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Sutherland L, Lang J, Gonzalez-Juarbe N, Pickett BE. Secondary Analysis of Human Bulk RNA-Seq Dataset Suggests Potential Mechanisms for Letrozole Resistance in Estrogen-Positive (ER+) Breast Cancer. Curr Issues Mol Biol 2024; 46:7114-7133. [PMID: 39057065 PMCID: PMC11275280 DOI: 10.3390/cimb46070424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Estrogen receptor-positive (ER+) breast cancer is common among postmenopausal women and is frequently treated with Letrozole, which inhibits aromatase from synthesizing estrogen from androgens. Decreased estrogen slows the growth of tumors and can be an effective treatment. The increase in Letrozole resistance poses a unique problem for patients. To better understand the underlying molecular mechanism(s) of Letrozole resistance, we reanalyzed transcriptomic data by comparing individuals who responded to Letrozole therapy (responders) to those who were resistant to treatment (non-responders). We identified SOX11 and S100A9 as two significant differentially expressed genes (DEGs) between these patient cohorts, with "PLK1 signaling events" being the most significant signaling pathway. We also identified PRDX4 and E2F8 gene products as being the top mechanistic transcriptional markers for ER+ treatment resistance. Many of the significant DEGs that we identified play a known role in ER+ breast cancer or other types of cancer, which partially validate our results. Several of the gene products we identified are novel in the context of ER+ breast cancer. Many of the genes that we identified warrant further research to elucidate the more specific molecular mechanisms of Letrozole resistance in this patient population and could potentially be used as prognostic markers with further wet lab validation. We anticipate that these findings could contribute to improved detection and therapeutic outcomes in aromatase-resistant ER+ breast cancer patients.
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Affiliation(s)
- Lincoln Sutherland
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA; (L.S.); (J.L.)
| | - Jacob Lang
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA; (L.S.); (J.L.)
| | - Norberto Gonzalez-Juarbe
- J. Craig Venter Institute, Rockville, MD 20850, USA;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA; (L.S.); (J.L.)
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2
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Fuentes‐Antrás J, Bedard PL, Cescon DW. Seize the engine: Emerging cell cycle targets in breast cancer. Clin Transl Med 2024; 14:e1544. [PMID: 38264947 PMCID: PMC10807317 DOI: 10.1002/ctm2.1544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/10/2023] [Accepted: 12/31/2023] [Indexed: 01/25/2024] Open
Abstract
Breast cancer arises from a series of molecular alterations that disrupt cell cycle checkpoints, leading to aberrant cell proliferation and genomic instability. Targeted pharmacological inhibition of cell cycle regulators has long been considered a promising anti-cancer strategy. Initial attempts to drug critical cell cycle drivers were hampered by poor selectivity, modest efficacy and haematological toxicity. Advances in our understanding of the molecular basis of cell cycle disruption and the mechanisms of resistance to CDK4/6 inhibitors have reignited interest in blocking specific components of the cell cycle machinery, such as CDK2, CDK4, CDK7, PLK4, WEE1, PKMYT1, AURKA and TTK. These targets play critical roles in regulating quiescence, DNA replication and chromosome segregation. Extensive preclinical data support their potential to overcome CDK4/6 inhibitor resistance, induce synthetic lethality or sensitise tumours to immune checkpoint inhibitors. This review provides a biological and drug development perspective on emerging cell cycle targets and novel inhibitors, many of which exhibit favourable safety profiles and promising activity in clinical trials.
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Affiliation(s)
- Jesús Fuentes‐Antrás
- Division of Medical Oncology and HematologyDepartment of MedicinePrincess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoOntarioCanada
- NEXT OncologyHospital Universitario QuironSalud MadridMadridSpain
| | - Philippe L. Bedard
- Division of Medical Oncology and HematologyDepartment of MedicinePrincess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoOntarioCanada
| | - David W. Cescon
- Division of Medical Oncology and HematologyDepartment of MedicinePrincess Margaret Cancer CentreUniversity Health NetworkUniversity of TorontoTorontoOntarioCanada
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3
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Atasoy-Zeybek A, Hawse GP, Nagelli CV, Lopez De Padilla C, Abdel MP, Evans CH. Transcriptomic changes during the replicative senescence of human articular chondrocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.565835. [PMID: 37986862 PMCID: PMC10659330 DOI: 10.1101/2023.11.07.565835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Osteoarthritis (OA) is a degenerative joint disease and a leading cause of disability worldwide. Aging is a major risk factor for OA, but the specific mechanisms underlying this connection remain unclear. Although chondrocytes rarely divide in adult articular cartilage, they undergo replicative senescence in vitro which provides an opportunity to study changes related to aging under controlled laboratory conditions. In this pilot study, we performed bulk RNA sequencing on early- and late-passage human articular chondrocytes to identify transcriptomic changes associated with cellular aging. Chondrocytes were isolated from the articular cartilage of three donors, two with OA (age 70-80 years) and one with healthy cartilage (age 26 years). Chondrocytes were serially passaged until replicative senescence and RNA extracted from early- and late-passage cells. Principal component analysis of all genes showed clear separation between early- and late-passage chondrocytes, indicating substantial age-related differences in gene expression. Differentially expressed genes (DEGs) analysis confirmed distinct transcriptomic profiles between early- and late-passage chondrocytes. Hierarchical clustering revealed contrasting expression patterns between the two isolates from osteoarthritic samples and the healthy sample. Focused analysis of DEGs on transcripts associated with turnover of the extra-cellular matrix and the senescence-associated secretory phenotype (SASP) showed consistent downregulation of Col2A1 and ACAN, and upregulation of MMP19, ADAMTS4, and ADAMTS8 in late passage chondrocytes across all samples. SASP components including IL-1α, IL-1β, IL-6, IL-7, p16INK4A (CDKN2A) and CCL2 demonstrated significant upregulation in late passage chondrocytes originally isolated from OA samples. Pathway analysis between sexes with OA revealed shared pathways such as extracellular matrix (ECM) organization, collagen formation, skeletal and muscle development, and nervous system development. Sex-specific differences were observed, with males showing distinctions in ECM organization, regulation of the cell cycle process as well as neuron differentiation. In contrast, females exhibited unique variations in the regulation of the cell cycle process, DNA metabolic process, and the PID-PLK1 pathway.
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Affiliation(s)
- Aysegul Atasoy-Zeybek
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Gresin P. Hawse
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Christopher V. Nagelli
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Consuelo Lopez De Padilla
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Christopher H. Evans
- Musculoskeletal Gene Therapy Research Laboratory, Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
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4
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Lashen AG, Toss MS, Wootton L, Green AR, Mongan NP, Madhusudan S, Rakha E. Characteristics and prognostic significance of polo-like kinase-1 (PLK1) expression in breast cancer. Histopathology 2023; 83:414-425. [PMID: 37222669 DOI: 10.1111/his.14960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/25/2023]
Abstract
AIM Polo-like kinase-1 (PLK1) plays a crucial role in cell cycle progression, and it is considered a potential therapeutic target in many cancers. Although the role of PLK1 is well established in triple-negative breast cancer (TNBC) as an oncogene, its role in luminal BC is still controversial. In this study, we aimed to evaluate the prognostic and predictive role of PLK1 in BC and its molecular subtypes. METHODS A large BC cohort (n = 1208) were immunohistochemically stained for PLK1. The association with clinicopathological, molecular subtypes, and survival data was analysed. PLK1 mRNA was evaluated in the publicly available datasets (n = 6774), including The Cancer Genome Atlas and the Kaplan-Meier Plotter tool. RESULTS 20% of the study cohort showed high cytoplasmic PLK1 expression. High PLK1 expression was significantly associated with a better outcome in the whole cohort, luminal BC. In contrast, high PLK1 expression was associated with a poor outcome in TNBC. Multivariate analyses indicated that high PLK1 expression is independently associated with longer survival in luminal BC, and in poorer prognosis in TNBC. At the mRNA levels, PLK1 expression was associated with short survival in TNBC consistent with the protein expression. However, in luminal BC, its prognostic value significantly varies between cohorts. CONCLUSION The prognostic role of PLK1 in BC is molecular subtype-dependent. As PLK1 inhibitors are introduced to clinical trials for several cancer types, our study supports evaluation of the pharmacological inhibition of PLK1 as an attractive therapeutic target in TNBC. However, in luminal BC, PLK1 prognostic role remains controversial.
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Affiliation(s)
- Ayat G Lashen
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- Department of Pathology, Faculty of Medicine, Menoufia University, Shebin El Kom, Egypt
- Nottingham Breast Cancer Research Centre, University of Nottingham, Nottingham, UK
| | - Michael S Toss
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham Breast Cancer Research Centre, University of Nottingham, Nottingham, UK
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust Sheffield, Sheffield, UK
| | - Louisa Wootton
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Andrew R Green
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham Breast Cancer Research Centre, University of Nottingham, Nottingham, UK
| | - Nigel P Mongan
- School of Veterinary Medicine and Sciences, University of Nottingham, Nottingham, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Srinivasan Madhusudan
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- Department of Oncology, Nottingham University Hospitals, Nottingham, UK
| | - Emad Rakha
- Academic Unit for Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
- Department of Pathology, Faculty of Medicine, Menoufia University, Shebin El Kom, Egypt
- Department of Pathology, Hamad Medical Corporation, Doha, Qatar
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Accattatis FM, Caruso A, Carleo A, Del Console P, Gelsomino L, Bonofiglio D, Giordano C, Barone I, Andò S, Bianchi L, Catalano S. CEBP-β and PLK1 as Potential Mediators of the Breast Cancer/Obesity Crosstalk: In Vitro and In Silico Analyses. Nutrients 2023; 15:2839. [PMID: 37447165 DOI: 10.3390/nu15132839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Over the last two decades, obesity has reached pandemic proportions in several countries, and expanding evidence is showing its contribution to several types of malignancies, including breast cancer (BC). The conditioned medium (CM) from mature adipocytes contains a complex of secretes that may mimic the obesity condition in studies on BC cell lines conducted in vitro. Here, we report a transcriptomic analysis on MCF-7 BC cells exposed to adipocyte-derived CM and focus on the predictive functional relevance that CM-affected pathways/processes and related biomarkers (BMs) may have in BC response to obesity. CM was demonstrated to increase cell proliferation, motility and invasion as well as broadly alter the transcript profiles of MCF-7 cells by significantly modulating 364 genes. Bioinformatic functional analyses unraveled the presence of five highly relevant central hubs in the direct interaction networks (DIN), and Kaplan-Meier analysis sorted the CCAAT/enhancer binding protein beta (CEBP-β) and serine/threonine-protein kinase PLK1 (PLK1) as clinically significant biomarkers in BC. Indeed, CEBP-β and PLK1 negatively correlated with BC overall survival and were up-regulated by adipocyte-derived CM. In addition to their known involvement in cell proliferation and tumor progression, our work suggests them as a possible "deus ex machina" in BC response to fat tissue humoral products in obese women.
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Affiliation(s)
- Felice Maria Accattatis
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Amanda Caruso
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, Carl-Neuberg-Straße, 30625 Hannover, Germany
| | - Piercarlo Del Console
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Luca Gelsomino
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Daniela Bonofiglio
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Cinzia Giordano
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Ines Barone
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
| | - Laura Bianchi
- Section of Functional Proteomics, Department of Life Sciences, Via Aldo Moro, University of Siena, 53100 Siena, Italy
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
- Centro Sanitario, Via P. Bucci, University of Calabria, Arcavacata di Rende (CS), 87036 Cosenza, Italy
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6
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Zhang H, Song W, Ma X, Yu M, Chen L, Tao Y. Acetylation stabilizes the signaling protein WISP2 by preventing its degradation to suppress the progression of acute myeloid leukemia. J Biol Chem 2023; 299:102971. [PMID: 36736423 PMCID: PMC9996369 DOI: 10.1016/j.jbc.2023.102971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Acute myeloid leukemia (AML) is challenging to treat due to its heterogeneity, prompting a deep understanding of its pathogenesis mechanisms, diagnosis, and treatment. Here, we found reduced expression and acetylation levels of WISP2 in bone marrow mononuclear cells from AML patients and that AML patients with lower WISP2 expression tended to have reduced survival. At the functional level, overexpression of WISP2 in leukemia cells (HL-60 and Kasumi-1) suppressed cell proliferation, induced cell apoptosis, and exerted antileukemic effects in an in vivo model of AML. Our mechanistic investigation demonstrated that WISP2 deacetylation was regulated by the deacetylase histone deacetylase (HDAC)3. In addition, we determined that crosstalk between acetylation and ubiquitination was involved in the modulation of WISP2 expression in AML. Deacetylation of WISP2 decreased the stability of the WISP2 protein by boosting its ubiquitination mediated by NEDD4 and proteasomal degradation. Moreover, pan-HDAC inhibitors (valproic acid and trichostatin A) and an HDAC3-specific inhibitor (RGFP966) induced WISP2 acetylation at lysine K6 and prevented WISP2 degradation. This regulation led to inhibition of proliferation and induction of apoptosis in AML cells. In summary, our study revealed that WISP2 contributes to tumor suppression in AML, which provided an experimental framework for WISP2 as a candidate for gene therapy of AML.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China; Institute of Blood and Marrow Transplantation, Jining Medical University, Jining, Shandong, China
| | - Wenjun Song
- Institute of Blood and Marrow Transplantation, Jining Medical University, Jining, Shandong, China; Graduate School, Department of Clinical Medicine, Jining Medical University, Jining, Shandong, China
| | - Xinying Ma
- Institute of Blood and Marrow Transplantation, Jining Medical University, Jining, Shandong, China; Graduate School, Department of Clinical Medicine, Jining Medical University, Jining, Shandong, China
| | - Mingxiao Yu
- Institute of Blood and Marrow Transplantation, Jining Medical University, Jining, Shandong, China; Graduate School, Department of Clinical Medicine, Jining Medical University, Jining, Shandong, China
| | - Lulu Chen
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China; Institute of Blood and Marrow Transplantation, Jining Medical University, Jining, Shandong, China
| | - Yanling Tao
- Department of Pediatric Hematology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China.
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Stafford JM, Wyatt MD, McInnes C. Inhibitors of the PLK1 polo-box domain: drug design strategies and therapeutic opportunities in cancer. Expert Opin Drug Discov 2023; 18:65-81. [PMID: 36524399 DOI: 10.1080/17460441.2023.2159942] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Polo Like Kinase 1 (PLK1) is a key regulator of mitosis and its overexpression is frequently observed in a wide variety of human cancers, while often being associated with poor survival rates. Therefore, it is considered a potential and attractive target for cancer therapeutic development. The Polo like kinase family is characterized by the presence of a unique C terminal polobox domain (PBD) involved in regulating kinase activity and subcellular localization. Among the two functionally essential, druggable sites with distinct properties that PLK1 offers, targeting the PBD presents an alternative approach for therapeutic development. AREAS COVERED Significant progress has been made in progressing from the peptidic PBD inhibitors first identified, to peptidomimetic and recently drug-like small molecules. In this review, the rationale for targeting the PBD over the ATP binding site is discussed, along with recent progress, challenges, and outlook. EXPERT OPINION The PBD has emerged as a viable alternative target for the inhibition of PLK1, and progress has been made in using compounds to elucidate mechanistic aspects of activity regulation and in determining roles of the PBD. Studies have resulted in proof of concept of in vivo efficacy suggesting promise for PBD binders in clinical development.
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Affiliation(s)
- Jessy M Stafford
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Michael D Wyatt
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
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8
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Soman A, Asha Nair S. Unfolding the cascade of SERPINA3: Inflammation to cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188760. [PMID: 35843512 DOI: 10.1016/j.bbcan.2022.188760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 10/17/2022]
Abstract
SERine Protease INhibitor clade A member 3 (SERPINA3), a member of the SERine-Protease INhibitor (SERPIN) superfamily, principally works as a protease inhibitor in maintaining cellular homeostasis. It is a matricellular acute-phase glycoprotein that appears to be the sole nuclear-binding secretory serpin. Several studies have emerged in recent years demonstrating its link to cancer and disease biology. SERPINA3 seems to have cancer- and compartment-specific biological functions, acting either as a tumour promoter or suppressor in different cancers. However, the localization, mechanism of action and the effectors of SERPINA3 in physiological and pathological scenarios remain obscure. Our review aims to consolidate the current evidence of SERPINA3 in various cancers, highlighting its association with the cancer hallmarks and ratifying its status as an emerging cancer biomarker. The elucidation of SERPINA3-mediated cancer progression and its targeting might shed light on the realm of cancer therapeutics.
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Affiliation(s)
- Anjana Soman
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India; Research Centre, University of Kerala, Thiruvananthapuram, India
| | - S Asha Nair
- Cancer Research Program 4, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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9
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Fang L, Liu Q, Cui H, Zheng Y, Wu C. Bioinformatics Analysis Highlight Differentially Expressed CCNB1 and PLK1 Genes as Potential Anti-Breast Cancer Drug Targets and Prognostic Markers. Genes (Basel) 2022; 13:654. [PMID: 35456460 PMCID: PMC9027215 DOI: 10.3390/genes13040654] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
Breast cancer is one of the most common malignant tumors in women worldwide. Early diagnosis, treatment, and prognosis of breast cancer are global challenges. Identification of valid predictive diagnosis and prognosis biomarkers and drug targets are crucial for breast cancer prevention. This study characterizes differentially expressed genes (DEGs) based on the TCGA database by using DESeq2, edgeR, and limma. A total of 2032 DEGs, including 1026 up-regulated genes and 1006 down-regulated genes were screened. Followed with WGCNA, PPI analysis, GEPIA 2, and HPA database verification, thirteen hub genes including CDK1, BUB1, BUB1B, CDC20, CCNB2, CCNB1, KIF2C, NDC80, CDCA8, CENPF, BIRC5, AURKB, PLK1, MAD2L1, and CENPE were obtained, and they may serve as potential therapeutic targets of breast cancer. Especially, overexpression of CCNB1 and PLK1 are strongly associated with the low survival rate of breast cancer patients, demonstrating their potentiality as prognostic markers. Moreover, CCNB1 and PLK1 are highly expressed in all breast cancer stages, suggesting that they could be further studied as potential drug targets. Taken together, our study highlights CCNB1 and PLK1 as potential anti-breast cancer drug targets and prognostic markers.
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Affiliation(s)
- Leiming Fang
- School of Biomedical Engineering, Dalian University of Technology, Dalian 116024, China; (L.F.); (Q.L.); (H.C.)
| | - Qi Liu
- School of Biomedical Engineering, Dalian University of Technology, Dalian 116024, China; (L.F.); (Q.L.); (H.C.)
| | - Hongtu Cui
- School of Biomedical Engineering, Dalian University of Technology, Dalian 116024, China; (L.F.); (Q.L.); (H.C.)
| | - Yunji Zheng
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China;
| | - Chengjun Wu
- School of Biomedical Engineering, Dalian University of Technology, Dalian 116024, China; (L.F.); (Q.L.); (H.C.)
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10
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Huo Y, Li X, Xu P, Bao Z, Liu W. Analysis of Breast Cancer Based on the Dysregulated Network. Front Genet 2022; 13:856075. [PMID: 35242172 PMCID: PMC8886234 DOI: 10.3389/fgene.2022.856075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer is a heterogeneous disease, and its development is closely associated with the underlying molecular regulatory network. In this paper, we propose a new way to measure the regulation strength between genes based on their expression values, and construct the dysregulated networks (DNs) for the four subtypes of breast cancer. Our results show that the key dysregulated networks (KDNs) are significantly enriched in critical breast cancer-related pathways and driver genes; closely related to drug targets; and have significant differences in survival analysis. Moreover, the key dysregulated genes could serve as potential driver genes, drug targets, and prognostic markers for each breast cancer subtype. Therefore, the KDN is expected to be an effective and novel way to understand the mechanisms of breast cancer.
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Affiliation(s)
- Yanhao Huo
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
| | - Xianbin Li
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
| | - Peng Xu
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China.,School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Zhenshen Bao
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China.,School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Wenbin Liu
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
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11
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Wright RHG, Vastolo V, Oliete JQ, Carbonell-Caballero J, Beato M. Global signalling network analysis of luminal T47D breast cancer cells in response to progesterone. Front Endocrinol (Lausanne) 2022; 13:888802. [PMID: 36034422 PMCID: PMC9403329 DOI: 10.3389/fendo.2022.888802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Breast cancer cells enter into the cell cycle following progestin exposure by the activation of signalling cascades involving a plethora of enzymes, transcription factors and co-factors that transmit the external signal from the cell membrane to chromatin, ultimately leading to a change of the gene expression program. Although many of the events within the signalling network have been described in isolation, how they globally team up to generate the final cell response is unclear. METHODS In this study we used antibody microarrays and phosphoproteomics to reveal a dynamic global signalling map that reveals new key regulated proteins and phosphor-sites and links between previously known and novel pathways. T47D breast cancer cells were used, and phospho-sites and pathways highlighted were validated using specific antibodies and phenotypic assays. Bioinformatic analysis revealed an enrichment in novel signalling pathways, a coordinated response between cellular compartments and protein complexes. RESULTS Detailed analysis of the data revealed intriguing changes in protein complexes involved in nuclear structure, epithelial to mesenchyme transition (EMT), cell adhesion, as well as transcription factors previously not associated with breast cancer cell proliferation. Pathway analysis confirmed the key role of the MAPK signalling cascade following progesterone and additional hormone regulated phospho-sites were identified. Full network analysis shows the activation of new signalling pathways previously not associated with progesterone signalling in T47D breast cancer cells such as ERBB and TRK. As different post-translational modifications can mediate complex crosstalk mechanisms and massive PARylation is also rapidly induced by progestins, we provide details of important chromatin regulatory complexes containing both phosphorylated and PARylated proteins. CONCLUSIONS This study contributes an important resource for the scientific community, as it identifies novel players and connections meaningful for breast cancer cell biology and potentially relevant for cancer management.
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Affiliation(s)
- Roni H. G. Wright
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
- *Correspondence: Roni H. G. Wright, ; Miguel Beato,
| | - Viviana Vastolo
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Javier Quilez Oliete
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - José Carbonell-Caballero
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- *Correspondence: Roni H. G. Wright, ; Miguel Beato,
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12
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Iliaki S, Beyaert R, Afonina IS. Polo-like kinase 1 (PLK1) signaling in cancer and beyond. Biochem Pharmacol 2021; 193:114747. [PMID: 34454931 DOI: 10.1016/j.bcp.2021.114747] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023]
Abstract
PLK1 is an evolutionary conserved Ser/Thr kinase that is best known for its role in cell cycle regulation and is expressed predominantly during the G2/S and M phase of the cell cycle. PLK1-mediated phosphorylation of specific substrates controls cell entry into mitosis, centrosome maturation, spindle assembly, sister chromatid cohesion and cytokinesis. In addition, a growing body of evidence describes additional roles of PLK1 beyond the cell cycle, more specifically in the DNA damage response, autophagy, apoptosis and cytokine signaling. PLK1 has an indisputable role in cancer as it controls several key transcription factors and promotes cell proliferation, transformation and epithelial-to-mesenchymal transition. Furthermore, deregulation of PLK1 results in chromosome instability and aneuploidy. PLK1 is overexpressed in many cancers, which is associated with poor prognosis, making PLK1 an attractive target for cancer treatment. Additionally, PLK1 is involved in immune and neurological disorders including Graft versus Host Disease, Huntington's disease and Alzheimer's disease. Unfortunately, newly developed small compound PLK1 inhibitors have only had limited success so far, due to low therapeutic response rates and toxicity. In this review we will highlight the current knowledge about the established roles of PLK1 in mitosis regulation and beyond. In addition, we will discuss its tumor promoting but also tumor suppressing capacities, as well as the available PLK1 inhibitors, elaborating on their efficacy and limitations.
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Affiliation(s)
- Styliani Iliaki
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, B-9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, B-9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium.
| | - Inna S Afonina
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, B-9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
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13
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Wu Y, Guo Y, Yu H, Guo T. RNA editing affects cis-regulatory elements and predicts adverse cancer survival. Cancer Med 2021; 10:6114-6127. [PMID: 34319007 PMCID: PMC8419749 DOI: 10.1002/cam4.4146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA editing exerts critical impacts on numerous biological processes and thus are implicated in crucial human phenotypes, including tumorigenesis and prognosis. While previous studies have analyzed aggregate RNA editing activity at the sample level and associated it with overall cancer survival, there is not yet a large-scale disease-specific survival study to examine genome-wide RNA editing sites' prognostic value taking into account the host gene expression and clinical variables. METHODS In this study, we solved comprehensive Cox proportional models of disease-specific survival on individual RNA-editing sites plus host gene expression and critical demographic covariates. This allowed us to interrogate the prognostic value of a large number of RNA-editing sites at single-nucleotide resolution. RESULTS As a result, we identified 402 gene-proximal RNA-editing sites that generally predict adverse cancer survival. For example, an RNA-editing site residing in ZNF264 indicates poor survival of uterine corpus endometrial carcinoma, with a hazard ratio of 2.13 and an adjusted p-value of 4.07 × 10-7 . Some of these prognostic RNA-editing sites mediate the binding of RNA binding proteins and microRNAs, thus propagating their impacts to extensive regulatory targets. CONCLUSIONS In conclusion, RNA editing affects cis-regulatory elements and predicts adverse cancer survival.
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Affiliation(s)
- Yuan‐Ming Wu
- School of Basic Medical SciencesGuizhou Medical UniversityGuiyangChina
- Stem Cell and Tissue Engineering Research CenterGuizhou Medical UniversityGuizhouChina
| | - Yan Guo
- Comprehensive Cancer CenterUniversity of New MexicoAlbuquerqueNMUSA
| | - Hui Yu
- Comprehensive Cancer CenterUniversity of New MexicoAlbuquerqueNMUSA
| | - Tao Guo
- Guizhou Provincial People’s HospitalGuiyangChina
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14
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Saha S, Dey S, Nath S. Steroid Hormone Receptors: Links With Cell Cycle Machinery and Breast Cancer Progression. Front Oncol 2021; 11:620214. [PMID: 33777765 PMCID: PMC7994514 DOI: 10.3389/fonc.2021.620214] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
Progression of cells through cell cycle consists of a series of events orchestrated in a regulated fashion. Such processes are influenced by cell cycle regulated expression of various proteins where multiple families of transcription factors take integral parts. Among these, the steroid hormone receptors (SHRs) represent a connection between the external hormone milieu and genes that control cellular proliferation. Therefore, understanding the molecular connection between the transcriptional role of steroid hormone receptors and cell cycle deserves importance in dissecting cellular proliferation in normal as well as malignant conditions. Deregulation of cell cycle promotes malignancies of various origins, including breast cancer. Indeed, SHR members play crucial role in breast cancer progression as well as management. This review focuses on SHR-driven cell cycle regulation and moving forward, attempts to discuss the role of SHR-driven crosstalk between cell cycle anomalies and breast cancer.
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Affiliation(s)
- Suryendu Saha
- Department of Basic and Translational Research, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Samya Dey
- Department of Basic and Translational Research, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Somsubhra Nath
- Department of Basic and Translational Research, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
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15
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Rooney J, Ryan N, Liu J, Houtman R, van Beuningen R, Hsieh JH, Chang G, Chen S, Christopher Corton J. A Gene Expression Biomarker Identifies Chemical Modulators of Estrogen Receptor α in an MCF-7 Microarray Compendium. Chem Res Toxicol 2021; 34:313-329. [PMID: 33405908 PMCID: PMC10683854 DOI: 10.1021/acs.chemrestox.0c00243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identification of chemicals that affect hormone-regulated systems will help to predict endocrine disruption. In our previous study, a 46 gene biomarker was found to be an accurate predictor of estrogen receptor (ER) α modulation in chemically treated MCF-7 cells. Here, potential ERα modulators were identified using the biomarker by screening a microarray compendium consisting of ∼1600 gene expression comparisons representing exposure to ∼1200 chemicals. A total of ∼170 chemicals were identified as potential ERα modulators. In the Connectivity Map 2.0 collection, 75 and 39 chemicals were predicted to activate or suppress ERα, and they included 12 and six known ERα agonists and antagonists/selective ERα modulators, respectively. Nineteen and eight of the total number were also identified as active in an ERα transactivation assay carried out in an MCF-7-derived cell line used to screen the Tox21 10K chemical library in agonist or antagonist modes, respectively. Chemicals predicted to modulate ERα in MCF-7 cells were examined further using global and targeted gene expression in wild-type and ERα-null cells, transactivation assays, and cell-free ERα coregulator interaction assays. Environmental chemicals classified as weak and very weak agonists were confirmed to activate ERα including apigenin, kaempferol, and oxybenzone. Novel activators included digoxin, nabumetone, ivermectin, and six progestins. Novel suppressors included emetine, mifepristone, niclosamide, and proscillaridin. Our strategy will be useful to identify environmentally relevant ERα modulators in future high-throughput transcriptomic screens.
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Affiliation(s)
- John Rooney
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
- Present address: Integrated Lab Services, Research Triangle Park, NC
| | - Natalia Ryan
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
- Present address: Bayer Crop Science, Research Triangle Park, NC
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
| | - René Houtman
- PamGene International B.V., Den Bosch, The Netherlands
- Present address: Precision Medicine Lab, Oss, The Netherlands
| | | | - Jui-Hua Hsieh
- Kelly Government Solutions, Research Triangle Park, North Carolina
| | - Gregory Chang
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte,California 91010
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte,California 91010
| | - J. Christopher Corton
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
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16
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Jeong JH, Yun JW, Kim HY, Heo CY, Lee S. Elucidation of Novel Therapeutic Targets for Breast Cancer with ESR1-CCDC170 Fusion. J Clin Med 2021; 10:jcm10040582. [PMID: 33557149 PMCID: PMC7913953 DOI: 10.3390/jcm10040582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/09/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022] Open
Abstract
Among the various types of breast cancer, the luminal B subtype is the most common in young women, and ESR1-CCDC170 (E:C) fusion is the most frequent oncogenic fusion driver of the luminal B subtype. Nevertheless, treatments targeting E:C fusion has not been well established yet. Hence, the aim of this study is to investigate potential therapies targeting E:C fusion based on systematic bioinformatical analysis of the Cancer Genome Atlas (TCGA) data. One thousand related genes were extracted using transcriptome analysis, and major signaling pathways associated with breast cancer were identified with over-representation analysis. Then, we conducted drug-target network analysis based on the OncoKB and CIViC databases, and finally selected potentially applicable drug candidates. Six major cancer-related signaling pathways (p53, ATR/ATM, FOXM1, hedgehog, cell cycle, and Aurora B) were significantly altered in E:C fusion-positive cases of breast cancer. Further investigation revealed that nine genes (AURKB, HDAC2, PLK1, CENPA, CHEK1, CHEK2, RB1, CCNA2, and MDM2) in coordination with E:C fusion were found to be common denominators in three or more of these pathways, thereby making them promising gene biomarkers for target therapy. Among the 21 putative actionable drugs inferred by drug-target network analysis, palbociclib, alpelisib, ribociclib, dexamethasone, checkpoint kinase inhibitor AXD 7762, irinotecan, milademetan tosylate, R05045337, cisplatin, prexasertib, and olaparib were considered promising drug candidates targeting genes involved in at least two E:C fusion-related pathways.
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Affiliation(s)
- Jae Heon Jeong
- Integrated Major in Innovative Medical Science, College of Medicine, Seoul National University, Seoul 08826, Korea;
- Interdisciplinary Program for Bioengineering, College of Engineering, Seoul National University, Seoul 08826, Korea;
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Jae Won Yun
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul 08826, Korea;
| | - Ha Young Kim
- Interdisciplinary Program for Bioengineering, College of Engineering, Seoul National University, Seoul 08826, Korea;
| | - Chan Yeong Heo
- Interdisciplinary Program for Bioengineering, College of Engineering, Seoul National University, Seoul 08826, Korea;
- Department of Plastic and Reconstructive Surgery, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Department of Plastic and Reconstructive Surgery, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (C.Y.H.); (S.L.); Tel.: +82-31-787-8124 (S.L.)
| | - Sejoon Lee
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
- Correspondence: (C.Y.H.); (S.L.); Tel.: +82-31-787-8124 (S.L.)
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17
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Montaudon E, Nikitorowicz-Buniak J, Sourd L, Morisset L, El Botty R, Huguet L, Dahmani A, Painsec P, Nemati F, Vacher S, Chemlali W, Masliah-Planchon J, Château-Joubert S, Rega C, Leal MF, Simigdala N, Pancholi S, Ribas R, Nicolas A, Meseure D, Vincent-Salomon A, Reyes C, Rapinat A, Gentien D, Larcher T, Bohec M, Baulande S, Bernard V, Decaudin D, Coussy F, Le Romancer M, Dutertre G, Tariq Z, Cottu P, Driouch K, Bièche I, Martin LA, Marangoni E. PLK1 inhibition exhibits strong anti-tumoral activity in CCND1-driven breast cancer metastases with acquired palbociclib resistance. Nat Commun 2020; 11:4053. [PMID: 32792481 PMCID: PMC7426966 DOI: 10.1038/s41467-020-17697-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/16/2020] [Indexed: 02/08/2023] Open
Abstract
A significant proportion of patients with oestrogen receptor (ER) positive breast cancers (BC) develop resistance to endocrine treatments (ET) and relapse with metastatic disease. Here we perform whole exome sequencing and gene expression analysis of matched primary breast tumours and bone metastasis-derived patient-derived xenografts (PDX). Transcriptomic analyses reveal enrichment of the G2/M checkpoint and up-regulation of Polo-like kinase 1 (PLK1) in PDX. PLK1 inhibition results in tumour shrinkage in highly proliferating CCND1-driven PDX, including different RB-positive PDX with acquired palbociclib resistance. Mechanistic studies in endocrine resistant cell lines, suggest an ER-independent function of PLK1 in regulating cell proliferation. Finally, in two independent clinical cohorts of ER positive BC, we find a strong association between high expression of PLK1 and a shorter metastases-free survival and poor response to anastrozole. In conclusion, our findings support clinical development of PLK1 inhibitors in patients with advanced CCND1-driven BC, including patients progressing on palbociclib treatment.
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Affiliation(s)
- Elodie Montaudon
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | | | - Laura Sourd
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Ludivine Morisset
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Rania El Botty
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Léa Huguet
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Ahmed Dahmani
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Pierre Painsec
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Fariba Nemati
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, Paris, France
| | | | | | | | - Camilla Rega
- Institute of Cancer Research, 123 Old Brompton Road, SW7 3RP, London, UK
| | | | - Nikiana Simigdala
- Institute of Cancer Research, 123 Old Brompton Road, SW7 3RP, London, UK
| | - Sunil Pancholi
- Institute of Cancer Research, 123 Old Brompton Road, SW7 3RP, London, UK
| | - Ricardo Ribas
- Institute of Cancer Research, 123 Old Brompton Road, SW7 3RP, London, UK
| | - André Nicolas
- Department of Pathology, Institut Curie, Paris, France
| | | | | | - Cécile Reyes
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Audrey Rapinat
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - David Gentien
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Thibaut Larcher
- INRA, APEX-PAnTher, Oniris, Rue De La Géraudière Cedex 3, 44322, Nantes, France
| | - Mylène Bohec
- Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France
| | - Sylvain Baulande
- Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France
| | | | - Didier Decaudin
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Florence Coussy
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Muriel Le Romancer
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, 28 Rue Laennec, 69000, Lyon, France
| | | | - Zakia Tariq
- Department of Genetics, Institut Curie, Paris, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, Paris, France
| | | | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris, France
| | - Lesley-Ann Martin
- Institute of Cancer Research, 123 Old Brompton Road, SW7 3RP, London, UK
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France.
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18
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Ogara MF, Rodríguez-Seguí SA, Marini M, Nacht AS, Stortz M, Levi V, Presman DM, Vicent GP, Pecci A. The glucocorticoid receptor interferes with progesterone receptor-dependent genomic regulation in breast cancer cells. Nucleic Acids Res 2020; 47:10645-10661. [PMID: 31598691 PMCID: PMC6846950 DOI: 10.1093/nar/gkz857] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 09/19/2019] [Accepted: 10/04/2019] [Indexed: 12/30/2022] Open
Abstract
The glucocorticoid and progesterone receptors (GR and PR) are closely related members of the steroid receptor family. Despite sharing similar structural and functional characteristics; the cognate hormones display very distinct physiological responses. In mammary epithelial cells, PR activation is associated with the incidence and progression of breast cancer, whereas the GR is related to growth suppression and differentiation. Despite their pharmacological relevance, only a few studies have compared GR and PR activities in the same system. Using a PR+/GR+ breast cancer cell line, here we report that either glucocorticoid-free or dexamethasone (DEX)-activated GR inhibits progestin-dependent gene expression associated to epithelial-mesenchymal-transition and cell proliferation. When both receptors are activated with their cognate hormones, PR and GR can form part of the same complex according to co-immunoprecipitation, quantitative microscopy and sequential ChIP experiments. Moreover, genome-wide studies in cells treated with either DEX or R5020, revealed the presence of several regions co-bound by both receptors. Surprisingly, GR also binds novel genomic sites in cells treated with R5020 alone. This progestin-induced GR binding was enriched in REL DNA motifs and located close to genes coding for chromatin remodelers. Understanding GR behavior in the context of progestin-dependent breast cancer could provide new targets for tumor therapy.
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Affiliation(s)
- Maria F Ogara
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Santiago A Rodríguez-Seguí
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.,Departamento de Fisiología, Biología Molecular y Celular, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Melisa Marini
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Ana Silvina Nacht
- Centro de Regulación Genómica, Barcelona 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Martin Stortz
- Departamento de Fisiología, Biología Molecular y Celular, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.,Departamento de Química Biológica, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Guillermo P Vicent
- Centro de Regulación Genómica, Barcelona 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.,Department of Molecular Genomics, Institute of Molecular Biology of Barcelona, IBMB-CSIC. Baldiri Reixac 4, Barcelona 08028, Spain
| | - Adali Pecci
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.,Departamento de Química Biológica, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
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19
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Zhang R, Wei R, Du W, Zhang L, Du T, Geng Y, Wei X. Long noncoding RNA ENST00000413528 sponges microRNA-593-5p to modulate human glioma growth via polo-like kinase 1. CNS Neurosci Ther 2019; 25:842-854. [PMID: 30924320 PMCID: PMC6630009 DOI: 10.1111/cns.13121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/08/2019] [Accepted: 02/28/2019] [Indexed: 12/11/2022] Open
Abstract
AIMS In this study, we examined the expression of lncRNA ENST00000413528 in glioma and determined its role in glioma development. METHODS LncRNA ENST00000413528 was detected in glioma tissues by lncRNA microarray. Then, we performed real-time PCR, CCK-8, colony formation assay, flow cytometry, caspase-3/7 assay and animal experiment to detect the function of ENST00000413528 in glioma after ENST00000413528 knockdown. Subsequent bioinformatics analysis, luciferase reporter assays and RNA immunoprecipitation (RIP) assay western blotting indicated possible downstream regulatory molecules. The expression of PLK1 in glioma tissues was also examined by immunohistochemistry staining. RESULTS Expression of ENST00000413528 was significantly increased in glioma tissues and LN229 and U251 cells. PLK1 protein could not be detected in peritumoral brain edema (PTBE) tissues; however, it showed an increasing number of positively cytoplasmic stained from WHO-Grade II to Grade III gliomas. Knockdown of ENST00000413528 in glioma cells inhibited cell proliferation and colony formation abilities, induced the G0/G1 arrest of the cell cycle, and promoted apoptosis. The dual reporter assay and RNA immunoprecipitation assay verified the interaction between ENST00000413528 and miR-593. We also demonstrated that polo-like kinase 1 (PLK1) was regulated by miR-593; PLK1 messenger RNA lacking 3'UTR partially reversed the effects caused by ENST00000413528 knockdown or miR-593 upregulation. CONCLUSION lncRNA ENST00000413528 is closely related to the development of glioma via the miR-593-5p/PLK1 pathway.
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Affiliation(s)
- Ren Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ruo‐Lun Wei
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Wei Du
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Li‐Wei Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Tao Du
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ya‐Dong Geng
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xin‐ting Wei
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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20
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Park C, Yoon K, Kim J, Park IH, Park SJ, Kim MK, Jang W, Cho SY, Park B, Kong S, Lee ES. Integrative molecular profiling identifies a novel cluster of estrogen receptor-positive breast cancer in very young women. Cancer Sci 2019; 110:1760-1770. [PMID: 30811755 PMCID: PMC6500962 DOI: 10.1111/cas.13982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/07/2019] [Accepted: 02/19/2019] [Indexed: 11/28/2022] Open
Abstract
Very young breast cancer patients are more common in Asian countries than Western countries and are thought to have worse prognosis than older patients. The aim of the current study was to identify molecular characteristics of young patients with estrogen receptor (ER)-positive breast cancer by analyzing mutations and copy number variants (CNV), and by applying expression profiling. The whole exome and transcriptome of 47 Korean young breast cancer (KYBR) patients (age <35) were analyzed. Genomic profiles were constructed using mutations, CNV and differential gene expression from sequencing data. Pathway analyses were also performed using gene sets to identify biological processes. Our data were compared with young ER+ breast cancer patients in The Cancer Genome Atlas (TCGA) dataset. TP53, PIK3CA and GATA3 were highly recurrent somatic mutation genes. APOBEC-associated mutation signature was more frequent in KYBR compared with young TCGA patients. Integrative profiling was used to classify our patients into 3 subgroups based on molecular characteristics. Group A showed luminal A-like subtype and IGF1R signal dysregulation. Luminal B patients were classified into groups B and C, which showed chromosomal instability and enrichment for APOBEC3A/B deletions, respectively. Group B was characterized by 11q13 (CCND1) amplification and activation of the ubiquitin-mediated proteolysis pathway. Group C showed 17q12 (ERBB2) amplification and lower ER and progesterone receptor expression. Group C was also distinguished by immune activation and lower epithelial-mesenchyme transition (EMT) degree compared with group B. This study showed that integrative genomic profiling could classify very young patients with breast cancer into molecular subgroups that are potentially linked to different clinical characteristics.
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Affiliation(s)
- Charny Park
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - Kyong‐Ah Yoon
- Laboratory of BiochemistryCollege of Veterinary MedicineKonkuk UniversitySeoulKorea
| | - Jihyun Kim
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - In Hae Park
- Center for Breast CancerHospitalNational Cancer CenterGoyangKorea
| | - Soo Jin Park
- Center for Breast CancerHospitalNational Cancer CenterGoyangKorea
| | - Min Kyeong Kim
- Translational Cancer Research BranchDivision of Translational ScienceNational Cancer CenterGoyangKorea
| | - Wooyeong Jang
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - Soo Young Cho
- Clinical Genomics Analysis BranchResearch InstituteNational Cancer CenterGoyangKorea
| | - Boyoung Park
- Graduate School for Cancer Science and PolicyNational Cancer CenterGoyangKorea
| | - Sun‐Young Kong
- Translational Cancer Research BranchDivision of Translational ScienceNational Cancer CenterGoyangKorea
- Graduate School for Cancer Science and PolicyNational Cancer CenterGoyangKorea
| | - Eun Sook Lee
- Center for Breast CancerHospitalNational Cancer CenterGoyangKorea
- Graduate School for Cancer Science and PolicyNational Cancer CenterGoyangKorea
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21
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de Cárcer G. The Mitotic Cancer Target Polo-Like Kinase 1: Oncogene or Tumor Suppressor? Genes (Basel) 2019; 10:E208. [PMID: 30862113 PMCID: PMC6470689 DOI: 10.3390/genes10030208] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/21/2022] Open
Abstract
The master mitotic regulator, Polo-like kinase 1 (Plk1), is an essential gene for the correct execution of cell division. Plk1 has strong clinical relevance, as it is considered a bona fide cancer target, it is found overexpressed in a large collection of different cancer types and this tumoral overexpression often correlates with poor patient prognosis. All these data led the scientific community to historically consider Plk1 as an oncogene. Although there is a collection of scientific reports showing how Plk1 can contribute to tumor progression, recent data from different laboratories using mouse models, show that Plk1 can surprisingly play as a tumor suppressor. Therefore, the fact that Plk1 is an oncogene is now under debate. This review summarizes the proposed mechanisms by which Plk1 can play as an oncogene or as a tumor suppressor, and extrapolates this information to clinical features.
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Affiliation(s)
- Guillermo de Cárcer
- Cell Cycle & Cancer Biomarkers Group, Cancer Biology Department, Instituto de Investigaciones Biomédicas"Alberto Sols" (IIBm), Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid,(CSIC-UAM), C/Arturo Duperier 4, 28029 Madrid, Spain.
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22
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Liu X, Chen Y, Li Y, Petersen RB, Huang K. Targeting mitosis exit: A brake for cancer cell proliferation. Biochim Biophys Acta Rev Cancer 2019; 1871:179-191. [PMID: 30611728 DOI: 10.1016/j.bbcan.2018.12.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/16/2022]
Abstract
The transition from mitosis to interphase, referred to as mitotic exit, is a critical mitotic process which involves activation and inactivation of multiple mitotic kinases and counteracting protein phosphatases. Loss of mitotic exit checkpoints is a common feature of cancer cells, leading to mitotic dysregulation and confers cancer cells with oncogenic characteristics, such as aberrant proliferation and microtubule-targeting agent (MTA) resistance. Since MTA resistance results from cancer cells prematurely exiting mitosis (mitotic slippage), blocking mitotic exit is believed to be a promising anticancer strategy. Moreover, based on this theory, simultaneous inhibition of mitotic exit and additional cell cycle phases would likely achieve synergistic antitumor effects. In this review, we divide the molecular regulators of mitotic exit into four categories based on their different regulatory functions: 1) the anaphase-promoting complex/cyclosome (APC/C, a ubiquitin ligase), 2) cyclin B, 3) mitotic kinases and phosphatases, 4) kinesins and microtubule-binding proteins. We also review the regulators of mitotic exit and propose prospective anticancer strategies targeting mitotic exit, including their strengths and possible challenges to their use.
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Affiliation(s)
- Xinran Liu
- Tongji School of Pharmacy, Huazhong University of Science & Technology, Wuhan, Hubei 430030, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Huazhong University of Science & Technology, Wuhan, Hubei 430030, China
| | - Yangkai Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mt. Pleasant, MI 48858, USA
| | - Kun Huang
- Tongji School of Pharmacy, Huazhong University of Science & Technology, Wuhan, Hubei 430030, China.
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23
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Personalized prediction of genes with tumor-causing somatic mutations based on multi-modal deep Boltzmann machine. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2018.02.096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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24
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Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells. Cancers (Basel) 2018; 10:cancers10100371. [PMID: 30301163 PMCID: PMC6210734 DOI: 10.3390/cancers10100371] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/01/2018] [Indexed: 01/18/2023] Open
Abstract
Breast cancer prognosis and response to endocrine therapy strongly depends on the expression of the estrogen and progesterone receptors (ER and PR, respectively). Although much is known about ERα gene (ESR1) regulation after hormonal stimulation, how it is regulated in hormone-free condition is not fully understood. We used ER-/PR-positive breast cancer cells to investigate the role of PR in ESR1 regulation in the absence of hormones. We show that PR binds to the low-methylated ESR1 promoter and maintains both gene expression and DNA methylation of the ESR1 locus in hormone-deprived breast cancer cells. Depletion of PR reduces ESR1 expression, with a concomitant increase in gene promoter methylation. The high amount of methylation in the ESR1 promoter of PR-depleted cells persists after the stable re-expression of PR and inhibits PR binding to this genomic region. As a consequence, the rescue of PR expression in PR-depleted cells is insufficient to restore ESR1 expression. Consistently, DNA methylation impedes PR binding to consensus progesterone responsive elements. These findings contribute to understanding the complex crosstalk between PR and ER and suggest that the analysis of ESR1 promoter methylation in breast cancer cells can help to design more appropriate targeted therapies for breast cancer patients.
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25
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de Cárcer G, Venkateswaran SV, Salgueiro L, El Bakkali A, Somogyi K, Rowald K, Montañés P, Sanclemente M, Escobar B, de Martino A, McGranahan N, Malumbres M, Sotillo R. Plk1 overexpression induces chromosomal instability and suppresses tumor development. Nat Commun 2018; 9:3012. [PMID: 30069007 PMCID: PMC6070485 DOI: 10.1038/s41467-018-05429-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 07/06/2018] [Indexed: 02/06/2023] Open
Abstract
Polo-like kinase 1 (Plk1) is overexpressed in a wide spectrum of human tumors, being frequently considered as an oncogene and an attractive cancer target. However, its contribution to tumor development is unclear. Using a new inducible knock-in mouse model we report here that Plk1 overexpression results in abnormal chromosome segregation and cytokinesis, generating polyploid cells with reduced proliferative potential. Mechanistically, these cytokinesis defects correlate with defective loading of Cep55 and ESCRT complexes to the abscission bridge, in a Plk1 kinase-dependent manner. In vivo, Plk1 overexpression prevents the development of Kras-induced and Her2-induced mammary gland tumors, in the presence of increased rates of chromosome instability. In patients, Plk1 overexpression correlates with improved survival in specific breast cancer subtypes. Therefore, despite the therapeutic benefits of inhibiting Plk1 due to its essential role in tumor cell cycles, Plk1 overexpression has tumor-suppressive properties by perturbing mitotic progression and cytokinesis.
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Affiliation(s)
- Guillermo de Cárcer
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain.
| | - Sharavan Vishaan Venkateswaran
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - Lorena Salgueiro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Aicha El Bakkali
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Kalman Somogyi
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Konstantina Rowald
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Pablo Montañés
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Manuel Sanclemente
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Beatriz Escobar
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Alba de Martino
- Histopathology Unit, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Marcos Malumbres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain.
| | - Rocío Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany.
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26
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Wang J, Zhang X, Ling J, Wang Y, Xu X, Liu Y, Jin C, Ju J, Yuan Y, He F, Zhao C, Wang J, Tian C. KRAB-containing zinc finger protein ZNF496 inhibits breast cancer cell proliferation by selectively repressing ERα activity. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30048-8. [PMID: 30012466 DOI: 10.1016/j.bbagrm.2018.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/25/2018] [Accepted: 07/10/2018] [Indexed: 12/20/2022]
Abstract
KRAB-containing zinc finger proteins (KZNF) constitute the largest family of transcriptional regulators in humans and play critical roles in normal development and tumorigenesis. However, the function and mechanism of most KZNFs remain unclear. Here, we report that ZNF496, a KZNF family member, interacts with the DNA binding domain (DBD) of estrogen receptor alpha (ERα) via its C2H2 domain. This interaction decreases ERα binding to chromatin DNA and results in the repression of ERα transactivation, the selective suppression of ERα target genes, and ultimately in a reduction of ERα-positive cell growth in the presence of E2. An analysis of clinical data revealed that the downregulation of ZNF496 expression is observed only in ERα-positive and not in ERα-negative breast cancer tissues when compared with that in matched adjacent tissues. Lastly, we also observed that the downregulation of ZNF496 is associated with poor recurrence-free survival among patients with breast cancer. Collectively, our findings demonstrate that ZNF496 is a novel ERα-binding protein that acts as a target gene-specific ERα corepressor and inhibits the growth of ERα-positive breast cancer cells.
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Affiliation(s)
- Jinlong Wang
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Department of Pathology, The 422th Hospital of PLA, Zhanjiang, Guangdong Province 524000, China
| | - Xiuyuan Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jiming Ling
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yun Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; College of Animal Science, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Xiaolin Xu
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chaozhi Jin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jiyu Ju
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chunling Zhao
- School of Bioscience and Technology, Weifang Medical University, Weifang, Shandong Province 261053, China.
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
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27
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Nickel A, Blücher C, Kadri OA, Schwagarus N, Müller S, Schaab M, Thiery J, Burkhardt R, Stadler SC. Adipocytes induce distinct gene expression profiles in mammary tumor cells and enhance inflammatory signaling in invasive breast cancer cells. Sci Rep 2018; 8:9482. [PMID: 29930291 PMCID: PMC6013441 DOI: 10.1038/s41598-018-27210-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/25/2018] [Indexed: 12/14/2022] Open
Abstract
Obesity is a known risk factor for breast cancer. Since obesity rates are constantly rising worldwide, understanding the molecular details of the interaction between adipose tissue and breast tumors becomes an urgent task. To investigate potential molecular changes in breast cancer cells induced by co-existing adipocytes, we used a co-culture system of different breast cancer cell lines (MCF-7 and T47D: ER+/PR+/HER2- and MDA-MB-231: ER-/PR-/HER2-) and murine 3T3-L1 adipocytes. Here, we report that co-culture with adipocytes revealed distinct changes in global gene expression pattern in the different breast cancer cell lines. Our microarray data revealed that in both ER+ cell lines, top upregulated genes showed significant enrichment for hormone receptor target genes. In triple-negative MDA-MB-231 cells, co-culture with adipocytes led to the induction of pro-inflammatory genes, mainly involving genes of the Nf-κB signaling pathway. Moreover, co-cultured MDA-MB-231 cells showed increased secretion of the pro-inflammatory interleukins IL-6 and IL-8. Using a specific NF-κB inhibitor, these effects were significantly decreased. Finally, migratory capacities were significantly increased in triple-negative breast cancer cells upon co-culture with adipocytes, indicating an enhanced aggressive cell phenotype. Together, our studies illustrate that factors secreted by adipocytes have a significant impact on the molecular biology of breast cancer cells.
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Affiliation(s)
- Annina Nickel
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Christina Blücher
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Omaeir Al Kadri
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Nancy Schwagarus
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Silvana Müller
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Michael Schaab
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Ralph Burkhardt
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Sonja C Stadler
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.
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28
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Gates LA, Gu G, Chen Y, Rohira AD, Lei JT, Hamilton RA, Yu Y, Lonard DM, Wang J, Wang SP, Edwards DG, Lavere PF, Shao J, Yi P, Jain A, Jung SY, Malovannaya A, Li S, Shao J, Roeder RG, Ellis MJ, Qin J, Fuqua SAW, O'Malley BW, Foulds CE. Proteomic profiling identifies key coactivators utilized by mutant ERα proteins as potential new therapeutic targets. Oncogene 2018; 37:4581-4598. [PMID: 29748621 PMCID: PMC6095836 DOI: 10.1038/s41388-018-0284-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 12/05/2022]
Abstract
Approximately 75% of breast cancers are estrogen receptor alpha (ERα)-positive and are treatable with endocrine therapies, but often patients develop lethal resistant disease. Frequent mutations (10–40%) in the ligand-binding domain (LBD) codons in the gene encoding ERα (ESR1) have been identified, resulting in ligand-independent, constitutively active receptors. In addition, ESR1 chromosomal translocations can occur, resulting in fusion proteins that lack the LBD and are entirely unresponsive to all endocrine treatments. Thus, identifying coactivators that bind to these mutant ERα proteins may offer new therapeutic targets for endocrine-resistant cancer. To define coactivator candidate targets, a proteomics approach was performed profiling proteins recruited to the two most common ERα LBD mutants, Y537S and D538G, and an ESR1-YAP1 fusion protein. These mutants displayed enhanced coactivator interactions as compared to unliganded wild-type ERα. Inhibition of these coactivators decreased the ability of ESR1 mutants to activate transcription and promote breast cancer growth in vitro and in vivo. Thus, we have identified specific coactivators that may be useful as targets for endocrine-resistant breast cancers.
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Affiliation(s)
- Leah A Gates
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Guowei Gu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yue Chen
- Employee of Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130, USA
| | - Aarti D Rohira
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ross A Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yang Yu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jin Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shu-Ping Wang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - David G Edwards
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Philip F Lavere
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiangyong Shao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Antrix Jain
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anna Malovannaya
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shunqiang Li
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Jieya Shao
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jun Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suzanne A W Fuqua
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA.
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29
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Pu SY, Yu Q, Wu H, Jiang JJ, Chen XQ, He YH, Kong QP. ERCC6L, a DNA helicase, is involved in cell proliferation and associated with survival and progress in breast and kidney cancers. Oncotarget 2018; 8:42116-42124. [PMID: 28178669 PMCID: PMC5522053 DOI: 10.18632/oncotarget.14998] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 01/16/2017] [Indexed: 12/21/2022] Open
Abstract
By analyzing 4987 cancer transcriptomes from The Cancer Genome Atlas (TCGA), we identified that excision repair cross-complementation group 6 like (ERCC6L), a newly discovered DNA helicase, is highly expressed in 12 solid cancers. However, its role and mechanism in tumorigenesis are largely unknown. In this study, we found that ERCC6L silencing by small interring RNA (siRNA) or short hairpin RNA (shRNA) significantly inhibited the proliferation of breast (MCF-7, MDA-MB-231) and kidney cancer cells (786-0). Furthermore, ERCC6L silencing induced cell cycle arrest at G0/G1 phase without affecting apoptosis. We then performed RNA sequencing (RNA-seq) analysis after ERCC6L silencing and identified that RAB31 was markedly downregulated at both the transcriptional and translational levels. Its downstream protein, phosphorylated MAPK and CDK2 were also inhibited by ERCC6L silencing. The xenograft experiment showed that silencing of ERCC6L strikingly inhibited tumor growth from the 7th day after xenograft in nude mice. In addition, higher ERCC6L expression was found to be significantly associated with worse clinical survival in breast and kidney cancers. In conclusion, our results suggest that ERCC6L may stimulates cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2, and it could be a potential biomarker for cancer prognosis and target for cancer treatment.
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Affiliation(s)
- Shao-Yan Pu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Qin Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Jun Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Qiong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Yong-Han He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
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30
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Raab M, Sanhaji M, Matthess Y, Hörlin A, Lorenz I, Dötsch C, Habbe N, Waidmann O, Kurunci-Csacsko E, Firestein R, Becker S, Strebhardt K. PLK1 has tumor-suppressive potential in APC-truncated colon cancer cells. Nat Commun 2018; 9:1106. [PMID: 29549256 PMCID: PMC5856809 DOI: 10.1038/s41467-018-03494-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 02/19/2018] [Indexed: 12/13/2022] Open
Abstract
The spindle assembly checkpoint (SAC) acts as a molecular safeguard in ensuring faithful chromosome transmission during mitosis, which is regulated by a complex interplay between phosphatases and kinases including PLK1. Adenomatous polyposis coli (APC) germline mutations cause aneuploidy and are responsible for familial adenomatous polyposis (FAP). Here we study the role of PLK1 in colon cancer cells with chromosomal instability promoted by APC truncation (APC-ΔC). The expression of APC-ΔC in colon cells reduces the accumulation of mitotic cells upon PLK1 inhibition, accelerates mitotic exit and increases the survival of cells with enhanced chromosomal abnormalities. The inhibition of PLK1 in mitotic, APC-∆C-expressing cells reduces the kinetochore levels of Aurora B and hampers the recruitment of SAC component suggesting a compromised mitotic checkpoint. Furthermore, Plk1 inhibition (RNAi, pharmacological compounds) promotes the development of adenomatous polyps in two independent Apc Min/+ mouse models. High PLK1 expression increases the survival of colon cancer patients expressing a truncated APC significantly.
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Affiliation(s)
- Monika Raab
- Department of Gynecology, Goethe-University, 60590, Frankfurt, Germany
| | - Mourad Sanhaji
- Department of Gynecology, Goethe-University, 60590, Frankfurt, Germany
| | - Yves Matthess
- Department of Gynecology, Goethe-University, 60590, Frankfurt, Germany
- German Cancer Consortium (DKTK)/ German Cancer Research Center, 69120, Heidelberg, Germany
| | - Albrecht Hörlin
- Institute of Pathology at the Department of Pathology, Goethe-University, 60590, Frankfurt, Germany
| | - Ioana Lorenz
- Department of Gynecology, Goethe-University, 60590, Frankfurt, Germany
| | - Christina Dötsch
- Department of Gynecology, Goethe-University, 60590, Frankfurt, Germany
| | - Nils Habbe
- Department of General and Visceral Surgery, Goethe-University, 60590, Frankfurt, Germany
| | - Oliver Waidmann
- Department of Gastroenterology and Hepatology, Goethe-University, 60590, Frankfurt, Germany
| | | | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, AU 31681, Australia
- Department of Molecular Translational Medicine, Monash University, Clayton, VIC, 3800, Australia
| | - Sven Becker
- Department of Gynecology, Goethe-University, 60590, Frankfurt, Germany
| | - Klaus Strebhardt
- Department of Gynecology, Goethe-University, 60590, Frankfurt, Germany.
- German Cancer Consortium (DKTK)/ German Cancer Research Center, 69120, Heidelberg, Germany.
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31
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Li C, Luo L, Wei S, Wang X. Identification of the potential crucial genes in invasive ductal carcinoma using bioinformatics analysis. Oncotarget 2018; 9:6800-6813. [PMID: 29467930 PMCID: PMC5805516 DOI: 10.18632/oncotarget.23239] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/01/2017] [Indexed: 02/06/2023] Open
Abstract
Invasive ductal carcinoma (IDC) is a common histological type of breast cancer. The aim of this study was to identify the potential crucial genes associated with IDC and to provide valid biological information for further investigations. The gene expression profiles of GSE10780 which contained 42 histologically normal breast tissues and 143 IDC tissues were downloaded from the GEO database. Functional and pathway enrichment analysis of differentially expressed genes (DEGs) were performed and protein-protein interaction (PPI) network was analyzed using Cytoscape. In total, 999 DEGs were identified, including 667 up-regulated and 332 down-regulated DEGs. Gene ontology analysis demonstrated that most DEGs were significantly enriched in mitotic cell cycle, adhesion and protein binding process. Through PPI network analysis, a significant module was screened out, and the top 10 hub genes, CDK1, CCNB1, CENPE, CENPA, PLK1, CDC20, MAD2L1, HIST1H2BK, KIF2C and CCNA2 were identified from the PPI network. The expression levels of the 10 genes were validated in Oncomine database. KIF2C, MAD2L1 and PLK1 were associated with the overall survival. And we used cBioPortal to explore the genetic alterations of hub genes and potential drugs. In conclusion, the present study identified DEGs between normal and IDC samples, which could improve our understanding of the molecular mechanisms in the development of IDC, and these candidate genes might be used as therapeutic targets for IDC.
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Affiliation(s)
- Chunguang Li
- Department of Oncological Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, P. R. China
| | - Liangtao Luo
- Department of General Surgery, First Renmin Hospital, Tianmen, Hubei, P. R. China
| | - Sheng Wei
- Department of General Surgery, Traditional Chinese Medicine Hospital, Xishui, Hubei, P. R. China
| | - Xiongbiao Wang
- Department of General Surgery, First Renmin Hospital, Yangxin, Hubei, P. R. China
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32
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Pan Z, Chen Y, Liu J, Jiang Q, Yang S, Guo L, He G. Design, synthesis, and biological evaluation of polo-like kinase 1/eukaryotic elongation factor 2 kinase (PLK1/EEF2K) dual inhibitors for regulating breast cancer cells apoptosis and autophagy. Eur J Med Chem 2018; 144:517-528. [PMID: 29288948 DOI: 10.1016/j.ejmech.2017.12.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 01/09/2023]
Abstract
Both PLK1 and EEF2K are serine⁄threonine kinases that play important roles in the proliferation and programmed cell death of various types of cancer. They are highly expressed in breast cancer tissues. Based on the multiple-complexes generated pharmacophore models of PLK1 and homology models of EEF2K, the integrated virtual screening is performed to discover novel PLK1/EEF2K dual inhibitors. The top ten hit compounds are selected and tested in vitro, and five of them display PLK1 and EEF2K inhibition in vitro. Based on the docking modes of the most potent hit compound, a series of derivatives are synthesized, characterized and biological assayed on the PLK1, EEF2K as well as breast cancer cell proliferation models. Compound 18i with satisfied inhibitory potency are shifted to molecular mechanism studies contained molecular dynamics simulations, cell cycles, apoptosis and autophagy assays. Our results suggested that these novel PLK1/EEF2K dual inhibitors can be used as lead compounds for further development breast cancer chemotherapy.
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Affiliation(s)
- Zhaoping Pan
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; State Key Laboratory of Biotherapy and Department of Breast Surgery, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yujuan Chen
- State Key Laboratory of Biotherapy and Department of Breast Surgery, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Jingyan Liu
- State Key Laboratory of Biotherapy and Department of Breast Surgery, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Qinglin Jiang
- State Key Laboratory of Biotherapy and Department of Breast Surgery, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; School of Pharmacy and Sichuan Province College Key Laboratory of Structure-Specific Small Molecule Drugs, Chengdu Medical College, Chengdu 610500, China.
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Department of Breast Surgery, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Li Guo
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
| | - Gu He
- Key Laboratory of Drug-Targeting of Education Ministry and Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China; State Key Laboratory of Biotherapy and Department of Breast Surgery, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
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33
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García-Aranda M, Redondo M. Protein Kinase Targets in Breast Cancer. Int J Mol Sci 2017; 18:ijms18122543. [PMID: 29186886 PMCID: PMC5751146 DOI: 10.3390/ijms18122543] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 01/10/2023] Open
Abstract
With 1.67 million new cases and 522,000 deaths in the year 2012, breast cancer is the most common type of diagnosed malignancy and the second leading cause of cancer death in women around the world. Despite the success of screening programs and the development of adjuvant therapies, a significant percentage of breast cancer patients will suffer a metastatic disease that, to this day, remains incurable and justifies the research of new therapies to improve their life expectancy. Among the new therapies that have been developed in recent years, the emergence of targeted therapies has been a milestone in the fight against cancer. Over the past decade, many studies have shown a causal role of protein kinase dysregulations or mutations in different human diseases, including cancer. Along these lines, cancer research has demonstrated a key role of many protein kinases during human tumorigenesis and cancer progression, turning these molecules into valid candidates for new targeted therapies. The subsequent discovery and introduction in 2001 of the kinase inhibitor imatinib, as a targeted treatment for chronic myelogenous leukemia, revolutionized cancer genetic pathways research, and lead to the development of multiple small-molecule kinase inhibitors against various malignancies, including breast cancer. In this review, we analyze studies published to date about novel small-molecule kinase inhibitors and evaluate if they would be useful to develop new treatment strategies for breast cancer patients.
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Affiliation(s)
- Marilina García-Aranda
- Biochemistry Department, Hospital Costa del Sol, Carretera de Cádiz km, 187, 29600 Marbella, Málaga, Spain.
| | - Maximino Redondo
- Biochemistry Department, Hospital Costa del Sol, Carretera de Cádiz km, 187, 29600 Marbella, Málaga, Spain.
- Biochemistry Department, Facultad de Medicina de la Universidad de Málaga, Bulevar Louis Pasteur 32, 29010 Málaga, Spain.
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34
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Shi SH, Zhang W, Jiang J, Sun L. Identification of altered pathways in breast cancer based on individualized pathway aberrance score. Oncol Lett 2017; 14:1287-1294. [PMID: 28789343 PMCID: PMC5529805 DOI: 10.3892/ol.2017.6292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/20/2016] [Indexed: 11/06/2022] Open
Abstract
The objective of the present study was to identify altered pathways in breast cancer based on the individualized pathway aberrance score (iPAS) method combined with the normal reference (nRef). There were 4 steps to identify altered pathways using the iPAS method: Data preprocessing conducted by the robust multi-array average (RMA) algorithm; gene-level statistics based on average Z; pathway-level statistics according to iPAS; and a significance test dependent on 1 sample Wilcoxon test. The altered pathways were validated by calculating the changed percentage of each pathway in tumor samples and comparing them with pathways from differentially expressed genes (DEGs). A total of 688 altered pathways with P<0.01 were identified, including kinesin (KIF)- and polo-like kinase (PLK)-mediated events. When the percentage of change reached 50%, 310 pathways were involved in the total 688 altered pathways, which may validate the present results. In addition, there were 324 DEGs and 155 common genes between DEGs and pathway genes. DEGs and common genes were enriched in the same 9 significant terms, which also were members of altered pathways. The iPAS method was suitable for identifying altered pathways in breast cancer. Altered pathways (such as KIF and PLK mediated events) were important for understanding breast cancer mechanisms and for the future application of customized therapeutic decisions.
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Affiliation(s)
- Sheng-Hong Shi
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Wei Zhang
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Jing Jiang
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Long Sun
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315000, P.R. China
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35
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Augmented expression of polo-like kinase 1 indicates poor clinical outcome for breast patients: a systematic review and meta-analysis. Oncotarget 2017; 8:57723-57732. [PMID: 28915707 PMCID: PMC5593679 DOI: 10.18632/oncotarget.17301] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/09/2017] [Indexed: 12/15/2022] Open
Abstract
Polo-like kinases 1 (PLK1), a key regulator of mitosis, plays an essential role in maintaining genomic stability. Up-regulation of PLK1 was found in tumorigenesis and tumor progression of diverse cancers. However, the clinicopathological and prognostic implications of PLK1 in breast cancer (BC) have yet to be unveiled. Therefore, using PubMed, Web of Science, Embase, and Chinese databases, we conducted a meta-analysis to define the potential clinical value of PLK1 in BC. Eleven eligible articles with 2481 patients enrolled were included in the present meta-analysis, of which eight studies reported on the relationship between PLK1 expression and clinicopathological features, and nine studies provided survival data in BC patients. Furthermore, the results revealed that high PLK1 levels were significantly associated with larger tumor size (OR=1.703, 95%CIs: 1.315-2.205, P<0.001), higher pathological grading (OR=6.028, 95%CIs: 2.639-13.772, P<0.001), and lymph node metastasis (OR= 1.524, 95%CIs: 1.192-1.950, P=0.001). Moreover, PLK1 was found to be a valuable factor for distinguishing lobular BC from ductal BC with the pooled OR=0.215(95%CIs: 0.083-0.557, P=0.002). Analysis of included data showed that high PLK1 expression significantly indicated worse overall survival for BC patients (HR= 3.438, 95%CIs: 2.293-5.154, P<0.001), as well as worse cancer specific survival and disease-free survival (HR=2.414, 95%CIs: 1.633-3.567, P<0.001 and HR= 2.261, 95%CIs: 1.796-2.951, P<0.001, respectively). This quantitative meta-analysis suggests that high PLK1 expression is a credible indicator for the progression of BC and confirms a higher risk of a worse survival rate in patients with BC.
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36
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de Castro IJ, Budzak J, Di Giacinto ML, Ligammari L, Gokhan E, Spanos C, Moralli D, Richardson C, de las Heras JI, Salatino S, Schirmer EC, Ullman KS, Bickmore WA, Green C, Rappsilber J, Lamble S, Goldberg MW, Vinciotti V, Vagnarelli P. Repo-Man/PP1 regulates heterochromatin formation in interphase. Nat Commun 2017; 8:14048. [PMID: 28091603 PMCID: PMC5241828 DOI: 10.1038/ncomms14048] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022] Open
Abstract
Repo-Man is a protein phosphatase 1 (PP1) targeting subunit that regulates mitotic progression and chromatin remodelling. After mitosis, Repo-Man/PP1 remains associated with chromatin but its function in interphase is not known. Here we show that Repo-Man, via Nup153, is enriched on condensed chromatin at the nuclear periphery and at the edge of the nucleopore basket. Repo-Man/PP1 regulates the formation of heterochromatin, dephosphorylates H3S28 and it is necessary and sufficient for heterochromatin protein 1 binding and H3K27me3 recruitment. Using a novel proteogenomic approach, we show that Repo-Man is enriched at subtelomeric regions together with H2AZ and H3.3 and that depletion of Repo-Man alters the peripheral localization of a subset of these regions and alleviates repression of some polycomb telomeric genes. This study shows a role for a mitotic phosphatase in the regulation of the epigenetic landscape and gene expression in interphase.
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Affiliation(s)
- Inês J. de Castro
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - James Budzak
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Maria L. Di Giacinto
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Lorena Ligammari
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Ezgi Gokhan
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
| | - Daniela Moralli
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Silvia Salatino
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Katharine S. Ullman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Catherine Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
- Technische Universitat Berlin, 13355 Berlin, Germany
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Martin W. Goldberg
- School of Biological and Medical Science, Durham University, Durham DH1 3LE, UK
| | - Veronica Vinciotti
- College of Engineering, Design and Technology, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
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37
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Cebrián A, Gómez Del Pulgar T, Fernández-Aceñero MJ, Borrero-Palacios A, Del Puerto-Nevado L, Martínez-Useros J, Marín-Arango JP, Caramés C, Vega-Bravo R, Rodríguez-Remírez M, Manzarbeitia F, García-Foncillas J. Decreased PLK1 expression denotes therapy resistance and unfavourable disease-free survival in rectal cancer patients receiving neoadjuvant chemoradiotherapy. Pathol Res Pract 2016; 212:1133-1137. [PMID: 27712975 DOI: 10.1016/j.prp.2016.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/02/2016] [Accepted: 09/19/2016] [Indexed: 12/12/2022]
Abstract
AIM Polo-like kinase 1 (Plk1) plays a key role in mitotic cell division and DNA damage repair. It has been observed that either up-regulated or down-regulated Plk1 could induce mitotic defects that results in aneuploidy and tumorigenesis, probably depending on the context. Few previous reports have associated Plk1 expression with prognosis and response to radiotherapy in rectal carcinomas. The aim of this study is to investigate the prognostic impact of Plk1 expression and its role in predicting response to neoadjuvant cheomoradiotherapy in rectal cancer. METHODS AND RESULTS Immunohistochemical analysis of Plk1 expression was performed in the pre-treatment tumour specimens from 75 rectal cancer patients. We analysed the assocation between Plk1 expression and clinicopathological parameters, pathologic response and outcome. Opposed to previous reports on this issue, low expression of Plk1 was significantly associated with a high grade of differentiation (P=0.0007) and higher rate of distant metastasis (P=0.014). More importantly, decreased levels of Plk1 were associated with absence of response after neoadjuvant therapy (P=0.049). Moreover, low Plk1 expression emerged as an unfavourable prognostic factor for disease-free survival in the non-responder group of patients (P=0.037). CONCLUSIONS Decreased Plk1 expression was associated with poor pathologic response and worse disease-free survival in rectal cancer patients receiving neoadjuvant chemoradiotherapy, suggesting Plk1 as a clinically relevant marker to predict chemoradiotherapy response and outcome.
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Affiliation(s)
- Arancha Cebrián
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain.
| | - Teresa Gómez Del Pulgar
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Maria Jesús Fernández-Aceñero
- Pathology Department, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Aurea Borrero-Palacios
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Laura Del Puerto-Nevado
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Javier Martínez-Useros
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Juan Pablo Marín-Arango
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Cristina Caramés
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Ricardo Vega-Bravo
- Pathology Department, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - María Rodríguez-Remírez
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Felix Manzarbeitia
- Pathology Department, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
| | - Jesús García-Foncillas
- Translational Oncology Division, Oncohealth Institute, Health Research Institute FJD-UAM, University Hospital "Fundacion Jimenez Diaz", 28040 Madrid Spain
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38
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Bhat-Nakshatri P, Goswami CP, Badve S, Magnani L, Lupien M, Nakshatri H. Molecular Insights of Pathways Resulting from Two Common PIK3CA Mutations in Breast Cancer. Cancer Res 2016; 76:3989-4001. [DOI: 10.1158/0008-5472.can-15-3174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/31/2016] [Indexed: 11/16/2022]
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39
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Ji M, Li P, Sheng N, Liu L, Pan H, Wang C, Cai L, Ma Y. Sialic Acid-Targeted Nanovectors with Phenylboronic Acid-Grafted Polyethylenimine Robustly Enhance siRNA-Based Cancer Therapy. ACS APPLIED MATERIALS & INTERFACES 2016; 8:9565-76. [PMID: 27007621 DOI: 10.1021/acsami.5b11866] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Small interference RNA (siRNA)-based therapy holds great potential for cancer treatment. However, its clinical application remains unsatisfied due to the lack of a safe and effective RNA delivery system. Aberrantly elevated sialyation on cell membrane has been reported as an attractive target for cancer diagnosis and therapy. In this study, phenylboronic acid (PBA) was conjugated onto low molecular weight polyethylenimine (PEI1.8k) to generate amphiphilic PBA-grafted PEI1.8k (PEI-PBA) nanovector, which was designed to facilitate cancer-targeted RNA delivery through the recognition of sialic structures on a cancer cell membrane. PEI-PBA simultaneously encapsulated siRNA to form PEI-PBA/siRNA nanocomplexes with great biocompatibility, serum stability and RNase resistance. The cell culture study showed that PEI-PBA/siRNA dramatically increased siRNA uptake up to 70-90% in several cancer cell lines, which relied on the interaction between PBA and sialic acid on cell membrane. Moreover, the PEI-PBA nanovector effectively promoted the lysosome escape of siRNA, decreasing the expression of target gene Polo-like kinase 1 (PLK-1) in cancer cells. The systemic administration of PEI-PBA/PLK-1 siRNA (PEI-PBA/siPLK1) nanocomplexes not only facilitated tumor-targeted siRNA delivery but also significantly decreased PLK-1 expression in tumors, thereby robustly inducing tumor apoptosis and cell cycle arrest. Additionally, the administration of PEI-PBA/siPLK1 did not cause significant systemic toxicity or immunotoxicity. Hence, sialic acid-targeted PEI-PBA could be a highly efficient and safe nanovector to improve the efficacy of cancer siRNA therapy.
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Affiliation(s)
- Manyi Ji
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
- Nano Science and Technology Institute, University of Science and Technology of China , Suzhou 215123, People's Republic of China
| | - Ping Li
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
| | - Nan Sheng
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
- Nano Science and Technology Institute, University of Science and Technology of China , Suzhou 215123, People's Republic of China
| | - Lanlan Liu
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
| | - Hong Pan
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
| | - Ce Wang
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
| | - Lintao Cai
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
| | - Yifan Ma
- Key Lab of Health Informatics of Chinese Academy of Sciences, Guangdong Key Laboratory of Nanomedicine, Shenzhen Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen 518055, People's Republic of China
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40
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Zheng Y, Murphy LC. Regulation of steroid hormone receptors and coregulators during the cell cycle highlights potential novel function in addition to roles as transcription factors. NUCLEAR RECEPTOR SIGNALING 2016; 14:e001. [PMID: 26778927 PMCID: PMC4714463 DOI: 10.1621/nrs.14001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/01/2015] [Indexed: 01/15/2023]
Abstract
Cell cycle progression is tightly controlled by several kinase families including Cyclin-Dependent Kinases, Polo-Like Kinases, and Aurora Kinases. A large amount of data show that steroid hormone receptors and various components of the cell cycle, including cell cycle regulated kinases, interact, and this often results in altered transcriptional activity of the receptor. Furthermore, steroid hormones, through their receptors, can also regulate the transcriptional expression of genes that are required for cell cycle regulation. However, emerging data suggest that steroid hormone receptors may have roles in cell cycle progression independent of their transcriptional activity. The following is a review of how steroid receptors and their coregulators can regulate or be regulated by the cell cycle machinery, with a particular focus on roles independent of transcription in G2/M.
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Affiliation(s)
- Yingfeng Zheng
- Department of Biochemistry and Medical Genetics (YZ, LCM), University of Manitoba; Manitoba Institute of Cell Biology (YZ, LCM), CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Leigh C Murphy
- Department of Biochemistry and Medical Genetics (YZ, LCM), University of Manitoba; Manitoba Institute of Cell Biology (YZ, LCM), CancerCare Manitoba, Winnipeg, Manitoba, Canada
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Gabr H, Rivera-Mulia JC, Gilbert DM, Kahveci T. Computing interaction probabilities in signaling networks. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2015; 2015:10. [PMID: 26587014 PMCID: PMC4642599 DOI: 10.1186/s13637-015-0031-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/30/2015] [Indexed: 01/17/2023]
Abstract
Biological networks inherently have uncertain topologies. This arises from many factors. For instance, interactions between molecules may or may not take place under varying conditions. Genetic or epigenetic mutations may also alter biological processes like transcription or translation. This uncertainty is often modeled by associating each interaction with a probability value. Studying biological networks under this probabilistic model has already been shown to yield accurate and insightful analysis of interaction data. However, the problem of assigning accurate probability values to interactions remains unresolved. In this paper, we present a novel method for computing interaction probabilities in signaling networks based on transcription levels of genes. The transcription levels define the signal reachability probability between membrane receptors and transcription factors. Our method computes the interaction probabilities that minimize the gap between the observed and the computed signal reachability probabilities. We evaluate our method on four signaling networks from the Kyoto Encyclopedia of Genes and Genomes (KEGG). For each network, we compute its edge probabilities using the gene expression profiles for seven major leukemia subtypes. We use these values to analyze how the stress induced by different leukemia subtypes affects signaling interactions.
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Affiliation(s)
- Haitham Gabr
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, Florida, USA
| | | | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Tamer Kahveci
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, Florida, USA
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Prashanth Kumar B, Rajput S, Bharti R, Parida S, Mandal M. BI2536 – A PLK inhibitor augments paclitaxel efficacy in suppressing tamoxifen induced senescence and resistance in breast cancer cells. Biomed Pharmacother 2015; 74:124-32. [DOI: 10.1016/j.biopha.2015.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 07/09/2015] [Indexed: 02/02/2023] Open
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TFAP2C expression in breast cancer: correlation with overall survival beyond 10 years of initial diagnosis. Breast Cancer Res Treat 2015; 152:519-31. [PMID: 26160249 DOI: 10.1007/s10549-015-3492-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/02/2015] [Indexed: 01/15/2023]
Abstract
Recurrence and death in a significant number of patients with ERα-positive breast cancer occurs 10-20 years after diagnosis. Prognostic markers for late events have been more elusive. TFAP2C (AP2γ) regulates the expression of ERα, the ERα pioneer factors FOXA1 and GATA3, and controls ERα-dependent transcription. The purpose of this investigation is to determine the long-term prognostic value of TFAP2C. A tissue microarray (TMA) consisting of breast tumors from 451 patients with median follow-up time of 10.3 years was created and tested for the expression of TFAP2C by immunohistochemistry. Wilcoxon Rank-Sum and Kruskal-Wallis tests were used to determine if TFAP2C H-scores correlate with other tumor markers. Cox proportional hazards regression models were used to determine whether TFAP2C H-scores and other tumor markers were related to overall and disease-free survival in univariate and multivariable models. TFPAC2 overexpression did not impact overall survival during the first 10 years after diagnosis, but was associated with a shorter survival after 10 years (HR 3.40, 95 % CI 1.58, 7.30; p value = 0.002). This late divergence persisted in ER-positive (HR 2.86, 95 % CI 1.29, 6.36; p value = 0.01) and endocrine therapy-positive subgroups (HR 4.19, 95 % CI 1.72, 10.23; p value = 0.002). For the ER+ and endocrine therapy subgroup, the HR was 3.82 (95 % CI 1.53, 9.50; p value = 0.004). TFAP2C H-scores were not correlated with other tumor markers or related to disease-free survival. In this hypothesis-generating study, we show that higher TFAP2C scores correlate with poor overall survival after 10 years of diagnosis in ERα-positive and endocrine therapy-treated subgroups.
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McCarroll JA, Dwarte T, Baigude H, Dang J, Yang L, Erlich RB, Kimpton K, Teo J, Sagnella SM, Akerfeldt MC, Liu J, Phillips PA, Rana TM, Kavallaris M. Therapeutic targeting of polo-like kinase 1 using RNA-interfering nanoparticles (iNOPs) for the treatment of non-small cell lung cancer. Oncotarget 2015; 6:12020-34. [PMID: 25557168 PMCID: PMC4494920 DOI: 10.18632/oncotarget.2664] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/27/2014] [Indexed: 01/29/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) remains the most common cause of cancer death worldwide due its resistance to chemotherapy and aggressive tumor growth. Polo-like kinase 1 (PLK1) is a serine-threonine protein kinase which is overexpressed in cancer cells, and plays a major role in regulating tumor growth. A number of PLK1 inhibitors are in clinical trial; however, poor tumor bioavailability and off-target effects limit their efficacy. Short-interfering-RNA (siRNA) holds promise as a class of therapeutics, which can selectively silence disease-causing genes. However, siRNA cannot enter cells without a delivery vehicle. Herein, we investigated whether RNAi-interfering nanoparticles could deliver siRNA to NSCLC cells and silence PLK1 expression in vitro and in vivo. iNOP-7 was non-toxic, and delivered siRNA with high efficiency to NSCLC cells. iNOP-7-PLK1 siRNA silenced PLK1 expression and reduced NSCLC growth in vitro. Notably, iNOP-7 delivered siRNA to orthotopic lung tumors in mice, and administration of iNOP-7-PLK1 siRNA reduced lung tumor burden. These novel data show that iNOP-7 can deliver siRNA against PLK1 to NSCLC cells, and decrease cell proliferation both in vitro and in vivo. iNOP-7-PLK1 siRNA may provide a novel therapeutic strategy for the treatment of NSCLC as well as other cancers which aberrantly express this gene.
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Affiliation(s)
- Joshua A. McCarroll
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW, NSW, Australia
| | - Tanya Dwarte
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
| | - Huricha Baigude
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
| | - Jason Dang
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Lu Yang
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
| | - Rafael B. Erlich
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW, NSW, Australia
| | - Kathleen Kimpton
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
| | - Joann Teo
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW, NSW, Australia
| | - Sharon M. Sagnella
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW, NSW, Australia
| | - Mia C. Akerfeldt
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
| | - Jie Liu
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW, NSW, Australia
| | - Phoebe A. Phillips
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW, NSW, Australia
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW, NSW, Australia
| | - Tariq M. Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Centre, Randwick, UNSW Australia (UNSW), NSW, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, UNSW, NSW, Australia
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Robichaux JP, Hallett RM, Fuseler JW, Hassell JA, Ramsdell AF. Mammary glands exhibit molecular laterality and undergo left-right asymmetric ductal epithelial growth in MMTV-cNeu mice. Oncogene 2015; 34:2003-10. [PMID: 24909172 PMCID: PMC4261057 DOI: 10.1038/onc.2014.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 04/01/2014] [Accepted: 04/21/2014] [Indexed: 02/07/2023]
Abstract
Significant left-right (L-R) differences in tumor incidence and disease outcome occur for cancers of paired organs, including the breasts; however, the basis for this laterality is unknown. Here, we show that despite their morphologic symmetry, left versus right mammary glands in wild-type mice have baseline differences in gene expression that are L-R independently regulated during pubertal development, including genes that regulate luminal progenitor cell renewal, luminal cell differentiation, mammary tumorigenesis, tamoxifen sensitivity and chemotherapeutic resistance. In MMTV-cNeu(Tg/Tg) mice, which model HER2/Neu-amplified breast cancer, baseline L-R differences in mammary gene expression are amplified, sustained or inverted in a gene-specific manner and the mammary ductal epithelium undergoes L-R asymmetric growth and patterning. Comparative genomic analysis of mouse L-R mammary gene expression profiles with gene expression profiles of human breast tumors revealed significant linkage between right-sided gene expression and decreased breast cancer patient survival. Collectively, these findings are the first to demonstrate that mammary glands are lateralized organs, and, moreover, that mammary glands have L-R differential susceptibility to HER2/Neu oncogene-mediated effects on ductal epithelial growth and differentiation. We propose that intrinsic molecular laterality may have a role in L-R asymmetric breast tumor incidence and, furthermore, that interplay between the L-R molecular landscape and oncogene activity may contribute to the differential disease progression and patient outcome that are associated with tumor situs.
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Affiliation(s)
- Jacqulyne P. Robichaux
- Department of Regenerative Medicine and Cell Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
| | - Robin M. Hallett
- Department of Biochemistry and Biomedical Sciences, Centre for Functional Genomics, McMaster University, Ontario, Canada
| | - John W. Fuseler
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC 29208
| | - John A. Hassell
- Department of Biochemistry and Biomedical Sciences, Centre for Functional Genomics, McMaster University, Ontario, Canada
| | - Ann F. Ramsdell
- Department of Regenerative Medicine and Cell Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC 29208
- Program In Women’s and Gender Studies, College of Arts and Sciences, University of South Carolina, Columbia, SC 29208
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46
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Bhola NE, Jansen VM, Bafna S, Giltnane JM, Balko JM, Estrada MV, Meszoely I, Mayer I, Abramson V, Ye F, Sanders M, Dugger TC, Allen EV, Arteaga CL. Kinome-wide functional screen identifies role of PLK1 in hormone-independent, ER-positive breast cancer. Cancer Res 2015; 75:405-14. [PMID: 25480943 PMCID: PMC4297507 DOI: 10.1158/0008-5472.can-14-2475] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Estrogen receptor (ER) α-positive breast cancers initially respond to antiestrogens but eventually become estrogen independent and recur. ER(+) breast cancer cells resistant to long-term estrogen deprivation (LTED) exhibit hormone-independent ER transcriptional activity and growth. A kinome-wide siRNA screen using a library targeting 720 kinases identified Polo-like kinase 1 (PLK1) as one of the top genes whose downregulation resulted in inhibition of estrogen-independent ER transcriptional activity and growth of LTED cells. High PLK1 mRNA and protein correlated with a high Ki-67 score in primary ER(+) breast cancers after treatment with the aromatase inhibitor letrozole. RNAi-mediated knockdown of PLK1 inhibited ER expression, estrogen-independent growth, and ER transcription in MCF7 and HCC1428 LTED cells. Pharmacologic inhibition of PLK1 with volasertib, a small-molecule ATP-competitive PLK1 inhibitor, decreased LTED cell growth, ER transcriptional activity, and ER expression. Volasertib in combination with the ER antagonist, fulvestrant, decreased MCF7 xenograft growth in ovariectomized mice more potently than each drug alone. JUNB, a component of the AP-1 complex, was expressed 16-fold higher in MCF7/LTED compared with parental MCF7 cells. Furthermore, JUNB and BCL2L1 (which encodes antiapoptotic BCL-xL) mRNA levels were markedly reduced upon volasertib treatment in MCF7/LTED cells, while they were increased in parental MCF7 cells. Finally, JUNB knockdown decreased ER expression and transcriptional activity in MCF7/LTED cells, suggesting that PLK1 drives ER expression and estrogen-independent growth via JUNB. These data support a critical role of PLK1 in acquired hormone-independent growth of ER(+) human breast cancer and is therefore a promising target in tumors that have escaped estrogen deprivation therapy.
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Affiliation(s)
- Neil E Bhola
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Valerie M Jansen
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Sangeeta Bafna
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jennifer M Giltnane
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee. Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Justin M Balko
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee. Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Mónica V Estrada
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ingrid Meszoely
- Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee. Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ingrid Mayer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee. Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Vandana Abramson
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee. Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Fei Ye
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Melinda Sanders
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee. Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Teresa C Dugger
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Eliezer V Allen
- Department of Medical Oncology, Broad Institute of MIT at Harvard, Cambridge, Massachusetts
| | - Carlos L Arteaga
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee. Breast Cancer Research Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.
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47
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Bruce MC, McAllister D, Murphy LC. The kinome associated with estrogen receptor-positive status in human breast cancer. Endocr Relat Cancer 2014; 21:R357-70. [PMID: 25056177 DOI: 10.1530/erc-14-0232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Estrogen receptor alpha (ERα) regulates and is regulated by kinases involved in several functions associated with the hallmarks of cancer. The following literature review strongly suggests that distinct kinomes exist for ERα-positive and -negative human breast cancers. Importantly, consistent with the known heterogeneity of ERα-positive cancers, different subgroups exist, which can be defined by different kinome signatures, which in turn are correlated with clinical outcome. Strong evidence supports the interplay of kinase networks, suggesting that targeting a single node may not be sufficient to inhibit the network. Therefore, identifying the important hubs/nodes associated with each clinically relevant kinome in ER+ tumors could offer the ability to implement the best therapy options at diagnosis, either endocrine therapy alone or together with other targeted therapies, for improved overall outcome.
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Affiliation(s)
- M Christine Bruce
- Department of Biochemistry and Medical GeneticsManitoba Institute of Cell Biology, University of Manitoba and CancerCare Manitoba, 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
| | - Danielle McAllister
- Department of Biochemistry and Medical GeneticsManitoba Institute of Cell Biology, University of Manitoba and CancerCare Manitoba, 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
| | - Leigh C Murphy
- Department of Biochemistry and Medical GeneticsManitoba Institute of Cell Biology, University of Manitoba and CancerCare Manitoba, 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
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48
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GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data. Sci Rep 2014; 4:6347. [PMID: 25213199 PMCID: PMC4161965 DOI: 10.1038/srep06347] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/19/2014] [Indexed: 12/11/2022] Open
Abstract
RNA-Seq is quickly becoming the preferred method for comprehensively characterizing whole transcriptome activity, and the analysis of count data from RNA-Seq requires new computational tools. We developed GSAASeqSP, a novel toolset for genome-wide gene set association analysis of sequence count data. This toolset offers a variety of statistical procedures via combinations of multiple gene-level and gene set-level statistics, each having their own strengths under different sample and experimental conditions. These methods can be employed independently, or results generated from multiple or all methods can be integrated to determine more robust profiles of significantly altered biological pathways. Using simulations, we demonstrate the ability of these methods to identify association signals and to measure the strength of the association. We show that GSAASeqSP analyses of RNA-Seq data from diverse tissue samples provide meaningful insights into the biological mechanisms that differentiate these samples. GSAASeqSP is a powerful platform for investigating molecular underpinnings of complex traits and diseases arising from differential activity within the biological pathways. GSAASeqSP is available at http://gsaa.unc.edu.
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49
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Hu J, Tzeng JY. Integrative gene set analysis of multi-platform data with sample heterogeneity. ACTA ACUST UNITED AC 2014; 30:1501-7. [PMID: 24489370 DOI: 10.1093/bioinformatics/btu060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MOTIVATION Gene set analysis is a popular method for large-scale genomic studies. Because genes that have common biological features are analyzed jointly, gene set analysis often achieves better power and generates more biologically informative results. With the advancement of technologies, genomic studies with multi-platform data have become increasingly common. Several strategies have been proposed that integrate genomic data from multiple platforms to perform gene set analysis. To evaluate the performances of existing integrative gene set methods under various scenarios, we conduct a comparative simulation analysis based on The Cancer Genome Atlas breast cancer dataset. RESULTS We find that existing methods for gene set analysis are less effective when sample heterogeneity exists. To address this issue, we develop three methods for multi-platform genomic data with heterogeneity: two non-parametric methods, multi-platform Mann-Whitney statistics and multi-platform outlier robust T-statistics, and a parametric method, multi-platform likelihood ratio statistics. Using simulations, we show that the proposed multi-platform Mann-Whitney statistics method has higher power for heterogeneous samples and comparable performance for homogeneous samples when compared with the existing methods. Our real data applications to two datasets of The Cancer Genome Atlas also suggest that the proposed methods are able to identify novel pathways that are missed by other strategies. AVAILABILITY AND IMPLEMENTATION http://www4.stat.ncsu.edu/∼jytzeng/Software/Multiplatform_gene_set_analysis/
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Affiliation(s)
- Jun Hu
- Bioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA, Division of Bioinformatics, Omicsoft Inc., 200 Cascade Pointe Lane, Suite 101, Cary, NC 27513, USA, Department of Statistics, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and Department of Statistics, National Cheng-Kung University, No.1, University Road, Tainan 701, TaiwanBioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA, Division of Bioinformatics, Omicsoft Inc., 200 Cascade Pointe Lane, Suite 101, Cary, NC 27513, USA, Department of Statistics, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and Department of Statistics, National Cheng-Kung University, No.1, University Road, Tainan 701, Taiwan
| | - Jung-Ying Tzeng
- Bioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA, Division of Bioinformatics, Omicsoft Inc., 200 Cascade Pointe Lane, Suite 101, Cary, NC 27513, USA, Department of Statistics, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and Department of Statistics, National Cheng-Kung University, No.1, University Road, Tainan 701, TaiwanBioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA, Division of Bioinformatics, Omicsoft Inc., 200 Cascade Pointe Lane, Suite 101, Cary, NC 27513, USA, Department of Statistics, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and Department of Statistics, National Cheng-Kung University, No.1, University Road, Tainan 701, TaiwanBioinformatics Research Center, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA, Division of Bioinformatics, Omicsoft Inc., 200 Cascade Pointe Lane, Suite 101, Cary, NC 27513, USA, Department of Statistics, North Carolina State University, Ricks Hall, 1 Lampe Dr., Raleigh, NC 27607, USA and Department of Statistics, National Cheng-Kung University, No.1, University Road, Tainan 701, Taiwan
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50
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Ji J, Jia S, Ji K, Jiang WG. Wnt1 inducible signalling pathway protein-2 (WISP‑2/CCN5): roles and regulation in human cancers (review). Oncol Rep 2013; 31:533-9. [PMID: 24337439 DOI: 10.3892/or.2013.2909] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/27/2013] [Indexed: 11/05/2022] Open
Abstract
Wnt1 inducible signalling pathway protein-2 (WISP‑2), also known as CCN5, CT58, CTGF-L, CTGF-3, HICP and Cop1, is one of the 3 WNT1 inducible proteins that belongs to the CCN family. This family of members has been shown to play multiple roles in a number of pathophysiological processes, including cell proliferation, adhesion, wound healing, extracellular matrix regulation, epithelial-mesenchymal transition, angiogenesis, fibrosis, skeletal development and embryo implantation. Recent results suggest that WISP-2 is relevant to tumorigenesis and malignant transformation, particularly in breast cancer, colorectal cancer and hepatocarcinoma. Notably, its roles in cancer appear to vary depending on cell/tumour type and the microenvironment. The striking difference in the structure of WISP-2 in comparison with the other 2 family members may contribute to its difference in functions, which leads to the hypothesis that WISP-2 may act as a dominant-negative regulator of other CCN family members. In the present review, we summarise the roles, regulation and underlying mechanism of WISP-2 in human cancers.
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Affiliation(s)
- Jiafu Ji
- Department of Gastro-enterological Cancers, Peking University Cancer Hospital, Beijing, P.R. China
| | - Shuqin Jia
- Cardiff University-Peking University Joint Cancer Institute, Beijing, P.R. China
| | - Ke Ji
- Cardiff University-Peking University Joint Cancer Institute, Beijing, P.R. China
| | - Wen G Jiang
- Metastasis and Angiogenesis Research Group, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
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