1
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Fuentes-Mattei E, Bayraktar R, Manshouri T, Silva AM, Ivan C, Gulei D, Fabris L, Soares do Amaral N, Mur P, Perez C, Torres-Claudio E, Dragomir MP, Badillo-Perez A, Knutsen E, Narayanan P, Golfman L, Shimizu M, Zhang X, Zhao W, Ho WT, Estecio MR, Bartholomeusz G, Tomuleasa C, Berindan-Neagoe I, Zweidler-McKay PA, Estrov Z, Zhao ZJ, Verstovsek S, Calin GA, Redis RS. miR-543 regulates the epigenetic landscape of myelofibrosis by targeting TET1 and TET2. JCI Insight 2024; 9:e178762. [PMID: 38329131 DOI: 10.1172/jci.insight.178762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
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2
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Knutsen E, Das Sajib S, Fiskaa T, Lorens J, Gudjonsson T, Mælandsmo GM, Johansen SD, Seternes OM, Perander M. Identification of a core EMT signature that separates basal-like breast cancers into partial- and post-EMT subtypes. Front Oncol 2023; 13:1249895. [PMID: 38111531 PMCID: PMC10726128 DOI: 10.3389/fonc.2023.1249895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a cellular plasticity program critical for embryonic development and tissue regeneration, and aberrant EMT is associated with disease including cancer. The high degree of plasticity in the mammary epithelium is reflected in extensive heterogeneity among breast cancers. Here, we have analyzed RNA-sequencing data from three different mammary epithelial cell line-derived EMT models and identified a robust mammary EMT gene expression signature that separates breast cancers into distinct subgroups. Most strikingly, the basal-like breast cancers form two subgroups displaying partial-EMT and post-EMT gene expression patterns. We present evidence that key EMT-associated transcription factors play distinct roles at different stages of EMT in mammary epithelial cells.
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Affiliation(s)
- Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
- Centre for Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
| | - Saikat Das Sajib
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Tonje Fiskaa
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - James Lorens
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Thorarinn Gudjonsson
- Department of Anatomy, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Hematology, Landspitali, University Hospital, Reykjavik, Iceland
| | - Gunhild M. Mælandsmo
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Steinar Daae Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
- Genomics Division, Faculty of Bioscience and Aquaculture, Nord University, Bodø, Norway
| | - Ole-Morten Seternes
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
- Centre for Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
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3
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Drula R, Pardini B, Fu X, De los Santos MC, Jurj A, Pang L, El-Daly SM, Fabris L, Knutsen E, Dragomir MP, Bayraktar R, Li Y, Chen M, Del Vecchio F, Berland L, Dae J, Fan D, Shimizu M, Tran AM, Barzi M, Pioppini C, Gutierrez AM, Ivan C, Meas S, Hall CS, Alahari SK, Berindan-Neagoe I, Fabbri M, Lucci A, Arun B, Anfossi S, Calin GA. 17β-estradiol promotes extracellular vesicle release and selective miRNA loading in ERα-positive breast cancer. Proc Natl Acad Sci U S A 2023; 120:e2122053120. [PMID: 37252969 PMCID: PMC10266002 DOI: 10.1073/pnas.2122053120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/14/2023] [Indexed: 06/01/2023] Open
Abstract
The causes and consequences of abnormal biogenesis of extracellular vesicles (EVs) are not yet well understood in malignancies, including in breast cancers (BCs). Given the hormonal signaling dependence of estrogen receptor-positive (ER+) BC, we hypothesized that 17β-estradiol (estrogen) might influence EV production and microRNA (miRNA) loading. We report that physiological doses of 17β-estradiol promote EV secretion specifically from ER+ BC cells via inhibition of miR-149-5p, hindering its regulatory activity on SP1, a transcription factor that regulates the EV biogenesis factor nSMase2. Additionally, miR-149-5p downregulation promotes hnRNPA1 expression, responsible for the loading of let-7's miRNAs into EVs. In multiple patient cohorts, we observed increased levels of let-7a-5p and let-7d-5p in EVs derived from the blood of premenopausal ER+ BC patients, and elevated EV levels in patients with high BMI, both conditions associated with higher levels of 17β-estradiol. In brief, we identified a unique estrogen-driven mechanism by which ER+ BC cells eliminate tumor suppressor miRNAs in EVs, with effects on modulating tumor-associated macrophages in the microenvironment.
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Affiliation(s)
- Rares Drula
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337Cluj Napoca, Romania
| | - Barbara Pardini
- Italian Institute for Genomic Medicine, c/o FPO-IRCCS Candiolo, 10060Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060Candiolo, Italy
| | - Xiao Fu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Department of Medical Oncology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 Shaanxi, China
| | - Mireia Cruz De los Santos
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, 17164Solna, Sweden
| | - Ancuta Jurj
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337Cluj Napoca, Romania
| | - Lan Pang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Sherien M. El-Daly
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Medical Biochemistry Department, Medical Research and Clinical Studies Institute, National Research Centre, Cairo12622, Egypt
| | - Linda Fabris
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Department of Medical Biology, Faculty of Health Sciences, UiT, The Artic University of Norway, N-9037Tromso, Norway
- Centre for Clinical Research and Education, University Hospital of North Norway, N-9037Tromso, Norway
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10178Berlin, Germany
- German Cancer Research Center (DKFZ), Partner Site Berlin, and German Cancer Consortium (DKTK), 69120Heidelberg, Germany
- Berlin Institute of Health, 10178Berlin, Germany
| | - Recep Bayraktar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Yongfeng Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, 310022 Zhejiang, P.R. China
| | - Meng Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Filippo Del Vecchio
- University of Hawaii Cancer Center, Cancer Biology Program, Honolulu, HI96813
| | - Léa Berland
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Department of Research Imaging, Dana Farber Cancer Institute, Boston, MA02215
| | - Jessica Dae
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- College of Natural Sciences, The University of Texas at Austin, Austin, TX78712
| | - Daniel Fan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- College of Natural Sciences, The University of Texas at Austin, Austin, TX78712
| | - Masayoshi Shimizu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Anh M. Tran
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Department of Chemistry, Mount Holyoke College, South Hadley, MA01075
| | - Mercedes Barzi
- Department of Pediatrics, Duke University, Durham, NC27708
| | - Carlotta Pioppini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Department of Nephrology and Medical Intensive Care, Charité—Universitätsmedizin Berlin, 10117Berlin, Germany
| | - Angelica M. Gutierrez
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Salyna Meas
- Breast Surgical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Carolyn S. Hall
- Breast Surgical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Suresh K. Alahari
- Department of Biochemistry and Molecular Biology, Stanley S Scott Cancer Center, Louisiana State University School of Medicine, New Orleans, LA70112
| | - Ioana Berindan-Neagoe
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337Cluj Napoca, Romania
| | - Muller Fabbri
- University of Hawaii Cancer Center, Cancer Biology Program, Honolulu, HI96813
- Center for Cancer and Immunology Research, Children’s National Hospital, WashingtonDC20010
| | - Anthony Lucci
- Breast Surgical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Banu Arun
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Simone Anfossi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX77030
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX77030
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4
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Dragomir MP, Fuentes-Mattei E, Winkle M, Okubo K, Bayraktar R, Knutsen E, Qdaisat A, Chen M, Li Y, Shimizu M, Pang L, Liu K, Liu X, Anfossi S, Zhang H, Koch I, Tran AM, Mohapatra S, Ton A, Kaplan M, Anderson MW, Rothfuss SJ, Silasi R, Keshari RS, Ferracin M, Ivan C, Rodriguez-Aguayo C, Lopez-Berestein G, Georgescu C, Banerjee PP, Basar R, Li Z, Horst D, Vasilescu C, Bertilaccio MTS, Rezvani K, Lupu F, Yeung SC, Calin GA. Anti-miR-93-5p therapy prolongs sepsis survival by restoring the peripheral immune response. J Clin Invest 2023:158348. [PMID: 37261908 DOI: 10.1172/jci158348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
Sepsis remains a leading cause of human death and currently has no pathogenesis-specific therapy. Hampered progress is partly due to a lack of insight into deep mechanistic processes. In the last decade, deciphering the functions of small non-coding microRNAs (miRNAs) in sepsis pathogenesis became a dynamic research topic. To screen for new miRNA targets for sepsis therapeutics, we used human samples for miRNA array from peripheral blood mononuclear cells from sepsis patients and controls, blood samples from two cohorts of sepsis patients, and multiple animal models: mouse cecum ligation-puncture (CLP)-induced sepsis, mouse viral miRNA challenge, and baboon Gram-positive and Gram-negative sepsis models. miR-93-5p met the criteria for a therapeutic target, being overexpressed in baboons that died early after induction of sepsis, downregulated in humans who survived after sepsis, and correlated with negative clinical prognosticators for sepsis. Therapeutically, inhibiting miR-93-5p prolonged the overall survival of mice with CLP-induced sepsis, with a stronger effect in older mice. Mechanistically, anti-miR-93-5p therapy reduced inflammatory monocytes and increased circulating effector memory T cells, especially the CD4+ subset. AGO2-immunoprecipitation in miR-93-knockout T cells identified important regulatory receptors, such as CD28, as direct miR-93-5p target genes. In conclusion, miR-93-5p is a potential therapeutic target in sepsis through regulating both innate and adaptive immunity with possibly more benefit for the elderly than the young patients.
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Affiliation(s)
- Mihnea P Dragomir
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Enrique Fuentes-Mattei
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Melanie Winkle
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Keishi Okubo
- Department of Digestive Surgery, Breast and Thyroid Surgery, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Recep Bayraktar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway, Tromsø, Norway
| | - Aiham Qdaisat
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Meng Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Yongfeng Li
- Department of Breast Surgery, Institute of Cancer and Basic Medicine (ICBM), Zhejiang, China
| | - Masayoshi Shimizu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Lan Pang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Kevin Liu
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Xiuping Liu
- Department of Experimental Therapeutics, Healgen Scientific, Houston, United States of America
| | - Simone Anfossi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Huanyu Zhang
- Department of Pediatric Surgery, The Affiliated Hospital of Qingdao University, Shandong, China
| | - Ines Koch
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anh M Tran
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Swati Mohapatra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Anh Ton
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Mecit Kaplan
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Matthew W Anderson
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Spencer J Rothfuss
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Robert Silasi
- Cardiovascular Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Ravi S Keshari
- Cardiovascular Biology, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Constantin Georgescu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Pinaki P Banerjee
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Catalin Vasilescu
- Department of Surgery, Fundeni Clinical Hospital, Bucharest, Romania
| | - Maria Teresa S Bertilaccio
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The Univerisity of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Florea Lupu
- Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Sai-Ching Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
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5
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Mohapatra S, Knutsen E, Gagea MI, Fabris L, Calin GA. Abstract 3795: Deciphering the in vivo roles of a novel long non-coding RNA in chronic lymphocytic leukemia and Richter syndrome. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
The ultraconserved regions (UCRs) are the genomic segments manifesting perfect conservation between the orthologous genomes of humans, rats, and mice that get transcribed into mono-exonic long non-coding RNAs (lncRNAs) known as transcribed ultraconserved regions (T-UCRs). Increasing evidence demonstrates the importance of T-UCRs in human cancers, however, their involvement in the pathogenesis of Chronic Lymphocytic Leukemia (CLL) is poorly understood. Our lab has recently identified a lncRNA transcribed from a UCR and named it TRUC-16 (Translational Regulatory UltraConserved gene affecting p16), which is overexpressed in CLL and correlates with treatment-free survival. We have developed a transgenic C57BL6 mouse model to overexpress TRUC-16 in B cells. We monitored the number and development of B cell subsets over time in peripheral blood and lymphoid organs (lymph nodes, spleen, and bone marrow), and performed immunophenotyping to assess clonality and proportion of the cells considered to be the origin for CLL (i.e. B1 cells and IgM memory B cells that are CD5+). We followed mice survival (n=10 for each gender) and performed necropsy with histopathologic and immunophenotypic analysis. If blood sampling suggests developing a CLL-like state, we will monitor for evolution to Richter Syndrome by flow cytometry analysis and biochemistry markers. We have validated the TRUC-16 overexpression specific to the B-cell compartment in the mice cohorts and have observed lymphoma in several organs. Interestingly, TRUC-16 overexpressing mice showed significantly higher splenic weights compared to controls. The mice were found to develop adulthood lymphoma that we are now analyzing molecularly and phenotypically. We are planning to further characterize the subtype of lymphoma by utilizing specific diagnostic markers through immunohistochemistry and flow cytometry. This is the first-ever transgenic mice modeling overexpression of UCR in the context of cancer. Validation of the functional correlation between the TRUC-16 phenotype and CLL patients’ clinical data will provide a valuable resource to pursue a multitude of preclinical studies to find targets that might help better understand the disease pathophysiology.
Citation Format: Swati Mohapatra, Erik Knutsen, Mihai Iurascu Gagea, Linda Fabris, George Adrian Calin. Deciphering the in vivo roles of a novel long non-coding RNA in chronic lymphocytic leukemia and Richter syndrome. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3795.
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Affiliation(s)
- Swati Mohapatra
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Erik Knutsen
- 2UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Linda Fabris
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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6
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Untergasser A, Hellemans J, Pfaffl MW, Ruijter JM, van den Hoff MJB, Dragomir MP, Adamoski D, Dias SMG, Reis RM, Ferracin M, Dias-Neto E, Marsh I, Kubista M, Fabbri M, Goel A, Slabý O, Knutsen E, Chen B, Negrini M, Mimori K, Pichler M, Papatriantafyllou M, Anfossi S, Schmittgen TD, Huggett J, Bustin S, Vandesompele J, Calin GA. Disclosing quantitative RT-PCR raw data during manuscript submission:a call for action. Mol Oncol 2023; 17:713-717. [PMID: 36916500 PMCID: PMC10158759 DOI: 10.1002/1878-0261.13418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Accuracy and transparency of scientific data are becoming more and more relevant with the increasing concern regarding the evaluation of data reproducibility in many research areas. This concern is also true for quantifying coding and non-coding RNAs, with the remarkable increase in publications reporting RNA profiling and sequencing studies. To address the problem, we propose the following recommendations: 1) accurate documentation of experimental procedures in Materials and Methods (and not only in the supplementary information, as many journals have a strict mandate for making Materials and Methods as visible as possible in the main text); 2) submission of RT-qPCR raw data for all experiments reported; and 3) adoption of a unified, simple format for submitted RT-qPCR raw data. The Real-time PCR Data Essential Spreadsheet Format (RDES) was created for this purpose.
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Affiliation(s)
- Andreas Untergasser
- Zentrum für Molekulare Biologie der Universität Heidelberg, Im Neuenheimer Feld 329, D-69120, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Genomics Core Facility, D-69117, Heidelberg, Germany
| | | | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Jan M Ruijter
- Department of Medical Biology, Amsterdam UMC, location AMC, University of Amsterdam, Meibergdreef 15, 1105AZ, Amsterdam, The Netherlands
| | - Maurice J B van den Hoff
- Department of Medical Biology, Amsterdam UMC, location AMC, University of Amsterdam, Meibergdreef 15, 1105AZ, Amsterdam, The Netherlands
| | - Mihnea P Dragomir
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Health, Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Zip Code 13083-970, Sao Paulo, Campinas, Brazil
| | - Sandra Martha Gomes Dias
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Zip Code 13083-970, Sao Paulo, Campinas, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,3B's- PT, Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.,IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, Centro Internacional de Pesquisa, AC Camargo Cancer Center, São Paulo, SP, Brazil.,Laboratory of Neurosciences (LIM27), Institute of Psychiatry, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ian Marsh
- New South Wales Department of Primary Industries, Macarthur Agricultural Institute, PMB 4008, Narellan, New South Wales, 2567, Elizabeth, Australia
| | - Mikael Kubista
- TATAA Biocenter AB, Sofierogatan 3A:2 412 51, Göteborg, Sweden.,Institute of Biotechnology CAS, v. v. i., Vestec, Czech Republic
| | - Muller Fabbri
- Center for Cancer and Immunology Research, Children's National Hospital, 20010, Washington, DC, USA
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA.,City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ondřej Slabý
- Department of Biology, Faculty of Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - BaoQing Chen
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Massimo Negrini
- Laboratory for Technologies of Advanced Therapies (LTTA), Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria.,Translational Oncology, University Hospital of Augsburg Stenglinstrasse 2 86156, Augsburg, Germany
| | | | - Simone Anfossi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, Unites States
| | - Thomas D Schmittgen
- Department of Pharmaceutics, University of Florida College of Pharmacy, Gainesville, Florida
| | - Jim Huggett
- National Measurement Laboratory, LGC, Teddington, United Kingdom; School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Stephen Bustin
- Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, United Kingdom
| | - Jo Vandesompele
- CellCarta, 9052 Zwijnaarde, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, Unites States.,The Center for Non-codingRNAs, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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7
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Karagiorgou Z, Fountas PN, Manou D, Knutsen E, Theocharis AD. Proteoglycans Determine the Dynamic Landscape of EMT and Cancer Cell Stemness. Cancers (Basel) 2022; 14:5328. [PMID: 36358747 PMCID: PMC9653992 DOI: 10.3390/cancers14215328] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 03/15/2024] Open
Abstract
Proteoglycans (PGs) are pivotal components of extracellular matrices, involved in a variety of processes such as migration, invasion, morphogenesis, differentiation, drug resistance, and epithelial-to-mesenchymal transition (EMT). Cellular plasticity is a crucial intermediate phenotypic state acquired by cancer cells, which can modulate EMT and the generation of cancer stem cells (CSCs). PGs affect cell plasticity, stemness, and EMT, altering the cellular shape and functions. PGs control these functions, either by direct activation of signaling cascades, acting as co-receptors, or through regulation of the availability of biological compounds such as growth factors and cytokines. Differential expression of microRNAs is also associated with the expression of PGs and their interplay is implicated in the fine tuning of cancer cell phenotype and potential. This review summarizes the involvement of PGs in the regulation of EMT and stemness of cancer cells and highlights the molecular mechanisms.
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Affiliation(s)
- Zoi Karagiorgou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Panagiotis N. Fountas
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Dimitra Manou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, 9010 Tromsø, Norway
- Centre for Clinical Research and Education, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Achilleas D. Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26504 Patras, Greece
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8
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Klec C, Knutsen E, Schwarzenbacher D, Jonas K, Pasculli B, Heitzer E, Rinner B, Krajina K, Prinz F, Gottschalk B, Ulz P, Deutsch A, Prokesch A, Jahn SW, Lellahi SM, Perander M, Barbano R, Graier WF, Parrella P, Calin GA, Pichler M. ALYREF, a novel factor involved in breast carcinogenesis, acts through transcriptional and post-transcriptional mechanisms selectively regulating the short NEAT1 isoform. Cell Mol Life Sci 2022; 79:391. [PMID: 35776213 PMCID: PMC9249705 DOI: 10.1007/s00018-022-04402-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022]
Abstract
The RNA-binding protein ALYREF (THOC4) is involved in transcriptional regulation and nuclear mRNA export, though its role and molecular mode of action in breast carcinogenesis are completely unknown. Here, we identified high ALYREF expression as a factor for poor survival in breast cancer patients. ALYREF significantly influenced cellular growth, apoptosis and mitochondrial energy metabolism in breast cancer cells as well as breast tumorigenesis in orthotopic mouse models. Transcriptional profiling, phenocopy and rescue experiments identified the short isoform of the lncRNA NEAT1 as a molecular trigger for ALYREF effects in breast cancer. Mechanistically, we found that ALYREF binds to the NEAT1 promoter region to enhance the global NEAT1 transcriptional activity. Importantly, by stabilizing CPSF6, a protein that selectively activates the post-transcriptional generation of the short isoform of NEAT1, as well as by direct binding and stabilization of the short isoform of NEAT1, ALYREF selectively fine-tunes the expression of the short NEAT1 isoform. Overall, our study describes ALYREF as a novel factor contributing to breast carcinogenesis and identifies novel molecular mechanisms of regulation the two isoforms of NEAT1.
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Affiliation(s)
- Christiane Klec
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Katharina Jonas
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Barbara Pasculli
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz (MUG), Graz, Austria
| | - Beate Rinner
- Biomedical Research, Medical University of Graz (MUG), Graz, Austria
| | - Katarina Krajina
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Felix Prinz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Benjamin Gottschalk
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cellular Signaling, Metabolism and Aging, Medical University of Graz (MUG), Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics, Medical University of Graz (MUG), Graz, Austria
| | - Alexander Deutsch
- Division of Hematology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Andreas Prokesch
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Stephan W Jahn
- Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - S Mohammad Lellahi
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Raffaela Barbano
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Wolfgang F Graier
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cellular Signaling, Metabolism and Aging, Medical University of Graz (MUG), Graz, Austria
| | - Paola Parrella
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - George Adrian Calin
- Department of Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria.
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria.
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9
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Tellez-Gabriel M, Tekpli X, Reine TM, Hegge B, Nielsen SR, Chen M, Moi L, Normann LS, Busund LTR, Calin GA, Mælandsmo GM, Perander M, Theocharis AD, Kolset SO, Knutsen E. Serglycin Is Involved in TGF-β Induced Epithelial-Mesenchymal Transition and Is Highly Expressed by Immune Cells in Breast Cancer Tissue. Front Oncol 2022; 12:868868. [PMID: 35494005 PMCID: PMC9047906 DOI: 10.3389/fonc.2022.868868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
Serglycin is a proteoglycan highly expressed by immune cells, in which its functions are linked to storage, secretion, transport, and protection of chemokines, proteases, histamine, growth factors, and other bioactive molecules. In recent years, it has been demonstrated that serglycin is also expressed by several other cell types, such as endothelial cells, muscle cells, and multiple types of cancer cells. Here, we show that serglycin expression is upregulated in transforming growth factor beta (TGF-β) induced epithelial-mesenchymal transition (EMT). Functional studies provide evidence that serglycin plays an important role in the regulation of the transition between the epithelial and mesenchymal phenotypes, and it is a significant EMT marker gene. We further find that serglycin is more expressed by breast cancer cell lines with a mesenchymal phenotype as well as the basal-like subtype of breast cancers. By examining immune staining and single cell sequencing data of breast cancer tissue, we show that serglycin is highly expressed by infiltrating immune cells in breast tumor tissue.
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Affiliation(s)
- Marta Tellez-Gabriel
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trine M. Reine
- Department of Interphase Genetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Beate Hegge
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Stephanie R. Nielsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Meng Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Line Moi
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - Lisa Svartdal Normann
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Research and Innovation, Vestre Viken Hospital Trust, Drammen, Norway
| | - Lill-Tove R. Busund
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Gunhild M. Mælandsmo
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Achilleas D. Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras, Greece
| | | | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Centre for Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
- *Correspondence: Erik Knutsen,
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10
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Emblem Å, Knutsen E, Jørgensen TE, Fure H, Johansen SD, Brekke OL, Mollnes TE, Karlsen BO. Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene. Noncoding RNA 2022; 8:ncrna8020024. [PMID: 35447887 PMCID: PMC9027897 DOI: 10.3390/ncrna8020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Many severe inflammation conditions are complement-dependent with the complement component C5a-C5aR1 axis as an important driver. At the RNA level, the blood transcriptome undergoes programmed expression of coding and long non-coding RNAs to combat invading microorganisms. Understanding the expression of long non-coding RNAs containing Alu elements in inflammation is important for reconstructing cell fate trajectories leading to severe disease. We have assembled a pipeline for computation mining of new Alu-containing long non-coding RNAs by intersecting immune genes with known Alu coordinates in the human genome. By applying the pipeline to patient bulk RNA-seq data with sepsis, we found immune genes containing 48 Alu insertion as robust candidates for further study. Interestingly, 1 of the 48 candidates was located within the complement system receptor gene C5aR1 and holds promise as a target for RNA therapeutics.
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Affiliation(s)
- Åse Emblem
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
| | - Erik Knutsen
- Department of Medical Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Tor Erik Jørgensen
- Genomics Division—FBA, Nord University, 8026 Bodø, Norway; (T.E.J.); (S.D.J.)
| | - Hilde Fure
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
| | | | - Ole-Lars Brekke
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
- Department of Clinical Medicine, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Tom Eirik Mollnes
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Immunology, Oslo University Hospital Rikshospitalet, University of Oslo, 0372 Oslo, Norway
| | - Bård Ove Karlsen
- Research Laboratory and Department of Laboratory Medicine, Nordland Hospital Trust, 8005 Bodø, Norway; (Å.E.); (H.F.); (O.-L.B.); (T.E.M.)
- Correspondence:
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11
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Dragomir MP, Knutsen E, Calin GA. Classical and noncanonical functions of miRNAs in cancers. Trends Genet 2021; 38:379-394. [PMID: 34728089 DOI: 10.1016/j.tig.2021.10.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Alterations in microRNAs (miRNAs) expression are causative in the initiation and progression of human cancers. The molecular events responsible for the widespread differential expression of miRNAs in malignancy are exemplified by their location in cancer-associated genomic regions, epigenetic mechanisms, transcriptional dysregulation, chemical modifications and editing, and alterations in miRNA biogenesis proteins. The classical miRNA function is synonymous with post-transcriptional repression of target protein genes. However, several studies have reported miRNAs functioning outside this paradigm and some of these novel modes of regulation of gene expression have been implicated in cancers. Here, we summarize key aspects of miRNA involvement in cancer, with a special focus on these lesser-studied mechanisms of action.
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Affiliation(s)
- Mihnea P Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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12
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Pereira Zambalde E, Bayraktar R, Schultz Jucoski T, Ivan C, Rodrigues AC, Mathias C, Knutsen E, Silveira de Lima R, Fiori Gradia D, de Souza Fonseca Ribeiro EM, Hannash S, Adrian Calin G, Carvalhode Oliveira J. A novel lncRNA derived from an ultraconserved region: lnc- uc.147, a potential biomarker in luminal A breast cancer. RNA Biol 2021; 18:416-429. [PMID: 34387142 DOI: 10.1080/15476286.2021.1952757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The human genome contains 481 ultraconserved regions (UCRs), which are genomic stretches of over 200 base pairs conserved among human, rat, and mouse. The majority of these regions are transcriptionally active (T-UCRs), and several have been found to be differentially expressed in tumours. Some T-UCRs have been functionally characterized, but of those few have been associated to breast cancer (BC). Using TCGA data, we found 302 T-UCRs related to clinical features in BC: 43% were associated with molecular subtypes, 36% with oestrogen-receptor positivity, 17% with HER2 expression, 12% with stage, and 10% with overall survival. The expression levels of 12 T-UCRs were further analysed in a cohort of 82 Brazilian BC patients using RT-qPCR. We found that uc.147 is high expressed in luminal A and B patients. For luminal A, a subtype usually associated with better prognosis, high uc.147 expression was associated with a poor prognosis and suggested as an independent prognostic factor. The lncRNA from uc.147 (lnc-uc.147) is located in the nucleus. Northern blotting results show that uc.147 is a 2,8 kb monoexonic trancript, and its sequence was confirmed by RACE. The silencing of uc.147 increases apoptosis, arrests cell cycle, and reduces cell viability and colony formation in BC cell lines. Additionally, we identifed 19 proteins that interact with lnc-uc.147 through mass spectrometry and demonstrated a high correlation of lnc-uc.147 with the neighbour gene expression and miR-18 and miR-190b. This is the first study to analyse the expression of all T-UCRs in BC and to functionally assess the lnc-uc.147.
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Affiliation(s)
- Erika Pereira Zambalde
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil.,Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Tayana Schultz Jucoski
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Cristina Ivan
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Carolina Rodrigues
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Carolina Mathias
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Erik Knutsen
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT - the Arctic University of Norway, Tromsø, Norway
| | | | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | | | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George Adrian Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaqueline Carvalhode Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
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13
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Brun VH, Knutsen E, Stenvold H, Halvorsen H. Severe hypercalcemia caused by parathyroid hormone in a rectal cancer metastasis: a case report. BMC Endocr Disord 2021; 21:4. [PMID: 33413267 PMCID: PMC7792014 DOI: 10.1186/s12902-020-00664-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hypercalcemia of malignancy is relatively common in several cancers. However, in colorectal cancer, paraneoplastic phenomena that cause hypercalcemia is uncommon. In the few cases that are reported, secretion of parathyroid hormone-related peptide mediates the effect. We describe the first case of severe hypercalcemia mediated by intact parathyroid hormone secretion from a bone metastasis of colorectal origin. This was a diagnostic and therapeutic challenge. CASE PRESENTATION A 68-year-old male treated for rectal adenocarcinoma 10 years earlier developed a bone metastasis. After initial treatment of the metastasis with surgery and irradiation, he developed a relapse with severe hypercalcemia and corresponding elevated parathyroid hormone levels. The workup showed no signs of parathyroid adenomas, but the metastasis produced intact parathyroid hormone. The hypercalcemia was successfully treated by irradiation and osteoclast inhibitor, and the patient received chemotherapy. Survival was 24 months from the onset of hypercalcemia. CONCLUSIONS Proper diagnosis of the uncommon endocrine disturbance allowed targeted therapy and avoidance of neck exploration for wrongly suspecting primary hyperparathyroidism. Intact parathyroid hormone should be measured in cases of malignant hypercalcemia.
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Affiliation(s)
- Vegard Heimly Brun
- Department of Breast- and Endocrine Surgery, University Hospital of North Norway, Sykehusvegen 38, 9019, Tromsø, Norway.
- UiT The Arctic University of Norway, Faculty of Health Sciences, Hansine Hansens veg 18, 9019, Tromsø, Norway.
| | - Erik Knutsen
- UiT The Arctic University of Norway, Faculty of Health Sciences, Hansine Hansens veg 18, 9019, Tromsø, Norway
| | - Helge Stenvold
- Department of Oncology, University Hospital of North Norway, Sykehusvegen 38, 9019, Tromsø, Norway
| | - Hanne Halvorsen
- Department of Clinical Pathology, University Hospital of North Norway, Sykehusvegen 38, 9019, Tromsø, Norway
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14
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Abstract
Knockout (KO) of long non-coding RNAs (lncRNAs) enables functional characterization of this still poorly described group of transcripts. One of the most efficient and simplest methods to achieve complete KO of a lncRNA is by employing CRISPR/Cas gene editing. As most lncRNAs are not well annotated, their individual functional regions are often not defined, and the majority of the transcripts are not affected by single nucleotide mutations. Therefore, CRISPR/Cas KO is more challenging for lncRNAs as compared to KO of protein coding genes. Strategies for lncRNAs KO include complete removal of the entire gene, removal of the promoter and transcriptional start site, abolishing exon-exon junctions, or removing the transcriptional termination site. Here, we describe the methodology to perform CRISPR/Cas9 KO of lncRNAs in vitro using electroporation as the method of transfection of presynthesized single guide RNAs (sgRNAs) and Cas9 enzyme.
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Affiliation(s)
- Ingrid Arctander Rosenlund
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mihnea P Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.
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15
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Tellez-Gabriel M, Knutsen E, Perander M. Current Status of Circulating Tumor Cells, Circulating Tumor DNA, and Exosomes in Breast Cancer Liquid Biopsies. Int J Mol Sci 2020; 21:E9457. [PMID: 33322643 PMCID: PMC7763984 DOI: 10.3390/ijms21249457] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the most common cancer among women worldwide. Although the five-, ten- and fifteen-year survival rates are good for breast cancer patients diagnosed with early-stage disease, some cancers recur many years after completion of primary therapy. Tumor heterogeneity and clonal evolution may lead to distant metastasis and therapy resistance, which are the main causes of breast cancer-associated deaths. In the clinic today, imaging techniques like mammography and tissue biopsies are used to diagnose breast cancer. Even though these methods are important in primary diagnosis, they have limitations when it comes to longitudinal monitoring of residual disease after treatment, disease progression, therapy responses, and disease recurrence. Over the last few years, there has been an increasing interest in the diagnostic, prognostic, and predictive potential of circulating cancer-derived material acquired through liquid biopsies in breast cancer. Thanks to the development of sensitive devices and platforms, a variety of tumor-derived material, including circulating cancer cells (CTCs), circulating DNA (ctDNA), and biomolecules encapsulated in extracellular vesicles, can now be extracted and analyzed from body fluids. Here we will review the most recent studies on breast cancer, demonstrating the clinical potential and utility of CTCs and ctDNA. We will also review literature illustrating the potential of circulating exosomal RNA and proteins as future biomarkers in breast cancer. Finally, we will discuss some of the advantages and limitations of liquid biopsies and the future perspectives of this field in breast cancer management.
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Affiliation(s)
- Marta Tellez-Gabriel
- Department of Medical Biology, Faculty of Health Sciences, UiT—The Arctic University of Norway, 9011 Tromsø, Norway; (E.K.); (M.P.)
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16
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Chen B, Dragomir MP, Fabris L, Bayraktar R, Knutsen E, Liu X, Tang C, Li Y, Shimura T, Ivkovic TC, De los Santos MC, Anfossi S, Shimizu M, Shah MY, Ling H, Shen P, Multani AS, Pardini B, Burks JK, Katayama H, Reineke LC, Huo L, Syed M, Song S, Ferracin M, Oki E, Fromm B, Ivan C, Bhuvaneshwar K, Gusev Y, Mimori K, Menter D, Sen S, Matsuyama T, Uetake H, Vasilescu C, Kopetz S, Parker-Thornburg J, Taguchi A, Hanash SM, Girnita L, Slaby O, Goel A, Varani G, Gagea M, Li C, Ajani JA, Calin GA. The Long Noncoding RNA CCAT2 Induces Chromosomal Instability Through BOP1-AURKB Signaling. Gastroenterology 2020; 159:2146-2162.e33. [PMID: 32805281 PMCID: PMC7725986 DOI: 10.1053/j.gastro.2020.08.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Chromosomal instability (CIN) is a carcinogenesis event that promotes metastasis and resistance to therapy by unclear mechanisms. Expression of the colon cancer-associated transcript 2 gene (CCAT2), which encodes a long noncoding RNA (lncRNA), associates with CIN, but little is known about how CCAT2 lncRNA regulates this cancer enabling characteristic. METHODS We performed cytogenetic analysis of colorectal cancer (CRC) cell lines (HCT116, KM12C/SM, and HT29) overexpressing CCAT2 and colon organoids from C57BL/6N mice with the CCAT2 transgene and without (controls). CRC cells were also analyzed by immunofluorescence microscopy, γ-H2AX, and senescence assays. CCAT2 transgene and control mice were given azoxymethane and dextran sulfate sodium to induce colon tumors. We performed gene expression array and mass spectrometry to detect downstream targets of CCAT2 lncRNA. We characterized interactions between CCAT2 with downstream proteins using MS2 pull-down, RNA immunoprecipitation, and selective 2'-hydroxyl acylation analyzed by primer extension analyses. Downstream proteins were overexpressed in CRC cells and analyzed for CIN. Gene expression levels were measured in CRC and non-tumor tissues from 5 cohorts, comprising more than 900 patients. RESULTS High expression of CCAT2 induced CIN in CRC cell lines and increased resistance to 5-fluorouracil and oxaliplatin. Mice that expressed the CCAT2 transgene developed chromosome abnormalities, and colon organoids derived from crypt cells of these mice had a higher percentage of chromosome abnormalities compared with organoids from control mice. The transgenic mice given azoxymethane and dextran sulfate sodium developed more and larger colon polyps than control mice given these agents. Microarray analysis and mass spectrometry indicated that expression of CCAT2 increased expression of genes involved in ribosome biogenesis and protein synthesis. CCAT2 lncRNA interacted directly with and stabilized BOP1 ribosomal biogenesis factor (BOP1). CCAT2 also increased expression of MYC, which activated expression of BOP1. Overexpression of BOP1 in CRC cell lines resulted in chromosomal missegregation errors, and increased colony formation, and invasiveness, whereas BOP1 knockdown reduced viability. BOP1 promoted CIN by increasing the active form of aurora kinase B, which regulates chromosomal segregation. BOP1 was overexpressed in polyp tissues from CCAT2 transgenic mice compared with healthy tissue. CCAT2 lncRNA and BOP1 mRNA or protein were all increased in microsatellite stable tumors (characterized by CIN), but not in tumors with microsatellite instability compared with nontumor tissues. Increased levels of CCAT2 lncRNA and BOP1 mRNA correlated with each other and with shorter survival times of patients. CONCLUSIONS We found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis by stabilizing and inducing expression of BOP1 an activator of aurora kinase B. Strategies to target this pathway might be developed for treatment of patients with microsatellite stable colorectal tumors.
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Affiliation(s)
- Baoqing Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China,Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Linda Fabris
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Xu Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Yongfeng Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tadanobu Shimura
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA
| | - Tina Catela Ivkovic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mireia Cruz De los Santos
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Masayoshi Shimizu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maitri Y. Shah
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Shen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Asha S. Multani
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,present address: Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.,present address: Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucas C. Reineke
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Longfei Huo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muddassir Syed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Takatoshi Matsuyama
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Hiroyuki Uetake
- Department of Specialized Surgeries, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Catalin Vasilescu
- Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,“Carol Davila University of Medicine and Pharmacy”, Bucharest, Romania
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jan Parker-Thornburg
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leonard Girnita
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institute and Karolinska University Hospital, SE-171 647 Stockholm, Sweden
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA.,present address: Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston Texas 77030, USA
| | - Chunlai Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jaffer A. Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Lead Contact
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Dragomir MP, Moisoiu V, Manaila R, Pardini B, Knutsen E, Anfossi S, Amit M, Calin GA. A Holistic Perspective: Exosomes Shuttle between Nerves and Immune Cells in the Tumor Microenvironment. J Clin Med 2020; 9:jcm9113529. [PMID: 33142779 PMCID: PMC7693842 DOI: 10.3390/jcm9113529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
One of the limitations of cancer research has been the restricted focus on tumor cells and the omission of other non-malignant cells that are constitutive elements of this systemic disease. Current research is focused on the bidirectional communication between tumor cells and other components of the tumor microenvironment (TME), such as immune and endothelial cells, and nerves. A major success of this bidirectional approach has been the development of immunotherapy. Recently, a more complex landscape involving a multi-lateral communication between the non-malignant components of the TME started to emerge. A prime example is the interplay between immune and endothelial cells, which led to the approval of anti-vascular endothelial growth factor-therapy combined with immune checkpoint inhibitors and classical chemotherapy in non-small cell lung cancer. Hence, a paradigm shift approach is to characterize the crosstalk between different non-malignant components of the TME and understand their role in tumorigenesis. In this perspective, we discuss the interplay between nerves and immune cells within the TME. In particular, we focus on exosomes and microRNAs as a systemic, rapid and dynamic communication channel between tumor cells, nerves and immune cells contributing to cancer progression. Finally, we discuss how combinatorial therapies blocking this tumorigenic cross-talk could lead to improved outcomes for cancer patients.
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Affiliation(s)
- Mihnea P. Dragomir
- Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 022328 Bucharest, Romania
- Institute of Pathology, Charité University Hospital, 10117 Berlin, Germany
- Correspondence: (M.P.D.); (G.A.C.)
| | - Vlad Moisoiu
- Faculty of Physics, Babeş-Bolyai University, 400084 Cluj-Napoca, Romania;
| | - Roxana Manaila
- Clinical Institute of Urology and Renal Transplantation, 400006 Cluj-Napoca, Romania;
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway;
| | - Simone Anfossi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Moran Amit
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (M.P.D.); (G.A.C.)
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18
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Pichler M, Rodriguez-Aguayo C, Nam SY, Dragomir MP, Bayraktar R, Anfossi S, Knutsen E, Ivan C, Fuentes-Mattei E, Lee SK, Ling H, Ivkovic TC, Huang G, Huang L, Okugawa Y, Katayama H, Taguchi A, Bayraktar E, Bhattacharya R, Amero P, He WR, Tran AM, Vychytilova-Faltejskova P, Klec C, Bonilla DL, Zhang X, Kapitanovic S, Loncar B, Gafà R, Wang Z, Cristini V, Hanash S, Bar-Eli M, Lanza G, Slaby O, Goel A, Rigoutsos I, Lopez-Berestein G, Calin GA. Therapeutic potential of FLANC, a novel primate-specific long non-coding RNA in colorectal cancer. Gut 2020; 69:1818-1831. [PMID: 31988194 PMCID: PMC7382985 DOI: 10.1136/gutjnl-2019-318903] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/21/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the function of a novel primate-specific long non-coding RNA (lncRNA), named FLANC, based on its genomic location (co-localised with a pyknon motif), and to characterise its potential as a biomarker and therapeutic target. DESIGN FLANC expression was analysed in 349 tumours from four cohorts and correlated to clinical data. In a series of multiple in vitro and in vivo models and molecular analyses, we characterised the fundamental biological roles of this lncRNA. We further explored the therapeutic potential of targeting FLANC in a mouse model of colorectal cancer (CRC) metastases. RESULTS FLANC, a primate-specific lncRNA feebly expressed in normal colon cells, was significantly upregulated in cancer cells compared with normal colon samples in two independent cohorts. High levels of FLANC were associated with poor survival in two additional independent CRC patient cohorts. Both in vitro and in vivo experiments demonstrated that the modulation of FLANC expression influenced cellular growth, apoptosis, migration, angiogenesis and metastases formation ability of CRC cells. In vivo pharmacological targeting of FLANC by administration of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine nanoparticles loaded with a specific small interfering RNA, induced significant decrease in metastases, without evident tissue toxicity or pro-inflammatory effects. Mechanistically, FLANC upregulated and prolonged the half-life of phosphorylated STAT3, inducing the overexpression of VEGFA, a key regulator of angiogenesis. CONCLUSIONS Based on our findings, we discovered, FLANC as a novel primate-specific lncRNA that is highly upregulated in CRC cells and regulates metastases formation. Targeting primate-specific transcripts such as FLANC may represent a novel and low toxic therapeutic strategy for the treatment of patients.
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Affiliation(s)
- Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Research Unit of Non-Coding RNA and Genome Editing, Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Su Youn Nam
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Gastroenterology Department, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enrique Fuentes-Mattei
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sang Kil Lee
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina Catela Ivkovic
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Guoliang Huang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: China-America Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, Guangdong, P.R. China
| | - Li Huang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ayumu Taguchi
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Emine Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajat Bhattacharya
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Ruixian He
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anh M. Tran
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Petra Vychytilova-Faltejskova
- Molecular Oncology II - Solid Cancers, Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Czech Republic
| | - Christiane Klec
- Research Unit of Non-Coding RNA and Genome Editing, Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Diana L. Bonilla
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinna Zhang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Medical and Molecular Genetics Department, Indiana University, Indianapolis, IN, USA
| | - Sanja Kapitanovic
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Bozo Loncar
- Department of Surgery, Clinical Hospital Dubrava, Zagreb, Croatia
| | - Roberta Gafà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Zhihui Wang
- Mathematics in Medicine Program, The Houston Methodist Research Institute HMRI R8-122, 6670 Bertner Ave, Houston, TX 77030
| | - Vittorio Cristini
- Mathematics in Medicine Program, The Houston Methodist Research Institute HMRI R8-122, 6670 Bertner Ave, Houston, TX 77030
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giovanni Lanza
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Ondrej Slaby
- Molecular Oncology II - Solid Cancers, Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX,Present address: Department of Molecular Diagnostics, Therapeutics and Translational Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center and Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Corresponding authors George A. Calin, M.D., Ph.D. Professor, Department of Experimental Therapeutics, Center for RNA Interference and Non-Coding RNAs, Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, P.O. Box 301429, Houston, Texas 77030-1429, and Gabriel Lopez-Berestein, M.D., Professor, Department of Experimental Therapeutics, Center for RNA Interference and Non-Coding RNAs, Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, P.O. Box 301429, Houston, Texas 77030-1429,
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19
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Dragomir MP, Manyam GC, Ott LF, Berland L, Knutsen E, Ivan C, Lipovich L, Broom BM, Calin GA. FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs. Noncoding RNA 2020; 6:E41. [PMID: 32977531 PMCID: PMC7712257 DOI: 10.3390/ncrna6040041] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs.
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Affiliation(s)
- Mihnea P. Dragomir
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 022328 Bucharest, Romania
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.); (B.M.B.)
| | - Leonie Florence Ott
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Léa Berland
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
| | - Erik Knutsen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Department of Medical Biology, Faculty of Health Sciences, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Cristina Ivan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Centre, Houston, TX 77054, USA
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA;
| | - Bradley M. Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.); (B.M.B.)
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.F.O.); (L.B.); (E.K.); (C.I.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Centre, Houston, TX 77054, USA
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20
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Amit M, Takahashi H, Dragomir MP, Lindemann A, Gleber-Netto FO, Pickering CR, Anfossi S, Osman AA, Cai Y, Wang R, Knutsen E, Shimizu M, Ivan C, Rao X, Wang J, Silverman DA, Tam S, Zhao M, Caulin C, Zinger A, Tasciotti E, Dougherty PM, El-Naggar A, Calin GA, Myers JN. Loss of p53 drives neuron reprogramming in head and neck cancer. Nature 2020; 578:449-454. [PMID: 32051587 DOI: 10.1038/s41586-020-1996-3] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/15/2020] [Indexed: 12/22/2022]
Abstract
The solid tumour microenvironment includes nerve fibres that arise from the peripheral nervous system1,2. Recent work indicates that newly formed adrenergic nerve fibres promote tumour growth, but the origin of these nerves and the mechanism of their inception are unknown1,3. Here, by comparing the transcriptomes of cancer-associated trigeminal sensory neurons with those of endogenous neurons in mouse models of oral cancer, we identified an adrenergic differentiation signature. We show that loss of TP53 leads to adrenergic transdifferentiation of tumour-associated sensory nerves through loss of the microRNA miR-34a. Tumour growth was inhibited by sensory denervation or pharmacological blockade of adrenergic receptors, but not by chemical sympathectomy of pre-existing adrenergic nerves. A retrospective analysis of samples from oral cancer revealed that p53 status was associated with nerve density, which was in turn associated with poor clinical outcomes. This crosstalk between cancer cells and neurons represents mechanism by which tumour-associated neurons are reprogrammed towards an adrenergic phenotype that can stimulate tumour progression, and is a potential target for anticancer therapy.
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Affiliation(s)
- Moran Amit
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Hideaki Takahashi
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Otorhinolaryngology Head and Neck Surgery, Yokohama City University, Yokohama, Japan
| | - Mihnea Paul Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Antje Lindemann
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Frederico O Gleber-Netto
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abdullah A Osman
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Cai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rong Wang
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Masayoshi Shimizu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiayu Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deborah A Silverman
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samantha Tam
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mei Zhao
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlos Caulin
- Department of Otolaryngology, Head and Neck Surgery, University of Arizona, Tucson, AZ, USA.,University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Assaf Zinger
- Regenerative Medicine Program, Houston Methodist Research Institute, Houston, TX, USA.,Department of Orthopedics and Sports Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Ennio Tasciotti
- Regenerative Medicine Program, Houston Methodist Research Institute, Houston, TX, USA.,Department of Orthopedics and Sports Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Patrick M Dougherty
- Department of Pain Medicine, Division of Anesthesiology, Critical Care, and Pain Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adel El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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21
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Knutsen E, Lellahi SM, Aure MR, Nord S, Fismen S, Larsen KB, Gabriel MT, Hedberg A, Bjørklund SS, Bofin AM, Mælandsmo GM, Sørlie T, Mortensen ES, Perander M. The expression of the long NEAT1_2 isoform is associated with human epidermal growth factor receptor 2-positive breast cancers. Sci Rep 2020; 10:1277. [PMID: 31992741 PMCID: PMC6987222 DOI: 10.1038/s41598-020-57759-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 12/21/2019] [Indexed: 12/21/2022] Open
Abstract
The long non-coding RNA NEAT1 locus is transcribed into two overlapping isoforms, NEAT1_1 and NEAT1_2, of which the latter is essential for the assembly of nuclear paraspeckles. NEAT1 is abnormally expressed in a wide variety of human cancers. Emerging evidence suggests that the two isoforms have distinct functions in gene expression regulation, and recently it was shown that NEAT1_2, but not NEAT1_1, expression predicts poor clinical outcome in cancer. Here, we report that NEAT1_2 expression correlates with HER2-positive breast cancers and high-grade disease. We provide evidence that NEAT1_1 and NEAT1_2 have distinct expression pattern among different intrinsic breast cancer subtypes. Finally, we show that NEAT1_2 expression and paraspeckle formation increase upon lactation in humans, confirming what has previously been demonstrated in mice.
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Affiliation(s)
- Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Seyed Mohammad Lellahi
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Silje Fismen
- Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - Kenneth Bowitz Larsen
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Marta Tellez Gabriel
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Annica Hedberg
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Sunniva Stordal Bjørklund
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | - Anna Mary Bofin
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gunhild Mari Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Elin Synnøve Mortensen
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway.
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22
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Fuentes-Mattei E, Bayraktar R, Manshouri T, Silva AM, Ivan C, Gulei D, Fabris L, Soares do Amaral N, Mur P, Perez C, Torres-Claudio E, Dragomir MP, Badillo-Perez A, Knutsen E, Narayanan P, Golfman L, Shimizu M, Zhang X, Zhao W, Ho WT, Estecio MR, Bartholomeusz G, Tomuleasa C, Berindan-Neagoe I, Zweidler-McKay PA, Estrov Z, Zhao ZJ, Verstovsek S, Calin GA, Redis RS. miR-543 regulates the epigenetic landscape of myelofibrosis by targeting TET1 and TET2. JCI Insight 2020; 5:121781. [PMID: 31941838 PMCID: PMC7030823 DOI: 10.1172/jci.insight.121781] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 12/04/2019] [Indexed: 12/13/2022] Open
Abstract
Myelofibrosis (MF) is a myeloproliferative neoplasm characterized by cytopenia and extramedullary hematopoiesis, resulting in splenomegaly. Multiple pathological mechanisms (e.g., circulating cytokines and genetic alterations, such as JAKV617F mutation) have been implicated in the etiology of MF, but the molecular mechanism causing resistance to JAK2V617F inhibitor therapy remains unknown. Among MF patients who were treated with the JAK inhibitor ruxolitinib, we compared noncoding RNA profiles of ruxolitinib therapy responders versus nonresponders and found miR-543 was significantly upregulated in nonresponders. We validated these findings by reverse transcription-quantitative PCR. in this same cohort, in 2 additional independent MF patient cohorts from the United States and Romania, and in a JAK2V617F mouse model of MF. Both in vitro and in vivo models were used to determine the underlying molecular mechanism of miR-543 in MF. Here, we demonstrate that miR-543 targets the dioxygenases ten-eleven translocation 1 (TET1) and 2 (TET2) in patients and in vitro, causing increased levels of global 5-methylcytosine, while decreasing the acetylation of histone 3, STAT3, and tumor protein p53. Mechanistically, we found that activation of STAT3 by JAKs epigenetically controls miR-543 expression via binding the promoter region of miR-543. Furthermore, miR-543 upregulation promotes the expression of genes related to drug metabolism, including CYP3A4, which is involved in ruxolitinib metabolism. Our findings suggest miR-543 as a potentially novel biomarker for the prognosis of MF patients with a high risk of treatment resistance and as a potentially new target for the development of new treatment options.
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Affiliation(s)
| | | | - Taghi Manshouri
- Department of Leukemia, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | - Andreia M. Silva
- Department of Experimental Therapeutics and
- Instituto de Investigação e Inovação em Saúde (i3S)
- Instituto de Engenharia Biomédica (INEB), and
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Cristina Ivan
- Department of Experimental Therapeutics and
- Center for RNA Interference and Non-coding RNAs, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | - Diana Gulei
- Department of Experimental Therapeutics and
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania
- Department of Functional Genomics, The Oncology Institute, Cluj-Napoca, Romania
| | | | - Nayra Soares do Amaral
- Department of Experimental Therapeutics and
- Molecular Morphology Laboratory, Department of Investigative Pathology, AC Camargo Cancer Center, São Paulo, Brazil
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Perez
- Department of Experimental Therapeutics and
- Mayagüez Campus, University of Puerto Rico, Mayagüez, Puerto Rico, USA
| | - Elizabeth Torres-Claudio
- Department of Experimental Therapeutics and
- University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics and
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania
- Department of Surgery, Fundeni Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | | | | | | | - Leonard Golfman
- Department of Pediatrics, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | | | - Xinna Zhang
- Center for RNA Interference and Non-coding RNAs, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | - Wanke Zhao
- Department of Pathology, Health Sciences Center, University of Oklahoma, Oklahoma City, Oklahoma, USA
| | - Wanting Tina Ho
- Department of Pathology, Health Sciences Center, University of Oklahoma, Oklahoma City, Oklahoma, USA
| | - Marcos Roberto Estecio
- Department of Epigenetics and Molecular Carcinogenesis and
- Center for Cancer Epigenetics, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | | | - Ciprian Tomuleasa
- Department of Hematology, The Oncology Institute Ion Chiricuta, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania
- Department of Functional Genomics, The Oncology Institute, Cluj-Napoca, Romania
| | | | - Zeev Estrov
- Department of Leukemia, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | - Zhizhuang J. Zhao
- Department of Pathology, Health Sciences Center, University of Oklahoma, Oklahoma City, Oklahoma, USA
| | - Srdan Verstovsek
- Department of Leukemia, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
| | - George A. Calin
- Department of Experimental Therapeutics and
- Center for RNA Interference and Non-coding RNAs, MD Anderson Cancer Center, The University of Texas, Houston, Texas, USA
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23
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Abstract
MicroRNAs (miRNAs) are synonymous with post-transcriptional repression of target genes. A number of studies, however, have reported miRNAs functioning outside this paradigm, and this SnapShot outlines these unconventional ways in which miRNAs can exert regulatory functions. To view this SnapShot, open or download the PDF.
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Affiliation(s)
- Mihnea Paul Dragomir
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - George Adrian Calin
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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24
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Braicu C, Gulei D, Cojocneanu R, Raduly L, Jurj A, Knutsen E, Calin GA, Berindan‐Neagoe I. miR-181a/b therapy in lung cancer: reality or myth? Mol Oncol 2019; 13:9-25. [PMID: 30548184 PMCID: PMC6322195 DOI: 10.1002/1878-0261.12420] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/30/2018] [Accepted: 12/04/2018] [Indexed: 12/24/2022] Open
Abstract
Despite substantial progress in oncology, lung cancer remains the number one malignancy in terms of both incidence and mortality rates, and there thus remains an urgent need for new therapeutic alternatives. MicroRNA (miRNA) have an important role in cancer initiation and progression due to their capacity to interfere with transcriptional signaling and regulate key cellular processes. miR-181a and miR-181b (miR-181a/b), which are located on chromosomes 1 and 9, are pathologically expressed in the tumor tissue and plasma of patients diagnosed with lung cancer. The miR-181a/b regulatory mechanisms are sophisticated and are directly related to different target genes. In recent years, an ever-increasing number of studies have focused on the biological relevance of miR-181a/b in key cellular processes. In this paper, we aim to discuss the challenging experimental data related to miR-181a/b and their potential use for the development of new therapeutic approaches in lung cancer. We will further present the ongoing issues regarding the regulation of their multiple target genes, and their potential use as biomarkers and therapeutic targets in this deadly malignancy.
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Affiliation(s)
- Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine‘Iuliu Hatieganu’ University of Medicine and PharmacyCluj‐NapocaRomania
| | - Diana Gulei
- MedFuture Research Center for Advanced Medicine‘Iuliu Hatieganu’ University of Medicine and PharmacyCluj‐NapocaRomania
| | - Roxana Cojocneanu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine‘Iuliu Hatieganu’ University of Medicine and PharmacyCluj‐NapocaRomania
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine‘Iuliu Hatieganu’ University of Medicine and PharmacyCluj‐NapocaRomania
| | - Ancuta Jurj
- Research Center for Functional Genomics, Biomedicine and Translational Medicine‘Iuliu Hatieganu’ University of Medicine and PharmacyCluj‐NapocaRomania
| | - Erik Knutsen
- Department of Experimental TherapeuticsThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - George Adrian Calin
- Department of Experimental TherapeuticsThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
- Center for RNA Inference and Non‐Coding RNAThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Ioana Berindan‐Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine‘Iuliu Hatieganu’ University of Medicine and PharmacyCluj‐NapocaRomania
- MedFuture Research Center for Advanced Medicine‘Iuliu Hatieganu’ University of Medicine and PharmacyCluj‐NapocaRomania
- Department of Functional Genomics and Experimental PathologyThe Oncology Institute ‘Prof. Dr. Ion Chiricuta’Cluj‐NapocaRomania
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25
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Shen P, Reineke LC, Knutsen E, Chen M, Pichler M, Ling H, Calin GA. Metformin blocks MYC protein synthesis in colorectal cancer via mTOR-4EBP-eIF4E and MNK1-eIF4G-eIF4E signaling. Mol Oncol 2018; 12:1856-1870. [PMID: 30221473 PMCID: PMC6210051 DOI: 10.1002/1878-0261.12384] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 08/04/2018] [Accepted: 08/14/2018] [Indexed: 12/26/2022] Open
Abstract
The antidiabetic drug metformin has been associated with reduced colorectal cancer (CRC) risk and improved prognosis of CRC patients. However, the detailed mechanisms underlying such beneficial effects remain unknown. In this study, we aimed to evaluate metformin activity in CRC models and unveil the underlying molecular mechanisms. We showed that metformin inhibits CRC cell proliferation by arresting cells in the G1 phase of the cell cycle and dramatically reduces colony formation of CRC cells. We discovered that metformin causes a robust reduction of MYC protein level. Through the use of luciferase assay and coincubation with either protein synthesis or proteasome inhibitors, we demonstrated that regulation of MYC by metformin is independent of the proteasome and 3' UTR-mediated regulation, but depends on protein synthesis. Data from polysome profiling and ribopuromycylation assays showed that metformin induced widespread inhibition of protein synthesis. Repression of protein synthesis by metformin preferentially affects cell cycle-associated proteins, by altering signaling through the mTOR-4EBP-eIF4E and MNK1-eIF4G-eIF4E axes. The inhibition of MYC protein synthesis may underlie metformin's beneficial effects on CRC risk and prognosis.
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Affiliation(s)
- Peng Shen
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucas C Reineke
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Meng Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Division of Oncology, Research Unit of Non-Coding RNA and Genome Editing in Cancer, Medical University of Graz, Austria
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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26
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Lellahi SM, Rosenlund IA, Hedberg A, Kiær LT, Mikkola I, Knutsen E, Perander M. The long noncoding RNA NEAT1 and nuclear paraspeckles are up-regulated by the transcription factor HSF1 in the heat shock response. J Biol Chem 2018; 293:18965-18976. [PMID: 30305397 DOI: 10.1074/jbc.ra118.004473] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/02/2018] [Indexed: 01/08/2023] Open
Abstract
The long noncoding RNA (lncRNA) NEAT1 (nuclear enriched abundant transcript 1) is the architectural component of nuclear paraspeckles, and it has recently gained considerable attention as it is abnormally expressed in pathological conditions such as cancer and neurodegenerative diseases. NEAT1 and paraspeckle formation are increased in cells upon exposure to a variety of environmental stressors and believed to play an important role in cell survival. The present study was undertaken to further investigate the role of NEAT1 in cellular stress response pathways. We show that NEAT1 is a novel target gene of heat shock transcription factor 1 (HSF1) and is up-regulated when the heat shock response pathway is activated by sulforaphane (SFN) or elevated temperature. HSF1 binds specifically to a newly identified conserved heat shock element in the NEAT1 promoter. In line with this, SFN induced the formation of NEAT1-containing paraspeckles via an HSF1-dependent mechanism. HSF1 plays a key role in the cellular response to proteotoxic stress by promoting the expression of a series of genes, including those encoding molecular chaperones. We have found that the expression of HSP70, HSP90, and HSP27 is amplified and sustained during heat shock in NEAT1-depleted cells compared with control cells, indicating that NEAT1 feeds back via an unknown mechanism to regulate HSF1 activity. This interrelationship is potentially significant in human diseases such as cancer and neurodegenerative disorders.
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Affiliation(s)
| | | | | | | | - Ingvild Mikkola
- Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
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27
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Hedberg A, Knutsen E, Løvhaugen AS, Jørgensen TE, Perander M, Johansen SD. Cancer-specific SNPs originate from low-level heteroplasmic variants in human mitochondrial genomes of a matched cell line pair. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:82-91. [PMID: 29671673 DOI: 10.1080/24701394.2018.1461852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Low-level mitochondrial heteroplasmy is a common phenomenon in both normal and cancer cells. Here, we investigate the link between low-level heteroplasmy and mitogenome mutations in a human breast cancer matched cell line by high-throughput sequencing. We identified 23 heteroplasmic sites, of which 15 were common between normal cells (Hs578Bst) and cancer cells (Hs578T). Most sites were clustered within the highly conserved Complex IV and ribosomal RNA genes. Two heteroplasmic variants in normal cells were found as fixed mutations in cancer cells. This indicates a positive selection of these variants in cancer cells. RNA-Seq analysis identified upregulated L-strand specific transcripts in cancer cells, which include three mitochondrial long non-coding RNA molecules. We hypothesize that this is due to two cancer cell-specific mutations in the control region.
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Affiliation(s)
- Annica Hedberg
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Erik Knutsen
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Anne Silje Løvhaugen
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Tor Erik Jørgensen
- b Genomics Group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
| | - Maria Perander
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Steinar D Johansen
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway.,b Genomics Group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
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28
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Fiskaa T, Knutsen E, Nikolaisen MA, Jørgensen TE, Johansen SD, Perander M, Seternes OM. Distinct Small RNA Signatures in Extracellular Vesicles Derived from Breast Cancer Cell Lines. PLoS One 2016; 11:e0161824. [PMID: 27579604 PMCID: PMC5006963 DOI: 10.1371/journal.pone.0161824] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/14/2016] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is a heterogeneous disease, and different subtypes of breast cancer show distinct cellular morphology, gene expression, metabolism, motility, proliferation, and metastatic potential. Understanding the molecular features responsible for this heterogeneity is important for correct diagnosis and better treatment strategies. Extracellular vesicles (EVs) and their associated molecules have gained much attention as players in intercellular communication, ability to precondition specific organs for metastatic invasion, and for their potential role as circulating cancer biomarkers. EVs are released from the cells and contain proteins, DNA, and long and small RNA species. Here we show by high-throughput small RNA-sequencing that EVs from nine different breast cancer cell lines share common characteristics in terms of small RNA content that are distinct from their originating cells. Most strikingly, a highly abundant small RNA molecule derived from the nuclear 28S rRNA is vastly enriched in EVs. The miRNA profiles in EVs correlate with the cellular miRNA expression pattern, but with a few exceptions that includes miR-21. This cancer-associated miRNA is retained in breast cancer cell lines. Finally, we report that EVs from breast cancer cell lines cluster together based on their small RNA signature when compared to EVs derived from other cancer cell lines. Altogether, our data demonstrate that breast cancer cell lines manifest a specific small RNA signature in their released EVs. This opens up for further evaluation of EVs as breast cancer biomarkers.
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Affiliation(s)
- Tonje Fiskaa
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
- * E-mail:
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
| | - Marlen Aas Nikolaisen
- Department of Pharmacy, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
| | - Tor Erik Jørgensen
- Marine Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Steinar Daae Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
- Marine Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
| | - Ole Morten Seternes
- Department of Pharmacy, Faculty of Health Sciences, UiT–The Arctic University of Norway, MH-building Breivika, Tromsø, N-9037, Norway
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El-Gewely MR, Andreassen M, Walquist M, Ursvik A, Knutsen E, Nystad M, Coucheron DH, Myrmel KS, Hennig R, Johansen SD. Differentially Expressed MicroRNAs in Meningiomas Grades I and II Suggest Shared Biomarkers with Malignant Tumors. Cancers (Basel) 2016; 8:E31. [PMID: 26950155 PMCID: PMC4810115 DOI: 10.3390/cancers8030031] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/19/2016] [Accepted: 02/24/2016] [Indexed: 12/18/2022] Open
Abstract
Meningiomas represent the most common primary tumors of the central nervous system, but few microRNA (miRNA) profiling studies have been reported so far. Deep sequencing of small RNA libraries generated from two human meningioma biopsies WHO grades I (benign) and II (atypical) were compared to excess dura controls. Nineteen differentially expressed miRNAs were validated by RT-qPCR using tumor RNA from 15 patients and 5 meninges controls. Tumor suppressor miR-218 and miR-34a were upregulated relative to normal controls, however, miR-143, miR-193b, miR-451 and oncogenic miR-21 were all downregulated. From 10 selected putative mRNA targets tested by RT-qPCR only four were differentially expressed relative to normal controls. PTEN and E-cadherin (CDH1) were upregulated, but RUNX1T1 was downregulated. Proliferation biomarker p63 was upregulated with nuclear localization, but not detected in most normal arachnoid tissues. Immunoreactivity of E-cadherin was detected in the outermost layer of normal arachnoids, but was expressed throughout the tumors. Nuclear Cyclin D1 expression was positive in all studied meningiomas, while its expression in arachnoid was limited to a few trabecular cells. Meningiomas of grades I and II appear to share biomarkers with malignant tumors, but with some additional tumor suppressor biomarkers expression. Validation in more patients is of importance.
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Affiliation(s)
- Mohamed Raafat El-Gewely
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Morten Andreassen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Mari Walquist
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Anita Ursvik
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Mona Nystad
- Department of Clinical Medicine, Women's Health and Perinatology Research Group, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
- Department of Obstetrics and Gynecology, University Hospital of North Norway, NO-9038 Tromsø, Norway.
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, NO-9038 Tromsø, Norway.
| | - Dag H Coucheron
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | | | - Rune Hennig
- Department of Neurosurgery, University Hospital of North Norway, NO-9038 Tromsø, Norway.
- Department of Clinical Medicine, Division of Neurosurgery, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
- Marine Genomics Group, Faculty of Biosciences and Aquaculture, Nord University NO-8049 Bodø, Norway.
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Roth SA, Knutsen E, Fiskaa T, Utnes P, Bhavsar S, Hald ØH, Løkke C, Mestdagh P, Johansen SD, Flægstad T, Einvik C. Next generation sequencing of microRNAs from isogenic neuroblastoma cell lines isolated before and after treatment. Cancer Lett 2015; 372:128-36. [PMID: 26708804 DOI: 10.1016/j.canlet.2015.11.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
Abstract
Neuroblastoma is a pediatric cancer of the developing sympathetic nervous system. High risk neuroblastoma patients typically undergo an initial remission in response to treatment, followed by recurrence of aggressive tumors that have become refractory to further treatment. Recent works have underlined the involvement of microRNAs (miRNAs) in neuroblastoma development and evolution of drug resistance. In this study we have used deep sequencing technology to identify miRNAs differentially expressed in neuroblastoma cell lines isolated from 6 patients at diagnosis and at relapse after intensive treatments. This approach revealed a panel of 42 differentially expressed miRNAs, 8 of which were upregulated and 34 were downregulated. Most strikingly, the 14q32 miRNA clusters encode 22 of the downregulated miRNAs. Reduced expression of 14q32 miRNAs in tumors associated with poor prognosis factors was confirmed in a cohort consisting of 226 primary neuroblastomas. In order to gain insight into the nature of the genes that may be affected by the differentially expressed miRNAs we utilized Ingenuity Pathway Analysis (IPA). This analysis revealed several biological functions and canonical pathways associated with cancer progression and drug resistance. The results of this study contribute to the identification of miRNAs involved in the complex processes of surviving therapeutic treatment and developing drug resistance in neuroblastoma.
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Affiliation(s)
- Sarah Andrea Roth
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway
| | - Erik Knutsen
- RNA and Molecular Pathology (RAMP), Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway
| | - Tonje Fiskaa
- RNA and Molecular Pathology (RAMP), Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway
| | - Peter Utnes
- Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway
| | - Swapnil Bhavsar
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway
| | - Øyvind H Hald
- Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway
| | - Cecilie Løkke
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway
| | - Pieter Mestdagh
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Steinar D Johansen
- RNA and Molecular Pathology (RAMP), Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway; Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
| | - Trond Flægstad
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway; Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway
| | - Christer Einvik
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway; Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway.
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Knutsen E, Fiskaa T, Figenschau S, Brun E, Fismen S, Seternes O, Mortensen E, Johansen S, Perander M. 326: Expression analyses of long non-coding RNAs in breast cancer. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50290-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Manning CN, Havlioglu N, Knutsen E, Sakiyama-Elbert SE, Silva MJ, Thomopoulos S, Gelberman RH. The early inflammatory response after flexor tendon healing: a gene expression and histological analysis. J Orthop Res 2014; 32:645-52. [PMID: 24464937 PMCID: PMC4076155 DOI: 10.1002/jor.22575] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/05/2013] [Indexed: 02/04/2023]
Abstract
Despite advances in surgical techniques over the past three decades, tendon repairs remain prone to poor clinical outcomes. Previous attempts to improve tendon healing have focused on the later stages of healing (i.e., proliferation and matrix synthesis). The early inflammatory phase of tendon healing, however, is not fully understood and its modulation during healing has not yet been studied. Therefore, the purpose of this work was to characterize the early inflammatory phase of flexor tendon healing with the goal of identifying inflammation-related targets for future treatments. Canine flexor tendons were transected and repaired using techniques identical to those used clinically. The inflammatory response was monitored for 9 days. Temporal changes in immune cell populations and gene expression of inflammation-, matrix degradation-, and extracellular matrix-related factors were examined. Gene expression patterns paralleled changes in repair-site cell populations. Of the observed changes, the most dramatic effect was a greater than 4,000-fold up-regulation in the expression of the pro-inflammatory factor IL-1β. While an inflammatory response is likely necessary for healing to occur, high levels of pro-inflammatory cytokines may result in collateral tissue damage and impaired tendon healing. These findings suggest that future tendon treatment approaches consider modulation of the inflammatory phase of healing.
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Affiliation(s)
- CN Manning
- Dept. of Orthopaedic Surgery, Washington University, St Louis, MO
| | - N Havlioglu
- Dept. of Pathology, Saint Louis University Hospital, St Louis, MO
| | - E Knutsen
- Dept. of Orthopaedic Surgery, Washington University, St Louis, MO
| | | | - MJ Silva
- Dept. of Orthopaedic Surgery, Washington University, St Louis, MO
| | - S Thomopoulos
- Dept. of Orthopaedic Surgery, Washington University, St Louis, MO
,Corresponding Authors: Stavros Thomopoulos, Ph.D. (study design and in vivo studies), Richard H. Gelberman, M.D. (clinical relevance and surgical methods). Washington University, 425 South Euclid, Campus Box 8233, St Louis, MO 63110, Phone: 314-362-8605, Fax: 314-362-0334,
| | - RH Gelberman
- Dept. of Orthopaedic Surgery, Washington University, St Louis, MO
,Corresponding Authors: Stavros Thomopoulos, Ph.D. (study design and in vivo studies), Richard H. Gelberman, M.D. (clinical relevance and surgical methods). Washington University, 425 South Euclid, Campus Box 8233, St Louis, MO 63110, Phone: 314-362-8605, Fax: 314-362-0334,
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Knutsen E, Fiskaa T, Ursvik A, Jørgensen TE, Perander M, Lund E, Seternes OM, Johansen SD, Andreassen M. Performance comparison of digital microRNA profiling technologies applied on human breast cancer cell lines. PLoS One 2013; 8:e75813. [PMID: 24116077 PMCID: PMC3793004 DOI: 10.1371/journal.pone.0075813] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 08/20/2013] [Indexed: 12/21/2022] Open
Abstract
MicroRNA profiling represents an important first-step in deducting individual RNA-based regulatory function in a cell, tissue, or at a specific developmental stage. Currently there are several different platforms to choose from in order to make the initial miRNA profiles. In this study we investigate recently developed digital microRNA high-throughput technologies. Four different platforms were compared including next generation SOLiD ligation sequencing and Illumina HiSeq sequencing, hybridization-based NanoString nCounter, and miRCURY locked nucleic acid RT-qPCR. For all four technologies, full microRNA profiles were generated from human cell lines that represent noninvasive and invasive tumorigenic breast cancer. This study reports the correlation between platforms, as well as a more extensive analysis of the accuracy and sensitivity of data generated when using different platforms and important consideration when verifying results by the use of additional technologies. We found all the platforms to be highly capable for microRNA analysis. Furthermore, the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS and RT-qPCR. Based on these findings we propose new guidelines and considerations when performing microRNA profiling.
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Affiliation(s)
- Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Tonje Fiskaa
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Anita Ursvik
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Tor Erik Jørgensen
- Marine Genomics group, Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Eiliv Lund
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ole Morten Seternes
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Steinar D. Johansen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Marine Genomics group, Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
- * E-mail: (SJ); (MA)
| | - Morten Andreassen
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- * E-mail: (SJ); (MA)
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Ohlsson BG, Englund MC, Karlsson AL, Knutsen E, Erixon C, Skribeck H, Liu Y, Bondjers G, Wiklund O. Oxidized low density lipoprotein inhibits lipopolysaccharide-induced binding of nuclear factor-kappaB to DNA and the subsequent expression of tumor necrosis factor-alpha and interleukin-1beta in macrophages. J Clin Invest 1996; 98:78-89. [PMID: 8690807 PMCID: PMC507403 DOI: 10.1172/jci118780] [Citation(s) in RCA: 136] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A large body of evidence suggests that oxidized LDL (oxLDL) has a role in atherogenesis. One effect is the impact on macrophage function. We have studied the effects of oxLDL and oxysterols on the binding of the transcription factors nuclear factor (NF)-kappaB and AP-1 to DNA. These transcription factors are involved in the regulation of several genes and expressed during activation of macrophages, for example by endotoxin (LPS). OxLDL did not induce binding of NF-kappaB. However, the LPS-induced response to NF-kappaB was substantially reduced after preincubation with oxLDL. Medium and highly oxidized LDL also decreased the constitutive DNA-binding of AP-1. Similar effects on AP-1-binding were seen with the oxysterols, 7beta-hydroxycholesterol, 24- hydroxy-, 25-hydroxy-, and 27-hydroxy-cholesterol. Our data therefore suggest an effect of oxLDL on the DNA-binding of AP-1, which might be mediated by the oxysterol content of oxLDL. A decreased LPS-induced TNF-alpha and IL-1beta mRNA and protein expression were found in macrophages incubated with oxLDL before LPS-exposure. These observations suggest that macrophages that internalize extensively oxidized LDL are suppressed in their response to inflammatory stimulation.
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Affiliation(s)
- B G Ohlsson
- The Wallenberg Laboratory for Cardiovascular Research, Sahlgren's Hospital, University of Göteborg, Sweden
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Knutsen E, DuRand C. Previously unrecognized physical illnesses in psychiatric patients. Hosp Community Psychiatry 1991; 42:182-6. [PMID: 1997369 DOI: 10.1176/ps.42.2.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Studies of the prevalence of previously unrecognized physical illness among psychiatric patients have paid little attention to the treatment implications of such illness. The authors describe a study in California in which 78 inpatients received an augmented evaluation one to two weeks after their admission evaluation. The retest evaluation detected previously unrecognized physical conditions that were judged to be causal among patients and physical conditions that were judged to exacerbate the psychiatric condition among 56 patients. The authors discuss the treatment implications of the most common type of conditions detected, neurological and nutritional. They also delineate the barriers to recognizing and then treating previously unrecognized physical illnesses.
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Affiliation(s)
- E Knutsen
- Medical Evaluation Research Project, Napa State Hospital, Imola, CA
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36
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Knutsen E. Psychiatry-important advances in clinical medicine: underdiagnosis of bipolar disorder: causes and implications. West J Med 1983; 138:409-410. [PMID: 18749321 PMCID: PMC1021489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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Abstract
An examination of tardive dyskinesia in 213 schizophrenic outpatients using the Abnormal Involuntary Movement Scale (AIMS) indicates that increasing age is significantly associated with the presence of this disorder while sex is not. Both sexes showed significant linear increases with increasing age. Although males did not evidence the statistically significant curvilinear trend previously reported in an inpatient study using the same methodology, they displayed an attenuated effect at the older age levels. A comparison of prevalence values between the outpatient sample and the inpatient sample previously studied indicated no greater prevalence in the outpatients. However, an examination of differences in AIMS total scores between these samples suggested the presence of many more marginal and mild movements in the outpatients. Reasons for the differences between the inpatient and outpatient studies are discussed.
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Knutsen E. Dental standards ... in Sweden. Dent Mag Oral Top 1970; 87:69-70. [PMID: 5268366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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