1
|
Nie K, He ZJ, Kong LJ. NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway. J Cancer Res Clin Oncol 2024; 150:411. [PMID: 39237674 PMCID: PMC11377494 DOI: 10.1007/s00432-024-05935-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024]
Abstract
PURPOSE The aim of this study was to explore the potential correlation between the nuclear receptor subfamily 3 group C member 2 (NR3C2) and outcomes of colon cancer, along with the mechanisms underlying this association. METHOD mRNA (messenger RNA) data and clinical records pertaining to colon cancer were retrieved from The Cancer Genome Atlas (TCGA) database. The analysis of NR3C2 expression discrepancies between normal colon and tumor tissues was conducted using R software. In addition, we also studied the relationship between NR3C2 expression and prognosis, pathological parameters. The relative role of NR3C2 were further predicted through bioinformatics methods and receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of NR3C2 in colon cancer. Single-cell data from colon cancer samples in the GEO (Gene Expression Omnibus) database further investigated the mechanism of the lower survival associated with NR3C2 dysregulation. NR3C2 expression in three fresh colon cancer samples and their respective paracancer samples was determined. Furthermore, colon cancer cell models overexpressing NR3C2 and with knockdown NR3C2 were constructed by lentiviral vector transfection. Cell Counting Kit-8 assay, transplantation of tumors in nude mice and transwell assays were used to examine the proliferation, migration and invasion of colon cancer cells. The effect on the Wnt/β-catenin pathway, activities of cellular autophagy and cell apoptosis were examined by assessing the expression levels of several key proteins, including Bcl-2, Bax, and LC3. RESULTS We found that NR3C2 was found a significantly lower level in colon cancer tissues than in adjacent tissues, which was associated with distant and lymphatic metastases, clinical stage, and poor clinical outcome, and it was an independent prognostic factor and potential marker of colon cancer. Single-cell transcriptome data identified the subset of circulating T and B cells with high expression of NR3C2, which is involved in TNF signaling pathway. Functional experiments show that downregulation of NR3C2 resultsed in the activation of the Wnt/β-catenin signaling pathway, and promotesd the proliferation and invasion of colon cancer cells while suppressing cell autophagy and apoptosis. CONCLUSION NR3C2 may regulate Wnt/β-catenin to affect the proliferation, invasion apoptosis and autophagy of colon cancer, and this axis is a potential target for the treatment of colon cancer.
Collapse
Affiliation(s)
- Ke Nie
- Department of Laboratory Medicine, The People's Hospital of Changshou District of Chongqing City, Chongqing, 401220, China
| | - Zhong-Jiang He
- Gastrointestinal Surgery, The People's Hospital of Yubei District of Chongqing City, Chongqing, 401120, China.
| | - Ling-Jun Kong
- Gastrointestinal Surgery, The People's Hospital of Yubei District of Chongqing City, Chongqing, 401120, China
| |
Collapse
|
2
|
Yang S, Tang W, Azizian A, Gaedcke J, Ohara Y, Cawley H, Hanna N, Ghadimi M, Lal T, Sen S, Creighton CJ, Gao J, Putluri N, Ambs S, Hussain P. MIF/NR3C2 axis regulates glucose metabolism reprogramming in pancreatic cancer through MAPK-ERK and AP-1 pathways. Carcinogenesis 2024; 45:582-594. [PMID: 38629149 PMCID: PMC11317528 DOI: 10.1093/carcin/bgae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/10/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
Inflammation and aberrant cellular metabolism are widely recognized as hallmarks of cancer. In pancreatic ductal adenocarcinoma (PDAC), inflammatory signaling and metabolic reprogramming are tightly interwoven, playing pivotal roles in the pathogenesis and progression of the disease. However, the regulatory functions of inflammatory mediators in metabolic reprogramming in pancreatic cancer have not been fully explored. Earlier, we demonstrated that pro-inflammatory mediator macrophage migration inhibitory factor (MIF) enhances disease progression by inhibiting its downstream transcriptional factor nuclear receptor subfamily 3 group C member 2 (NR3C2). Here, we provide evidence that MIF and NR3C2 interactively regulate metabolic reprogramming, resulting in MIF-induced cancer growth and progression in PDAC. MIF positively correlates with the HK1 (hexokinase 1), HK2 (hexokinase 2) and LDHA (lactate dehydrogenase) expression and increased pyruvate and lactate production in PDAC patients. Additionally, MIF augments glucose uptake and lactate efflux by upregulating HK1, HK2 and LDHA expression in pancreatic cancer cells in vitro and in mouse models of PDAC. Conversely, a reduction in HK1, HK2 and LDHA expression is observed in tumors with high NR3C2 expression in PDAC patients. NR3C2 suppresses HK1, HK2 and LDHA expression, thereby inhibiting glucose uptake and lactate efflux in pancreatic cancer. Mechanistically, MIF-mediated regulation of glycolytic metabolism involves the activation of the mitogen-activated protein kinase-ERK signaling pathway, whereas NR3C2 interacts with the activator protein 1 to regulate glycolysis. Our findings reveal an interactive role of the MIF/NR3C2 axis in regulating glucose metabolism supporting tumor growth and progression and may be a potential target for designing novel approaches for improving disease outcome.
Collapse
Affiliation(s)
- Shouhui Yang
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Azadeh Azizian
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Yuuki Ohara
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helen Cawley
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nader Hanna
- Division of Surgical Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Trisha Lal
- Howard University College of Medicine, Washington, DC, USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Dan L. Duncan Comprehensive Cancer Center, Advanced Technology Core, Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Perwez Hussain
- Pancreatic Cancer Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
3
|
Manickasamy MK, Jayaprakash S, Girisa S, Kumar A, Lam HY, Okina E, Eng H, Alqahtani MS, Abbas M, Sethi G, Kumar AP, Kunnumakkara AB. Delineating the role of nuclear receptors in colorectal cancer, a focused review. Discov Oncol 2024; 15:41. [PMID: 38372868 PMCID: PMC10876515 DOI: 10.1007/s12672-023-00808-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/20/2023] [Indexed: 02/20/2024] Open
Abstract
Colorectal cancer (CRC) stands as one of the most prevalent form of cancer globally, causing a significant number of deaths, surpassing 0.9 million in the year 2020. According to GLOBOCAN 2020, CRC ranks third in incidence and second in mortality in both males and females. Despite extensive studies over the years, there is still a need to establish novel therapeutic targets to enhance the patients' survival rate in CRC. Nuclear receptors (NRs) are ligand-activated transcription factors (TFs) that regulate numerous essential biological processes such as differentiation, development, physiology, reproduction, and cellular metabolism. Dysregulation and anomalous expression of different NRs has led to multiple alterations, such as impaired signaling cascades, mutations, and epigenetic changes, leading to various diseases, including cancer. It has been observed that differential expression of various NRs might lead to the initiation and progression of CRC, and are correlated with poor survival outcomes in CRC patients. Despite numerous studies on the mechanism and role of NRs in this cancer, it remains of significant scientific interest primarily due to the diverse functions that various NRs exhibit in regulating key hallmarks of this cancer. Thus, modulating the expression of NRs with their agonists and antagonists, based on their expression levels, holds an immense prospect in the diagnosis, prognosis, and therapeutical modalities of CRC. In this review, we primarily focus on the role and mechanism of NRs in the pathogenesis of CRC and emphasized the significance of targeting these NRs using a variety of agents, which may represent a novel and effective strategy for the prevention and treatment of this cancer.
Collapse
Affiliation(s)
- Mukesh Kumar Manickasamy
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Sujitha Jayaprakash
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Sosmitha Girisa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Aviral Kumar
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Hiu Yan Lam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117699, Singapore
| | - Elena Okina
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117699, Singapore
| | - Huiyan Eng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117699, Singapore
| | - Mohammed S Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, 61421, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester, LE1 7RH, UK
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, 61421, Abha, Saudi Arabia
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117699, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117600, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, 117699, Singapore.
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India.
| |
Collapse
|
4
|
Nagata Y, Goto T, Teramoto Y, Matsukawa T, Fujimoto N, Miyamoto H. Mineralocorticoid receptor signaling inhibits bladder cancer progression. Am J Cancer Res 2024; 14:696-708. [PMID: 38455412 PMCID: PMC10915320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/11/2024] [Indexed: 03/09/2024] Open
Abstract
The biological or clinical significance of mineralocorticoid receptor (MR) in urothelial cancer remains largely unknown. The present study aimed to determine the functional role of MR in bladder cancer progression. In two of the human bladder cancer lines expressing MR, treatment with a natural MR ligand, aldosterone, significantly reduced cell proliferation and migration, which was restored by three MR antagonists clinically used, spironolactone (except colony formation of androgen receptor-positive cells cultured in the presence of androgens), eplerenone, and esaxerenone. Similarly, MR knockdown via shRNA virus infection resulted in significant increases in cell viability/migration, as well as colony formation, compared with control sublines. In addition, MR knockdown augmented the expression of β-catenin, c-fos, and N-cadherin, and lowered that of E-cadherin and p53, indicating the induction of the cadherin switching. Immunohistochemistry in surgical specimens detected MR signals in 58 (92.1%; 36.5% weakly-positive/1+, 44.4% moderately-positive/2+, and 11.1% strongly-positive/3+) of 63 muscle-invasive bladder cancers, which was significantly lower than in adjacent non-neoplastic urothelial tissues (100%; 15.7% 1+, 37.3% 2+, and 47.1% 3+). Moreover, patients with MR-high (3+) tumor had a significantly lower risk of cancer-specific mortality (P=0.039). Multivariable analysis further showed that strong MR expression was an independent predictor of cancer-specific survival in patients with muscle-invasive bladder cancer (hazard ratio 0.117, P=0.039). These findings suggest that MR signaling functions as a tumor suppressor in urothelial carcinoma and prevents tumor growth. Accordingly, there is a possibility that the concurrent use of anti-mineralocorticoids, particularly eplerenone and esaxerenone, in patients with bladder cancer rather contributes to the promotion of disease progression.
Collapse
Affiliation(s)
- Yujiro Nagata
- Department of Pathology and Laboratory Medicine, University of Rochester Medical CenterRochester, NY, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical CenterRochester, NY, USA
- Department of Urology, University of Occupational and Environmental Health School of MedicineKitakyushu, Japan
| | - Takuro Goto
- Department of Pathology and Laboratory Medicine, University of Rochester Medical CenterRochester, NY, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical CenterRochester, NY, USA
| | - Yuki Teramoto
- Department of Pathology and Laboratory Medicine, University of Rochester Medical CenterRochester, NY, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical CenterRochester, NY, USA
| | - Takuo Matsukawa
- Department of Pathology and Laboratory Medicine, University of Rochester Medical CenterRochester, NY, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical CenterRochester, NY, USA
- Department of Urology, University of Occupational and Environmental Health School of MedicineKitakyushu, Japan
| | - Naohiro Fujimoto
- Department of Urology, University of Occupational and Environmental Health School of MedicineKitakyushu, Japan
| | - Hiroshi Miyamoto
- Department of Pathology and Laboratory Medicine, University of Rochester Medical CenterRochester, NY, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical CenterRochester, NY, USA
- Department of Urology, University of Rochester Medical CenterRochester, NY, USA
- Departments of Pathology and Urology, Johns Hopkins University School of MedicineBaltimore, MD, USA
| |
Collapse
|
5
|
Wani SA, Hussain S, Gray JS, Nayak D, Tang H, Perez LM, Long MD, Siddappa M, McCabe CJ, Sucheston-Campbell LE, Freeman MR, Campbell MJ. Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.15.571947. [PMID: 38168185 PMCID: PMC10760102 DOI: 10.1101/2023.12.15.571947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The current study in prostate cancer (PCa) focused on the genomic mechanisms at the cross-roads of pro-differentiation signals and the emergence of lineage plasticity. We explored an understudied cistromic mechanism involving RARγ's ability to govern AR cistrome-transcriptome relationships, including those associated with more aggressive PCa features. The RARγ complex in PCa cell models was enriched for canonical cofactors, as well as proteins involved in RNA processing and bookmarking. Identifying the repertoire of miR-96 bound and regulated gene targets, including those recognition elements marked by m6A, revealed their significant enrichment in the RARγ complex. RARγ significantly enhanced the AR cistrome, particularly in active enhancers and super-enhancers, and overlapped with the binding of bookmarking factors. Furthermore, RARγ expression led to nucleosome-free chromatin enriched with H3K27ac, and significantly enhanced the AR cistrome in G2/M cells. RARγ functions also antagonized the transcriptional actions of the lineage master regulator ONECUT2. Similarly, gene programs regulated by either miR-96 or antagonized by RARγ were enriched in alternative lineages and more aggressive PCa phenotypes. Together these findings reveal an under-investigated role for RARγ, modulated by miR-96, to bookmark enhancer sites during mitosis. These sites are required by the AR to promote transcriptional competence, and emphasize luminal differentiation, while antagonizing ONECUT2.
Collapse
Affiliation(s)
- Sajad A Wani
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Shahid Hussain
- Division of Cancer Biology, Cedars Sinai Cancer, and Los Angeles, CA 90048
- Board of Governors Innovation Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Jaimie S Gray
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Debasis Nayak
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Hancong Tang
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Lillian M Perez
- Division of Cancer Therapeutics, Cedars Sinai Cancer, Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Mark D Long
- Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263
| | - Manjunath Siddappa
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH 43210
| | - Christopher J McCabe
- Institute of Metabolism and Systems Research (IMSR), and Centre of Endocrinology, Diabetes and Metabolism (CEDAM), University of Birmingham, Birmingham, UK
| | | | - Michael R Freeman
- Division of Cancer Therapeutics, Cedars Sinai Cancer, Departments of Urology and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Moray J Campbell
- Division of Cancer Biology, Cedars Sinai Cancer, and Los Angeles, CA 90048
- Board of Governors Innovation Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| |
Collapse
|
6
|
Kałuzińska-Kołat Ż, Kołat D, Kośla K, Płuciennik E, Bednarek AK. Delineating the glioblastoma stemness by genes involved in cytoskeletal rearrangements and metabolic alterations. World J Stem Cells 2023; 15:302-322. [PMID: 37342224 PMCID: PMC10277965 DOI: 10.4252/wjsc.v15.i5.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 05/26/2023] Open
Abstract
Literature data on glioblastoma ongoingly underline the link between metabolism and cancer stemness, the latter is one responsible for potentiating the resistance to treatment, inter alia due to increased invasiveness. In recent years, glioblastoma stemness research has bashfully introduced a key aspect of cytoskeletal rearrangements, whereas the impact of the cytoskeleton on invasiveness is well known. Although non-stem glioblastoma cells are less invasive than glioblastoma stem cells (GSCs), these cells also acquire stemness with greater ease if characterized as invasive cells and not tumor core cells. This suggests that glioblastoma stemness should be further investigated for any phenomena related to the cytoskeleton and metabolism, as they may provide new invasion-related insights. Previously, we proved that interplay between metabolism and cytoskeleton existed in glioblastoma. Despite searching for cytoskeleton-related processes in which the investigated genes might have been involved, not only did we stumble across the relation to metabolism but also reported genes that were found to be implicated in stemness. Thus, dedicated research on these genes in GSCs seems justifiable and might reveal novel directions and/or biomarkers that could be utilized in the future. Herein, we review the previously identified cytoskeleton/metabolism-related genes through the prism of glioblastoma stemness.
Collapse
Affiliation(s)
- Żaneta Kałuzińska-Kołat
- Department of Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Katarzyna Kośla
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| |
Collapse
|
7
|
Nagata Y, Matsukawa T, Goto T, Teramoto Y, Jiang G, Fujimoto N, Miyamoto H. Protective role of mineralocorticoid receptor signaling in urothelial tumorigenesis. Am J Cancer Res 2023; 13:408-418. [PMID: 36895984 PMCID: PMC9989624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 01/12/2023] [Indexed: 03/11/2023] Open
Abstract
The expression status of mineralocorticoid receptor (MR) and its biological significance in human urothelial carcinoma remain unknown. The present study aimed to determine the functional role of MR in the development of urothelial cancer. In human normal urothelial SVHUC cells with exposure to a chemical carcinogen 3-methylcholanthrene (MCA), we assessed the effects of a natural MR ligand, aldosterone, and 3 MR antagonists, including spironolactone, eplerenone, and esaxerenone, as well as knockdown of MR via shRNA virus infection, on their neoplastic/malignant transformation. The in vitro system with carcinogen challenge showed that aldosterone and anti-mineralocorticoids significantly prevented and promoted, respectively, the neoplastic transformation of SVHUC cells. Similarly, MR knockdown in SVHUC cells considerably induced MCA-mediated neoplastic transformation, compared with a control subline. In addition, MR knockdown or antagonist treatment resulted in increases in the expression of β-catenin, c-Fos, and N-cadherin, and a decrease in that of E-cadherin. Meanwhile, spironolactone, which is known to possess anti-androgenic activity, rather suppressed the neoplastic transformation of a SVHUC subline stably expressing wild-type androgen receptor, indicating its dominant effect via the androgen receptor pathway. Immunohistochemistry in surgical specimens detected MR signals in 77 (98.7%; 23.1% weak/1+, 42.3% moderate/2+, and 33.3% strong/3+) of 78 non-invasive bladder tumors, which was significantly (P<0.001) lower than in adjacent non-neoplastic urothelial tissues (100%; 20.5% 2+ and 79.5% 3+). Moreover, the risks for disease recurrence after transurethral surgery were marginally lower in female patients with MR-high (2+/3+) tumor (P=0.068) and significantly lower in all patients with MR-high/glucocorticoid receptor-high tumor (P=0.025), compared with respective controls. These findings suggest that MR signaling functions as a suppressor for urothelial tumorigenesis.
Collapse
Affiliation(s)
- Yujiro Nagata
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center Rochester, NY 14642, USA.,James P. Wilmot Cancer Institute, University of Rochester Medical Center Rochester, NY 14642, USA.,Department of Urology, University of Occupational and Environmental Health School of Medicine Kitakyushu, Japan
| | - Takuo Matsukawa
- Department of Urology, University of Occupational and Environmental Health School of Medicine Kitakyushu, Japan
| | - Takuro Goto
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center Rochester, NY 14642, USA.,James P. Wilmot Cancer Institute, University of Rochester Medical Center Rochester, NY 14642, USA
| | - Yuki Teramoto
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center Rochester, NY 14642, USA.,James P. Wilmot Cancer Institute, University of Rochester Medical Center Rochester, NY 14642, USA
| | - Guiyang Jiang
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center Rochester, NY 14642, USA.,James P. Wilmot Cancer Institute, University of Rochester Medical Center Rochester, NY 14642, USA
| | - Naohiro Fujimoto
- Department of Urology, University of Occupational and Environmental Health School of Medicine Kitakyushu, Japan
| | - Hiroshi Miyamoto
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center Rochester, NY 14642, USA.,James P. Wilmot Cancer Institute, University of Rochester Medical Center Rochester, NY 14642, USA.,Department of Urology, University of Rochester Medical Center Rochester, NY 14642, USA.,Department of Pathology and Urology, Johns Hopkins University School of Medicine Baltimore, MD 21287, USA
| |
Collapse
|
8
|
Shatnawi A, Ayoub NM, Alkhalifa AE, Ibrahim DR. Estrogen-Related Receptors Gene Expression and Copy Number Alteration Association With the Clinicopathologic Characteristics of Breast Cancer. BREAST CANCER: BASIC AND CLINICAL RESEARCH 2022; 16:11782234221086713. [PMID: 35359609 PMCID: PMC8961373 DOI: 10.1177/11782234221086713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose: It has been suggested that dysregulation of transcription factors expression
or activity plays significant roles in breast cancer (BC) severity and poor
prognosis. Therefore, our study aims to thoroughly evaluate the
estrogen-related receptor isoforms (ESRRs) expression and copy number
alteration (CNA) status and their association with clinicopathologic
characteristics in BC. Methods: A METABRIC dataset consist of 2509 BC patients’ samples was obtained from the
cBioPortal public domain. The gene expression, putative CNA, and relevant
tumor information of ESRRs were retrieved. ESRRs messenger RNA (mRNA)
expression in BC cell lines was obtained from the Cancer Cell Line
Encyclopedia (CCLE). Association and correlation analysis of ESRRs
expression with BC clinicopathologic characteristics and molecular subtype
were performed. Kaplan–Meier survival analysis was conducted to evaluate the
prognostic value of ESRRs expression on patient survival. Results: ESRRα expression correlated negatively with patients’ age and overall
survival, whereas positively correlated with tumor size, the number of
positive lymph nodes, and Nottingham prognostic index (NPI). Conversely,
ESRRγ expression was positively correlated with patients’ age and negatively
correlated with NPI. ESRRα and ESRRγ expression were significantly
associated with tumor grade, expression of hormone receptors, human
epidermal growth factor receptor 2 (HER2), and molecular subtype, whereas
ESRRβ was only associated with tumor stage. A significant and distinct
association of each of ESRRs CNA with various clinicopathologic and
prognostic factors was also observed. Kaplan–Meier survival analysis
demonstrated no significant difference for survival curves among BC patients
with high or low expression of ESRRα, β, or γ. On stratification, high ESRRα
expression significantly reduced survival among premenopausal patients,
patients with grade I/II, and early-stage disease. In BC cell lines, only
ESRRα expression was significantly higher in HER2-positive cells. No
significant association was observed between ESRRβ expression and any of the
clinicopathologic characteristics examined. Conclusions: In this clinical dataset, ESRRα and ESRRγ mRNA expression and CNA show a
significant correlation and association with distinct clinicopathologic and
prognostic parameters known to influence treatment outcomes; however, ESRRβ
failed to show a robust role in BC pathogenesis. ESRRα and ESRRγ can be
employed as therapeutic targets in BC-targeted therapy. However, the role of
ESRRβ in BC pathogenesis remains unclear.
Collapse
Affiliation(s)
- Aymen Shatnawi
- Department of Pharmaceutical and Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV, USA
| | - Nehad M Ayoub
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Amer E Alkhalifa
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Dalia R Ibrahim
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| |
Collapse
|
9
|
Molecular Signatures of Tumour and Its Microenvironment for Precise Quantitative Diagnosis of Oral Squamous Cell Carcinoma: An International Multi-Cohort Diagnostic Validation Study. Cancers (Basel) 2022; 14:cancers14061389. [PMID: 35326543 PMCID: PMC8945999 DOI: 10.3390/cancers14061389] [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: 02/15/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Heterogeneity in oral potentially malignant disorder (OPMD) poses a problem for accurate prognosis that impacts on treatment strategy and patient outcome. A holistic assessment based on gene expression signatures from both the tumour cells and their microenvironment is necessary to provide a more precise prognostic assessment than just tumour cell signatures alone. METHODS We reformulated our previously established multigene qPCR test, quantitative Malignancy Index Diagnostic System (qMIDS) with new genes involved in matrix/stroma and immune modulation of the tumour microenvironment. An algorithm calculates and converts a panel of 16 gene mRNA expression levels into a qMIDS index to quantify risk of malignancy for each sample. RESULTS The new qMIDSV2 assay was validated in a UK oral squamous cell carcinoma (OSCC) cohort (n = 282) of margin and tumour core samples demonstrating significantly better diagnostic performance (AUC = 0.945) compared to previous qMIDSV1 (AUC = 0.759). Performance of qMIDSV2 were independently validated in Chinese (n = 35; AUC = 0.928) and Indian (n = 95; AUC = 0.932) OSCC cohorts. Further, 5-year retrospective analysis on an Indian dysplastic lesion cohort (n = 30) showed that qMIDSV2 was able to significantly differentiate between lesions without transformation and those with malignant transformation. CONCLUSIONS This study validated a novel multi-gene qPCR test on a total of 535 tissue specimens from UK, China and India, demonstrating a rapid minimally invasive method that has a potential application for dysplasia risk stratification. Further study is required to establish if qMIDSV2 could be used to improve OPMD patient management, guide treatment strategy and reduce oral cancer burden.
Collapse
|
10
|
Gangwar SK, Kumar A, Jose S, Alqahtani MS, Abbas M, Sethi G, Kunnumakkara AB. Nuclear receptors in oral cancer-emerging players in tumorigenesis. Cancer Lett 2022; 536:215666. [DOI: 10.1016/j.canlet.2022.215666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 12/24/2022]
|
11
|
Genomic Insights into Non-steroidal Nuclear Receptors in Prostate and Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1390:227-239. [DOI: 10.1007/978-3-031-11836-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
A Comprehensive Bioinformatic Analysis of NOTCH Pathway Involvement in Stomach Adenocarcinoma. DISEASE MARKERS 2021; 2021:4739868. [PMID: 34925644 PMCID: PMC8674080 DOI: 10.1155/2021/4739868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/12/2021] [Indexed: 01/02/2023]
Abstract
Background Activation of NOTCH signaling pathways, which are key regulators of multiple cellular functions, has been frequently implicated in cancer pathogenesis, and NOTCH inhibitors have received much recent focus in the context of cancer therapeutics. However, the role and possible involvement of NOTCH pathways in stomach adenocarcinoma (STAD) are unclear. Here, putative regulatory mechanisms and functions of NOTCH pathways in STAD were investigated. Methods Publicly available data from the TCGA-STAD database were utilized to explore the involvement of canonical NOTCH pathways in STAD by analyzing RNA expression levels of NOTCH receptors, ligands, and downstream genes. Statistical analysis of the data pertaining to cancer and noncancerous samples was performed using R software packages and public databases/webservers. Results Significant differential gene expression between control and STAD samples was noted for all NOTCH receptors (NOTCH1, 2, 3, and 4), the delta-like NOTCH ligands (DLL-3 and 4), and typical downstream genes (HES1 and HEY1). Four genes (NOTCH1, NOTCH2, NOTCH3, and HEY1) presented prognostic values for the STAD outcome in terms of overall survival. Functional enrichment analysis indicated that NOTCH family genes-strongly correlated genes were mainly enriched in several KEGG signaling pathways such as the PI3K-Akt signaling pathway, human papillomavirus infection, focal adhesion, Rap1 signaling pathway, and ECM-receptor interaction. Gene set enrichment analysis (GSEA) results showed that NOTCH family genes-significantly correlated genes were mainly enriched in four signaling pathways, ECM (extracellular matrix), tumor angiogenesis, inflammatory response, and immune regulation. Conclusions NOTCH family genes may play an essential role in the progression of STAD by modulating immune cells and mediating ECM synthesis, angiogenesis, focal adhesion, and PI3K-Akt signaling. Multiple NOTCH family genes are valuable candidate biomarkers or therapeutic targets for the management of STAD.
Collapse
|
13
|
Jiang J, Yuan J, Hu Z, Xu M, Zhang Y, Long M, Fan Y, Montone K, Tanyi JL, Tavana O, Chan HM, Zhang L, Hu X. Systematic pan-cancer characterization of nuclear receptors identifies potential cancer biomarkers and therapeutic targets. Cancer Res 2021; 82:46-59. [PMID: 34750098 DOI: 10.1158/0008-5472.can-20-3458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/15/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022]
Abstract
The nuclear receptor (NR) superfamily is one of the major druggable gene families, representing targets of approximately 13.5% of approved drugs. Certain NRs, such as estrogen receptor and androgen receptor, have been well demonstrated to be functionally involved in cancer and serve as informative biomarkers and therapeutic targets in oncology. However, the spectrum of NR dysregulation across cancers remains to be comprehensively characterized. Through computational integration of genetic, genomic, and pharmacologic profiles, we characterized the expression, recurrent genomic alterations, and cancer dependency of NRs at a large scale across primary tumor specimens and cancer cell lines. Expression levels of NRs were highly cancer-type specific and globally downregulated in tumors compared to corresponding normal tissue. Although the majority of NRs showed copy number losses in cancer, both recurrent focal gains and losses were identified in select NRs. Recurrent mutations and transcript fusions of NRs were observed in a small portion of cancers, serving as actionable genomic alterations. Analysis of large-scale CRISPR and RNAi screening datasets identified 10 NRs as strongly selective essential genes for cancer cell growth. In a subpopulation of tumor cells, growth dependencies correlated significantly with expression or genomic alterations. Overall, our comprehensive characterization of NRs across cancers may facilitate the identification and prioritization of potential biomarkers and therapeutic targets, as well as the selection of patients for precision cancer treatment.
Collapse
Affiliation(s)
| | - Jiao Yuan
- Ob and Gyn, University of Pennsylvania
| | - Zhongyi Hu
- Department of Obstetrics and Gynecology, University of Pennsylvania
| | - Mu Xu
- Department of Obstetrics and Gynecology, University of Pennsylvania
| | | | - Meixiao Long
- Comprehensive Cancer Center, The Ohio State University
| | - Yi Fan
- Radiation Oncology, University of Pennsylvania
| | | | | | | | - Ho Man Chan
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca (United States)
| | - Lin Zhang
- Department of Obstetrics and Gynecology, University of Pennsylvania
| | | |
Collapse
|
14
|
Dong Y, Hao L, Fang K, Han XX, Yu H, Zhang JJ, Cai LJ, Fan T, Zhang WD, Pang K, Ma WM, Wang XT, Han CH. A network pharmacology perspective for deciphering potential mechanisms of action of Solanum nigrum L. in bladder cancer. BMC Complement Med Ther 2021; 21:45. [PMID: 33494738 PMCID: PMC7836472 DOI: 10.1186/s12906-021-03215-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Solanum nigrum L. decoction has been used as a folklore medicine in China to prevent the postoperative recurrence of bladder cancer (BC). However, there are no previous pharmacological studies on the protective mechanisms of this activity of the plant. Thus, this study aimed to perform a systematic analysis and to predict the potential action mechanisms underlying S. nigrum activity in BC based on network pharmacology. METHODS Based on network pharmacology, the active ingredients of S. nigrum and the corresponding targets were identified using the Traditional Chinese Medicines for Systems Pharmacology Database and Analysis Platform database, and BC-related genes were screened using GeneCards and the Online Mendelian Inheritance in Man database. In addition, ingredient-target (I-T) and protein-protein interaction (PPI) networks were constructed using STRING and Cytoscape, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted, and then the pathways directly related to BC were integrated manually to reveal the pharmacological mechanism underlying S. nigrum-medicated therapeutic effects in BC. RESULTS Seven active herbal ingredients from 39 components of S. nigrum were identified, which shared 77 common target genes related to BC. I-T network analysis revealed that quercetin was associated with all targets and that NCOA2 was targeted by four ingredients. Besides, interleukin 6 had the highest degree value in the PPI network, indicating a hub role. A subsequent gene enrichment analysis yielded 86 significant GO terms and 89 significant pathways, implying that S. nigrum had therapeutic benefits in BC through multi-pathway effects, including the HIF-1, TNF, P53, MAPK, PI3K/Akt, apoptosis and bladder cancer pathway. CONCLUSIONS S. nigrum may mediate pharmacological effects in BC through multi-target and various signaling pathways. Further validation is required experimentally. Network pharmacology approach provides a predicative novel strategy to reveal the holistic mechanism of action of herbs.
Collapse
Affiliation(s)
- Yang Dong
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China.,Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Lin Hao
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China.,Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Kun Fang
- Xuzhou Clinical Medical College of Integrated Traditional Chinese and Western Medicine Affiliated to Nanjing University of Traditional Chinese Medicine, Xuzhou, China
| | - Xiao-Xiao Han
- Center of Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hui Yu
- Yantai Hospital of Traditional Chinese Medicine, Yantai, China
| | - Jian-Jun Zhang
- Department of Urology, Suqian People's Hospital of Nanjing Drum-Tower Hospital Group, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
| | - Long-Jun Cai
- Department of Urology, Suqian People's Hospital of Nanjing Drum-Tower Hospital Group, The Affiliated Suqian Hospital of Xuzhou Medical University, Suqian, China
| | - Tao Fan
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China
| | - Wen-da Zhang
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China
| | - Kun Pang
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China
| | - Wei-Ming Ma
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China
| | - Xi-Tao Wang
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China
| | - Cong-Hui Han
- Department of Urology, XuZhou Central Hospital Affiliated to Nanjing University of Chinese Medicine, Jiefang South Road, No. 199, Jiangsu, Xuzhou, China. .,Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China. .,Department of Biotechnology, College of Life Sciences, Jiangsu Normal University, Xuzhou, China.
| |
Collapse
|
15
|
Font-Díaz J, Jiménez-Panizo A, Caelles C, Vivanco MDM, Pérez P, Aranda A, Estébanez-Perpiñá E, Castrillo A, Ricote M, Valledor AF. Nuclear receptors: Lipid and hormone sensors with essential roles in the control of cancer development. Semin Cancer Biol 2020; 73:58-75. [PMID: 33309851 DOI: 10.1016/j.semcancer.2020.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022]
Abstract
Nuclear receptors (NRs) are a superfamily of ligand-activated transcription factors that act as biological sensors and use a combination of mechanisms to modulate positively and negatively gene expression in a spatial and temporal manner. The highly orchestrated biological actions of several NRs influence the proliferation, differentiation, and apoptosis of many different cell types. Synthetic ligands for several NRs have been the focus of extensive drug discovery efforts for cancer intervention. This review summarizes the roles in tumour growth and metastasis of several relevant NR family members, namely androgen receptor (AR), estrogen receptor (ER), glucocorticoid receptor (GR), thyroid hormone receptor (TR), retinoic acid receptors (RARs), retinoid X receptors (RXRs), peroxisome proliferator-activated receptors (PPARs), and liver X receptors (LXRs). These studies are key to develop improved therapeutic agents based on novel modes of action with reduced side effects and overcoming resistance.
Collapse
Affiliation(s)
- Joan Font-Díaz
- Department of Cell Biology, Physiology and Immunology, School of Biology, University of Barcelona, Barcelona, 08028, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, 08028, Spain
| | - Alba Jiménez-Panizo
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, 08028, Spain; Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, 08028, Spain
| | - Carme Caelles
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, 08028, Spain; Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, University of Barcelona, Barcelona, 08028, Spain
| | - María dM Vivanco
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology Park, Derio, 48160, Spain
| | - Paloma Pérez
- Instituto de Biomedicina de Valencia (IBV)-CSIC, Valencia, 46010, Spain
| | - Ana Aranda
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28029, Spain
| | - Eva Estébanez-Perpiñá
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, 08028, Spain; Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, 08028, Spain
| | - Antonio Castrillo
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28029, Spain; Unidad de Biomedicina, (Unidad Asociada al CSIC), Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Universidad de Las Palmas, Gran Canaria, 35001, Spain
| | - Mercedes Ricote
- Area of Myocardial Pathophysiology, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Annabel F Valledor
- Department of Cell Biology, Physiology and Immunology, School of Biology, University of Barcelona, Barcelona, 08028, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, 08028, Spain.
| |
Collapse
|
16
|
Li Y, Luo Y. Performance-weighted-voting model: An ensemble machine learning method for cancer type classification using whole-exome sequencing mutation. QUANTITATIVE BIOLOGY 2020; 8:347-358. [PMID: 34336363 DOI: 10.1007/s40484-020-0226-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background With improvements in next-generation DNA sequencing technology, lower cost is needed to collect genetic data. More machine learning techniques can be used to help with cancer analysis and diagnosis. Methods We developed an ensemble machine learning system named performance-weighted-voting model for cancer type classification in 6,249 samples across 14 cancer types. Our ensemble system consists of five weak classifiers (logistic regression, SVM, random forest, XGBoost and neural networks). We first used cross-validation to get the predicted results for the five classifiers. The weights of the five weak classifiers can be obtained based on their predictive performance by solving linear regression functions. The final predicted probability of the performance-weighted-voting model for a cancer type can be determined by the summation of each classifier's weight multiplied by its predicted probability. Results Using the somatic mutation count of each gene as the input feature, the overall accuracy of the performance-weighted-voting model reached 71.46%, which was significantly higher than the five weak classifiers and two other ensemble models: the hard-voting model and the soft-voting model. In addition, by analyzing the predictive pattern of the performance-weighted-voting model, we found that in most cancer types, higher tumor mutational burden can improve overall accuracy. Conclusion This study has important clinical significance for identifying the origin of cancer, especially for those where the primary cannot be determined. In addition, our model presents a good strategy for using ensemble systems for cancer type classification.
Collapse
Affiliation(s)
- Yawei Li
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
17
|
Siddappa M, Wani SA, Long MD, Leach DA, Mathé EA, Bevan CL, Campbell MJ. Identification of transcription factor co-regulators that drive prostate cancer progression. Sci Rep 2020; 10:20332. [PMID: 33230156 PMCID: PMC7683598 DOI: 10.1038/s41598-020-77055-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
In prostate cancer (PCa), and many other hormone-dependent cancers, there is clear evidence for distorted transcriptional control as disease driver mechanisms. Defining which transcription factor (TF) and coregulators are altered and combine to become oncogenic drivers remains a challenge, in part because of the multitude of TFs and coregulators and the diverse genomic space on which they function. The current study was undertaken to identify which TFs and coregulators are commonly altered in PCa. We generated unique lists of TFs (n = 2662), coactivators (COA; n = 766); corepressors (COR; n = 599); mixed function coregulators (MIXED; n = 511), and to address the challenge of defining how these genes are altered we tested how expression, copy number alterations and mutation status varied across seven prostate cancer (PCa) cohorts (three of localized and four advanced disease). Testing of significant changes was undertaken by bootstrapping approaches and the most significant changes were identified. For one commonly and significantly altered gene were stably knocked-down expression and undertook cell biology experiments and RNA-Seq to identify differentially altered gene networks and their association with PCa progression risks. COAS, CORS, MIXED and TFs all displayed significant down-regulated expression (q.value < 0.1) and correlated with protein expression (r 0.4-0.55). In localized PCa, stringent expression filtering identified commonly altered TFs and coregulator genes, including well-established (e.g. ERG) and underexplored (e.g. PPARGC1A, encodes PGC1α). Reduced PPARGC1A expression significantly associated with worse disease-free survival in two cohorts of localized PCa. Stable PGC1α knockdown in LNCaP cells increased growth rates and invasiveness and RNA-Seq revealed a profound basal impact on gene expression (~ 2300 genes; FDR < 0.05, logFC > 1.5), but only modestly impacted PPARγ responses. GSEA analyses of the PGC1α transcriptome revealed that it significantly altered the AR-dependent transcriptome, and was enriched for epigenetic modifiers. PGC1α-dependent genes were overlapped with PGC1α-ChIP-Seq genes and significantly associated in TCGA with higher grade tumors and worse disease-free survival. These methods and data demonstrate an approach to identify cancer-driver coregulators in cancer, and that PGC1α expression is clinically significant yet underexplored coregulator in aggressive early stage PCa.
Collapse
Affiliation(s)
- Manjunath Siddappa
- College of Pharmacy, Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, 536 Parks Hall, 500 West 12th Ave, Columbus, OH, 43210, USA
| | - Sajad A Wani
- College of Pharmacy, Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, 536 Parks Hall, 500 West 12th Ave, Columbus, OH, 43210, USA
| | - Mark D Long
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Damien A Leach
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Ewy A Mathé
- Biomedical Informatics Department, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.,Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Dr, Rockville, MD, 20892, USA
| | - Charlotte L Bevan
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Moray J Campbell
- College of Pharmacy, Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, 536 Parks Hall, 500 West 12th Ave, Columbus, OH, 43210, USA. .,The James, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA. .,Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
18
|
Lněničková K, Šadibolová M, Matoušková P, Szotáková B, Skálová L, Boušová I. The Modulation of Phase II Drug-Metabolizing Enzymes in Proliferating and Differentiated CaCo-2 Cells by Hop-Derived Prenylflavonoids. Nutrients 2020; 12:nu12072138. [PMID: 32708388 PMCID: PMC7400824 DOI: 10.3390/nu12072138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Prenylflavonoids in the human organism exhibit various health-beneficial activities, although they may interfere with drugs via the modulation of the expression and/or activity of drug-metabolizing enzymes. As intestinal cells are exposed to the highest concentrations of prenylflavonoids, we decided to study the cytotoxicity and modulatory effects of the four main hop-derived prenylflavonoids on the activities and mRNA expression of the main drug-conjugating enzymes in human CaCo-2 cells. Proliferating CaCo-2 cells were used for these purposes as a model of colorectal cancer cells, and differentiated CaCo-2 cells were used as an enterocyte-like model. All the tested prenylflavonoids inhibited the CaCo-2 cells proliferation, with xanthohumol proving the most effective (IC50 8.5 µM). The prenylflavonoids modulated the activities and expressions of the studied enzymes to a greater extent in the differentiated, as opposed to the proliferating, CaCo-2 cells. In the differentiated cells, all the prenylflavonoids caused a marked increase in glutathione S-transferase and catechol-O-methyltransferase activities, while the activity of sulfotransferase was significantly inhibited. Moreover, the prenylflavonoids upregulated the mRNA expression of uridine diphosphate (UDP)-glucuronosyl transferase 1A6 and downregulated that of glutathione S-transferase 1A1/2.
Collapse
Affiliation(s)
- Kateřina Lněničková
- Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 3, 77515 Olomouc, Czech Republic;
| | - Michaela Šadibolová
- Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 50005 Hradec Králové, Czech Republic; (M.Š.); (P.M.); (B.S.); (L.S.)
| | - Petra Matoušková
- Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 50005 Hradec Králové, Czech Republic; (M.Š.); (P.M.); (B.S.); (L.S.)
| | - Barbora Szotáková
- Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 50005 Hradec Králové, Czech Republic; (M.Š.); (P.M.); (B.S.); (L.S.)
| | - Lenka Skálová
- Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 50005 Hradec Králové, Czech Republic; (M.Š.); (P.M.); (B.S.); (L.S.)
| | - Iva Boušová
- Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 50005 Hradec Králové, Czech Republic; (M.Š.); (P.M.); (B.S.); (L.S.)
- Correspondence: ; Tel.: +420-495-067-406
| |
Collapse
|
19
|
Li H, Tian X, Wang P, Hu J, Qin R, Xu R, Liu K, Hao J, Tian N. LINC01128 resisted acute myeloid leukemia through regulating miR-4260/NR3C2. Cancer Biol Ther 2020; 21:615-622. [PMID: 32338183 DOI: 10.1080/15384047.2020.1740054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Acute myeloid leukemia (AML) is a prevalent class of blood disease with a high occurrence rate and relapse rate. The role of dysregulated microRNAs (miRNAs) in AML is emerging. MiR-4260 was identified to be a carcinogenic miRNA in colorectal cancer, but never has it been reported in AML. We aimed to study the function and mechanism of miR-4260 in AML. The miR-4260 level was higher in AML cell lines than the normal cell lines. Inhibition of miR-4260 hindered proliferation and increased apoptosis of AML cells. Mechanistically, long intergenic non-protein coding RNA 1128 (LINC01128) competed with nuclear receptor subfamily 3 group C member 2 (NR3C2) for miR-4260 so as to upregulate NR3C2. We identified the reduced levels of LINC01128 and NR3C2 in AML and it was suggested through rescue assays that LINC01128 repressed AML progression through regulating miR-4260/NR3C2 axis. In conclusion, we firstly uncovered that LINC01128 resisted acute myeloid leukemia through regulating miR-4260/NR3C2, providing novel clues for the treatment improvement of AML.
Collapse
Affiliation(s)
- Haixia Li
- The Third Department of Rehabilitation (Department of Integrated Chinese and Western Medicine), Hunan Children's Hospital , Changsha, Hunan, China.,Hunan University of Chinese Medicine , Changsha, Hunan, China
| | - Xuefei Tian
- College of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine
| | - Paoqiu Wang
- The Third Department of Rehabilitation (Department of Integrated Chinese and Western Medicine), Hunan Children's Hospital , Changsha, Hunan, China
| | - Jihong Hu
- The First Department of Rehabilitation, Hunan Children's Hospital , Changsha, Hunan, China
| | - Rong Qin
- The Second Department of Rehabilitation, Hunan Children's Hospital , Changsha, Hunan, China
| | - Ronghua Xu
- Department of Hematology, The First Hospital of Hunan University of Traditional Chinese Medicine , Changsha, Hunan, China
| | - Kai Liu
- Department of Hematology, The First Hospital of Hunan University of Traditional Chinese Medicine , Changsha, Hunan, China
| | - Jingquan Hao
- Department of Hematology, The First Hospital of Hunan University of Traditional Chinese Medicine , Changsha, Hunan, China
| | - Nie Tian
- Department of Hematology, The First Hospital of Hunan University of Traditional Chinese Medicine , Changsha, Hunan, China
| |
Collapse
|
20
|
Pan-cancer analyses of human nuclear receptors reveal transcriptome diversity and prognostic value across cancer types. Sci Rep 2020; 10:1873. [PMID: 32024906 PMCID: PMC7002682 DOI: 10.1038/s41598-020-58842-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/08/2020] [Indexed: 12/19/2022] Open
Abstract
The human nuclear receptor (NR) superfamily comprises 48 ligand-dependent transcription factors that play regulatory roles in physiology and pathophysiology. In cancer, NRs have long served as predictors of disease stratification, treatment response, and clinical outcome. The Cancer Genome Atlas (TCGA) Pan-Cancer project provides a wealth of genetic data for a large number of human cancer types. Here, we examined NR transcriptional activity in 8,526 patient samples from 33 TCGA ‘Pan-Cancer’ diseases and 11 ‘Pan-Cancer’ organ systems using RNA sequencing data. The web-based Kaplan-Meier (KM) plotter tool was then used to evaluate the prognostic potential of NR gene expression in 21/33 cancer types. Although, most NRs were significantly underexpressed in cancer, NR expression (moderate to high expression levels) was predominantly restricted (46%) to specific tissues, particularly cancers representing gynecologic, urologic, and gastrointestinal ‘Pan-Cancer’ organ systems. Intriguingly, a relationship emerged between recurrent positive pairwise correlation of Class IV NRs in most cancers. NR expression was also revealed to play a profound effect on patient overall survival rates, with ≥5 prognostic NRs identified per cancer type. Taken together, these findings highlighted the complexity of NR transcriptional networks in cancer and identified novel therapeutic targets for specific cancer types.
Collapse
|
21
|
Fernandez AI, Geng X, Chaldekas K, Harris B, Duttargi A, Berry VL, Berry DL, Mahajan A, Cavalli LR, Győrffy B, Tan M, Riggins RB. The orphan nuclear receptor estrogen-related receptor beta (ERRβ) in triple-negative breast cancer. Breast Cancer Res Treat 2020; 179:585-604. [PMID: 31741180 PMCID: PMC7153462 DOI: 10.1007/s10549-019-05485-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Triple-negative breast cancer (TNBC)/basal-like breast cancer (BLBC) is a highly aggressive form of breast cancer. We previously reported that a small molecule agonist ligand for the orphan nuclear receptor estrogen-related receptor beta (ERRβ or ESRRB) has growth inhibitory and anti-mitotic activity in TNBC cell lines. In this study, we evaluate the association of ESRRB mRNA, copy number levels, and protein expression with demographic, clinicopathological, and gene expression features in breast tumor clinical specimens. METHODS ESRRB mRNA-level expression and clinical associations were analyzed using RNAseq data. Array-based comparative genomic hybridization determined ESRRB copy number in African-American and Caucasian women. Transcription factor activity was measured using promoter-reporter luciferase assays in TNBC cell lines. Semi-automatic quantification of immunohistochemistry measured ERRβ protein expression on a 150-patient tissue microarray series. RESULTS ESRRB mRNA expression is significantly lower in TNBC/BLBC versus other breast cancer subtypes. There is no evidence of ESRRB copy number loss. ESRRB mRNA expression is correlated with the expression of genes associated with neuroactive ligand-receptor interaction, metabolic pathways, and deafness. These genes contain G/C-rich transcription factor binding motifs. The ESRRB message is alternatively spliced into three isoforms, which we show have different transcription factor activity in basal-like versus other TNBC cell lines. We further show that the ERRβ2 and ERRβsf isoforms are broadly expressed in breast tumors at the protein level. CONCLUSIONS Decreased ESRRB mRNA expression and distinct patterns of ERRβ isoform subcellular localization and transcription factor activity are key features in TNBC/BLBC.
Collapse
Affiliation(s)
- Aileen I Fernandez
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA.
- Department of Oncology, Georgetown University, 3970 Reservoir Rd NW, E412 Research Bldg., Washington, DC, 20057, USA.
| | - Xue Geng
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - Krysta Chaldekas
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - Brent Harris
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - Anju Duttargi
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - V Layne Berry
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - Deborah L Berry
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - Akanksha Mahajan
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - Luciane R Cavalli
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
- Research Institute Pelé Pequeno Príncipe Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group and Semmelweis University 2nd Department of Pediatrics, Budapest, Hungary
| | - Ming Tan
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA
| | - Rebecca B Riggins
- Department of Oncology, Georgetown University, Washington, DC, 22209, USA.
- Department of Oncology, Georgetown University, 3970 Reservoir Rd NW, E412 Research Bldg., Washington, DC, 20057, USA.
| |
Collapse
|
22
|
Muralidhar S, Filia A, Nsengimana J, Poźniak J, O'Shea SJ, Diaz JM, Harland M, Randerson-Moor JA, Reichrath J, Laye JP, van der Weyden L, Adams DJ, Bishop DT, Newton-Bishop J. Vitamin D-VDR Signaling Inhibits Wnt/β-Catenin-Mediated Melanoma Progression and Promotes Antitumor Immunity. Cancer Res 2019; 79:5986-5998. [PMID: 31690667 DOI: 10.1158/0008-5472.can-18-3927] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/12/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022]
Abstract
1α,25-Dihydroxyvitamin D3 signals via the vitamin D receptor (VDR). Higher serum vitamin D is associated with thinner primary melanoma and better outcome, although a causal mechanism has not been established. As patients with melanoma commonly avoid sun exposure, and consequent vitamin D deficiency might worsen outcomes, we interrogated 703 primary melanoma transcriptomes to understand the role of vitamin D-VDR signaling and replicated the findings in The Cancer Genome Atlas metastases. VDR expression was independently protective for melanoma-related death in both primary and metastatic disease. High tumor VDR expression was associated with upregulation of pathways mediating antitumor immunity and corresponding with higher imputed immune cell scores and histologically detected tumor-infiltrating lymphocytes. High VDR-expressing tumors had downregulation of proliferative pathways, notably Wnt/β-catenin signaling. Deleterious low VDR levels resulted from promoter methylation and gene deletion in metastases. Vitamin D deficiency (<25 nmol/L ∼ 10 ng/mL) shortened survival in primary melanoma in a VDR-dependent manner. In vitro functional validation studies showed that elevated vitamin D-VDR signaling inhibited Wnt/β-catenin signaling genes. Murine melanoma cells overexpressing VDR produced fewer pulmonary metastases than controls in tail-vein metastasis assays. In summary, vitamin D-VDR signaling contributes to controlling pro-proliferative/immunosuppressive Wnt/β-catenin signaling in melanoma and this is associated with less metastatic disease and stronger host immune responses. This is evidence of a causal relationship between vitamin D-VDR signaling and melanoma survival, which should be explored as a therapeutic target in primary resistance to checkpoint blockade. SIGNIFICANCE: VDR expression could potentially be used as a biomarker to stratify patients with melanoma that may respond better to immunotherapy.
Collapse
Affiliation(s)
- Sathya Muralidhar
- University of Leeds School of Medicine, Leeds, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Anastasia Filia
- Centre for Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Joanna Poźniak
- University of Leeds School of Medicine, Leeds, United Kingdom
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sally J O'Shea
- University of Leeds School of Medicine, Leeds, United Kingdom
- Faculty of Medicine and Health, University College Cork, Cork, Ireland
- Mater Private Hospital Cork, Citygate, Mahon, Cork, Ireland
| | - Joey M Diaz
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Mark Harland
- University of Leeds School of Medicine, Leeds, United Kingdom
| | | | - Jörg Reichrath
- Center for Clinical and Experimental Photodermatology, The Saarland University Hospital, Homburg, Germany
| | - Jonathan P Laye
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Louise van der Weyden
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - D T Bishop
- University of Leeds School of Medicine, Leeds, United Kingdom
| | | |
Collapse
|
23
|
Joseph C, Al-Izzi S, Alsaleem M, Kurozumi S, Toss MS, Arshad M, Goh FQ, Alshankyty IM, Aleskandarany MA, Ali S, Ellis IO, Mongan NP, Green AR, Rakha EA. Retinoid X receptor gamma (RXRG) is an independent prognostic biomarker in ER-positive invasive breast cancer. Br J Cancer 2019; 121:776-785. [PMID: 31558802 PMCID: PMC6889395 DOI: 10.1038/s41416-019-0589-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/22/2019] [Accepted: 09/05/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Retinoid X Receptor Gamma (RXRG) is a member of the nuclear receptor superfamily and plays a role in tumour suppression. This study aims to explore the prognostic significance of RXRG in breast cancer. METHODS Primary breast cancer tissue microarrays (n = 923) were immuno-stained for RXRG protein and correlated with clinicopathological features, and patient outcome. RESULTS Nuclear RXRG expression was significantly associated with smaller tumour size (p = 0.036), lower grade (p < 0.001), lobular histology (p = 0.016), lower Nottingham Prognostic Index (p = 0.04) and longer breast cancer-specific survival (p < 0.001), and longer time to distant metastasis (p = 0.002). RXRG expression showed positive association with oestrogen receptor (ER)-related biomarkers: GATA3, FOXA1, STAT3 and MED7 (all p < 0.001) and a negative correlation with the Ki67 proliferation marker. Multivariate analysis demonstrated RXRG protein as an independent predictor of longer breast cancer-specific survival and distant metastasis-free survival. In the external validation cohorts, RXRG expression was associated with improved patients' outcome (p = 0.025). In ER-positive tumours, high expression of RXRG was associated with better patient outcome regardless of adjuvant systemic therapy. ER signalling pathway was the top predicted master regulator of RXRG protein expression (p = 0.005). CONCLUSION This study provides evidence for the prognostic value of RXRG in breast cancer particularly the ER-positive tumours.
Collapse
Affiliation(s)
- Chitra Joseph
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Sara Al-Izzi
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Mansour Alsaleem
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Sasagu Kurozumi
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Michael S Toss
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK.,Histopathology Department, Faculty of Medicine, Menoufia University, Shebin El Kom, Egypt
| | - Maariya Arshad
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Fang Qin Goh
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Ibraheem M Alshankyty
- Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed A Aleskandarany
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK.,Histopathology Department, Faculty of Medicine, Menoufia University, Shebin El Kom, Egypt
| | - Simak Ali
- Faculty of Medicine, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Ian O Ellis
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Nigel P Mongan
- Cancer Biology and Translational Research, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham and Nottingham University Hospital NHS Trust, Nottingham, UK. .,Histopathology Department, Faculty of Medicine, Menoufia University, Shebin El Kom, Egypt.
| |
Collapse
|
24
|
Ide H, Inoue S, Mizushima T, Kashiwagi E, Zheng Y, Miyamoto H. Role of glucocorticoid signaling in urothelial tumorigenesis: Inhibition by prednisone presumably through inducing glucocorticoid receptor transrepression. Mol Carcinog 2019; 58:2297-2305. [PMID: 31535408 DOI: 10.1002/mc.23118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/31/2022]
Abstract
Glucocorticoids, including dexamethasone (DEX) and prednisone (PRED), have been prescribed in patients with neoplastic disease as cytotoxic agents or comedications. Nonetheless, it remains uncertain whether they have an impact on the development of bladder cancer. We, therefore, assessed the functional role of the glucocorticoid-mediated glucocorticoid receptor (GR) signaling in urothelial tumorigenesis. Tumor formation was significantly delayed in xenograft-bearing mice with implantation of control bladder cancer UMUC3 cells or nonneoplastic urothelial SVHUC cells undergoing malignant transformation induced by a chemical carcinogen 3-methylcholanthrene (MCA), compared with respective GR knockdown xenografts. Using the in vitro system with MCA-SVHUC cells, we screened 11 GR ligands, including DEX, and found significant inhibitory effects of PRED on their neoplastic transformation. The effects of PRED were restored by a GR antagonist RU486 in GR-positive MCA-SVHUC cells, while PRED failed to inhibit the neoplastic transformation of GR knockdown cells. Significant decreases in the expression levels of oncogenes (c-Fos/c-Jun) and significant increases in those of a tumor suppressor UGT1A were seen in MCA-SVHUC-control cells (vs GR-short hairpin RNA) or PRED-treated MCA-SVHUC-control cells (vs mock). In addition, N-butyl-N-(4-hydroxybutyl) nitrosamine induced bladder cancer in all of eight mock-treated mice vs seven (87.5%) of DEX-treated (P = .302) or four (50%) of PRED-treated (P = .021) animals. Finally, DEX was found to considerably induce both transactivation (activation of glucocorticoid-response element mediated transcription and expression of its targets) and transrepression (suppression of nuclear factor-kappa B transactivation and expression of its regulated genes) of GR in SVHUC cells, while PRED more selectively induced GR transrepression. These findings suggest that PRED could prevent urothelial tumorigenesis presumably via inducing GR transrepression.
Collapse
Affiliation(s)
- Hiroki Ide
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Satoshi Inoue
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York.,James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York
| | - Taichi Mizushima
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York.,James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York
| | - Eiji Kashiwagi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yichun Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York
| | - Hiroshi Miyamoto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York.,James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York.,Department of Urology, University of Rochester Medical Center, Rochester, New York
| |
Collapse
|
25
|
Moens U, Macdonald A. Effect of the Large and Small T-Antigens of Human Polyomaviruses on Signaling Pathways. Int J Mol Sci 2019; 20:ijms20163914. [PMID: 31408949 PMCID: PMC6720190 DOI: 10.3390/ijms20163914] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 12/12/2022] Open
Abstract
Viruses are intracellular parasites that require a permissive host cell to express the viral genome and to produce new progeny virus particles. However, not all viral infections are productive and some viruses can induce carcinogenesis. Irrespective of the type of infection (productive or neoplastic), viruses hijack the host cell machinery to permit optimal viral replication or to transform the infected cell into a tumor cell. One mechanism viruses employ to reprogram the host cell is through interference with signaling pathways. Polyomaviruses are naked, double-stranded DNA viruses whose genome encodes the regulatory proteins large T-antigen and small t-antigen, and structural proteins that form the capsid. The large T-antigens and small t-antigens can interfere with several host signaling pathways. In this case, we review the interplay between the large T-antigens and small t-antigens with host signaling pathways and the biological consequences of these interactions.
Collapse
Affiliation(s)
- Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9019 Tromsø, Norway.
| | - Andrew Macdonald
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
26
|
Cheng HS, Lee JXT, Wahli W, Tan NS. Exploiting vulnerabilities of cancer by targeting nuclear receptors of stromal cells in tumor microenvironment. Mol Cancer 2019; 18:51. [PMID: 30925918 PMCID: PMC6441226 DOI: 10.1186/s12943-019-0971-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/21/2019] [Indexed: 12/27/2022] Open
Abstract
The tumor microenvironment is a complex and dynamic cellular community comprising the tumor epithelium and various tumor-supporting cells such as immune cells, fibroblasts, immunosuppressive cells, adipose cells, endothelial cells, and pericytes. The interplay between the tumor microenvironment and tumor cells represents a key contributor to immune evasiveness, physiological hardiness and the local and systemic invasiveness of malignant cells. Nuclear receptors are master regulators of physiological processes and are known to play pro-/anti-oncogenic activities in tumor cells. However, the actions of nuclear receptors in tumor-supporting cells have not been widely studied. Given the excellent druggability and extensive regulatory effects of nuclear receptors, understanding their biological functionality in the tumor microenvironment is of utmost importance. Therefore, the present review aims to summarize recent evidence about the roles of nuclear receptors in tumor-supporting cells and their implications for malignant processes such as tumor proliferation, evasion of immune surveillance, angiogenesis, chemotherapeutic resistance, and metastasis. Based on findings derived mostly from cell culture studies and a few in vivo animal cancer models, the functions of VDR, PPARs, AR, ER and GR in tumor-supporting cells are relatively well-characterized. Evidence for other receptors, such as RARβ, RORγ, and FXR, is limited yet promising. Hence, the nuclear receptor signature in the tumor microenvironment may harbor prognostic value. The clinical prospects of a tumor microenvironment-oriented cancer therapy exploiting the nuclear receptors in different tumor-supporting cells are also encouraging. The major challenge, however, lies in the ability to develop a highly specific drug delivery system to facilitate precision medicine in cancer therapy.
Collapse
Affiliation(s)
- Hong Sheng Cheng
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Jeannie Xue Ting Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Walter Wahli
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore, 308232, Singapore.,INRA ToxAlim, UMR1331, Chemin de Tournefeuille, Toulouse Cedex 3, France.,Center for Integrative Genomics, University of Lausanne, Le Génopode, CH-1015, Lausanne, Switzerland
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore, 308232, Singapore.
| |
Collapse
|
27
|
Nagata Y, Goto T, Miyamoto H. The Role of Mineralocorticoid Receptor Signaling in Genitourinary Cancers. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Yujiro Nagata
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Urology, University of Occupational and Environmental Health School of Medicine, Kitakyushu, Fukuoka 807-8555, Japan
| | - Takuro Goto
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Hiroshi Miyamoto
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Urology, University of Rochester Medical Center, Rochester, NY 14642, USA
| |
Collapse
|
28
|
Long MD, Singh PK, Russell JR, Llimos G, Rosario S, Rizvi A, van den Berg PR, Kirk J, Sucheston-Campbell LE, Smiraglia DJ, Campbell MJ. The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression. Oncogene 2019; 38:421-444. [PMID: 30120411 PMCID: PMC6336686 DOI: 10.1038/s41388-018-0450-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/25/2018] [Accepted: 06/26/2018] [Indexed: 01/22/2023]
Abstract
Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARγ) are commonly reduced in prostate cancer (PCa). Therefore, we sought to establish the cellular and gene regulatory consequences of reduced RARγ expression, and determine RARγ regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARγ levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RARγ cistrome, which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RARγ to regulate androgen signaling, RARγ knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RARγ downregulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RARγ expression and function. Capture of the miR-96 targetome by biotin-miR-96 identified that RARγ and a number of RARγ interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RARγ target genes (e.g., SOX15) that significantly associated with worse disease-free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p = 0.015). In summary, miR-96 targets a RARγ network to govern AR signaling, PCa progression and disease outcome.
Collapse
MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/mortality
- Adenocarcinoma/pathology
- Androgens
- Animals
- Cell Line, Tumor
- Disease Progression
- Enhancer Elements, Genetic
- Fetal Proteins/metabolism
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Kaplan-Meier Estimate
- Male
- Mice
- MicroRNAs/physiology
- Microtubule-Associated Proteins/metabolism
- Neoplasm Proteins/physiology
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/metabolism
- Neoplasms, Hormone-Dependent/mortality
- Neoplasms, Hormone-Dependent/pathology
- Nuclear Proteins/metabolism
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/mortality
- Prostatic Neoplasms/pathology
- RNA Interference
- RNA, Neoplasm/physiology
- RNA, Small Interfering/genetics
- Receptors, Androgen/metabolism
- Receptors, Retinoic Acid/physiology
- Signal Transduction
- Retinoic Acid Receptor gamma
Collapse
Affiliation(s)
- Mark D Long
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Prashant K Singh
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - James R Russell
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Gerard Llimos
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Spencer Rosario
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Abbas Rizvi
- College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick R van den Berg
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
- Leiden institute of Physics, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Jason Kirk
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Lara E Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Dominic J Smiraglia
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center (RPCCC), Buffalo, NY, 14263, USA
| | - Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, 536 Parks Hall, Columbus, OH, 43210, USA.
| |
Collapse
|
29
|
Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas. Nat Commun 2018; 9:5330. [PMID: 30552315 PMCID: PMC6294258 DOI: 10.1038/s41467-018-07232-8] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
Understanding metabolic dysregulation in different disease settings is vital for the safe and effective incorporation of metabolism-targeted therapeutics in the clinic. Here, using transcriptomic data for 10,704 tumor and normal samples from The Cancer Genome Atlas, across 26 disease sites, we present a novel bioinformatics pipeline that distinguishes tumor from normal tissues, based on differential gene expression for 114 metabolic pathways. We confirm pathway dysregulation in separate patient populations, demonstrating the robustness of our approach. Bootstrapping simulations were then applied to assess the biological significance of these alterations. We provide distinct examples of the types of analysis that can be accomplished with this tool to understand cancer specific metabolic dysregulation, highlighting novel pathways of interest, and patterns of metabolic flux, in both common and rare disease sites. Further, we show that Master Metabolic Transcriptional Regulators explain why metabolic differences exist, can segregate patient populations, and predict responders to different metabolism-targeted therapeutics.
Collapse
|
30
|
Zhao Z, Zhang M, Duan X, Deng T, Qiu H, Zeng G. Low NR3C2 levels correlate with aggressive features and poor prognosis in non‐distant metastatic clear‐cell renal cell carcinoma. J Cell Physiol 2018; 233:6825-6838. [PMID: 29693713 DOI: 10.1002/jcp.26550] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/16/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Zhijian Zhao
- Department of Urology and Guangdong Key Laboratory of Urology The First Affiliated Hospital of Guangzhou Medical University Guangzhou China
| | - Mengping Zhang
- Department of Oncology The First Affiliated Hospital of Sun Yat‐sen University Guangzhou China
| | - Xiaolu Duan
- Department of Urology and Guangdong Key Laboratory of Urology The First Affiliated Hospital of Guangzhou Medical University Guangzhou China
| | - Tuo Deng
- Department of Urology and Guangdong Key Laboratory of Urology The First Affiliated Hospital of Guangzhou Medical University Guangzhou China
| | - Huijuan Qiu
- Department of VIP, Sun Yat‐Sen University Cancer Center, State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Guangzhou China
| | - Guohua Zeng
- Department of Urology and Guangdong Key Laboratory of Urology The First Affiliated Hospital of Guangzhou Medical University Guangzhou China
| |
Collapse
|
31
|
Dhiman VK, Bolt MJ, White KP. Nuclear receptors in cancer — uncovering new and evolving roles through genomic analysis. Nat Rev Genet 2017; 19:160-174. [DOI: 10.1038/nrg.2017.102] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
32
|
Abstract
The vitamin D receptor (VDR) binds the secosteroid hormone 1,25(OH)2D3 with high affinity and regulates gene programs that control a serum calcium levels, as well as cell proliferation and differentiation. A significant focus has been to exploit the VDR in cancer settings. Although preclinical studies have been strongly encouraging, to date clinical trials have delivered equivocal findings that have paused the clinical translation of these compounds. However, it is entirely possible that mining of genomic data will help to refine precisely what are the key anticancer actions of vitamin D compounds and where these can be used most effectively.
Collapse
Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, 536 Parks Hall, Columbus, OH 43210, USA.
| | - Donald L Trump
- Department of Medicine, Inova Schar Cancer Institute, Virginia Commonwealth University, 3221 Gallows Road, Fairfax, VA 22031, USA
| |
Collapse
|
33
|
Long MD, Campbell MJ. Integrative genomic approaches to dissect clinically-significant relationships between the VDR cistrome and gene expression in primary colon cancer. J Steroid Biochem Mol Biol 2017; 173:130-138. [PMID: 28027912 DOI: 10.1016/j.jsbmb.2016.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/01/2016] [Accepted: 12/23/2016] [Indexed: 12/13/2022]
Abstract
Recently, we undertook a pan-cancer analyses of the nuclear hormone receptor (NR) superfamily in The Cancer Genome Atlas (TCGA), and revealed that the vitamin D receptor (NR1I1/VDR) was commonly and significantly down-regulated specifically in colon adenocarcinoma cohort (COAD). To examine the consequence of down-regulated VDR expression we re-analyzed VDR chromatin immunoprecipitation sequencing (ChIP-Seq) data from LS180 colon cancer cells (GSE31939). This analysis identified 1809 loci that displayed significant (p.adj<0.01) differential binding of the VDR in response 1,25(OH)2D3 treatment; 947 peaks annotated to 672 genes. We examined expression patterns in the COAD cohort of 286 tumors compared to 41 normal samples and revealed that VDR bound genes were significantly positively correlated to VDR expression compared to the background transcriptome, suggesting direct regulation by VDR. Gene set enrichment analyses revealed significant enrichment for genes known to be regulated by a number of other transcription factors including SMADs and JUN. Filtering VDR associated genes for those that were commonly and significantly altered in COAD revealed a cohort of 27 differentially expressed genes. The expression patterns of these genes clustered tumors and significantly associated with disease free survival. For instance, males with low expression of Lectin, Galactoside Binding Soluble 4 (LGALS4, encodes the colon tumor suppressor, Galactin 4) had significantly shorted disease free survival. These analyses suggest that reduced expression of VDR in colon cancer (but neither loss nor mutation) changes the actions of the VDR by both dampening the expression of tumor suppressors (e.g. LGALS4) whilst either stabilizing or not down-regulating expression of oncogenes (e.g. Carbonic Anhydrase 9 (CA9)). These integrative genomic approaches are relatively generic and applicable to the study of any transcription factor.
Collapse
Affiliation(s)
- Mark D Long
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Moray J Campbell
- College of Pharmacy, Pharmaceutics and Pharmaceutical Chemistry, 536 Parks Hall, 500 West 12th Ave., The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
34
|
Campbell MJ. Bioinformatic approaches to interrogating vitamin D receptor signaling. Mol Cell Endocrinol 2017; 453:3-13. [PMID: 28288905 DOI: 10.1016/j.mce.2017.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022]
Abstract
Bioinformatics applies unbiased approaches to develop statistically-robust insight into health and disease. At the global, or "20,000 foot" view bioinformatic analyses of vitamin D receptor (NR1I1/VDR) signaling can measure where the VDR gene or protein exerts a genome-wide significant impact on biology; VDR is significantly implicated in bone biology and immune systems, but not in cancer. With a more VDR-centric, or "2000 foot" view, bioinformatic approaches can interrogate events downstream of VDR activity. Integrative approaches can combine VDR ChIP-Seq in cell systems where significant volumes of publically available data are available. For example, VDR ChIP-Seq studies can be combined with genome-wide association studies to reveal significant associations to immune phenotypes. Similarly, VDR ChIP-Seq can be combined with data from Cancer Genome Atlas (TCGA) to infer the impact of VDR target genes in cancer progression. Therefore, bioinformatic approaches can reveal what aspects of VDR downstream networks are significantly related to disease or phenotype.
Collapse
Affiliation(s)
- Moray J Campbell
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, 536 Parks Hall, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
35
|
Affiliation(s)
- Madduri Srinivasarao
- Purdue Institute for Drug
Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Philip S. Low
- Purdue Institute for Drug
Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
36
|
Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer. Sci Rep 2017; 7:44997. [PMID: 28349958 PMCID: PMC5368637 DOI: 10.1038/srep44997] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
In this study, an attempt has been made to identify expression-based gene biomarkers that can discriminate early and late stage of clear cell renal cell carcinoma (ccRCC) patients. We have analyzed the gene expression of 523 samples to identify genes that are differentially expressed in the early and late stage of ccRCC. First, a threshold-based method has been developed, which attained a maximum accuracy of 71.12% with ROC 0.67 using single gene NR3C2. To improve the performance of threshold-based method, we combined two or more genes and achieved maximum accuracy of 70.19% with ROC of 0.74 using eight genes on the validation dataset. These eight genes include four underexpressed (NR3C2, ENAM, DNASE1L3, FRMPD2) and four overexpressed (PLEKHA9, MAP6D1, SMPD4, C11orf73) genes in the late stage of ccRCC. Second, models were developed using state-of-art techniques and achieved maximum accuracy of 72.64% and 0.81 ROC using 64 genes on validation dataset. Similar accuracy was obtained on 38 genes selected from subset of genes, involved in cancer hallmark biological processes. Our analysis further implied a need to develop gender-specific models for stage classification. A web server, CancerCSP, has been developed to predict stage of ccRCC using gene expression data derived from RNAseq experiments.
Collapse
|
37
|
The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate Cancer. Biomolecules 2017; 7:biom7010015. [PMID: 28216563 PMCID: PMC5372727 DOI: 10.3390/biom7010015] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/23/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022] Open
Abstract
The process of DNA CpG methylation has been extensively investigated for over 50 years and revealed associations between changing methylation status of CpG islands and gene expression. As a result, DNA CpG methylation is implicated in the control of gene expression in developmental and homeostasis processes, as well as being a cancer-driver mechanism. The development of genome-wide technologies and sophisticated statistical analytical approaches has ushered in an era of widespread analyses, for example in the cancer arena, of the relationships between altered DNA CpG methylation, gene expression, and tumor status. The remarkable increase in the volume of such genomic data, for example, through investigators from the Cancer Genome Atlas (TCGA), has allowed dissection of the relationships between DNA CpG methylation density and distribution, gene expression, and tumor outcome. In this manner, it is now possible to test that the genome-wide correlations are measurable between changes in DNA CpG methylation and gene expression. Perhaps surprisingly is that these associations can only be detected for hundreds, but not thousands, of genes, and the direction of the correlations are both positive and negative. This, perhaps, suggests that CpG methylation events in cancer systems can act as disease drivers but the effects are possibly more restricted than suspected. Additionally, the positive and negative correlations suggest direct and indirect events and an incomplete understanding. Within the prostate cancer TCGA cohort, we examined the relationships between expression of genes that control DNA methylation, known targets of DNA methylation and tumor status. This revealed that genes that control the synthesis of S-adenosyl-l-methionine (SAM) associate with altered expression of DNA methylation targets in a subset of aggressive tumors.
Collapse
|