Characterizing temporal genomic heterogeneity in pediatric low-grade gliomas

Abstract

Recent discoveries have provided valuable insight into the genomic landscape of pediatric low-grade gliomas (LGGs) at diagnosis, facilitating molecularly targeted treatment. However, little is known about their temporal and therapy-related genomic heterogeneity. An adequate understanding of the evolution of pediatric LGGs' genomic profiles over time is critically important in guiding decisions about targeted therapeutics and diagnostic biopsy at recurrence. Fluorescence in situ hybridization, mutation-specific immunohistochemistry, and/or targeted sequencing were performed on paired tumor samples from primary diagnostic and subsequent surgeries. Ninety-four tumor samples from 45 patients (41 with two specimens, four with three specimens) from three institutions underwent testing. Conservation of BRAF fusion, BRAF^V600E mutation, and FGFR1 rearrangement status was observed in 100%, 98%, and 96% of paired specimens, respectively. No loss or gain of IDH1 mutations or NTRK2, MYB, or MYBL1 rearrangements were detected over time. Histologic diagnosis remained the same in all tumors, with no acquired H3K27M mutations or malignant transformation. Changes in CDKN2A deletion status at recurrence occurred in 11 patients (42%), with acquisition of hemizygous CDKN2A deletion in seven and loss in four. Shorter time to progression and shorter time to subsequent surgery were observed among patients with acquired CDKN2A deletions compared to patients without acquisition of this alteration [median time to progression: 5.5 versus 16.0 months (p = 0.048); median time to next surgery: 17.0 months versus 29.0 months (p = 0.031)]. Most targetable genetic aberrations in pediatric LGGs, including BRAF alterations, are conserved at recurrence and following chemotherapy or irradiation. However, changes in CDKN2A deletion status over time were demonstrated. Acquisition of CDKN2A deletion may define a higher risk subgroup of pediatric LGGs with a poorer prognosis. Given the potential for targeted therapies for tumors harboring CDKN2A deletions, biopsy at recurrence may be indicated in certain patients, especially those with rapid progression.

Keywords: BRAF; CDKN2A; Genomics; Paired; Pediatric low-grade gliomas; Recurrence; Tumor evolution.

Fig. 1

Genomic profiles of paired primary and recurrent and/or progressive tumor samples from 45 pediatric patients with LGGs analyzed in this study, grouped by histopathologic classification. Patients’ age (years), sex, tumor location, treatment received between primary and subsequent surgeries (systemic therapy [“S”], irradiation [“I”], or both [“B”]), and time interval (months) between respective surgeries are indicated. Each row of circles represents a tumor pair (or triplet) from an individual patient. The left half of a circle represents the primary diagnostic tumor sample, the right half represents the second subsequent surgical sample, and a third semicircle (with *) represents a third surgical sample if applicable. Dark blue, dark gray, and light blue semi-circles indicate positivity, negativity, or testing not able to be performed for the given genetic alteration, respectively

Fig. 2

Histologic and molecular findings in paired samples from representative patients. a The pilocytic astrocytoma from Patient #18 retained a BRAF fusion. Note that the partial duplication of 3′BRAF (7q34) b is most commonly associated with the BRAF-KIAA1549 fusion product. c The ganglioglioma from Patient #40 retained a BRAF^V600E mutation (d BRAF V600E IHC, 400x). e The pilocytic astrocytoma from Patient #2 acquired a hemizygous deletion (loss of one copy) of CDKN2A (f), while the diffuse astrocytoma (g) from Patient #33 lost this alteration (h). (2A, E, and G, H&E x100; 2C, x200)

Fig. 3

Kaplan Meier curves illustrating associations between temporal CDKN2A deletion status and time to progression (a, c, e) or time to next surgery (b, d, f) among patients who had CDKN2A deletion testing performed on paired tumor specimens. Shown are comparisons between patients whose tumors acquired CDKN2A deletions versus patients whose tumors did not acquire this genetic alteration (a, b), versus patients whose tumors had conserved CDKN2A deletions from diagnosis (c, d), and versus patients whose tumors lost CDKN2A deletions (e, f)