Biology subjects

Badie, B.

Publications and source records attributed to Badie, B..

7 recordsLinked to original sources

bioRxiv2026

Therapeutic Targeting of the TGFβ Pathway Augments CAR T cell Efficacy in Glioblastoma

Chimeric Antigen Receptor (CAR) T therapy represents a promising approach to improve outcomes for patients with high-grade gliomas (HGG). Recently, we reported on a phase I trial assessing the local delivery of CAR T cells for HGG. Despite notable clinical benefits to CAR T treatment, clinical responses were highly variable between patients. Here we report that TGF{beta} levels in the tumor cavity fluid (TCF) decreased following CAR T treatment and that lower TGF{beta} levels positively correlated with improved patient responses to CAR T therapy. Patients were stratified based on baseline TGF{beta} levels in the TCF before CAR T therapy. Single-cell RNA sequencing of patient tumor tissues identified significant upregulation of genes associated with angiogenesis and epithelial-to-mesenchymal transition, and IL6 and SLRP pathways in TGF{beta} high patients, while IL2, chemokine signaling and NK-mediated cytotoxicity pathways were significantly upregulated in TGF{beta} low patients. Preclinically, we demonstrated that systemic treatment with a TGF{beta}R1 inhibitor markedly improved CAR T efficacy in syngeneic murine glioma models, correlating with changes in the tumor microenvironment (TME) that benefited both endogenous and CAR T cell phenotype and trafficking. Further studies demonstrated that inhibition of the TGF{beta} pathway in CAR T cells, through either TGF{beta}R1 inhibitor or CRISPR/Cas9 knockout of TGF{beta}R2 (TGF{beta}R2-KO), significantly enhanced CAR T cell expansion and antitumor activity. Collectively, our clinical and preclinical findings strongly indicate that targeting the TGF{beta} pathway could significantly enhance CAR T therapy for patients with high-grade gliomas.

cancer biology↗

bioRxiv2026

A long-term organotypic slice culture model of patient high-grade glioma preserving tumor heterogeneity and architecture, and specificity of CAR T cell targeting

ABSTRACT Background: High grade glioma (HGG), encompassing IDH-wildtype glioblastoma (CNS WHO grade 4), diffuse midline glioma (CNS WHO grade 4), oligodendroglioma (IDH-mutant and 1p/19q-codeleted) CNS WHO grade 3, together with IDH-mutant astrocytoma of CNS grade 3 and grade 4, represents the most lethal group of adult diffuse gliomas. Despite significant efforts, obtaining improvements in patient survival has been limited, in part, by difficulties in comprehensive ex vivo modeling of the complexities of HGG. Although organotypic slice cultures and other platforms have shown promise, existing models often fail to capture the intrinsic cellular heterogeneity, microenvironment, and architecture of HGG, restricting investigations into their fundamental biology as well as design of novel therapeutics. Methods: We developed a patient-derived HGG organotypic slice culture (GOSC) platform demonstrating long-term preservation of intrinsic tumor characteristics. Vibratome-sectioned slices were cultured in defined medium under conditions approximating those in situ: reduced oxygen (4%), low glucose (2.5 mM), and no added growth factors. The characteristics of GOSCs after 28 days in culture, including expression of immunotherapy targets, were compared to parental tumors using histological staining, immunofluorescence, multiplexed PhenoCycler (CODEX) imaging, bulk RNA-seq expression profiling, and CAR T cell killing assays. Results: GOSCs preserved the histopathology, cell heterogeneity, tumor microenvironment, and tissue architecture of their parental tumors throughout at least 28 days in culture. Importantly, GOSCs retained parental patterns of immunotherapy target expression, and CAR T cells co-cultured with GOSCs demonstrated target-specific killing consistent with parental tumors. Conclusions: This ex vivo GOSC platform offers long-term preservation of the cellular and structural properties of parental HGG tumors, thereby providing a robust tool for extended preclinical studies, and facilitating development and evaluation of advanced tumor-targeting strategies.

cancer biology↗

bioRxiv2026

Patient-Derived Glioma Models Preserve Tumor Heterogeneity and Identify Stearoyl-CoA Desaturase1 (SCD1) as a Candidate Biomarker for Precision Immunotherapy

Background: Pediatric and adult brain tumors, including glioblastoma, astrocytoma, ependymoma, and medulloblastoma, remain associated with poor prognosis despite advances in surgery, radiation, and chemotherapy. Therapeutic resistance, tumor heterogeneity, and treatment-related toxicity highlight the need for clinically relevant models that enable precision medicine and immunotherapy development. Methods: Freshly dispersed tumors (FDTs), low-passage patient-derived brain tumor (PBT) spheroid lines, and matched patient-derived xenograft (PDX) models were established from patients with primary brain tumors. Models were characterized using single-cell and bulk RNA sequencing, whole-exome sequencing, multiparameter flow cytometry, and immunohistochemistry. PBTs were compared with matched FDTs to evaluate model fidelity. Results: PBT lines were established in approximately 68% of cases and retained key patient-specific genomic alterations, including IDH1, MGMT, TP53, and PTEN, with expression of therapeutically relevant targets, including IL13R2, EGFR, HER2, WNT1, JAK1/2, and NOTCH1-4. Gene expression profiles of PBTs closely correlated with matched FDTs (R = 0.38, P = 0.0038). PBT and PDX models preserved intratumoral heterogeneity and non-clonal populations, enabling identification of therapy-resistant subclones during in vitro selection. Molecular analyses identified Stearoyl-CoA Desaturase1 (SCD1) as an overexpressed biomarker across glioma PBTs and matched patient tumors. Ingenuity Pathway Analysis identified SCD1 as an upstream regulator of EGFR-, TP53-, and CYCS-associated signaling networks implicated in tumor progression and immune suppression. Conclusions: Clinically relevant PBT and matched PDX models recapitulate molecular, transcriptional, and histopathological characteristics of primary brain tumors. These platforms provide tools for biomarker discovery, therapeutic testing, and precision immunotherapy development, while identifying SCD1 as a biomarker and therapeutic target in glioma.

cancer biology↗

bioRxiv2025

Overcoming myeloid-driven resistance to CAR T therapy by targeting SPP1

Chimeric antigen receptor (CAR) T cell therapy faces notable limitations in treatment of solid tumors. The suppressive tumor microenvironment (TME), characterized by complex interactions among immune and stromal cells, is gaining recognition in conferring resistance to CAR T cell therapy. Despite the abundance and diversity of macrophages in the TME, their intricate involvement in modulating responses to CAR T cell therapies remains poorly understood. Here, we conducted single-cell RNA sequencing (scRNA-seq) on tumors from 41 glioma patients undergoing IL13R2-targeted CAR T cell therapy, identifying elevated suppressive SPP1 signatures predominantly in macrophages from patients who were resistant to treatment. Further integrative scRNA-seq analysis of high-grade gliomas as well as an interferon-signaling deficient syngeneic mouse model--both resistant to CAR T therapy--demonstrated the role of congruent suppressive pathways in mediating resistance to CAR T cells and a dominant role for SPP1+ macrophages. SPP1 blockade with an anti-SPP1 antibody abrogates the suppressive TME effects and substantially prolongs survival in IFN signaling-deficient and glioma syngeneic mouse models resistant to CAR T cell therapy. These findings illuminate the role of SPP1+ macrophages in fueling a suppressive TME and driving solid tumor resistance to CAR cell therapies. Targeting SPP1 may serve as a universal strategy to reprogram immune dynamics in solid tumors mitigating resistance to CAR T cell therapies.

cancer biology↗

bioRxiv2022

Selective IL13Rα2-Targeted Functionality of IL13-Ligand CARs is Enhanced by Inclusion of 4-1BB Co-Stimulation

ABSTRACTChimeric antigen receptor (CAR) T cell immunotherapy is emerging as a powerful strategy for cancer therapy; however, an important safety consideration is the potential for off-tumor recognition of normal tissue. This is particularly important as ligand-based CARs are optimized for clinical translation. Our group has developed and clinically translated an IL13(E12Y) ligand- based CAR targeting the cancer antigen IL13R2 for treatment of glioblastoma (GBM). There remains limited understanding of how IL13-ligand CAR design impacts the activity and selectivity for the intended tumor-associated target IL13R2 versus the more ubiquitous unintended target IL13R1. In this study, we functionally compared IL13(E12Y)-CARs incorporating different intracellular signaling domains, including first-generation CD3{zeta}- containing CARs (IL13{zeta}), second-generation 4-1BB- (CD137) or CD28-containing CARs (IL13- BB{zeta} or IL13-28{zeta}), and third-generation CARs containing both 4-1BB and CD28 (IL13-28BB{zeta}). In vitro co-culture assays at high tumor burden establish that 2nd generation IL13-BB{zeta} or IL13- 28{zeta} outperform first-generation IL13{zeta} and 3rd generation IL13-28BB{zeta} CAR designs, with IL13- BB{zeta} providing superior CAR proliferation and in vivo anti-tumor potency in human xenograft mouse models. IL13-28{zeta} displayed a lower threshold for antigen recognition, resulting in higher off-target IL13R1 reactivity both in vitro and in vivo. Syngeneic mouse models of GBM also demonstrate safety and anti-tumor potency of murine IL13-BB{zeta} CAR T cells delivered systemically after lymphodepletion. These findings support the use of IL13-BB{zeta} CARs for greater selective recognition of IL13R2 over IL13R1, higher proliferative potential, and superior anti-tumor responsiveness. This study exemplifies the potential of modulating factors outside the antigen targeting domain of a CAR to improve selective tumor recognition..

immunology↗

bioRxiv2021

CAR T cell therapy drives endogenous locoregional T cell dynamics in a responding patient with glioblastoma

CAR T cell therapy has transformed clinical care and management of patients with certain hematological cancers. However, it remains unclear whether the success of CAR T cell therapy relies solely on CAR T cell engagement with tumor antigen, or if it also requires the stimulation of an individual patients endogenous T cell response. Here, we performed combined analysis of longitudinal, single cell RNA and T cell receptor sequencing on glioblastoma tumors, peripheral blood (PB), and cerebrospinal fluid (CSF) from a patient with recurrent multifocal glioblastoma that underwent a remarkable response followed by recurrence on IL13RA2-targeted CAR T cell therapy (Brown et al. 2016). Single cell analysis of a tumor resected prior to CAR T cell therapy revealed the existence of an inflamed tumor microenvironment including a CD8+ cytotoxic, clonally expanded and antigen specific T cell population that disappeared in the recurrent setting. Longitudinal tracking of T cell receptors uncovered distinct T cell dynamics classes in the CSF during CAR T cell therapy. These included T cell clones with transient dynamics, representing intraventricular CAR T cell delivery and endogenous T cell recruitment from the PB into the CSF; and a group of T cells in the cerebrospinal fluid, that tracked with clonally expanded tumor resident T cells and whose dynamics contracted concomitantly with tumor volume. Our results suggest the existence of an endogenous T cell population that was invigorated by intraventricular CAR T cell infusions, and combined with the therapy to produce a complete response.

immunology↗

bioRxiv2020

Chlorotoxin Redirects Chimeric Antigen Receptor T Cells for Specific and Effective Targeting of Glioblastoma

While chimeric antigen receptor (CAR) T cells have demonstrated antitumor activity against glioblastoma (GBM), tumor heterogeneity remains a critical challenge. To more effectively target heterogeneous GBMs, we report the development of a novel peptide-based CAR exploiting the GBM-binding potential of chlorotoxin (CLTX). CLTX bound a greater proportion of tumor cells than GBM-associated antigens EGFR, HER2 and IL13R2. CAR T cells bearing CLTX as the targeting domain (CLTX-CAR), mediated potent in vitro and in vivo anti-GBM activity, and efficiently targeted tumors lacking expression of other GBM-associated antigens. Importantly, CLTX-CAR T cells exhibited no observable off-target effector activity against normal cells, or when adoptively transferred into mice. Effective targeting by CLTX-CAR T cells required cell surface expression of matrix metalloproteinase-2 (MMP-2). Our results are the first demonstration of a peptide toxin utilized as a CAR targeting domain, expanding the repertoire of tumor-selective CAR T cells with the potential to reduce antigen escape. One Sentence SummaryChimeric antigen receptors incorporating chlorotoxin as the tumor targeting domain recognize and kill glioblastoma with high specificity and potency.

immunology↗