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Combined proteomics and miRNomics of a glioblastoma immunotherapy cohort reveal resistance factor candidates and potential counterstrategies

ABSTRACT: Glioblastoma is the most prevalent and aggressive brain cancer. With a median overall survival of ~15-20 months under standard therapy, novel treatment approaches are desperately needed. A recent phase II clinical trial with a personalized immunotherapy based on tumor lysate-charged dendritic cells (DCs), however, failed to prolong survival. Here, we investigated tumor tissue from patients from this trial to explore glioblastoma (immuno)resistancesurvival-related factors. and strategies to overcome them. We followed an innovative approach of combining mass spectrometry-based quantitative proteomics (n=36) with microRNA sequencing plus RT-qPCR (n=38). Protein quantification identified e.g. huntingtin interacting protein 1 (HIP1), retinol binding protein 1 (RBPP1), ferritin heavy chain (FTH1) and focal adhesion kinase 2 (FAK2) as resistance factor candidates. MicroRNA analysis identified miR-216b, miR-216a, miR-708 and let-7i as molecules potentially associated with overcoming resistancefavourable tissue characteristics as they were enriched in patients with a comparably longer survival. In silico target prediction and subsequent analyses indicated focal adhesion as a pathway of interest. Taken together, we here mapped possible drivers of glioblastoma outcome under immunotherapy’s (immuno)resistance in one of the largest DC vaccination tissue analysis cohorts so far – demonstrating usefulness and feasibility of combined proteomics/miRNomics approaches. Future research should investigate agents that sensitize glioblastoma to (immuno)therapy – potentially building on insights generated here.

OTHER RELATED OMICS DATASETS IN: PXD012616

ORGANISM(S): Homo sapiens

PROVIDER: GSE132554 | GEO | 2020/01/27

REPOSITORIES: GEO

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Project description:Background: Patients with glioblastoma (GBM) have a dramatically poor prognosis. The recent REGOMA trial suggested an overall survival benefit of regorafenib in recurrent GBM patients. Considering the extreme genetic heterogeneity of GBMs, we aimed to identify molecular biomarkers predictive of differential response to the drug. The study provides evidence that a signature based on the expression of five biomarkers could help identifying a subgroup of GBM patients exhibiting a striking survival advantage when treated with regorafenib. Despite the presented results must be confirmed in larger replication cohorts, the study highlights potential biomarker options to help guiding the clinical decision among regorafenib and other treatments in patients with relapsing GBM. Methods.Total RNA was extracted from tumor samples of patients enrolled in the REGOMA trial. Genome-wide transcriptome and miRNA profiles were associated with patients' Overall Survival (OS) and Progression Free Survival (PFS). Results. At first step, a set of 11 gene transcripts (HIF1A, CTSK, SLC2A1, KLHL12, CDKN1A, CA12, WDR1, CD53, CBR4, NIFK-AS1, RAB30-DT) and 10 miRNAs (miR-93-5p, miR-203a-3p, miR-17-5p, let-7c-3p, miR-101-3p, miR-3607-3p, miR-6516-3p, miR-301a-3p, miR-23b-3p, miR-222-3p) was filtered by comparing survival between regorafenib and lomustine arms. As second step, a minisignature of two gene transcripts (HIF1A, CDKN1A) and three miRNAs (miR-3607-3p, miR-301a-3p, miR-93-5p) identified a subgroup of patients showing prolonged survival after regorafenib administration (median OS range 10.6 - 20.8 months). Conclusions. The study provides evidence that a signature based on the expression of five biomarkers could help identifying a subgroup of GBM patients exhibiting a striking survival advantage when treated with regorafenib. Despite the presented results must be confirmed in larger replication cohorts, the study highlights potential biomarker options to help guiding the clinical decision among regorafenib and other treatments in patients with relapsing GBM.

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Combined proteomics and miRNomics of a glioblastoma immunotherapy cohort reveal resistance factor candidates and potential counterstrategies

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