A Functional Precision Medicine Pipeline Combines Comparative Transcriptomics and Tumor Organoid Modeling to Identify Bespoke Treatment Strategies for Glioblastoma

Abstract

Li Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome caused by germline mutations in TP53. TP53 is the most common mutated gene in human cancer, occurring in 30–50% of glioblastomas (GBM). Here, we highlight a precision medicine platform to identify potential targets for a GBM patient with LFS. We used a comparative transcriptomics approach to identify genes that are uniquely overexpressed in the LFS GBM patient relative to a cancer compendium of 12,747 tumor RNA sequencing data sets, including 200 GBMs. STAT1 and STAT2 were identified as being significantly overexpressed in the LFS patient, indicating ruxolitinib, a Janus kinase 1 and 2 inhibitors, as a potential therapy. The LFS patient had the highest level of STAT1 and STAT2 expression in an institutional high-grade glioma cohort of 45 patients, further supporting the cancer compendium results. To empirically validate the comparative transcriptomics pipeline, we used a combination of adherent and organoid cell culture techniques, including ex vivo patient-derived organoids (PDOs) from four patient-derived cell lines, including the LFS patient. STAT1 and STAT2 expression levels in the four patient-derived cells correlated with levels identified in the respective parent tumors. In both adherent and organoid cultures, cells from the LFS patient were among the most sensitive to ruxolitinib compared to patient-derived cells with lower STAT1 and STAT2 expression levels. A spheroid-based drug screening assay (3D-PREDICT) was performed and used to identify further therapeutic targets. Two targeted therapies were selected for the patient of interest and resulted in radiographic disease stability. This manuscript supports the use of comparative transcriptomics to identify personalized therapeutic targets in a functional precision medicine platform for malignant brain tumors.

Receptor tyrosine kinase (RTK) targeting in pediatric high-grade glioma and diffuse midline glioma: Pre-clinical models and precision medicine

“…A cryopreserved GBO repository has been developed and used to screen a library of 22 compounds that inhibit tumor invasion into surrounding tissue ( 110 ). GBOs have also been used to study response to chimeric antigen T (CAR-T) cell immunotherapy in the setting of the EGFRvIII variant ( 111 ), mTOR inhibitors in PTEN loss ( 112 ), and STAT inhibitors in Li-Fraumeni syndrome ( 113 ). These studies support that GBOs are a reliable tool for developing personalized therapies.…”

Mechanistic and pharmacodynamic studies of DuoBody-CD3x5T4 in preclinical tumor models

“…After washing, viability marker DRAQ7 (BD Biosciences) was added at a 1:200 dilution before data acquisition on the CytoFLEX LX flow cytometer (Beckman Coulter). 3D patient-derived spheroid cultures were generated, and response testing was performed using KIYATEC proprietary technologies, including the KIYA-PREDICT (KIYATEC) testing platform ( Shuford et al, 2019 , 2021 ; Appleton et al, 2021 ; Reed et al, 2021 ). After 72 h of treatment, spheroid viability was assessed on a TECAN infinite M1000pro (Mannedorf) using a CellTiter-Glo 3D (Promega) assay.…”

Li–Fraumeni Syndrome: Mutation of TP53 Is a Biomarker of Hereditary Predisposition to Tumor: New Insights and Advances in the Treatment

“…These findings inspired a new approach where the use of a comparative transcriptomic analysis identified a group of genes precisely overexpressed in LFS glioblastoma multiforme (GBM) patients among a cancer compendium of 12.747 tumor RNA sequencing data sets, including 200 GBMs, opening the way for the identification of personalized drug treatments [ 112 ]. STAT1 and STAT2 genes are identified to be overexpressed in LFS patients and ruxolitinib was the JNK inhibitor, which could be used as a potential therapy to block the JNK/STAT1,2 pathway [ 112 ]. The research of actionable targets by using genomic and transcriptomic approaches and patient-derived organoids could represent the basis of many therapeutic trials in cancer.…”