutic options.
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Affiliation(s)
- Pablo Antón-García
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Elham Bavafaye Haghighi
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Katja Rose
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Georg Vladimirov
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Andreas Hecht
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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18
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Ku SC, Liu HL, Su CY, Yeh IJ, Yen MC, Anuraga G, Ta HDK, Chiao CC, Xuan DTM, Prayugo FB, Wang WJ, Wang CY. Comprehensive analysis of prognostic significance of cadherin (CDH) gene family in breast cancer. Aging (Albany NY) 2022; 14:8498-8567. [PMID: 36315446 PMCID: PMC9648792 DOI: 10.18632/aging.204357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Breast cancer is one of the leading deaths in all kinds of malignancies; therefore, it is important for early detection. At the primary tumor site, tumor cells could take on mesenchymal properties, termed the epithelial-to-mesenchymal transition (EMT). This process is partly regulated by members of the cadherin (CDH) family of genes, and it is an essential step in the formation of metastases. There has been a lot of study of the roles of some of the CDH family genes in cancer; however, a holistic approach examining the roles of distinct CDH family genes in the development of breast cancer remains largely unexplored. In the present study, we used a bioinformatics approach to examine expression profiles of CDH family genes using the Oncomine, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), cBioPortal, MetaCore, and Tumor IMmune Estimation Resource (TIMER) platforms. We revealed that CDH1/2/4/11/12/13 messenger (m)RNA levels are overexpressed in breast cancer cells compared to normal cells and were correlated with poor prognoses in breast cancer patients’ distant metastasis-free survival. An enrichment analysis showed that high expressions of CDH1/2/4/11/12/13 were significantly correlated with cell adhesion, the extracellular matrix remodeling process, the EMT, WNT/beta-catenin, and interleukin-mediated immune responses. Collectively, CDH1/2/4/11/12/13 are thought to be potential biomarkers for breast cancer progression and metastasis.
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Affiliation(s)
- Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of General Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Hsin-Liang Liu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Che-Yu Su
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - I-Jeng Yeh
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Chung-Chieh Chiao
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Wei-Jan Wang
- Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 40676, Taiwan
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
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19
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Warrick JI, Knowles MA, Hurst CD, Shuman L, Raman JD, Walter V, Putt J, Dyrskjøt L, Groeneveld C, Castro MAA, Robertson AG, DeGraff DJ. A transcriptional network of cell cycle dysregulation in noninvasive papillary urothelial carcinoma. Sci Rep 2022; 12:16538. [PMID: 36192513 PMCID: PMC9529892 DOI: 10.1038/s41598-022-20927-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Human cancers display a restricted set of expression profiles, despite diverse mutational drivers. This has led to the hypothesis that select sets of transcription factors act on similar target genes as an integrated network, buffering a tumor’s transcriptional state. Noninvasive papillary urothelial carcinoma (NIPUC) with higher cell cycle activity has higher risk of recurrence and progression. In this paper, we describe a transcriptional network of cell cycle dysregulation in NIPUC, which was delineated using the ARACNe algorithm applied to expression data from a new cohort (n = 81, RNA sequencing), and two previously published cohorts. The transcriptional network comprised 121 transcription factors, including the pluripotency factors SOX2 and SALL4, the sex hormone binding receptors ESR1 and PGR, and multiple homeobox factors. Of these 121 transcription factors, 65 and 56 were more active in tumors with greater and less cell cycle activity, respectively. When clustered by activity of these transcription factors, tumors divided into High Cell Cycle versus Low Cell Cycle groups. Tumors in the High Cell Cycle group demonstrated greater mutational burden and copy number instability. A putative mutational driver of cell cycle dysregulation, such as homozygous loss of CDKN2A, was found in only 50% of High Cell Cycle NIPUC, suggesting a prominent role of transcription factor activity in driving cell cycle dysregulation. Activity of the 121 transcription factors strongly associated with expression of EZH2 and other members of the PRC2 complex, suggesting regulation by this complex influences expression of the transcription factors in this network. Activity of transcription factors in this network also associated with signatures of pluripotency and epithelial-to-mesenchymal transition (EMT), suggesting they play a role in driving evolution to invasive carcinoma. Consistent with this, these transcription factors differed in activity between NIPUC and invasive urothelial carcinoma.
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Affiliation(s)
- Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA. .,Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
| | - Margaret A Knowles
- Divison of Molecular Medicine, Leeds Institute of Molecular Research at St James's, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Carolyn D Hurst
- Divison of Molecular Medicine, Leeds Institute of Molecular Research at St James's, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Lauren Shuman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Jay D Raman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Vonn Walter
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Jeffrey Putt
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Clarice Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Équipe Oncologie Moleculaire, Institut Curie, Paris, France
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR, 81520-260, Brazil
| | | | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA. .,Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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20
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Goettsch KA, Zhang L, Singh AB, Dhawan P, Bastola DK. Reliable epithelial-mesenchymal transition biomarkers for colorectal cancer detection. Biomark Med 2022; 16:889-901. [PMID: 35892269 PMCID: PMC9442548 DOI: 10.2217/bmm-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aims: To combat increases in colorectal cancer (CRC) incidence and mortality, biomarkers among differentially expressed genes (DEGs) have been identified to objectively detect cancer. However, DEGs are numerous, and additional parameters may identify more reliable biomarkers. Here, CRC DEGs were filtered into a prioritized list of biomarkers. Materials & methods: Two independent datasets (COAD-READ [n = 698] and GSE50760 [n = 36]) were input alternatively to the recently published data-driven reference method. Results were filtered based on epithelial-mesenchymal transition enrichment (χ-square statistic: 919.05; p = 2.2e-16) to produce 37 potential CRC biomarkers. Results: All 37 genes reliably classified CRC samples and ETV4, CLDN1 and CA2 together were top-ranked by DDR (accuracy: 89%; F1 score: 0.89). Conclusion: Biological and statistical information were combined to produce a better set of CRC detection biomarkers.
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Affiliation(s)
- Kaitlin A Goettsch
- School of Interdisciplinary Informatics, College of Information Science & Technology, University of Nebraska at Omaha, 1110 S. 67th Street, Omaha, NE 68182, USA
| | - Ling Zhang
- School of Interdisciplinary Informatics, College of Information Science & Technology, University of Nebraska at Omaha, 1110 S. 67th Street, Omaha, NE 68182, USA
| | - Amar B Singh
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, 42nd & Emile Streets, Omaha, NE 68198, USA.,Veterans Affairs Nebraska - Western Iowa Health Care System, Research Service, Omaha, NE 68105, USA
| | - Punita Dhawan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, 42nd & Emile Streets, Omaha, NE 68198, USA
| | - Dhundy K Bastola
- School of Interdisciplinary Informatics, College of Information Science & Technology, University of Nebraska at Omaha, 1110 S. 67th Street, Omaha, NE 68182, USA
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21
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Plasma membrane phosphatidylinositol (4,5)-bisphosphate is critical for determination of epithelial characteristics. Nat Commun 2022; 13:2347. [PMID: 35534464 PMCID: PMC9085759 DOI: 10.1038/s41467-022-30061-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/13/2022] [Indexed: 11/20/2022] Open
Abstract
Epithelial cells provide cell-cell adhesion that is essential to maintain the integrity of multicellular organisms. Epithelial cell-characterizing proteins, such as epithelial junctional proteins and transcription factors are well defined. However, the role of lipids in epithelial characterization remains poorly understood. Here we show that the phospholipid phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] is enriched in the plasma membrane (PM) of epithelial cells. Epithelial cells lose their characteristics upon depletion of PM PI(4,5)P2, and synthesis of PI(4,5)P2 in the PM results in the development of epithelial-like morphology in osteosarcoma cells. PM localization of PARD3 is impaired by depletion of PM PI(4,5)P2 in epithelial cells, whereas expression of the PM-targeting exocyst-docking region of PARD3 induces osteosarcoma cells to show epithelial-like morphological changes, suggesting that PI(4,5)P2 regulates epithelial characteristics by recruiting PARD3 to the PM. These results indicate that a high level of PM PI(4,5)P2 plays a crucial role in the maintenance of epithelial characteristics. Epithelial cells provide cell-cell adhesion to maintain the integrity of multicellular organisms. Here the authors show that phospholipid phosphatidylinositol (4,5)-bisphosphate is critical for the maintenance of epithelial characteristics.
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22
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Genest M, Comunale F, Planchon D, Govindin P, Noly D, Vacher S, Bièche I, Robert B, Malhotra H, Schoenit A, Tashireva LA, Casas J, Gauthier-Rouvière C, Bodin S. Upregulated flotillins and sphingosine kinase 2 derail AXL vesicular traffic to promote epithelial-mesenchymal transition. J Cell Sci 2022; 135:274986. [PMID: 35394045 DOI: 10.1242/jcs.259178] [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: 07/21/2021] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Altered endocytosis and vesicular trafficking are major players during tumorigenesis. Flotillin overexpression, a feature observed in many invasive tumors and identified as a marker of poor prognosis, induces a deregulated endocytic and trafficking pathway called upregulated flotillin-induced trafficking (UFIT). Here, we found that in non-tumoral mammary epithelial cells, induction of the UFIT pathway promotes epithelial-to-mesenchymal transition (EMT) and accelerates the endocytosis of several transmembrane receptors, including AXL, in flotillin-positive late endosomes. AXL overexpression, frequently observed in cancer cells, is linked to EMT and metastasis formation. In flotillin-overexpressing non-tumoral mammary epithelial cells and in invasive breast carcinoma cells, we found that the UFIT pathway-mediated AXL endocytosis allows its stabilization and depends on sphingosine kinase 2, a lipid kinase recruited in flotillin-rich plasma membrane domains and endosomes. Thus, the deregulation of vesicular trafficking following flotillin upregulation, and through sphingosine kinase 2, emerges as a new mechanism of AXL overexpression and EMT-inducing signaling pathway activation.
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Affiliation(s)
- Mallory Genest
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Franck Comunale
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Damien Planchon
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Pauline Govindin
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Dune Noly
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, Paris 75005, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris 75005, France
| | - Bruno Robert
- IRCM, Campus Val d'Aurelle, 208 avenue des Apothicaires, 34298 Montpellier, France
| | - Himanshu Malhotra
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Andreas Schoenit
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Liubov A Tashireva
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634050, Russia
| | - Josefina Casas
- Research Unit on BioActive Molecules (RUBAM), Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain.,Liver and Digestive Diseases Networking Biomedical Research Centre (CIBER-EHD), 28029 Madrid, Spain
| | | | - Stéphane Bodin
- CRBM, University of Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
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23
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Transcriptional and post-transcriptional control of epithelial-mesenchymal plasticity: why so many regulators? Cell Mol Life Sci 2022; 79:182. [PMID: 35278142 PMCID: PMC8918127 DOI: 10.1007/s00018-022-04199-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
The dynamic transition between epithelial-like and mesenchymal-like cell states has been a focus for extensive investigation for decades, reflective of the importance of Epithelial-Mesenchymal Transition (EMT) through development, in the adult, and the contributing role EMT has to pathologies including metastasis and fibrosis. Not surprisingly, regulation of the complex genetic networks that underlie EMT have been attributed to multiple transcription factors and microRNAs. What is surprising, however, are the sheer number of different regulators (hundreds of transcription factors and microRNAs) for which critical roles have been described. This review seeks not to collate these studies, but to provide a perspective on the fundamental question of whether it is really feasible that so many regulators play important roles and if so, what does this tell us about EMT and more generally, the genetic machinery that controls complex biological processes.
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Canonical TGFβ signaling induces collective invasion in colorectal carcinogenesis through a Snail1- and Zeb1-independent partial EMT. Oncogene 2022; 41:1492-1506. [PMID: 35075245 PMCID: PMC8897192 DOI: 10.1038/s41388-022-02190-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 12/21/2021] [Accepted: 01/12/2022] [Indexed: 12/12/2022]
Abstract
Local invasion is the initial step towards metastasis, the main cause of cancer mortality. In human colorectal cancer (CRC), malignant cells predominantly invade as cohesive collectives and may undergo partial epithelial-mesenchymal transition (pEMT) at the invasive front. How this particular mode of stromal infiltration is generated is unknown. Here we investigated the impact of oncogenic transformation and the microenvironment on tumor cell invasion using genetically engineered organoids as CRC models. We found that inactivation of the Apc tumor suppressor combined with expression of oncogenic KrasG12D and dominant-negative Trp53R172H did not cell-autonomously induce invasion in vitro. However, oncogenic transformation primed organoids for activation of a collective invasion program upon exposure to the prototypical microenvironmental factor TGFβ1. Execution of this program co-depended on a permissive extracellular matrix which was further actively remodeled by invading organoids. Although organoids shed some epithelial properties particularly at the invasive edge, TGFβ1-stimulated organoids largely maintained epithelial gene expression while additionally implementing a mesenchymal transcription pattern, resulting in a pEMT phenotype that did not progress to a fully mesenchymal state. Notably, while TGFβ1 induced pEMT and promoted collective invasion, it abrogated self-renewal capacity of TKA organoids which correlated with the downregulation of intestinal stem cell (ISC) marker genes. Mechanistically, induction of the non-progressive pEMT required canonical TGFβ signaling mediated by Smad transcription factors (TFs), whereas the EMT master regulators Snail1 and Zeb1 were dispensable. Gene expression profiling provided further evidence for pEMT of TGFβ1-treated organoids and showed that their transcriptomes resemble those of human poor prognosis CMS4 cancers which likewise exhibit pEMT features. We propose that collective invasion in colorectal carcinogenesis is triggered by microenvironmental stimuli through activation of a novel, transcription-mediated form of non-progressive pEMT independently of classical EMT regulators.
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Li Q, Jin Y, Shen Z, Liu H, Shen Y, Wu Z. Construction of a Ferroptosis-Related Gene Signature for Head and Neck Squamous Cell Carcinoma Prognosis Prediction. Int J Gen Med 2022; 14:10117-10129. [PMID: 34992433 PMCID: PMC8711242 DOI: 10.2147/ijgm.s343233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/08/2021] [Indexed: 12/22/2022] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignant cancers, and few studies have demonstrated the value of ferroptosis-related genes in prognosis. Methods The original counts of RNA sequencing data and clinicopathological data were obtained from TCGA and GSE65858 datasets. Common ferroptosis-related genes related to prognosis were identified from the training set and were included in LASSO to determine the best prognosis. To evaluate the efficacy, time-dependent ROC and Kaplan–Meier (KM) survival analyses were applied. Moreover, univariate and multivariate Cox regression analyses were used to screen independent parameters of prognosis and build a nomogram. Eventually, possible biological pathways were proposed based on GSEA. Results Among 242 ferroptosis-related genes, we identified that the FLT3, IL6, Keap1, NQO1, SOCS1 and TRIB3 genes were significantly connected with HNSCC patient prognosis as a six-gene signature. After, the patients were divided into high- and low-risk groups based on the six-gene signature. The KM survival curves demonstrated that the high-risk group had worse OS (p < 0.0001) and higher AUC values (0.654, 0.735, and 0.679 for 1-, 3-, and 5-year survival, respectively) for the prognostic signature of the six genes compared with other genes, which were also validated in the GSE65858 dataset. Moreover, GSEA suggested that the epithelial mesenchymal transition pathway was abundant and that the mesenchymal status in the high-risk group was substantially higher than that in the low-risk group. Finally, the immune microenvironment and differences in the content of immune cell types were demonstrated. Conclusion We established a six-ferroptosis-related-gene model crossing clinical prognostic parameters that can predict HNSCC patient prognosis and provide a reliable prognostic evaluation tool to assist clinical treatment decisions.
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Affiliation(s)
- Qun Li
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, People's Republic of China
| | - Yangli Jin
- Department of Doppler Ultrasonic, Ningbo Yinzhou No.2 Hospital, Ningbo, Zhejiang, People's Republic of China
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, People's Republic of China
| | - Huigao Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Zhenhai Longsai Hospital, Ningbo, Zhejiang, People's Republic of China
| | - Yi Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, People's Republic of China
| | - Zhenhua Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, People's Republic of China
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Wang Q, Karvelsson ST, Kotronoulas A, Gudjonsson T, Halldorsson S, Rolfsson O. Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) is upregulated in breast epithelial-mesenchymal transition and responds to oxidative stress. Mol Cell Proteomics 2021; 21:100185. [PMID: 34923141 PMCID: PMC8803663 DOI: 10.1016/j.mcpro.2021.100185] [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: 05/26/2021] [Revised: 10/20/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Breast cancer cells that have undergone partial epithelial–mesenchymal transition (EMT) are believed to be more invasive than cells that have completed EMT. To study metabolic reprogramming in different mesenchymal states, we analyzed protein expression following EMT in the breast epithelial cell model D492 with single-shot LFQ supported by a SILAC proteomics approach. The D492 EMT cell model contains three cell lines: the epithelial D492 cells, the mesenchymal D492M cells, and a partial mesenchymal, tumorigenic variant of D492 that overexpresses the oncogene HER2. The analysis classified the D492 and D492M cells as basal-like and D492HER2 as claudin-low. Comparative analysis of D492 and D492M to tumorigenic D492HER2 differentiated metabolic markers of migration from those of invasion. Glutamine-fructose-6-phosphate transaminase 2 (GFPT2) was one of the top dysregulated enzymes in D492HER2. Gene expression analysis of the cancer genome atlas showed that GFPT2 expression was a characteristic of claudin-low breast cancer. siRNA-mediated knockdown of GFPT2 influenced the EMT marker vimentin and both cell growth and invasion in vitro and was accompanied by lowered metabolic flux through the hexosamine biosynthesis pathway (HBP). Knockdown of GFPT2 decreased cystathionine and sulfide:quinone oxidoreductase (SQOR) in the transsulfuration pathway that regulates H2S production and mitochondrial homeostasis. Moreover, GFPT2 was within the regulation network of insulin and EGF, and its expression was regulated by reduced glutathione (GSH) and suppressed by the oxidative stress regulator GSK3-β. Our results demonstrate that GFPT2 controls growth and invasion in the D492 EMT model, is a marker for oxidative stress, and associated with poor prognosis in claudin-low breast cancer. GFPT2 is upregulated following EMT. GFPT2 is a marker for claudin-low breast cancer. GFPT2 affects vimentin, cell proliferation, and cell invasion. GFPT2 responds to oxidative stress. GFPT2 is regulated by insulin and EGF.
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Affiliation(s)
- Qiong Wang
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Sigurdur Trausti Karvelsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Aristotelis Kotronoulas
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Thorarinn Gudjonsson
- Stem Cell Research Unit, Biomedical Center, Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavík, Iceland
| | - Skarphedinn Halldorsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Ottar Rolfsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland.
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27
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Raghavan S, Winter PS, Navia AW, Williams HL, DenAdel A, Lowder KE, Galvez-Reyes J, Kalekar RL, Mulugeta N, Kapner KS, Raghavan MS, Borah AA, Liu N, Väyrynen SA, Costa AD, Ng RW, Wang J, Hill EK, Ragon DY, Brais LK, Jaeger AM, Spurr LF, Li YY, Cherniack AD, Booker MA, Cohen EF, Tolstorukov MY, Wakiro I, Rotem A, Johnson BE, McFarland JM, Sicinska ET, Jacks TE, Sullivan RJ, Shapiro GI, Clancy TE, Perez K, Rubinson DA, Ng K, Cleary JM, Crawford L, Manalis SR, Nowak JA, Wolpin BM, Hahn WC, Aguirre AJ, Shalek AK. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell 2021; 184:6119-6137.e26. [PMID: 34890551 PMCID: PMC8822455 DOI: 10.1016/j.cell.2021.11.017] [Citation(s) in RCA: 186] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 09/24/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023]
Abstract
Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding back in vivo-relevant factors and show plasticity in culture models. Further, we prove that non-genetic modulation of cell state can strongly influence drug responses, uncovering state-specific vulnerabilities. This work provides a broadly applicable framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity and manipulating cell state to target associated vulnerabilities.
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Affiliation(s)
- Srivatsan Raghavan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,These authors contributed equally
| | - Peter S. Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,These authors contributed equally,Correspondence: (P.S.W.), (A.J.A.), (A.K.S.)
| | - Andrew W. Navia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,These authors contributed equally
| | - Hannah L. Williams
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,These authors contributed equally
| | - Alan DenAdel
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA,Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Kristen E. Lowder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennyfer Galvez-Reyes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Radha L. Kalekar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nolawit Mulugeta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin S. Kapner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Manisha S. Raghavan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashir A. Borah
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nuo Liu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sara A. Väyrynen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA
| | - Andressa Dias Costa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA
| | - Raymond W.S. Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Junning Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Emma K. Hill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dorisanne Y. Ragon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Lauren K. Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alex M. Jaeger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liam F. Spurr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yvonne Y. Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew D. Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Harvard Medical School, Boston, MA 02115, USA
| | - Matthew A. Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Elizabeth F. Cohen
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Michael Y. Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Isaac Wakiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bruce E. Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Ewa T. Sicinska
- Harvard Medical School, Boston, MA 02115, USA,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tyler E. Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan J. Sullivan
- Harvard Medical School, Boston, MA 02115, USA,Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Thomas E. Clancy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kimberly Perez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Douglas A. Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA,Department of Biostatistics, Brown University, Providence, RI 02912, USA,Microsoft Research New England, Cambridge, MA 02142, USA
| | - Scott R. Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jonathan A. Nowak
- Harvard Medical School, Boston, MA 02115, USA,Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,These authors contributed equally,Senior author
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,These authors contributed equally,Senior author
| | - Andrew J. Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA,These authors contributed equally,Senior author,Correspondence: (P.S.W.), (A.J.A.), (A.K.S.)
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Harvard Medical School, Boston, MA 02115, USA,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA,These authors contributed equally,Senior author,Lead contact,Correspondence: (P.S.W.), (A.J.A.), (A.K.S.)
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Frey P, Devisme A, Rose K, Schrempp M, Freihen V, Andrieux G, Boerries M, Hecht A. SMAD4 mutations do not preclude epithelial-mesenchymal transition in colorectal cancer. Oncogene 2021; 41:824-837. [PMID: 34857888 PMCID: PMC8816731 DOI: 10.1038/s41388-021-02128-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 11/14/2022]
Abstract
Transforming growth factor beta (TGFβ) superfamily signaling is a prime inducer of epithelial-mesenchymal transitions (EMT) that foster cancer cell invasion and metastasis, a major cause of cancer-related deaths. Yet, TGFβ signaling is frequently inactivated in human tumor entities including colorectal cancer (CRC) and pancreatic adenocarcinoma (PAAD) with a high proportion of mutations incapacitating SMAD4, which codes for a transcription factor (TF) central to canonical TGFβ and bone morphogenetic protein (BMP) signaling. Beyond its role in initiating EMT, SMAD4 was reported to crucially contribute to subsequent gene regulatory events during EMT execution. It is therefore widely assumed that SMAD4-mutant (SMAD4mut) cancer cells are unable to undergo EMT. Here, we scrutinized this notion and probed for potential SMAD4-independent EMT execution using SMAD4mut CRC cell lines. We show that SMAD4mut cells exhibit morphological changes, become invasive, and regulate EMT marker genes upon induction of the EMT-TF SNAIL1. Furthermore, SNAIL1-induced EMT in SMAD4mut cells was found to be entirely independent of TGFβ/BMP receptor activity. Global assessment of the SNAIL1-dependent transcriptome confirmed the manifestation of an EMT gene regulatory program in SMAD4mut cells highly related to established EMT signatures. Finally, analyses of human tumor transcriptomes showed that SMAD4 mutations are not underrepresented in mesenchymal tumor samples and that expression patterns of EMT-associated genes are similar in SMAD4mut and SMAD4 wild-type (SMAD4wt) cases. Altogether, our findings suggest that alternative TFs take over the gene regulatory functions of SMAD4 downstream of EMT-TFs, arguing for considerable plasticity of gene regulatory networks operating in EMT execution. Further, they establish that EMT is not categorically precluded in SMAD4mut tumors, which is relevant for their diagnostic and therapeutic evaluation.
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Affiliation(s)
- Patrick Frey
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Antoine Devisme
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katja Rose
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Monika Schrempp
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vivien Freihen
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Hecht
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany. .,Faculty of Biology, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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29
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Title AC, Silva PN, Godbersen S, Hasenöhrl L, Stoffel M. The miR-200-Zeb1 axis regulates key aspects of β-cell function and survival in vivo. Mol Metab 2021; 53:101267. [PMID: 34116231 PMCID: PMC8258987 DOI: 10.1016/j.molmet.2021.101267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The miR-200-Zeb1 axis regulates the epithelial-to-mesenchymal transition (EMT), differentiation, and resistance to apoptosis. A better understanding of these processes in diabetes is highly relevant, as β-cell dedifferentiation and apoptosis contribute to the loss of functional β-cell mass and diabetes progression. Furthermore, EMT promotes the loss of β-cell identity in the in vitro expansion of human islets. Though the miR-200 family has previously been identified as a regulator of β-cell apoptosis in vivo, studies focusing on Zeb1 are lacking. The aim of this study was thus to investigate the role of Zeb1 in β-cell function and survival in vivo. METHODS miR-200 and Zeb1 are involved in a double-negative feedback loop. We characterized a mouse model in which miR-200 binding sites in the Zeb1 3'UTR are mutated (Zeb1200), leading to a physiologically relevant upregulation of Zeb1 mRNA expression. The role of Zeb1 was investigated in this model via metabolic tests and analysis of isolated islets. Further insights into the distinct contributions of the miR-200 and Zeb1 branches of the feedback loop were obtained by crossing the Zeb1200 allele into a background of miR-141-200c overexpression. RESULTS Mild Zeb1 derepression in vivo led to broad transcriptional changes in islets affecting β-cell identity, EMT, insulin secretion, cell-cell junctions, the unfolded protein response (UPR), and the response to ER stress. The aggregation and insulin secretion of dissociated islets of mice homozygous for the Zeb1200 mutation (Zeb1200M) were impaired, and Zeb1200M islets were resistant to thapsigargin-induced ER stress ex vivo. Zeb1200M mice had increased circulating proinsulin levels but no overt metabolic phenotype, reflecting the strong compensatory ability of islets to maintain glucose homeostasis. CONCLUSIONS This study signifies the importance of the miR-200-Zeb1 axis in regulating key aspects of β-cell function and survival. A better understanding of this axis is highly relevant in developing therapeutic strategies for inducing β-cell redifferentiation and maintaining β-cell identity in in vitro islet expansion.
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Affiliation(s)
- Alexandra C Title
- Institute of Molecular Health Sciences (IMHS), ETH Zürich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland; Competence Center Personalized Medicine, ETH Zürich, Voltastrasse 24, 8044, Zürich, Switzerland
| | - Pamuditha N Silva
- Institute of Molecular Health Sciences (IMHS), ETH Zürich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Svenja Godbersen
- Institute of Molecular Health Sciences (IMHS), ETH Zürich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Lynn Hasenöhrl
- Institute of Molecular Health Sciences (IMHS), ETH Zürich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences (IMHS), ETH Zürich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland; Competence Center Personalized Medicine, ETH Zürich, Voltastrasse 24, 8044, Zürich, Switzerland; Medical Faculty, University of Zürich, 8091, Zürich, Switzerland.
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Chen YL, Wang CY, Fang JH, Hsu HP. Serine/threonine-protein kinase 24 is an inhibitor of gastric cancer metastasis through suppressing CDH1 gene and enhancing stemness. Am J Cancer Res 2021; 11:4277-4293. [PMID: 34659887 PMCID: PMC8493374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023] Open
Abstract
Gastric cancer patients often present with distant metastasis and advanced stages. Suppressing serine/threonine-protein kinase 24 (STK24, also known as MST3) is known to promote gastric tumorigenesis. Here, we investigated the effects from STK24 on the metastasis of gastric cancer. We used CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 technology for genetic knockout of STK24 at the genomic DNA level in human MKN45 and mouse M12 gastric cancer cells. To assess the consequences of STK24 knockdown, western blot, cell migration, and wound healing assays were conducted in vitro. An in vivo mouse model of liver metastasis was established and tested, and bioinformatics analyses were performed. The knockdown of the STK24 gene enhanced cell migration and increased liver metastasis in the mouse model of gastric cancer. STK24-silenced tumors suppressed CD4+ T cells and enhanced the expansion of CD11b+Ly6C+ myeloid-derived suppressor cells (MDSCs) and F4/80+ macrophages in the spleen of the mice. In MKN45 cells, STK24 silencing resulted in downregulation of E-cadherin (gene CDH1, Cadherin-1, or epithelial cadherin). In 38 paired specimens of gastric adenocarcinomas and normal tissues, we examined STK24 and CDH1 expression levels via western blot; a positive correlation between the expression levels of STK24 and CDH1 was found (R2 = 0.5507, P = 9.72 × 10-8). Furthermore, in Oncomine database and Kaplan-Meier plotter analysis, the loss of CDH1, increase in CCL2, and upregulation of CD44 were correlated with poor prognosis of gastric cancer patients. Our results demonstrate that knockdown of STK24 increases cell migration through suppressing CDH1 and enhancing CD44. In experimental model of metastatic gastric cancer in syngeneic inbred mice, STK24 is important for immune suppression through expansion of CD11b+Ly6C+ MDSCs and F4/80+ macrophages. We confirmed that STK24 is an inhibitor of gastric cancer metastasis.
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Affiliation(s)
- Yi-Ling Chen
- Department of Senior Citizen Service Management, Chia Nan University of Pharmacy and ScienceTainan, Taiwan
- Department of Health and Nutrition, Chia Nan University of Pharmacy and ScienceTainan, Taiwan
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei, Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei, Taiwan
| | - Jung-Hua Fang
- Laboratory Animal Center, College of Medicine, National Cheng Kung UniversityTainan, Taiwan
| | - Hui-Ping Hsu
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung UniversityTainan, Taiwan
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Baasch S, Giansanti P, Kolter J, Riedl A, Forde AJ, Runge S, Zenke S, Elling R, Halenius A, Brabletz S, Hengel H, Kuster B, Brabletz T, Cicin-Sain L, Arens R, Vlachos A, Rohr JC, Stemmler MP, Kopf M, Ruzsics Z, Henneke P. Cytomegalovirus subverts macrophage identity. Cell 2021; 184:3774-3793.e25. [PMID: 34115982 DOI: 10.1016/j.cell.2021.05.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/26/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022]
Abstract
Cytomegaloviruses (CMVs) have co-evolved with their mammalian hosts for millions of years, leading to remarkable host specificity and high infection prevalence. Macrophages, which already populate barrier tissues in the embryo, are the predominant immune cells at potential CMV entry sites. Here we show that, upon CMV infection, macrophages undergo a morphological, immunophenotypic, and metabolic transformation process with features of stemness, altered migration, enhanced invasiveness, and provision of the cell cycle machinery for viral proliferation. This complex process depends on Wnt signaling and the transcription factor ZEB1. In pulmonary infection, mouse CMV primarily targets and reprograms alveolar macrophages, which alters lung physiology and facilitates primary CMV and secondary bacterial infection by attenuating the inflammatory response. Thus, CMV profoundly perturbs macrophage identity beyond established limits of plasticity and rewires specific differentiation processes, allowing viral spread and impairing innate tissue immunity.
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Affiliation(s)
- Sebastian Baasch
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Piero Giansanti
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Julia Kolter
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - André Riedl
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Aaron James Forde
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Solveig Runge
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Simon Zenke
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Roland Elling
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany
| | - Anne Halenius
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Simone Brabletz
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hartmut Hengel
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University Munich, 85354 Freising, Germany
| | - Thomas Brabletz
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Luka Cicin-Sain
- Immune Aging and Chronic Infections Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hanover Medical School (MHH), 30625 Hanover, Germany
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Jan Christopher Rohr
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany
| | - Marc Philippe Stemmler
- Department of Experimental Medicine I, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Zsolt Ruzsics
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Philipp Henneke
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Center for Pediatrics and Adolescent Medicine, University Medical Center, 79106 Freiburg, Germany.
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AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency. Proc Natl Acad Sci U S A 2021; 118:2104841118. [PMID: 34088849 DOI: 10.1073/pnas.2104841118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Somatic cell transcription factors are critical to maintaining cellular identity and constitute a barrier to human somatic cell reprogramming; yet a comprehensive understanding of the mechanism of action is lacking. To gain insight, we examined epigenome remodeling at the onset of human nuclear reprogramming by profiling human fibroblasts after fusion with murine embryonic stem cells (ESCs). By assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing we identified enrichment for the activator protein 1 (AP-1) transcription factor c-Jun at regions of early transient accessibility at fibroblast-specific enhancers. Expression of a dominant negative AP-1 mutant (dnAP-1) reduced accessibility and expression of fibroblast genes, overcoming the barrier to reprogramming. Remarkably, efficient reprogramming of human fibroblasts to induced pluripotent stem cells was achieved by transduction with vectors expressing SOX2, KLF4, and inducible dnAP-1, demonstrating that dnAP-1 can substitute for exogenous human OCT4. Mechanistically, we show that the AP-1 component c-Jun has two unexpected temporally distinct functions in human reprogramming: 1) to potentiate fibroblast enhancer accessibility and fibroblast-specific gene expression, and 2) to bind to and repress OCT4 as a complex with MBD3. Our findings highlight AP-1 as a previously unrecognized potent dual gatekeeper of the somatic cell state.
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Bannerman D, Pascual-Gil S, Floryan M, Radisic M. Bioengineering strategies to control epithelial-to-mesenchymal transition for studies of cardiac development and disease. APL Bioeng 2021; 5:021504. [PMID: 33948525 PMCID: PMC8068500 DOI: 10.1063/5.0033710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is a process that occurs in a wide range of tissues and environments, in response to numerous factors and conditions, and plays a critical role in development, disease, and regeneration. The process involves epithelia transitioning into a mobile state and becoming mesenchymal cells. The investigation of EMT processes has been important for understanding developmental biology and disease progression, enabling the advancement of treatment approaches for a variety of disorders such as cancer and myocardial infarction. More recently, tissue engineering efforts have also recognized the importance of controlling the EMT process. In this review, we provide an overview of the EMT process and the signaling pathways and factors that control it, followed by a discussion of bioengineering strategies to control EMT. Important biological, biomaterial, biochemical, and physical factors and properties that have been utilized to control EMT are described, as well as the studies that have investigated the modulation of EMT in tissue engineering and regenerative approaches in vivo, with a specific focus on the heart. Novel tools that can be used to characterize and assess EMT are discussed and finally, we close with a perspective on new bioengineering methods that have the potential to transform our ability to control EMT, ultimately leading to new therapies.
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Jarroux J, Foretek D, Bertrand C, Gabriel M, Szachnowski U, Saci Z, Guo S, Londoño-Vallejo A, Pinskaya M, Morillon A. HOTAIR lncRNA promotes epithelial-mesenchymal transition by redistributing LSD1 at regulatory chromatin regions. EMBO Rep 2021; 22:e50193. [PMID: 33960111 PMCID: PMC8366456 DOI: 10.15252/embr.202050193] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Epithelial‐to‐mesenchymal transition (EMT) describes the loss of epithelial traits and gain of mesenchymal traits by normal cells during development and by neoplastic cells during cancer metastasis. The long noncoding RNA HOTAIR triggers EMT, in part by serving as a scaffold for PRC2 and thus promoting repressive histone H3K27 methylation. In addition to PRC2, HOTAIR interacts with the LSD1 lysine demethylase, an epigenetic regulator of cell fate during development and differentiation, but little is known about the role of LSD1 in HOTAIR function during EMT. Here, we show that HOTAIR requires its LSD1‐interacting domain, but not its PRC2‐interacting domain, to promote the migration of epithelial cells. This activity is suppressed by LSD1 overexpression. LSD1‐HOTAIR interactions induce partial reprogramming of the epithelial transcriptome altering LSD1 distribution at promoter and enhancer regions. Thus, we uncover an unexpected role of HOTAIR in EMT as an LSD1 decommissioning factor, counteracting its activity in the control of epithelial identity.
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Affiliation(s)
- Julien Jarroux
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Dominika Foretek
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Claire Bertrand
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Marc Gabriel
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Zohra Saci
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Shuling Guo
- Ionis Pharmaceuticals, Inc, Carlsbad, CA, USA
| | - Arturo Londoño-Vallejo
- Telomeres and Cancer, CNRS UMR3244, Sorbonne Université, PSL Université, Institut Curie, Centre de Recherche, Paris, France
| | - Marina Pinskaya
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
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Yang J, Wang X, Huang B, Liu R, Xiong H, Ye F, Zeng C, Fu X, Li L. An IFNγ/STAT1/JMJD3 Axis Induces ZEB1 Expression and Promotes Aggressiveness in Lung Adenocarcinoma. Mol Cancer Res 2021; 19:1234-1246. [PMID: 33771881 DOI: 10.1158/1541-7786.mcr-20-0948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/14/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Active IFNγ signaling is a common feature of tumors responding to PD-1 checkpoint blockade. IFNγ exhibits both anti- and protumor activities. Here, we show that the treatment of lung adenocarcinoma cells with IFNγ led to a rapid increase of ZEB1 expression and a significant change in epithelial-to-mesenchymal transition (EMT)-associated gene expression pattern. Moreover, functional analyses show that IFNγ promoted cell migration in vitro and metastasis in vivo. We demonstrate that ZEB1 is required for IFNγ-promoted EMT, cell migration, and metastasis, as RNAi-mediated knockdown of ZEB1 abrogated EMT, cell migration, and metastasis induced by IFNγ. We show that IFNγ induced upregulation of JMJD3 significantly reduced H3K27 trimethylation in the promoter of the ZEB1 gene, which led to activation of ZEB1 gene transcription. IFNγ-induced JMJD3 expression was JAK1/2-STAT1 dependent. Inhibition of JMJD3 abrogated IFNγ-induced ZEB1 expression. IFNγ-induced ZEB1 also reduced miR-200 expression. Downregulation of ZEB1 increased miR-200 expression, which led to a reduction of PD-L1 expression induced by IFNγ. It is worth noting that knockdown of ZEB1 did not affect IFNγ-mediated antiproliferation and induction of CXCL9 and CXCL10. Thus, downregulation of ZEB1 may prevent the protumor activity of IFNγ while retaining its antitumor function. This study expands our understanding of IFNγ-mediated signaling and helps to identify therapeutic targets to improve current immunotherapies. IMPLICATIONS: IFNγ increases ZEB1 expression in a STAT1-JMJD3 dependent manner, and consequently promotes cancer cell aggressiveness. This study provides a potential target to minimize the procancer effect of IFNγ while preserving its antitumor function.
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Affiliation(s)
- Jianjian Yang
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Xue Wang
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Bing Huang
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Rong Liu
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Hui Xiong
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Fan Ye
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Chenxi Zeng
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Xiangning Fu
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.
| | - Lequn Li
- Thoracic Surgery Laboratory, Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.
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Preoperative immune landscape predisposes adverse outcomes in hepatocellular carcinoma patients with liver transplantation. NPJ Precis Oncol 2021; 5:27. [PMID: 33772139 PMCID: PMC7997876 DOI: 10.1038/s41698-021-00167-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/03/2021] [Indexed: 01/15/2023] Open
Abstract
Immune class in hepatocellular carcinoma (HCC) has been shown to possess immunogenic power; however, how preestablished immune landscapes in premalignant and early HCC stages impact the clinical outcomes of HCC patients remains unexplored. We sequenced bulk transcriptomes for 62 malignant tumor samples from a Korean HCC cohort in which 38 patients underwent total hepatectomy, as well as for 15 normal and 47 adjacent nontumor samples. Using in silico deconvolution of expression mixtures, 22 immune cell fractions for each sample were inferred, and validated with immune cell counting by immunohistochemistry. Cell type-specific immune signatures dynamically shifted from premalignant stages to the late HCC stage. Total hepatectomy patients displayed elevated immune infiltration and prolonged disease-free survival compared to the partial hepatectomy patients. However, patients who exhibited an infiltration of regulatory T cells (Tregs) during the pretransplantation period displayed a high risk of tumor relapse with suppressed immune responses, and pretreatment was a potential driver of Treg infiltration in the total hepatectomy group. Treg infiltration appeared to be independent of molecular classifications based on transcriptomic data. Our study provides not only comprehensive immune signatures in adjacent nontumor lesions and early malignant HCC stages but also clinical guidance for HCC patients who will undergo liver transplantation.
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37
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Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma. Nat Med 2021; 27:289-300. [PMID: 33495604 DOI: 10.1038/s41591-020-01212-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 12/14/2020] [Indexed: 11/08/2022]
Abstract
Synovial sarcoma (SyS) is an aggressive neoplasm driven by the SS18-SSX fusion, and is characterized by low T cell infiltration. Here, we studied the cancer-immune interplay in SyS using an integrative approach that combines single-cell RNA sequencing (scRNA-seq), spatial profiling and genetic and pharmacological perturbations. scRNA-seq of 16,872 cells from 12 human SyS tumors uncovered a malignant subpopulation that marks immune-deprived niches in situ and is predictive of poor clinical outcomes in two independent cohorts. Functional analyses revealed that this malignant cell state is controlled by the SS18-SSX fusion, is repressed by cytokines secreted by macrophages and T cells, and can be synergistically targeted with a combination of HDAC and CDK4/CDK6 inhibitors. This drug combination enhanced malignant-cell immunogenicity in SyS models, leading to induced T cell reactivity and T cell-mediated killing. Our study provides a blueprint for investigating heterogeneity in fusion-driven malignancies and demonstrates an interplay between immune evasion and oncogenic processes that can be co-targeted in SyS and potentially in other malignancies.
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Abstract
Drug metabolizing enzymes catalyze the biotransformation of many of drugs and chemicals. The drug metabolizing enzymes are distributed among several evolutionary families and catalyze a range of detoxication reactions, including oxidation/reduction, conjugative, and hydrolytic reactions that serve to detoxify potentially toxic compounds. This detoxication function requires that drug metabolizing enzymes exhibit substrate promiscuity. In addition to their catalytic functions, many drug metabolizing enzymes possess functions unrelated to or in addition to catalysis. Such proteins are termed 'moonlighting proteins' and are defined as proteins with multiple biochemical or biophysical functions that reside in a single protein. This review discusses the diverse moonlighting functions of drug metabolizing enzymes and the roles they play in physiological functions relating to reproduction, vision, cell signaling, cancer, and transport. Further research will likely reveal new examples of moonlighting functions of drug metabolizing enzymes.
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Affiliation(s)
- Philip G Board
- John Curtin School of Medical Research, ANU College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, NY, USA
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Knott EL, Leidenheimer NJ. A Targeted Bioinformatics Assessment of Adrenocortical Carcinoma Reveals Prognostic Implications of GABA System Gene Expression. Int J Mol Sci 2020; 21:ijms21228485. [PMID: 33187258 PMCID: PMC7697095 DOI: 10.3390/ijms21228485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Adrenocortical carcinoma (ACC) is a rare but deadly cancer for which few treatments exist. Here, we have undertaken a targeted bioinformatics study of The Cancer Genome Atlas (TCGA) ACC dataset focusing on the 30 genes encoding the γ-aminobutyric acid (GABA) system—an under-studied, evolutionarily-conserved system that is an emerging potential player in cancer progression. Our analysis identified a subset of ACC patients whose tumors expressed a distinct GABA system transcriptome. Transcript levels of ABAT (encoding a key GABA shunt enzyme), were upregulated in over 40% of tumors, and this correlated with several favorable clinical outcomes including patient survival; while enrichment and ontology analysis implicated two cancer-related biological pathways involved in metastasis and immune response. The phenotype associated with ABAT upregulation revealed a potential metabolic heterogeneity among ACC tumors associated with enhanced mitochondrial metabolism. Furthermore, many GABAA receptor subunit-encoding transcripts were expressed, including two (GABRB2 and GABRD) prognostic for patient survival. Transcripts encoding GABAB receptor subunits and GABA transporters were also ubiquitously expressed. The GABA system transcriptome of ACC tumors is largely mirrored in the ACC NCI-H295R cell line, suggesting that this cell line may be appropriate for future functional studies investigating the role of the GABA system in ACC cell growth phenotypes and metabolism.
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The glutathione peroxidase 8 (GPX8)/IL-6/STAT3 axis is essential in maintaining an aggressive breast cancer phenotype. Proc Natl Acad Sci U S A 2020; 117:21420-21431. [PMID: 32817494 DOI: 10.1073/pnas.2010275117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One of the emerging hallmarks of cancer illustrates the importance of metabolic reprogramming, necessary to synthesize the building blocks required to fulfill the high demands of rapidly proliferating cells. However, the proliferation-independent instructive role of metabolic enzymes in tumor plasticity is still unclear. Here, we provide evidence that glutathione peroxidase 8 (GPX8), a poorly characterized enzyme that resides in the endoplasmic reticulum, is an essential regulator of tumor aggressiveness. We found that GPX8 expression was induced by the epithelial-mesenchymal transition (EMT) program. Moreover, in breast cancer patients, GPX8 expression significantly correlated with known mesenchymal markers and poor prognosis. Strikingly, GPX8 knockout in mesenchymal-like cells (MDA-MB-231) resulted in an epithelial-like morphology, down-regulation of EMT characteristics, and loss of cancer stemness features. In addition, GPX8 knockout significantly delayed tumor initiation and decreased its growth rate in mice. We found that these GPX8 loss-dependent phenotypes were accompanied by the repression of crucial autocrine factors, in particular, interleukin-6 (IL-6). In these cells, IL-6 bound to the soluble receptor (sIL6R), stimulating the JAK/STAT3 signaling pathway by IL-6 trans-signaling mechanisms, so promoting cancer aggressiveness. We observed that in GPX8 knockout cells, this signaling mechanism was impaired as sIL6R failed to activate the JAK/STAT3 signaling pathway. Altogether, we present the GPX8/IL-6/STAT3 axis as a metabolic-inflammatory pathway that acts as a robust regulator of cancer cell aggressiveness.
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Spatial and morphological reorganization of endosymbiosis during metamorphosis accommodates adult metabolic requirements in a weevil. Proc Natl Acad Sci U S A 2020; 117:19347-19358. [PMID: 32723830 DOI: 10.1073/pnas.2007151117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bacterial intracellular symbiosis (endosymbiosis) is widespread in nature and impacts many biological processes. In holometabolous symbiotic insects, metamorphosis entails a complete and abrupt internal reorganization that creates a constraint for endosymbiont transmission from larvae to adults. To assess how endosymbiosis copes-and potentially evolves-throughout this major host-tissue reorganization, we used the association between the cereal weevil Sitophilus oryzae and the bacterium Sodalis pierantonius as a model system. S. pierantonius are contained inside specialized host cells, the bacteriocytes, that group into an organ, the bacteriome. Cereal weevils require metabolic inputs from their endosymbiont, particularly during adult cuticle synthesis, when endosymbiont load increases dramatically. By combining dual RNA-sequencing analyses and cell imaging, we show that the larval bacteriome dissociates at the onset of metamorphosis and releases bacteriocytes that undergo endosymbiosis-dependent transcriptomic changes affecting cell motility, cell adhesion, and cytoskeleton organization. Remarkably, bacteriocytes turn into spindle cells and migrate along the midgut epithelium, thereby conveying endosymbionts to midgut sites where future mesenteric caeca will develop. Concomitantly, endosymbiont genes encoding a type III secretion system and a flagellum apparatus are transiently up-regulated while endosymbionts infect putative stem cells and enter their nuclei. Infected cells then turn into new differentiated bacteriocytes and form multiple new bacteriomes in adults. These findings show that endosymbiosis reorganization in a holometabolous insect relies on a synchronized host-symbiont molecular and cellular "choreography" and illustrates an adaptive feature that promotes bacteriome multiplication to match increased metabolic requirements in emerging adults.
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Liu M, An H, Zhang Y, Sun W, Cheng S, Wang R, Wang X, Feng L. Molecular analysis of Chinese oesophageal squamous cell carcinoma identifies novel subtypes associated with distinct clinical outcomes. EBioMedicine 2020; 57:102831. [PMID: 32580137 PMCID: PMC7317223 DOI: 10.1016/j.ebiom.2020.102831] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Oesophageal squamous cell carcinoma (ESCC) is a highly heterogeneous cancer with a distinct incidence and prognosis. Molecular events driving ESCC subtypes and prognosis have not been established, and little is known regarding Chinese ESCC patients in Xinjiang, China. METHODS Here, we first integrated the genomic and transcriptomic data of 125 Chinese ESCC patients from Xinjiang Tumor Hospital (Urumqi, China). Two independent datasets of GSE53624 and The Cancer Genome Atlas (TCGA) ESCC were used to confirm the results of this study. DNA mutation and overall survival (OS) were analysed independently in the Chinese ESCC cohorts. FINDINGS Genomic analyses revealed a consistent mutation signatures and discordance among mutated genes across the different ESCC cohorts. In addition, transcriptomic profiling identified three Chinese ESCC subtypes associated with clinical and molecular attributes, including patient survival, lymph node status and genetic profile. Moreover, Chinese ESCC subtypes have distinct metabolic, inflammatory, metastatic, and cell proliferation features and unique potential therapeutics. Furthermore, the expression of cell cycle- and/or cell proliferation-related genes was higher in cyclin D1 (CCND1)-amplified tumours than in CCND1-normal tumours from Chinese ESCC patients, suggesting that CCND1 amplification promoted cell proliferation. INTERPRETATION Our findings provide a framework to facilitate the rational categorization of ESCC in Chinese patients and a foundation for new therapies. FUNDING This study was supported by the Research Fund of Key Laboratory of Xinjiang oncology (Grant no.2017D04006) and the Outstanding Youth Science and technology training project fund of Xinjiang, China (Grant no. 2017Q058).
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Affiliation(s)
- Meng Liu
- Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi 830011, Xinjiang, China.
| | - Haiyin An
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.
| | - Yuan Zhang
- Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang, China.
| | - Wei Sun
- Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang, China.
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.
| | - Ruozheng Wang
- Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang, China; Key Laboratory of Cancer Immunotherapy and Radiotherapy, Chinese Academy of Medical Sciences, Urumqi 830011, Xinjiang, China.
| | - Xiyan Wang
- Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011, Xinjiang, China.
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China.
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Waldbillig F, Nitschke K, Abdelhadi A, von Hardenberg J, Nuhn P, Nientiedt M, Weis CA, Michel MS, Erben P, Worst TS. Phosphodiesterase SMPDL3B Gene Expression as Independent Outcome Prediction Marker in Localized Prostate Cancer. Int J Mol Sci 2020; 21:ijms21124373. [PMID: 32575490 PMCID: PMC7352472 DOI: 10.3390/ijms21124373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/11/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022] Open
Abstract
Current outcome prediction markers for localized prostate cancer (PCa) are insufficient. The impact of the lipid-modifying Sphingomyelin Phosphodiesterase Acid Like 3B (SMPDL3B) in PCa is unknown. Two cohorts of patients with PCa who underwent radical prostatectomy (n = 40, n = 56) and benign prostate hyperplasia (BPH) controls (n = 8, n = 11) were profiled for SMPDL3B expression with qRT-PCR. Publicly available PCa cohorts (Memorial Sloane Kettering Cancer Centre (MSKCC; n = 131, n = 29 controls) and The Cancer Genome Atlas (TCGA; n = 497, n = 53 controls)) served for validation. SMPDL3B's impact on proliferation and migration was analyzed in PC3 cells by siRNA knockdown. In both cohorts, a Gleason score and T stage independent significant overexpression of SMPDL3B was seen in PCa compared to BPH (p < 0.001 each). A lower expression of SMPDL3B was associated with a shorter overall survival (OS) (p = 0.005) in long term follow-up. A SMPDL3B overexpression in PCa tissue was confirmed in the validation cohorts (p < 0.001 each). In the TCGA patients with low SMPDL3B expression, biochemical recurrence-free survival (p = 0.011) and progression-free interval (p < 0.001) were shorter. Knockdown of SMPDL3B impaired PC3 cell migration but not proliferation (p = 0.0081). In summary, SMPLD3B is highly overexpressed in PCa tissue, is inversely associated with localized PCa prognosis, and impairs PCa cell migration.
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Affiliation(s)
- Frank Waldbillig
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
- Correspondence: ; Tel.: +49-621-383-2201
| | - Katja Nitschke
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
| | - Abdallah Abdelhadi
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
| | - Jost von Hardenberg
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
| | - Philipp Nuhn
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
| | - Malin Nientiedt
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
| | - Cleo-Aron Weis
- Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany;
| | - Maurice Stephan Michel
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
| | - Philipp Erben
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
| | - Thomas Stefan Worst
- Department of Urology and Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany; (K.N.); (A.A.); (J.v.H.); (P.N.); (M.N.); (M.S.M.); (P.E.); (T.S.W.)
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van der Heijden M, Essers PBM, Verhagen CVM, Willems SM, Sanders J, de Roest RH, Vossen DM, Leemans CR, Verheij M, Brakenhoff RH, van den Brekel MWM, Vens C. Epithelial-to-mesenchymal transition is a prognostic marker for patient outcome in advanced stage HNSCC patients treated with chemoradiotherapy. Radiother Oncol 2020; 147:186-194. [PMID: 32413532 DOI: 10.1016/j.radonc.2020.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND The prognosis of patients with HPV-negative advanced stage head and neck squamous cell carcinoma (HNSCC) remains poor. No prognostic markers other than TNM staging are routinely used in clinic. Epithelial-to-mesenchymal transition (EMT) has been shown to be a strong prognostic factor in other cancer types. The purpose of this study was to determine the role of EMT in HPV-negative HNSCC outcomes. METHODS Pretreatment tumor material from patients of two cohorts, totalling 174 cisplatin-based chemoradiotherapy treated HPV-negative HNSCC patients, was RNA-sequenced. Seven different EMT gene expression signatures were used for EMT status classification and generation of HNSCC-specific EMT models using Random Forest machine learning. RESULTS Mesenchymal classification by all EMT signatures consistently enriched for poor prognosis patients in both cohorts of 98 and 76 patients. Uni- and multivariate analyses show important HR of 1.6-5.8, thereby revealing EMT's role in HNSCC outcome. Discordant classification by these signatures prompted the generation of an HNSCC-specific EMT profile based on the concordantly classified samples in the first cohort (cross-validation AUC > 0.98). The independent validation cohort confirmed the association of mesenchymal classification by the HNSCC-EMT model with poor overall survival (HR = 3.39, p < 0.005) and progression free survival (HR = 3.01, p < 0.005) in multivariate analysis with TNM. Analysis of an additional HNSCC cohort from PET-positive patients with metastatic disease prior to treatment further supports this relationship and reveals a strong link of EMT to the propensity to metastasize. CONCLUSIONS EMT in HPV-negative HNSCC co-defines patient outcome after chemoradiotherapy. The generated HNSCC-EMT prediction models can function as strong prognostic biomarkers.
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Affiliation(s)
- Martijn van der Heijden
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul B M Essers
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Caroline V M Verhagen
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, The Netherlands
| | - Joyce Sanders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Reinout H de Roest
- Department of Otolaryngology/Head and Neck Surgery, VUmc Cancer Center Amsterdam, The Netherlands
| | - David M Vossen
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - C René Leemans
- Department of Otolaryngology/Head and Neck Surgery, VUmc Cancer Center Amsterdam, The Netherlands
| | - Marcel Verheij
- Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruud H Brakenhoff
- Department of Otolaryngology/Head and Neck Surgery, VUmc Cancer Center Amsterdam, The Netherlands
| | - Michiel W M van den Brekel
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Oral and Maxillofacial Surgery, Academic Medical Center, Amsterdam, The Netherlands
| | - Conchita Vens
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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Lin N, Li W, Wang X, Hou S, Yu D, Zhao X, Jin C, Yao G, Yan W, You Y. Upregulation of miR-340 Inhibits Tumor Growth and Mesenchymal Transition via Targeting c-MET in Glioblastoma. Cancer Manag Res 2020; 12:3343-3352. [PMID: 32494198 PMCID: PMC7229788 DOI: 10.2147/cmar.s250772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
Background Epithelial-mesenchymal Transition (EMT) is involved in various cancers including glioblastoma. Our previous study has shown that miR-340 negatively correlated with EMT process in glioblastoma. Purpose In the present study, we aim to explore the underlying molecular mechanisms of miR-340 in EMT process of glioblastomas. Materials and Methods Using RT-qPCR assay, we analyzed the expression of miR-340 in glioma cell lines and normal human glia (NHA) cell line. Using CCK8, Colony formation assays, transwell and Western blot assays, we investigated tumor growth and EMT process. Using luciferase reporter assay, we confirmed a target of miR-340. Results Our results showed that miR-340 was down-regulated in glioma cell lines (U87, U251 and LN229) compared to NHA cells. MiR-340 overexpression remarkably inhibited cell proliferation and invasion as well as up-regulated E-cadherin expression and down-regulated N-cadherin, Vimentin, ZEB1, Slug and Snail expressions in U251 and LN229 cells. Further studies have confirmed c-MET as a target gene of miR-340. The EMT-inhibitory effect of miR-340 was lost after c-MET expression was restored. We also identified the antitumorigenic activity of miR-340 in vivo. Conclusion These results demonstrated that miR-340 functioned as a tumor suppressor via targeting EMT process and could be a potential therapeutic candidate for treating glioblastomas.
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Affiliation(s)
- Ning Lin
- Department of Neurosurgery, Chuzhou Clinical College of Anhui Medical University, The First People's Hospital Chuzhou, Chuzhou, People's Republic of China
| | - Wentao Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Xiefeng Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Shiqiang Hou
- Department of Neurosurgery, Chuzhou Clinical College of Anhui Medical University, The First People's Hospital Chuzhou, Chuzhou, People's Republic of China
| | - Dong Yu
- Department of Neurosurgery, Chuzhou Clinical College of Anhui Medical University, The First People's Hospital Chuzhou, Chuzhou, People's Republic of China
| | - Xingyuan Zhao
- Department of Neurosurgery, Chuzhou Clinical College of Anhui Medical University, The First People's Hospital Chuzhou, Chuzhou, People's Republic of China
| | - Chunjing Jin
- Laboratory Medicine Center, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Guoquan Yao
- Department of Neurosurgery, Chuzhou Clinical College of Anhui Medical University, The First People's Hospital Chuzhou, Chuzhou, People's Republic of China
| | - Wei Yan
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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Canonical BMP Signaling Executes Epithelial-Mesenchymal Transition Downstream of SNAIL1. Cancers (Basel) 2020; 12:cancers12041019. [PMID: 32326239 PMCID: PMC7226241 DOI: 10.3390/cancers12041019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a pivotal process in development and disease. In carcinogenesis, various signaling pathways are known to trigger EMT by inducing the expression of EMT transcription factors (EMT-TFs) like SNAIL1, ultimately promoting invasion, metastasis and chemoresistance. However, how EMT is executed downstream of EMT-TFs is incompletely understood. Here, using human colorectal cancer (CRC) and mammary cell line models of EMT, we demonstrate that SNAIL1 critically relies on bone morphogenetic protein (BMP) signaling for EMT execution. This activity requires the transcription factor SMAD4 common to BMP/TGFβ pathways, but is TGFβ signaling-independent. Further, we define a signature of BMP-dependent genes in the EMT-transcriptome, which orchestrate EMT-induced invasiveness, and are found to be regulated in human CRC transcriptomes and in developmental EMT processes. Collectively, our findings substantially augment the knowledge of mechanistic routes whereby EMT can be effectuated, which is relevant for the conceptual understanding and therapeutic targeting of EMT processes.
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Zadora PK, Chumduri C, Imami K, Berger H, Mi Y, Selbach M, Meyer TF, Gurumurthy RK. Integrated Phosphoproteome and Transcriptome Analysis Reveals Chlamydia-Induced Epithelial-to-Mesenchymal Transition in Host Cells. Cell Rep 2020; 26:1286-1302.e8. [PMID: 30699355 DOI: 10.1016/j.celrep.2019.01.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 10/05/2018] [Accepted: 12/31/2018] [Indexed: 12/26/2022] Open
Abstract
Chlamydia trachomatis (Ctr) causes a range of infectious diseases and is epidemiologically associated with cervical and ovarian cancers. To obtain a panoramic view of Ctr-induced signaling, we performed global phosphoproteomic and transcriptomic analyses. We identified numerous Ctr phosphoproteins and Ctr-regulated host phosphoproteins. Bioinformatics analysis revealed that these proteins were predominantly related to transcription regulation, cellular growth, proliferation, and cytoskeleton organization. In silico kinase substrate motif analysis revealed that MAPK and CDK were the most overrepresented upstream kinases for upregulated phosphosites. Several of the regulated host phosphoproteins were transcription factors, including ETS1 and ERF, that are downstream targets of MAPK. Functional analysis of phosphoproteome and transcriptome data confirmed their involvement in epithelial-to-mesenchymal transition (EMT), a phenotype that was validated in infected cells, along with the essential role of ERK1/2, ETS1, and ERF for Ctr replication. Our data reveal the extent of Ctr-induced signaling and provide insights into its pro-carcinogenic potential.
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Affiliation(s)
- Piotr K Zadora
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Cindrilla Chumduri
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany; Department of Hepatology and Gastroenterology, Charité University Medicine, 13353 Berlin, Germany
| | - Koshi Imami
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Hilmar Berger
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Yang Mi
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.
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Basturk O, Weigelt B, Adsay V, Benhamida JK, Askan G, Wang L, Arcila ME, Zamboni G, Fukushima N, Gularte-Mérida R, Da Cruz Paula A, Selenica P, Kumar R, Pareja F, Maher CA, Scholes J, Oda Y, Santini D, Doyle LA, Petersen I, Flucke U, Koelsche C, Reynolds SJ, Yavas A, von Deimling A, Reis-Filho JS, Klimstra DS. Sclerosing epithelioid mesenchymal neoplasm of the pancreas - a proposed new entity. Mod Pathol 2020; 33:456-467. [PMID: 31383964 PMCID: PMC7000300 DOI: 10.1038/s41379-019-0334-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
Abstract
We have encountered pancreatic tumors with unique histologic features, which do not conform to any of the known tumors of the pancreas or other anatomical sites. We aimed to define their clinicopathologic features and whether they are characterized by recurrent molecular signatures. Eight cases were identified; studied histologically and by immunohistochemistry. Selected cases were also subjected to whole-exome sequencing (WES; n = 4), RNA-sequencing (n = 6), Archer FusionPlex assay (n = 5), methylation profiling using the Illumina MethylationEPIC (850k) array platform (n = 6), and TERT promoter sequencing (n = 5). Six neoplasms occurred in females. The mean age was 43 years (range: 26-75). Five occurred in the head/neck of the pancreas. All patients were treated surgically; none received neoadjuvant/adjuvant therapy. All patients are free of disease after 53 months of median follow-up (range: 8-94). The tumors were well-circumscribed, and the median size was 1.8 cm (range: 1.3-5.8). Microscopically, the unencapsulated tumors had a geographic pattern of epithelioid cell nests alternating with spindle cell fascicles. Some areas showed dense fibrosis, in which enmeshed tumor cells imparted a slit-like pattern. The predominant epithelioid cells had scant cytoplasm and round-oval nuclei with open chromatin. The spindle cells displayed irregular, hyperchromatic nuclei. Mitoses were rare. No lymph node metastases were identified. All tumors were positive for vimentin, CD99 and cytokeratin (patchy), while negative for markers of solid pseudopapillary neoplasm, neuroendocrine, acinar, myogenic/rhabdoid, vascular, melanocytic, or lymphoid differentiation, gastrointestinal stromal tumor as well as MUC4. Whole-exome sequencing revealed no recurrent somatic mutations or amplifications/homozygous deletions in any known oncogenes or tumor suppressor genes. RNA-sequencing and the Archer FusionPlex assay did not detect any recurrent likely pathogenic gene fusions. Single sample gene set enrichment analysis revealed that these tumors display a likely mesenchymal transcriptomic program. Unsupervised analysis (t-SNE) of their methylation profiles against a set of different mesenchymal neoplasms demonstrated a distinct methylation pattern. Here, we describe pancreatic neoplasms with unique morphologic/immunophenotypic features and a distinct methylation pattern, along with a lack of abnormalities in any of key genetic drivers, supporting that these neoplasms represent a novel entity with an indolent clinical course. Given their mesenchymal transcriptomic features, we propose the designation of "sclerosing epithelioid mesenchymal neoplasm" of the pancreas.
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Affiliation(s)
- Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Volkan Adsay
- Department of Pathology, Koç University, Istanbul,
Turkey
| | - Jamal K. Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Gokce Askan
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Giuseppe Zamboni
- Department of Pathology, University of Verona and IRCCS
Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | | | | | - Arnaud Da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | | | - John Scholes
- Department of Pathology, St. Francis Hospital and Medical
Center, Hartford, CT, USA
| | - Yoshinao Oda
- Department of Pathology, Kyushu University, Fukuoka,
Fukuoka Prefecture, Japan
| | - Donatella Santini
- Department of Pathology, Azienda Ospedaliera-Universitaria
di Bologna, Italy
| | - Leona A. Doyle
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA, USA
| | - Iver Petersen
- Department of Pathology, SRH Poliklinik Gera GmbH, Gera,
Germany
| | - Uta Flucke
- Department of Pathology, Radboud University Medical
Center, Nijmegen, The Netherlands
| | | | | | - Aslihan Yavas
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Andreas von Deimling
- Department of Pathology, University Hospital Heidelberg
and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
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Satish L, Evdokiou A, Geletu E, Hahn JM, Supp DM. Pirfenidone inhibits epithelial-mesenchymal transition in keloid keratinocytes. BURNS & TRAUMA 2020; 8:tkz007. [PMID: 32405508 DOI: 10.1093/burnst/tkz007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/15/2019] [Accepted: 12/11/2019] [Indexed: 01/23/2023]
Abstract
Background Keloids are benign fibroproliferative skin lesions that are difficult to treat and become a lifetime predicament for patients. Several treatment modalities have been put forth, but as yet no satisfactory approach to the prevention or treatment of keloids has been identified. The process of epithelial-to-mesenchymal transition (EMT) has been implicated in keloid scarring, as keloid keratinocytes display an EMT-like phenotype. This study investigated the potential of pirfenidone, an antifibrotic agent, to counteract EMT-like alterations in keloid keratinocytes, including gene expression, cell migratory and proliferative functions. Methods Normal and keloid keratinocytes were isolated from discarded normal skin tissues and from resected keloid tissues, respectively. Cells were quiesced for 24 h without epidermal growth factor DS-Qi1MCDigital and were exposed to transforming growth factor-beta1 (TGF-β1; 10 ng/mL), with or without pirfenidone (400 μg/mL), for an additional 24 h. The effects of pirfenidone on cytotoxicity, cell migration, cell proliferation, and on expression of genes and proteins involved in EMT were assayed. Statistical significance was determined by two-way ANOVA using Sigma Plot. Results We found that pirfenidone did not elicit any cytotoxic effect at concentrations up to 1000 μg/mL. A statistically significant dose-dependent decrease in basal cell proliferation rate was noted in both normal and keloid keratinocytes when exposed to pirfenidone at concentrations ranging from 200 to 1000 μg/mL. Pirfenidone significantly decreased basal cell migration in both normal and keloid keratinocytes, but a significant decrease in TGF-β1-induced cell migration was seen only in keloid keratinocytes. Significant inhibition of the expression of TGF-β1-induced core EMT genes, namely hyaluronan synthase 2, vimentin, cadherin-11, and wingless-type MMTV integration site family, member 5A along with fibronectin-1, was observed in both normal and keloid keratinocytes treated with pirfenidone. In addition, the protein levels of vimentin and fibronectin were significantly reduced by pirfenidone (400 μg/mL) in both normal and keloid keratinocytes. Conclusions For the first time, this study shows the efficacy of pirfenidone in inhibiting the EMT-like phenotype in keratinocytes derived from keloids, suggesting that pirfenidone may counteract a critical contributor of keloid progression and recurrence.
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Affiliation(s)
- Latha Satish
- Research Department, Shriners Hospitals for Children-Cincinnati, Cincinnati, OH 45229 USA.,Department of Pathology & Laboratory Medicine, University of Cincinnati, Cincinnati, OH 45229, USA, and
| | - Alexander Evdokiou
- Research Department, Shriners Hospitals for Children-Cincinnati, Cincinnati, OH 45229 USA
| | - Eleni Geletu
- Research Department, Shriners Hospitals for Children-Cincinnati, Cincinnati, OH 45229 USA
| | - Jennifer M Hahn
- Research Department, Shriners Hospitals for Children-Cincinnati, Cincinnati, OH 45229 USA
| | - Dorothy M Supp
- Research Department, Shriners Hospitals for Children-Cincinnati, Cincinnati, OH 45229 USA.,Department of Surgery, University of Cincinnati, Cincinnati, OH 45229, USA
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Barneh F, Mirzaie M, Nickchi P, Tan TZ, Thiery JP, Piran M, Salimi M, Goshadrou F, Aref AR, Jafari M. Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer. Brief Bioinform 2020; 20:717-731. [PMID: 29726962 DOI: 10.1093/bib/bby030] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/04/2018] [Indexed: 02/07/2023] Open
Abstract
With the advent of high-throughput technologies leading to big data generation, increasing number of gene signatures are being published to predict various features of diseases such as prognosis and patient survival. However, to use these signatures for identifying therapeutic targets, use of additional bioinformatic tools is indispensible part of research. Here, we have generated a pipeline comprised of nearly 15 bioinformatic tools and enrichment statistical methods to propose and validate a drug combination strategy from already approved drugs and present our approach using published pan-cancer epithelial-mesenchymal transition (EMT) signatures as a case study. We observed that histone deacetylases were critical targets to tune expression of multiple epithelial versus mesenchymal genes. Moreover, SRC and IKBK were the principal intracellular kinases regulating multiple signaling pathways. To confirm the anti-EMT efficacy of the proposed target combination in silico, we validated expression of targets in mesenchymal versus epithelial subtypes of ovarian cancer. Additionally, we inhibited the pinpointed proteins in vitro using an invasive lung cancer cell line. We found that whereas low-dose mono-therapy failed to limit cell dispersion from collagen spheroids in a microfluidic device as a metric of EMT, the combination fully inhibited dissociation and invasion of cancer cells toward cocultured endothelial cells. Given the approval status and safety profiles of the suggested drugs, the proposed combination set can be considered in clinical trials.
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Affiliation(s)
- Farnaz Barneh
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Payman Nickchi
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, BC, Canada
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore, Translational Centre for Development and Research, National University Health System, MD11, #03-10, 10 Medical Drive, Singapore 117597, Singapore
| | - Jean Paul Thiery
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore.,Institut Gustave Roussy, Inserm Unit 1186 Comprehensive Cancer Center, Villejuif, France.,CNRS UMR 7057 Matter and Complex Systems, University Paris Denis Diderot, Paris, France
| | - Mehran Piran
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Salimi
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Goshadrou
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir R Aref
- Department of Medical Oncology, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston 02215, USA
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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