Homozygous deletion of CDKN2A by fluorescence in situ hybridization is prognostic in grade 4, but not grade 2 or 3, IDH-mutant astrocytomas

Daniel F Marker,Thomas M Pearce

doi:10.1186/s40478-020-01044-y

Daniel F Marker, Thomas M Pearce

Open Access

https://doi.org/10.1186/s40478-020-01044-y

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Abstract

IDH-mutant astrocytomas have a more indolent natural history and better prognosis than their IDH-wild type counterparts, but are still graded according to schemes developed prior to the recognition of this type of neoplasm as a distinct entity. Homozygous deletion of CDKN2A has been proposed as a molecular correlate of aggressive behavior in these tumors, and may be incorporated into future grading systems in an effort to improve prognostic stratification. Fluorescence in situ hybridization (FISH) is a common ancillary testing modality used to assess CDKN2A status, but the specifics of how to best interpret FISH results for prognostication of gliomas have not been clearly defined in the literature. To address this issue, we performed a retrospective analysis of prospectively collected CDKN2A FISH data from 108 primary and 43 recurrent IDH-mutant astrocytomas diagnosed between 2007–2020 at the University of Pittsburgh Medical Center. High level CDKN2A homozygous deletion was rare in primary tumors and was identified more frequently in recurrent tumors. Multivariate Cox Proportional-Hazards analysis demonstrated that histologic grade and CDKN2A status are independent predictors of survival, and the prognostic value of CDKN2A is maximized by applying a threshold of ≥ 30% of tumor cells with homozygous deletion by FISH to define a positive result. At this threshold, CDKN2A deletion significantly stratified survival of histologic grade 4 tumors, but grade 2 and 3 tumors rarely exceeded this cutoff value and did not show worse survival. Lower thresholds identified additional lower grade tumors, but were not prognostically useful. Compared to prior studies, the lack of prognostic significance of CDKN2A homozygous deletion by FISH in grade 2–3 IDH-mutant astrocytomas may reflect differences in cohort populations or technical differences between testing modalities. Definitive criteria for determining CDKN2A homozygous deletion by various methodologies will be critical if this is to be included in future grading schemes.

Highlights

Incorporation of somatic molecular alterations into the classification and grading of brain tumors continues to drive an ongoing revolution in the field of neuro-oncology
High percentage homozygous CDKN2A deletion is a rare event in primary IDHm astrocytomas, but is more frequent in recurrent tumors As a first step, we looked for evidence of a natural cutpoint to distinguish tumors with intact CDKN2A from those with homozygous deletion, as would be seen if the percentage of cells with homozygous deletion followed a bimodal distribution
Tumors of histologic grade 4 were over-represented in the tail of the distribution, confirming a relationship between CDKN2A status and aggressive tumor behavior, but no intuitively obvious cutoff value emerged from this analysis

Summary

Introduction

Incorporation of somatic molecular alterations into the classification and grading of brain tumors continues to drive an ongoing revolution in the field of neuro-oncology. Some of the morphologic features used to grade IDHwt tumors do a poor job of stratifying IDHm astrocytoma survival, mitotic activity [2,3,4]. To address these shortcomings, a number of groups have investigated molecular correlates of aggressive behavior in IDHm astrocytomas [5,6,7,8,9,10,11]. Homozygous deletion of the CDKN2A gene, which encodes the cell-cycle regulators p16INK4A and p14ARF, has emerged as a leading candidate molecular marker of high-grade behavior in these tumors [3, 7, 10,11,12]

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