Acta Neuropathol. 2022 Oct 22.
Patrick J Cimino,
Courtney Ketchum,
Rust Turakulov,
Omkar Singh,
Zied Abdullaev,
Caterina Giannini,
Peter Pytel,
Giselle Yvette Lopez,
Howard Colman,
MacLean P Nasrallah,
Mariarita Santi,
Igor Lima Fernandes,
Jeff Nirschl,
Sonika Dahiya,
Stewart Neill,
David Solomon,
Eilis Perez,
David Capper,
Haresh Mani,
Dario Caccamo,
Matthew Ball,
Michael Badruddoja,
Rati Chkheidze,
Sandra Camelo-Piragua,
Joseph Fullmer,
Sanda Alexandrescu,
Gabrielle Yeaney,
Charles Eberhart,
Maria Martinez-Lage,
Jie Chen,
Leor Zach,
B K Kleinschmidt-DeMasters,
Marco Hefti,
Maria-Beatriz Lopes,
Nicholas Nuechterlein,
Craig Horbinski,
Fausto J Rodriguez,
Martha Quezado,
Drew Pratt,
Kenneth Aldape.
High-grade astrocytoma with piloid features (HGAP) is a recently recognized glioma type whose classification is dependent on its global epigenetic signature. HGAP is characterized by alterations in the mitogen-activated protein kinase (MAPK) pathway, often co-occurring with CDKN2A/B homozygous deletion and/or ATRX mutation. Experience with HGAP is limited and to better understand this tumor type, we evaluated an expanded cohort of patients (n = 144) with these tumors, as defined by DNA methylation array testing, with a subset additionally evaluated by next-generation sequencing (NGS). Among evaluable cases, we confirmed the high prevalence CDKN2A/B homozygous deletion, and/or ATRX mutations/loss in this tumor type, along with a subset showing NF1 alterations. Five of 93 (5.4%) cases sequenced harbored TP53 mutations and RNA fusion analysis identified a single tumor containing an NTRK2 gene fusion, neither of which have been previously reported in HGAP. Clustering analysis revealed the presence of three distinct HGAP subtypes (or groups = g) based on whole-genome DNA methylation patterns, which we provisionally designated as gNF1 (n = 18), g1 (n = 72), and g2 (n = 54) (median ages 43.5 years, 47 years, and 32 years, respectively). Subtype gNF1 is notable for enrichment with patients with Neurofibromatosis Type 1 (33.3%, p = 0.0008), confinement to the posterior fossa, hypermethylation in the NF1 enhancer region, a trend towards decreased progression-free survival (p = 0.0579), RNA processing pathway dysregulation, and elevated non-neoplastic glia and neuron cell content (p < 0.0001 and p < 0.0001, respectively). Overall, our expanded cohort broadens the genetic, epigenetic, and clinical phenotype of HGAP and provides evidence for distinct epigenetic subtypes in this tumor type.
Keywords: DNA Methylation; HGAP; High-grade astrocytoma with piloid features; NF1; Neurofibromatosis type 1