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Murray-Nerger LA, Lozano C, Burton EM, Liao Y, Ungerleider NA, Guo R, Gewurz BE. The nucleic acid binding protein SFPQ represses EBV lytic reactivation by promoting histone H1 expression. Nat Commun 2024; 15:4156. [PMID: 38755141 PMCID: PMC11099029 DOI: 10.1038/s41467-024-48333-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Epstein-Barr virus (EBV) uses a biphasic lifecycle of latency and lytic reactivation to infect >95% of adults worldwide. Despite its central role in EBV persistence and oncogenesis, much remains unknown about how EBV latency is maintained. We used a human genome-wide CRISPR/Cas9 screen to identify that the nuclear protein SFPQ was critical for latency. SFPQ supported expression of linker histone H1, which stabilizes nucleosomes and regulates nuclear architecture, but has not been previously implicated in EBV gene regulation. H1 occupied latent EBV genomes, including the immediate early gene BZLF1 promoter. Upon reactivation, SFPQ was sequestered into sub-nuclear puncta, and EBV genomic H1 occupancy diminished. Enforced H1 expression blocked EBV reactivation upon SFPQ knockout, confirming it as necessary downstream of SFPQ. SFPQ knockout triggered reactivation of EBV in B and epithelial cells, as well as of Kaposi's sarcoma-associated herpesvirus in B cells, suggesting a conserved gamma-herpesvirus role. These findings highlight SFPQ as a major regulator of H1 expression and EBV latency.
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Affiliation(s)
- Laura A Murray-Nerger
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Virology, Boston, MA, 02115, USA
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Clarisel Lozano
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Eric M Burton
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Virology, Boston, MA, 02115, USA
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Yifei Liao
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Program in Virology, Boston, MA, 02115, USA
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | | | - Rui Guo
- Department of Molecular Biology and Microbiology, Tufts University, Medford, MA, 02155, USA
| | - Benjamin E Gewurz
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Program in Virology, Boston, MA, 02115, USA.
- Center for Integrated Solutions to Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
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2
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Ashton AW, Dhanjal HK, Rossner B, Mahmood H, Patel VI, Nadim M, Lota M, Shahid F, Li Z, Joyce D, Pajkos M, Dosztányi Z, Jiao X, Pestell RG. Acetylation of nuclear receptors in health and disease: an update. FEBS J 2024; 291:217-236. [PMID: 36471658 DOI: 10.1111/febs.16695] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/17/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a common reversible post-translational modification of proteins that plays a key role in regulating gene expression. Nuclear receptors (NRs) include ligand-inducible transcription factors and orphan receptors for which the ligand is undetermined, which together regulate the expression of genes involved in development, metabolism, homeostasis, reproduction and human diseases including cancer. Since the original finding that the ERα, AR and HNF4 are acetylated, we now understand that the vast majority of NRs are acetylated and that this modification has profound effects on NR function. Acetylation sites are often conserved and involve both ordered and disordered regions of NRs. The acetylated residues function as part of an intramolecular signalling platform intersecting phosphorylation, methylation and other modifications. Acetylation of NR has been shown to impact recruitment into chromatin, co-repressor and coactivator complex formation, sensitivity and specificity of regulation by ligand and ligand antagonists, DNA binding, subcellular distribution and transcriptional activity. A growing body of evidence in mice indicates a vital role for NR acetylation in metabolism. Additionally, mutations of the NR acetylation site occur in human disease. This review focuses on the role of NR acetylation in coordinating signalling in normal physiology and disease.
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Affiliation(s)
- Anthony W Ashton
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Lankenau Institute for Medical Research, Wynnewood, PA, USA
| | | | - Benjamin Rossner
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Huma Mahmood
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Vivek I Patel
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Mohammad Nadim
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Manpreet Lota
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Farhan Shahid
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Zhiping Li
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, USA
| | - David Joyce
- Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Matyas Pajkos
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Xuanmao Jiao
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, USA
| | - Richard G Pestell
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, USA
- The Wistar Cancer Center, Philadelphia, PA, USA
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3
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Takayama KI, Matsuoka S, Adachi S, Honma T, Yoshida M, Doi T, Shin-ya K, Yoshida M, Osada H, Inoue S. Identification of small-molecule inhibitors against the interaction of RNA-binding protein PSF and its target RNA for cancer treatment. PNAS NEXUS 2023; 2:pgad203. [PMID: 37388923 PMCID: PMC10304769 DOI: 10.1093/pnasnexus/pgad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023]
Abstract
Diverse cellular activities are modulated through a variety of RNAs, including long noncoding RNAs (lncRNAs), by binding to certain proteins. The inhibition of oncogenic proteins or RNAs is expected to suppress cancer cell proliferation. We have previously demonstrated that PSF interaction with its target RNAs, such as androgen-induced lncRNA CTBP1-AS, is critical for hormone therapy resistance in prostate and breast cancers. However, the action of protein-RNA interactions remains almost undruggable to date. High-throughput screening (HTS) has facilitated the discovery of drugs for protein-protein interactions. In the present study, we developed an in vitro alpha assay using Flag peptide-conjugated lncRNA, CTBP1-AS, and PSF. We then constructed an effective HTS screening system to explore small compounds that inhibit PSF-RNA interactions. Thirty-six compounds were identified and dose-dependently inhibited PSF-RNA interaction in vitro. Moreover, chemical optimization of these lead compounds and evaluation of cancer cell proliferation revealed two promising compounds, N-3 and C-65. These compounds induced apoptosis and inhibited cell growth in prostate and breast cancer cells. By inhibiting PSF-RNA interaction, N-3 and C-65 up-regulated signals that are repressed by PSF, such as the cell cycle signals by p53 and p27. Furthermore, using a mouse xenograft model for hormone therapy-resistant prostate cancer, we revealed that N-3 and C-65 can significantly suppress tumor growth and downstream target gene expression, such as the androgen receptor (AR). Thus, our findings highlight a therapeutic strategy through the development of inhibitors for RNA-binding events in advanced cancers.
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Affiliation(s)
- Ken-ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, itabashi-ku, Tokyo 173-0015, Japan
| | - Seiji Matsuoka
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shungo Adachi
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Masahito Yoshida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Drug Discovery Chemical Bank Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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Hodges SL, Bouza AA, Isom LL. Therapeutic Potential of Targeting Regulated Intramembrane Proteolysis Mechanisms of Voltage-Gated Ion Channel Subunits and Cell Adhesion Molecules. Pharmacol Rev 2022; 74:1028-1048. [PMID: 36113879 PMCID: PMC9553118 DOI: 10.1124/pharmrev.121.000340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/13/2022] [Indexed: 10/03/2023] Open
Abstract
Several integral membrane proteins undergo regulated intramembrane proteolysis (RIP), a tightly controlled process through which cells transmit information across and between intracellular compartments. RIP generates biologically active peptides by a series of proteolytic cleavage events carried out by two primary groups of enzymes: sheddases and intramembrane-cleaving proteases (iCLiPs). Following RIP, fragments of both pore-forming and non-pore-forming ion channel subunits, as well as immunoglobulin super family (IgSF) members, have been shown to translocate to the nucleus to function in transcriptional regulation. As an example, the voltage-gated sodium channel β1 subunit, which is also an IgSF-cell adhesion molecule (CAM), is a substrate for RIP. β1 RIP results in generation of a soluble intracellular domain, which can regulate gene expression in the nucleus. In this review, we discuss the proposed RIP mechanisms of voltage-gated sodium, potassium, and calcium channel subunits as well as the roles of their generated proteolytic products in the nucleus. We also discuss other RIP substrates that are cleaved by similar sheddases and iCLiPs, such as IgSF macromolecules, including CAMs, whose proteolytically generated fragments function in the nucleus. Importantly, dysfunctional RIP mechanisms are linked to human disease. Thus, we will also review how understanding RIP events and subsequent signaling processes involving ion channel subunits and IgSF proteins may lead to the discovery of novel therapeutic targets. SIGNIFICANCE STATEMENT: Several ion channel subunits and immunoglobulin superfamily molecules have been identified as substrates of regulated intramembrane proteolysis (RIP). This signal transduction mechanism, which generates polypeptide fragments that translocate to the nucleus, is an important regulator of gene transcription. RIP may impact diseases of excitability, including epilepsy, cardiac arrhythmia, and sudden death syndromes. A thorough understanding of the role of RIP in gene regulation is critical as it may reveal novel therapeutic strategies for the treatment of previously intractable diseases.
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Affiliation(s)
- Samantha L Hodges
- Departments of Pharmacology (S.L.H., A.A.B., L.L.I.), Neurology (L.L.I.), and Molecular & Integrative Physiology (L.L.I.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Alexandra A Bouza
- Departments of Pharmacology (S.L.H., A.A.B., L.L.I.), Neurology (L.L.I.), and Molecular & Integrative Physiology (L.L.I.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Lori L Isom
- Departments of Pharmacology (S.L.H., A.A.B., L.L.I.), Neurology (L.L.I.), and Molecular & Integrative Physiology (L.L.I.), University of Michigan Medical School, Ann Arbor, Michigan
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5
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Jafari H, Hussain S, Campbell MJ. Nuclear Receptor Coregulators in Hormone-Dependent Cancers. Cancers (Basel) 2022; 14:2402. [PMID: 35626007 PMCID: PMC9139824 DOI: 10.3390/cancers14102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/10/2022] Open
Abstract
Nuclear receptors (NRs) function collectively as a transcriptional signaling network that mediates gene regulatory actions to either maintain cellular homeostasis in response to hormonal, dietary and other environmental factors, or act as orphan receptors with no known ligand. NR complexes are large and interact with multiple protein partners, collectively termed coregulators. Coregulators are essential for regulating NR activity and can dictate whether a target gene is activated or repressed by a variety of mechanisms including the regulation of chromatin accessibility. Altered expression of coregulators contributes to a variety of hormone-dependent cancers including breast and prostate cancers. Therefore, understanding the mechanisms by which coregulators interact with and modulate the activity of NRs provides opportunities to develop better prognostic and diagnostic approaches, as well as novel therapeutic targets. This review aims to gather and summarize recent studies, techniques and bioinformatics methods used to identify distorted NR coregulator interactions that contribute as cancer drivers in hormone-dependent cancers.
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Affiliation(s)
- Hedieh Jafari
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA;
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Shahid Hussain
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Moray J. Campbell
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
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6
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Shadrina OA, Kikhay TF, Agapkina YY, Gottikh MB. SFPQ and NONO Proteins and Long Non-Coding NEAT1 RNA: Cellular Functions and Role in the HIV-1 Life Cycle. Mol Biol 2022. [DOI: 10.1134/s0026893322020133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Katano-Toki A, Yoshino S, Nakajima Y, Tomaru T, Nishikido A, Ishida E, Horiguchi K, Saito T, Ozawa A, Satoh T, Yamada M. SFPQ associated with a co-activator for PPARγ, HELZ2, regulates key nuclear factors for adipocyte differentiation. Biochem Biophys Res Commun 2021; 562:139-145. [PMID: 34052659 DOI: 10.1016/j.bbrc.2021.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
We recently isolated a novel co-activator of peroxisome proliferator-activated receptor γ, helicase with zinc finger 2 (HELZ2). HELZ2 null mice were resistant to diet-induced obesity and NAFFL/NASH, and HELZ2 was phosphorylated at tyrosine residues. In order to find a factor related to HELZ2, we analyzed products co-immunoprecipitated with phosphorylated HELZ2 by mass spectrometry analyses. We identified proline- and glutamine-rich (SFPQ) as a protein associating with tyrosine-phosphorylated HELZ2. The knockdown of SFPQ in 3T3-L1 cells downregulated mRNA levels of transcription factors including Krox20, Cebpβ, and Cebpδ: key factors for early-stage adipocyte differentiation. In addition, knockdown of SFPQ inhibited 3T3-L1 cell differentiation to mature adipocytes. These findings demonstrated that SFPQ associating with HELZ2 is an important novel transcriptional regulator of adipocyte differentiation.
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Affiliation(s)
- Akiko Katano-Toki
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan.
| | - Satoshi Yoshino
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Yasuyo Nakajima
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takuya Tomaru
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Ayaka Nishikido
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Emi Ishida
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kazuhiko Horiguchi
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tsugumichi Saito
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Atsushi Ozawa
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tetsurou Satoh
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Masanobu Yamada
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
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8
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Takayama KI, Honma T, Suzuki T, Kondoh Y, Osada H, Suzuki Y, Yoshida M, Inoue S. Targeting Epigenetic and Posttranscriptional Gene Regulation by PSF Impairs Hormone Therapy-Refractory Cancer Growth. Cancer Res 2021; 81:3495-3508. [PMID: 33975881 DOI: 10.1158/0008-5472.can-20-3819] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/05/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022]
Abstract
RNA-binding protein PSF functions as an epigenetic modifier by interacting with long noncoding RNAs and the corepressor complex. PSF also promotes RNA splicing events to enhance oncogenic signals. In this study, we conducted an in vitro chemical array screen and identified multiple small molecules that interact with PSF. Several molecules inhibited RNA binding by PSF and decreased prostate cancer cell viability. Among these molecules and its derivatives was a promising molecule, No. 10-3 [7,8-dihydroxy-4-(4-methoxyphenyl)chromen-2-one], that was the most effective at blocking PSF RNA-binding ability and suppressing treatment-resistant prostate and breast cancer cell proliferation. Exposure to No. 10-3 inhibited PSF target gene expression at the mRNA level. Treatment with No. 10-3 reversed epigenetically repressed PSF downstream targets, such as cell-cycle inhibitors, at the transcriptional level. Chromatin immunoprecipitation sequencing in prostate cancer cells revealed that No. 10-3 enhances histone acetylation to induce expression of apoptosis as well as cell-cycle inhibitors. Furthermore, No. 10-3 exhibited antitumor efficacy in a hormone therapy-resistant prostate cancer xenograft mouse model, suppressing treatment-resistant tumor growth. Taken together, this study highlights the feasibility of targeting PSF-mediated epigenetic and RNA-splicing activities for the treatment of aggressive cancers. SIGNIFICANCE: This study identifies small molecules that target PSF-RNA interactions and suppress hormone therapy-refractory cancer growth, suggesting the potential of targeting PSF-mediated gene regulation for cancer treatment.
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Affiliation(s)
- Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Drug Discovery Chemical Bank Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Drug Discovery Chemical Bank Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan. .,Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
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9
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Liang S, Takahashi H, Hirose T, Kuramitsu Y, Hatakeyama S, Yoshiyama H, Wang R, Hamada JI, Iizasa H. NONO Is a Negative Regulator of SOX2 Promoter. Cancer Genomics Proteomics 2021; 17:359-367. [PMID: 32576581 DOI: 10.21873/cgp.20195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND/AIM Sex determining region Y (SRY)-box 2 (SOX2) is a transcription factor essential for the maintenance of proliferation and self-renewal of cancer stem cells and is associated with breast cancer initiation. Regulation of cancer stem cell plasticity by SOX2 requires both positive and negative SOX2 transcription factors, but the negative regulator is still largely unknown. MATERIALS AND METHODS SOX2 promoter-binding proteins were identified by liquid chromatography-mass spectrometry/mass spectrometry, luciferase assay, and chromatin immunoprecipitation. The effects of one such transcription factor on SOX2 expression was investigated by knockdown and overexpression experiments. RESULTS Non-POU domain-containing octamer-binding protein (NONO) (also known as 54-kDa nuclear RNA-binding protein, P54NRB) was identified as a SOX2 promoter-binding protein and a negative regulator of SOX2 expression. Its activity was controlled by its coiled-coil domain and the C-terminal domain. CONCLUSION These results suggest that NONO acts as a key regulator of SOX2 transcription through the repression of SOX2 promoter activity in breast cancer cells.
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Affiliation(s)
- Shanshan Liang
- The Key Laboratory of Biomarker High-throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Oncology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, P.R. China.,Department of Microbiology, Faculty of Medicine, Shimane University, Shimane, Japan.,Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Hidehisa Takahashi
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Japan.,Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama City University Graduate School of Medical Science, Yokohama, Japan
| | - Tetsuro Hirose
- Division of RNA Bio-function, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yasuhiro Kuramitsu
- Health Science University of Hokkaido School of Nursing & Social Services, Hokkaido, Japan
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, Shimane, Japan
| | - Ruoyu Wang
- The Key Laboratory of Biomarker High-throughput Screening and Target Translation of Breast and Gastrointestinal Tumor, Oncology Department, Affiliated Zhongshan Hospital of Dalian University, Dalian, P.R. China
| | - Jun-Ichi Hamada
- Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan .,Health Science University of Hokkaido School of Nursing & Social Services, Hokkaido, Japan
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, Shimane, Japan .,Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
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10
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The Emerging Role of the RNA-Binding Protein SFPQ in Neuronal Function and Neurodegeneration. Int J Mol Sci 2020; 21:ijms21197151. [PMID: 32998269 PMCID: PMC7582472 DOI: 10.3390/ijms21197151] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are a class of proteins known for their diverse roles in RNA biogenesis, from regulating transcriptional processes in the nucleus to facilitating translation in the cytoplasm. With higher demand for RNA metabolism in the nervous system, RBP misregulation has been linked to a wide range of neurological and neurodegenerative diseases. One of the emerging RBPs implicated in neuronal function and neurodegeneration is splicing factor proline- and glutamine-rich (SFPQ). SFPQ is a ubiquitous and abundant RBP that plays multiple regulatory roles in the nucleus such as paraspeckle formation, DNA damage repair, and various transcriptional regulation processes. An increasing number of studies have demonstrated the nuclear and also cytoplasmic roles of SFPQ in neurons, particularly in post-transcriptional regulation and RNA granule formation. Not surprisingly, the misregulation of SFPQ has been linked to pathological features shown by other neurodegenerative disease-associated RBPs such as aberrant RNA splicing, cytoplasmic mislocalization, and aggregation. In this review, we discuss recent findings on the roles of SFPQ with a particular focus on those in neuronal development and homeostasis as well as its implications in neurodegenerative diseases.
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11
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Palomares KT, Parobchak N, Ithier MC, Aleksunes LM, Castaño PM, So M, Faro R, Heller D, Wang B, Rosen T. Fetal Exosomal Platelet-activating Factor Triggers Functional Progesterone Withdrawal in Human Placenta. Reprod Sci 2020; 28:252-262. [PMID: 32780361 DOI: 10.1007/s43032-020-00283-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/31/2020] [Indexed: 11/27/2022]
Abstract
In most mammals, labor is heralded by the withdrawal of progesterone. In humans, circulating progesterone levels increase as gestation advances while placental expression of progesterone receptor A (PR-A) declines. As a result of PR-A downregulation, the non-canonical NF-κB pathway is activated, an event implicated in triggering labor. Here, we sought to identify fetal-derived mediator(s) that represses placental PR-A in human placenta leading to activation of pro-labor signaling. Lipidomic profiling demonstrated enrichment of platelet-activating factor (PAF) in exosomes originating from the human fetus. Exposure of primary cytotrophoblasts to fetal exosomes from term pregnancies reduced PR-A expression by > 50%, and PAF also reduced PR-A message levels in a dose-dependent manner. Notably, fetal exosomes from preterm pregnancies had lower PAF levels and no effect on PR-A expression. Synthetic PAF-induced DNA methylation increases by 20% at the PR-A promoter, leading to recruitment of corepressors and downregulation of PR-A in cytotrophoblast. Furthermore, suppression of PR-A by PAF-stimulated expression of the pro-labor genes, corticotropin-releasing hormone (CRH) and cyclooxygenase-2 (COX-2), which was reversed by disruption of the DNA methyltransferases 3B and 3L. Taken together, PAF represents a novel fetal-derived candidate for initiation of labor by stimulating methylation and repression of PR-A and activating pro-labor signaling in trophoblast.
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Affiliation(s)
- Kristy T Palomares
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, NJ, 08901, USA
| | - Nataliya Parobchak
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Mayra Cruz Ithier
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Lauren M Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, 08854, USA
| | - Paula M Castaño
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Melody So
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
| | - Revital Faro
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, NJ, 08901, USA
| | - Debra Heller
- Department of Pathology and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Bingbing Wang
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA.
| | - Todd Rosen
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA.
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12
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Guo P, Chen S, Li D, Zhang J, Luo J, Zhang A, Yu D, Bloom MS, Chen L, Chen W. SFPQ is involved in regulating arsenic-induced oxidative stress by interacting with the miRNA-induced silencing complexes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114160. [PMID: 32066060 DOI: 10.1016/j.envpol.2020.114160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/06/2020] [Accepted: 02/09/2020] [Indexed: 06/10/2023]
Abstract
Arsenic exposure contributed to the development of human diseases. Arsenic exerted multiple organ toxicities mainly by triggering oxidative stress. However, the signaling pathway underlying oxidative stress is unclear. We previously found that the expression of SFPQ, a splicing factor, was positively associated with urinary arsenic concentration in an arsenic-exposed population, suggesting an oxidative stress regulatory role for SFPQ. To test this hypothesis, we established cell models of oxidative stress in human hepatocyte cells (L02) treated with NaAsO2. Reactive oxygen species (ROS) synthesis displayed a time- and dose-dependent increase with NaAsO2 treatment. SFPQ suppression resulted in a 36%-53% decrease in ROS generation, leading to enhanced cellular damage determined by 8-OHdG, comet tail moment, and micronucleus analysis. Particularly, SFPQ deficiency attenuated expression of the oxidase genes DUOX1, DUOX2, NCF2, and NOX2. A fluorescent-based RNA electrophoretic mobility shift assay (FREMSA) and dual-luciferase reporter system revealed that miR-92b-5p targeted DUOX2 mRNA degradation. An RNA immunoprecipitation assay showed an interaction between SFPQ and miR-92b-5p of the miRNA-induced silencing complex (miRISC). Notably, NaAsO2 treatment diminished the interaction between SFPQ and miR92b-5p, accompanied by decreased binding between miR-92b-5p and 3'-UTR of DUOX2. However, SFPQ deficiency suppressed the dissociation of miR-92b-5p from 3'-UTR of DUOX2, indicating that miR-92b-5p regulated the SFPQ-dependent DUOX2 expression. Taken together, we reveal that SFPQ responds to arsenic-induced oxidative stress by interacting with the miRISC. These findings offer new insight into the potential role of SFPQ in regulating cellular stress response.
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Affiliation(s)
- Ping Guo
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shen Chen
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Daochuan Li
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jinmiao Zhang
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiao Luo
- School of Public Health, Qingdao University, Qingdao 266071, China
| | - Aihua Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao 266071, China
| | - Michael S Bloom
- Departments of Environmental Health Sciences & Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, NY 12144, USA
| | - Liping Chen
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
| | - Wen Chen
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
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13
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Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone. PLoS Genet 2020; 16:e1008770. [PMID: 32453730 PMCID: PMC7274477 DOI: 10.1371/journal.pgen.1008770] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/05/2020] [Accepted: 04/08/2020] [Indexed: 01/18/2023] Open
Abstract
Hormone-dependent activation of enhancers includes histone hyperacetylation and mediator recruitment. Histone hyperacetylation is mostly explained by a bimodal switch model, where histone deacetylases (HDACs) disassociate from chromatin, and histone acetyl transferases (HATs) are recruited. This model builds on decades of research on steroid receptor regulation of transcription. Yet, the general concept of the bimodal switch model has not been rigorously tested genome wide. We have used a genomics approach to study enhancer hyperacetylation by the thyroid hormone receptor (TR), described to operate as a bimodal switch. H3 acetylation, HAT and HDAC ChIP-seq analyses of livers from hypo- and hyperthyroid wildtype, TR deficient and NCOR1 disrupted mice reveal three types of thyroid hormone (T3)-regulated enhancers. One subset of enhancers is bound by HDAC3-NCOR1 in the absence of hormone and constitutively occupy TR and HATs irrespective of T3 levels, suggesting a poised enhancer state in absence of hormone. In presence of T3, HDAC3-NCOR1 dissociates from these enhancers leading to histone hyperacetylation, suggesting a histone acetylation rheostat function of HDACs at poised enhancers. Another subset of enhancers, not occupied by HDACs, is hyperacetylated in a T3-dependent manner, where TR is recruited to chromatin together with HATs. Lastly, a subset of enhancers, is not occupied directly by TR yet requires TR for histone hyperacetylation. This indirect enhancer activation involves co-association with TR bound enhancers within super-enhancers or topological associated domains. Collectively, this demonstrates various mechanisms controlling hormone-dependent transcription and adds significant details to the otherwise simple bimodal switch model. Thyroid hormone (T3) is a central regulator of growth, thermogenesis, heart rate and metabolism. In the liver T3 binds thyroid hormone receptor beta (TRβ) controlling expression of genes involved in processes such as lipid and cholesterol metabolism. The molecular mechanisms controlling TR-dependent gene regulation are centred on a bimodal switch model. In the absence of T3 co-repressors bind TR reducing gene expression. When hormone binds TR, co-repressors dissociate, and co-activators are recruited inducing gene expression. This model predominates the current understanding of T3-regulated gene expression. However, only a few studies have tested this model by genome-wide approaches. We have quantified histone3 acetylation genome-wide in the liver of hypo- and hyperthyroid mice and identified gene regulatory regions regulated by T3. Probing TR and co-regulators at these regulatory regions, and analysing histone3 acetylation in mouse models for disrupted co-repressor and TR activity, reveal additional insights to the mechanisms regulating T3-dependent gene expression. We suggest a revision of the prevailing bimodal switch model which helps understanding T3-regulated gene expression in tissues such as liver. We hope that this study, together with future studies, will add new perspectives on nuclear receptor-mediated transcriptional regulation to reveal general principles.
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14
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Mitobe Y, Iino K, Takayama KI, Ikeda K, Suzuki T, Aogi K, Kawabata H, Suzuki Y, Horie-Inoue K, Inoue S. PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2. Cancer Res 2020; 80:2230-2242. [PMID: 32213542 DOI: 10.1158/0008-5472.can-19-3095] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 01/15/2020] [Accepted: 03/18/2020] [Indexed: 11/16/2022]
Abstract
Endocrine therapy is standard treatment for estrogen receptor (ER)-positive breast cancer, yet long-term treatment often causes acquired resistance, which results in recurrence and metastasis. Recent studies have revealed that RNA-binding proteins (RBP) are involved in tumorigenesis. Here, we demonstrate that PSF/SFPQ is an RBP that potentially predicts poor prognosis of patients with ER-positive breast cancer by posttranscriptionally regulating ERα (ESR1) mRNA expression. Strong PSF immunoreactivity correlated with shorter overall survival in patients with ER-positive breast cancer. PSF was predominantly expressed in a model of tamoxifen-resistant breast cancer cells, and depletion of PSF attenuated proliferation of cultured cells and xenografted tumors. PSF expression was significantly associated with estrogen signaling. PSF siRNA downregulated ESR1 mRNA by inhibiting nuclear export of the RNA. Integrative analyses of microarray and RNA immunoprecipitation sequencing also identified SCFD2, TRA2B, and ASPM as targets of PSF. Among the PSF targets, SCFD2 was a poor prognostic indicator of breast cancer and SCFD2 knockdown significantly suppressed breast cancer cell proliferation. Collectively, this study shows that PSF plays a pathophysiologic role in ER-positive breast cancer by posttranscriptionally regulating expression of its target genes such as ESR1 and SCFD2. Overall, PSF and SCFD2 could be potential diagnostic and therapeutic targets for primary and hormone-refractory breast cancers. SIGNIFICANCE: This study defines oncogenic roles of RNA-binding protein PSF, which exhibits posttranscriptional regulation in ER-positive breast cancer.
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Affiliation(s)
- Yuichi Mitobe
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Kaori Iino
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
| | - Kazuhiro Ikeda
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kenjiro Aogi
- Department of Surgery, National Shikoku Cancer Center, Matsuyama, Ehime, Japan
| | - Hidetaka Kawabata
- Department of Breast and Endocrine Surgery, Toranomon Hospital, Minato-ku, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan. .,Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
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15
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Feng P, Li L, Deng T, Liu Y, Ling N, Qiu S, Zhang L, Peng B, Xiong W, Cao L, Zhang L, Ye M. NONO and tumorigenesis: More than splicing. J Cell Mol Med 2020; 24:4368-4376. [PMID: 32168434 PMCID: PMC7176863 DOI: 10.1111/jcmm.15141] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 12/24/2022] Open
Abstract
The non-POU domain-containing octamer-binding protein NONO/p54nrb , which belongs to the Drosophila behaviour/human splicing (DBHS) family, is a multifunctional nuclear protein rarely functioning alone. Emerging solid evidences showed that NONO engages in almost every step of gene regulation, including but not limited to mRNA splicing, DNA unwinding, transcriptional regulation, nuclear retention of defective RNA and DNA repair. NONO is involved in many biological processes including cell proliferation, apoptosis, migration and DNA damage repair. Dysregulation of NONO has been found in many types of cancer. In this review, we summarize the current and fast-growing knowledge about the regulation of NONO, its biological function and implications in tumorigenesis and cancer progression. Overall, significant findings about the roles of NONO have been made, which might make NONO to be a new biomarker or/and a possible therapeutic target for cancers.
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Affiliation(s)
- Peifu Feng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Ling Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Tanggang Deng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Yan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Neng Ling
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Siyuan Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Lin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Bo Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Wei Xiong
- Ophthalmology and Eye Research Center, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Lanqin Cao
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha, China
| | - Lei Zhang
- Department of Nephrology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, China
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16
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Das S, Zhang E, Senapati P, Amaram V, Reddy MA, Stapleton K, Leung A, Lanting L, Wang M, Chen Z, Kato M, Oh HJ, Guo Q, Zhang X, Zhang B, Zhang H, Zhao Q, Wang W, Wu Y, Natarajan R. A Novel Angiotensin II-Induced Long Noncoding RNA Giver Regulates Oxidative Stress, Inflammation, and Proliferation in Vascular Smooth Muscle Cells. Circ Res 2019; 123:1298-1312. [PMID: 30566058 DOI: 10.1161/circresaha.118.313207] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RATIONALE AngII (angiotensin II)-mediated vascular smooth muscle cell (VSMC) dysfunction plays a major role in hypertension. Long noncoding RNAs have elicited much interest, but their molecular roles in AngII actions and hypertension are unclear. OBJECTIVE To investigate the regulation and functions of a novel long noncoding RNA growth factor- and proinflammatory cytokine-induced vascular cell-expressed RNA ( Giver), in AngII-mediated VSMC dysfunction. METHODS AND RESULTS RNA-sequencing and real-time quantitative polymerase chain reactions revealed that treatment of rat VSMC with AngII increased the expression of Giver and Nr4a3, an adjacent gene encoding a nuclear receptor. Similar changes were observed in rat and mouse aortas treated ex vivo with AngII. RNA-FISH (fluorescence in situ hybridization) and subcellular fractionation showed predominantly nuclear localization of Giver. AngII increased Giver expression via recruitment of Nr4a3 to Giver promoter. Microarray profiling and real-time quantitative polymerase chain reaction validation in VSMC showed that Giver knockdown attenuated the expression of genes involved in oxidative stress ( Nox1) and inflammation ( Il6, Ccl2, Tnf) but increased Nr4a3. Conversely, endogenous Giver overexpression showed opposite effects supporting its role in oxidative stress and inflammation. Chromatin immunoprecipitation assays showed Giver overexpression also increased Pol II (RNA polymerase II) enrichment and decreased repressive histone modification histone H3 trimethylation on lysine 27 at Nox1 and inflammatory gene promoters. Accordingly, Giver knockdown inhibited AngII-induced oxidative stress and proliferation in rat VSMC. RNA-pulldown combined with mass spectrometry showed Giver interacts with nuclear and chromatin remodeling proteins and corepressors, including NONO (non-pou domain-containing octamer-binding protein). Moreover, NONO knockdown elicited similar effects as Giver knockdown on the expression of key Giver-regulated genes. Notably, GIVER and NR4A3 were increased in AngII-treated human VSMC and in arteries from hypertensive patients but attenuated in hypertensive patients treated with ACE (angiotensin-converting enzyme) inhibitors or angiotensin receptor blockers. Furthermore, human GIVER also exhibits partial functional conservation with rat Giver. CONCLUSIONS Giver and its regulator Nr4a3 are important players in AngII-mediated VSMC dysfunction and could be novel targets for antihypertensive therapy.
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Affiliation(s)
- Sadhan Das
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Erli Zhang
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Center for Structural Heart Diseases (E.Z., W.W., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Parijat Senapati
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Vishnu Amaram
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (V.A., K.S., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Marpadga A Reddy
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Kenneth Stapleton
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (V.A., K.S., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Amy Leung
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Linda Lanting
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Mei Wang
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Zhuo Chen
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Mitsuo Kato
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Hyung Jung Oh
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
| | - Qianyun Guo
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyue Zhang
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Zhang
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haitong Zhang
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qinghao Zhao
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Wang
- Center for Structural Heart Diseases (E.Z., W.W., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongjian Wu
- Department of Cardiology (E.Z., Q.G., X.Z., B.Z., H.Z., Q.Z., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Center for Structural Heart Diseases (E.Z., W.W., Y.W.), State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rama Natarajan
- From the Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute (S.D., E.Z., P.S., V.A., M.A.R., K.S., A.L., L.L., M.W., Z.C., M.K., H.J.O., R.N.), Beckman Research Institute of City of Hope, Duarte, CA.,Irell and Manella Graduate School of Biological Sciences (V.A., K.S., R.N.), Beckman Research Institute of City of Hope, Duarte, CA
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Yu JSE, Colborne S, Hughes CS, Morin GB, Nielsen TO. The FUS-DDIT3 Interactome in Myxoid Liposarcoma. Neoplasia 2019; 21:740-751. [PMID: 31220736 PMCID: PMC6584455 DOI: 10.1016/j.neo.2019.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Myxoid liposarcoma is a malignant lipogenic tumor that develops in deep soft tissues. While local control rates are good, current chemotherapy options remain ineffective against metastatic disease. Myxoid liposarcoma is characterized by the FUS-DDIT3 fusion oncoprotein that is proposed to function as an aberrant transcription factor, but its exact mechanism of action has remained unclear. To identify the key functional interacting partners of FUS-DDIT3, this study utilized immunoprecipitation-mass spectrometry (IP-MS) to identify the FUS-DDIT3 interactome in whole cell lysates of myxoid liposarcoma cells, and results showed an enrichment of RNA processing proteins. Further quantitative MS analyses of FUS-DDIT3 complexes isolated from nuclear lysates showed that members of several chromatin regulatory complexes were present in the FUS-DDIT3 interactome, including NuRD, SWI/SNF, PRC1, PRC2, and MLL1 COMPASS-like complexes. Co-immunoprecipitation validated the associations of FUS-DDIT3 with BRG1/SMARCA4, BAF155/SMARCC1, BAF57/SMARCE1, and KDM1A. Data from this study provides candidates for functional validation as potential therapeutic targets, particularly for emerging epigenetic drugs.
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Affiliation(s)
- Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
| | - Shane Colborne
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | | | - Gregg B Morin
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
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18
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de Silva HC, Lin MZ, Phillips L, Martin JL, Baxter RC. IGFBP-3 interacts with NONO and SFPQ in PARP-dependent DNA damage repair in triple-negative breast cancer. Cell Mol Life Sci 2019; 76:2015-2030. [PMID: 30725116 PMCID: PMC11105386 DOI: 10.1007/s00018-019-03033-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/09/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022]
Abstract
Women with triple-negative breast cancer (TNBC) are generally treated by chemotherapy but their responsiveness may be blunted by DNA double-strand break (DSB) repair. We previously reported that IGFBP-3 forms nuclear complexes with EGFR and DNA-dependent protein kinase (DNA-PKcs) to modulate DSB repair by non-homologous end-joining (NHEJ) in TNBC cells. To discover IGFBP-3 binding partners involved in chemoresistance through stimulation of DSB repair, we analyzed the IGFBP-3 interactome by LC-MS/MS and confirmed interactions by coimmunoprecipitation and proximity ligation assay. Functional effects were demonstrated by DNA end-joining in vitro and measurement of γH2AX foci. In response to 20 µM etoposide, the DNA/RNA-binding protein, non-POU domain-containing octamer-binding protein (NONO) and its dimerization partner splicing factor, proline/glutamine-rich (SFPQ) formed complexes with IGFBP-3, demonstrated in basal-like TNBC cell lines HCC1806 and MDA-MB-468. NONO binding to IGFBP-3 was also shown in a cell-free biochemical assay. IGFBP-3 complexes with NONO and SFPQ were blocked by inhibiting EGFR with gefitinib or DNA-PKcs with NU7026, and by the PARP inhibitors veliparib and olaparib, which also reduced DNA end-joining activity and delayed the resolution of the γH2AX signal (i.e. inhibited DNA DSB repair). Downregulation of the long noncoding RNA in NHEJ pathway 1 (LINP1) by siRNA also blocked IGFBP-3 interaction with NONO-SFPQ. These findings suggest a PARP-dependent role for NONO and SFPQ in IGFBP-3-dependent DSB repair and the involvement of LINP1 in the complex formation. We propose that targeting of the DNA repair function of IGFBP-3 may enhance chemosensitivity in basal-like TNBC, thus improving patient outcomes.
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Affiliation(s)
- Hasanthi C de Silva
- Kolling Institute, Royal North Shore Hospital, The University of Sydney, St. Leonards, NSW, 2065, Australia
| | - Mike Z Lin
- Kolling Institute, Royal North Shore Hospital, The University of Sydney, St. Leonards, NSW, 2065, Australia
- Orange Family Medical Centre, 95 Peisley Street, Orange, NSW, 2800, Australia
| | - Leo Phillips
- Kolling Institute, Royal North Shore Hospital, The University of Sydney, St. Leonards, NSW, 2065, Australia
| | - Janet L Martin
- Kolling Institute, Royal North Shore Hospital, The University of Sydney, St. Leonards, NSW, 2065, Australia
| | - Robert C Baxter
- Kolling Institute, Royal North Shore Hospital, The University of Sydney, St. Leonards, NSW, 2065, Australia.
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19
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Tuna M, Amos CI, Mills GB. Molecular mechanisms and pathobiology of oncogenic fusion transcripts in epithelial tumors. Oncotarget 2019; 10:2095-2111. [PMID: 31007851 PMCID: PMC6459343 DOI: 10.18632/oncotarget.26777] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Recurrent fusion transcripts, which are one of the characteristic hallmarks of cancer, arise either from chromosomal rearrangements or from transcriptional errors in splicing. DNA rearrangements include intrachromosomal or interchromosomal translocation, tandem duplication, deletion, inversion, or result from chromothripsis, which causes complex rearrangements. In addition, fusion proteins can be created through transcriptional read-through. Fusion genes can be transcribed to fusion transcripts and translated to chimeric proteins, with many having demonstrated transforming activities through multiple mechanisms in cells. Fusion proteins represent novel therapeutic targets and diagnostic biomarkers of diagnosis, disease status, or progression. This review focuses on the mechanisms underlying the formation of oncogenic fusion genes and transcripts and their impact on the pathobiology of epithelial tumors.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I. Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Gordon B. Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR, USA
- Precision Oncology, Knight Cancer Institute, Portland, OR, USA
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20
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Li D, Chen Y, Mei H, Jiao W, Song H, Ye L, Fang E, Wang X, Yang F, Huang K, Zheng L, Tong Q. Ets-1 promoter-associated noncoding RNA regulates the NONO/ERG/Ets-1 axis to drive gastric cancer progression. Oncogene 2018; 37:4871-4886. [PMID: 29773901 PMCID: PMC6117270 DOI: 10.1038/s41388-018-0302-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 03/20/2018] [Accepted: 04/16/2018] [Indexed: 01/12/2023]
Abstract
Emerging studies have indicated the essential functions of long noncoding RNAs (lncRNAs) during cancer progression. However, whether lncRNAs contribute to the upregulation of v-ets erythroblastosis virus E26 oncogene homolog 1 (Ets-1), an established oncogenic protein facilitating tumor invasion and metastasis, in gastric cancer remains elusive. Herein, we identified Ets-1 promoter-associated noncoding RNA (pancEts-1) as a novel lncRNA associated with the gastric cancer progression via mining of publicly available datasets and rapid amplification of cDNA ends. RNA pull-down, RNA immunoprecipitation, in vitro binding, and RNA electrophoretic mobility shift assays indicated the binding of pancEts-1 to non-POU domain containing octamer binding (NONO) protein. Mechanistically, pancEts-1 facilitated the physical interaction between NONO and Ets related gene (ERG), resulting in increased ERG transactivation and transcription of Ets-1 associated with gastric cancer progression. In addition, pancEts-1 facilitated the growth and aggressiveness of gastric cancer cells via interacting with NONO. In gastric cancer tissues, pancEts-1, NONO, and ERG were upregulated and significantly correlated with Ets-1 levels. High levels of pancEts-1, NONO, ERG, or Ets-1 were respectively associated with poor survival of gastric cancer patients, whereas simultaneous expression of all of them (HR = 3.012, P = 0.105) was not an independent prognostic factor for predicting clinical outcome. Overall, these results demonstrate that lncRNA pancEts-1 exhibits oncogenic properties that drive the progression of gastric cancer via regulating the NONO/ERG/Ets-1 axis.
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Affiliation(s)
- Dan Li
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Yajun Chen
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Hong Mei
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Wanju Jiao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Huajie Song
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Lin Ye
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Erhu Fang
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Xiaojing Wang
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Feng Yang
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Kai Huang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China. .,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China.
| | - Qiangsong Tong
- Department of Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China. .,Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022, Wuhan, Hubei Province, China.
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21
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Overexpression of p54 nrb/NONO induces differential EPHA6 splicing and contributes to castration-resistant prostate cancer growth. Oncotarget 2018. [PMID: 29535823 PMCID: PMC5828187 DOI: 10.18632/oncotarget.24063] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The non-POU domain-containing octamer binding protein p54nrb/NONO is a multifunctional nuclear protein involved in RNA splicing, processing, and transcriptional regulation of nuclear hormone receptors. Through chromosome copy number analysis via whole-exome sequencing, we revealed amplification of the chromosome Xq11.22-q21.33 locus containing the androgen receptor (AR) and NONO genes in androgen-independent, castration-resistant prostate cancer (CRPC)-like LNCaP-SF cells. Moreover, NONO was frequently amplified and overexpressed in patients with CRPC. RNA sequencing data revealed that a truncated ephrin type-A receptor 6 (EPHA6) splice variant (EPHA6-001) was overexpressed in LNCaP-SF cells, and knockdown of NONO or EPHA6-001 prevented EPHA6-001 expression and reduced proliferation and invasion by LNCaP-SF cells grown under androgen deprivation conditions. Growth inhibition and differential splicing of EPHA6 mRNA by p54nrb/NONO were confirmed in gene silencing experiments in 22Rv1 PCa cells. Importantly, NONO knockdown in LNCaP-SF cells led to reduced tumor growth in castrated mice. These findings indicate that p54nrb/NONO is amplified and overexpressed in CRPC cells and clinical samples, and facilitates CRPC growth by mediating aberrant EPHA6 splicing. We therefore propose that p54nrb/NONO constitutes a novel and attractive therapeutic target for CRPC.
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22
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Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS. Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes. Mol Cell 2017; 68:1023-1037.e15. [PMID: 29272703 PMCID: PMC5858919 DOI: 10.1016/j.molcel.2017.11.030] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 12/24/2022]
Abstract
Heterochromatin is integral to cell identity maintenance by impeding the activation of genes for alternate cell fates. Heterochromatic regions are associated with histone 3 lysine 9 trimethylation (H3K9me3) or H3K27me3, but these modifications are also found in euchromatic regions that permit transcription. We discovered that resistance to sonication is a reliable indicator of the heterochromatin state, and we developed a biophysical method (gradient-seq) to discriminate subtypes of H3K9me3 and H3K27me3 domains in sonication-resistant heterochromatin (srHC) versus euchromatin. These classifications are more accurate than the histone marks alone in predicting transcriptional silence and resistance of alternate fate genes to activation during direct cell conversion. Our proteomics of H3K9me3-marked srHC and functional screens revealed diverse proteins, including RBMX and RBMXL1, that impede gene induction during cellular reprogramming. Isolation of srHC with gradient-seq provides a genome-wide map of chromatin structure, elucidating subtypes of repressed domains that are uniquely predictive of diverse other chromatin properties.
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Affiliation(s)
- Justin S Becker
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Ryan L McCarthy
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Greg Donahue
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Kelsey E Kaeding
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Zhiying He
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Shu Lin
- Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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23
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Huang CJ, Das U, Xie W, Ducasse M, Tucker HO. Altered stoichiometry and nuclear delocalization of NonO and PSF promote cellular senescence. Aging (Albany NY) 2017; 8:3356-3374. [PMID: 27992859 PMCID: PMC5270673 DOI: 10.18632/aging.101125] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/26/2016] [Indexed: 12/21/2022]
Abstract
While cellular senescence is a critical mechanism to prevent malignant transformation of potentially mutated cells, persistence of senescent cells can also promote cancer and aging phenotypes. NonO/p54nrb and PSF are multifunctional hnRNPs typically found as a complex exclusively within the nuclei of all mammalian cells. We demonstrate here that either increase or reduction of expression of either factor results in cellular senescence. Coincident with this, we observe expulsion of NonO and PSF-containing nuclear paraspeckles and posttranslational modification at G2/M. That senescence is mediated most robustly by overexpression of a cytoplasmic C-truncated form of NonO further indicated that translocation of NonO and PSF from the nucleus is critical to senescence induction. Modulation of NonO and PSF expression just prior to or coincident with senescence induction disrupts the normally heterodimeric NonO-PSF nuclear complex resulting in a dramatic shift in stoichiometry to heterotetramers and monomer with highest accumulation within the cytoplasm. This is accompanied by prototypic cell cycle checkpoint activation and chromatin condensation. These observations identify yet another role for these multifunctional factors and provide a hitherto unprecedented mechanism for cellular senescence and nuclear-cytoplasmic trafficking.
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Affiliation(s)
- Ching-Jung Huang
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Austin, TX 78712, USA
| | - Utsab Das
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Austin, TX 78712, USA
| | - Weijun Xie
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Austin, TX 78712, USA
| | - Miryam Ducasse
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Austin, TX 78712, USA
| | - Haley O Tucker
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Austin, TX 78712, USA
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24
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Richard P, Vethantham V, Manley JL. Roles of Sumoylation in mRNA Processing and Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:15-33. [PMID: 28197904 DOI: 10.1007/978-3-319-50044-7_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SUMO has gained prominence as a regulator in a number of cellular processes. The roles of sumoylation in RNA metabolism, however, while considerable, remain less well understood. In this chapter we have assembled data from proteomic analyses, localization studies and key functional studies to extend SUMO's role to the area of mRNA processing and metabolism. Proteomic analyses have identified multiple putative sumoylation targets in complexes functioning in almost all aspects of mRNA metabolism, including capping, splicing and polyadenylation of mRNA precursors. Possible regulatory roles for SUMO have emerged in pre-mRNA 3' processing, where SUMO influences the functions of polyadenylation factors and activity of the entire complex. SUMO is also involved in regulating RNA editing and RNA binding by hnRNP proteins, and recent reports have suggested the involvement of the SUMO pathway in mRNA export. Together, these reports suggest that SUMO is involved in regulation of many aspects of mRNA metabolism and hold the promise for exciting future studies.
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Affiliation(s)
- Patricia Richard
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | | | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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25
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SFPQ associates to LSD1 and regulates the migration of newborn pyramidal neurons in the developing cerebral cortex. Int J Dev Neurosci 2016; 57:1-11. [PMID: 28034769 DOI: 10.1016/j.ijdevneu.2016.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
The development of the cerebral cortex requires the coordination of multiple processes ranging from the proliferation of progenitors to the migration and establishment of connectivity of the newborn neurons. Epigenetic regulation carried out by the COREST/LSD1 complex has been identified as a mechanism that regulates the development of pyramidal neurons of the cerebral cortex. We now identify the association of the multifunctional RNA-binding protein SFPQ to LSD1 during the development of the cerebral cortex. In vivo reduction of SFPQ dosage by in utero electroporation of a shRNA results in impaired radial migration of newborn pyramidal neurons, in a similar way to that observed when COREST or LSD1 expressions are decreased. Diminished SFPQ expression also associates to decreased proliferation of progenitor cells, while it does not affect the acquisition of neuronal fate. These results are compatible with the idea that SFPQ, plays an important role regulating proliferation and migration during the development of the cerebral cortex.
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26
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Glorieux C, Sandoval JM, Fattaccioli A, Dejeans N, Garbe JC, Dieu M, Verrax J, Renard P, Huang P, Calderon PB. Chromatin remodeling regulates catalase expression during cancer cells adaptation to chronic oxidative stress. Free Radic Biol Med 2016; 99:436-450. [PMID: 27591797 DOI: 10.1016/j.freeradbiomed.2016.08.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/27/2016] [Accepted: 08/28/2016] [Indexed: 12/31/2022]
Abstract
Regulation of ROS metabolism plays a major role in cellular adaptation to oxidative stress in cancer cells, but the molecular mechanism that regulates catalase, a key antioxidant enzyme responsible for conversion of hydrogen peroxide to water and oxygen, remains to be elucidated. Therefore, we investigated the transcriptional regulatory mechanism controlling catalase expression in three human mammary cell lines: the normal mammary epithelial 250MK primary cells, the breast adenocarcinoma MCF-7 cells and an experimental model of MCF-7 cells resistant against oxidative stress resulting from chronic exposure to H2O2 (Resox), in which catalase was overexpressed. Here we identify a novel promoter region responsible for the regulation of catalase expression at -1518/-1226 locus and the key molecules that interact with this promoter and affect catalase transcription. We show that the AP-1 family member JunB and retinoic acid receptor alpha (RARα) mediate catalase transcriptional activation and repression, respectively, by controlling chromatin remodeling through a histone deacetylases-dependent mechanism. This regulatory mechanism plays an important role in redox adaptation to chronic exposure to H2O2 in breast cancer cells. Our study suggests that cancer adaptation to oxidative stress may be regulated by transcriptional factors through chromatin remodeling, and reveals a potential new mechanism to target cancer cells.
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Affiliation(s)
- Christophe Glorieux
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510275 Guangzhou, China.
| | - Juan Marcelo Sandoval
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Facultad de Ciencias de la Salud, Universidad Arturo Prat, 1100000 Iquique, Chile
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Nicolas Dejeans
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium
| | - James C Garbe
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marc Dieu
- Mass Spectrometry University of Namur (MaSUN), University of Namur, 5000 Namur, Belgium
| | - Julien Verrax
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Peng Huang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510275 Guangzhou, China; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pedro Buc Calderon
- Université catholique de Louvain, Louvain Drug Research Institute, Toxicology and Cancer Biology Research Group, 1200 Brussels, Belgium; Facultad de Ciencias de la Salud, Universidad Arturo Prat, 1100000 Iquique, Chile.
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27
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Knott GJ, Bond CS, Fox AH. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res 2016; 44:3989-4004. [PMID: 27084935 PMCID: PMC4872119 DOI: 10.1093/nar/gkw271] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Nuclear proteins are often given a concise title that captures their function, such as 'transcription factor,' 'polymerase' or 'nuclear-receptor.' However, for members of the Drosophila behavior/human splicing (DBHS) protein family, no such clean-cut title exists. DBHS proteins are frequently identified engaging in almost every step of gene regulation, including but not limited to, transcriptional regulation, RNA processing and transport, and DNA repair. Herein, we present a coherent picture of DBHS proteins, integrating recent structural insights on dimerization, nucleic acid binding modalities and oligomerization propensity with biological function. The emerging paradigm describes a family of dynamic proteins mediating a wide range of protein-protein and protein-nucleic acid interactions, on the whole acting as a multipurpose molecular scaffold. Overall, significant steps toward appreciating the role of DBHS proteins have been made, but we are only beginning to understand the complexity and broader importance of this family in cellular biology.
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Affiliation(s)
- Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Archa H Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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Telorac J, Prykhozhij SV, Schöne S, Meierhofer D, Sauer S, Thomas-Chollier M, Meijsing SH. Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements. Nucleic Acids Res 2016; 44:6142-56. [PMID: 27016732 PMCID: PMC5291246 DOI: 10.1093/nar/gkw203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/16/2016] [Indexed: 01/13/2023] Open
Abstract
Out of the myriad of potential DNA binding sites of the glucocorticoid receptor (GR) found in the human genome, only a cell-type specific minority is actually bound, indicating that the presence of a recognition sequence alone is insufficient to specify where GR binds. Cooperative interactions with other transcription factors (TFs) are known to contribute to binding specificity. Here, we reasoned that sequence signals preventing GR recruitment to certain loci provide an alternative means to confer specificity. Motif analyses uncovered candidate Negative Regulatory Sequences (NRSs) that interfere with genomic GR binding. Subsequent functional analyses demonstrated that NRSs indeed prevent GR binding to nearby response elements. We show that NRS activity is conserved across species, found in most tissues and that they also interfere with the genomic binding of other TFs. Interestingly, the effects of NRSs appear not to be a simple consequence of changes in chromatin accessibility. Instead, we find that NRSs interact with proteins found at sub-nuclear structures called paraspeckles and that these proteins might mediate the repressive effects of NRSs. Together, our studies suggest that the joint influence of positive and negative sequence signals partition the genome into regions where GR can bind and those where it cannot.
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Affiliation(s)
- Jonas Telorac
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Sergey V Prykhozhij
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Sascha Sauer
- CU Systems Medicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Morgane Thomas-Chollier
- Computational Systems Biology, Institut de Biologie de l'Ecole Normale, Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
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Obesity-induced DNA hypermethylation of the adiponectin gene mediates insulin resistance. Nat Commun 2015; 6:7585. [PMID: 26139044 PMCID: PMC4506505 DOI: 10.1038/ncomms8585] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/21/2015] [Indexed: 12/28/2022] Open
Abstract
Adiponectin plays a key role in the regulation of the whole-body energy homeostasis by modulating glucose and lipid metabolism. Although obesity-induced reduction of adiponectin expression is primarily ascribed to a transcriptional regulation failure, the underlying mechanisms are largely undefined. Here we show that DNA hypermethylation of a particular region of the adiponectin promoter suppresses adiponectin expression through epigenetic control and, in turn, exacerbates metabolic diseases in obesity. Obesity-induced, pro-inflammatory cytokines promote DNMT1 expression and its enzymatic activity. Activated DNMT1 selectively methylates and stimulates compact chromatin structure in the adiponectin promoter, impeding adiponectin expression. Suppressing DNMT1 activity with a DNMT inhibitor resulted in the amelioration of obesity-induced glucose intolerance and insulin resistance in an adiponectin-dependent manner. These findings suggest a critical role of adiponectin gene epigenetic control by DNMT1 in governing energy homeostasis, implying that modulating DNMT1 activity represents a new strategy for the treatment of obesity-related diseases.
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30
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Yarosh CA, Iacona JR, Lutz CS, Lynch KW. PSF: nuclear busy-body or nuclear facilitator? WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:351-67. [PMID: 25832716 PMCID: PMC4478221 DOI: 10.1002/wrna.1280] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 01/25/2023]
Abstract
PTB-associated splicing factor (PSF) is an abundant and essential nucleic acid-binding protein that participates in a wide range of gene regulatory processes and cellular response pathways. At the protein level, PSF consists of multiple domains, many of which remain poorly characterized. Although grouped in a family with the proteins p54nrb/NONO and PSPC1 based on sequence homology, PSF contains additional protein sequence not included in other family members. Consistently, PSF has also been implicated in functions not ascribed to p54nrb/NONO or PSPC1. Here, we provide a review of the cellular activities in which PSF has been implicated and what is known regarding the mechanisms by which PSF functions in each case. We propose that the complex domain arrangement of PSF allows for its diversity of function and integration of activities. Finally, we discuss recent evidence that individual activities of PSF can be regulated independently from one another through the activity of domain-specific co-factors.
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Affiliation(s)
- Christopher A Yarosh
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph R Iacona
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences-New Jersey Medical School, Newark, NJ, USA
| | - Carol S Lutz
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences-New Jersey Medical School, Newark, NJ, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
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Lee M, Sadowska A, Bekere I, Ho D, Gully BS, Lu Y, Iyer KS, Trewhella J, Fox AH, Bond CS. The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation. Nucleic Acids Res 2015; 43:3826-40. [PMID: 25765647 PMCID: PMC4402515 DOI: 10.1093/nar/gkv156] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/18/2015] [Indexed: 12/14/2022] Open
Abstract
SFPQ, (a.k.a. PSF), is a human tumor suppressor protein that regulates many important functions in the cell nucleus including coordination of long non-coding RNA molecules into nuclear bodies. Here we describe the first crystal structures of Splicing Factor Proline and Glutamine Rich (SFPQ), revealing structural similarity to the related PSPC1/NONO heterodimer and a strikingly extended structure (over 265 Å long) formed by an unusual anti-parallel coiled-coil that results in an infinite linear polymer of SFPQ dimers within the crystals. Small-angle X-ray scattering and transmission electron microscopy experiments show that polymerization is reversible in solution and can be templated by DNA. We demonstrate that the ability to polymerize is essential for the cellular functions of SFPQ: disruptive mutation of the coiled-coil interaction motif results in SFPQ mislocalization, reduced formation of nuclear bodies, abrogated molecular interactions and deficient transcriptional regulation. The coiled-coil interaction motif thus provides a molecular explanation for the functional aggregation of SFPQ that directs its role in regulating many aspects of cellular nucleic acid metabolism.
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Affiliation(s)
- Mihwa Lee
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Agata Sadowska
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Indra Bekere
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Diwei Ho
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Benjamin S Gully
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Yanling Lu
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - K Swaminathan Iyer
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - Archa H Fox
- Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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Snijders AP, Hautbergue GM, Bloom A, Williamson JC, Minshull TC, Phillips HL, Mihaylov SR, Gjerde DT, Hornby DP, Wilson SA, Hurd PJ, Dickman MJ. Arginine methylation and citrullination of splicing factor proline- and glutamine-rich (SFPQ/PSF) regulates its association with mRNA. RNA (NEW YORK, N.Y.) 2015; 21:347-59. [PMID: 25605962 PMCID: PMC4338332 DOI: 10.1261/rna.045138.114] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 11/15/2014] [Indexed: 05/19/2023]
Abstract
Splicing factor proline- and glutamine-rich (SFPQ) also commonly known as polypyrimidine tract-binding protein-associated-splicing factor (PSF) and its binding partner non-POU domain-containing octamer-binding protein (NONO/p54nrb), are highly abundant, multifunctional nuclear proteins. However, the exact role of this complex is yet to be determined. Following purification of the endogeneous SFPQ/NONO complex, mass spectrometry analysis identified a wide range of interacting proteins, including those involved in RNA processing, RNA splicing, and transcriptional regulation, consistent with a multifunctional role for SFPQ/NONO. In addition, we have identified several sites of arginine methylation in SFPQ/PSF using mass spectrometry and found that several arginines in the N-terminal domain of SFPQ/PSF are asymmetrically dimethylated. Furthermore, we find that the protein arginine N-methyltransferase, PRMT1, catalyzes this methylation in vitro and that this is antagonized by citrullination of SFPQ. Arginine methylation and citrullination of SFPQ/PSF does not affect complex formation with NONO. However, arginine methylation was shown to increase the association with mRNA in mRNP complexes in mammalian cells. Finally we show that the biochemical properties of the endogenous complex from cell lysates are significantly influenced by the ionic strength during purification. At low ionic strength, the SFPQ/NONO complex forms large heterogeneous protein assemblies or aggregates, preventing the purification of the SFPQ/NONO complex. The ability of the SFPQ/NONO complex to form varying protein assemblies, in conjunction with the effect of post-translational modifications of SFPQ modulating mRNA binding, suggests key roles affecting mRNP dynamics within the cell.
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Affiliation(s)
- Ambrosius P Snijders
- ChELSI Institute, Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - Alex Bloom
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - James C Williamson
- ChELSI Institute, Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Thomas C Minshull
- ChELSI Institute, Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Helen L Phillips
- ChELSI Institute, Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Simeon R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | | | - David P Hornby
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Stuart A Wilson
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Paul J Hurd
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Mark J Dickman
- ChELSI Institute, Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom
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p54nrb/NONO regulates cyclic AMP-dependent glucocorticoid production by modulating phosphodiesterase mRNA splicing and degradation. Mol Cell Biol 2015; 35:1223-37. [PMID: 25605330 DOI: 10.1128/mcb.00993-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glucocorticoid production in the adrenal cortex is activated in response to an increase in cyclic AMP (cAMP) signaling. The nuclear protein p54(nrb)/NONO belongs to the Drosophila behavior/human splicing (DBHS) family and has been implicated in several nuclear processes, including transcription, splicing, and RNA export. We previously identified p54(nrb)/NONO as a component of a protein complex that regulates the transcription of CYP17A1, a gene required for glucocorticoid production. Based on the multiple mechanisms by which p54(nrb)/NONO has been shown to control gene expression and the ability of the protein to be recruited to the CYP17A1 promoter, we sought to further define the molecular mechanism by which p54(nrb)/NONO confers optimal cortisol production. We show here that silencing p54(nrb)/NONO expression in H295R human adrenocortical cells decreases the ability of the cells to increase intracellular cAMP production and subsequent cortisol biosynthesis in response to adrenocorticotropin hormone (ACTH) stimulation. Interestingly, the expression of multiple phosphodiesterase (PDE) isoforms, including PDE2A, PDE3A, PDE3B, PDE4A, PDE4D, and PDE11A, was induced in p54(nrb)/NONO knockdown cells. Investigation of the mechanism by which silencing of p54(nrb)/NONO led to increased expression of select PDE isoforms revealed that p54(nrb)/NONO regulates the splicing of a subset of PDE isoforms. Importantly, we also identify a role for p54(nrb)/NONO in regulating the stability of PDE transcripts by facilitating the interaction between the exoribonuclease XRN2 and select PDE transcripts. In summary, we report that p54(nrb)/NONO modulates cAMP-dependent signaling, and ultimately cAMP-stimulated glucocorticoid biosynthesis by regulating the splicing and degradation of PDE transcripts.
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Satoh T, Katano-Toki A, Tomaru T, Yoshino S, Ishizuka T, Horiguchi K, Nakajima Y, Ishii S, Ozawa A, Shibusawa N, Hashimoto K, Mori M, Yamada M. Coordinated regulation of transcription and alternative splicing by the thyroid hormone receptor and its associating coregulators. Biochem Biophys Res Commun 2014; 451:24-9. [PMID: 25019984 DOI: 10.1016/j.bbrc.2014.07.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/06/2014] [Indexed: 12/17/2022]
Abstract
Emerging evidence has indicated that the transcription and processing of precursor mRNA (pre-mRNA) are functionally coupled to modulate gene expression. In collaboration with coregulators, several steroid hormone receptors have previously been shown to directly affect alternative pre-mRNA splicing coupled to hormone-induced gene transcription; however, the roles of the thyroid hormone receptor (TR) and its coregulators in alternative splicing coordinated with transcription remain unknown. In the present study, we constructed a luciferase reporter and CD44 alternative splicing (AS) minigene driven by a minimal promoter carrying 2 copies of the palindromic thyroid hormone-response element. We then examined whether TR could modulate pre-mRNA processing coupled to triiodothyronine (T3)-induced gene transcription using luciferase reporter and splicing minigene assays in HeLa cells. In the presence of cotransfected TRβ1, T3 increased luciferase activities along with the inclusion of the CD44 variable exons 4 and 5 in a dose- and time-dependent manner. In contrast, cotransfected TRβ1 did not affect the exon-inclusion of the CD44 minigene driven by the cytomegalovirus promoter. T3-induced two-exon inclusion was significantly increased by the cotransfection of the TR-associated protein, 150-kDa, a subunit of the TRAP/Mediator complex that has recently been shown to function as a splicing factor. In contrast, T3-induced two-exon inclusion was significantly decreased by cotransfection of the polypyrimidine tract-binding protein-associated splicing factor, which was previously shown to function as a corepressor of TR. These results demonstrated that liganded TR in cooperation with its associating cofactors could modulate alternative pre-mRNA splicing coupled to gene transcription.
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Affiliation(s)
- Tetsurou Satoh
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan.
| | - Akiko Katano-Toki
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takuya Tomaru
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Satoshi Yoshino
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takahiro Ishizuka
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kazuhiko Horiguchi
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Yasuyo Nakajima
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Sumiyasu Ishii
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Atsushi Ozawa
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Nobuyuki Shibusawa
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Koshi Hashimoto
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Masatomo Mori
- Kitakanto Molecular Novel Research Institute for Obesity and Metabolism, Midori, Japan
| | - Masanobu Yamada
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
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Small G Proteins Dexras1 and RHES and Their Role in Pathophysiological Processes. Int J Cell Biol 2014; 2014:308535. [PMID: 24817889 PMCID: PMC3979064 DOI: 10.1155/2014/308535] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/18/2014] [Indexed: 11/23/2022] Open
Abstract
Dexras1 and RHES, monomeric G proteins, are members of small GTPase family that are involved in modulation of pathophysiological processes. Dexras1 and RHES levels are modulated by hormones and Dexras1 expression undergoes circadian fluctuations. Both these GTPases are capable of modulating calcium ion channels which in turn can potentially modulate neurosecretion/hormonal release. These two GTPases have been reported to prevent the aberrant cell growth and induce apoptosis in cell lines. Present review focuses on role of these two monomeric GTPases and summarizes their role in pathophysiological processes.
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36
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Zanfardino M, Spampanato C, De Cicco R, Buommino E, De Filippis A, Baiano S, Barra A, Morelli F. Simvastatin reduces melanoma progression in a murine model. Int J Oncol 2013; 43:1763-70. [PMID: 24101161 PMCID: PMC3833984 DOI: 10.3892/ijo.2013.2126] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/04/2013] [Indexed: 12/27/2022] Open
Abstract
Statins are a class of drugs that inhibit the rate-limiting step in the cholesterol biosynthetic pathway and show an anticancer effect, probably through the inhibition of cell proliferation. To date, the exact mechanism of cancer cell growth arrest induced by statins is not known. We report that simvastatin is able to induce apoptosis in melanoma cells but not in normal cells and also able to contrast the growth of tumor in an experimental melanoma murine model. We observed a delay in the tumor development in almost the 50% of the simvastatin administered animals and a strong reduction of the tumor volume with a differences of ~150% compared to the controls. Also the survival rate was significantly higher in mice that received the drug with a survival increase of ~130% compared to the controls. The tumor growth reduction in mice was supported by the results of cell migration assay, confirming that simvastatin clearly reduced cell migration. Moreover, simvastatin induced a strong downregulation of NonO gene expression, an important growth factor involved in the splicing regulation. This result could explain the decrease of melanoma cells proliferation, suggesting a possible action mechanism. The results derived from our experiments may sustain the many reports on the anticancer inhibitory property of statins and encourage new studies on this drug for a possible use in therapy, probably in combination with conventional chemotherapy.
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Affiliation(s)
- Mario Zanfardino
- Institute of Genetics and Biophysics A. Buzzati Traverso, CNR Naples, Naples, Italy
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Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification. J Virol 2013; 87:8697-712. [PMID: 23740976 DOI: 10.1128/jvi.00950-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic RNA viruses are known to utilize host factors; however, the identity of these factors and their role in the virus life cycle remain largely undefined. Here, we report a method to identify proteins bound to the viral RNA during amplification in cell culture: thiouracil cross-linking mass spectrometry (TUX-MS). TUX-MS relies on incorporation of a zero-distance cross-linker into the viral RNA during infection. Proteins bound to viral RNA are cross-linked prior to cell lysis, purified, and identified using mass spectrometry. Using the TUX-MS method, an unbiased screen for poliovirus (PV) host factors was conducted. All host and viral proteins that are known to interact with the poliovirus RNA were identified. In addition, TUX-MS identified an additional 66 host proteins that have not been previously described in poliovirus amplification. From these candidates, eight were selected and validated. Furthermore, we demonstrate that small interfering RNA (siRNA)-mediated knockdown of two of these uncharacterized host factors results in either a decrease in copy number of positive-stranded RNA or a decrease in PV translation. These data demonstrate that TUX-MS is a robust, unbiased method to identify previously unknown host cell factors that influence virus growth. This method is broadly applicable to a range of RNA viruses, such as flaviviruses, alphaviruses, picornaviruses, bunyaviruses, and coronaviruses.
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38
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Transcription of the human microsomal epoxide hydrolase gene (EPHX1) is regulated by an HNF-4α/CAR/RXR/PSF complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1000-9. [PMID: 23714182 DOI: 10.1016/j.bbagrm.2013.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 05/13/2013] [Accepted: 05/17/2013] [Indexed: 11/23/2022]
Abstract
Microsomal epoxide hydrolase (mEH) is a bifunctional protein that plays a central role in the metabolism of numerous xenobiotics as well as mediating the sodium-dependent transport of bile acids into hepatocytes where they are involved in cholesterol excretion and metabolism, lipid digestion and regulating numerous signaling pathways. Previous studies have demonstrated the critical role of GATA-4 and a C/EBPα-NF/Y complex in the regulation of the mEH gene (EPHX1). In this study we show that HNF-4α and CAR/RXR also bind to the proximal promoter region and regulate EPHX1 expression. Bile acids, which inhibit the expression of HNF-4α also decrease the expression of EPHX1. Studies also established that the binding of HNF-4α was essential for the activation of EPHX1 activity by CAR suggesting the formation of a complex between these adjacent factors. The nature of this regulatory complex was further explored using a biotinylated oligonucleotide of this region in conjunction with BioMag beads and mass spectrometric analysis which demonstrated the presence of an additional inhibitory factor (PSF), confirmed by co-immunoprecipitation and ChIP analyses, which interacted with DNA-bound CAR/RXR/HNF-4α forming a 4-component regulatory complex.
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39
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Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer. EMBO J 2013; 32:1665-80. [PMID: 23644382 DOI: 10.1038/emboj.2013.99] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/04/2013] [Indexed: 11/08/2022] Open
Abstract
High-throughput techniques have identified numerous antisense (AS) transcripts and long non-coding RNAs (ncRNAs). However, their significance in cancer biology remains largely unknown. Here, we report an androgen-responsive long ncRNA, CTBP1-AS, located in the AS region of C-terminal binding protein 1 (CTBP1), which is a corepressor for androgen receptor. CTBP1-AS is predominantly localized in the nucleus and its expression is generally upregulated in prostate cancer. CTBP1-AS promotes both hormone-dependent and castration-resistant tumour growth. Mechanistically, CTBP1-AS directly represses CTBP1 expression by recruiting the RNA-binding transcriptional repressor PSF together with histone deacetylases. CTBP1-AS also exhibits global androgen-dependent functions by inhibiting tumour-suppressor genes via the PSF-dependent mechanism thus promoting cell cycle progression. Our findings provide new insights into the functions of ncRNAs that directly contribute to prostate cancer progression.
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40
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Tsukahara T, Haniu H, Matsuda Y. PTB-associated splicing factor (PSF) is a PPARγ-binding protein and growth regulator of colon cancer cells. PLoS One 2013; 8:e58749. [PMID: 23516550 PMCID: PMC3596311 DOI: 10.1371/journal.pone.0058749] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/05/2013] [Indexed: 11/19/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor that plays an essential role in cell proliferation, apoptosis, and inflammation. It is over-expressed in many types of cancer, including colon, stomach, breast, and lung cancer, suggesting that regulation of PPARγ might affect cancer pathogenesis. Here, using a proteomic approach, we identify PTB-associated splicing factor (PSF) as a novel PPARγ-interacting protein and demonstrate that PSF is involved in several important regulatory steps of colon cancer cell proliferation. To investigate the relationship between PSF and PPARγ in colon cancer, we evaluated the effects of PSF expression in DLD-1 and HT-29 colon cancer cell lines, which express low and high levels of PPARγ, respectively PSF affected the ability of PPARγ to bind, and expression of PSF siRNA significantly suppressed the proliferation of colon cancer cells. Furthermore, PSF knockdown induced apoptosis via activation of caspase-3. Interestingly, DLD-1 cells were more susceptible to PSF knockdown-induced cell death than HT-29 cells. Our data suggest that PSF is an important regulator of cell death that plays critical roles in the survival and growth of colon cancer cells. The PSF-PPARγ axis may play a role in the control of colorectal carcinogenesis. Taken together, this study is the first to describe the effects of PSF on cell proliferation, tumor growth, and cell signaling associated with PPARγ.
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Affiliation(s)
- Tamotsu Tsukahara
- Department of Integrative Physiology and Bio-System Control, Shinshu University School of Medicine, Asahi, Matsumoto, Nagano, Japan.
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Icardi L, De Bosscher K, Tavernier J. The HAT/HDAC interplay: multilevel control of STAT signaling. Cytokine Growth Factor Rev 2012; 23:283-91. [PMID: 22989617 DOI: 10.1016/j.cytogfr.2012.08.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 08/20/2012] [Indexed: 12/13/2022]
Abstract
Besides the transcription-promoting role of histone acetyltransferases (HATs) and the transcription-delimiting function of histone deacetylases (HDACs) through histone acetylation and deacetylation respectively, HATs and HDACs also regulate the activity of several non-histone proteins. This includes signal transducers and activators of transcription (STATs), key proteins in cytokine signaling. Unlike Tyr phosphorylation/dephosphorylation, which mainly acts as an on/off switch of STAT activity, the control exerted by HATs and HDACs appears multifaceted and far more complex than initially imagined. Our review focuses on the latest trends and novel hypotheses to explain differential context-dependent STAT regulation by complex posttranslational modification patterns. We chart the knowledge on how STATs interact with HATs and HDACs, and additionally bring a transcriptional regulatory and gene-set specific role for HDACs in the picture. Indeed, a growing amount of evidence demonstrates, paradoxically, that not only HAT but also HDAC activity can be required for STAT-dependent transcription, in a STAT subtype- and cell type-dependent manner. Referring to recent reports, we review and discuss the various molecular mechanisms that have recently been proposed to account for this peculiar regulation, in an attempt to shed more light on the difficult yet important question on how STAT specificity is being generated.
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Affiliation(s)
- Laura Icardi
- Department of Medical Protein Research, VIB, Ghent, Belgium
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Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin remodeling and splicing. Blood 2012; 120:e83-92. [PMID: 22976956 DOI: 10.1182/blood-2011-12-401471] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) is characterized by molecular heterogeneity. As commonly altered genomic regions point to candidate genes involved in leukemogenesis, we used microarray-based comparative genomic hybridization and single nucleotide polymorphism profiling data of 391 AML cases to further narrow down genomic regions of interest. Targeted resequencing of 1000 genes located in the critical regions was performed in a representative cohort of 50 AML samples comprising all major cytogenetic subgroups. We identified 120 missense/nonsense mutations as well as 60 insertions/deletions affecting 73 different genes (∼ 3.6 tumor-specific aberrations/AML). While most of the newly identified alterations were nonrecurrent, we observed an enrichment of mutations affecting genes involved in epigenetic regulation including known candidates like TET2, TET1, DNMT3A, and DNMT1, as well as mutations in the histone methyltransferases NSD1, EZH2, and MLL3. Furthermore, we found mutations in the splicing factor SFPQ and in the nonclassic regulators of mRNA processing CTCF and RAD21. These splicing-related mutations affected 10% of AML patients in a mutually exclusive manner. In conclusion, we could identify a large number of alterations in genes involved in aberrant splicing and epigenetic regulation in genomic regions commonly altered in AML, highlighting their important role in the molecular pathogenesis of AML.
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43
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Distinct roles of DBHS family members in the circadian transcriptional feedback loop. Mol Cell Biol 2012; 32:4585-94. [PMID: 22966205 DOI: 10.1128/mcb.00334-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Factors interacting with core circadian clock components are essential to achieve transcriptional feedback necessary for metazoan clocks. Here, we show that all three members of the Drosophila behavior human splicing (DBHS) family of RNA-binding proteins play a role in the mammalian circadian oscillator, abrogating or altering clock function when overexpressed or depleted in cells. Although these proteins are members of so-called nuclear paraspeckles, depletion of paraspeckles themselves via silencing of the structural noncoding RNA (ncRNA) Neat1 did not affect overall clock function, suggesting that paraspeckles are not required for DBHS-mediated circadian effects. Instead, we show that the proteins bound to circadian promoter DNA in a fashion that required the PERIOD (PER) proteins and potently repressed E-box-mediated transcription but not cytomegalovirus (CMV) promoter-mediated transcription when they were exogenously recruited. Nevertheless, mice with one or both copies of these genes deleted show only small changes in period length or clock gene expression in vivo. Data from transient transfections show that each of these proteins can either repress or activate, depending on the context. Taken together, our data suggest that all of the DBHS family members serve overlapping or redundant roles as transcriptional cofactors at circadian clock-regulated genes.
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Krietsch J, Caron MC, Gagné JP, Ethier C, Vignard J, Vincent M, Rouleau M, Hendzel MJ, Poirier GG, Masson JY. PARP activation regulates the RNA-binding protein NONO in the DNA damage response to DNA double-strand breaks. Nucleic Acids Res 2012; 40:10287-301. [PMID: 22941645 PMCID: PMC3488241 DOI: 10.1093/nar/gks798] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
After the generation of DNA double-strand breaks (DSBs), poly(ADP-ribose) polymerase-1 (PARP-1) is one of the first proteins to be recruited and activated through its binding to the free DNA ends. Upon activation, PARP-1 uses NAD+ to generate large amounts of poly(ADP-ribose) (PAR), which facilitates the recruitment of DNA repair factors. Here, we identify the RNA-binding protein NONO, a partner protein of SFPQ, as a novel PAR-binding protein. The protein motif being primarily responsible for PAR-binding is the RNA recognition motif 1 (RRM1), which is also crucial for RNA-binding, highlighting a competition between RNA and PAR as they share the same binding site. Strikingly, the in vivo recruitment of NONO to DNA damage sites completely depends on PAR, generated by activated PARP-1. Furthermore, we show that upon PAR-dependent recruitment, NONO stimulates nonhomologous end joining (NHEJ) and represses homologous recombination (HR) in vivo. Our results therefore place NONO after PARP activation in the context of DNA DSB repair pathway decision. Understanding the mechanism of action of proteins that act in the same pathway as PARP-1 is crucial to shed more light onto the effect of interference on PAR-mediated pathways with PARP inhibitors, which have already reached phase III clinical trials but are until date poorly understood.
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Affiliation(s)
- Jana Krietsch
- Cancer Research Unit, Laval University Medical Research Center, CHUQ-CRCHUL, Genome Stability Laboratory, Laval University Cancer Research Center, Hôtel-Dieu de Québec, QC, Canada G1R 2J6
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45
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Xie N, Liu L, Li Y, Yu C, Lam S, Shynlova O, Gleave M, Challis JRG, Lye S, Dong X. Expression and function of myometrial PSF suggest a role in progesterone withdrawal and the initiation of labor. Mol Endocrinol 2012; 26:1370-9. [PMID: 22669741 DOI: 10.1210/me.2012-1088] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Progesterone (P4), acting through its receptor (PR), is essential for the maintenance of pregnancy. P4 acts by suppressing uterine contractility and the expression of contraction-associated proteins (CAP) such as connexin 43 (Cx43). P4 levels must be reduced or its actions blocked to allow the increased expression of CAP genes and the initiation of labor. Although the importance of progesterone in pregnancy has been known for about 80 yr, the fundamental mechanisms by which P4/PR maintains myometrial quiescence and by which this signaling is blocked at term labor remain to be determined. In this manuscript, we demonstrate that ligand-bound PR interacts with the Cx43 gene promoter through activator protein-1 transcription factors. We show that the ability of PR to repress Cx43 transcription is conferred through the recruitment of the PR coregulator, polypyrimidine tract binding protein-associated splicing factor (PSF), and the further recruitment of the yeast switch independent 3 homolog A/histone deacetylase corepressor complex. PSF expression is elevated during pregnancy but falls toward term as a result of increased mechanical stretch of the myometrium and a rise in the concentrations of circulating estrogen. These data together indicate that PSF is a critical regulator of P4/PR signaling and labor. We suggest that decreased PSF at term may result in a de-repression of PR transcriptional control of CAP genes and thereby contributes to a functional withdrawal of progesterone at term labor.
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Affiliation(s)
- Ning Xie
- Vancouver Prostate Center, Department of Urologic Sciences, University of British Columbia, Vancouver Canada
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Rasd1 modulates the coactivator function of NonO in the cyclic AMP pathway. PLoS One 2011; 6:e24401. [PMID: 21915321 PMCID: PMC3168489 DOI: 10.1371/journal.pone.0024401] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 08/08/2011] [Indexed: 11/19/2022] Open
Abstract
All living organisms exhibit autonomous daily physiological and behavioural rhythms to help them synchronize with the environment. Entrainment of circadian rhythm is achieved via activation of cyclic AMP (cAMP) and mitogen-activated protein kinase signaling pathways. NonO (p54nrb) is a multifunctional protein involved in transcriptional activation of the cAMP pathway and is involved in circadian rhythm control. Rasd1 is a monomeric G protein implicated to play a pivotal role in potentiating both photic and nonphotic responses of the circadian rhythm. In this study, we have identified and validated NonO as an interacting partner of Rasd1 via affinity pulldown, co-immunoprecipitation and indirect immunofluorescence studies. The GTP-hydrolysis activity of Rasd1 is required for the functional interaction. Functional interaction of Rasd1-NonO in the cAMP pathway was investigated via reporter gene assays, chromatin immunoprecipitation and gene knockdown. We showed that Rasd1 and NonO interact at the CRE-site of specific target genes. These findings reveal a novel mechanism by which the coregulator activity of NonO can be modulated.
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Ray P, Kar A, Fushimi K, Havlioglu N, Chen X, Wu JY. PSF suppresses tau exon 10 inclusion by interacting with a stem-loop structure downstream of exon 10. J Mol Neurosci 2011; 45:453-66. [PMID: 21881826 DOI: 10.1007/s12031-011-9634-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 08/17/2011] [Indexed: 01/24/2023]
Abstract
Microtubule binding protein Tau has been implicated in a wide range of neurodegenerative disorders collectively classified as tauopathies. Exon 10 of the human tau gene, which codes for a microtubule binding repeat region, is alternatively spliced to form Tau protein isoforms containing either four or three microtubule binding repeats, Tau4R and Tau3R, respectively. The levels of different Tau splicing isoforms are fine-tuned by alternative splicing with the ratio of Tau4R/Tau3R maintained approximately at one in adult neurons. Mutations that disrupt tau exon 10 splicing regulation cause an imbalance of different tau splicing isoforms and have been associated with tauopathy. To search for factors interacting with tau pre-messenger RNA (pre-mRNA) and regulating tau exon 10 alternative splicing, we performed a yeast RNA-protein interaction screen and identified polypyrimidine tract binding protein associated splicing factor (PSF) as a candidate tau exon 10 splicing regulator. UV crosslinking experiments show that PSF binds to the stem-loop structure at the 5' splice site downstream of tau exon 10. This PSF-interacting RNA element is distinct from known PSF binding sites previously identified in other genes. Overexpression of PSF promotes tau exon 10 exclusion, whereas down-regulation of the endogenous PSF facilitates exon 10 inclusion. Immunostaining shows that PSF is expressed in the human brain regions affected by tauopathy. Our data reveal a new player in tau exon 10 alternative splicing regulation and uncover a previously unknown mechanism of PSF in regulating tau pre-mRNA splicing.
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Affiliation(s)
- Payal Ray
- Department of Neurology, Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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48
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Abstract
Circadian rhythms in mammals are generated by a feedback loop in which the three PERIOD (PER) proteins, acting in a large complex, inhibit the transcriptional activity of the CLOCK-BMAL1 dimer, which represses their own expression. Although fundamental, the mechanism of negative feedback in the mammalian clock, or any eukaryotic clock, is unknown. We analyzed protein constituents of PER complexes purified from mouse tissues and identified PSF (polypyrimidine tract-binding protein-associated splicing factor). Our analysis indicates that PSF within the PER complex recruits SIN3A, a scaffold for assembly of transcriptional inhibitory complexes and that the PER complex thereby rhythmically delivers histone deacetylases to the Per1 promoter, which repress Per1 transcription. These findings provide a function for the PER complex and a molecular mechanism for circadian clock negative feedback.
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Affiliation(s)
| | | | | | - Charles J. Weitz
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115 USA
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Nuclear receptors TR2 and TR4 recruit multiple epigenetic transcriptional corepressors that associate specifically with the embryonic β-type globin promoters in differentiated adult erythroid cells. Mol Cell Biol 2011; 31:3298-311. [PMID: 21670149 DOI: 10.1128/mcb.05310-11] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear receptors TR2 and TR4 (TR2/TR4) were previously shown to bind in vitro to direct repeat elements in the mouse and human embryonic and fetal β-type globin gene promoters and to play critical roles in the silencing of these genes. By chromatin immunoprecipitation (ChIP) we show that, in adult erythroid cells, TR2/TR4 bind to the embryonic β-type globin promoters but not to the adult β-globin promoter. We purified protein complexes containing biotin-tagged TR2/TR4 from adult erythroid cells and identified DNMT1, NuRD, and LSD1/CoREST repressor complexes, as well as HDAC3 and TIF1β, all known to confer epigenetic gene silencing, as potential corepressors of TR2/TR4. Coimmunoprecipitation assays of endogenous abundance proteins indicated that TR2/TR4 complexes consist of at least four distinct molecular species. In ChIP assays we found that, in undifferentiated murine adult erythroid cells, many of these corepressors associate with both the embryonic and the adult β-type globin promoters but, upon terminal differentiation, they specifically dissociate only from the adult β-globin promoter concomitant with its activation but remain bound to the silenced embryonic globin gene promoters. These data suggest that TR2/TR4 recruit an array of transcriptional corepressors to elicit adult stage-specific silencing of the embryonic β-type globin genes through coordinated epigenetic chromatin modifications.
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Rosen MD, Privalsky ML. Thyroid hormone receptor mutations in cancer and resistance to thyroid hormone: perspective and prognosis. J Thyroid Res 2011; 2011:361304. [PMID: 21760978 PMCID: PMC3134260 DOI: 10.4061/2011/361304] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 03/16/2011] [Indexed: 12/13/2022] Open
Abstract
Thyroid hormone, operating through its receptors, plays crucial roles in the control of normal human physiology and development; deviations from the norm can give rise to disease. Clinical endocrinologists often must confront and correct the consequences of inappropriately high or low thyroid hormone synthesis. Although more rare, disruptions in thyroid hormone endocrinology due to aberrations in the receptor also have severe medical consequences. This review will focus on the afflictions that are caused by, or are closely associated with, mutated thyroid hormone receptors. These include Resistance to Thyroid Hormone Syndrome, erythroleukemia, hepatocellular carcinoma, renal clear cell carcinoma, and thyroid cancer. We will describe current views on the molecular bases of these diseases, and what distinguishes the neoplastic from the non-neoplastic. We will also touch on studies that implicate alterations in receptor expression, and thyroid hormone levels, in certain oncogenic processes.
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Affiliation(s)
- Meghan D Rosen
- Department of Microbiology, University of California-Davis, Davis, CA 95616, USA
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