Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma

Abstract

Purpose: Glioblastoma is the most frequent and lethal primary brain tumor. Development of novel therapies relies on the availability of relevant preclinical models. We have established a panel of 96 glioblastoma patient-derived xenografts (PDX) and undertaken its genomic and phenotypic characterization.Experimental Design: PDXs were established from glioblastoma, IDH-wildtype (n ¼ 93), glioblastoma, IDH-mutant (n ¼ 2), diffuse midline glioma, H3 K27M-mutant (n ¼ 1), and both primary (n ¼ 60) and recurrent (n ¼ 34) tumors. Tumor growth rates, histopathology, and treatment response were characterized. Integrated molecular profiling was performed by whole-exome sequencing (WES, n ¼ 83), RNAsequencing (n ¼ 68), and genome-wide methylation profiling (n ¼ 76). WES data from 24 patient tumors was compared with derivative models.Results: PDXs recapitulate many key phenotypic and molecular features of patient tumors. Orthotopic PDXs show charac-teristic tumor morphology and invasion patterns, but largely lack microvascular proliferation and necrosis. PDXs capture common and rare molecular drivers, including alterations of TERT, EGFR, PTEN, TP53, BRAF, and IDH1, most at frequencies comparable with human glioblastoma. However, PDGFRA amplification was absent. RNA-sequencing and genome-wide methylation profiling demonstrated broad representation of glioblastoma molecular subtypes. MGMT promoter methylation correlated with increased survival in response to temozolomide. WES of 24 matched patient tumors showed preservation of most genetic driver alterations, including EGFR amplification. However, in four patient-PDX pairs, driver alterations were gained or lost on engraftment, consistent with clonal selection.Conclusions: Our PDX panel captures the molecular heterogeneity of glioblastoma and recapitulates many salient genetic and phenotypic features. All models and genomic data are openly available to investigators.

Establishment and Characterisation of Heterotopic Patient-Derived Xenografts for Glioblastoma

“…Gene expression analyses also indicate a high similarity between PDXs and the patient sample they derive from [48,50,52]. Additionally, a recent study by whole-exome sequencing in glioblastoma and their parent tumours showed that most genetic driver mutations are conserved in PDXs, although gain and loss were also observed, indicating potential clonal selection [53]. It can be speculated that with increasing passage, the number of genetic and transcriptomic alterations will increase in the specific mouse microenvironment.…”

Primary and recurrent glioma patient-derived orthotopic xenografts (PDOX) represent relevant patient avatars for precision medicine

“…We find that prominent angiogenic features are rare in mice compared to rats, which may arise from differences in brain size and/or in molecular interaction between species, suggesting that for studies targeting angiogenesis, rat PDOX models may be more appropriate. Others also reported gradients of invasive and angiogenic features across GBM xenografts, with limited endothelial proliferation and necrosis in mouse brains 67,77 , while large subcutaneous tumors displayed extensive angiogenesis 67 .…”

“…Most glioma PDX models are derived by subcutaneous implantation of tumor fragments 66,67 , which may not accurately mimic the complex and distinctive brain microenvironment. As direct implantation of tissue fragments to rodent brains is challenging, GBM orthotopic xenografts usually rely on single cell dissociation followed by in vitro cultures prior to xenotransplantation 51,66,[68][69][70] , where cultures are often maintained for unspecified time and passage number.…”

“…This is in concordance with the general selection of aggressive tumors upon PDX generation in different tumor types, including pediatric brain tumors 73 . So far, only a handful of IDH1mut glioma models were described, which all suffer from long development time and/or changes in IDH1 status 67,[74][75][76][77][78] . Successful IDH1mut models in our cohort were defined molecularly as high-grade astrocytomas with abundant chromosomal aberrations, CDKN2A/B loss, ATRX and TP53 mutations and G-CIMP-low signature.…”

Selective Vulnerability of Senescent Glioblastoma Cells to Bcl-XL Inhibition

“…Conversely, four of the GBM lines used (10,76,120,123) were derived from patient with recurrent tumors who had previously undergone chemotherapy and radiation. [27] Although GBM123 was among the weaker responders, all others showed similarly augmented response to BCL-XL inhibition after re-induction of senescence with radiation or TMZ. Also of note, certain lines tested (including GBM 6 and 10) have been previously reported as radio-resistant with nominal prolongation of survival in xenografts upon radiation.…”