Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Abstract

Background: Diffuse pleural mesothelioma (DPM) is an aggressive malignancy that, despite recent treatment advances, has unacceptably poor outcomes. Therapeutic research in DPM is inhibited by a paucity of preclinical models that faithfully recapitulate the human disease.

Methods: We established 22 patient-derived xenografts (PDX) from 22 patients with DPM and performed multi-omic analyses to deconvolute the mutational landscapes, global expression profiles, and molecular subtypes of these PDX models and compared features to those of the matched primary patient tumors. Targeted next-generation sequencing (NGS; MSK-IMPACT), immunohistochemistry, and histologic subtyping were performed on all available samples. RNA sequencing was performed on all available PDX samples. Clinical outcomes and treatment history were annotated for all patients. Platinum-doublet progression-free survival (PFS) was determined from the start of chemotherapy until radiographic/clinical progression and grouped into < or ≥ 6 months.

Results: PDX models were established from both treatment naïve and previously treated samples and were noted to closely resemble the histology, genomic landscape, and proteomic profiles of the parent tumor. After establishing the validity of the models, transcriptomic analyses demonstrated overexpression in WNT/β-catenin, hedgehog, and TGF-β signaling and a consistent suppression of immune-related signaling in PDXs derived from patients with worse clinical outcomes.

Conclusions: These data demonstrate that DPM PDX models closely resemble the genotype and phenotype of parental tumors, and identify pathways altered in DPM for future exploration in preclinical studies.

Fig. 1

Generation of PDX models and patient treatment histories. A Graphical overview of PDX collection and analysis. Samples were obtained by surgical resection (pleurectomy/decortication), biopsy, and aspirations. Both PDX and human samples were analyzed by IHC, targeted next generation sequencing (MSK-IMPACT), and histologic subtyping when material was available. RNA sequencing was performed on all PDX models with available data. The “n” represents the number of samples run at each step of the analysis. B Swimmers plot showing the clinical course of all 22 patients where the red arrow denotes the time of tissue collection for the PDX and C details of systemic therapy received prior to PDX collection in the 11 applicable patients. E, epithelioid; B, biphasic; S, sarcomatoid

Fig. 2

Comparative immunohistochemistry and next generation sequencing of patient samples and PDX models. A Concordance of IHC markers between PDX and patient samples. BAP1 concordance was defined as loss/retained. WT1, mesothelin, VISTA, and PD-L1 concordance was defined as the PDX and patient sample expression being within ±25% expression of each other. B Genomic landscape of patients’ samples (n = 19), C PDX samples (n = 22), and D paired patient/PDX samples (n = 19) with available material using MSK-IMPACT targeted next generation sequencing. Genes were annotated if noted to have at least one alteration in the patient cohort

Fig. 3

Gene expression changes in mesothelioma PDX models as a function of histologic subtype. A Sample to sample subtype correlation plot using the top 100 highest variance genes. The spearman correlation was used, and the samples were ordered using hierarchical clustering with complete linkage. B Principal component analysis plot showing mesothelioma PDX samples color-coded based on subtype annotation. C Volcano plot showing top differentially expressed genes (DEGs) in epithelioid vs non-epithelioid subtype comparison D Pathway enrichment analyses on the DEGs of the epithelioid vs non-epithelioid subtype comparison

Fig. 4

Gene expression changes in mesothelioma PDX models grouped by platinum doublet and clinical outcomes in the contributing patients. A Heatmap of gene expression of PDX samples for top genes altered by PFS on platinum doublet (< 6 months vs ≥ 6 months). B Pathway enrichment analyses of the top pathways altered by platinum doublet PFS (< 6 months vs ≥ 6 months) in PDXs. C Heatmap of gene expression of PDX samples for top genes altered between OS (< 2 years vs ≥ 2 years). D Pathway enrichment analyses of the top pathways altered between OS (< 2 years vs ≥ 2 years)

Fig. 5

Gene expression changes in mesothelioma PDX models grouped by platinum/pemetrexed exposure at the time of PDX sample collection and OncoCast-DPM risk score. A Heatmap of gene expression of PDX samples for top genes altered by exposure to platinum/pemetrexed at the time of PDX sample collection. B Pathway enrichment analyses of the top pathways altered by exposure to platinum/pemetrexed vs untreated at the time of PDX sample collection. C Heatmap of gene expression of PDX samples for top 50 genes altered between OncoCast-MPM high vs low risk groups. D Pathway enrichment analyses of the top pathways altered between OncoCast-MPM high vs low risk