Molecular and clonal evolution in recurrent metastatic gliosarcoma

Abstract

We discuss the molecular evolution of gliosarcoma, a mesenchymal type of glioblastoma (GBM), using the case of a 37-yr-old woman who developed two recurrences and an extracranial metastasis. She was initially diagnosed with isocitrate dehydrogenase (IDH) wild-type gliosarcoma in the frontal lobe and treated with surgery followed by concurrent radiotherapy with temozolomide. Five months later the tumor recurred in the left frontal lobe, outside the initially resected area, and was treated with further surgery and radiotherapy. Six months later the patient developed a second left frontal recurrence and was again treated with surgery and radiotherapy. Six weeks later, further recurrence was observed in the brain and bone, and biopsy confirmed metastases in the pelvic bones. To understand the clonal relationships between the four tumor instances and the origin of metastasis, we performed whole-genome sequencing of the intracranial tumors and the tumor located in the right iliac bone. We compared their mutational and copy-number profiles and inferred the clonal phylogeny. The tumors harbored shared alterations in GBM driver genes, including mutations in TP53, NF1, and RB1, and CDKN2A deletion. Whole-genome doubling was identified in the first recurrence and the extracranial metastasis. Comparisons of the metastatic to intracranial tumors highlighted a high similarity in molecular profile but contrasting evidence regarding the origin of the metastasis. Subclonal reconstruction suggested a parallel evolution of the recurrent tumors, and that the metastatic tumor was largely derived from the first recurrence. We conclude that metastasis in glioma can be a late event in tumorigenesis.

Keywords: IDH; glioblastoma; glioma; neoplasm of the nervous system.

Figure 1.

Clinical presentation of metastatic gliosarcoma. (A–C) Magnetic resonance imaging (MRI) of initial tumor diagnosis for the primary (P), first recurrent (R1), and second recurrent (R2) tumors, respectively. (D) Computed tomography (CT) scan of initial diagnosis of metastatic (M) tumor. (E–H) Hematoxylin and eosin stain of biopsy specimens from tumors P, R1, R2, and M, respectively. (I) Timeline of patient diagnoses and treatments. Sample designations are denoted in parentheses after the procedure they were collected from. (GTR) Gross tumor resection, (RT) radiotherapy, (TMZ) temozolomide.

Figure 2.

Comparative distribution of alterations among primary and recurrent tumors. (A) Upset plot of somatic mutations present in tumor samples. (B) Heatmap of mutations and focal copy-number alterations in glioma driver genes. An asterisk denotes mutation detection with insufficient coverage.

Figure 3.

Mutational signature profiles of primary and recurrent tumors. (A) Barplot of the relative contribution of COSMIC signatures derived from all mutations. (B) Heatmap of pairwise cosine similarity of mutational signatures derived from all mutations. The size of the circle correlates with the total number of mutations present in the tumor pairs, and the circle color correlates with the cosine similarity value for the given tumor pair. (C) Barplot of the relative contribution of COSMIC signatures derived from mutations private to a single sample.

Figure 4.

Copy-number alterations in primary and recurrent tumors. (A) Copy-number profiles of tumor samples as estimated by Sequenza. Copy number is reported as depth ratio, in which a depth ratio of 1 corresponds to a total copy-number equal to the tumor ploidy. Sequenza estimates of tumor ploidy were 1.9, 2.8, 2.3, and 2.5 for tumors P, R1, R2, and M, respectively. (B) Pairwise comparisons of arm-level aneuploidy scores, as calculated by the Taylor et al. method (Taylor et al. 2018). A given chromosome arm was considered aneuploid if ≥80% was altered in the same direction. Chromosome arms were given a score of +1 for copy-number gain, −1 for copy-number loss, and 0 otherwise. For each subpanel, the tumor with the earliest diagnosis of the pair is on the left. Spearman's correlation coefficient was calculated for the aneuploidy scores of each tumor pair and is reported above each subfigure. The aneuploid genome fraction was calculated by summing the length of all altered chromosome arms and dividing by the length of the genome.

Figure 5.

Subclonal composition of primary and recurrent tumors. Phylogenetic tree inferred by PhyloWGS from copy-number, somatic variant, and tumor purity data for patient primary (P) and recurrent (R1, R2, M) samples. Clonal evolution progresses from top to bottom, with each row representing a clonal generation. Each numbered node corresponds to a set of acquired mutations, which represents a tumor clone. Acquired mutations on driver genes are annotated on tree branches. Colored squares within each node denote samples for which the clone cancer cell fraction (CCF) is >0.1. Sample clone CCFs are depicted to the right of each generation. The thickness of the points correspond to the number of single-nucleotide variants (SNVs) comprising a given clone.