Genetic, Epigenetic, and Immunologic Profiling of MMR-Deficient Relapsed Glioblastoma

• Published in: Clinical cancer research 2019-03, Vol.25 (6), p.1828-1837
• Main Authors: Indraccolo, Stefano, Lombardi, Giuseppe, Fassan, Matteo, Pasqualini, Lorenza, Giunco, Silvia, Marcato, Raffaella, Gasparini, Alessandra, Candiotto, Cinzia, Nalio, Silvia, Fiduccia, Pasquale, Fanelli, Giuseppe Nicolò, Pambuku, Ardi, Della Puppa, Alessandro, D'Avella, Domenico, Bonaldi, Laura, Gardiman, Marina Paola, Bertorelle, Roberta, De Rossi, Anita, Zagonel, Vittorina
• Format: Article
• Language: English
• Subjects: Biomarkers, Tumor - genetics; Biomarkers, Tumor - immunology; Brain - pathology; Brain - surgery; Brain Neoplasms - genetics; Brain Neoplasms - immunology; Brain Neoplasms - pathology; Brain Neoplasms - therapy; Chemoradiotherapy, Adjuvant; DNA Methylation; DNA Mismatch Repair; Epigenesis, Genetic; Female; Gene Expression Profiling; Genes, MHC Class I - genetics; Glioblastoma - genetics; Glioblastoma - immunology; Glioblastoma - mortality; Glioblastoma - therapy; Histocompatibility Antigens Class I - genetics; Histocompatibility Antigens Class I - metabolism; Humans; Male; Middle Aged; Mutation; Neoplasm Recurrence, Local - genetics; Neoplasm Recurrence, Local - immunology; Neoplasm Recurrence, Local - mortality; Neoplasm Recurrence, Local - surgery; Progression-Free Survival; Retrospective Studies; Telomere Homeostasis - genetics; Tumor Microenvironment - genetics; Tumor Microenvironment - immunology; Whole Exome Sequencing
• ISSN: 1078-0432; 1557-3265
• DOI: 10.1158/1078-0432.ccr-18-1892

In-depth characterization of recurrent glioblastoma (rGBM) might contribute to a better understanding of the mechanisms behind tumor progression and enable rGBM treatment with targeted drugs. In this study, GBM samples were collected at diagnosis and recurrence from adult patients treated with Stupp protocol. Expression of mismatch repair (MMR) proteins was evaluated by IHC, followed by whole exome sequencing (WES) of tumor samples showing loss of MSH6 reactivity. Established genetic, epigenetic, and immunologic markers were assessed by standard methods and correlated with loss of MMR proteins and patient survival. Expression of MMR proteins was partially or completely lost in 25.9% rGBM samples. Specifically, 12 samples showed partial or total MSH6 expression reduction. Conversely, 96.4% of GBM samples at diagnosis expressed MMR markers. WES disclosed lack of variants in MMR genes in primary samples, whereas two MSH6-negative rGBM samples shared a c.3438+1G>A* splicing variant with a potential loss of function effect. MSH6-negative rGBM specimens had high tumor mutational burden (TMB), but no microsatellite instability. In contrast, GBM samples with partial loss of MMR proteins disclosed low TMB. MMR-deficient rGBM showed significant telomere shortening and MGMT methylation and are characterized by highly heterogeneous MHC class I expression. Multilevel profiling of MMR-deficient rGBM uncovered hypermutated genotype uncoupled from enriched expression of immune-related markers. Assessment of MHC class I expression and TMB should be included in protocols aiming to identify rGBM patients potentially eligible for treatment with drugs targeting immune-checkpoint inhibitors.