Publications
bioRxivApr 2025 DOI:
10.1101/2025.04.25.650703

Personalized CRISPR Knock-In Cytokine Gene Therapy to Remodel the Tumor Microenvironment and Enhance CAR T Cell Therapy in Solid Tumors

Launspach, Michael; Macos, Julia; Afzal, Shoaib; Hohmann, John G.; Beez, Stefanie; Pilgram, Maximilian; Ven, Casper F. T. van der; Lachiheb, Chahrazad; Andersch, Lena; Jens, Marvin; Appis, Marc Lucas; Zirngibl, Felix; Kath, Jonas; Stecklum, Maria; Anders, Kathleen; Wagner, Dimitrios L.; Kuehn, Ralf; Eggert, Angelika; Kuenkele, Annette
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Genes
Abstract
The immunosuppressive tumor microenvironment (TME) remains a central barrier to effective immunotherapy in solid tumors. To address this, we developed a novel gene therapeutic strategy that enables localized remodeling of the TME via tumor-intrinsic cytokine expression. Central to this approach is CancerPAM, a multi-omics bioinformatics pipeline that identifies and ranks patient-specific, tumor-exclusive CRISPR-Cas9 knock-in sites with high specificity and integration efficiency. Using neuroblastoma - a pediatric solid tumor with a suppressive TME - as a model, we applied CancerPAM to sequencing data from cell lines and patients to identify optimal integration sites for pro-inflammatory cytokines (CXCL10, CXCL11, IFNG). CRISPR-mediated CXCL10 knock-in into tumor cells significantly enhanced CAR T cell infiltration and antitumor efficacy both in vitro and in vivo. In vivo, CXCL10-expressing tumors showed significantly increased early CAR T cell infiltration and prolonged survival compared to controls. CancerPAM rankings correlated strongly with target-site specificity and knock-in efficiency, validating its predictive performance. Our findings establish CancerPAM as a powerful tool for safe and effective CRISPR-based interventions and provide a conceptual framework for integrating cytokine-driven TME remodeling with cellular immunotherapies. This personalized strategy holds promise for enhancing CAR T cells and other immunotherapies across immune-refractory solid tumors.
Product Used
Genes

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