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  1. Article ; Online: Automated tumor immunophenotyping predicts clinical benefit from anti-PD-L1 immunotherapy.

    Li, Xiao / Eastham, Jeffrey / Giltnane, Jennifer M / Zou, Wei / Zijlstra, Andries / Tabatsky, Evgeniy / Banchereau, Romain / Chang, Ching-Wei / Nabet, Barzin Y / Patil, Namrata S / Molinero, Luciana / Chui, Steve / Harryman, Maureen / Lau, Shari / Rangell, Linda / Waumans, Yannick / Kockx, Mark / Orlova, Darya / Koeppen, Hartmut

    The Journal of pathology

    2024  

    Abstract: Cancer immunotherapy has transformed the clinical approach to patients with malignancies, as profound benefits can be seen in a subset of patients. To identify this subset, biomarker analyses increasingly focus on phenotypic and functional evaluation of ... ...

    Abstract Cancer immunotherapy has transformed the clinical approach to patients with malignancies, as profound benefits can be seen in a subset of patients. To identify this subset, biomarker analyses increasingly focus on phenotypic and functional evaluation of the tumor microenvironment to determine if density, spatial distribution, and cellular composition of immune cell infiltrates can provide prognostic and/or predictive information. Attempts have been made to develop standardized methods to evaluate immune infiltrates in the routine assessment of certain tumor types; however, broad adoption of this approach in clinical decision-making is still missing. We developed approaches to categorize solid tumors into 'desert', 'excluded', and 'inflamed' types according to the spatial distribution of CD8+ immune effector cells to determine the prognostic and/or predictive implications of such labels. To overcome the limitations of this subjective approach, we incrementally developed four automated analysis pipelines of increasing granularity and complexity for density and pattern assessment of immune effector cells. We show that categorization based on 'manual' observation is predictive for clinical benefit from anti-programmed death ligand 1 therapy in two large cohorts of patients with non-small cell lung cancer or triple-negative breast cancer. For the automated analysis we demonstrate that a combined approach outperforms individual pipelines and successfully relates spatial features to pathologist-based readouts and the patient's response to therapy. Our findings suggest that tumor immunophenotype generated by automated analysis pipelines should be evaluated further as potential predictive biomarkers for cancer immunotherapy. © 2024 The Pathological Society of Great Britain and Ireland.
    Language English
    Publishing date 2024-03-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 3119-7
    ISSN 1096-9896 ; 0022-3417
    ISSN (online) 1096-9896
    ISSN 0022-3417
    DOI 10.1002/path.6274
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics.

    Banchereau, Romain / Cepika, Alma-Martina / Banchereau, Jacques / Pascual, Virginia

    Annual review of immunology

    2017  Volume 35, Page(s) 337–370

    Abstract: Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated ... ...

    Abstract Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.
    MeSH term(s) Autoimmune Diseases/diagnosis ; Autoimmune Diseases/immunology ; Datasets as Topic ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammation/diagnosis ; Inflammation/immunology ; Information Storage and Retrieval ; Molecular Targeted Therapy ; Monitoring, Immunologic ; Prognosis ; Transcriptome
    Language English
    Publishing date 2017-01-30
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 604953-9
    ISSN 1545-3278 ; 0732-0582
    ISSN (online) 1545-3278
    ISSN 0732-0582
    DOI 10.1146/annurev-immunol-051116-052225
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Clinico-Genomic Characterization of Patients with Metastatic Urothelial Carcinoma in Real-World Practice Identifies a Novel Bladder Immune Performance Index (BIPI).

    Szabados, Bernadett / Ponz-Sarvisé, Mariano / Machado, Robson / Saldana, Diego / Kadel, Edward E / Banchereau, Romain / Bouquet, Fanny / Garmhausen, Marius / Powles, Thomas / Schröder, Carsten

    Clinical cancer research : an official journal of the American Association for Cancer Research

    2022  Volume 28, Issue 18, Page(s) 4083–4091

    Abstract: Purpose: This retrospective analysis of the largest available clinico-genomic database used de-identified patient-level electronic health record-derived real-world data (RWD) combined with FoundationOne comprehensive genomic profiling (CGP) to ... ...

    Abstract Purpose: This retrospective analysis of the largest available clinico-genomic database used de-identified patient-level electronic health record-derived real-world data (RWD) combined with FoundationOne comprehensive genomic profiling (CGP) to characterize patients with metastatic urothelial carcinoma (mUC) treated in the real-world setting, detect potential biomarkers, and develop a bladder immune performance index (BIPI).
    Experimental design: Patients with mUC who started front-line single-agent immune checkpoint inhibitors (ICI) and an unmatched group treated with front-line platinum-based chemotherapy between January 1, 2011, and September 30, 2019, were selected. Clinical and genomic data were correlated with overall survival (OS). A novel BIPI predicting outcome with ICIs was developed using machine learning methods and validated using data from a phase II trial (NCT02951767).
    Results: In ICI-treated patients (n = 118), high tumor mutational burden (≥10 mutations/megabase) was associated with improved OS (HR, 0.58; 95% CI, 0.35-0.95; P = 0.03). In chemotherapy-treated patients (n = 268), those with high APOBEC mutational signature had worse OS (HR, 1.43; 95% CI, 1.06-1.94; P = 0.02). Neither FGFR3 mutations nor DNA damage-repair pathway alterations were associated with OS. A novel BIPI combining clinical and genomic variables (nonmetastatic at initial diagnosis, normal or above normal albumin level at baseline, prior surgery for organ-confined disease, high tumor mutational burden) identified ICI-treated patients with longest OS and was validated in an independent dataset.
    Conclusions: Contemporary RWD including FoundationOne CGP can be used to characterize outcomes in real-world patients according to biomarkers beyond PD-L1. A validated, novel clinico-genomic BIPI demonstrated satisfactory prognostic performance for OS in patients with mUC receiving front-line ICI therapy.
    MeSH term(s) Carcinoma, Transitional Cell/drug therapy ; Clinical Trials, Phase II as Topic ; Genomics ; Humans ; Retrospective Studies ; Urinary Bladder ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/genetics
    Language English
    Publishing date 2022-07-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1225457-5
    ISSN 1557-3265 ; 1078-0432
    ISSN (online) 1557-3265
    ISSN 1078-0432
    DOI 10.1158/1078-0432.CCR-22-0200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade.

    Nabet, Barzin Y / Hamidi, Habib / Lee, Myung Chang / Banchereau, Romain / Morris, Stefanie / Adler, Leah / Gayevskiy, Velimir / Elhossiny, Ahmed M / Srivastava, Minu K / Patil, Namrata S / Smith, Kiandra A / Jesudason, Rajiv / Chan, Caleb / Chang, Patrick S / Fernandez, Matthew / Rost, Sandra / McGinnis, Lisa M / Koeppen, Hartmut / Gay, Carl M /
    Minna, John D / Heymach, John V / Chan, Joseph M / Rudin, Charles M / Byers, Lauren A / Liu, Stephen V / Reck, Martin / Shames, David S

    Cancer cell

    2024  Volume 42, Issue 3, Page(s) 429–443.e4

    Abstract: Atezolizumab (anti-PD-L1), combined with carboplatin and etoposide (CE), is now a standard of care for extensive-stage small-cell lung cancer (ES-SCLC). A clearer understanding of therapeutically relevant SCLC subsets could identify rational combination ... ...

    Abstract Atezolizumab (anti-PD-L1), combined with carboplatin and etoposide (CE), is now a standard of care for extensive-stage small-cell lung cancer (ES-SCLC). A clearer understanding of therapeutically relevant SCLC subsets could identify rational combination strategies and improve outcomes. We conduct transcriptomic analyses and non-negative matrix factorization on 271 pre-treatment patient tumor samples from IMpower133 and identify four subsets with general concordance to previously reported SCLC subtypes (SCLC-A, -N, -P, and -I). Deeper investigation into the immune heterogeneity uncovers two subsets with differing neuroendocrine (NE) versus non-neuroendocrine (non-NE) phenotypes, demonstrating immune cell infiltration hallmarks. The NE tumors with low tumor-associated macrophage (TAM) but high T-effector signals demonstrate longer overall survival with PD-L1 blockade and CE versus CE alone than non-NE tumors with high TAM and high T-effector signal. Our study offers a clinically relevant approach to discriminate SCLC patients likely benefitting most from immunotherapies and highlights the complex mechanisms underlying immunotherapy responses.
    MeSH term(s) Humans ; Lung Neoplasms/genetics ; Immune Checkpoint Inhibitors/therapeutic use ; Small Cell Lung Carcinoma/genetics ; Carboplatin/therapeutic use ; Etoposide/therapeutic use ; Immunotherapy
    Chemical Substances Immune Checkpoint Inhibitors ; Carboplatin (BG3F62OND5) ; Etoposide (6PLQ3CP4P3)
    Language English
    Publishing date 2024-02-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2078448-X
    ISSN 1878-3686 ; 1535-6108
    ISSN (online) 1878-3686
    ISSN 1535-6108
    DOI 10.1016/j.ccell.2024.01.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Immunomodulatory effects and improved outcomes with cisplatin- versus carboplatin-based chemotherapy plus atezolizumab in urothelial cancer.

    Galsky, Matthew D / Guan, Xiangnan / Rishipathak, Deepali / Rapaport, Aaron S / Shehata, Hesham M / Banchereau, Romain / Yuen, Kobe / Varfolomeev, Eugene / Hu, Ruozhen / Han, Chia-Jung / Li, Haocheng / Liang, Yuxin / Vucic, Domagoj / Wang, Li / Zhu, Jun / Yu, Haocheng / Herbst, Rebecca H / Hajaj, Emma / Kiner, Evgeny /
    Bamias, Aristotelis / De Santis, Maria / Davis, Ian D / Arranz, José Ángel / Kikuchi, Eiji / Bernhard, Sandrine / Williams, Patrick / Lee, Chooi / Mellman, Ira / Sanjabi, Shomyseh / Johnston, Robert / Black, Peter C / Grande, Enrique / Mariathasan, Sanjeev

    Cell reports. Medicine

    2024  Volume 5, Issue 2, Page(s) 101393

    Abstract: In metastatic urothelial cancer (mUC), cisplatin versus carboplatin leads to durable disease control in a subset of patients. The IMvigor130 trial reveals more favorable effects with atezolizumab combined with gemcitabine and cisplatin (GemCis) versus ... ...

    Abstract In metastatic urothelial cancer (mUC), cisplatin versus carboplatin leads to durable disease control in a subset of patients. The IMvigor130 trial reveals more favorable effects with atezolizumab combined with gemcitabine and cisplatin (GemCis) versus gemcitabine and carboplatin (GemCarbo). This study investigates the immunomodulatory effects of cisplatin as a potential explanation for these observations. Our findings indicate that improved outcomes with GemCis versus GemCarbo are primarily observed in patients with pretreatment tumors exhibiting features of restrained adaptive immunity. In addition, GemCis versus GemCarbo ± atezolizumab induces transcriptional changes in circulating immune cells, including upregulation of antigen presentation and T cell activation programs. In vitro experiments demonstrate that cisplatin, compared with carboplatin, exerts direct immunomodulatory effects on cancer cells, promoting dendritic cell activation and antigen-specific T cell killing. These results underscore the key role of immune modulation in cisplatin's efficacy in mUC and highlight the importance of specific chemotherapy backbones in immunotherapy combination regimens.
    MeSH term(s) Humans ; Antibodies, Monoclonal, Humanized ; Carboplatin/therapeutic use ; Carcinoma, Transitional Cell/drug therapy ; Carcinoma, Transitional Cell/chemically induced ; Carcinoma, Transitional Cell/pathology ; Cisplatin/therapeutic use ; Deoxycytidine/therapeutic use ; Gemcitabine ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/pathology ; Urologic Neoplasms/drug therapy ; Urologic Neoplasms/chemically induced ; Urologic Neoplasms/pathology
    Chemical Substances Antibodies, Monoclonal, Humanized ; atezolizumab (52CMI0WC3Y) ; Carboplatin (BG3F62OND5) ; Cisplatin (Q20Q21Q62J) ; Deoxycytidine (0W860991D6) ; Gemcitabine
    Language English
    Publishing date 2024-01-26
    Publishing country United States
    Document type Clinical Trial ; Journal Article
    ISSN 2666-3791
    ISSN (online) 2666-3791
    DOI 10.1016/j.xcrm.2024.101393
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Publisher Correction: Clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial.

    Powles, Thomas / Kockx, Mark / Rodriguez-Vida, Alejo / Duran, Ignacio / Crabb, Simon J / Van Der Heijden, Michiel S / Szabados, Bernadett / Pous, Albert Font / Gravis, Gwenaelle / Herranz, Urbano Anido / Protheroe, Andrew / Ravaud, Alain / Maillet, Denis / Mendez, Maria Jose / Suarez, Cristina / Linch, Mark / Prendergast, Aaron / van Dam, Pieter-Jan / Stanoeva, Diana /
    Daelemans, Sofie / Mariathasan, Sanjeev / Tea, Joy S / Mousa, Kelly / Banchereau, Romain / Castellano, Daniel

    Nature medicine

    2023  Volume 29, Issue 12, Page(s) 3271

    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-023-02312-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Influenza vaccines differentially regulate the interferon response in human dendritic cell subsets.

    Athale, Shruti / Banchereau, Romain / Thompson-Snipes, LuAnn / Wang, Yuanyuan / Palucka, Karolina / Pascual, Virginia / Banchereau, Jacques

    Science translational medicine

    2017  Volume 9, Issue 382

    Abstract: Human dendritic cells (DCs) play a fundamental role in the initiation of long-term adaptive immunity during vaccination against influenza. Understanding the early response of human DCs to vaccine exposure is thus essential to determine the nature and ... ...

    Abstract Human dendritic cells (DCs) play a fundamental role in the initiation of long-term adaptive immunity during vaccination against influenza. Understanding the early response of human DCs to vaccine exposure is thus essential to determine the nature and magnitude of maturation signals that have been shown to strongly correlate with vaccine effectiveness. In 2009, the H1N1 influenza epidemics fostered the commercialization of the nonadjuvanted monovalent H1N1 California vaccine (MIV-09) to complement the existing nonadjuvanted trivalent Fluzone 2009-2010 vaccine (TIV-09). In retrospective studies, MIV-09 displayed lower effectiveness than TIV-09. We show that TIV-09 induces monocyte-derived DCs (moDCs), blood conventional DCs (cDCs), and plasmacytoid DCs (pDCs) to express CD80, CD83, and CD86 and secrete cytokines. TIV-09 stimulated the secretion of type I interferons (IFNs) IFN-α and IFN-β and type III IFN interleukin-29 (IL-29) by moDC and cDC subsets. The vaccine also induced the production of IL-6, tumor necrosis factor, and the chemokines IFN-γ-inducible protein 10 (IP-10) and macrophage inflammatory protein-1β (MIP-1β). Conversely, MIV-09 did not induce the production of type I IFNs in moDCs and blood cDCs. Furthermore, it inhibited the TIV-09-induced secretion of type I IFNs by these DCs. However, both vaccines induced pDCs to secrete type I IFNs, indicating that different influenza vaccines activate distinct molecular signaling pathways in DC subsets. These results suggest that subtypes of nonadjuvanted influenza vaccines trigger immunity through different mechanisms and that the ability of a vaccine to induce an IFN response in DCs may offset the absence of adjuvant and increase vaccine efficacy.
    Language English
    Publishing date 2017-03-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.aaf9194
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Systems approaches to human autoimmune diseases.

    Banchereau, Romain / Cepika, Alma-Martina / Pascual, Virginia

    Current opinion in immunology

    2013  Volume 25, Issue 5, Page(s) 598–605

    Abstract: Systemic autoimmune diseases result from interactions between genes and environmental triggers that lead to dysregulation of both innate and adaptive immunity. Systems biology approaches enable the global characterization of complex systems at the DNA, ... ...

    Abstract Systemic autoimmune diseases result from interactions between genes and environmental triggers that lead to dysregulation of both innate and adaptive immunity. Systems biology approaches enable the global characterization of complex systems at the DNA, RNA and protein levels. Recent technological breakthroughs such as deep sequencing or high-throughput proteomics are revealing novel inflammatory pathways involved in autoimmunity. Herein, we review recent developments, challenges and promising avenues in the use of systems approaches to understand human systemic autoimmune and autoinflammatory diseases.
    MeSH term(s) Animals ; Autoimmune Diseases/genetics ; Autoimmune Diseases/immunology ; Autoimmunity ; Epigenesis, Genetic ; Genome-Wide Association Study ; Humans ; Systems Biology/methods ; Transcriptome
    Language English
    Publishing date 2013-09-18
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1035767-1
    ISSN 1879-0372 ; 0952-7915
    ISSN (online) 1879-0372
    ISSN 0952-7915
    DOI 10.1016/j.coi.2013.08.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Systems approaches to human autoimmune diseases

    Banchereau, Romain / Cepika, Alma-Martina / Pascual, Virginia

    Current Opinion in Immunology. 2013 Oct., v. 25, no. 5

    2013  

    Abstract: Systemic autoimmune diseases result from interactions between genes and environmental triggers that lead to dysregulation of both innate and adaptive immunity. Systems biology approaches enable the global characterization of complex systems at the DNA, ... ...

    Abstract Systemic autoimmune diseases result from interactions between genes and environmental triggers that lead to dysregulation of both innate and adaptive immunity. Systems biology approaches enable the global characterization of complex systems at the DNA, RNA and protein levels. Recent technological breakthroughs such as deep sequencing or high-throughput proteomics are revealing novel inflammatory pathways involved in autoimmunity. Herein, we review recent developments, challenges and promising avenues in the use of systems approaches to understand human systemic autoimmune and autoinflammatory diseases.
    Keywords DNA ; RNA ; adaptive immunity ; autoimmune diseases ; autoimmunity ; genes ; high-throughput nucleotide sequencing ; humans ; proteomics
    Language English
    Dates of publication 2013-10
    Size p. 598-605.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1035767-1
    ISSN 1879-0372 ; 0952-7915
    ISSN (online) 1879-0372
    ISSN 0952-7915
    DOI 10.1016/j.coi.2013.08.005
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer.

    Patil, Namrata S / Nabet, Barzin Y / Müller, Sören / Koeppen, Hartmut / Zou, Wei / Giltnane, Jennifer / Au-Yeung, Amelia / Srivats, Shyam / Cheng, Jason H / Takahashi, Chikara / de Almeida, Patricia E / Chitre, Avantika S / Grogan, Jane L / Rangell, Linda / Jayakar, Sangeeta / Peterson, Maureen / Hsia, Allison W / O'Gorman, William E / Ballinger, Marcus /
    Banchereau, Romain / Shames, David S

    Cancer cell

    2022  Volume 40, Issue 3, Page(s) 289–300.e4

    Abstract: Inhibitors of the programmed cell death-1 (PD-1/PD-L1) signaling axis are approved to treat non-small cell lung cancer (NSCLC) patients, based on their significant overall survival (OS) benefit. Using transcriptomic analysis of 891 NSCLC tumors from ... ...

    Abstract Inhibitors of the programmed cell death-1 (PD-1/PD-L1) signaling axis are approved to treat non-small cell lung cancer (NSCLC) patients, based on their significant overall survival (OS) benefit. Using transcriptomic analysis of 891 NSCLC tumors from patients treated with either the PD-L1 inhibitor atezolizumab or chemotherapy from two large randomized clinical trials, we find a significant B cell association with extended OS with PD-L1 blockade, independent of CD8
    MeSH term(s) B7-H1 Antigen/genetics ; B7-H1 Antigen/therapeutic use ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Non-Small-Cell Lung/pathology ; Humans ; Immune Checkpoint Inhibitors ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Plasma Cells/pathology
    Chemical Substances B7-H1 Antigen ; Immune Checkpoint Inhibitors
    Language English
    Publishing date 2022-02-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078448-X
    ISSN 1878-3686 ; 1535-6108
    ISSN (online) 1878-3686
    ISSN 1535-6108
    DOI 10.1016/j.ccell.2022.02.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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