Immunogenomics of Hypermutated Glioblastoma: A Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy

Abstract

We present the case of a patient with a left frontal glioblastoma with primitive neuroectodermal tumor features and hypermutated genotype in the setting of a POLE germline alteration. During standard-of-care chemoradiation, the patient developed a cervical spine metastasis and was subsequently treated with pembrolizumab. Shortly thereafter, the patient developed an additional metastatic spinal lesion. Using whole-exome DNA sequencing and clonal analysis, we report changes in the subclonal architecture throughout treatment. Furthermore, a persistently high neoantigen load was observed within all tumors. Interestingly, following initiation of pembrolizumab, brisk lymphocyte infiltration was observed in the subsequently resected metastatic spinal lesion and an objective radiographic response was noted in a progressive intracranial lesion, suggestive of active central nervous system (CNS) immunosurveillance following checkpoint blockade therapy.

Significance: It is unclear whether hypermutated glioblastomas are susceptible to checkpoint blockade in adults. Herein, we provide proof of principle that glioblastomas with DNA-repair defects treated with checkpoint blockade may result in CNS immune activation, leading to clinically and immunologically significant responses. These patients may represent a genomically stratified group for whom immunotherapy could be considered. Cancer Discov; 6(11); 1230-6. ©2016 AACR.See related commentary by Snyder and Wolchok, p. 1210This article is highlighted in the In This Issue feature, p. 1197.

Conflict of interest statement

The authors have no conflicts of interest to disclose.

©2016 American Association for Cancer Research.

Figures

Figure 1

Presentation and progression of glioblastoma with PNET features in an adult patient. A) A left frontoinsular enhancing tumor was identified at presentation and resected. Following concomitant temozolomide and radiation treatment, an intradural/extramedullary C7-T2 metastasis was identified and also resected. Following a course of Pembrolizumab, a second intradural/extramedullary metastasis at T7-8 was resected. All tumors were glioblastoma with PNET features. (B) Mutational burden as detected by whole exome DNA sequencing. Each tumor harbored between 9–11,000 non-synonymous mutations. (C) All tumors carried a nearly identical spectrum of mutations, with the majority C>G alterations. (D) Relative expression of MGMT by RNA-seq across each tumor.

Figure 2

Clonal evolution of a glioblastoma and two metastases. (A) Three-dimensional clustering of variant allele frequencies infers nine distinct clonal populations. Points represent individual single-nucleotide variants, and lines connect the median variant allele frequencies of each cluster. (B) Simplified view showing only subclones present in the primary tumor (left), the C7-T2 metastasis (center) and the T7-8 metastasis (right). (C) Nested view showing the origins of each subclone in the primary tumor (left), the C7-T2 metastasis (center) and the T7-8 metastasis (right).

Figure 3

Predicted neoantigen burden and response to checkpoint blockade treatment. (A) Defining immunologically-relevant mutations through successive filtering steps, resulting in only expressed missense mutations that are present in every cell of the tumors and are predicted to create neoantigens. (B) Coronal T1 post-contrast (top) and axial T2/FLAIR (bottom) brain MRI sequences at progression (left panel), 3 weeks after Pembrolizumab initiation (middle panel), and 13 weeks after Pembrolizumab treatment (right panel). On post-contrast images, the right frontal enhancing lesion (blue arrow) decreases in intensity following Pembrolizumab. Enhancement near the site of initial resection (red arrow) disappears. On the T2/FLAIR sequence, the right frontal horn lesion (white arrow) increases in intensity and then decreases. (C) mRNA expression of key immune response-related genes. (D) Tumor-infiltrating lymphocytes following Pembrolizumab treatment. The glioblastoma metastatic specimens before (top panel) and after (bottom panel) Pembrolizumab were stained with antibodies to CD3, CD4, and CD8.