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Porras L, Ismail H, Mader S. Positive Regulation of Estrogen Receptor Alpha in Breast Tumorigenesis. Cells 2021; 10:cells10112966. [PMID: 34831189 PMCID: PMC8616513 DOI: 10.3390/cells10112966] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 12/31/2022] Open
Abstract
Estrogen receptor alpha (ERα, NR3A1) contributes through its expression in different tissues to a spectrum of physiological processes, including reproductive system development and physiology, bone mass maintenance, as well as cardiovascular and central nervous system functions. It is also one of the main drivers of tumorigenesis in breast and uterine cancer and can be targeted by several types of hormonal therapies. ERα is expressed in a subset of luminal cells corresponding to less than 10% of normal mammary epithelial cells and in over 70% of breast tumors (ER+ tumors), but the basis for its selective expression in normal or cancer tissues remains incompletely understood. The mapping of alternative promoters and regulatory elements has delineated the complex genomic structure of the ESR1 gene and shed light on the mechanistic basis for the tissue-specific regulation of ESR1 expression. However, much remains to be uncovered to better understand how ESR1 expression is regulated in breast cancer. This review recapitulates the current body of knowledge on the structure of the ESR1 gene and the complex mechanisms controlling its expression in breast tumors. In particular, we discuss the impact of genetic alterations, chromatin modifications, and enhanced expression of other luminal transcription regulators on ESR1 expression in tumor cells.
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Schumacher FR, Basourakos SP, Lewicki PJ, Vince R, Spratt DE, Barbieri CE, Shoag JE. Race and Genetic Alterations in Prostate Cancer. JCO Precis Oncol 2021; 5:PO.21.00324. [PMID: 34746633 PMCID: PMC8563071 DOI: 10.1200/po.21.00324] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Fredrick R. Schumacher
- Fredrick R. Schumacher, PhD, Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH; Spyridon P. Basourakos, MD, and Patrick J. Lewicki, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; Randy Vince, MD, Department of Urology, University of Michigan, Ann Arbor, MI; Daniel E. Spratt, MD, Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH; Christopher E. Barbieri, MD, PhD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; and Jonathan E. Shoag, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Spyridon P. Basourakos
- Fredrick R. Schumacher, PhD, Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH; Spyridon P. Basourakos, MD, and Patrick J. Lewicki, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; Randy Vince, MD, Department of Urology, University of Michigan, Ann Arbor, MI; Daniel E. Spratt, MD, Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH; Christopher E. Barbieri, MD, PhD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; and Jonathan E. Shoag, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Patrick J. Lewicki
- Fredrick R. Schumacher, PhD, Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH; Spyridon P. Basourakos, MD, and Patrick J. Lewicki, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; Randy Vince, MD, Department of Urology, University of Michigan, Ann Arbor, MI; Daniel E. Spratt, MD, Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH; Christopher E. Barbieri, MD, PhD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; and Jonathan E. Shoag, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Randy Vince
- Fredrick R. Schumacher, PhD, Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH; Spyridon P. Basourakos, MD, and Patrick J. Lewicki, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; Randy Vince, MD, Department of Urology, University of Michigan, Ann Arbor, MI; Daniel E. Spratt, MD, Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH; Christopher E. Barbieri, MD, PhD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; and Jonathan E. Shoag, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Daniel E. Spratt
- Fredrick R. Schumacher, PhD, Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH; Spyridon P. Basourakos, MD, and Patrick J. Lewicki, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; Randy Vince, MD, Department of Urology, University of Michigan, Ann Arbor, MI; Daniel E. Spratt, MD, Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH; Christopher E. Barbieri, MD, PhD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; and Jonathan E. Shoag, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Christopher E. Barbieri
- Fredrick R. Schumacher, PhD, Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH; Spyridon P. Basourakos, MD, and Patrick J. Lewicki, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; Randy Vince, MD, Department of Urology, University of Michigan, Ann Arbor, MI; Daniel E. Spratt, MD, Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH; Christopher E. Barbieri, MD, PhD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; and Jonathan E. Shoag, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Jonathan E. Shoag
- Fredrick R. Schumacher, PhD, Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH; Spyridon P. Basourakos, MD, and Patrick J. Lewicki, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; Randy Vince, MD, Department of Urology, University of Michigan, Ann Arbor, MI; Daniel E. Spratt, MD, Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH; Christopher E. Barbieri, MD, PhD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY; and Jonathan E. Shoag, MD, Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH
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Dai S, Qu L, Li J, Chen Y. Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations. Nucleic Acids Res 2021; 49:10235-10249. [PMID: 34551426 PMCID: PMC8501956 DOI: 10.1093/nar/gkab807] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 01/12/2023] Open
Abstract
Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors that play numerous regulatory roles in eukaryotes during developmental and adult life. Dysfunction of FOX proteins has been implicated in a variety of human diseases, including cancer, neurodevelopment disorders and genetic diseases. The FOX family members share a highly conserved DNA-binding domain (DBD), which is essential for DNA recognition, binding and function. Since the first FOX structure was resolved in 1993, >30 FOX structures have been reported to date. It is clear now that the structure and DNA recognition mechanisms vary among FOX members; however, a systematic review on this aspect is lacking. In this manuscript, we present an overview of the mechanisms by which FOX transcription factors bind DNA, including protein structures, DNA binding properties and disease-causing mutations. This review should enable a better understanding of FOX family transcription factors for basic researchers and clinicians.
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Affiliation(s)
- Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Linzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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54
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Wang Y, Yu J. Dissecting multiple roles of SUMOylation in prostate cancer. Cancer Lett 2021; 521:88-97. [PMID: 34464672 DOI: 10.1016/j.canlet.2021.08.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022]
Abstract
Protein modification with small ubiquitin-like modifiers (SUMOs) plays dual roles in prostate cancer (PCa) tumorigenesis and development. Any intermediary of the SUMO conjugation cycle going awry may forfeit the balance between tumorigenic potential and anticancer effects. Deregulated SUMOylation on the androgen receptor and oncoproteins also takes part in this pathological process, as exemplified by STAT3/NF-κB and tumor suppressors such as PTEN and p53. Here, we outline recent developments and discoveries of SUMOylation in PCa and present an overview of its multiple roles in PCa tumorigenesis/promotion and suppression, while elucidating its potential as a therapeutic target for PCa.
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Affiliation(s)
- Yishu Wang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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55
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Ren N, Liu Q, Yan L, Huang Q. Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition. Int J Mol Sci 2021; 22:8792. [PMID: 34445492 PMCID: PMC8395720 DOI: 10.3390/ijms22168792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
Functional characterization of cancer risk-associated single nucleotide polymorphism (SNP) identified by genome-wide association studies (GWAS) has become a big challenge. To identify the regulatory risk SNPs that can lead to transcriptional misregulation, we performed parallel reporter gene assays with both alleles of 213 prostate cancer risk-associated GWAS SNPs in 22Rv1 cells. We disclosed 32 regulatory SNPs that exhibited different regulatory activities with two alleles. For one of the regulatory SNPs, rs684232, we found that the variation altered chromatin binding of transcription factor FOXA1 on the DNA region and led to aberrant gene expression of VPS53, FAM57A, and GEMIN4, which play vital roles in prostate cancer malignancy. Our findings reveal the roles and underlying mechanism of rs684232 in prostate cancer progression and hold great promise in benefiting prostate cancer patients with prognostic prediction and target therapies.
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Affiliation(s)
| | | | | | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; (N.R.); (Q.L.); (L.Y.)
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56
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Somatic Alterations Impact AR Transcriptional Activity and Efficacy of AR-Targeting Therapies in Prostate Cancer. Cancers (Basel) 2021; 13:cancers13163947. [PMID: 34439101 PMCID: PMC8393938 DOI: 10.3390/cancers13163947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary For patients whose prostate cancer spreads beyond the confines of the prostate, treatment options continue to increase. However, we are missing the information that is needed to choose for each patient the best treatment at each step of his cancer progression so we can ensure that maximal remissions and prolonged survival are achieved. In this review, we examine whether a better understanding of how the activity of the target for the default first treatment, the androgen receptor, is regulated in prostate cancer tissues can improve prostate cancer treatment plans. We consider the evidence for variability of androgen receptor activity among patients and examine the molecular basis for this variable action. We summarize clinical evidence supporting that information on a prostate cancer’s genomic composition may inform on its level of androgen receptor action, which may facilitate choice for the most effective first-line therapy and ultimately improve prostate cancer treatment plans overall. Abstract Inhibiting the activity of the ligand-activated transcription factor androgen receptor (AR) is the default first-line treatment for metastatic prostate cancer (CaP). Androgen deprivation therapy (ADT) induces remissions, however, their duration varies widely among patients. The reason for this heterogeneity is not known. A better understanding of its molecular basis may improve treatment plans and patient survival. AR’s transcriptional activity is regulated in a context-dependent manner and relies on an interplay between its associated transcriptional regulators, DNA recognition motifs, and ligands. Alterations in one or more of these factors induce shifts in the AR cistrome and transcriptional output. Significant variability in AR activity is seen in both castration-sensitive (CS) and castration-resistant CaP (CRPC). Several AR transcriptional regulators undergo somatic alterations that impact their function in clinical CaPs. Some alterations occur in a significant fraction of cases, resulting in CaP subtypes, while others affect only a few percent of CaPs. Evidence is emerging that these alterations may impact the response to CaP treatments such as ADT, radiation therapy, and chemotherapy. Here, we review the contribution of recurring somatic alterations on AR cistrome and transcriptional output and the efficacy of CaP treatments and explore strategies to use these insights to improve treatment plans and outcomes for CaP patients.
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Torres AG, Rodríguez-Escribà M, Marcet-Houben M, Santos Vieira HG, Camacho N, Catena H, Murillo Recio M, Rafels-Ybern À, Reina O, Torres FM, Pardo-Saganta A, Gabaldón T, Novoa EM, Ribas de Pouplana L. Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins. Nucleic Acids Res 2021; 49:7011-7034. [PMID: 34125917 PMCID: PMC8266599 DOI: 10.1093/nar/gkab461] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the transformation of the homodimeric bacterial enzyme TadA, which generates I34 in tRNAArg and tRNALeu, into the heterodimeric eukaryotic enzyme ADAT, which modifies up to eight different tRNAs. The emergence of ADAT and its larger set of substrates, strongly influenced the tRNA composition and codon usage of eukaryotic genomes. However, the selective advantages that drove the expansion of I34-tRNAs remain unknown. Here we investigate the functional relevance of I34-tRNAs in human cells and show that a full complement of these tRNAs is necessary for the translation of low-complexity protein domains enriched in amino acids cognate for I34-tRNAs. The coding sequences for these domains require codons translated by I34-tRNAs, in detriment of synonymous codons that use other tRNAs. I34-tRNA-dependent low-complexity proteins are enriched in functional categories related to cell adhesion, and depletion in I34-tRNAs leads to cellular phenotypes consistent with these roles. We show that the distribution of these low-complexity proteins mirrors the distribution of I34-tRNAs in the phylogenetic tree.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Marcet-Houben
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
| | | | - Noelia Camacho
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Helena Catena
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Murillo Recio
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Àlbert Rafels-Ybern
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Francisco Miguel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Ana Pardo-Saganta
- Centre for Applied Medical Research (CIMA Universidad de Navarra), Pamplona 31008, Spain
| | - Toni Gabaldón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,University Pompeu Fabra, Barcelona, Catalonia 08003, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
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58
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Paakinaho V, Palvimo JJ. Genome-wide crosstalk between steroid receptors in breast and prostate cancers. Endocr Relat Cancer 2021; 28:R231-R250. [PMID: 34137734 PMCID: PMC8345902 DOI: 10.1530/erc-21-0038] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022]
Abstract
Steroid receptors (SRs) constitute an important class of signal-dependent transcription factors (TFs). They regulate a variety of key biological processes and are crucial drug targets in many disease states. In particular, estrogen (ER) and androgen receptors (AR) drive the development and progression of breast and prostate cancer, respectively. Thus, they represent the main specific drug targets in these diseases. Recent evidence has suggested that the crosstalk between signal-dependent TFs is an important step in the reprogramming of chromatin sites; a signal-activated TF can expand or restrict the chromatin binding of another TF. This crosstalk can rewire gene programs and thus alter biological processes and influence the progression of disease. Lately, it has been postulated that there may be an important crosstalk between the AR and the ER with other SRs. Especially, progesterone (PR) and glucocorticoid receptor (GR) can reprogram chromatin binding of ER and gene programs in breast cancer cells. Furthermore, GR can take the place of AR in antiandrogen-resistant prostate cancer cells. Here, we review the current knowledge of the crosstalk between SRs in breast and prostate cancers. We emphasize how the activity of ER and AR on chromatin can be modulated by other SRs on a genome-wide scale. We also highlight the knowledge gaps in the interplay of SRs and their complex interactions with other signaling pathways and suggest how to experimentally fill in these gaps.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jorma J Palvimo
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Correspondence should be addressed to J J Palvimo:
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Kukkonen K, Taavitsainen S, Huhtala L, Uusi-Makela J, Granberg KJ, Nykter M, Urbanucci A. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers (Basel) 2021; 13:3325. [PMID: 34283056 PMCID: PMC8268970 DOI: 10.3390/cancers13133325] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of chromatin and epigenetics has been defined as the overarching cancer hallmark. By disrupting transcriptional regulation in normal cells and mediating tumor progression by promoting cancer cell plasticity, this process has the ability to mediate all defined hallmarks of cancer. In this review, we collect and assess evidence on the contribution of chromatin and epigenetic dysregulation in prostate cancer. We highlight important mechanisms leading to prostate carcinogenesis, the emergence of castration-resistance upon treatment with androgen deprivation therapy, and resistance to antiandrogens. We examine in particular the contribution of chromatin structure and epigenetics to cell lineage commitment, which is dysregulated during tumorigenesis, and cell plasticity, which is altered during tumor progression.
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Affiliation(s)
- Konsta Kukkonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Laura Huhtala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Joonas Uusi-Makela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Kirsi J. Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
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60
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Vettorazzi S, Nalbantoglu D, Gebhardt JCM, Tuckermann J. A guide to changing paradigms of glucocorticoid receptor function-a model system for genome regulation and physiology. FEBS J 2021; 289:5718-5743. [PMID: 34213830 DOI: 10.1111/febs.16100] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/08/2021] [Accepted: 07/01/2021] [Indexed: 12/13/2022]
Abstract
The glucocorticoid receptor (GR) is a bona fide ligand-regulated transcription factor. Cloned in the 80s, the GR has become one of the best-studied and clinically most relevant members of the nuclear receptor superfamily. Cooperative activity of GR with other transcription factors and a plethora of coregulators contribute to the tissue- and context-specific response toward the endogenous and pharmacological glucocorticoids (GCs). Furthermore, nontranscriptional activities in the cytoplasm are emerging as an additional function of GR. Over the past 40 years, the concepts of GR mechanisms of action had been constantly changing. Different methodologies in the pregenomic and genomic era of molecular biological research and recent cutting-edge technology in single-cell and single-molecule analysis are steadily evolving the views, how the GR in particular and transcriptional regulation in general act in physiological and pathological processes. In addition to the development of technologies for GR analysis, the use of model organisms provides insights how the GR in vivo executes GC action in tissue homeostasis, inflammation, and energy metabolism. The model organisms, namely the mouse, but also rats, zebrafish, and recently fruit flies carrying mutations of the GR became a major driving force to analyze the molecular function of GR in disease models. This guide provides an overview of the exciting research and paradigm shifts in the GR field from past to present with a focus on GR transcription factor networks, GR DNA-binding and single-cell analysis, and model systems.
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Affiliation(s)
- Sabine Vettorazzi
- Institute of Comparative Molecular Endocrinology (CME), Ulm University, Germany
| | - Denis Nalbantoglu
- Institute of Comparative Molecular Endocrinology (CME), Ulm University, Germany
| | | | - Jan Tuckermann
- Institute of Comparative Molecular Endocrinology (CME), Ulm University, Germany
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61
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Islam Z, Ali AM, Naik A, Eldaw M, Decock J, Kolatkar PR. Transcription Factors: The Fulcrum Between Cell Development and Carcinogenesis. Front Oncol 2021; 11:681377. [PMID: 34195082 PMCID: PMC8236851 DOI: 10.3389/fonc.2021.681377] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Higher eukaryotic development is a complex and tightly regulated process, whereby transcription factors (TFs) play a key role in controlling the gene regulatory networks. Dysregulation of these regulatory networks has also been associated with carcinogenesis. Transcription factors are key enablers of cancer stemness, which support the maintenance and function of cancer stem cells that are believed to act as seeds for cancer initiation, progression and metastasis, and treatment resistance. One key area of research is to understand how these factors interact and collaborate to define cellular fate during embryogenesis as well as during tumor development. This review focuses on understanding the role of TFs in cell development and cancer. The molecular mechanisms of cell fate decision are of key importance in efforts towards developing better protocols for directed differentiation of cells in research and medicine. We also discuss the dysregulation of TFs and their role in cancer progression and metastasis, exploring TF networks as direct or indirect targets for therapeutic intervention, as well as specific TFs’ potential as biomarkers for predicting and monitoring treatment responses.
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Affiliation(s)
- Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Ameena Mohamed Ali
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Adviti Naik
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Mohamed Eldaw
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Prasanna R Kolatkar
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
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62
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Forkhead Transcription Factors in Health and Disease. Trends Genet 2021; 37:460-475. [DOI: 10.1016/j.tig.2020.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
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63
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Increased Hospitalization and Mortality from COVID-19 in Prostate Cancer Patients. Cancers (Basel) 2021; 13:cancers13071630. [PMID: 33915795 PMCID: PMC8037308 DOI: 10.3390/cancers13071630] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cancer patients with COVID-19 have a poor disease course. Among tumor types, prostate cancer and COVID-19 share several risk factors, and the interaction of prostate cancer and COVID-19 is purported to have an adverse outcome. METHODS This was a single-institution retrospective study on 286,609 patients who underwent the COVID-19 test at Mount Sinai Hospital system from March 2020 to December 2020. Chi-square/Fisher's exact tests were used to summarize baseline characteristics of categorical data, and Mann-Whitney U test was used for continuous variables. Univariable logistic regression analysis to compare the hospitalization and mortality rates and the strength of association was obtained by the odds ratio and confidence interval. RESULTS This study aimed to compare hospitalization and mortality rates between men with COVID-19 and prostate cancer and those who were COVID-19-positive with non-prostate genitourinary malignancy or any solid cancer, and with breast cancer patients. We also compared our studies to others that reported the incidence and severity of COVID-19 in prostate cancer patients. Our studies highlight that patients with prostate cancer had higher susceptibility to COVID-19-related pathogenesis, resulting in higher mortality and hospitalization rates. Hospitalization and mortality rates were higher in prostate cancer patients with COVID-19 when compared with COVID-19 patients with non-prostate genitourinary (GU) malignancies.
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64
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Gupta S, Halabi S, Kemeny G, Anand M, Giannakakou P, Nanus DM, George DJ, Gregory SG, Armstrong AJ. Circulating Tumor Cell Genomic Evolution and Hormone Therapy Outcomes in Men with Metastatic Castration-Resistant Prostate Cancer. Mol Cancer Res 2021; 19:1040-1050. [PMID: 33771885 DOI: 10.1158/1541-7786.mcr-20-0975] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/11/2021] [Accepted: 03/01/2021] [Indexed: 01/24/2023]
Abstract
Men with circulating tumor cell (CTC) AR-V7-positive metastatic castration-resistant prostate cancer (mCRPC) have worse outcomes when treated with enzalutamide/abiraterone. However, most men lack CTC AR-V7 detection, and additional predictive biomarkers are needed. We conducted a retrospective secondary analysis of the prospective PROPHECY trial (NCT02269982) of men with mCRPC undergoing treatment with enzalutamide/abiraterone, analyzing pooled CTC and germline DNA for whole-genome copy-number alterations (CNA) in 73 samples from 48 men over time along with pooled CTC and germline whole-exome sequencing on 22 paired samples before and following progression on androgen receptor (AR) inhibitor therapy to identify somatic genomic alterations associated with acquired resistance. We observed broad interpatient and longitudinal CTC genomic heterogeneity from AR-V7-negative men with mCRPC, including common gains of KDM6A, MYCN, and AR, and loss of ZFHX3, BRCA1, and PTEN. Men who had progression-free survival of ≤3 months despite enzalutamide/abiraterone treatment were more likely to have baseline CTC genomic loss of CHD1, PTEN, PHLPP1, and ZFHX3 and gains of BRCA2, KDM5D, MYCN, and SPARC. After progression on abiraterone/enzalutamide, we observed clonal evolution of CTCs harboring TP53 mutations and gain of ATM, KDM6A, and MYC, and loss of NCOR1, PTEN, RB1, and RUNX2. CTC genomic findings were independently confirmed in a separate cohort of mCRPC men who progressed despite prior treatment with abiraterone/enzalutamide (NCT02204943). IMPLICATIONS: We identified common and reproducible genomic alterations in CTCs from AR-V7-negative mCRPC men associated with poor outcomes during enzalutamide/abiraterone treatment, including CNAs in genes linked to lineage plasticity and epigenetic signaling, DNA repair, AR, TP53/RB1, PTEN, and WNT pathways.
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Affiliation(s)
- Santosh Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolin.,Epic Sciences, San Diego, California
| | - Susan Halabi
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Gabor Kemeny
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Monika Anand
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | | | - David M Nanus
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Daniel J George
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Departments of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Simon G Gregory
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolin
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina. .,Departments of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
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65
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Elian FA, Are U, Ghosh S, Nuin P, Footz T, McMullen TPW, Brindley DN, Walter MA. FOXQ1 is Differentially Expressed Across Breast Cancer Subtypes with Low Expression Associated with Poor Overall Survival. BREAST CANCER-TARGETS AND THERAPY 2021; 13:171-188. [PMID: 33688250 PMCID: PMC7935334 DOI: 10.2147/bctt.s282860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022]
Abstract
Purpose Forkhead box Q1 (FOXQ1) has been shown to contribute to the development and progression of cancers, including ovarian and breast cancer (BC). However, research exploring FOXQ1 expression, copy number variation (CNV), and prognostic value across different BC subtypes is limited. Our purpose was to evaluate FOXQ1 mRNA expression, CNV, and prognostic value across BC subtypes. Materials and Methods We determined FOXQ1 expression and CNV in BC patient tumors using RT-qPCR and qPCR, respectively. We also analyzed FOXQ1 expression and CNV in BC cell lines in the CCLE database using K-means clustering. The prognostic value of FOXQ1 expression in the TCGA-BRCA database was assessed using univariate and multivariate Cox's regression analysis as well as using the online tools OncoLnc, GEPIA, and UALCAN. Results Our analyses reveal that FOXQ1 mRNA is differentially expressed between different subtypes of BC and is significantly decreased in luminal BC and HER2 patients when compared to normal breast tissue samples. Furthermore, analysis of BC cell lines showed that FOXQ1 mRNA expression was independent of CNV. Moreover, patients with low FOXQ1 mRNA expression had significantly poorer overall survival compared to those with high FOXQ1 mRNA expression. Finally, low FOXQ1 expression had a critical impact on the prognostic values of BC patients and was an independent predictor of overall survival when it was adjusted for BC subtypes and to two other FOX genes, FOXF2 and FOXM1. Conclusion Our study reveals for the first time that FOXQ1 is differentially expressed across BC subtypes and that low expression of FOXQ1 is indicative of poor prognosis in patients with BC.
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Affiliation(s)
- Fahed A Elian
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ubah Are
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Sunita Ghosh
- Department of Medical Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Mathematical and Statistical Sciences, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Paulo Nuin
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Tim Footz
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Todd P W McMullen
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - David N Brindley
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Michael A Walter
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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66
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Launonen KM, Paakinaho V, Sigismondo G, Malinen M, Sironen R, Hartikainen JM, Laakso H, Visakorpi T, Krijgsveld J, Niskanen EA, Palvimo JJ. Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells. Oncogene 2021; 40:4567-4579. [PMID: 34127815 PMCID: PMC8266679 DOI: 10.1038/s41388-021-01887-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/18/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023]
Abstract
Treatment of prostate cancer confronts resistance to androgen receptor (AR)-targeted therapies. AR-associated coregulators and chromatin proteins hold a great potential for novel therapy targets. Here, we employed a powerful chromatin-directed proteomics approach termed ChIP-SICAP to uncover the composition of chromatin protein network, the chromatome, around endogenous AR in castration resistant prostate cancer (CRPC) cells. In addition to several expected AR coregulators, the chromatome contained many nuclear proteins not previously associated with the AR. In the context of androgen signaling in CRPC cells, we further investigated the role of a known AR-associated protein, a chromatin remodeler SMARCA4 and that of SIM2, a transcription factor without a previous association with AR. To understand their role in chromatin accessibility and AR target gene expression, we integrated data from ChIP-seq, RNA-seq, ATAC-seq and functional experiments. Despite the wide co-occurrence of SMARCA4 and AR on chromatin, depletion of SMARCA4 influenced chromatin accessibility and expression of a restricted set of AR target genes, especially those involved in cell morphogenetic changes in epithelial-mesenchymal transition. The depletion also inhibited the CRPC cell growth, validating SMARCA4's functional role in CRPC cells. Although silencing of SIM2 reduced chromatin accessibility similarly, it affected the expression of a much larger group of androgen-regulated genes, including those involved in cellular responses to external stimuli and steroid hormone stimulus. The silencing also reduced proliferation of CRPC cells and tumor size in chick embryo chorioallantoic membrane assay, further emphasizing the importance of SIM2 in CRPC cells and pointing to the functional relevance of this potential prostate cancer biomarker in CRPC cells. Overall, the chromatome of AR identified in this work is an important resource for the field focusing on this important drug target.
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Affiliation(s)
- Kaisa-Mari Launonen
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ville Paakinaho
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Gianluca Sigismondo
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marjo Malinen
- grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Reijo Sironen
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M. Hartikainen
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
| | - Hanna Laakso
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tapio Visakorpi
- grid.412330.70000 0004 0628 2985Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland ,grid.511163.10000 0004 0518 4910Fimlab Laboratories, Tampere, Finland
| | - Jeroen Krijgsveld
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Einari A. Niskanen
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jorma J. Palvimo
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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67
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Wang L, Xu M, Kao CY, Tsai SY, Tsai MJ. Small molecule JQ1 promotes prostate cancer invasion via BET-independent inactivation of FOXA1. J Clin Invest 2020; 130:1782-1792. [PMID: 31874106 DOI: 10.1172/jci126327] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Recent findings have shown that inhibitors targeting bromodomain and extraterminal domain (BET) proteins, such as the small molecule JQ1, are potent growth inhibitors of many cancers and hold promise for cancer therapy. However, some reports have also revealed that JQ1 can activate additional oncogenic pathways and may affect epithelial-to-mesenchymal transition (EMT). Therefore, it is important to address the potential unexpected effect of JQ1 treatment, such as cell invasion and metastasis. Here, we showed that in prostate cancer, JQ1 inhibited cancer cell growth but promoted invasion and metastasis in a BET protein-independent manner. Multiple invasion pathways including EMT, bone morphogenetic protein (BMP) signaling, chemokine signaling, and focal adhesion were activated by JQ1 to promote invasion. Notably, JQ1 induced upregulation of invasion genes through inhibition of Forkhead box protein A1 (FOXA1), an invasion suppressor in prostate cancer. JQ1 directly interacted with FOXA1 and inactivated FOXA1 binding to its interacting repressors TLE3, HDAC7, and NFIC, thereby blocking FOXA1-repressive function and activating the invasion genes. Our findings indicate that JQ1 has an unexpected effect of promoting invasion in prostate cancer. Thus, the ill effect of JQ1 or its derived therapeutic agents cannot be ignored during cancer treatment, especially in FOXA1-related cancers.
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Affiliation(s)
- Leiming Wang
- Department of Molecular and Cellular Biology, and
| | - Mafei Xu
- Department of Molecular and Cellular Biology, and
| | | | - Sophia Y Tsai
- Department of Molecular and Cellular Biology, and.,Department of Medicine and Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, and.,Department of Medicine and Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
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68
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Estrogen Receptor on the move: Cistromic plasticity and its implications in breast cancer. Mol Aspects Med 2020; 78:100939. [PMID: 33358533 DOI: 10.1016/j.mam.2020.100939] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/27/2023]
Abstract
Estrogen Receptor (ERα) is a hormone-driven transcription factor, critically involved in driving tumor cell proliferation in the vast majority of breast cancers (BCas). ERα binds the genome at cis-regulatory elements, dictating the expression of a large spectrum of responsive genes in 3D genomic space. While initial reports described a rather static ERα chromatin binding repertoire, we now know that ERα DNA interactions are highly versatile, altered in breast tumor development and progression, and deviate between tumors from patients with differential outcome. Multiple cellular signaling cascades are known to impinge on ERα genomic function, changing its cistrome to retarget the receptor to other regions of the genome and reprogram its impact on breast cell biology. This review describes the current state-of-the-art on which factors manipulate the ERα cistrome and how this alters the response to both endogenous and exogenous hormonal stimuli, ultimately impacting BCa cell progression and response to commonly used therapeutic interventions. Novel insights in ERα cistrome dynamics may pave the way for better patient diagnostics and the development of novel therapeutic interventions, ultimately improving cancer care and patient outcome.
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69
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Dong B, Miao J, Wang Y, Luo W, Ji Z, Lai H, Zhang M, Cheng X, Wang J, Fang Y, Zhu HH, Chua CW, Fan L, Zhu Y, Pan J, Wang J, Xue W, Gao WQ. Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer. Commun Biol 2020; 3:778. [PMID: 33328604 PMCID: PMC7745034 DOI: 10.1038/s42003-020-01476-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Neuroendocrine prostate cancer is one of the most aggressive subtypes of prostate tumor. Although much progress has been made in understanding the development of neuroendocrine prostate cancer, the cellular architecture associated with neuroendocrine differentiation in human prostate cancer remain incompletely understood. Here, we use single-cell RNA sequencing to profile the transcriptomes of 21,292 cells from needle biopsies of 6 castration-resistant prostate cancers. Our analyses reveal that all neuroendocrine tumor cells display a luminal-like epithelial phenotype. In particular, lineage trajectory analysis suggests that focal neuroendocrine differentiation exclusively originate from luminal-like malignant cells rather than basal compartment. Further tissue microarray analysis validates the generality of the luminal phenotype of neuroendocrine cells. Moreover, we uncover neuroendocrine differentiation-associated gene signatures that may help us to further explore other intrinsic molecular mechanisms deriving neuroendocrine prostate cancer. In summary, our single-cell study provides direct evidence into the cellular states underlying neuroendocrine transdifferentiation in human prostate cancer.
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Affiliation(s)
- Baijun Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Juju Miao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yanqing Wang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Wenqin Luo
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Zhongzhong Ji
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Huadong Lai
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Man Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiaomu Cheng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinming Wang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuxiang Fang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Helen He Zhu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Chee Wai Chua
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Liancheng Fan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yinjie Zhu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jiahua Pan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jia Wang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Wei Xue
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China. .,School of Biomedical Engineering and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China.
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70
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Paakinaho V, Swinstead EE, Presman DM, Grøntved L, Hager GL. Meta-analysis of Chromatin Programming by Steroid Receptors. Cell Rep 2020; 28:3523-3534.e2. [PMID: 31553919 DOI: 10.1016/j.celrep.2019.08.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022] Open
Abstract
Transcription factors (TFs) must access chromatin to bind to their response elements and regulate gene expression. A widely accepted model proposes that only a special subset of TFs, pioneer factors, can associate with condensed chromatin and initiate chromatin opening. We previously reported that steroid receptors (SRs), not considered pioneer factors, can assist the binding of an archetypal pioneer, the forkhead box protein 1 (FOXA1), at a subset of receptor-activated enhancers. These findings have been challenged recently, with the suggestion that newly acquired data fully support the prevailing pioneer model. Here, we reexamine our results and confirm the original conclusions. We also analyze and discuss a number of available datasets relevant to chromatin penetration by SRs and find a general consensus supporting our original observations. Hence, we propose that chromatin opening at some sites can be initiated by SRs, with a parallel recruitment of factors often treated as having a unique pioneer function. This Matters Arising paper is in response to Glont et al. (2019), published in Cell Reports.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, 70211 Kuopio, Finland
| | - Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892-5055, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892-5055, USA.
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71
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Michmerhuizen AR, Spratt DE, Pierce LJ, Speers CW. ARe we there yet? Understanding androgen receptor signaling in breast cancer. NPJ Breast Cancer 2020; 6:47. [PMID: 33062889 PMCID: PMC7519666 DOI: 10.1038/s41523-020-00190-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
The role of androgen receptor (AR) activation and expression is well understood in prostate cancer. In breast cancer, expression and activation of AR is increasingly recognized for its role in cancer development and its importance in promoting cell growth in the presence or absence of estrogen. As both prostate and breast cancers often share a reliance on nuclear hormone signaling, there is increasing appreciation of the overlap between activated cellular pathways in these cancers in response to androgen signaling. Targeting of the androgen receptor as a monotherapy or in combination with other conventional therapies has proven to be an effective clinical strategy for the treatment of patients with prostate cancer, and these therapeutic strategies are increasingly being investigated in breast cancer. This overlap suggests that targeting androgens and AR signaling in other cancer types may also be effective. This manuscript will review the role of AR in various cellular processes that promote tumorigenesis and metastasis, first in prostate cancer and then in breast cancer, as well as discuss ongoing efforts to target AR for the more effective treatment and prevention of cancer, especially breast cancer.
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Affiliation(s)
- Anna R Michmerhuizen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI USA
| | - Lori J Pierce
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI USA
| | - Corey W Speers
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI USA
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72
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Chen Y, Lan T. Molecular Origin, Expression Regulation, and Biological Function of Androgen Receptor Splicing Variant 7 in Prostate Cancer. Urol Int 2020; 105:337-353. [PMID: 32957106 DOI: 10.1159/000510124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022]
Abstract
The problem of resistance to therapy in prostate cancer (PCa) is multifaceted. Key determinants of drug resistance include tumor burden and growth kinetics, tumor heterogeneity, physical barriers, immune system and microenvironment, undruggable cancer drivers, and consequences of therapeutic pressures. With regard to the fundamental importance of the androgen receptor (AR) in all stages of PCa from tumorigenesis to progression, AR is postulated to have a continued critical role in castration-resistant prostate cancer (CRPC). Suppression of AR signaling mediated by the full-length AR (AR-FL) is the therapeutic goal of all AR-directed therapies. However, AR-targeting agents ultimately lead to AR aberrations that promote PCa progression and drug resistance. Among these AR aberrations, androgen receptor variant 7 (AR-V7) is gaining attention as a potential predictive marker for as well as one of the resistance mechanisms to the most current anti-AR therapies in CRPC. Meanwhile, development of next-generation drugs that directly or indirectly target AR-V7 signaling is urgently needed. In the present review of the current literature, we have summarized the origin, alternative splicing, expression induction, protein conformation, interaction with coregulators, relationship with AR-FL, transcriptional activity, and biological function of AR-V7 in PCa development and therapeutic resistance. We hope this review will help further understand the molecular origin, expression regulation, and role of AR-V7 in the progression of PCa and provide insight into the design of novel selective inhibitors of AR-V7 in PCa treatment.
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Affiliation(s)
- Ye Chen
- Department of Surgery and Anesthesiology, Joint Logistic Support 940 Hospital of CPLA, Lanzhou, China
| | - Tian Lan
- Department of Urology, Joint Logistic Support 940 Hospital of CPLA, Lanzhou, China,
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73
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Pioneer of prostate cancer: past, present and the future of FOXA1. Protein Cell 2020; 12:29-38. [PMID: 32946061 PMCID: PMC7815845 DOI: 10.1007/s13238-020-00786-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/18/2020] [Indexed: 01/27/2023] Open
Abstract
Prostate cancer is the most commonly diagnosed non-cutaneous cancers in North American men. While androgen deprivation has remained as the cornerstone of prostate cancer treatment, resistance ensues leading to lethal disease. Forkhead box A1 (FOXA1) encodes a pioneer factor that induces open chromatin conformation to allow the binding of other transcription factors. Through direct interactions with the Androgen Receptor (AR), FOXA1 helps to shape AR signaling that drives the growth and survival of normal prostate and prostate cancer cells. FOXA1 also possesses an AR-independent role of regulating epithelial-to-mesenchymal transition (EMT). In prostate cancer, mutations converge onto the coding sequence and cis-regulatory elements (CREs) of FOXA1, leading to functional alterations. In addition, FOXA1 activity in prostate cancer can be modulated post-translationally through various mechanisms such as LSD1-mediated protein demethylation. In this review, we describe the latest discoveries related to the function and regulation of FOXA1 in prostate cancer, pointing to their relevance to guide future clinical interventions.
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74
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Yang Z, Xu JX, Fang DP, Ke J. Analysis of key genes reveal lysine demethylase 5B promotes prostate cancer progression. Oncol Lett 2020; 20:62. [PMID: 32863895 PMCID: PMC7436301 DOI: 10.3892/ol.2020.11923] [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: 08/03/2019] [Accepted: 01/14/2020] [Indexed: 11/29/2022] Open
Abstract
Prostate cancer (PCa) is one of the most common types of cancer in males globally. However, the molecular mechanisms underlying PCa progression remain largely unclear. In the present study, Gene Expression Omnibus (GEO) datasets and datasets from The Cancer Genome Atlas (TCGA) were used to analyze the expression of lysine demethylase 5B (KDM5B) in PCa. Proliferation, cell cycle and migration assays were used to detect the functional roles of KDM5B. It was found KDM5B was upregulated in PCa tissues by analyzing GEO and TCGA datasets. KDM5B knockdown significantly suppressed proliferation and cell cycle progression in PCa cells. In additional, KDM5B knockdown inhibited PCa cell migration. By analyzing a TCGA dataset, KDM5B was found to be upregulated in patients at N1 stage compared with N0 stage PCa, in patients at T3+T4 stages compared with T2 stage and in patients with Gleason score ≥8 compared with those with score ≤7. Kaplan-Meier analysis revealed that higher expression of KDM5B was associated with shorter biochemical recurrence-free survival and overall survival time in patients with PCa. These results suggest that expression of KDM5B may serve as a biomarker to predict the outcome of PCa.
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Affiliation(s)
- Zhi Yang
- Department of Urology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, Wuhan, Hubei 430015, P.R. China
| | - Jian-Xin Xu
- Department of Urology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, Wuhan, Hubei 430015, P.R. China
| | - Deng-Pan Fang
- Department of Urology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, Wuhan, Hubei 430015, P.R. China
| | - Jian Ke
- Department of Urology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, Wuhan, Hubei 430015, P.R. China
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75
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Hight SK, Mootz A, Kollipara RK, McMillan E, Yenerall P, Otaki Y, Li LS, Avila K, Peyton M, Rodriguez-Canales J, Mino B, Villalobos P, Girard L, Dospoy P, Larsen J, White MA, Heymach JV, Wistuba II, Kittler R, Minna JD. An in vivo functional genomics screen of nuclear receptors and their co-regulators identifies FOXA1 as an essential gene in lung tumorigenesis. Neoplasia 2020; 22:294-310. [PMID: 32512502 PMCID: PMC7281309 DOI: 10.1016/j.neo.2020.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 01/04/2023]
Abstract
Using a mini-library of 1062 lentiviral shRNAs targeting 40 nuclear hormone receptors and 70 of their co-regulators, we searched for potential therapeutic targets that would be important during in vivo tumor growth using a parallel in vitro and in vivo shRNA screening strategy in the non-small cell lung cancer (NSCLC) line NCI-H1819. We identified 21 genes essential for in vitro growth, and nine genes specifically required for tumor survival in vivo, but not in vitro: NCOR2, FOXA1, HDAC1, RXRA, RORB, RARB, MTA2, ETV4, and NR1H2. We focused on FOXA1, since it lies within the most frequently amplified genomic region in lung adenocarcinomas. We found that 14q-amplification in NSCLC cell lines was a biomarker for FOXA1 dependency for both in vivo xenograft growth and colony formation, but not mass culture growth in vitro. FOXA1 knockdown identified genes involved in electron transport among the most differentially regulated, indicating FOXA1 loss may lead to a decrease in cellular respiration. In support of this, FOXA1 amplification was correlated with increased sensitivity to the complex I inhibitor phenformin. Integrative ChipSeq analyses reveal that FOXA1 functions in this genetic context may be at least partially independent of NKX2-1. Our findings are consistent with a neomorphic function for amplified FOXA1, driving an oncogenic transcriptional program. These data provide new insight into the functional consequences of FOXA1 amplification in lung adenocarcinomas, and identify new transcriptional networks for exploration of therapeutic vulnerabilities in this patient population.
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MESH Headings
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/metabolism
- Adenocarcinoma of Lung/pathology
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Cell Proliferation
- Female
- Gene Expression Regulation, Neoplastic
- Genome-Wide Association Study
- Genomics/methods
- Hepatocyte Nuclear Factor 3-alpha/genetics
- Hepatocyte Nuclear Factor 3-alpha/metabolism
- Humans
- Insulin-Like Growth Factor Binding Protein 3/genetics
- Insulin-Like Growth Factor Binding Protein 3/metabolism
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Receptors, Cytoplasmic and Nuclear
- Thrombospondin 1/genetics
- Thrombospondin 1/metabolism
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Suzie K Hight
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Allison Mootz
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth McMillan
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Paul Yenerall
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Eugene McDermott Center for Human Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yoichi Otaki
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of General Surgical Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Long-Shan Li
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kimberley Avila
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Peyton
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jaime Rodriguez-Canales
- Department of Translational and Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Mino
- Department of Translational and Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Pamela Villalobos
- Department of Translational and Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Patrick Dospoy
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jill Larsen
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michael A White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John V Heymach
- Department Thoracic and Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational and Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ralf Kittler
- Eugene McDermott Center for Human Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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76
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Chakravarty D, Nair SS, Hammouda N, Ratnani P, Gharib Y, Wagaskar V, Mohamed N, Lundon D, Dovey Z, Kyprianou N, Tewari AK. Sex differences in SARS-CoV-2 infection rates and the potential link to prostate cancer. Commun Biol 2020; 3:374. [PMID: 32641750 PMCID: PMC7343823 DOI: 10.1038/s42003-020-1088-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 01/08/2023] Open
Abstract
The recent outbreak of infections and the pandemic caused by SARS-CoV-2 represent one of the most severe threats to human health in more than a century. Emerging data from the United States and elsewhere suggest that the disease is more severe in men. Knowledge gained, and lessons learned, from studies of the biological interactions and molecular links that may explain the reasons for the greater severity of disease in men, and specifically in the age group at risk for prostate cancer, will lead to better management of COVID-19 in prostate cancer patients. Such information will be indispensable in the current and post-pandemic scenarios.
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Affiliation(s)
- Dimple Chakravarty
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Sujit S Nair
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nada Hammouda
- Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Parita Ratnani
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yasmine Gharib
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vinayak Wagaskar
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nihal Mohamed
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dara Lundon
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zachary Dovey
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Natasha Kyprianou
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ashutosh K Tewari
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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77
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FOXA1 Expression in Nasopharyngeal Carcinoma: Association with Clinicopathological Characteristics and EMT Markers. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4234632. [PMID: 32685483 PMCID: PMC7330629 DOI: 10.1155/2020/4234632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 05/07/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
Abstract
The forkhead box (FOXA) family of transcription factors regulates gene expression and chromatin structure during tumorigenesis and embryonic development. Until now, the relationship between FOXA1 and the nasopharyngeal carcinoma (NPC) has not yet been reported. Therefore, our purpose is to analyze the expression of FOXA1 in 56 NPC patients compared to 10 normal nasopharyngeal mucosae and to correlate the expression with the clinicopathological features. Besides, we investigated the association between FOXA1 and LMP1 gene expression, as well as the EMT markers namely the E-cadherin and Twist1. Among 56 NPC tissues, 34 (60.7%) cases were positive for FOXA1. Furthermore, we noticed that FOXA1 expression correlated with TNM (p = 0.037), and age at diagnosis (p = 0.05). Moreover, positive expression of FOXA1 is likely to be associated with prolonged disease-free survival and overall survival rates. On the other hand, we observed a positive association between the expression of E-cadherin and FOXA1 (p = 0.0051) whereas Twist1 correlated negatively with FOXA1 (p = 0.004). Furthermore, knowing that LMP1 plays a key role in the pathogenesis of NPC, we explored the association of FOXA1 with the LMP1 gene expression in both NPC cell lines and tissues. We found that, in the C666-1 which displays low levels of LMP1, the expression of FOXA1 is high, and inversely in the C15 cell line that expresses a high level of LMP1, the level of FOXA1 is low. Besides, in accordance to our results, we found that in NPC tissues there is a negative association between LMP1 and FOXA1. In conclusion, our results suggest that the overexpression of FOXA1 is associated with a nonaggressive behavior and favorable prognosis in NPC patients. FOXA1 could contribute in the EMT process through key factors as E-cadherin, Twist1, and LMP1.
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78
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Lin CJ, Lo UG, Hsieh JT. The regulatory pathways leading to stem-like cells underlie prostate cancer progression. Asian J Androl 2020; 21:233-240. [PMID: 30178777 PMCID: PMC6498735 DOI: 10.4103/aja.aja_72_18] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) is the most common cause of malignancy in males and the third leading cause of cancer mortality in the United States. The standard care for primary PCa with local invasive disease mainly is surgery and radiation. For patients with distant metastases, androgen deprivation therapy (ADT) is a gold standard. Regardless of a favorable outcome of ADT, patients inevitably relapse to an end-stage castration-resistant prostate cancer (CRPC) leading to mortality. Therefore, revealing the mechanism and identifying cellular components driving aggressive PCa is critical for prognosis and therapeutic intervention. Cancer stem cell (CSC) phenotypes characterized as poor differentiation, cancer initiation with self-renewal capabilities, and therapeutic resistance are proposed to contribute to the onset of CRPC. In this review, we discuss the role of CSC in CRPC with the evidence of CSC phenotypes and the possible underlying mechanisms.
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Affiliation(s)
- Chun-Jung Lin
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - U-Ging Lo
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jer-Tsong Hsieh
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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79
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Levitsky V, Zemlyanskaya E, Oshchepkov D, Podkolodnaya O, Ignatieva E, Grosse I, Mironova V, Merkulova T. A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. Nucleic Acids Res 2020; 47:e139. [PMID: 31750523 PMCID: PMC6868382 DOI: 10.1093/nar/gkz800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 08/12/2019] [Accepted: 09/09/2019] [Indexed: 01/20/2023] Open
Abstract
Recognition of composite elements consisting of two transcription factor binding sites gets behind the studies of tissue-, stage- and condition-specific transcription. Genome-wide data on transcription factor binding generated with ChIP-seq method facilitate an identification of composite elements, but the existing bioinformatics tools either require ChIP-seq datasets for both partner transcription factors, or omit composite elements with motifs overlapping. Here we present an universal Motifs Co-Occurrence Tool (MCOT) that retrieves maximum information about overrepresented composite elements from a single ChIP-seq dataset. This includes homo- and heterotypic composite elements of four mutual orientations of motifs, separated with a spacer or overlapping, even if recognition of motifs within composite element requires various stringencies. Analysis of 52 ChIP-seq datasets for 18 human transcription factors confirmed that for over 60% of analyzed datasets and transcription factors predicted co-occurrence of motifs implied experimentally proven protein-protein interaction of respecting transcription factors. Analysis of 164 ChIP-seq datasets for 57 mammalian transcription factors showed that abundance of predicted composite elements with an overlap of motifs compared to those with a spacer more than doubled; and they had 1.5-fold increase of asymmetrical pairs of motifs with one more conservative 'leading' motif and another one 'guided'.
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Affiliation(s)
- Victor Levitsky
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.,Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.,Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Olga Podkolodnaya
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Elena Ignatieva
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.,Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ivo Grosse
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Victoria Mironova
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.,Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Tatyana Merkulova
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.,Department of Molecular Genetics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
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80
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Xia Z, Su Y, Petersen P, Qi L, Kim AE, Figueiredo JC, Lin Y, Nan H, Sakoda LC, Albanes D, Berndt SI, Bézieau S, Bien S, Buchanan DD, Casey G, Chan AT, Conti DV, Drew DA, Gallinger SJ, Gauderman WJ, Giles GG, Gruber SB, Gunter MJ, Hoffmeister M, Jenkins MA, Joshi AD, Le Marchand L, Lewinger JP, Li L, Lindor NM, Moreno V, Murphy N, Nassir R, Newcomb PA, Ogino S, Rennert G, Song M, Wang X, Wolk A, Woods MO, Brenner H, White E, Slattery ML, Giovannucci EL, Chang‐Claude J, Pharoah PDP, Hsu L, Campbell PT, Peters U. Functional informed genome-wide interaction analysis of body mass index, diabetes and colorectal cancer risk. Cancer Med 2020; 9:3563-3573. [PMID: 32207560 PMCID: PMC7221445 DOI: 10.1002/cam4.2971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/28/2020] [Accepted: 02/21/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Body mass index (BMI) and diabetes are established risk factors for colorectal cancer (CRC), likely through perturbations in metabolic traits (e.g. insulin resistance and glucose homeostasis). Identification of interactions between variation in genes and these metabolic risk factors may identify novel biologic insights into CRC etiology. METHODS To improve statistical power and interpretation for gene-environment interaction (G × E) testing, we tested genetic variants that regulate expression of a gene together for interaction with BMI (kg/m2 ) and diabetes on CRC risk among 26 017 cases and 20 692 controls. Each variant was weighted based on PrediXcan analysis of gene expression data from colon tissue generated in the Genotype-Tissue Expression Project for all genes with heritability ≥1%. We used a mixed-effects model to jointly measure the G × E interaction in a gene by partitioning the interactions into the predicted gene expression levels (fixed effects), and residual G × E effects (random effects). G × BMI analyses were stratified by sex as BMI-CRC associations differ by sex. We used false discovery rates to account for multiple comparisons and reported all results with FDR <0.2. RESULTS Among 4839 genes tested, genetically predicted expressions of FOXA1 (P = 3.15 × 10-5 ), PSMC5 (P = 4.51 × 10-4 ) and CD33 (P = 2.71 × 10-4 ) modified the association of BMI on CRC risk for men; KIAA0753 (P = 2.29 × 10-5 ) and SCN1B (P = 2.76 × 10-4 ) modified the association of BMI on CRC risk for women; and PTPN2 modified the association between diabetes and CRC risk in both sexes (P = 2.31 × 10-5 ). CONCLUSIONS Aggregating G × E interactions and incorporating functional information, we discovered novel genes that may interact with BMI and diabetes on CRC risk.
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81
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Moore NL, Hanson AR, Ebrahimie E, Hickey TE, Tilley WD. Anti-proliferative transcriptional effects of medroxyprogesterone acetate in estrogen receptor positive breast cancer cells are predominantly mediated by the progesterone receptor. J Steroid Biochem Mol Biol 2020; 199:105548. [PMID: 31805393 DOI: 10.1016/j.jsbmb.2019.105548] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 11/19/2019] [Indexed: 01/14/2023]
Abstract
Medroxyprogesterone acetate (MPA) is a first generation progestin that has been in clinical use for various hormonal conditions in women since the 1960s. Although developed as a progesterone receptor (PR) agonist, MPA also has strong binding affinity for other steroid receptors. This promiscuity confounds the mechanistic action of MPA in target cells that express multiple steroid receptors. This study is the first to assess the relative contribution of progesterone, androgen and glucocorticoid receptors in mediating the transcriptional activity of MPA on endogenous targets in breast cancer cells that endogenously express all three receptors at comparable levels. Gene expression profiling in estrogen receptor positive (ER+) ZR-75-1 breast cancer cells demonstrated that although the MPA-regulated transcriptome strongly overlapped with that of Progesterone (PROG), 5α-dihydrotestosterone (DHT) and Dexamethasone (DEX), it clustered most strongly with that of PROG, suggesting that MPA predominantly acts via the progesterone receptor (PR) rather than androgen receptor (AR) or glucocorticoid receptor (GR). Subsequent experiments manipulating levels of these receptors, either through specific culture conditions or with lentiviral shRNAs targeting individual receptors, also revealed a stronger contribution of PR compared to AR and GR on the expression of endogenous target genes that are either commonly regulated by all ligands or specifically regulated only by MPA. A predominant contribution of PR to MPA action in ER+ T-47D breast cancer cells was also observed, although a stronger role for AR was evident in T-47D compared to that observed in ZR-75-1 cells. Network analysis of ligand-specific and commonly regulated genes demonstrated that MPA utilises different transcription factors and signalling pathways to inhibit proliferation compared with PROG. This study reaffirms the importance of PR in mediating MPA action in an endogenous breast cancer context where multiple steroid receptors are co-expressed and has potential implications for PR-targeting therapeutic strategies in ER+ breast cancer.
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Affiliation(s)
- Nicole L Moore
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Adrienne R Hanson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Esmaeil Ebrahimie
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia.
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82
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Li J, Xu C, Lee HJ, Ren S, Zi X, Zhang Z, Wang H, Yu Y, Yang C, Gao X, Hou J, Wang L, Yang B, Yang Q, Ye H, Zhou T, Lu X, Wang Y, Qu M, Yang Q, Zhang W, Shah NM, Pehrsson EC, Wang S, Wang Z, Jiang J, Zhu Y, Chen R, Chen H, Zhu F, Lian B, Li X, Zhang Y, Wang C, Wang Y, Xiao G, Jiang J, Yang Y, Liang C, Hou J, Han C, Chen M, Jiang N, Zhang D, Wu S, Yang J, Wang T, Chen Y, Cai J, Yang W, Xu J, Wang S, Gao X, Wang T, Sun Y. A genomic and epigenomic atlas of prostate cancer in Asian populations. Nature 2020; 580:93-99. [PMID: 32238934 DOI: 10.1038/s41586-020-2135-x] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/17/2020] [Indexed: 12/24/2022]
Abstract
Prostate cancer is the second most common cancer in men worldwide1. Over the past decade, large-scale integrative genomics efforts have enhanced our understanding of this disease by characterizing its genetic and epigenetic landscape in thousands of patients2,3. However, most tumours profiled in these studies were obtained from patients from Western populations. Here we produced and analysed whole-genome, whole-transcriptome and DNA methylation data for 208 pairs of tumour tissue samples and matched healthy control tissue from Chinese patients with primary prostate cancer. Systematic comparison with published data from 2,554 prostate tumours revealed that the genomic alteration signatures in Chinese patients were markedly distinct from those of Western cohorts: specifically, 41% of tumours contained mutations in FOXA1 and 18% each had deletions in ZNF292 and CHD1. Alterations of the genome and epigenome were correlated and were predictive of disease phenotype and progression. Coding and noncoding mutations, as well as epimutations, converged on pathways that are important for prostate cancer, providing insights into this devastating disease. These discoveries underscore the importance of including population context in constructing comprehensive genomic maps for disease.
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Affiliation(s)
- Jing Li
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Center for Translational Medicine, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shancheng Ren
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Xiaoyuan Zi
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | | | - Haifeng Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yongwei Yu
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chenghua Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaofeng Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianguo Hou
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Bo Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qing Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Huamao Ye
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tie Zhou
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xin Lu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yan Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Min Qu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qingsong Yang
- Department of Radiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wenhui Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shuo Wang
- Department of Urology, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zengjun Wang
- State Key Laboratory of Reproductive Medicine and Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Jiang
- Department of Urology, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yan Zhu
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Rui Chen
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Huan Chen
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Feng Zhu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bijun Lian
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | | | - Yun Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chao Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yue Wang
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China.,Department of Histology and Embryology, Second Military Medical University, Shanghai, China
| | - Guangan Xiao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Junfeng Jiang
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China.,Department of Histology and Embryology, Second Military Medical University, Shanghai, China
| | - Yue Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chaozhao Liang
- Department of Urology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jianquan Hou
- Department of Urology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Conghui Han
- Department of Urology, Xuzhou Central Hospital, The Affiliated Xuzhou Hospital of Medical College of Southeast University, Xuzhou, China
| | - Ming Chen
- Department of Urology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Ning Jiang
- Department of Urology, Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Dahong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Song Wu
- Department of Urology Institute of Shenzhen University, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Jinjian Yang
- Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tao Wang
- Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongliang Chen
- Department of Urology, Shaoxing Central Hospital, Shaoxing, China
| | - Jiantong Cai
- Department of Urology, Shishi Hospital, Shishi, China
| | - Wenzeng Yang
- Department of Urology, The Affiliated Hospital of Hebei University, Baoding, China
| | - Jun Xu
- Department of Urology, Huadong Hospital, Fudan University, Shanghai, China
| | - Shaogang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan, China
| | - Xu Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China. .,Shanghai Key Laboratory of Cell Engineering, Shanghai, China.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA. .,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
| | - Yinghao Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China. .,Shanghai Key Laboratory of Cell Engineering, Shanghai, China.
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83
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Zhang M, Lai Y, Vasquez JL, James DI, Smith KM, Waddell ID, Ogilvie DJ, Liu Y, Agoulnik IU. Androgen Receptor and Poly(ADP-ribose) Glycohydrolase Inhibition Increases Efficiency of Androgen Ablation in Prostate Cancer Cells. Sci Rep 2020; 10:3836. [PMID: 32123273 PMCID: PMC7052214 DOI: 10.1038/s41598-020-60849-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
There is mounting evidence of androgen receptor signaling inducing genome instability and changing DNA repair capacity in prostate cancer cells. Expression of genes associated with base excision repair (BER) is increased with prostate cancer progression and correlates with poor prognosis. Poly(ADP-ribose) polymerase (PARP) and poly(ADP-ribose) glycohydrolase (PARG) are key enzymes in BER that elongate and degrade PAR polymers on target proteins. While PARP inhibitors have been tested in clinical trials and are a promising therapy for prostate cancer patients with TMPRSS2-ERG fusions and mutations in DNA repair genes, PARG inhibitors have not been evaluated. We show that PARG is a direct androgen receptor (AR) target gene. AR is recruited to the PARG locus and induces PARG expression. Androgen ablation combined with PARG inhibition synergistically reduces BER capacity in independently derived LNCaP and LAPC4 prostate cancer cell lines. A combination of PARG inhibition with androgen ablation or with the DNA damaging drug, temozolomide, significantly reduces cellular proliferation and increases DNA damage. PARG inhibition alters AR transcriptional output without changing AR protein levels. Thus, AR and PARG are engaged in reciprocal regulation suggesting that the success of androgen ablation therapy can be enhanced by PARG inhibition in prostate cancer patients.
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Affiliation(s)
- Manqi Zhang
- Biochemistry Ph.D. Program, Florida International University, Miami, FL, USA
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, College of Arts, Sciences and Education, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Judy L Vasquez
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Dominic I James
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
| | - Kate M Smith
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
| | - Ian D Waddell
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
- CRL, Chesterford Research Park, CB10 1XL, Alderley Park, UK
| | - Donald J Ogilvie
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK104TG, UK
| | - Yuan Liu
- Department of Chemistry and Biochemistry, College of Arts, Sciences and Education, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Irina U Agoulnik
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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84
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Epigenetic modulations and lineage plasticity in advanced prostate cancer. Ann Oncol 2020; 31:470-479. [PMID: 32139297 DOI: 10.1016/j.annonc.2020.02.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 12/25/2022] Open
Abstract
Prostate cancer is the most common cancer and second leading cause of cancer-related death in American men. Antiandrogen therapies are part of the standard of therapeutic regimen for advanced or metastatic prostate cancers; however, patients who receive these treatments are more likely to develop castration-resistant prostate cancer (CRPC) or neuroendocrine prostate cancer (NEPC). In the development of CRPC or NEPC, numerous genetic signaling pathways have been under preclinical investigations and in clinical trials. Accumulated evidence shows that DNA methylation, chromatin integrity, and accessibility for transcriptional regulation still play key roles in prostate cancer initiation and progression. Better understanding of how epigenetic change regulates the progression of prostate cancer and the interaction between epigenetic and genetic modulators driving NEPC may help develop a better risk stratification and more effective treatment regimens for prostate cancer patients.
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85
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Androgen receptor-binding sites are highly mutated in prostate cancer. Nat Commun 2020; 11:832. [PMID: 32047165 PMCID: PMC7012874 DOI: 10.1038/s41467-020-14644-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/20/2020] [Indexed: 12/20/2022] Open
Abstract
Androgen receptor (AR) signalling is essential in nearly all prostate cancers. Any alterations to AR-mediated transcription can have a profound effect on carcinogenesis and tumor growth. While mutations of the AR protein have been extensively studied, little is known about those somatic mutations that occur at the non-coding regions where AR binds DNA. Using clinical whole genome sequencing, we show that AR binding sites have a dramatically increased rate of mutations that is greater than any other transcription factor and specific to only prostate cancer. Demonstrating this may be common to lineage-specific transcription factors, estrogen receptor binding sites were also found to have elevated rate of mutations in breast cancer. We provide evidence that these mutations at AR binding sites, and likely other related transcription factors, are caused by faulty repair of abasic sites. Overall, this work demonstrates that non-coding AR binding sites are frequently mutated in prostate cancer and can impact enhancer activity.
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86
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Elix CC, Salgia MM, Otto-Duessel M, Copeland BT, Yoo C, Lee M, Tew BY, Ann D, Pal SK, Jones JO. Peroxisome proliferator-activated receptor gamma controls prostate cancer cell growth through AR-dependent and independent mechanisms. Prostate 2020; 80:162-172. [PMID: 31769890 PMCID: PMC8985763 DOI: 10.1002/pros.23928] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Prostate cancer (PC) remains a leading cause of cancer mortality and the most successful chemopreventative and treatment strategies for PC come from targeting the androgen receptor (AR). Although AR plays a key role, it is likely that other molecular pathways also contribute to PC, making it essential to identify and develop drugs against novel targets. Recent studies have identified peroxisome proliferator-activated receptor gamma (PPARγ), a nuclear receptor that regulates fatty acid (FA) metabolism, as a novel target in PC, and suggest that inhibitors of PPARγ could be used to treat existing disease. We hypothesized that PPARγ acts through AR-dependent and independent mechanisms to control PC development and growth and that PPARγ inhibition is a viable PC treatment strategy. METHODS Immunohistochemistry was used to determine expression of PPARү in a cohort of patients with PC. Standard molecular techniques were used to investigate the PPARү signaling in PC cells as well a xenograft mouse model to test PPARү inhibition in vivo. Kaplan-Meier curves were created using cBioportal. RESULTS We confirmed the expression of PPARү in human PC. We then showed that small molecule inhibition of PPARγ decreases the growth of AR-positive and -negative PC cells in vitro and that T0070907, a potent PPARγ antagonist, significantly decreased the growth of human PC xenografts in nude mice. We found that PPARγ antagonists or small interfering RNA (siRNA) do not affect mitochondrial activity nor do they cause apoptosis; instead, they arrest the cell cycle. In AR-positive PC cells, antagonists and siRNAs reduce AR transcript and protein levels, which could contribute to growth inhibition. AR-independent effects on growth appear to be mediated by effects on FA metabolism as the specific FASN inhibitor, Fasnall, inhibited PC cell growth but did not have an additive effect when combined with PPARγ antagonists. Patients with increased PPARү target gene expression, but not alterations in PPARү itself, were found to have significantly worse overall survival. CONCLUSIONS Having elucidated the direct cancer cell effects of PPARγ inhibition, our studies have helped to determine the role of PPARγ in PC growth, and support the hypothesis that PPARγ inhibition is an effective strategy for PC treatment.
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Affiliation(s)
- Catherine C Elix
- Department of Medical Oncology, City of Hope, Duarte, California
| | - Meghan M Salgia
- Department of Medical Oncology, City of Hope, Duarte, California
| | | | - Ben T Copeland
- Department of Medical Oncology, City of Hope, Duarte, California
| | - Christopher Yoo
- Department of Medical Oncology, City of Hope, Duarte, California
| | - Michael Lee
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, California
| | - Ben Yi Tew
- Department of Medical Oncology, City of Hope, Duarte, California
| | - David Ann
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, California
| | - Sumanta K Pal
- Department of Medical Oncology, City of Hope, Duarte, California
| | - Jeremy O Jones
- Department of Medical Oncology, City of Hope, Duarte, California
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87
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Bagherpoor Helabad M, Volkenandt S, Imhof P. Molecular Dynamics Simulations of a Chimeric Androgen Receptor Protein (SPARKI) Confirm the Importance of the Dimerization Domain on DNA Binding Specificity. Front Mol Biosci 2020; 7:4. [PMID: 32083093 PMCID: PMC7005049 DOI: 10.3389/fmolb.2020.00004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/10/2020] [Indexed: 11/21/2022] Open
Abstract
The DNA binding domains of Androgen/Glucocorticoid receptors (AR/GR), members of class I steroid receptors, bind as a homo-dimer to a cis-regulatory element. These response elements are arranged as inverted repeat (IR) of hexamer “AGAACA”, separated with a 3 base pairs spacer. DNA binding domains of the Androgen receptor, AR-DBDs, in addition, selectively recognize a direct-like repeat (DR) arrangement of this hexamer. A chimeric AR protein, termed SPARKI, in which the second zinc-binding motif of AR is swapped with that of GR, however, fails to recognize DR-like elements. By molecular dynamic simulations, we identify how the DNA binding domains of the wild type AR/GR, and also the chimeric SPARKI model, distinctly interact with both IR and DR response elements. AR binds more strongly to DR than GR binds to IR elements. A SPARKI model built from the structure of the AR (SPARKI-AR) shows significantly fewer hydrogen bond interactions in complex with a DR sequence than with an IR sequence. Moreover, a SPARKI model based on the structure of the GR (SPARKI-GR) shows a considerable distortion in its dimerization domain when complexed to a DR-DNA whereas it remains in a stable conformation in a complex with an IR-DNA. The diminished interaction of SPARKI-AR with and the instability of SPARKI-GR on DR response elements agree with SPARKI's lack of affinity for these sequences. The more GR-like binding specificity of the chimeric SPARKI protein is further emphasized by both SPARKI models binding even more strongly to IR elements than observed for the DNA binding domain of the GR.
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Affiliation(s)
| | - Senta Volkenandt
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Petra Imhof
- Department of Physics, Freie Universität Berlin, Berlin, Germany
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88
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Zhou J, Li Y, Cao H, Yang M, Chu L, Li T, Yu Z, Yu R, Qiu B, Wang Q, Li X, Xie J. CATA: a comprehensive chromatin accessibility database for cancer. Database (Oxford) 2020; 2022:6520815. [PMID: 35134148 PMCID: PMC9246274 DOI: 10.1093/database/baab085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/05/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
Accessible chromatin refers to the active regions of a chromosome that are bound by many transcription factors (TFs). Changes in chromatin accessibility play a critical role in tumorigenesis. With the emergence of novel methods like Assay for Transposase-accessible Chromatin Sequencing, a sequencing method that maps chromatin-accessible regions (CARs) and enables the computational analysis of TF binding at chromatin-accessible sites, the regulatory landscape in cancer can be dissected. Herein, we developed a comprehensive cancer chromatin accessibility database named CATA, which aims to provide available resources of cancer CARs and to annotate their potential roles in the regulation of genes in a cancer type-specific manner. In this version, CATA stores 2 991 163 CARs from 23 cancer types, binding information of 1398 TFs within the CARs, and provides multiple annotations about these regions, including common single nucleotide polymorphisms (SNPs), risk SNPs, copy number variation, somatic mutations, motif changes, expression quantitative trait loci, methylation and CRISPR/Cas9 target loci. Moreover, CATA supports cancer survival analysis of the CAR-associated genes and provides detailed clinical information of the tumor samples. Database URL: CATA is available at http://www.xiejjlab.bio/cata/.
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Affiliation(s)
- Jianyuan Zhou
- Central Laboratory of Molecular Biology, Medical College of Jiaying University, 146 Huangtang Road, Meizhou 514031, China
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong
- First Medical University, and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan 250000, China
| | | | | | - Min Yang
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Lingyu Chu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Taisong Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Zhengmin Yu
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Rui Yu
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Bo Qiu
- Central Laboratory of Molecular Biology, Medical College of Jiaying University, 146 Huangtang Road, Meizhou 514031, China
| | - Qiuyu Wang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Jianjun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
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89
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Yuan F, Hankey W, Wu D, Wang H, Somarelli J, Armstrong AJ, Huang J, Chen Z, Wang Q. Molecular determinants for enzalutamide-induced transcription in prostate cancer. Nucleic Acids Res 2019; 47:10104-10114. [PMID: 31501863 PMCID: PMC6821169 DOI: 10.1093/nar/gkz790] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/04/2019] [Indexed: 11/25/2022] Open
Abstract
Enzalutamide, a second-generation androgen receptor (AR) antagonist, has demonstrated clinical benefit in men with prostate cancer. However, it only provides a temporary response and modest increase in survival, indicating a rapid evolution of resistance. Previous studies suggest that enzalutamide may function as a partial transcriptional agonist, but the underlying mechanisms for enzalutamide-induced transcription remain poorly understood. Here, we show that enzalutamide stimulates expression of a novel subset of genes distinct from androgen-responsive genes. Treatment of prostate cancer cells with enzalutamide enhances recruitment of pioneer factor GATA2, AR, Mediator subunits MED1 and MED14, and RNA Pol II to regulatory elements of enzalutamide-responsive genes. Mechanistically, GATA2 globally directs enzalutamide-induced transcription by facilitating AR, Mediator and Pol II loading to enzalutamide-responsive gene loci. Importantly, the GATA2 inhibitor K7174 inhibits enzalutamide-induced transcription by decreasing binding of the GATA2/AR/Mediator/Pol II transcriptional complex, contributing to sensitization of prostate cancer cells to enzalutamide treatment. Our findings provide mechanistic insight into the future combination of GATA2 inhibitors and enzalutamide for improved AR-targeted therapy.
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Affiliation(s)
- Fuwen Yuan
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - William Hankey
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dayong Wu
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Hongyan Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jason Somarelli
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew J Armstrong
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University School of Medicine, Durham, NC 27710, USA.,Departments of Surgery, Pharmacology, and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.,Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhong Chen
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qianben Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.,Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University School of Medicine, Durham, NC 27710, USA
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90
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Copeland BT, Du J, Pal SK, Jones JO. Factors that influence the androgen receptor cistrome in benign and malignant prostate cells. Mol Oncol 2019; 13:2616-2632. [PMID: 31520575 PMCID: PMC6887583 DOI: 10.1002/1878-0261.12572] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/14/2019] [Accepted: 09/11/2019] [Indexed: 01/24/2023] Open
Abstract
The androgen receptor (AR) plays key roles in the development of prostate tissue and the development and progression of prostate cancer (PC). AR guides cytodifferentiation and homeostasis in benign luminal epithelial cells; however, in PC, AR instead drives the uncontrolled proliferation of these cells. This ‘AR malignancy shift’ (AMS) is a central event in tumorigenesis. Using a ChIP‐seq approach in primary human tissues, cell lines, and mouse models, we demonstrate that the AMS occurs in every sample analyzed, suggesting that it is necessary for PC development. Using molecular and genetic techniques, we demonstrate that forkhead box (FOX)A1, HOXB13, GATA2, and c‐JUN are involved in the regulation of the AMS. AR‐binding sites (ARBS) are enriched for FOX, HOX, and GATA motifs in PC cells but not for c‐JUN motifs in benign cells. We show that the SPOP mutation commonly found in localized PCs can cause the AMS but is not transformative on its own and must be coupled to another mutation to transform cells. We show that the AMS occurs in mouse models of PC as well and that chronic low T, which is associated with increased PC risk and aggressiveness in humans, also causes the AMS in mice. We have discovered a previously unrecognized, fundamental tenet of PC, one which explains how and why AR signaling is different in cancer and benign cells. Our work has the potential to be used to stratify patients with localized PC for specific treatments. Furthermore, our work suggests that the AMS is a novel target for the treatment and/or prevention of PC.
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Affiliation(s)
- Ben T Copeland
- Deparment of Medical Oncology, City of Hope, Duarte, CA, USA
| | - Juan Du
- Integrative Genomics Core, City of Hope, Duarte, CA, USA
| | - Sumanta K Pal
- Deparment of Medical Oncology, City of Hope, Duarte, CA, USA
| | - Jeremy O Jones
- Deparment of Medical Oncology, City of Hope, Duarte, CA, USA
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91
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Feng Q, He B. Androgen Receptor Signaling in the Development of Castration-Resistant Prostate Cancer. Front Oncol 2019; 9:858. [PMID: 31552182 PMCID: PMC6738163 DOI: 10.3389/fonc.2019.00858] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
Most prostate cancers are androgen-sensitive malignancies whose growths depend on the transcriptional activity of the androgen receptor (AR). In the 1940s, Charles Huggins demonstrated that the surgical removal of testes in men can result in a dramatic improvement in symptoms and can induce prostate cancer regression. Since then, androgen deprivation therapies have been the standard first-line treatment for advanced prostate cancer, including: surgical castration, medical castration, antiandrogens, and androgen biosynthesis inhibitors. These therapies relieve symptoms, reduce tumor burden, and prolong patient survival, while having relatively modest side effects. Unfortunately, hormone deprivation therapy rarely cures the cancer itself. Prostate cancer almost always recurs, resulting in deadly castration-resistant prostate cancer. The underlying escape mechanisms include androgen receptor gene/enhancer amplification, androgen receptor mutations, androgen receptor variants, coactivator overexpression, intratumoral de novo androgen synthesis, etc. Whereas, the majority of the castration-resistant prostate cancers continuously rely on the androgen axis, a subset of recurrent cancers have completely lost androgen receptor expression, undergone divergent clonal evolution or de-differentiation, and become truly androgen receptor-independent small-cell prostate cancers. There is an urgent need for the development of novel targeted and immune therapies for this subtype of prostate cancer, when more deadly small-cell prostate cancers are induced by thorough androgen deprivation and androgen receptor ablation.
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Affiliation(s)
- Qin Feng
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, United States
| | - Bin He
- Departments of Surgery and Urology, Immunobiology & Transplant Science Center, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, United States
- Department of Medicine-Cancer Biology, Weill Cornell Medicine, Cornell University, New York, NY, United States
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92
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Blom S, Erickson A, Östman A, Rannikko A, Mirtti T, Kallioniemi O, Pellinen T. Fibroblast as a critical stromal cell type determining prognosis in prostate cancer. Prostate 2019; 79:1505-1513. [PMID: 31269283 PMCID: PMC6813917 DOI: 10.1002/pros.23867] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Tumor stroma associates with prostate cancer (PCa) progression, but its specific cellular composition and association to patient survival outcome have not been characterized. METHODS We analyzed stromal composition in human PCa using multiplex immunohistochemistry and quantitative, high-resolution image analysis in two retrospective, formalin-fixed paraffin embedded observational clinical cohorts (Cohort I, n = 117; Cohort II, n = 340) using PCa-specific mortality as outcome measurement. RESULTS A high proportion of fibroblasts associated with aggressive disease and castration-resistant prostate cancer (CRPC). In a multivariate analysis, increase in fibroblast proportion predicted poor cancer-specific outcome independently in the two clinical cohorts studied. CONCLUSIONS Fibroblasts were the most important cell type in determining prognosis in PCa and associated with CRPC. Thus, the stromal composition could be critically important in developing diagnostic and therapeutic approaches to aggressive prostate cancer.
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Affiliation(s)
- Sami Blom
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Andrew Erickson
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Arne Östman
- Science for Life Laboratory, Department of Oncology and PathologyKarolinska InstitutetStockholmSweden
| | - Antti Rannikko
- Department of UrologyHelsinki University and Helsinki University HospitalHelsinkiFinland
| | - Tuomas Mirtti
- Department of PathologyUniversity of HelsinkiHelsinkiFinland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Science for Life Laboratory, Department of Oncology and PathologyKarolinska InstitutetStockholmSweden
| | - Teijo Pellinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
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Selective targeting of PARP-2 inhibits androgen receptor signaling and prostate cancer growth through disruption of FOXA1 function. Proc Natl Acad Sci U S A 2019; 116:14573-14582. [PMID: 31266892 DOI: 10.1073/pnas.1908547116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Androgen receptor (AR) is a ligand-activated transcription factor and a key driver of prostate cancer (PCa) growth and progression. Understanding the factors influencing AR-mediated gene expression provides new opportunities for therapeutic intervention. Poly(ADP-ribose) Polymerase (PARP) is a family of enzymes, which posttranslationally modify a range of proteins and regulate many different cellular processes. PARP-1 and PARP-2 are two well-characterized PARP members, whose catalytic activity is induced by DNA-strand breaks and responsible for multiple DNA damage repair pathways. PARP inhibitors are promising therapeutic agents that show synthetic lethality against many types of cancer (including PCa) with homologous recombination (HR) DNA-repair deficiency. Here, we show that, beyond DNA damage repair function, PARP-2, but not PARP-1, is a critical component in AR transcriptional machinery through interacting with the pioneer factor FOXA1 and facilitating AR recruitment to genome-wide prostate-specific enhancer regions. Analyses of PARP-2 expression at both mRNA and protein levels show significantly higher expression of PARP-2 in primary PCa tumors than in benign prostate tissues, and even more so in castration-resistant prostate cancer (CRPC) tumors. Selective targeting of PARP-2 by genetic or pharmacological means blocks interaction between PARP-2 and FOXA1, which in turn attenuates AR-mediated gene expression and inhibits AR-positive PCa growth. Next-generation antiandrogens act through inhibiting androgen synthesis (abiraterone) or blocking ligand binding (enzalutamide). Selective targeting of PARP-2, however, may provide an alternative therapeutic approach for AR inhibition by disruption of FOXA1 function, which may be beneficial to patients, irrespective of their DNA-repair deficiency status.
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94
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Hernández-Llodrà S, Segalés L, Safont A, Juanpere N, Lorenzo M, Fumadó L, Rodríguez-Vida A, Cecchini L, Bellmunt J, Lloreta-Trull J. SPOP and FOXA1 mutations are associated with PSA recurrence in ERG wt tumors, and SPOP downregulation with ERG-rearranged prostate cancer. Prostate 2019; 79:1156-1165. [PMID: 31090082 DOI: 10.1002/pros.23830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/24/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND ERG fusion-related prostate cancer (PrCa) is the most prevalent oncogenic driver subclass. SPOP, FOXA1, and IDH1 mutations are other three main oncogenic driver subclasses in non-ETS-fusion PrCa. ERG protein levels seem to be increased in SPOP-mutated cases, and different studies reported that SPOP mutations and ERG fusions are mutually exclusive. The aim of this study has been to analyze the alterations in non-ETS-oncogenic drivers in PrCa. METHODS SPOP, FOXA1, and IDH mutations were investigated by polymerase chain reaction (PCR) and Sanger direct sequencing. ERG, SPOP, and TMPRSS2-ERG messenger RNA expression was assessed by quantitative real-time PCR from complementary DNA, and the presence of the fusion was also analyzed by nonquantitative PCR. The clinical pathological features were retrieved from the charts of the 111 patients included in the study (MARBiobanc, Barcelona, Spain). RESULTS Loss of SPOP expression (25.2%) was associated with ERG overexpression (P = 0.0036). SPOP mutations were found in 5.4% cases, all with wild-type (wt) ERG (P = 0.007). FOXA1 mutations were found in 8.2% cases, most of them ERG wt (P = 0.06). No IDH1 mutations were found. SPOP or FOXA1 mutations were found in 1.7% of ERG-rearranged, and 34.2% of non-ERG-rearranged cases (P < 0.0001). SPOP or FOXA1 alterations (mutations or expression loss) were significantly more common in GG5, while isolated ERG overexpression was more common in GG1 tumors (P = 0.042). SPOP-or FOXA1-mutated cases were associated with a shorter time to prostate-specific antigen (PSA) recurrence in the univariate (P = 0.0009), and with the PSA recurrence risk in the multivariate (P = 0.023) analysis. CONCLUSIONS In conclusion, SPOP and FOXA1 mutations may have prognostic value in ERG wt tumors. Interestingly, in absence of SPOP mutations, downregulation of this gene is a feature of many ERG-rearranged prostate tumors.
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Affiliation(s)
| | - Laura Segalés
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ainara Safont
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Juanpere
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Pathology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Marta Lorenzo
- Department of Pathology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Lluís Fumadó
- Department of Urology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Alejo Rodríguez-Vida
- Department of Oncology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Lluís Cecchini
- Department of Urology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
| | - Joaquim Bellmunt
- IMIM-Hospital del Mar Research Institute, Barcelona, Spain
- Harvard Medical School, Boston, Massachusetts
| | - Josep Lloreta-Trull
- Department of Health and Experimental Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Pathology, Hospital del Mar-Parc de Salut Mar-IMIM, Barcelona, Spain
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95
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Zhang S, Bai L, Chen Q, Ren Y, Zhang K, Wu Q, Huang H, Li W, Zhang Y, Zhang J, Liu Y. Identification of the O-GalNAcylation site(s) on FOXA1 catalyzed by ppGalNAc-T2 enzyme in vitro. Biochem Biophys Res Commun 2019; 514:157-165. [PMID: 31029427 DOI: 10.1016/j.bbrc.2019.04.146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 01/05/2023]
Abstract
FOXA1 functions as a pioneer factor of transcriptional regulation that binds to specific sites in the chromatin and recruits other transcription factors, promoting the initiation of gene transcription and mediating the regulation of downstream target gene expression. FOXA1 was reported to facilitate or reprogram ERα binding, thus playing a key function in breast cancer progression. Our previous results indicated that the O-linked N-acetylgalactosamine (O-GalNAc) modification of FOXA1 plays a potentially significant role in the ERα transcription network. However, further investigations are needed to identify the specific mechanism of modification and the specific glycosylation sites on FOXA1. In this study, we first suggested that FOXA1 could be O-GalNAcylated by ppGalNAc-T2 in vitro. By dividing and expressing recombinant FOXA1 as three segments, two O-GalNAcylation sites were found on FOXA1, both located at the C-terminal of the protein. Then, synthesized peptides, including the predicted O-GalNAc sites in the C-terminus of FOXA1, were used in a vitro reaction, and peptides mutated at the predicted O-GalNAc sites were employed as controls. Through an ESI-MS assay, S354 and S355 were identified as probable O-GalNAcylation sites on FOXA1. Additionally, we performed ESI-ETD-MS/MS analysis of the full-length O-GalNAcylated FOXA1 protein and identified S355 as the O-GalNAc modification site on FOXA1, consistent with the peptide reaction. In conclusion, our results demonstrated that FOXA1 can be O-GalNAcylated by ppGalNAc-T2 at S355 in vitro. These results will provide new insights for studying the role of O-GalNAcylation in the development of breast cancer.
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Affiliation(s)
- Siqi Zhang
- School of Life Science & Medicine, Dalian University of Technology, Panjin, China
| | - Lijuan Bai
- School of Life Science & Medicine, Dalian University of Technology, Panjin, China
| | - Qiushi Chen
- BGI-Shenzhen, Yantian District, Shenzhen, China
| | - Yan Ren
- BGI-Shenzhen, Yantian District, Shenzhen, China
| | - Keren Zhang
- BGI-Shenzhen, Yantian District, Shenzhen, China
| | - Qiong Wu
- School of Life Science & Medicine, Dalian University of Technology, Panjin, China
| | - Huang Huang
- School of Life Science & Medicine, Dalian University of Technology, Panjin, China
| | - Wenli Li
- School of Life Science & Medicine, Dalian University of Technology, Panjin, China
| | - Yan Zhang
- Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, China.
| | - Jianing Zhang
- School of Life Science & Medicine, Dalian University of Technology, Panjin, China.
| | - Yubo Liu
- School of Life Science & Medicine, Dalian University of Technology, Panjin, China.
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96
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Kwan EM, Fettke H, Docanto MM, To SQ, Bukczynska P, Mant A, Pook D, Ng N, Graham LJK, Mangiola S, Segelov E, Mahon K, Davis ID, Parente P, Pezaro C, Todenhöfer T, Horvath LG, Azad AA. Prognostic Utility of a Whole-blood Androgen Receptor-based Gene Signature in Metastatic Castration-resistant Prostate Cancer. Eur Urol Focus 2019; 7:63-70. [PMID: 31103601 DOI: 10.1016/j.euf.2019.04.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/27/2019] [Accepted: 04/30/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND The treatment paradigm for metastatic castration-resistant prostate cancer (mCRPC) has evolved significantly in recent years. Identifying predictive and/or prognostic biomarkers in the context of this rapidly expanding therapeutic armamentarium remains a pressing and unmet clinical need. OBJECTIVE To develop a prognostic whole-blood gene signature for mCRPC patients. DESIGN, SETTING, AND PARTICIPANTS As part of an ongoing prospective, multicentre biomarker research study (Australian Prostate Biomarker Alliance), we enrolled 115 mCRPC patients commencing chemotherapy (n = 34) or androgen receptor (AR) pathway inhibitors therapy (n = 81) and obtained pretreatment whole-blood samples in PAXgene RNA tubes. Gene expression was assessed using reverse transcription-polymerase chain reaction. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Gene transcripts correlating with overall survival (OS) at p < 0.10 in univariate Cox regression models were incorporated into a multigene signature. Kaplan-Meier survival estimates and multivariate analyses were used to assess association with clinical outcomes. Prognostic strength of the signature was estimated using a concordance probability estimate (CPE). RESULTS AND LIMITATIONS Based on univariate analysis for OS, the following genes were incorporated into a multigene signature: AR splice variant 7 (AR-V7), and three androgen-regulated genes: GRHL2, HOXB13, and FOXA1. The number of positive transcripts clearly stratified survival outcomes (median OS: not reached vs 24.8 mo vs 16.2 mo for 0, 1, and ≥2 transcripts, respectively; p = 0.0052). Notably, this multigene signature retained prognostic significance on multivariable analysis (hazard ratio, 2.1; 95% confidence interval, 1.1-4.0; p = 0.019). Moreover, CPE for this model was 0.78, indicating strong discriminative capacity. Limitations include short follow-up time. CONCLUSIONS Our data demonstrate the prognostic utility of a novel whole-blood AR-based signature in mCRPC patients commencing contemporary systemic therapies. Our pragmatic assay requires minimal processing, can be performed in most hospital laboratories, and could represent a key prognostic tool for risk stratification in mCRPC. PATIENT SUMMARY We found that expression of certain genes associated with the androgen receptor could help determine how long men with advanced prostate cancer survive after starting modern drug therapies.
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Affiliation(s)
- Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia; Department of Medical Oncology, Monash Health, Melbourne, VIC, Australia
| | - Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - Maria M Docanto
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - Sarah Q To
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - Patricia Bukczynska
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - Andrew Mant
- Medical Oncology Unit, Eastern Health, Melbourne, VIC, Australia; Eastern Health Clinical School, Monash University, Melbourne, VIC, Australia
| | - David Pook
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia; Department of Medical Oncology, Monash Health, Melbourne, VIC, Australia
| | - Nicole Ng
- Department of Medical Oncology, Monash Health, Melbourne, VIC, Australia
| | | | - Stefano Mangiola
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Eva Segelov
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia; Department of Medical Oncology, Monash Health, Melbourne, VIC, Australia
| | - Kate Mahon
- Medical Oncology, Chris O'Brien Lifehouse, Camperdown, NSW, Australia; University of Sydney, Sydney, NSW, Australia; Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ian D Davis
- Medical Oncology Unit, Eastern Health, Melbourne, VIC, Australia; Eastern Health Clinical School, Monash University, Melbourne, VIC, Australia
| | - Phillip Parente
- Medical Oncology Unit, Eastern Health, Melbourne, VIC, Australia; Eastern Health Clinical School, Monash University, Melbourne, VIC, Australia
| | - Carmel Pezaro
- Medical Oncology Unit, Eastern Health, Melbourne, VIC, Australia; Eastern Health Clinical School, Monash University, Melbourne, VIC, Australia
| | | | - Lisa G Horvath
- Medical Oncology, Chris O'Brien Lifehouse, Camperdown, NSW, Australia; Royal Prince Alfred Hospital, Camperdown, Sydney, NSW, Australia; University of Sydney, Sydney, NSW, Australia; Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia; Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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Holding AN, Giorgi FM, Donnelly A, Cullen AE, Nagarajan S, Selth LA, Markowetz F. VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer. Genome Biol 2019; 20:91. [PMID: 31084623 PMCID: PMC6515683 DOI: 10.1186/s13059-019-1698-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND VirtUaL ChIP-seq Analysis through Networks (VULCAN) infers regulatory interactions of transcription factors by overlaying networks generated from publicly available tumor expression data onto ChIP-seq data. We apply our method to dissect the regulation of estrogen receptor-alpha activation in breast cancer to identify potential co-regulators of the estrogen receptor's transcriptional response. RESULTS VULCAN analysis of estrogen receptor activation in breast cancer highlights the key components of the estrogen receptor complex alongside a novel interaction with GRHL2. We demonstrate that GRHL2 is recruited to a subset of estrogen receptor binding sites and regulates transcriptional output, as evidenced by changes in estrogen receptor-associated eRNA expression and stronger estrogen receptor binding at active enhancers after GRHL2 knockdown. CONCLUSIONS Our findings provide new insight into the role of GRHL2 in regulating eRNA transcription as part of estrogen receptor signaling. These results demonstrate VULCAN, available from Bioconductor, as a powerful predictive tool.
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Affiliation(s)
- Andrew N Holding
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
- The Alan Turing Institute, 96 Euston Road, Kings Cross, London, NW1 2DB, UK.
| | - Federico M Giorgi
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, Bologna, Italy
| | - Amanda Donnelly
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amy E Cullen
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Florian Markowetz
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
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98
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Gao Y, Li J, Zhang Z, Zhang R, Pollock A, Sun T. MicroRNA miR-7 and miR-17-92 in the Arcuate Nucleus of Mouse Hypothalamus Regulate Sex-Specific Diet-Induced Obesity. Mol Neurobiol 2019; 56:7508-7521. [DOI: 10.1007/s12035-019-1618-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/23/2019] [Indexed: 12/19/2022]
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99
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Stelloo S, Bergman AM, Zwart W. Androgen receptor enhancer usage and the chromatin regulatory landscape in human prostate cancers. Endocr Relat Cancer 2019; 26:R267-R285. [PMID: 30865928 DOI: 10.1530/erc-19-0032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance. Genome-wide chromatin association studies revealed that transcriptional regulation by AR mainly depends on binding to distal regulatory enhancer elements that control gene expression through chromatin looping to gene promoters. Changes in the chromatin epigenetic landscape and DNA sequence can locally alter AR-DNA-binding capacity and consequently impact transcriptional output and disease outcome. The vast majority of reports describing AR chromatin interactions have been limited to cell lines, identifying numerous other factors and interacting transcription factors that impact AR chromatin interactions. Do these factors also impact AR cistromics - the genome-wide chromatin-binding landscape of AR - in vivo? Recent technological advances now enable researchers to identify AR chromatin-binding sites and their target genes in human specimens. In this review, we provide an overview of the different factors that influence AR chromatin binding in prostate cancer specimens, which is complemented with knowledge from cell line studies. Finally, we discuss novel perspectives on studying AR cistromics in clinical samples.
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Affiliation(s)
- Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
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100
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Coons LA, Burkholder AB, Hewitt SC, McDonnell DP, Korach KS. Decoding the Inversion Symmetry Underlying Transcription Factor DNA-Binding Specificity and Functionality in the Genome. iScience 2019; 15:552-591. [PMID: 31152742 PMCID: PMC6542189 DOI: 10.1016/j.isci.2019.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/26/2018] [Accepted: 12/04/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding why a transcription factor (TF) binds to a specific DNA element in the genome and whether that binding event affects transcriptional output remains a great challenge. In this study, we demonstrate that TF binding in the genome follows inversion symmetry (IS). In addition, the specific DNA elements where TFs bind in the genome are determined by internal IS within the DNA element. These DNA-binding rules quantitatively define how TFs select the appropriate regulatory targets from a large number of similar DNA elements in the genome to elicit specific transcriptional and cellular responses. Importantly, we also demonstrate that these DNA-binding rules extend to DNA elements that do not support transcriptional activity. That is, the DNA-binding rules are obeyed, but the retention time of the TF at these non-functional DNA elements is not long enough to initiate and/or maintain transcription. We further demonstrate that IS is universal within the genome. Thus, IS is the DNA code that TFs use to interact with the genome and dictates (in conjunction with known DNA sequence constraints) which of those interactions are functionally active.
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Affiliation(s)
- Laurel A Coons
- Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, 111 T.W. Alexander Dr., Research Triangle Park, NC 27709, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Adam B Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Sylvia C Hewitt
- Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, 111 T.W. Alexander Dr., Research Triangle Park, NC 27709, USA
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth S Korach
- Receptor Biology Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, 111 T.W. Alexander Dr., Research Triangle Park, NC 27709, USA.
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