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Wei X, Li S, Li Z, Wang L, Fan W, Ruan K, Gao J. Fragment-based discovery of small molecule inhibitors of the HDGFRP2 PWWP domain. FEBS Lett 2024. [PMID: 39031937 DOI: 10.1002/1873-3468.14981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/20/2024] [Accepted: 06/19/2024] [Indexed: 07/22/2024]
Abstract
The PWWP domain of hepatoma-derived growth factor-related protein 2 (HDGFRP2) recognizes methylated histones to initiate the recruitment of homologous recombination repair proteins to damaged silent genes. The combined depletion of HDGFRP2 and its paralog PSIP1 effectively impedes the onset and progression of diffuse intrinsic pontine glioma (DIPG). Here, we discovered varenicline and 4-(4-bromo-1H-pyrazol-3-yl) pyridine (BPP) as inhibitors of the HDGFRP2 PWWP domain through a fragment-based screening method. The complex crystal structures reveal that both Varenicline and BPP engage with the aromatic cage of the HDGFRP2 PWWP domain, albeit via unique binding mechanisms. Notably, BPP represents the first single-digit micromolar inhibitor of the HDGFRP2 PWWP domain with a high ligand efficiency. As a dual inhibitor targeting both HDGFRP2 and PSIP1 PWWP domains, BPP offers an exceptional foundation for further optimization into a chemical tool to dissect the synergetic function of HDGFRP2 and PSIP1 in DIPG pathogenesis.
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Affiliation(s)
- Xiaoli Wei
- Department of Medical Oncology, The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shuju Li
- Department of Medical Oncology, The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zihuan Li
- Department of Medical Oncology, The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Lei Wang
- Department of Medical Oncology, The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Weiwei Fan
- Department of Medical Oncology, The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ke Ruan
- Department of Medical Oncology, The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jia Gao
- Department of Medical Oncology, The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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2
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Su F, Koeberle A. Regulation and targeting of SREBP-1 in hepatocellular carcinoma. Cancer Metastasis Rev 2024; 43:673-708. [PMID: 38036934 PMCID: PMC11156753 DOI: 10.1007/s10555-023-10156-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is an increasing burden on global public health and is associated with enhanced lipogenesis, fatty acid uptake, and lipid metabolic reprogramming. De novo lipogenesis is under the control of the transcription factor sterol regulatory element-binding protein 1 (SREBP-1) and essentially contributes to HCC progression. Here, we summarize the current knowledge on the regulation of SREBP-1 isoforms in HCC based on cellular, animal, and clinical data. Specifically, we (i) address the overarching mechanisms for regulating SREBP-1 transcription, proteolytic processing, nuclear stability, and transactivation and (ii) critically discuss their impact on HCC, taking into account (iii) insights from pharmacological approaches. Emphasis is placed on cross-talk with the phosphatidylinositol-3-kinase (PI3K)-protein kinase B (Akt)-mechanistic target of rapamycin (mTOR) axis, AMP-activated protein kinase (AMPK), protein kinase A (PKA), and other kinases that directly phosphorylate SREBP-1; transcription factors, such as liver X receptor (LXR), peroxisome proliferator-activated receptors (PPARs), proliferator-activated receptor γ co-activator 1 (PGC-1), signal transducers and activators of transcription (STATs), and Myc; epigenetic mechanisms; post-translational modifications of SREBP-1; and SREBP-1-regulatory metabolites such as oxysterols and polyunsaturated fatty acids. By carefully scrutinizing the role of SREBP-1 in HCC development, progression, metastasis, and therapy resistance, we shed light on the potential of SREBP-1-targeting strategies in HCC prevention and treatment.
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Affiliation(s)
- Fengting Su
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Andreas Koeberle
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria.
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3
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Seddighi S, Qi YA, Brown AL, Wilkins OG, Bereda C, Belair C, Zhang YJ, Prudencio M, Keuss MJ, Khandeshi A, Pickles S, Kargbo-Hill SE, Hawrot J, Ramos DM, Yuan H, Roberts J, Sacramento EK, Shah SI, Nalls MA, Colón-Mercado JM, Reyes JF, Ryan VH, Nelson MP, Cook CN, Li Z, Screven L, Kwan JY, Mehta PR, Zanovello M, Hallegger M, Shantaraman A, Ping L, Koike Y, Oskarsson B, Staff NP, Duong DM, Ahmed A, Secrier M, Ule J, Jacobson S, Reich DS, Rohrer JD, Malaspina A, Dickson DW, Glass JD, Ori A, Seyfried NT, Maragkakis M, Petrucelli L, Fratta P, Ward ME. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. Sci Transl Med 2024; 16:eadg7162. [PMID: 38277467 PMCID: PMC11325748 DOI: 10.1126/scitranslmed.adg7162] [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: 01/17/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.
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Affiliation(s)
- Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Colleen Bereda
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Aditya Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah E Kargbo-Hill
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Erika Kelmer Sacramento
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Syed I Shah
- Data Tecnica International, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Jennifer M Colón-Mercado
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Laurel Screven
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Puja R Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Martina Hallegger
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | | | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Björn Oskarsson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Nathan P Staff
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Aisha Ahmed
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK
| | - Jernej Ule
- Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Steven Jacobson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Reich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan D Rohrer
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Andrea Malaspina
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- Francis Crick Institute, London, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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4
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Saumer P, Scheffner M, Marx A, Stengel F. Interactome of intact chromatosome variants with site-specifically ubiquitylated and acetylated linker histone H1.2. Nucleic Acids Res 2024; 52:101-113. [PMID: 37994785 PMCID: PMC10783519 DOI: 10.1093/nar/gkad1113] [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: 04/05/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Post-translational modifications (PTMs) of histones have fundamental effects on chromatin structure and function. While the impact of PTMs on the function of core histones are increasingly well understood, this is much less the case for modifications of linker histone H1, which is at least in part due to a lack of proper tools. In this work, we establish the assembly of intact chromatosomes containing site-specifically ubiquitylated and acetylated linker histone H1.2 variants obtained by a combination of chemical biology approaches. We then use these complexes in a tailored affinity enrichment mass spectrometry workflow to identify and comprehensively characterize chromatosome-specific cellular interactomes and the impact of site-specific linker histone modifications on a proteome-wide scale. We validate and benchmark our approach by western-blotting and by confirming the involvement of chromatin-bound H1.2 in the recruitment of proteins involved in DNA double-strand break repair using an in vitro ligation assay. We relate our data to previous work and in particular compare it to data on modification-specific interaction partners of free H1. Taken together, our data supports the role of chromatin-bound H1 as a regulatory protein with distinct functions beyond DNA compaction and constitutes an important resource for future investigations of histone epigenetic modifications.
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Affiliation(s)
- Philip Saumer
- Department of Chemistry, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Martin Scheffner
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Department of Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
| | - Florian Stengel
- Konstanz Research School Chemical Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
- Department of Biology, University of Konstanz; Universitätsstraße 10, 78464 Konstanz, Germany
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5
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Rai R, Lightfoot S, Benbrook DM. Manipulation of metabolic responses enhances SHetA2 efficacy without toxicity in cervical cancer cell lines and xenografts. Gynecol Oncol 2024; 180:44-54. [PMID: 38052108 PMCID: PMC10922646 DOI: 10.1016/j.ygyno.2023.11.013] [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: 10/12/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 12/07/2023]
Abstract
OBJECTIVE The high frequency of cervical cancer recurrence after primary therapy necessitates alternative treatments. High-risk human papillomavirus (HR-HPV) causes cervical cancer and it's continued presence supports elevated metabolism, proliferation and survival of cancer cells. The low-to-no toxicity new investigational drug, SHetA2, counteracts high-risk human papillomavirus (HR-HPV) effects on cell proliferation and survival in cervical cancer cells and xenograft tumors by disrupting heat shock protein 70 chaperone protection of oncogenic proteins. Our objective was to study the involvement of metabolism in SHetA2 effects on cervical cancer cells and tumors. METHODS SHetA2-mediated proteomic and metabolic effects were measured in HR-HPV-positive CaSKi and SiHa and HR-HPV-negative C-33 A cervical cancer cell lines. Combined treatment with 2-deoxyglucose (2-DG) was evaluated in cell culture and SiHa xenografts. RESULTS SHetA2 inhibited oxidative phosphorylation (OxPhos) and altered levels of proteins involved in metabolism, protein synthesis, and DNA replication and repair. Cervical cancer cells responded by elevating glycolysis. Inhibition of the glycolytic responses using galactose media or 2-DG increased SHetA2 sensitivity of two HR-HPV-positive, but not an HR-HPV-negative cervical cancer cell line. Interaction of 2-DG and SHetA2 was synergistic in HR-HPV positive cell lines in association with augmentation of SHetA2 ATP reduction, but not SHetA2 DNA damage induction. These results were verified in a SiHa xenograft tumor model without evidence of toxicity. CONCLUSIONS Compensatory glycolysis counteracts OxPhos inhibition in SHetA2-treated HR-HPV-positive cervical cancer cell lines. Prevention of compensatory glycolysis with 2-DG or another glycolysis inhibitor has the potential to improve SHetA2 therapy without toxicity.
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Affiliation(s)
- Rajani Rai
- Section of Gynecologic Oncology, Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, USA
| | - Stanley Lightfoot
- Department of Pathology, University of Oklahoma Health Sciences Center, USA
| | - Doris Mangiaracina Benbrook
- Section of Gynecologic Oncology, Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Sciences Center, USA.
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6
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Zhang Z, Samsa WE, De Y, Zhang F, Reizes O, Almasan A, Gong Z. HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair. Nucleic Acids Res 2023; 51:2238-2256. [PMID: 36794849 PMCID: PMC10018360 DOI: 10.1093/nar/gkad073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 01/11/2023] [Accepted: 01/24/2023] [Indexed: 02/17/2023] Open
Abstract
The 53BP1-dependent end-joining pathway plays a critical role in double-strand break (DSB) repair. However, the regulators of 53BP1 in chromatin remain incompletely characterized. In this study, we identified HDGFRP3 (hepatoma-derived growth factor related protein 3) as a 53BP1-interacting protein. The HDGFRP3-53BP1 interaction is mediated by the PWWP domain of HDGFRP3 and the Tudor domain of 53BP1. Importantly, we observed that the HDGFRP3-53BP1 complex co-localizes with 53BP1 or γH2AX at sites of DSB and participates in the response to DNA damage repair. Loss of HDGFRP3 impairs classical non-homologous end-joining repair (NHEJ), curtails the accumulation of 53BP1 at DSB sites, and enhances DNA end-resection. Moreover, the HDGFRP3-53BP1 interaction is required for cNHEJ repair, 53BP1 recruitment at DSB sites, and inhibition of DNA end resection. In addition, loss of HDGFRP3 renders BRCA1-deficient cells resistant to PARP inhibitors by facilitating end-resection in BRCA1 deficient cells. We also found that the interaction of HDGFRP3 with methylated H4K20 was dramatically decreased; in contrast, the 53BP1-methylated H4K20 interaction was increased after ionizing radiation, which is likely regulated by protein phosphorylation and dephosphorylation. Taken together, our data reveal a dynamic 53BP1-methylated H4K20-HDGFRP3 complex that regulates 53BP1 recruitment at DSB sites, providing new insights into our understanding of the regulation of 53BP1-mediated DNA repair pathway.
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Affiliation(s)
- Zhen Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - William E Samsa
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Yanyan De
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Fan Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Ofer Reizes
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Alexandru Almasan
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
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7
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Seddighi S, Qi YA, Brown AL, Wilkins OG, Bereda C, Belair C, Zhang Y, Prudencio M, Keuss MJ, Khandeshi A, Pickles S, Hill SE, Hawrot J, Ramos DM, Yuan H, Roberts J, Kelmer Sacramento E, Shah SI, Nalls MA, Colon-Mercado J, Reyes JF, Ryan VH, Nelson MP, Cook C, Li Z, Screven L, Kwan JY, Shantaraman A, Ping L, Koike Y, Oskarsson B, Staff N, Duong DM, Ahmed A, Secrier M, Ule J, Jacobson S, Rohrer J, Malaspina A, Glass JD, Ori A, Seyfried NT, Maragkakis M, Petrucelli L, Fratta P, Ward ME. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525149. [PMID: 36747793 PMCID: PMC9900763 DOI: 10.1101/2023.01.23.525149] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to ALS and FTD, leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. However, the possibility of de novo protein synthesis from cryptic exon transcripts has not been explored. Here, we show that mRNA transcripts harboring cryptic exons generate de novo proteins both in TDP-43 deficient cellular models and in disease. Using coordinated transcriptomic and proteomic studies of TDP-43 depleted iPSC-derived neurons, we identified numerous peptides that mapped to cryptic exons. Cryptic exons identified in iPSC models were highly predictive of cryptic exons expressed in brains of patients with TDP-43 proteinopathy, including cryptic transcripts that generated de novo proteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that these de novo peptides were present in CSF from patients with ALS. The demonstration of cryptic exon translation suggests new mechanisms for ALS pathophysiology downstream of TDP-43 dysfunction and may provide a strategy for novel biomarker development.
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Affiliation(s)
- Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Oscar G Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
- The Francis Crick Institute, London, UK
| | - Colleen Bereda
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Yongjie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Matthew J Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Aditya Khandeshi
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Sarah Pickles
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Sarah E Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - James Hawrot
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Hebao Yuan
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jessica Roberts
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | | | - Syed I Shah
- Data Tecnica International, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Jenn Colon-Mercado
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Joel F Reyes
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Veronica H Ryan
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Casey Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Ziyi Li
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - Laurel Screven
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Justin Y Kwan
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | | | - Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Koike
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Björn Oskarsson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Nathan Staff
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Aisha Ahmed
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK
| | - Jerneg Ule
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Steven Jacobson
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jonathan Rohrer
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Andrea Malaspina
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
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8
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Wistner SC, MacDonald IA, Stanley KA, Hathaway NA. Characterization of Hepatoma-Derived Growth Factor-Related Protein 2 Interactions with Heterochromatin. Cells 2023; 12:325. [PMID: 36672260 PMCID: PMC9856275 DOI: 10.3390/cells12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
The expression of genetic information is tightly controlled by chromatin regulatory proteins, including those in the heterochromatin gene repression family. Many of these regulatory proteins work together on the chromatin substrate to precisely regulate gene expression during mammalian development, giving rise to many different tissues in higher organisms from a fixed genomic template. Here we identify and characterize the interactions of two related heterochromatin regulatory proteins, heterochromatin protein 1 alpha (HP1α) and M-phase phosphoprotein 8 (MPP8), with hepatoma-derived growth factor-related protein 2 (HRP2). We find in biochemical experiments that HRP2 copurifies and co-sediments with heterochromatin-associated proteins, including HP1α and MPP8. Using the Chromatin in vivo Assay in multiple cell types, we demonstrate that HP1α-mediated gene repression dynamics are altered by the presence of HRP2. Furthermore, the knockout of HRP2 in MDA-MB-231 cells results in significant changes to chromatin structure and stability, which alter gene expression patterns. Here, we detail a mechanism by which HRP2 contributes to epigenetic transcriptional regulation through engagement with heterochromatin-associated proteins to stabilize the chromatin landscape and influence gene expression.
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Affiliation(s)
- Sarah C. Wistner
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian A. MacDonald
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karly A. Stanley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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9
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Nagai M, Iemura K, Kikkawa T, Naher S, Hattori S, Hagihara H, Nagata KI, Anzawa H, Kugisaki R, Wanibuchi H, Abe T, Inoue K, Kinoshita K, Miyakawa T, Osumi N, Tanaka K. Deficiency of CHAMP1, a gene related to intellectual disability, causes impaired neuronal development and a mild behavioural phenotype. Brain Commun 2022; 4:fcac220. [PMID: 36106092 PMCID: PMC9465530 DOI: 10.1093/braincomms/fcac220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 05/12/2022] [Accepted: 08/26/2022] [Indexed: 11/24/2022] Open
Abstract
CHAMP1 is a gene associated with intellectual disability, which was originally identified as being involved in the maintenance of kinetochore–microtubule attachment. To explore the neuronal defects caused by CHAMP1 deficiency, we established mice that lack CHAMP1. Mice that are homozygous knockout for CHAMP1 were slightly smaller than wild-type mice and died soon after birth on pure C57BL/6J background. Although gross anatomical defects were not found in CHAMP1−/− mouse brains, mitotic cells were increased in the cerebral cortex. Neuronal differentiation was delayed in CHAMP1−/− neural stem cells in vitro, which was also suggested in vivo by CHAMP1 knockdown. In a behavioural test battery, adult CHAMP1 heterozygous knockout mice showed mild memory defects, altered social interaction, and depression-like behaviours. In transcriptomic analysis, genes related to neurotransmitter transport and neurodevelopmental disorder were downregulated in embryonic CHAMP1−/− brains. These results suggest that CHAMP1 plays a role in neuronal development, and CHAMP1-deficient mice resemble some aspects of individuals with CHAMP1 mutations.
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Affiliation(s)
- Masayoshi Nagai
- Department of Molecular Oncology, Institute of Development, Aging and Cancer (IDAC), Tohoku University , Sendai, Miyagi 980-8575 , Japan
| | - Kenji Iemura
- Department of Molecular Oncology, Institute of Development, Aging and Cancer (IDAC), Tohoku University , Sendai, Miyagi 980-8575 , Japan
| | - Takako Kikkawa
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine , Sendai, Miyagi 980-8575 , Japan
| | - Sharmin Naher
- Department of Developmental Neuroscience, Tohoku University Graduate School of Life Sciences , Sendai, Miyagi 980-8575 , Japan
| | - Satoko Hattori
- Division of Systems Medical Science, Institute for Comprehensive Medical Science (ICMS), Fujita Health University , Toyoake, Aichi 470-1192 , Japan
| | - Hideo Hagihara
- Division of Systems Medical Science, Institute for Comprehensive Medical Science (ICMS), Fujita Health University , Toyoake, Aichi 470-1192 , Japan
| | - Koh-ichi Nagata
- Department of Molecular Neurobiology, Institute of Developmental Research, Aichi Developmental Disability Center , Kasugai, Aichi 480-0392 , Japan
- Department of Neurochemistry, Nagoya University Graduate School of Medicine , Nagoya, Aichi 466-8550 , Japan
| | - Hayato Anzawa
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University , Sendai 980-8579 , Japan
| | - Risa Kugisaki
- Department of Molecular Oncology, Institute of Development, Aging and Cancer (IDAC), Tohoku University , Sendai, Miyagi 980-8575 , Japan
| | - Hideki Wanibuchi
- Department of Molecular Pathology, Osaka City University Graduate School of Medicine , Osaka 545-8585 , Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research , Kobe, Hyogo 650-0047 , Japan
| | - Kenichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research , Kobe, Hyogo 650-0047 , Japan
| | - Kengo Kinoshita
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University , Sendai 980-8579 , Japan
- Division of Integrated Genomics, Tohoku Medical Megabank Organization, Tohoku University , Sendai, 980-8573 , Japan
- Department of In Silico Analysis, Institute of Development, Aging and Cancer, Tohoku University , Sendai, 980-8575 , Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science (ICMS), Fujita Health University , Toyoake, Aichi 470-1192 , Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine , Sendai, Miyagi 980-8575 , Japan
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer (IDAC), Tohoku University , Sendai, Miyagi 980-8575 , Japan
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10
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CHAMP1 binds to REV7/FANCV and promotes homologous recombination repair. Cell Rep 2022; 40:111297. [PMID: 36044844 PMCID: PMC9472291 DOI: 10.1016/j.celrep.2022.111297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/13/2022] [Accepted: 08/09/2022] [Indexed: 11/22/2022] Open
Abstract
A critical determinant of DNA repair pathway choice is REV7, an adaptor that binds to various DNA repair proteins through its C-terminal seatbelt domain. The REV7 seatbelt binds to either REV3, activating translesion synthesis, or to SHLD3, activating non-homologous end joining (NHEJ) repair. Recent studies have identified another REV7 seatbelt-binding protein, CHAMP1 (chromosome alignment-maintaining phosphoprotein 1), though its possible role in DNA repair is unknown. Here, we show that binding of CHAMP1 to REV7 activates homologous recombination (HR) repair. Mechanistically, CHAMP1 binds directly to REV7 and reduces the level of the Shieldin complex, causing an increase in double-strand break end resection. CHAMP1 also interacts with POGZ in a heterochromatin complex further promoting HR repair. Importantly, in human tumors, CHAMP1 overexpression promotes HR, confers poly (ADP-ribose) polymerase inhibitor resistance, and correlates with poor prognosis. Thus, by binding to either SHLD3 or CHAMP1 through its seatbelt, the REV7 protein can promote either NHEJ or HR repair, respectively. Feng et al. demonstrate that CHAMP1 promotes homologous recombination by binding to REV7 and reducing the level of the Shieldin complex, causing an increase in double-strand break end resection. CHAMP1 and POGZ form a complex to further promote HR. Upregulation of CHAMP1 expression is a mechanism of acquired PARP inhibitor resistance.
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11
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CHAMP1-POGZ counteracts the inhibitory effect of 53BP1 on homologous recombination and affects PARP inhibitor resistance. Oncogene 2022; 41:2706-2718. [PMID: 35393543 DOI: 10.1038/s41388-022-02299-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/15/2022]
Abstract
DNA double-strand break (DSB) repair-pathway choice regulated by 53BP1 and BRCA1 contributes to genome stability. 53BP1 cooperates with the REV7-Shieldin complex and inhibits DNA end resection to block homologous recombination (HR) and affects the sensitivity to inhibitors for poly (ADP-ribose) polymerases (PARPs) in BRCA1-deficient cells. Here, we show that a REV7 binding protein, CHAMP1 (chromosome alignment-maintaining phosphoprotein 1), has an opposite function of REV7 in DSB repair and promotes HR through DNA end resection together with POGZ (POGO transposable element with ZNF domain). CHAMP1 was recruited to laser-micro-irradiation-induced DSB sites and promotes HR, but not NHEJ. CHAMP1 depletion suppressed the recruitment of BRCA1, but not the recruitment of 53BP1, suggesting that CHAMP1 regulates DSB repair pathway in favor of HR. Depletion of either CHAMP1 or POGZ impaired the recruitment of phosphorylated RPA2 and CtIP (CtBP-interacting protein) at DSB sites, implying that CHAMP1, in complex with POGZ, promotes DNA end resection for HR. Furthermore, loss of CHAMP1 and POGZ restored the sensitivity to a PARP inhibitor in cells depleted of 53BP1 together with BRCA1. These data suggest that CHAMP1and POGZ counteract the inhibitory effect of 53BP1 on HR by promoting DNA end resection and affect the resistance to PARP inhibitors.
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12
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Wang J, Zhu X, Dang L, Jiang H, Xie Y, Li X, Guo J, Wang Y, Peng Z, Wang M, Wang J, Wang S, Li Q, Wang Y, Wang Q, Ye L, Zhang L, Liu Z. Epigenomic reprogramming via HRP2-MINA dictates response to proteasome inhibitors in multiple myeloma with t(4;14) translocation. J Clin Invest 2022; 132:149526. [PMID: 35166240 PMCID: PMC8843744 DOI: 10.1172/jci149526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 12/27/2021] [Indexed: 11/17/2022] Open
Abstract
The chromosomal t(4;14) (p16;q32) translocation drives high expression of histone methyltransferase nuclear SET domain–containing 2 (NSD2) and plays vital roles in multiple myeloma (MM) evolution and progression. However, the mechanisms of NSD2-driven epigenomic alterations in chemoresistance to proteasome inhibitors (PIs) are not fully understood. Using a CRISPR/Cas9 sgRNA library in a bone marrow–bearing MM model, we found that hepatoma-derived growth factor 2 (HRP2) was a suppressor of chemoresistance to PIs and that its downregulation correlated with a poor response and worse outcomes in the clinic. We observed suppression of HRP2 in bortezomib-resistant MM cells, and knockdown of HRP2 induced a marked tolerance to PIs. Moreover, knockdown of HRP2 augmented H3K27me3 levels, consequentially intensifying transcriptome alterations promoting cell survival and restriction of ER stress. Mechanistically, HRP2 recognized H3K36me2 and recruited the histone demethylase MYC-induced nuclear antigen (MINA) to remove H3K27me3. Tazemetostat, a highly selective epigenetic inhibitor that reduces H3K27me3 levels, synergistically sensitized the anti-MM effects of bortezomib both in vitro and in vivo. Collectively, these results provide a better understanding of the origin of chemoresistance in patients with MM with the t(4;14) translocation and a rationale for managing patients with MM who have different genomic backgrounds.
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Affiliation(s)
- Jingjing Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Xu Zhu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lin Dang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hongmei Jiang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Ying Xie
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Xin Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Jing Guo
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Yixuan Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Ziyi Peng
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Mengqi Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Jingya Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Sheng Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China
| | - Qian Li
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, Tianjin, China
| | - Yafei Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, Tianjin, China
| | - Qiang Wang
- Center for Translational Research in Hematological Malignancies, Cancer Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Lingqun Ye
- Center for Translational Research in Hematological Malignancies, Cancer Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Lirong Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhiqiang Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Science, Tianjin Medical University, Heping, Tianjin, China.,Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, Tianjin, China
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13
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Heath J, Cheyou ES, Findlay S, Luo VM, Carpio EP, Lee J, Djerir B, Chen X, Morin T, Lebeau B, Karam M, Bagci H, Grapton D, Ursini‐Siegel J, Côté J, Witcher M, Richard S, Maréchal A, Orthwein A. POGZ promotes homology-directed DNA repair in an HP1-dependent manner. EMBO Rep 2022; 23:e51041. [PMID: 34758190 PMCID: PMC8728601 DOI: 10.15252/embr.202051041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 01/07/2023] Open
Abstract
The heterochromatin protein HP1 plays a central role in the maintenance of genome stability but little is known about how HP1 is controlled. Here, we show that the zinc finger protein POGZ promotes the presence of HP1 at DNA double-strand breaks (DSBs) in human cells. POGZ depletion delays the resolution of DSBs and sensitizes cells to different DNA-damaging agents, including cisplatin and talazoparib. Mechanistically, POGZ promotes homology-directed DNA repair by retaining the BRCA1/BARD1 complex at DSBs in an HP1-dependent manner. In vivo CRISPR inactivation of Pogz is embryonically lethal. Pogz haploinsufficiency (Pogz+ /delta) results in developmental delay, impaired intellectual abilities, hyperactive behaviour and a compromised humoral immune response in mice, recapitulating the main clinical features of the White Sutton syndrome (WHSUS). Pogz+ /delta mice are further radiosensitive and accumulate DSBs in diverse tissues, including the spleen and brain. Altogether, our findings identify POGZ as an important player in homology-directed DNA repair both in vitro and in vivo.
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Affiliation(s)
- John Heath
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Estelle Simo Cheyou
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Vincent M Luo
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Department of Microbiology and ImmunologyMcGill UniversityMontrealQCCanada
| | - Edgar Pinedo Carpio
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Jeesan Lee
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
| | - Billel Djerir
- Department of BiologyUniversité de SherbrookeSherbrookeQCCanada
| | - Xiaoru Chen
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
| | - Théo Morin
- Department of BiologyUniversité de SherbrookeSherbrookeQCCanada
| | - Benjamin Lebeau
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Martin Karam
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Halil Bagci
- Institut de Recherches Cliniques de Montréal (IRCM)MontrealQCCanada
- Département of Anatomy and Cell BiologyMcGill UniversityMontrealQCCanada
- Present address:
Institute of BiochemistryETH ZürichZürichSwitzerland
| | - Damien Grapton
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
| | - Josie Ursini‐Siegel
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
| | - Jean‐Francois Côté
- Institut de Recherches Cliniques de Montréal (IRCM)MontrealQCCanada
- Département of Anatomy and Cell BiologyMcGill UniversityMontrealQCCanada
- Département de Biochimie et Médecine MoléculaireUniversité de MontréalMontrealQCCanada
- Département de Médecine (Programmes de Biologie Moléculaire)Université de MontréalMontrealQCCanada
| | - Michael Witcher
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
| | - Stéphane Richard
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
| | | | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer CentreJewish General HospitalMontrealQCCanada
- Division of Experimental MedicineMcGill UniversityMontrealQCCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQCCanada
- Department of Microbiology and ImmunologyMcGill UniversityMontrealQCCanada
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14
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Yun HS, Lee J, Kim JY, Sim YJ, Lee CW, Park JK, Kim JS, Ahn J, Song JY, Baek JH, Hwang SG. A novel function of HRP-3 in regulating cell cycle progression via the HDAC-E2F1-Cyclin E pathway in lung cancer. Cancer Sci 2021; 113:145-155. [PMID: 34714604 PMCID: PMC8748221 DOI: 10.1111/cas.15183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
To improve the poor survival rate of lung cancer patients, we investigated the role of HDGF‐related protein 3 (HRP‐3) as a potential biomarker for lung cancer. The expression of endogenous HRP‐3 in human lung cancer tissues and xenograft tumor models is indicative of its clinical relevance in lung cancer. Additionally, we demonstrated that HRP‐3 directly binds to the E2F1 promoter on chromatin. Interestingly, HRP‐3 depletion in A549 cells impedes the binding of HRP‐3 to the E2F1 promoter; this in turn hampers the interaction between Histone H3/H4 and HDAC1/2 on the E2F1 promoter, while concomitantly inducing Histone H3/H4 acetylation around the E2F1 promoter. The enhanced Histone H3/H4 acetylation on the E2F1 promoter through HRP‐3 depletion increases the transcription level of E2F1. Furthermore, the increased E2F1 transcription levels lead to the enhanced transcription of Cyclin E, known as the E2F1‐responsive gene, thus inducing S‐phase accumulation. Therefore, our study provides evidence for the utility of HRP‐3 as a biomarker for the prognosis and treatment of lung cancer. Furthermore, we delineated the capacity of HRP‐3 to regulate the E2F1 transcription level via histone deacetylation.
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Affiliation(s)
- Hong Shik Yun
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Janet Lee
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Ju-Young Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ye-Ji Sim
- Radiation Biology Research Team, Research Center, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jong Kuk Park
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jae-Sung Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jiyeon Ahn
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jie-Young Song
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jeong-Hwa Baek
- Radiation Biology Research Team, Research Center, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Sang-Gu Hwang
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
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15
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The LEDGF/p75 Integrase Binding Domain Interactome Contributes to the Survival, Clonogenicity, and Tumorsphere Formation of Docetaxel-Resistant Prostate Cancer Cells. Cells 2021; 10:cells10102723. [PMID: 34685704 PMCID: PMC8534522 DOI: 10.3390/cells10102723] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/18/2022] Open
Abstract
Patients with prostate cancer (PCa) receiving docetaxel chemotherapy invariably develop chemoresistance. The transcription co-activator lens epithelium-derived growth factor p75 (LEDGF/p75), also known as DFS70 and PSIP1, is upregulated in several human cancers, including PCa and promotes resistance to docetaxel and other drugs. The C-terminal region of LEDGF/p75 contains an integrase binding domain (IBD) that tethers nuclear proteins, including the HIV-1 integrase and transcription factors, to active chromatin to promote viral integration and transcription of cellular survival genes. Here, we investigated the contribution of the LEDGF/p75 IBD interactome to PCa chemoresistance. Quantitative immunoblotting revealed that LEDGF/p75 and its IBD-interacting partners are endogenously upregulated in docetaxel-resistant PCa cell lines compared to docetaxel-sensitive parental cells. Using specific human autoantibodies, we co-immunoprecipitated LEDGF/p75 with its endogenous IBD-interacting partners JPO2, menin, MLL, IWS1, ASK1, and PogZ, as well as transcription factors c-MYC and HRP2, in docetaxel-resistant cells, and confirmed their nuclear co-localization by confocal microscopy. Depletion of LEDGF/p75 and selected interacting partners robustly decreased the survival, clonogenicity, and tumorsphere formation capacity of docetaxel-resistant cells. These results implicate the LEDGF/p75 IBD interactome in PCa chemoresistance and could lead to novel therapeutic strategies targeting this protein complex for the treatment of docetaxel-resistant tumors.
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16
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Waybright JM, Clinkscales SE, Barnash KD, Budziszewski GR, Rectenwald JM, Chiarella AM, Norris-Drouin JL, Cholensky SH, Pearce KH, Herring LE, McGinty RK, Hathaway NA, James LI. A Peptidomimetic Ligand Targeting the Chromodomain of MPP8 Reveals HRP2's Association with the HUSH Complex. ACS Chem Biol 2021; 16:1721-1736. [PMID: 34415726 DOI: 10.1021/acschembio.1c00429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interpretation of histone post-translational modifications (PTMs), specifically lysine methylation, by specific classes of "reader" proteins marks an important aspect of epigenetic control of gene expression. Methyl-lysine (Kme) readers often regulate gene expression patterns through the recognition of a specific Kme PTM while participating in or recruiting large protein complexes that contain enzymatic or chromatin remodeling activity. Understanding the composition of these Kme-reader-containing protein complexes can serve to further our understanding of the biological roles of Kme readers, while small molecule chemical tools can be valuable reagents in interrogating novel protein-protein interactions. Here, we describe our efforts to target the chromodomain of M-phase phosphoprotein 8 (MPP8), a member of the human silencing hub (HUSH) complex and a histone 3 lysine 9 trimethyl (H3K9me3) reader that is vital for heterochromatin formation and has specific roles in cancer metastasis. Utilizing a one-bead, one-compound (OBOC) combinatorial screening approach, we identified UNC5246, a peptidomimetic ligand capable of interacting with the MPP8 chromodomain in the context of the HUSH complex. Additionally, a biotinylated derivative of UNC5246 facilitated chemoproteomics studies which revealed hepatoma-derived growth factor-related protein 2 (HRP2) as a novel protein associated with MPP8. HRP2 was further shown to colocalize with MPP8 at the E-cadherin gene locus, suggesting a possible role in cancer cell plasticity.
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Affiliation(s)
- Jarod M. Waybright
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sarah E. Clinkscales
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | | | - Gabrielle R. Budziszewski
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Justin M. Rectenwald
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Anna M. Chiarella
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline L. Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie H. Cholensky
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Laura E. Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Robert K. McGinty
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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17
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Clairmont CS, D'Andrea AD. REV7 directs DNA repair pathway choice. Trends Cell Biol 2021; 31:965-978. [PMID: 34147298 DOI: 10.1016/j.tcb.2021.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
REV7 is a small multifunctional protein that participates in multiple DNA repair pathways, most notably translesion DNA synthesis and double-strand break (DSB) repair. While the role of REV7 in translesion synthesis has been known for several decades, its function in DSB repair is a recent discovery. Investigations into the DSB repair function of REV7 have led to the discovery of a new DNA repair complex known as Shieldin. Recent studies have also highlighted the importance of REV7's HORMA domain, an ancient structural motif, in REV7 function and have identified the HORMA regulators, TRIP13 and p31, as novel DNA repair factors. In this review, we discuss these recent findings and their implications for repair pathway choice, at both DSBs and replication forks. We suggest that REV7, in particular the activation state of its HORMA domain, can act as a critical determinant of mutagenic versus error-free repair in multiple contexts.
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Affiliation(s)
- Connor S Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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18
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Unlike Its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival. Cells 2021; 10:cells10010192. [PMID: 33477970 PMCID: PMC7835958 DOI: 10.3390/cells10010192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
HDGF-related protein 2 (HRP-2) is a member of the Hepatoma-Derived Growth Factor-related protein family that harbors the structured PWWP and Integrase Binding Domain, known to associate with methylated histone tails or cellular and viral proteins, respectively. Interestingly, HRP-2 is a paralog of Lens Epithelium Derived Growth Factor p75 (LEDGF/p75), which is essential for MLL-rearranged (MLL-r) leukemia but dispensable for hematopoiesis. Sequel to these findings, we investigated the role of HRP-2 in hematopoiesis and MLL-r leukemia. Protein interactions were investigated by co-immunoprecipitation and validated using recombinant proteins in NMR. A systemic knockout mouse model was used to study normal hematopoiesis and MLL-ENL transformation upon the different HRP-2 genotypes. The role of HRP-2 in MLL-r and other leukemic, human cell lines was evaluated by lentiviral-mediated miRNA targeting HRP-2. We demonstrate that MLL and HRP-2 interact through a conserved interface, although this interaction proved less dependent on menin than the MLL-LEDGF/p75 interaction. The systemic HRP-2 knockout mice only revealed an increase in neutrophils in the peripheral blood, whereas the depletion of HRP-2 in leukemic cell lines and transformed primary murine cells resulted in reduced colony formation independently of MLL-rearrangements. In contrast, primary murine HRP-2 knockout cells were efficiently transformed by the MLL-ENL fusion, indicating that HRP-2, unlike LEDGF/p75, is dispensable for the transformation of MLL-ENL leukemogenesis but important for leukemic cell survival.
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19
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Charmpi K, Guo T, Zhong Q, Wagner U, Sun R, Toussaint NC, Fritz CE, Yuan C, Chen H, Rupp NJ, Christiansen A, Rutishauser D, Rüschoff JH, Fankhauser C, Saba K, Poyet C, Hermanns T, Oehl K, Moore AL, Beisel C, Calzone L, Martignetti L, Zhang Q, Zhu Y, Martínez MR, Manica M, Haffner MC, Aebersold R, Wild PJ, Beyer A. Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biol 2020; 21:302. [PMID: 33317623 PMCID: PMC7737297 DOI: 10.1186/s13059-020-02188-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Background Tumor-specific genomic aberrations are routinely determined by high-throughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels and consequently biochemical states of tumor tissues. Results Here, we investigate the propagation of genomic effects along the axis of gene expression during prostate cancer progression. We quantify genomic, transcriptomic, and proteomic alterations based on 105 prostate samples, consisting of benign prostatic hyperplasia regions and malignant tumors, from 39 prostate cancer patients. Our analysis reveals the convergent effects of distinct copy number alterations impacting on common downstream proteins, which are important for establishing the tumor phenotype. We devise a network-based approach that integrates perturbations across different molecular layers, which identifies a sub-network consisting of nine genes whose joint activity positively correlates with increasingly aggressive tumor phenotypes and is predictive of recurrence-free survival. Further, our data reveal a wide spectrum of intra-patient network effects, ranging from similar to very distinct alterations on different molecular layers. Conclusions This study uncovers molecular networks with considerable convergent alterations across tumor sites and patients. It also exposes a diversity of network effects: we could not identify a single sub-network that is perturbed in all high-grade tumor regions.
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Affiliation(s)
- Konstantina Charmpi
- CECAD, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. .,Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China. .,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China.
| | - Qing Zhong
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Ulrich Wagner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Rui Sun
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Nora C Toussaint
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Christine E Fritz
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chunhui Yuan
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Hao Chen
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ailsa Christiansen
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jan H Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christian Fankhauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Karim Saba
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Department of Urology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Cedric Poyet
- Department of Urology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kathrin Oehl
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ariane L Moore
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | - Qiushi Zhang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Yi Zhu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | | | | | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. .,Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. .,Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany.
| | - Andreas Beyer
- CECAD, University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany.
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20
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Ding G, Xu X, Li D, Chen Y, Wang W, Ping D, Jia S, Cao L. Fisetin inhibits proliferation of pancreatic adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation. Cell Death Dis 2020; 11:893. [PMID: 33093461 PMCID: PMC7582166 DOI: 10.1038/s41419-020-03019-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/05/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022]
Abstract
Pancreatic adenocarcinoma (PDAC) is an extremely malignant tumor that is associated with low survival rates. Fisetin is a natural flavonoid that shows diverse antitumor effects, including DNA damage, in various cancers. Increasing studies have demonstrated that epigenetic modifications play critical roles in DNA-damage response. However, the epigenetic regulation mechanism of fisetin in cancers is hardly studied. RFXAP is a critical transcription factor for MHC II molecules, however, its transcriptional role in PDAC is poorly understood. The anti-PDAC effect of fisetin was measured by CCK-8, flow cytometry, xenograft tumor nude mice model. DNA-damage levels were examined by immunofluorescence. Bioinformatics analysis was used to examine the expression of RFXAP and other genes involved in DNA-damage response. ChIP sequencing was used to explore the transcriptional role of RFXAP. The expression of target gene KDM4A was measured by qRT-PCR and western blots. KDM4A promoter activity was analyzed using dual-luciferase reporter assay. RFXAP overexpressing or silencing of PDAC cells was used to explore the effect of RFXAP in DNA damage induced by fisetin. We found that fisetin inhibited cell proliferation and induced DNA damage and S-phase arrest in PDAC. Expression of RFXAP and other DNA-damage response genes were upregulated by fisetin. We revealed that RFXAP expression was relatively low in PDAC and correlated with tumor stage and poor prognosis. Then we explored the transcriptional role of RFXAP and found that RFXAP targeted KDM4A, a special demethylase specific for tri- and dimethylated histone H3K36. We found that overexpression of RFXAP upregulated KDM4A and attenuated methylation of H3K36, thereby impairing DNA repair and enhancing the DNA damage induced by fisetin, while RFXAP silencing showed the opposite effect. We also found the function of fisetin in enhancing the effect of chemotherapy on pancreatic cancer cells. Our findings revealed that fisetin induced DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation, thus causing inhibition of proliferation in PDAC.
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Affiliation(s)
- Guoping Ding
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Xiaodong Xu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Dan Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Department of General Surgery, School of Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310000, China
| | - Yuhao Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Emergency Department, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Weimin Wang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.,Department of General Surgery, Huzhou Hospital, Zhejiang University School of Medicine, Huzhou, 313003, Zhejiang, China
| | - Dongnan Ping
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Shengnan Jia
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China.
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China. .,Innovation Center for Minimally Invasive Technique and Device, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
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21
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Zhu X, Lan B, Yi X, He C, Dang L, Zhou X, Lu Y, Sun Y, Liu Z, Bai X, Zhang K, Li B, Li MJ, Chen Y, Zhang L. HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription. Nucleic Acids Res 2020; 48:6563-6582. [PMID: 32459350 PMCID: PMC7337902 DOI: 10.1093/nar/gkaa441] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/17/2022] Open
Abstract
Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we discover an HRP2-DPF3a-BAF epigenetic pathway that coordinates methylated histone H3 lysine 36 (H3K36me) and ATP-dependent chromatin remodeling to regulate chromatin dynamics and gene transcription during myogenic differentiation. Using siRNA screening targeting epigenetic modifiers, we identify hepatoma-derived growth factor-related protein 2 (HRP2) as a key regulator of myogenesis. Knockout of HRP2 in mice leads to impaired muscle regeneration. Mechanistically, through its HIV integrase binding domain (IBD), HRP2 associates with the BRG1/BRM-associated factor (BAF) chromatin remodeling complex by interacting directly with the BAF45c (DPF3a) subunit. Through its Pro-Trp-Trp-Pro (PWWP) domain, HRP2 preferentially binds to H3K36me2. Consistent with the biochemical studies, ChIP-seq analyses show that HRP2 colocalizes with DPF3a across the genome and that the recruitment of HRP2/DPF3a to chromatin is dependent on H3K36me2. Integrative transcriptomic and cistromic analyses, coupled with ATAC-seq, reveal that HRP2 and DPF3a activate myogenic genes by increasing chromatin accessibility through recruitment of BRG1, the ATPase subunit of the BAF complex. Taken together, these results illuminate a key role for the HRP2-DPF3a-BAF complex in the epigenetic coordination of gene transcription during myogenic differentiation.
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Affiliation(s)
- Xu Zhu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Bingxue Lan
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin 300070, China
| | - Chaoran He
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Lin Dang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xingquan Zhou
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yumei Lu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yongzhan Sun
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Zhiheng Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xue Bai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mulin Jun Li
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yupeng Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Lirong Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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22
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Xiao Y, Luo H, Yang WZ, Zeng Y, Shen Y, Ni X, Shi Z, Zhong J, Liang Z, Fu X, Tu H, Sun W, Shen WL, Hu J, Yang J. A Brain Signaling Framework for Stress-Induced Depression and Ketamine Treatment Elucidated by Phosphoproteomics. Front Cell Neurosci 2020; 14:48. [PMID: 32317933 PMCID: PMC7156020 DOI: 10.3389/fncel.2020.00048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/20/2020] [Indexed: 12/25/2022] Open
Abstract
Depression is a common affective disorder characterized by significant and persistent low mood. Ketamine, an N-methyl-D-aspartate receptor (NMDAR) antagonist, is reported to have a rapid and durable antidepressant effect, but the mechanisms are unclear. Protein phosphorylation is a post-translational modification that plays a crucial role in cell signaling. Thus, we present a phosphoproteomics approach to investigate the mechanisms underlying stress-induced depression and the rapid antidepressant effect of ketamine in mice. We analyzed the phosphoprotein changes induced by chronic unpredictable mild stress (CUMS) and ketamine treatment in two known mood control centers, the medial prefrontal cortex (mPFC) and the nucleus accumbens (NAc). We initially obtained >8,000 phosphorylation sites. Quantitation revealed 3,988 sites from the mPFC and 3,196 sites from the NAc. Further analysis revealed that changes in synaptic transmission-related signaling are a common feature. Notably, CUMS-induced changes were reversed by ketamine treatment, as shown by the analysis of commonly altered sites. Ketamine also induced specific changes, such as alterations in synapse organization, synaptic transmission, and enzyme binding. Collectively, our findings establish a signaling framework for stress-induced depression and the rapid antidepressant effect of ketamine.
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Affiliation(s)
- Yan Xiao
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Huoqing Luo
- School of Life Science and Technology, Shanghaitech University, Shanghai, China.,State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Institute of Neuroscience, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Z Yang
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and Technology, Shanghaitech University, Shanghai, China.,CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yeting Zeng
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yinbo Shen
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xinyan Ni
- School of Life Science and Technology, Shanghaitech University, Shanghai, China
| | - Zhaomei Shi
- School of Life Science and Technology, Shanghaitech University, Shanghai, China
| | - Jun Zhong
- Delta Omics Inc., Baltimore, MD, United States
| | - Ziqi Liang
- School of Life Science and Technology, Shanghaitech University, Shanghai, China
| | - Xiaoyu Fu
- School of Life Science and Technology, Shanghaitech University, Shanghai, China.,State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Institute of Neuroscience, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongqing Tu
- School of Life Science and Technology, Shanghaitech University, Shanghai, China.,State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Institute of Neuroscience, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhi Sun
- Chinese Institute For Brain Research, Beijing, China
| | - Wei L Shen
- School of Life Science and Technology, Shanghaitech University, Shanghai, China
| | - Ji Hu
- School of Life Science and Technology, Shanghaitech University, Shanghai, China
| | - Jiajun Yang
- Department of Neurology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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23
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Gao G, Zhang L, Villarreal OD, He W, Su D, Bedford E, Moh P, Shen J, Shi X, Bedford MT, Xu H. PRMT1 loss sensitizes cells to PRMT5 inhibition. Nucleic Acids Res 2019; 47:5038-5048. [PMID: 30916320 PMCID: PMC6547413 DOI: 10.1093/nar/gkz200] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/22/2019] [Accepted: 03/15/2019] [Indexed: 02/06/2023] Open
Abstract
PRMT5 is an arginine methyltransferase that accounts for the vast majority of the symmetric methylation in cells. PRMT5 exerts its function when complexed with MEP50/WDR77. This activity is often elevated in cancer cells and correlates with poor prognosis, making PRMT5 a therapeutic target. To investigate the PRMT5 signaling pathway and to identify genes whose loss-of-function sensitizes cancer cells to PRMT5 inhibition, we performed a CRISPR/Cas9 genetic screen in the presence of a PRMT5 inhibitor. We identified known components of the PRMT5 writer/reader pathway including PRMT5 itself, MEP50/WDR77, PPP4C, SMNDC1 and SRSF3. Interestingly, loss of PRMT1, the major asymmetric arginine methyltransferase, also sensitizes cells to PRMT5 inhibition. We investigated the interplay between PRMT5 and PRMT1, and found that combinatorial inhibitor treatment of small cell lung cancer and pancreatic cancer cell models have a synergistic effect. Furthermore, MTAP-deleted cells, which harbor an attenuated PRMT5–MEP50 signaling pathway, are generally more sensitive to PRMT1 inhibition. Together, these findings demonstrate that there is a degree of redundancy between the PRMT5 and PRMT1 pathways, even though these two enzymes deposit different types of arginine methylation marks. Targeting this redundancy provides a vulnerability for tumors carrying a co-deletion of MTAP and the adjacent CDKN2A tumor suppressor gene.
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Affiliation(s)
- Guozhen Gao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Liang Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Oscar D Villarreal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ella Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Phoebe Moh
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Han Xu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
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24
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Idini M, Wieringa P, Rocchiccioli S, Nieddu G, Ucciferri N, Formato M, Lepedda A, Moroni L. Glycosaminoglycan functionalization of electrospun scaffolds enhances Schwann cell activity. Acta Biomater 2019; 96:188-202. [PMID: 31265920 DOI: 10.1016/j.actbio.2019.06.054] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/06/2019] [Accepted: 06/27/2019] [Indexed: 12/13/2022]
Abstract
Nerve fibers of the peripheral nervous system (PNS) have a remarkable ability to regenerate up to an almost complete recovery of normal function following a crush or a Sunderland Type II injury. This process is governed by glial cells, known as Schwann cells, through their unique capacity to dedifferentiate into cells that drive the healing process. Despite that many progresses have occurred in restorative medicine and microsurgery, the regenerative process after a severe lesion of a major nerve trunk (e.g., Sunderland Types III-V) is often incomplete and functional recovery is unsatisfactory. In this aspect, it is known that glycosaminoglycans (GAGs) of the extracellular matrix are involved in proliferation, synaptogenesis, neural plasticity, and regeneration of the PNS. Here, we developed poly(caprolactone) (PCL) fibrous scaffolds functionalized with GAGs, which allowed us to assess their influence on the adhesion, proliferation, and differentiation of Schwann cells. We found that both aligned and random fiber scaffolds functionalized with GAGs resulted in increased cell proliferation on day 1. In addition, aligned functionalized scaffolds also resulted in increased GAG presence on day 1, probably because of cell extracellular matrix (ECM) formation and an increased syndecan-4 expression on day 7. A different modification and activation of Schwann cells in the presence of GAG versus no-GAG scaffolds was underlined by proteomic comparative analysis, where a general downregulation of the expression of intracellular/structural and synthetic proteins was shown on day 7 for GAG-functionalized scaffolds with regard to the nonfunctionalized ones. In conclusion, we have shown that GAG-functionalized scaffolds are effective in modulating Schwann cell behavior in terms of adhesion, proliferation, and differentiation and should be considered in strategies to improve PNS repair. STATEMENT OF SIGNIFICANCE: Nerve fibers functional recovery following a severe trauma of the Peripheral Nervous System (PNS) still represents a huge challenge for neurosurgery nowadays. In this respect, tissue engineering is committed to develop new constructs able to guide Schwann cells by mimicking the natural extracellular matrix environment. To this purpose, we successfully fabricated polycaprolactone (PCL) scaffolds with two well-defined fiber deposition patterns, functionalized with glycosaminoglycans (GAGs) and assessed for their potential as support for Schwann cells adhesion, growth and differentiation, by both classical biochemistry and LC-MS-based proteomic profiling. By this way, we showed that PCL-GAGs scaffolds could represent a promising artificial substrate that closely mimics the recently established pattern of Schwann cells migration into the regenerating nerve and, therefore, it should be considered in strategies to improve PNS repair.
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Affiliation(s)
- Michela Idini
- Dipartimento di Scienze Biomediche University of Sassari, Viale S. Pietro 43/B, 07100 Sassari, Italy
| | - Paul Wieringa
- Department of Complex Tissue Regeneration, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitsingel 40, 6229ER Maastricht, The Netherlands
| | - Silvia Rocchiccioli
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
| | - Gabriele Nieddu
- Dipartimento di Scienze Biomediche University of Sassari, Viale S. Pietro 43/B, 07100 Sassari, Italy
| | - Nadia Ucciferri
- Institute of Clinical Physiology, National Research Council, Via Moruzzi 1, 56124 Pisa, Italy
| | - Marilena Formato
- Dipartimento di Scienze Biomediche University of Sassari, Viale S. Pietro 43/B, 07100 Sassari, Italy
| | - Antonio Lepedda
- Dipartimento di Scienze Biomediche University of Sassari, Viale S. Pietro 43/B, 07100 Sassari, Italy
| | - Lorenzo Moroni
- Dipartimento di Scienze Biomediche University of Sassari, Viale S. Pietro 43/B, 07100 Sassari, Italy; Department of Complex Tissue Regeneration, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitsingel 40, 6229ER Maastricht, The Netherlands.
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25
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Milanesi E, Voinsky I, Hadar A, Srouji A, Maj C, Shekhtman T, Gershovits M, Gilad S, Chillotti C, Squassina A, Potash JB, Schulze TG, Goes FS, Zandi P, Kelsoe JR, Gurwitz D. RNA sequencing of bipolar disorder lymphoblastoid cell lines implicates the neurotrophic factor HRP-3 in lithium's clinical efficacy. World J Biol Psychiatry 2019; 20:449-461. [PMID: 28854847 DOI: 10.1080/15622975.2017.1372629] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Objectives: Lithium remains the oldest and most effective treatment for mood stabilisation in bipolar disorder (BD), even though at least half of patients are only partially responsive or do not respond. This study aimed to identify biomarkers associated with lithium response in BD, based on comparing RNA sequencing information derived from lymphoblastoid cell lines (LCLs) of lithium-responsive (LR) versus lithium non-responsive (LNR) BD patients, to assess gene expression variations that might bear on treatment outcome. Methods: RNA sequencing was carried out on 24 LCLs from female BD patients (12 LR and 12 LNR) followed by qPCR validation in two additional independent cohorts (41 and 17 BD patients, respectively). Results: Fifty-six genes showed nominal differential expression comparing LR and LNR (FC ≥ |1.3|, P ≤ 0.01). The differential expression of HDGFRP3 and ID2 was validated by qPCR in the independent cohorts. Conclusions: We observed higher expression levels of HDGFRP3 and ID2 in BD patients who favourably respond to lithium. Both of these genes are involved in neurogenesis, and HDGFRP3 has been suggested to be a neurotrophic factor. Additional studies in larger BD cohorts are needed to confirm the potential of HDGFRP3 and ID2 expression levels in blood cells as tentative favourable lithium response biomarkers.
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Affiliation(s)
- Elena Milanesi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel.,Genetics Unit, IRCCS, San Giovanni di Dio, Fatebenefratelli , Brescia , Italy
| | - Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Adva Hadar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Ala Srouji
- Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University Munich , Munich , Germany.,Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health , Mannheim , Germany
| | - Carlo Maj
- Genetics Unit, IRCCS, San Giovanni di Dio, Fatebenefratelli , Brescia , Italy
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California , San Diego , CA , USA
| | - Michael Gershovits
- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot , Israel
| | - Shlomit Gilad
- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot , Israel
| | - Caterina Chillotti
- Unit of Clinical Pharmacology, University Hospital of Cagliari , Cagliari , Italy
| | - Alessio Squassina
- Section of Neurosciences and Clinical Pharmacology, Department of Biomedical Sciences, School of Medicine, University of Cagliari , Cagliari , Italy
| | - James B Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine , Iowa City , IA , USA
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University Munich , Munich , Germany.,Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health , Mannheim , Germany.,Department of Psychiatry and Psychotherapy, University Medical Center Georg-August-University , Göttingen , Germany
| | - Fernando S Goes
- Department of Psychiatry, Johns Hopkins University , Baltimore , MD , USA
| | - Peter Zandi
- Department of Psychiatry, Johns Hopkins University , Baltimore , MD , USA
| | - John R Kelsoe
- Department of Psychiatry, University of California , San Diego , CA , USA
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel
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26
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MacDonald IA, Butler KV, Herring LE, Clinkscales SE, Yelagandula R, Stecher K, Bell O, Graves LM, Jin J, Hathaway NA. Pathway-Based High-Throughput Chemical Screen Identifies Compounds That Decouple Heterochromatin Transformations. SLAS DISCOVERY 2019; 24:802-816. [PMID: 31145866 DOI: 10.1177/2472555219849838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Heterochromatin protein 1 (HP1) facilitates the formation of repressive heterochromatin domains by recruiting histone lysine methyltransferase enzymes to chromatin, resulting in increased levels of histone H3K9me3. To identify chemical inhibitors of the HP1-heterochromatin gene repression pathway, we combined a cell-based assay that utilized chemical-mediated recruitment of HP1 to an endogenous active gene with high-throughput flow cytometry. Here we characterized small molecule inhibitors that block HP1-mediated heterochromatin formation. Our lead compounds demonstrated dose-dependent inhibition of HP1-stimulated gene repression and were validated in an orthogonal cell-based system. One lead inhibitor was improved by a change in stereochemistry, resulting in compound 2, which was further used to decouple the inverse relationship between H3K9 and H3K4 methylation states. We identified molecular components that bound compound 2, either directly or indirectly, by chemical affinity purification with a biotin-tagged derivative, followed by quantitative proteomic techniques. In summary, our pathway-based chemical screening approach resulted in the discovery of new inhibitors of HP1-mediated heterochromatin formation while identifying exciting new molecular interactions in the pathway to explore in the future. This modular platform can be expanded to test a wide range of chromatin modification pathways yielding inhibitors that are cell permeable and function in a physiologically relevant setting.
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Affiliation(s)
- Ian A MacDonald
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kyle V Butler
- 2 Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura E Herring
- 3 Department of Pharmacology, UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Sarah E Clinkscales
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ramesh Yelagandula
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Karin Stecher
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Oliver Bell
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,5 Department of Biochemistry and Molecular Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Lee M Graves
- 3 Department of Pharmacology, UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Jian Jin
- 2 Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathaniel A Hathaway
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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27
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Zhai B, Steinø A, Bacha J, Brown D, Daugaard M. Dianhydrogalactitol induces replication-dependent DNA damage in tumor cells preferentially resolved by homologous recombination. Cell Death Dis 2018; 9:1016. [PMID: 30283085 PMCID: PMC6170372 DOI: 10.1038/s41419-018-1069-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/30/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
1,2:5,6-Dianhydrogalactitol (DAG) is a bifunctional DNA-targeting agent causing N7-guanine alkylation and inter-strand DNA crosslinks currently in clinical trial for treatment of glioblastoma. While preclinical studies and clinical trials have demonstrated antitumor activity of DAG in a variety of malignancies, understanding the molecular mechanisms underlying DAG-induced cytotoxicity is essential for proper clinical qualification. Using non-small cell lung cancer (NSCLC) as a model system, we show that DAG-induced cytotoxicity materializes when cells enter S phase with unrepaired N7-guanine DNA crosslinks. In S phase, DAG-mediated DNA crosslink lesions translated into replication-dependent DNA double-strand breaks (DSBs) that subsequently triggered irreversible cell cycle arrest and loss of viability. DAG-treated NSCLC cells attempt to repair the DSBs by homologous recombination (HR) and inhibition of the HR repair pathway sensitized NSCLC cells to DAG-induced DNA damage. Accordingly, our work describes a molecular mechanism behind N7-guanine crosslink-induced cytotoxicity in cancer cells and provides a rationale for using DAG analogs to treat HR-deficient tumors.
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Affiliation(s)
- Beibei Zhai
- Vancouver Prostate Centre, Vancouver, BC, V6H 3Z6, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Anne Steinø
- DelMar Pharmaceuticals, Inc., Vancouver, BC, V5Z 1K5, Canada.,DelMar Pharmaceuticals, Inc., Menlo Park, CA, 94025, USA
| | - Jeffrey Bacha
- DelMar Pharmaceuticals, Inc., Vancouver, BC, V5Z 1K5, Canada.,DelMar Pharmaceuticals, Inc., Menlo Park, CA, 94025, USA
| | - Dennis Brown
- DelMar Pharmaceuticals, Inc., Vancouver, BC, V5Z 1K5, Canada.,DelMar Pharmaceuticals, Inc., Menlo Park, CA, 94025, USA
| | - Mads Daugaard
- Vancouver Prostate Centre, Vancouver, BC, V6H 3Z6, Canada. .,Department of Urologic Sciences, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada.
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28
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Hu Y, He C, Liu JP, Li NS, Peng C, Yang-Ou YB, Yang XY, Lu NH, Zhu Y. Analysis of key genes and signaling pathways involved in Helicobacter pylori-associated gastric cancer based on The Cancer Genome Atlas database and RNA sequencing data. Helicobacter 2018; 23:e12530. [PMID: 30175534 DOI: 10.1111/hel.12530] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Helicobacter pylori (H. pylori) infection is associated with the development of gastric cancer, although the mechanism is unclear. Herein, this study aimed to clarify the key genes and signaling pathways involved in H. pylori pathogenesis based on The Cancer Genome Atlas (TCGA) database and RNA sequencing analysis. MATERIALS AND METHODS Forty-nine gastric cancer samples (16 with H. pylori and 33 without H. pylori) and 35 cancer-adjacent normal samples from TCGA database were analyzed by bioinformatics. The differentially expressed genes between H. pylori-positive and H. pylori-negative patients were verified in 18 gastric cancer (GC) samples (9 with H. pylori and 9 without H. pylori), which were analyzed using RNA sequencing. Survival analysis was carried out to explore associations between the differentially expressed genes and prognosis. Bioinformatics analysis was performed to determine the signaling pathways associated with H. pylori. RESULTS The baseline level of clinical features from TCGA database and RNA sequencing showed no differences between the H. pylori-positive and H. pylori-negative GC groups (P > 0.05). TP53 was shown to be upregulated in the H. pylori-positive group in both TCGA database and RNA sequencing data, which also showed higher expression in the GC tissues than in adjacent normal tissues (P < 0.05). CCDC151, CHRNB2, GMPR2, HDGFRP2, and VSTM2L were shown to be downregulated in the H. pylori-positive group by both TCGA database and RNA sequencing, which also showed lower expression in the GC tissues than in adjacent normal tissues (P < 0.05). GC patients with low expression levels of HDGFRP2 had a poor prognosis (P < 0.05). Thirty-three signaling pathways and 10 biological processes were found to be positively associated with H. pylori infection (P < 0.05, FDR < 0.05). CONCLUSIONS These results indicate that some genes (TP53, CCDC151, CHRNB2, GMPR2, HDGFRP2, VSTM2L) and previously unidentified signaling pathways (eg, the Hippo signaling pathway) might play an important role in H. pylori-associated GC.
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Affiliation(s)
- Yi Hu
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
| | - Cong He
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
| | - Jian-Ping Liu
- Integrated Cardio Metabolic Centre, Karolinska Institute, Huddinge, Sweden
| | - Nian-Shuang Li
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
| | - Chao Peng
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
| | - Yao-Bin Yang-Ou
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
| | - Xiao-Yu Yang
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
| | - Nong-Hua Lu
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
| | - Yin Zhu
- Department of Gastroenterology, The First Affiliated Hospital Of Nanchang University, Nanchang, Jiangxi Province, China
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29
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Peng M, Cong K, Panzarino NJ, Nayak S, Calvo J, Deng B, Zhu LJ, Morocz M, Hegedus L, Haracska L, Cantor SB. Opposing Roles of FANCJ and HLTF Protect Forks and Restrain Replication during Stress. Cell Rep 2018; 24:3251-3261. [PMID: 30232006 PMCID: PMC6218949 DOI: 10.1016/j.celrep.2018.08.065] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/23/2018] [Accepted: 08/22/2018] [Indexed: 02/07/2023] Open
Abstract
The DNA helicase FANCJ is mutated in hereditary breast and ovarian cancer and Fanconi anemia (FA). Nevertheless, how loss of FANCJ translates to disease pathogenesis remains unclear. We addressed this question by analyzing proteins associated with replication forks in cells with or without FANCJ. We demonstrate that FANCJ-knockout (FANCJ-KO) cells have alterations in the replisome that are consistent with enhanced replication stress, including an aberrant accumulation of the fork remodeling factor helicase-like transcription factor (HLTF). Correspondingly, HLTF contributes to fork degradation in FANCJ-KO cells. Unexpectedly, the unrestrained DNA synthesis that characterizes HLTF-deficient cells is FANCJ dependent and correlates with S1 nuclease sensitivity and fork degradation. These results suggest that FANCJ and HLTF promote replication fork integrity, in part by counteracting each other to keep fork remodeling and elongation in check. Indicating one protein compensates for loss of the other, loss of both HLTF and FANCJ causes a more severe replication stress response.
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Affiliation(s)
- Min Peng
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ke Cong
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas J Panzarino
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sumeet Nayak
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jennifer Calvo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bin Deng
- Department of Biology/VGN Proteomics Facility, University of Vermont, Burlington, VT 05405, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Monika Morocz
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Lili Hegedus
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Lajos Haracska
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged 6726, Temesvari krt. 62, Hungary
| | - Sharon B Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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30
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Yang YF, Pan YH, Tian QH, Wu DC, Su SG. CBX1 Indicates Poor Outcomes and Exerts Oncogenic Activity in Hepatocellular Carcinoma. Transl Oncol 2018; 11:1110-1118. [PMID: 30031230 PMCID: PMC6074001 DOI: 10.1016/j.tranon.2018.07.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 06/26/2018] [Accepted: 07/02/2018] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of chromobox proteins contributes to the progression of human diseases. CBX1 has been implicated in epigenetic control of chromatin structure and gene expression, but its role in human cancers remains largely unknown. Here we show that CBX1 exhibits oncogenic activities in hepatocellular carcinoma (HCC) and indicates poor outcomes. The expression of CBX1 was noticeably increased, at both mRNA and protein levels, in HCC tissues and cell lines, compared with the nontumorous ones. High CBX1 expression was significantly associated with larger tumor size, poor tumor differentiation and tumor vascular invasion. Patients with elevated expression of CBX1 were frequently accompanied with unfavorable overall and disease-free survivals in two independent cohorts consisting of 648 HCC cases. The prognostic value of CBX1 was further confirmed by stratified survival analyses. Multivariate cox regression model suggested CBX1 as an independent factor for overall survival (hazard ratio = 1.735, 95% confident interval: 1.342–2.244, P < .001). In vitro data demonstrated that CBX1 overexpression promoted cell proliferation and migration, whereas the knockdown of CBX1 resulted in the opposite phenotypes. Mechanistically, CBX1 interacted with transcription factor HMGA2 to activate the Wnt/β-Catenin signaling pathway. Suppression of β-Catenin by siRNA or specific inhibitor XAV-939 markedly attenuated CBX1-mediated cell growth. Collectively, our findings indicate that CBX1 functions as an oncogene and may serve as a potential prognostic biomarker in HCC.
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Affiliation(s)
- Yu-Feng Yang
- Department of Pathology, Dongguan Third People's Hospital, Dongguan, China
| | - Ying-Hua Pan
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qiu-Hong Tian
- Department of Oncology, First Affiliated Hospital of NanChang University, NanChang, Jiangxi 330006, China
| | - Dan-Chun Wu
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shu-Guang Su
- Department of Pathology, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China.
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Sebastian R, Oberdoerffer P. Transcription-associated events affecting genomic integrity. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160288. [PMID: 28847825 PMCID: PMC5577466 DOI: 10.1098/rstb.2016.0288] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/25/2022] Open
Abstract
Accurate maintenance of genomic as well as epigenomic integrity is critical for proper cell and organ function. Continuous exposure to DNA damage is, thus, often associated with malignant transformation and degenerative diseases. A significant, chronic threat to genome integrity lies in the process of transcription, which can result in the formation of potentially harmful RNA : DNA hybrid structures (R-loops) and has been linked to DNA damage accumulation as well as dynamic chromatin reorganization. In sharp contrast, recent evidence suggests that active transcription, the resulting transcripts as well as R-loop formation can play multi-faceted roles in maintaining and restoring genome integrity. Here, we will discuss the emerging contributions of transcription as both a source of DNA damage and a mediator of DNA repair. We propose that both aspects have significant implications for genome maintenance, and will speculate on possible long-term consequences for the epigenetic integrity of transcribing cells.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
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