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Gosztyla ML, Zhan L, Olson S, Wei X, Naritomi J, Nguyen G, Street L, Goda GA, Cavazos FF, Schmok JC, Jain M, Uddin Syed E, Kwon E, Jin W, Kofman E, Tankka AT, Li A, Gonzalez V, Lécuyer E, Dominguez D, Jovanovic M, Graveley BR, Yeo GW. Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. Mol Cell 2024; 84:3826-3842.e8. [PMID: 39303722 DOI: 10.1016/j.molcel.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/19/2024] [Accepted: 08/06/2024] [Indexed: 09/22/2024]
Abstract
RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc-finger families. We show that multiple ZFPs are previously unknown regulators of RNA splicing, alternative polyadenylation, stability, or translation. The examined ZFPs show widespread sequence-specific RNA binding and preferentially bind proximal to transcription start sites. Additionally, several ZFPs associate with their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DNA/RNA-associated protein that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation.
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Affiliation(s)
- Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Jack Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Grady Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lena Street
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Grant A Goda
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Francisco F Cavazos
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Easin Uddin Syed
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; School of Pharmacy, Brac University, Dhaka 1212, Bangladesh
| | - Eunjeong Kwon
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Wenhao Jin
- Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexandra T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Allison Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Valerie Gonzalez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA.
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Wu M, Wu S, Guo R. Upregulation of ZMAT3 is Associated with the Poor Prognosis of Breast Cancer. Int J Gen Med 2024; 17:4003-4014. [PMID: 39286533 PMCID: PMC11404498 DOI: 10.2147/ijgm.s470303] [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: 05/20/2024] [Accepted: 09/08/2024] [Indexed: 09/19/2024] Open
Abstract
Background Breast cancer is the leading cause of cancer-related deaths among women worldwide. Identifying robust biomarkers for predicting outcomes is essential for improving patient care and reducing fatalities. ZMAT3, a zinc finger protein with potential carcinogenic properties, has been associated with various cancers. However, its role in breast cancer prognosis remains unclear. Methods We investigated the expression level of ZMAT3 in breast cancer tissues and its association with clinical outcomes through bioinformatics analysis and experimental validation. We examined the correlation between ZMAT3 expression and immune characteristics. ZMAT3 mRNA expression data from The Cancer Genome Atlas (TCGA) were analysed in relation to overall survival (OS), disease-specific survival (DSS) and progression-free interval (PFI) in patients with breast cancer. Immunohistochemistry (IHC) was performed on breast cancer tissues to assess ZMAT3 protein levels, with findings validated using qPCR and cell experiments. Results ZMAT3 mRNA levels were significantly upregulated in breast cancer samples compared to normal tissues. High ZMAT3 expression was significantly correlated with the poor OS, DSS and PFI. A significant positive correlation was observed between high ZMAT3 mRNA levels and the abundance of tumour-infiltrating lymphocytes (TILs), especially CD8+T cells and regulatory T cells (Tregs). Multivariate Cox regression analysis identified ZMAT3 as an independent prognostic factor for breast cancer. IHC staining confirmed increased ZMAT3 protein expression in breast cancer tissues, which was further validated by qPCR and cell function tests. Conclusion Our findings suggest that ZMAT3 is a prognostic biomarker linked to immune invasion in breast cancer. Elevated ZMAT3 expression correlates with adverse clinical outcomes, indicating its potential role in disease progression.
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Affiliation(s)
- Meng Wu
- Department of Pharmacy, the First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Shuang Wu
- Department of Pharmacy, the First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Rui Guo
- Department of Critical Care Medicine, the First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
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Bertazzon M, Hurtado-Pico A, Plaza-Sirvent C, Schuster M, Preußner M, Kuropka B, Liu F, Kirsten AZA, Schmitt XJ, König B, Álvaro-Benito M, Abualrous ET, Albert GI, Kliche S, Heyd F, Schmitz I, Freund C. The nuclear GYF protein CD2BP2/U5-52K is required for T cell homeostasis. Front Immunol 2024; 15:1415839. [PMID: 39308865 PMCID: PMC11412891 DOI: 10.3389/fimmu.2024.1415839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/11/2024] [Indexed: 09/25/2024] Open
Abstract
The question whether interference with the ubiquitous splicing machinery can lead to cell-type specific perturbation of cellular function is addressed here by T cell specific ablation of the general U5 snRNP assembly factor CD2BP2/U5-52K. This protein defines the family of nuclear GYF domain containing proteins that are ubiquitously expressed in eukaryotes with essential functions ascribed to early embryogenesis and organ function. Abrogating CD2BP2/U5-52K in T cells, allows us to delineate the consequences of splicing machinery interferences for T cell development and function. Increased T cell lymphopenia and T cell death are observed upon depletion of CD2BP2/U5-52K. A substantial increase in exon skipping coincides with the observed defect in the proliferation/differentiation balance in the absence of CD2BP2/U5-52K. Prominently, skipping of exon 7 in Mdm4 is observed, coinciding with upregulation of pro-apoptotic gene expression profiles upon CD2BP2/U5-52K depletion. Furthermore, we observe enhanced sensitivity of naïve T cells compared to memory T cells to changes in CD2BP2/U5-52K levels, indicating that depletion of this general splicing factor leads to modulation of T cell homeostasis. Given the recent structural characterization of the U5 snRNP and the crosslinking mass spectrometry data given here, design of inhibitors of the U5 snRNP conceivably offers new ways to manipulate T cell function in settings of disease.
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Affiliation(s)
- Miriam Bertazzon
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Almudena Hurtado-Pico
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | | | - Marc Schuster
- Systems-Oriented Immunology and Inflammation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marco Preußner
- Department of Chemistry and Biochemistry, RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benno Kuropka
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Fan Liu
- Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | | | - Xiao Jakob Schmitt
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benjamin König
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Miguel Álvaro-Benito
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
- School of Medicine, Universidad Complutense de Madrid, 12 de Octubre Health Research Institute, Madrid, Spain
| | - Esam T. Abualrous
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- Department of Physics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Gesa I. Albert
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Stefanie Kliche
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation GCI3, Otto-von-Guericke-University, Magdeburg, Germany
| | - Florian Heyd
- Department of Chemistry and Biochemistry, RNA Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Ingo Schmitz
- Department of Molecular Immunology, Ruhr-University Bochum, Bochum, Germany
| | - Christian Freund
- Department of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
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4
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Brennan MS, Brinkmann K, Romero Sola G, Healey G, Gibson L, Gangoda L, Potts MA, Lieschke E, Wilcox S, Strasser A, Herold MJ, Janic A. Combined absence of TRP53 target genes ZMAT3, PUMA and p21 cause a high incidence of cancer in mice. Cell Death Differ 2024; 31:159-169. [PMID: 38110554 PMCID: PMC10850490 DOI: 10.1038/s41418-023-01250-w] [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: 11/11/2022] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
Transcriptional activation of target genes is essential for TP53-mediated tumour suppression, though the roles of the diverse TP53-activated target genes in tumour suppression remains poorly understood. Knockdown of ZMAT3, an RNA-binding zinc-finger protein involved in regulating alternative splicing, in haematopoietic cells by shRNA caused leukaemia only with the concomitant absence of the PUMA and p21, the critical effectors of TRP53-mediated apoptosis and cell cycle arrest respectively. We were interested to further investigate the role of ZMAT3 in tumour suppression beyond the haematopoietic system. Therefore, we generated Zmat3 knockout and compound gene knockout mice, lacking Zmat3 and p21, Zmat3 and Puma or all three genes. Puma-/-p21-/-Zmat3-/- triple knockout mice developed tumours at a significantly higher frequency compared to wild-type, Puma-/-Zmat3-/- or p21-/-Zmat3-/-deficient mice. Interestingly, we observed that the triple knockout and Puma-/-Zmat3-/- double deficient animals succumbed to lymphoma, while p21-/-Zmat3-/- animals developed mainly solid cancers. This analysis suggests that in addition to ZMAT3 loss, additional TRP53-regulated processes must be disabled simultaneously for TRP53-mediated tumour suppression to fail. Our findings reveal that the absence of different TRP53 regulated tumour suppressive processes changes the tumour spectrum, indicating that different TRP53 tumour suppressive pathways are more critical in different tissues.
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Affiliation(s)
- Margs S Brennan
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Medicine Huddinge, Centre for Haematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Brinkmann
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Gerard Romero Sola
- Department of Medicine and Life Sciences, Universidad Pompeu Fabra, Barcelona, Spain
| | - Geraldine Healey
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia
| | - Leonie Gibson
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Lahiru Gangoda
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Margaret A Potts
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research (WEHI), 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, VIC, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia.
| | - Ana Janic
- Department of Medicine and Life Sciences, Universidad Pompeu Fabra, Barcelona, Spain.
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Spinelli R, Baboota RK, Gogg S, Beguinot F, Blüher M, Nerstedt A, Smith U. Increased cell senescence in human metabolic disorders. J Clin Invest 2023; 133:e169922. [PMID: 37317964 DOI: 10.1172/jci169922] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
Cell senescence (CS) is at the nexus between aging and associated chronic disorders, and aging increases the burden of CS in all major metabolic tissues. However, CS is also increased in adult obesity, type 2 diabetes (T2D), and nonalcoholic fatty liver disease independent of aging. Senescent tissues are characterized by dysfunctional cells and increased inflammation, and both progenitor cells and mature, fully differentiated and nonproliferating cells are afflicted. Recent studies have shown that hyperinsulinemia and associated insulin resistance (IR) promote CS in both human adipose and liver cells. Similarly, increased CS promotes cellular IR, showing their interdependence. Furthermore, the increased adipose CS in T2D is independent of age, BMI, and degree of hyperinsulinemia, suggesting premature aging. These results suggest that senomorphic/senolytic therapy may become important for treating these common metabolic disorders.
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Affiliation(s)
- Rosa Spinelli
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy
| | - Ritesh Kumar Baboota
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Evotec International GmbH, Göttingen, Germany
| | - Silvia Gogg
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Francesco Beguinot
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Annika Nerstedt
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ulf Smith
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Long KLP, Muroy SE, Sorooshyari SK, Ko MJ, Jaques Y, Sudmant P, Kaufer D. Transcriptomic profiles of stress susceptibility and resilience in the amygdala and hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527777. [PMID: 36798395 PMCID: PMC9934702 DOI: 10.1101/2023.02.08.527777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
A single, severe episode of stress can bring about myriad responses amongst individuals, ranging from cognitive enhancement to debilitating and persistent anxiety; however, the biological mechanisms that contribute to resilience versus susceptibility to stress are poorly understood. The dentate gyrus (DG) of the hippocampus and the basolateral nucleus of the amygdala (BLA) are key limbic regions that are susceptible to the neural and hormonal effects of stress. Previous work has also shown that these regions contribute to individual variability in stress responses; however, the molecular mechanisms underlying the role of these regions in susceptibility and resilience are unknown. In this study, we profiled the transcriptomic signatures of the DG and BLA of rats with divergent behavioral outcomes after a single, severe stressor. We subjected rats to three hours of immobilization with exposure to fox urine and conducted a behavioral battery one week after stress to identify animals that showed persistent, high anxiety-like behavior. We then conducted bulk RNA sequencing of the DG and BLA from susceptible, resilient, and unexposed control rats. Differential gene expression analyses revealed that the molecular signatures separating each of the three groups were distinct and non-overlapping between the DG and BLA. In the amygdala, key genes associated with insulin and hormonal signaling corresponded with vulnerability. Specifically, Inhbb, Rab31 , and Ncoa3 were upregulated in the amygdala of stress-susceptible animals compared to resilient animals. In the hippocampus, increased expression of Cartpt - which encodes a key neuropeptide involved in reward, reinforcement, and stress responses - was strongly correlated with vulnerability to anxiety-like behavior. However, few other genes distinguished stress-susceptible animals from control animals, while a larger number of genes separated stress-resilient animals from control and stress-susceptible animals. Of these, Rnf112, Tbx19 , and UBALD1 distinguished resilient animals from both control and susceptible animals and were downregulated in resilience, suggesting that an active molecular response in the hippocampus facilitates protection from the long-term consequences of severe stress. These results provide novel insight into the mechanisms that bring about individual variability in the behavioral responses to stress and provide new targets for the advancement of therapies for stress-induced neuropsychiatric disorders.
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7
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Humpton TJ, Hall H, Kiourtis C, Nixon C, Clark W, Hedley A, Shaw R, Bird TG, Blyth K, Vousden KH. p53-mediated redox control promotes liver regeneration and maintains liver function in response to CCl 4. Cell Death Differ 2022; 29:514-526. [PMID: 34628485 PMCID: PMC8901761 DOI: 10.1038/s41418-021-00871-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
The p53 transcription factor coordinates wide-ranging responses to stress that contribute to its function as a tumour suppressor. The responses to p53 induction are complex and range from mediating the elimination of stressed or damaged cells to promoting survival and repair. These activities of p53 can modulate tumour development but may also play a role in pathological responses to stress such as tissue damage and repair. Using a p53 reporter mouse, we have previously detected strong induction of p53 activity in the liver of mice treated with the hepatotoxin carbon tetrachloride (CCl4). Here, we show that p53 functions to support repair and recovery from CCl4-mediated liver damage, control reactive oxygen species (ROS) and limit the development of hepatocellular carcinoma (HCC), in part through the activation of a detoxification cytochrome P450, CYP2A5 (CYP2A6 in humans). Our work demonstrates an important role for p53-mediated redox control in facilitating the hepatic regenerative response after damage and identifies CYP2A5/CYP2A6 as a mediator of this pathway with potential prognostic utility in human HCC.
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Affiliation(s)
- Timothy J Humpton
- The Francis Crick Institute, London, NW1 1AT, UK.
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
| | - Holly Hall
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Christos Kiourtis
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - William Clark
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Robin Shaw
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Thomas G Bird
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- MRC Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
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8
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Best SA, Vandenberg CJ, Abad E, Whitehead L, Guiu L, Ding S, Brennan MS, Strasser A, Herold MJ, Sutherland KD, Janic A. Consequences of Zmat3 loss in c-MYC- and mutant KRAS-driven tumorigenesis. Cell Death Dis 2020; 11:877. [PMID: 33082333 PMCID: PMC7575595 DOI: 10.1038/s41419-020-03066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
TP53 is a critical tumor suppressor that is mutated in approximately 50% of human cancers. Unveiling the downstream target genes of TP53 that fulfill its tumor suppressor function is an area of intense investigation. Zmat3 (also known as Wig-1 or PAG608) is one such downstream target of p53, whose loss in hemopoietic stem cells lacking the apoptosis and cell cycle regulators, Puma and p21, respectively, promotes the development of leukemia. The function of Zmat3 in tumorigenesis however remains unclear. Here, to investigate which oncogenic drivers co-operate with Zmat3 loss to promote neoplastic transformation, we utilized Zmat3 knockout mice in models of c-MYC-driven lymphomagenesis and KrasG12D-driven lung adenocarcinoma development. Interestingly, unlike loss of p53, Zmat3 germline loss had little impact on the rate of tumor development or severity of malignant disease upon either the c-MYC or KrasG12D oncogenic activation. Furthermore, loss of Zmat3 failed to rescue KrasG12D primary lung tumor cells from oncogene-induced senescence. Taken together, we conclude that in the context of c-MYC-driven lymphomagenesis or mutant KrasG12D-driven lung adenocarcinoma development, additional co-occurring mutations are required to resolve Zmat3 tumor suppressive activity.
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Affiliation(s)
- Sarah A Best
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
| | - Cassandra J Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
| | - Etna Abad
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Lachlan Whitehead
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
| | - Laia Guiu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Sheryl Ding
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
| | - Margs S Brennan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia
| | - Kate D Sutherland
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia.
| | - Ana Janic
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003, Barcelona, Spain.
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9
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Chang HC, Chu CP, Lin SJ, Hsiao CK. Network hub-node prioritization of gene regulation with intra-network association. BMC Bioinformatics 2020; 21:101. [PMID: 32164570 PMCID: PMC7069025 DOI: 10.1186/s12859-020-3444-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
Background To identify and prioritize the influential hub genes in a gene-set or biological pathway, most analyses rely on calculation of marginal effects or tests of statistical significance. These procedures may be inappropriate since hub nodes are common connection points and therefore may interact with other nodes more often than non-hub nodes do. Such dependence among gene nodes can be conjectured based on the topology of the pathway network or the correlation between them. Results Here we develop a pathway activity score incorporating the marginal (local) effects of gene nodes as well as intra-network affinity measures. This score summarizes the expression levels in a gene-set/pathway for each sample, with weights on local and network information, respectively. The score is next used to examine the impact of each node through a leave-one-out evaluation. To illustrate the procedure, two cancer studies, one involving RNA-Seq from breast cancer patients with high-grade ductal carcinoma in situ and one microarray expression data from ovarian cancer patients, are used to assess the performance of the procedure, and to compare with existing methods, both ones that do and do not take into consideration correlation and network information. The hub nodes identified by the proposed procedure in the two cancer studies are known influential genes; some have been included in standard treatments and some are currently considered in clinical trials for target therapy. The results from simulation studies show that when marginal effects are mild or weak, the proposed procedure can still identify causal nodes, whereas methods relying only on marginal effect size cannot. Conclusions The NetworkHub procedure proposed in this research can effectively utilize the network information in combination with local effects derived from marker values, and provide a useful and complementary list of recommendations for prioritizing causal hubs.
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Affiliation(s)
- Hung-Ching Chang
- Division of Biostatistics, Institute of Epidemiology and Preventive Medicine, National Taiwan University, No. 17, Xu-Zhou Road, Taipei, 10055, Taiwan
| | - Chiao-Pei Chu
- Division of Biostatistics, Institute of Epidemiology and Preventive Medicine, National Taiwan University, No. 17, Xu-Zhou Road, Taipei, 10055, Taiwan
| | - Shu-Ju Lin
- Institute of Statistical Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Chuhsing Kate Hsiao
- Division of Biostatistics, Institute of Epidemiology and Preventive Medicine, National Taiwan University, No. 17, Xu-Zhou Road, Taipei, 10055, Taiwan. .,Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, 10055, Taiwan.
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10
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Zhou J, Li Z, Li J, Gao B, Song W. Chemotherapy Resistance Molecular Mechanism in Small Cell Lung Cancer. Curr Mol Med 2019; 19:157-163. [PMID: 30813876 DOI: 10.2174/1566524019666190226104909] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/08/2019] [Accepted: 02/18/2019] [Indexed: 12/11/2022]
Abstract
The malignancy of small cell lung cancer (SCLC) is the highest amongst all
lung cancer types. It is characterized by rapid growth, early occurrence of distant sites
metastasis, poor survival rates and is initially sensitive to chemotherapy and
radiotherapy. However, most patients eventually relapse or disease progresses because
of chemotherapy resistance. Because of lack of effective second-line therapies, the
prognosis of SCLC patients is usually poor. For the development of novel therapies, it is
necessary to understand the mechanisms of chemotherapy resistance in SCLC. The
mechanism is complex, because multiple factors could lead to chemotherapy resistance.
An overview of multiple events triggering the formation of chemotherapy resistance
phenotypes of SCLC cells is discussed.
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Affiliation(s)
- Jun Zhou
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, China
| | - Zhaopei Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, China
| | - Jun Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, China
| | - Binbin Gao
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, China
| | - Wei Song
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, China
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11
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Lee HC, Jung SH, Hwang HJ, Kang D, De S, Dudekula DB, Martindale JL, Park B, Park SK, Lee EK, Lee JH, Jeong S, Han K, Park HJ, Ko YG, Gorospe M, Lee JS. WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms. Nucleic Acids Res 2017; 45:6894-6910. [PMID: 28472401 PMCID: PMC5499809 DOI: 10.1093/nar/gkx307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
RNA-binding proteins (RBPs) are involved in mRNA splicing, maturation, transport, translation, storage and turnover. Here, we identified ACOT7 mRNA as a novel target of human WIG1. ACOT7 mRNA decay was triggered by the microRNA miR-9 in a WIG1-dependent manner via classic recruitment of Argonaute 2 (AGO2). Interestingly, AGO2 was also recruited to ACOT7 mRNA in a WIG1-dependent manner in the absence of miR-9, which indicates an alternative model whereby WIG1 controls AGO2-mediated gene silencing. The WIG1–AGO2 complex attenuated translation initiation via an interaction with translation initiation factor 5B (eIF5B). These results were confirmed using a WIG1 tethering system based on the MS2 bacteriophage coat protein and a reporter construct containing an MS2-binding site, and by immunoprecipitation of WIG1 and detection of WIG1-associated proteins using liquid chromatography-tandem mass spectrometry. We also identified WIG1-binding motifs using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation analyses. Altogether, our data indicate that WIG1 governs the miRNA-dependent and the miRNA-independent recruitment of AGO2 to lower the stability of and suppress the translation of ACOT7 mRNA.
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Affiliation(s)
- Hyung Chul Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Seung Hee Jung
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Hyun Jung Hwang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Donghee Kang
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Byungkyu Park
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Seung Kuk Park
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Jeong-Hwa Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Sunjoo Jeong
- Department of Molecular Biology, Dankook University, Yongin 16890, Korea
| | - Kyungsook Han
- Department of Computer Science and Engineering, Inha University, Incheon 22212, Korea
| | - Heon Joo Park
- Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Department of Microbiology, Inha University College of Medicine, Incheon 22212, Korea
| | - Young-Gyu Ko
- Division of Life Sciences, Korea University, Seoul 02841, Korea
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Jae-Seon Lee
- Department of Molecular Medicine, Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea.,Medical Research Center, Inha University College of Medicine, Incheon 22212, Korea
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12
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Bersani C, Huss M, Giacomello S, Xu LD, Bianchi J, Eriksson S, Jerhammar F, Alexeyenko A, Vilborg A, Lundeberg J, Lui WO, Wiman KG. Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis. Oncotarget 2016; 7:1895-911. [PMID: 26672765 PMCID: PMC4811505 DOI: 10.18632/oncotarget.6557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/15/2015] [Indexed: 02/06/2023] Open
Abstract
RNA-binding proteins (RBPs) play important roles in the regulation of gene expression through a variety of post-transcriptional mechanisms. The p53-induced RBP Wig-1 (Zmat3) binds RNA through its zinc finger domains and enhances stability of p53 and N-Myc mRNAs and decreases stability of FAS mRNA. To identify novel Wig-1-bound RNAs, we performed RNA-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) in HCT116 and Saos-2 cells. We identified 286 Wig-1-bound mRNAs common between the two cell lines. Sequence analysis revealed that AU-rich elements (AREs) are highly enriched in the 3′UTR of these Wig-1-bound mRNAs. Network enrichment analysis showed that Wig-1 preferentially binds mRNAs involved in cell cycle regulation. Moreover, we identified a 2D Wig-1 binding motif in HIF1A mRNA. Our findings confirm that Wig-1 is an ARE-BP that regulates cell cycle-related processes and provide a novel view of how Wig-1 may bind mRNA through a putative structural motif. We also significantly extend the repertoire of Wig-1 target mRNAs. Since Wig-1 is a transcriptional target of the tumor suppressor p53, these results have implications for our understanding of p53-dependent stress responses and tumor suppression.
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Affiliation(s)
- Cinzia Bersani
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Mikael Huss
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Li-Di Xu
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Julie Bianchi
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Sofi Eriksson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Fredrik Jerhammar
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Andrey Alexeyenko
- Department of Microbiology, Tumour and Cell biology, Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Anna Vilborg
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Joakim Lundeberg
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
| | - Klas G Wiman
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden
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13
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Olivos DJ, Mayo LD. Emerging Non-Canonical Functions and Regulation by p53: p53 and Stemness. Int J Mol Sci 2016; 17:ijms17121982. [PMID: 27898034 PMCID: PMC5187782 DOI: 10.3390/ijms17121982] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/10/2016] [Accepted: 11/15/2016] [Indexed: 01/15/2023] Open
Abstract
Since its discovery nearly 40 years ago, p53 has ascended to the forefront of investigated genes and proteins across diverse research disciplines and is recognized most exclusively for its role in cancer as a tumor suppressor. Levine and Oren (2009) reviewed the evolution of p53 detailing the significant discoveries of each decade since its first report in 1979. In this review, we will highlight the emerging non-canonical functions and regulation of p53 in stem cells. We will focus on general themes shared among p53's functions in non-malignant stem cells and cancer stem-like cells (CSCs) and the influence of p53 on the microenvironment and CSC niche. We will also examine p53 gain of function (GOF) roles in stemness. Mutant p53 (mutp53) GOFs that lead to survival, drug resistance and colonization are reviewed in the context of the acquisition of advantageous transformation processes, such as differentiation and dedifferentiation, epithelial-to-mesenchymal transition (EMT) and stem cell senescence and quiescence. Finally, we will conclude with therapeutic strategies that restore wild-type p53 (wtp53) function in cancer and CSCs, including RING finger E3 ligases and CSC maintenance. The mechanisms by which wtp53 and mutp53 influence stemness in non-malignant stem cells and CSCs or tumor-initiating cells (TICs) are poorly understood thus far. Further elucidation of p53's effects on stemness could lead to novel therapeutic strategies in cancer research.
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Affiliation(s)
- David J Olivos
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
- Department of Pediatrics, Herman B Wells Center for Pediatrics Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Lindsey D Mayo
- Department of Pediatrics, Herman B Wells Center for Pediatrics Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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14
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Giono LE, Nieto Moreno N, Cambindo Botto AE, Dujardin G, Muñoz MJ, Kornblihtt AR. The RNA Response to DNA Damage. J Mol Biol 2016; 428:2636-2651. [PMID: 26979557 DOI: 10.1016/j.jmb.2016.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 02/01/2023]
Abstract
Multicellular organisms must ensure genome integrity to prevent accumulation of mutations, cell death, and cancer. The DNA damage response (DDR) is a complex network that senses, signals, and executes multiple programs including DNA repair, cell cycle arrest, senescence, and apoptosis. This entails regulation of a variety of cellular processes: DNA replication and transcription, RNA processing, mRNA translation and turnover, and post-translational modification, degradation, and relocalization of proteins. Accumulated evidence over the past decades has shown that RNAs and RNA metabolism are both regulators and regulated actors of the DDR. This review aims to present a comprehensive overview of the current knowledge on the many interactions between the DNA damage and RNA fields.
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Affiliation(s)
- Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Nicolás Nieto Moreno
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Adrián E Cambindo Botto
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Gwendal Dujardin
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Centre for Genomic Regulation, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Manuel J Muñoz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
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15
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Deubiquitinase MYSM1 Is Essential for Normal Bone Formation and Mesenchymal Stem Cell Differentiation. Sci Rep 2016; 6:22211. [PMID: 26915790 PMCID: PMC4768166 DOI: 10.1038/srep22211] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/09/2016] [Indexed: 12/14/2022] Open
Abstract
Deubiquitinase MYSM1 has been shown to play a critical role in hematopoietic cell differentiation and hematopoietic stem cell (HSC) maintenance. Mesenchymal stem cells (MSCs) are multipotent stromal cells within the bone marrow. MSCs are progenitors to osteoblasts, chondrocytes, adipocytes, and myocytes. Although, MSCs have been extensively studied, the roles of MYSM1 in these cells remain unclear. Here we describe the function of MYSM1 on MSC maintenance and differentiation. In this report, we found that Mysm1−/− mice had a lower bone mass both in long bone and calvaria compared with their control counterpart. Preosteoblasts from Mysm1−/− mice did not show changes in proliferation or osteogenesis when compared to WT mice. Conversely, Mysm1−/− MSCs showed enhanced autonomous differentiation and accelerated adipogenesis. Our results demonstrate that MYSM1 plays a critical role in MSC maintenance and differentiation. This study also underscores the biological significance of deubiquitinase activity in MSC function. Mysm1 may represent a potential therapeutic target for controlling MSC lineage differentiation, and possibly for the treatment of metabolic bone diseases such as osteoporosis.
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16
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Chaturvedi P, Neelamraju Y, Arif W, Kalsotra A, Janga SC. Uncovering RNA binding proteins associated with age and gender during liver maturation. Sci Rep 2015; 5:9512. [PMID: 25824884 PMCID: PMC4379467 DOI: 10.1038/srep09512] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/09/2015] [Indexed: 11/09/2022] Open
Abstract
In the present study, we perform an association analysis focusing on the expression changes of 1344 RNA Binding proteins (RBPs) as a function of age and gender in human liver. We identify 88 and 45 RBPs to be significantly associated with age and gender respectively. Experimental verification of several of the predicted associations in mice confirmed our findings. Our results suggest that a small fraction of the gender-associated RBPs (~40%) are expressed higher in males than females. Altogether, these observations show that several of these RBPs are important and conserved regulators in maintaining liver function. Further analysis of the protein interaction network of RBPs associated with age and gender based on the centrality measures like degree, betweenness and closeness revealed that several of these RBPs might be prominent players in aging liver and impart gender specific alterations in gene expression via the formation of protein complexes. Indeed, both age and gender-associated RBPs in liver were found to show significantly higher clustering coefficients and network centrality measures compared to non-associated RBPs. The compendium of RBPs and this study will help us gain insight into the role of post-transcriptional regulatory molecules in aging and gender specific expression of genes.
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Affiliation(s)
- Praneet Chaturvedi
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202
| | - Yaseswini Neelamraju
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202
| | - Waqar Arif
- Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Auinash Kalsotra
- Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Sarath Chandra Janga
- 1] Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202 [2] Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana, 46202 [3] Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, Indiana, 46202
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17
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Xu LD, Muller S, Thoppe SR, Hellborg F, Kanter L, Lerner M, Zheng B, Lagercrantz SB, Grandér D, Wallin KL, Wiman KG, Larsson C, Andersson S. Expression of the p53 target Wig-1 is associated with HPV status and patient survival in cervical carcinoma. PLoS One 2014; 9:e111125. [PMID: 25379706 PMCID: PMC4224373 DOI: 10.1371/journal.pone.0111125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/19/2014] [Indexed: 12/24/2022] Open
Abstract
The p53 target gene WIG-1 (ZMAT3) is located in chromosomal region 3q26, that is frequently amplified in human tumors, including cervical cancer. We have examined the status of WIG-1 and the encoded Wig-1 protein in cervical carcinoma cell lines and tumor tissue samples. Our analysis of eight cervical cancer lines (Ca Ski, ME-180, MS751, SiHa, SW756, C-4I, C-33A, and HT-3) by spectral karyotype, comparative genomic hybridization and Southern blotting revealed WIG-1 is not the primary target for chromosome 3 gains. However, WIG-1/Wig-1 were readily expressed and WIG-1 mRNA expression was higher in the two HPV-negative cervical cell lines (C33-A, HT-3) than in HPV-positive lines. We then assessed Wig-1 expression by immunohistochemistry in 38 cervical tumor samples. We found higher nuclear Wig-1 expression levels in HPV-negative compared to HPV positive cases (p = 0.002) and in adenocarcinomas as compared to squamous cell lesions (p<0.0001). Cases with moderate nuclear Wig-1 staining and positive cytoplasmic Wig-1 staining showed longer survival than patients with strong nuclear and negative cytoplasmic staining (p = 0.042). Nuclear Wig-1 expression levels were positively associated with age at diagnosis (p = 0.023) and histologic grade (p = 0.034). These results are consistent with a growth-promoting and/or anti-cell death function of nuclear Wig-1 and suggest that Wig-1 expression can serve as a prognostic marker in cervical carcinoma.
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Affiliation(s)
- Li-Di Xu
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Susanne Muller
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Srinivasan R. Thoppe
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Fredrik Hellborg
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Lena Kanter
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Mikael Lerner
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Biying Zheng
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Svetlana Bajalica Lagercrantz
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Dan Grandér
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Keng Ling Wallin
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Klas G. Wiman
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
- * E-mail:
| | - Catharina Larsson
- Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Sonia Andersson
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska University Hospital-Solna, Stockholm, Sweden
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18
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Wig-1 regulates cell cycle arrest and cell death through the p53 targets FAS and 14-3-3σ. Oncogene 2014; 33:4407-17. [PMID: 24469038 PMCID: PMC4150987 DOI: 10.1038/onc.2013.594] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/31/2013] [Accepted: 12/16/2013] [Indexed: 01/29/2023]
Abstract
Wig-1, also known as ZMAT3, is a p53 target gene that encodes an RNA-binding zinc-finger protein involved in the regulation of mRNA stability through binding to AU-rich elements (AREs). We have used microarray analysis to identify novel Wig-1 target mRNAs. We identified 2447 transcripts with >fourfold differential expression between Wig-1 and control small interfering (si)RNA-treated HCT116 cells. Several p53 target genes were among the deregulated transcripts. We found that Wig-1 regulates FAS and 14-3-3σ mRNA independently of p53. We show that Wig-1 binds to FAS mRNA 3'-UTR and decreases its stability through an ARE in the 3'-UTR. Depletion of Wig-1 was associated with increased cell death and reduced cell cycle arrest upon DNA damage. Our results suggest a role of Wig-1 as a survival factor that directs the p53 stress response toward cell cycle arrest rather than apoptosis through the regulation of FAS and 14-3-3σ mRNA levels.
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19
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Vaughan C, Pearsall I, Yeudall A, Deb SP, Deb S. p53: its mutations and their impact on transcription. Subcell Biochem 2014; 85:71-90. [PMID: 25201189 DOI: 10.1007/978-94-017-9211-0_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
p53 is a tumor suppressor protein whose key function is to maintain the integrity of the cell. Mutations in p53 have been found in up to 50 % of all human cancers and cause an increase in oncogenic phenotypes such as proliferation and tumorigenicity. Both wild-type and mutant p53 have been shown to transactivate their target genes, either through directly binding to DNA, or indirectly through protein-protein interactions. This review discusses possible mechanisms behind both wild-type and mutant p53-mediated transactivation and touches on the concept of addiction to mutant p53 of cancer cells and how that may be used for future therapies.
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Affiliation(s)
- Catherine Vaughan
- Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA, 23298, USA
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20
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Mancini M, Saintigny G, Mahé C, Annicchiarico-Petruzzelli M, Melino G, Candi E. MicroRNA-152 and -181a participate in human dermal fibroblasts senescence acting on cell adhesion and remodeling of the extra-cellular matrix. Aging (Albany NY) 2013; 4:843-53. [PMID: 23238588 PMCID: PMC3560438 DOI: 10.18632/aging.100508] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ageing of human skin is associated with phenotypic changes in the cutaneous cells; the major functional markers of ageing occur as consequences of dermal and epidermal cell senescence and of structural and compositional remodeling of normally long-lived dermal extracellular matrix proteins. Understanding the contribution of the dermal cells in skin ageing is a key question, since this tissue is particularly important for skin integrity and its properties can affect the epidermis. Several microRNAs have been shown to be involved in the regulation of pathways involved in cellular senescence and exerted important effects on tissues ageing. In this study, we demonstrate that the expression of miR-152 and miR-181a increased during the human dermal fibroblasts senescence and that their overexpression, is sufficient to induce cellular senescence in early-passage cells. The increase of these miRNAs during cells senescence was accompanied by a decrease in integrin α5 and collagen XVI expression at mRNA and/or protein levels resulting in reduced cellular adhesion and suggesting extracellular matrix remodeling. These findings indicate that changes in miRNAs expression, by modulating the levels of adhesion proteins and extra-cellular matrix components, such as integrin α5 and collagen XVI, could contribute to the compositional remodelling of the dermis and epidermis occurring during skin aging.
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Affiliation(s)
- Mara Mancini
- University of Tor Vergata, Department of Experimental Medicine and Surgery, 00133 Rome, Italy
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21
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Madar S, Harel E, Goldstein I, Stein Y, Kogan-Sakin I, Kamer I, Solomon H, Dekel E, Tal P, Goldfinger N, Friedlander G, Rotter V. Mutant p53 attenuates the anti-tumorigenic activity of fibroblasts-secreted interferon beta. PLoS One 2013; 8:e61353. [PMID: 23630584 PMCID: PMC3632588 DOI: 10.1371/journal.pone.0061353] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 03/08/2013] [Indexed: 12/12/2022] Open
Abstract
Mutations in the p53 tumor suppressor protein are highly frequent in tumors and often endow cells with tumorigenic capacities. We sought to examine a possible role for mutant p53 in the cross-talk between cancer cells and their surrounding stroma, which is a crucial factor affecting tumor outcome. Here we present a novel model which enables individual monitoring of the response of cancer cells and stromal cells (fibroblasts) to co-culturing. We found that fibroblasts elicit the interferon beta (IFNβ) pathway when in contact with cancer cells, thereby inhibiting their migration. Mutant p53 in the tumor was able to alleviate this response via SOCS1 mediated inhibition of STAT1 phosphorylation. IFNβ on the other hand, reduced mutant p53 RNA levels by restricting its RNA stabilizer, WIG1. These data underscore mutant p53 oncogenic properties in the context of the tumor microenvironment and suggest that mutant p53 positive cancer patients might benefit from IFNβ treatment.
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Affiliation(s)
- Shalom Madar
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Einav Harel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Goldstein
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yan Stein
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ira Kogan-Sakin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Kamer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hilla Solomon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elya Dekel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Perry Tal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Goldfinger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Faculty of Biochemistry, Biological Services Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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22
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Abstract
p63 is a transcriptional factor implicated in cancer and development. The presence in TP63 gene of alternative promoters allows expression of one isoform containing the N-terminal transactivation domain (TA isoform) and one N-terminal truncated isoform (ΔN isoform). Complete ablation of all p63 isoforms produced mice with fatal developmental abnormalities, including lack of epidermal barrier, limbs and other epidermal appendages. Specific TAp63-null mice, although they developed normally, failed to undergo in DNA damage-induced apoptosis during primordial follicle meiotic arrest, suggesting a p63 involvement in maternal reproduction. Recent findings have elucidated the role in DNA damage response of a novel Hominidae p63 isoform, GTAp63, specifically expressed in human spermatic precursors. Thus, these findings suggest a unique strategy of p63 gene, to evolve in order to preserve the species as a guardian of reproduction. Elucidation of the biological basis of p63 function in reproduction may provide novel approaches to the control of human fertility.
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Affiliation(s)
- Ivano Amelio
- Medical Research Council; Toxicology Unit; Leicester University; Leicester, UK
- Department for Molecular Biomedical Research; VIB; Ghent University; Ghent, Belgium
- Department of Biomedical Molecular Biology; Ghent University; Ghent, Belgium
| | - Francesca Grespi
- Medical Research Council; Toxicology Unit; Leicester University; Leicester, UK
- Department for Molecular Biomedical Research; VIB; Ghent University; Ghent, Belgium
- Department of Biomedical Molecular Biology; Ghent University; Ghent, Belgium
| | | | - Gerry Melino
- Medical Research Council; Toxicology Unit; Leicester University; Leicester, UK
- Department for Molecular Biomedical Research; VIB; Ghent University; Ghent, Belgium
- Department of Biomedical Molecular Biology; Ghent University; Ghent, Belgium
- Biochemistry IDI-IRCCS Laboratory and Department of Experimental Medicine and Surgery; University of Rome “Tor Vergata;” Rome, Italy
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23
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Danielsson A, Claesson K, Parris TZ, Helou K, Nemes S, Elmroth K, Elgqvist J, Jensen H, Hultborn R. Differential gene expression in human fibroblasts after alpha-particle emitter211At compared with60Co irradiation. Int J Radiat Biol 2012; 89:250-8. [DOI: 10.3109/09553002.2013.746751] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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24
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Ramamoorthy M, Sykora P, Scheibye-Knudsen M, Dunn C, Kasmer C, Zhang Y, Becker KG, Croteau DL, Bohr VA. Sporadic Alzheimer disease fibroblasts display an oxidative stress phenotype. Free Radic Biol Med 2012; 53:1371-80. [PMID: 22885031 PMCID: PMC4617209 DOI: 10.1016/j.freeradbiomed.2012.07.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 06/13/2012] [Accepted: 07/17/2012] [Indexed: 11/16/2022]
Abstract
Alzheimer disease (AD) is a major health problem in the United States, affecting one in eight Americans over the age of 65. The number of elderly suffering from AD is expected to continue to increase over the next decade, as the average age of the U.S. population increases. The risk factors for and etiology of AD are not well understood; however, recent studies suggest that exposure to oxidative stress may be a contributing factor. Here, microarray gene expression signatures were compared in AD-patient-derived fibroblasts and normal fibroblasts exposed to hydrogen peroxide or menadione (to simulate conditions of oxidative stress). Using the 23K Illumina cDNA microarray to screen expression of >14,000 human genes, we identified a total of 1017 genes that are chronically up- or downregulated in AD fibroblasts, 215 of which were also differentially expressed in normal human fibroblasts within 12h after exposure to hydrogen peroxide or menadione. Pathway analysis of these 215 genes and their associated pathways revealed cellular functions that may be critically dysregulated by oxidative stress and play a critical role in the etiology and/or pathology of AD. We then examined the AD fibroblasts for the presence of oxidative DNA damage and found increased accumulation of 8-oxo-guanine. These results indicate the possible role of oxidative stress in the gene expression profile seen in AD.
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Affiliation(s)
- Mahesh Ramamoorthy
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Peter Sykora
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Morten Scheibye-Knudsen
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Christopher Dunn
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Cindy Kasmer
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kevin G. Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Deborah L. Croteau
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Vilhelm A. Bohr
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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25
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Abstract
Wig-1 is a transcriptional target of the p53 tumor suppressor and encodes an mRNA stability-regulating protein. We show here that Wig-1 knockdown causes a dramatic inhibition of N-Myc expression and triggers differentiation in neuroblastoma cells carrying amplified N-Myc. Transient Wig-1 knockdown significantly delays development of N-Myc-driven tumors in mice. We also show that N-Myc expression is induced upon moderate p53-activating stress, suggesting a role of the p53-Wig-1-N-Myc axis in promoting cell cycle re-entry upon p53-induced cell cycle arrest and DNA repair. Moreover, our findings raise possibilities for the improved treatment of poor prognosis neuroblastomas that carry amplified N-Myc.
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26
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Wen Y, Gamazon ER, Bleibel WK, Wing C, Mi S, McIlwee BE, Delaney SM, Duan S, Im HK, Dolan ME. An eQTL-based method identifies CTTN and ZMAT3 as pemetrexed susceptibility markers. Hum Mol Genet 2011; 21:1470-80. [PMID: 22171072 DOI: 10.1093/hmg/ddr583] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pemetrexed, approved for the treatment of non-small cell lung cancer and malignant mesothelioma, has adverse effects including neutropenia, leucopenia, thrombocytopenia, anemia, fatigue and nausea. The results we report here represent the first genome-wide study aimed at identifying genetic predictors of pemetrexed response. We utilized expression quantitative trait loci (eQTLs) mapping combined with drug-induced cytotoxicity data to gain mechanistic insights into the observed genetic associations with pemetrexed susceptibility. We found that CTTN and ZMAT3 expression signature explained >30% of the pemetrexed susceptibility phenotype variation for pemetrexed in the discovery population. Replication using PCR and a semi-high-throughput, scalable assay system confirmed the initial discovery results in an independent set of samples derived from the same ancestry. Furthermore, functional validation in both germline and tumor cells demonstrates a decrease in cell survival following knockdown of CTTN or ZMAT3. In addition to our particular findings on genetic and gene expression predictors of susceptibility phenotype for pemetrexed, the work presented here will be valuable to the robust discovery and validation of genetic determinants and gene expression signatures of various chemotherapeutic susceptibilities.
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Affiliation(s)
- Yujia Wen
- Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
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28
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Zinc induces cell cycle arrest and apoptosis by upregulation of WIG-1 in esophageal squamous cancer cell line EC109. Tumour Biol 2011; 32:801-8. [DOI: 10.1007/s13277-011-0182-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 04/27/2011] [Indexed: 10/18/2022] Open
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