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Pan G, Xie H, Xia Y. Disulfidptosis characterizes the tumor microenvironment and predicts immunotherapy sensitivity and prognosis in bladder cancer. Heliyon 2024; 10:e25573. [PMID: 38356551 PMCID: PMC10864973 DOI: 10.1016/j.heliyon.2024.e25573] [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: 07/28/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Background Bladder cancer (BLCA) is prone to metastasis and has poor prognosis with unsatisfactory treatment responsiveness. Disulfidptosis is a recently discovered, novel mode of cell death that is closely associated with human cancers. However, a comprehensive analysis of the relationship between disulfidptosis and BLCA is lacking. Therefore, this study aimed to explore the potential effect of disulfidptosis on BLCA and identify a biomarker for evaluating the prognosis and immunotherapy of patients with BLCA. Material and methods We acquired BLCA RNA sequencing data from The Cancer Genome Atlas Urothelial Bladder Carcinoma (TCGA-BLCA) cohort (containing 19 normal samples and 409 tumor samples) and the GES39281 cohort (containing 94 tumor samples) which were used for external validation of the signature. Initially, we performed unsupervised consensus clustering to explore disulfidptosis-related subgroups. We then conducted functional enrichment analysis on these subgroups to gain insights into their biological significance and evaluate their immunotherapy response and chemotherapy sensitivity. Next, we conducted Least Absolute Shrinkage and Selection Operator (LASSO) regression and multivariate Cox regression to construct a prognostic signature in the TCGA training set for prognosis-related differentially expressed genes (DEGs) in the disulfidptosis-related subgroups. Subsequently, we used a receiver operating characteristic (ROC) curve and independent prognostic analysis to validate the predictive performance of the signature in the TCGA testing and the GES39281 cohorts. Finally, we explored the therapeutic value of this signature in patients with BLCA, in terms of immunotherapy and chemotherapy. Result In this study, we obtained two subgroups: DRG-high (238 samples) and DRG-low (160 samples). The DRG-high group exhibited a poor survival rate compared to the DRG-low group and had a significant association with tumor grade, stage, and metastasis. Additionally, several pathways related to cancer and the immune system were enriched in the high-DRG group. Moreover, the DRG-high group exhibited higher expression of PD1 and CTLA4 and had a better response to immunotherapy in patients with both PD1 and CTLA4 positivity. Conversely, the DRG-high group was more sensitive to common chemotherapeutic agents. A prognostic signature was created, consisting of COL5A1, DIRAS3, NKG7, and POLR3G and validated as having a robust predictive capability. Patients in the low-risk-score group had more immune cells associated with tumor suppression and better immunotherapy outcomes. Conclusion This study contributes to our understanding of the characteristics of disulfidptosis-related subgroups in BLCA. Disulfidptosis-related signatures can be used to assess the prognosis and immunotherapy of patients with BLCA.
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Affiliation(s)
- Guizhen Pan
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huan Xie
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Yeye Xia
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Oncology, Chengdu Fifth People's Hospital, Sichuan, China
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2
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Tonduti D, Zambon AA, Ghezzi D, Lamantea E, Izzo R, Parazzini C, Baldoli C, van der Knaap MS, Fumagalli F. Expanding the Spectrum of NUBPL-Related Leukodystrophy. Neuropediatrics 2023; 54:161-166. [PMID: 36868263 DOI: 10.1055/s-0043-1764214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Mitochondrial leukodystrophies constitute a group of different conditions presenting with a wide range of clinical presentation but with some shared neuroradiological features. Genetic defects in NUBPL have been recognized as cause of a pediatric onset mitochondrial leukodystrophy characterized by onset at the end of the first year of life with motor delay or regression and cerebellar signs, followed by progressive spasticity. Early magnetic resonance imagings (MRIs) show white matter abnormalities with predominant involvement of frontoparietal regions and corpus callosum. A striking cerebellar involvement is usually observed. Later MRIs show spontaneous improvement of white matter abnormalities but worsening of the cerebellar involvement evolving to global atrophy and progressive involvement of brainstem. After the 7 cases initially described, 11 more subjects were reported. Some of them were similar to patients from the original series while few others broadened the phenotypic spectrum. We performed a literature review and report on a new patient who further expand the spectrum of NUBPL-related leukodystrophy. With our study we confirm that the association of cerebral white matter and cerebellar cortex abnormalities is a feature commonly observed in early stages of the disease but beside the original and so far prevalent presentation, there are also uncommon phenotypes: clinical onset can be earlier and more severe than previously thought and signs of extraneurological involvement can be observed. Brain white matter can be diffusely abnormal without anteroposterior gradient, can progressively worsen, and cystic degeneration can be present. Thalami can be involved. Basal ganglia can also become involved during disease evolution.
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Affiliation(s)
- Davide Tonduti
- Unit of Pediatric Neurology, C.O.A.L.A (Center for Diagnosis and Treatment of Leukodystrophies), V. Buzzi Children's Hospital, Milan, Italy.,Department of Biomedical and Clinical Sciences, L. Sacco University Hospital, Università degli Studi di Milano, Milan, Italy
| | - Alberto A Zambon
- Neuromuscular Repair Unit, Division of Neuroscience, Institute of Experimental Neurology (InSpe), IRCCS Ospedale San Raffaele, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Rossella Izzo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cecilia Parazzini
- Pediatric Radiology and Neuroradiology Unit, C.O.A.L.A (Center for Diagnosis and Treatment of Leukodystrophies), V. Buzzi Children's Hospital, Milan, Italy
| | - Cristina Baldoli
- Neuroradiology Unit and CERMAC, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Marjo S van der Knaap
- Department of Child Neurology, Emma Children's Hospital, Amsterdam Leukodystrophy Center, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, Netherlands.,Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Vrije Universiteit, Amsterdam, Netherlands.,Center for Neurogenomics and Cognitive Research, Integrative Neurophysiology, Vrije Universiteit, Amsterdam, Netherlands
| | - Francesca Fumagalli
- Units of Neurology and Neurophysiology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,San Raffaele Telethon Institute for Gene Therapy (SR-Tiget) and Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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3
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Peter S B, Vandana G S. Leukodystrophy Associated with Mitochondrial Complex 1 Deficiency Due to Mutation in NUBPL Gene-An Unusual Follow-Up Finding. Indian J Radiol Imaging 2022; 33:132-135. [PMID: 36855717 PMCID: PMC9968539 DOI: 10.1055/s-0042-1758195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Babu Peter S
- Barnard Institute of Radiology, Madras Medical College, Chennai, Tamil Nadu, India,Address for correspondence Babu Peter S, MDRD, DNB, FICR Professor of Radio-Diagnosis, Barnard Institute of Radiology, Madras Medical CollegeChennai 600003, Tamil NaduIndia
| | - Sree Vandana G
- Barnard Institute of Radiology, Madras Medical College, Chennai, Tamil Nadu, India
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Cheng C, Cleak J, Weiss L, Cater H, Stewart M, Wells S, Columbres RC, Shmara A, Morato Torres CA, Zafar F, Schüle B, Neumann J, Hatchwell E, Kimonis V. Early embryonic lethality in complex I associated p.L104P Nubpl mutant mice. Orphanet J Rare Dis 2022; 17:386. [PMID: 36280881 PMCID: PMC9594925 DOI: 10.1186/s13023-022-02446-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/14/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Variants in the mitochondrial complex I assembly factor, NUBPL are associated with a rare cause of complex I deficiency mitochondrial disease. Patients affected by complex I deficiency harboring homozygous NUBPL variants typically have neurological problems including seizures, intellectual disability, and ataxia associated with cerebellar hypoplasia. Thus far only 19 cases have been reported worldwide, and no treatment is available for this rare disease. METHODS To investigate the pathogenesis of NUBPL-associated complex I deficiency, and for translational studies, we generated a knock-in mouse harboring a patient-specific variant Nubpl c.311T>C; p. L104P reported in three families. RESULTS Similar to Nubpl global knockout mice, the Nubpl p. L104P homozygous mice are lethal at embryonic day E10.5, suggesting that the Nubpl p. L104P variant is likely a hypomorph allele. Given the recent link between Parkinson's disease and loss-of-function NUBPL variants, we also explored aging-related behaviors and immunocytochemical changes in Nubpl hemizygous mice and did not find significant behavioral and pathological changes for alpha-synuclein and oxidative stress markers . CONCLUSION Our data suggest that homozygotes with Nubpl variants, similar to the null mice, are lethal, and heterozygotes are phenotypically and neuropathologically normal. We propose that a tissue-specific knockout strategy is required to establish a mouse model of Nubpl-associated complex I deficiency disorder for future mechanistic and translational studies.
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Affiliation(s)
- Cheng Cheng
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA, USA
| | - James Cleak
- Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Lan Weiss
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Heather Cater
- Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Sara Wells
- Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Rod Carlo Columbres
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Alyaa Shmara
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA, USA
| | | | - Faria Zafar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan Neumann
- Transgenic Mouse Facility, University of California, Irvine, CA, USA
| | - Eli Hatchwell
- Population Bio UK, Inc, Begbroke Science Park, Begbroke, UK
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA, USA.
- Department of Neurology, University of California, Irvine, CA, USA.
- Department of Pathology, University of California, Irvine, CA, USA.
- Department of Environmental Medicine, University of California, Irvine, CA, USA.
- Children's Hospital of Orange County, Orange, CA, USA.
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Camponeschi F, Ciofi-Baffoni S, Calderone V, Banci L. Molecular Basis of Rare Diseases Associated to the Maturation of Mitochondrial [4Fe-4S]-Containing Proteins. Biomolecules 2022; 12:biom12071009. [PMID: 35883565 PMCID: PMC9313013 DOI: 10.3390/biom12071009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
The importance of mitochondria in mammalian cells is widely known. Several biochemical reactions and pathways take place within mitochondria: among them, there are those involving the biogenesis of the iron–sulfur (Fe-S) clusters. The latter are evolutionarily conserved, ubiquitous inorganic cofactors, performing a variety of functions, such as electron transport, enzymatic catalysis, DNA maintenance, and gene expression regulation. The synthesis and distribution of Fe-S clusters are strictly controlled cellular processes that involve several mitochondrial proteins that specifically interact each other to form a complex machinery (Iron Sulfur Cluster assembly machinery, ISC machinery hereafter). This machinery ensures the correct assembly of both [2Fe-2S] and [4Fe-4S] clusters and their insertion in the mitochondrial target proteins. The present review provides a structural and molecular overview of the rare diseases associated with the genes encoding for the accessory proteins of the ISC machinery (i.e., GLRX5, ISCA1, ISCA2, IBA57, FDX2, BOLA3, IND1 and NFU1) involved in the assembly and insertion of [4Fe-4S] clusters in mitochondrial proteins. The disease-related missense mutations were mapped on the 3D structures of these accessory proteins or of their protein complexes, and the possible impact that these mutations have on their specific activity/function in the frame of the mitochondrial [4Fe-4S] protein biogenesis is described.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence: (S.C.-B.); (V.C.); Tel.: +39-055-4574192 (S.C.-B.); +39-055-4574276 (V.C.)
| | - Vito Calderone
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
- Correspondence: (S.C.-B.); (V.C.); Tel.: +39-055-4574192 (S.C.-B.); +39-055-4574276 (V.C.)
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy; (F.C.); (L.B.)
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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Häfliger IM, Seefried FR, Drögemüller C. Reverse Genetic Screen for Deleterious Recessive Variants in the Local Simmental Cattle Population of Switzerland. Animals (Basel) 2021; 11:3535. [PMID: 34944310 PMCID: PMC8698008 DOI: 10.3390/ani11123535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
We herein report the result of a large-scale reverse genetic screen in the Swiss Simmental population, a local dual-purpose cattle breed. We aimed to detect possible recessively inherited variants affecting protein-coding genes, as such deleterious variants can impair fertility and rearing success significantly. We used 115,000 phased SNP data of almost 10 thousand cattle with pedigree data. This revealed evidence for 11 genomic regions of 1.17 Mb on average, with haplotypes (SH1 to SH11) showing a significant depletion in homozygosity and an allele frequency between 3.2 and 10.6%. For the proposed haplotypes, it was unfortunately not possible to evaluate associations with fertility traits as no corresponding data were available. For each haplotype region, possible candidate genes were listed based on their known function in development and disease. Subsequent mining of single-nucleotide variants and short indels in the genomes of 23 sequenced haplotype carriers allowed us to identify three perfectly linked candidate causative protein-changing variants: a SH5-related DIS3:p.Ile678fs loss-of-function variant, a SH8-related CYP2B6:p.Ile313Asn missense variant, and a SH9-related NUBPL:p.Ser143Tyr missense variant. None of these variants occurred in homozygous state in any of more than 5200 sequenced cattle of various breeds. Selection against these alleles in order to reduce reproductive failure and animal loss is recommended.
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Affiliation(s)
- Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
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7
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Dietz JV, Fox JL, Khalimonchuk O. Down the Iron Path: Mitochondrial Iron Homeostasis and Beyond. Cells 2021; 10:cells10092198. [PMID: 34571846 PMCID: PMC8468894 DOI: 10.3390/cells10092198] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the processes of and components involved in mitochondrial iron trafficking and storage, as well as mitochondrial iron–sulfur cluster biogenesis and heme biosynthesis. Recent findings and the most pressing topics for future research are highlighted.
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Affiliation(s)
- Jonathan V. Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
| | - Jennifer L. Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA;
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA;
- Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
- Fred and Pamela Buffett Cancer Center, Omaha, NE 68198, USA
- Correspondence:
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Eis PS, Huang N, Langston JW, Hatchwell E, Schüle B. Loss-of-Function NUBPL Mutation May Link Parkinson's Disease to Recessive Complex I Deficiency. Front Neurol 2020; 11:555961. [PMID: 33224084 PMCID: PMC7667465 DOI: 10.3389/fneur.2020.555961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/28/2020] [Indexed: 02/01/2023] Open
Abstract
In an unbiased genome-wide screen for copy number variants (CNVs) on a cohort of Parkinson's disease (PD) patients, we identified in one patient a complex chromosomal rearrangement involving the nucleotide binding protein-like (NUBPL) gene on chromosome 14q12. We noted that mutations in the NUBPL gene had been reported as causing autosomal recessive (AR) mitochondrial Complex I (CI) deficiency in children. The precise breakpoints of the rearrangement in our PD case were found to be identical to those described in a patient with AR CI deficiency who also harbored a second pathogenic mutation in NUBPL. Mitochondrial dysfunction has long been considered a strong contributor to PD, and there is substantial evidence that decreased CI activity plays a central role in PD pathogenesis. We hypothesize that pathogenic NUBPL variants may increase the risk for PD analogous to variants in the glucosylceramidase beta (GBA) gene that increase the risk of developing PD in heterozygous carriers.
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Affiliation(s)
- Peggy S Eis
- Population Bio, Inc., New York, NY, United States
| | - Neng Huang
- Valley Parkinson Clinic, Los Gatos, CA, United States
| | - J William Langston
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Eli Hatchwell
- Population Bio, UK, Begbroke, Oxfordshire, United Kingdom
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
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