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      Tracing specificity of immune landscape remodeling associated with distinct anticancer treatments

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          Summary

          Immune cells within the tumor microenvironment impact cancer progression, resistance, response to treatments. Despite remarkable outcomes for some cancer patients, immunotherapies remain unsatisfactory for others. Here, we designed an experimental setting using the Alb-R26 Met “inside-out” mouse model, faithfully recapitulating molecular features of liver cancer patients, to explore the effects of distinct anticancer targeted therapies on the tumor immune landscape. Using two treatments in clinical trials for different cancer types, Decitabine and MEK+BCL-XL blockage, we show their capability to trigger tumor regression in Alb-R26 Met mice and to superimpose distinct profiles of immune cell types and immune-checkpoints, impacting immunotherapy response. A machine learning approach processing tumor imaging and immune profile data identified a putative signature predicting tumor treatment response in mice and patients. Outcomes exemplify how the tumor immune microenvironment is differentially reshaped by distinct anticancer agents and highlight the importance of measuring its modulation during treatment to optimize oncotherapy and immunotherapy combinations.

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          Highlights

          • Alb-R26 Met liver cancer model recapitulates patient molecular and immune profiles

          • The distinct action of anticancer drugs on tumor immunity highlights its plasticity

          • Distinct anticancer agents differentially reshape the tumor immune landscape

          • Distinct treatments partially flatten immune heterogeneity of pre-treated tumors

          Abstract

          Microenvironment; Immune response; Cancer; Machine learning

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          Most cited references63

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          TIMER2.0 for analysis of tumor-infiltrating immune cells

          Abstract Tumor progression and the efficacy of immunotherapy are strongly influenced by the composition and abundance of immune cells in the tumor microenvironment. Due to the limitations of direct measurement methods, computational algorithms are often used to infer immune cell composition from bulk tumor transcriptome profiles. These estimated tumor immune infiltrate populations have been associated with genomic and transcriptomic changes in the tumors, providing insight into tumor–immune interactions. However, such investigations on large-scale public data remain challenging. To lower the barriers for the analysis of complex tumor–immune interactions, we significantly improved our previous web platform TIMER. Instead of just using one algorithm, TIMER2.0 (http://timer.cistrome.org/) provides more robust estimation of immune infiltration levels for The Cancer Genome Atlas (TCGA) or user-provided tumor profiles using six state-of-the-art algorithms. TIMER2.0 provides four modules for investigating the associations between immune infiltrates and genetic or clinical features, and four modules for exploring cancer-related associations in the TCGA cohorts. Each module can generate a functional heatmap table, enabling the user to easily identify significant associations in multiple cancer types simultaneously. Overall, the TIMER2.0 web server provides comprehensive analysis and visualization functions of tumor infiltrating immune cells.
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            Understanding the tumor immune microenvironment (TIME) for effective therapy

            The clinical successes in immunotherapy have been both astounding and at the same time unsatisfactory. Countless patients with varied tumor types have seen pronounced clinical response with immunotherapeutic intervention; however, many more patients have experienced minimal or no clinical benefit when provided the same treatment. As technology has advanced, so has the understanding of the complexity and diversity of the immune context of the tumor microenvironment and its influence on response to therapy. It has been possible to identify different subclasses of immune environment that have an influence on tumor initiation and response and therapy; by parsing the unique classes and subclasses of tumor immune microenvironment (TIME) that exist within a patient’s tumor, the ability to predict and guide immunotherapeutic responsiveness will improve, and new therapeutic targets will be revealed.
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              Hepatocellular Carcinoma

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                Author and article information

                Contributors
                Journal
                iScience
                iScience
                iScience
                Elsevier
                2589-0042
                20 February 2025
                21 March 2025
                20 February 2025
                : 28
                : 3
                : 112071
                Affiliations
                [1 ]Aix Marseille Univ, CNRS/IN2P3, CPPM, 13009 Marseille, France
                [2 ]Aix Marseille Univ, CNRS, Inserm, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
                [3 ]Aix Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), Turing Center for Living Systems, 13009 Marseille, France
                [4 ]Institut Universitaire de France, Paris, France
                Author notes
                []Corresponding author celia.sequera-hurtado@ 123456univ-amu.fr
                [∗∗ ]Corresponding author flavio.maina@ 123456univ-amu.fr
                [5]

                These authors contributed equally

                [6]

                Lead contact

                Article
                S2589-0042(25)00331-1 112071
                10.1016/j.isci.2025.112071
                11930375
                40124507
                f688d022-30d7-403e-9694-d9b2359c9dbb
                © 2025 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 3 March 2024
                : 18 July 2024
                : 10 February 2025
                Categories
                Article

                microenvironment,immune response,cancer,machine learning

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