The genetic landscape of anaplastic pleomorphic xanthoastrocytoma

Abstract

Pleomorphic xanthoastrocytoma (PXA) is an astrocytic neoplasm that is typically well circumscribed and can have a relatively favorable prognosis. Tumor progression to anaplastic PXA (WHO grade III), however, is associated with a more aggressive biologic behavior and worse prognosis. The factors that drive anaplastic progression are largely unknown. We performed comprehensive genomic profiling on a set of 23 PXAs from 19 patients, including 15 with anaplastic PXA. Four patients had tumor tissue from multiple recurrences, including two with anaplastic progression. We find that PXAs are genetically defined by the combination of CDKN2A biallelic inactivation and RAF alterations that were present in all 19 cases, most commonly as CDKN2A homozygous deletion and BRAF p.V600E mutation but also occasionally BRAF or RAF1 fusions or other rearrangements. The third most commonly altered gene in anaplastic PXA was TERT, with 47% (7/15) harboring TERT alterations, either gene amplification (n = 2) or promoter hotspot mutation (n = 5). In tumor pairs analyzed before and after anaplastic progression, two had increased copy number alterations and one had TERT promoter mutation at recurrence. Less commonly altered genes included TP53, BCOR, BCORL1, ARID1A, ATRX, PTEN, and BCL6. All PXA in this cohort were IDH and histone H3 wildtype, and did not contain alterations in EGFR. Genetic profiling performed on six regions from the same tumor identified intratumoral genomic heterogeneity, likely reflecting clonal evolution during tumor progression. Overall, anaplastic PXA is characterized by the combination of CDKN2A biallelic inactivation and oncogenic RAF kinase signaling as well as a relatively small number of additional genetic alterations, with the most common being TERT amplification or promoter mutation. These data define a distinct molecular profile for PXA and suggest additional genetic alterations, including TERT, may be associated with anaplastic progression.

Keywords: TERT promoter mutations; anaplastic PXA; glioma progression; intratumoral heterogeneity; pediatric glioma.

Figure 1

Clinical and genomic landscape of anaplastic pleomorphic xanthoastrocytoma (PXA). Clinical and genomic features of 15 anaplastic PXA (left) and 4 PXA (right). Tumors are arranged by age from young to old (from left to right) within each tumor grade and the percent of anaplastic tumors with the alteration are noted on the right for BRAF,RAF1,CDKN2A/B, and TERT. Progression‐free survival (PFS) and overall survival (OS) from the time of initial diagnosis and the patient status at last follow‐up are indicated.

Figure 2

Histologic features of anaplastic pleomorphic xanthoastrocytoma (PXA). Characteristic features of PXA, WHO grade II (left column), including pleomorphic, spindled, or focal epithelioid neoplastic cells with astrocytic morphology, pericellular reticulin, primarily solid, non‐infiltrative growth pattern highlighted by lack of neurofilament, and relatively low to moderate proliferation (mean mitotic index <1 mitosis per 10 high power fields, n = 4) Anaplastic PXA, WHO grade III (right column), shares many features with PXA but, in addition, areas can lack pericellular reticulin, exhibit infiltrative growth (entrapped axons highlighted by neurofilament, right image), and increased proliferation (mean mitotic index 14.4 mitoses per 10 high power fields, n = 15). Scale bar, 30 μm.

Figure 3

Comparison of clinical and genomic features of initial and recurrent tumor pairs. Summary of clinical and genomic tumor features from four patients with matched tumor tissue available from initial resection and subsequent recurrence (PXA#3, 6, 7) and from two different tumor recurrences (PXA#8) demonstrating changes in both single nucleotide variants and copy number alterations over time. After PXA # the i, denotes initial; r, denotes recurrent; and 1 or 2 denotes first or second recurrence. PXA#3i, 6i, 7r, and 8r² are also included in Figure 1.

Figure 4

Intratumoral heterogeneity in anaplastic anaplastic pleomorphic xanthoastrocytoma (PXA). (a) Multiple distinct anatomic regions of PXA#4 were sampled and denoted A‐F. These included A—anterior‐inferior tip of mass, B—medial‐inferior mass, C and D—adjacent central regions, E—lateral‐posterior mass, and F—superior‐lateral mass involving insular cortex. (b) Representative images from anatomically distinct regions (A, B, E, and F, from top to bottom) demonstrate mild to moderate variation in histologic appearance and Ki‐67 labeling index. As regions C, D, and E were similar, representative images from region E are shown. Scale bar, 30 μm. (c) Copy number alterations compared between different regions demonstrate tumor heterogeneity. Uniform homozygous deletion of CDKN2A at chromosome 9p21 across regional tumor samples compared to representative normal germline (N). In contrast, there is a focal loss of interstitial chromosome 6q only in a subset of regions, (C, D, E). The color vertical line indicates the CDKN2A genomic position (left) and color shading indicate region of loss on chromosome 6q (right). Samples have been grouped based on the presence (regions C, D, and E) or absence (regions A, F, and B) of the focal loss of interstitial chromosome 6q.