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Guarducci C, Nardone A, Russo D, Nagy Z, Heraud C, Grinshpun A, Zhang Q, Freelander A, Leventhal MJ, Feit A, Cohen Feit G, Feiglin A, Liu W, Hermida-Prado F, Kesten N, Ma W, De Angelis C, Morlando A, O'Donnell M, Naumenko S, Huang S, Nguyen QD, Huang Y, Malorni L, Bergholz JS, Zhao JJ, Fraenkel E, Lim E, Schiff R, Shapiro GI, Jeselsohn R. Selective CDK7 Inhibition Suppresses Cell Cycle Progression and MYC Signaling While Enhancing Apoptosis in Therapy-resistant Estrogen Receptor-positive Breast Cancer. Clin Cancer Res 2024; 30:1889-1905. [PMID: 38381406 PMCID: PMC11061603 DOI: 10.1158/1078-0432.ccr-23-2975] [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: 09/28/2023] [Revised: 01/09/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
PURPOSE Resistance to endocrine therapy (ET) and CDK4/6 inhibitors (CDK4/6i) is a clinical challenge in estrogen receptor (ER)-positive (ER+) breast cancer. Cyclin-dependent kinase 7 (CDK7) is a candidate target in endocrine-resistant ER+ breast cancer models and selective CDK7 inhibitors (CDK7i) are in clinical development for the treatment of ER+ breast cancer. Nonetheless, the precise mechanisms responsible for the activity of CDK7i in ER+ breast cancer remain elusive. Herein, we sought to unravel these mechanisms. EXPERIMENTAL DESIGN We conducted multi-omic analyses in ER+ breast cancer models in vitro and in vivo, including models with different genetic backgrounds. We also performed genome-wide CRISPR/Cas9 knockout screens to identify potential therapeutic vulnerabilities in CDK4/6i-resistant models. RESULTS We found that the on-target antitumor effects of CDK7 inhibition in ER+ breast cancer are in part p53 dependent, and involve cell cycle inhibition and suppression of c-Myc. Moreover, CDK7 inhibition exhibited cytotoxic effects, distinctive from the cytostatic nature of ET and CDK4/6i. CDK7 inhibition resulted in suppression of ER phosphorylation at S118; however, long-term CDK7 inhibition resulted in increased ER signaling, supporting the combination of ET with a CDK7i. Finally, genome-wide CRISPR/Cas9 knockout screens identified CDK7 and MYC signaling as putative vulnerabilities in CDK4/6i resistance, and CDK7 inhibition effectively inhibited CDK4/6i-resistant models. CONCLUSIONS Taken together, these findings support the clinical investigation of selective CDK7 inhibition combined with ET to overcome treatment resistance in ER+ breast cancer. In addition, our study highlights the potential of increased c-Myc activity and intact p53 as predictors of sensitivity to CDK7i-based treatments.
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Affiliation(s)
- Cristina Guarducci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Agostina Nardone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Douglas Russo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zsuzsanna Nagy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Capucine Heraud
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Albert Grinshpun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Qi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Allegra Freelander
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Mathew Joseph Leventhal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Computational and Systems Biology PhD program, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Avery Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gabriella Cohen Feit
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ariel Feiglin
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Weihan Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Francisco Hermida-Prado
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nikolas Kesten
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wen Ma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Carmine De Angelis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, Naples, Italy
| | - Antonio Morlando
- Bioinformatics Unit, Department of Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy
| | - Madison O'Donnell
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Sergey Naumenko
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, Massachusetts
| | - Shixia Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Quang-Dé Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ying Huang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Luca Malorni
- Translational Research Unit, Department of Oncology, Hospital of Prato, Azienda USL Toscana Centro, Prato, Italy
| | - Johann S. Bergholz
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Jean J. Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Rachel Schiff
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
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Indelicato E, Faserl K, Amprosi M, Nachbauer W, Schneider R, Wanschitz J, Sarg B, Boesch S. Skeletal muscle proteome analysis underpins multifaceted mitochondrial dysfunction in Friedreich's ataxia. Front Neurosci 2023; 17:1289027. [PMID: 38027498 PMCID: PMC10644315 DOI: 10.3389/fnins.2023.1289027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Friedreich's ataxia (FRDA) is a severe multisystemic disorder caused by a deficiency of the mitochondrial protein frataxin. While some aspects of FRDA pathology are developmental, the causes underlying the steady progression are unclear. The inaccessibility of key affected tissues to sampling is a main hurdle. Skeletal muscle displays a disease phenotype and may be sampled in vivo to address open questions on FRDA pathophysiology. Thus, we performed a quantitative mass spectrometry-based proteomics analysis in gastrocnemius skeletal muscle biopsies from genetically confirmed FRDA patients (n = 5) and controls. Obtained data files were processed using Proteome Discoverer and searched by Sequest HT engine against a UniProt human reference proteome database. Comparing skeletal muscle proteomics profiles between FRDA and controls, we identified 228 significant differentially expressed (DE) proteins, of which 227 were downregulated in FRDA. Principal component analysis showed a clear separation between FRDA and control samples. Interactome analysis revealed clustering of DE proteins in oxidative phosphorylation, ribosomal elements, mitochondrial architecture control, and fission/fusion pathways. DE findings in the muscle-specific proteomics suggested a shift toward fast-twitching glycolytic fibers. Notably, most DE proteins (169/228, 74%) are target of the transcription factor nuclear factor-erythroid 2. Our data corroborate a mitochondrial biosignature of FRDA, which extends beyond a mere oxidative phosphorylation failure. Skeletal muscle proteomics highlighted a derangement of mitochondrial architecture and maintenance pathways and a likely adaptive metabolic shift of contractile proteins. The present findings are relevant for the design of future therapeutic strategies and highlight the value of skeletal muscle-omics as disease state readout in FRDA.
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Affiliation(s)
- Elisabetta Indelicato
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Faserl
- Institute of Medical Biochemistry, Protein Core Facility, Medical University of Innsbruck, Innsbruck, Austria
| | - Matthias Amprosi
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wolfgang Nachbauer
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Rainer Schneider
- Institute of Biochemistry, Center of Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens University Innsbruck, Innsbruck, Austria
| | - Julia Wanschitz
- Laboratory of Tissue Diagnostics, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Sarg
- Institute of Medical Biochemistry, Protein Core Facility, Medical University of Innsbruck, Innsbruck, Austria
| | - Sylvia Boesch
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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Upadhya SR, Ryan CJ. Antibody reliability influences observed mRNA-protein correlations in tumour samples. Life Sci Alliance 2023; 6:e202201885. [PMID: 37169592 PMCID: PMC10176110 DOI: 10.26508/lsa.202201885] [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: 12/22/2022] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Reverse phase protein arrays (RPPA) have been used to quantify the abundance of hundreds of proteins across thousands of tumour samples in the Cancer Genome Atlas. By number of samples, this is the largest tumour proteomic dataset available and it provides an opportunity to systematically assess the correlation between mRNA and protein abundances. However, the RPPA approach is highly dependent on antibody reliability and approximately one-quarter of the antibodies used in the the Cancer Genome Atlas are deemed to be somewhat less reliable. Here, we assess the impact of antibody reliability on observed mRNA-protein correlations. We find that, in general, proteins measured with less reliable antibodies have lower observed mRNA-protein correlations. This is not true of the same proteins when measured using mass spectrometry. Furthermore, in cell lines, we find that when the same protein is quantified by both mass spectrometry and RPPA, the overall correlation between the two measurements is lower for proteins measured with less reliable antibodies. Overall our results reinforce the need for caution in using RPPA measurements from less reliable antibodies.
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Affiliation(s)
- Swathi Ramachandra Upadhya
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Colm J Ryan
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
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Juanes-Velasco P, Arias-Hidalgo C, Landeira-Viñuela A, Nuño-Soriano A, Fuentes-Vacas M, Góngora R, Hernández ÁP, Fuentes M. Functional proteomics based on protein microarray technology for biomedical research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:49-65. [PMID: 38220432 DOI: 10.1016/bs.apcsb.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
This chapter traces a route through Proteomics from its origins to the present day. The different proteomics applications are discussed with a focus on microarray technology. Analytical microarrays, functional microarrays and reverse phase microarrays and their different applications are discussed. Several studies are mentioned where the great versatility of this approach is shown. Finally, the advantages and future challenges of microarray technology are outlined.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ana Nuño-Soriano
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina Fuentes-Vacas
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafa Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.
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Fil D, Conley RL, Zuberi AR, Lutz CM, Gemelli T, Napierala M, Napierala JS. Neurobehavioral deficits of mice expressing a low level of G127V mutant frataxin. Neurobiol Dis 2023; 177:105996. [PMID: 36638893 PMCID: PMC9901512 DOI: 10.1016/j.nbd.2023.105996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/20/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Friedreich's ataxia (FRDA) is a neurodegenerative disease caused by reduced expression of the mitochondrial protein frataxin (FXN). Most FRDA patients are homozygous for large expansions of GAA repeats in intron 1 of FXN, while some are compound heterozygotes with an expanded GAA tract in one allele and a missense or nonsense mutation in the other. A missense mutation, changing a glycine to valine at position 130 (G130V), is prevalent among the clinical variants. We and others have demonstrated that levels of mature FXN protein in FRDA G130V samples are reduced below those detected in samples harboring homozygous repeat expansions. Little is known regarding expression and function of endogenous FXN-G130V protein due to lack of reagents and models that can distinguish the mutant FXN protein from the wild-type FXN produced from the GAA-expanded allele. We aimed to determine the effect of the G130V (murine G127V) mutation on Fxn expression and to define its multi-system impact in vivo. We used CRISPR/Cas9 to introduce the G127V missense mutation in the Fxn coding sequence and generated homozygous mice (FxnG127V/G127V). We also introduced the G127V mutation into a GAA repeat expansion FRDA mouse model (FxnGAA230/KO; KIKO) to generate a compound heterozygous strain (FxnG127V/GAA230). We performed neurobehavioral tests on cohorts of WT and Fxn mutant animals at three-month intervals for one year, and collected tissue samples to analyze molecular changes during that time. The endogenous Fxn G127V protein is detected at much lower levels in all tissues analyzed from FxnG127V/G127V mice compared to age and sex-matched WT mice without differences in Fxn transcript levels. FxnG127V/G127V mice are significantly smaller than WT counterparts, but perform similarly in most neurobehavioral tasks. RNA sequencing analysis revealed reduced expression of genes in oxidative phosphorylation and protein synthesis, underscoring the metabolic consequences in our mouse model expressing extremely low levels of Fxn. Results of these studies provide insight into the unique pathogenic mechanism of the FXN G130V mechanism and the tolerable limit of Fxn/FXN expression in vivo.
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Affiliation(s)
- Daniel Fil
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robbie L Conley
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aamir R Zuberi
- Technology Evaluation and Development, JAX Center for Precision Genetics, Rare Disease Translational Center, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Cathleen M Lutz
- The Rare and Orphan Disease Center, JAX Center for Precision Genetics, Rare Disease Translational Center, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Terry Gemelli
- Department of Neurology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Payne RM. Cardiovascular Research in Friedreich Ataxia: Unmet Needs and Opportunities. JACC Basic Transl Sci 2022; 7:1267-1283. [PMID: 36644283 PMCID: PMC9831864 DOI: 10.1016/j.jacbts.2022.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 01/18/2023]
Abstract
Friedreich Ataxia (FRDA) is an autosomal recessive disease in which a mitochondrial protein, frataxin, is severely decreased in its expression. In addition to progressive ataxia, patients with FRDA often develop a cardiomyopathy that can be hypertrophic. This cardiomyopathy is unlike the sarcomeric hypertrophic cardiomyopathies in that the hypertrophy is associated with massive mitochondrial proliferation within the cardiomyocyte rather than contractile protein overexpression. This is associated with atrial arrhythmias, apoptosis, and fibrosis over time, and patients often develop heart failure leading to premature death. The differences between this mitochondrial cardiomyopathy and the more common contractile protein hypertrophic cardiomyopathies can be a source of misunderstanding in the management of these patients. Although imaging studies have revealed much about the structure and function of the heart in this disease, we still lack an understanding of many important clinical and fundamental molecular events that determine outcome of the heart in FRDA. This review will describe the current basic and clinical understanding of the FRDA heart, and most importantly, identify major gaps in our knowledge that represent new directions and opportunities for research.
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Affiliation(s)
- R. Mark Payne
- Address for correspondence: Dr R. Mark Payne, Division of Pediatric Cardiology, Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut, R4 302b, Indianapolis, Indiana 46202, USA.
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