Optical genome mapping identifies a novel pediatric embryonal tumor with a ZNF532::NUTM1 fusion

Abstract

The molecular characteristics of pediatric brain tumors have not only allowed for tumor subgrouping but have led to the introduction of novel treatment options for patients with specific tumor alterations. Therefore, an accurate histologic and molecular diagnosis is critical for optimized management of all pediatric patients with brain tumors, including central nervous system embryonal tumors. We present a case where optical genome mapping identified a ZNF532::NUTM1 fusion in a patient with a unique tumor best characterized histologically as a central nervous system embryonal tumor with rhabdoid features. Additional analyses including immunohistochemistry for NUT protein, methylation array, whole genome, and RNA-sequencing was done to confirm the presence of the fusion in the tumor. This is the first description of a pediatric patient with a ZNF532::NUTM1 fusion, yet the histology of this tumor is similar to that of adult cancers with ZNF::NUTM1 fusions reported in the literature. Although rare, the distinct pathology and underlying molecular characteristics of the ZNF532::NUTM1 tumor separates this from other embryonal tumors. Therefore, screening for this or similar NUTM1 rearrangements should be considered for all patients with unclassified central nervous system tumors with rhabdoid features to ensure accurate diagnosis. Ultimately, with additional cases, we may be able to better inform therapeutic management for these patients. © 2023 The Pathological Society of Great Britain and Ireland.

Keywords: ZNF532::NUTM1; brain tumor; embryonal; optical genome mapping; pediatric.

Figure 1.. MRI and IHC images.

(A) Axial T2+contrast and (B) coronal T1+ contrast MRI imaging showed an enhancing supra-insular/inferior parietal mixed cystic/nodular neoplasm. (C) The lesion was completely removed by surgical resection. (D) H&E staining revealed a high-grade tumor organized in sheets (purple) with areas of necrosis (pale pink) (scale bar, 0.5 mm). (E,F) The undifferentiated tumor cells had an embryonal morphology and scattered larger cells with a vague (E) rhabdoid or (F) epithelioid morphology. Arrow in insets indicate (E) an epithelioid-like cell and (F) a rhabdoid cell with indented nucleus; scale bar, 0.05 mm). (G) Mitotic figures were abundant (arrow heads, arrow in inset indicates an example of a mitotic figure; scale bar, 0.05 mm). Ki-67 proliferative index was more than 90% (H; scale bar, 0.05 mm). (I) INI1 was retained as seen using IHC (scale bar, 0.05 mm). (J) BRG1 was retained as seen using IHC (scale bar, 0.05 mm). (K) A NUT antibody IHC (NeoGenomics) gave strong nuclear staining for NUT protein (scale bar, 0.1 mm).

Figure 2.. A ZNF532::NUTM1 fusion identified by optical genome mapping and confirmed by short-read sequencing.

(A) OGM genome browser view of the identified fusion. Top: in silico G-band staining of chromosome 18, followed by copy number and structural variant tracks. The green line and adjacent purple dots indicate the location of the insertion and corresponding breakpoints aligning to chromosome 15. The reference chromosomes 18 and 15 are shown in blue, with black vertical lines showing the DLE1 (Direct Labeling Enzyme 1) label locations. The assembled sample map is displayed in yellow, the red labels in the middle do not have alignment to chromosome 18, instead they align to chromosome 15. The total insertion size from chromosome 15 to 18 is approximately 200 kb. The left breakpoint on both chromosomes is magnified to show annotations for ZNF532 and NUTM1 genes, approximate breakpoint location and exons fused to exons. (B) Short-read sequencing alignments to the breakpoint location indicated by OGM. Read-pairs maps to two different chromosomes (chr18 and chr15), to confirm the identified translocation between an intron near the gene ZNF532 and exon 3 of the NUTM1 gene, respectively. (C) RNA-sequencing alignments also confirm the exon–exon fusion between ZNF532 (exon 7) and NUTM1 (exon 3). The split reads are designated using color, with part of the reads mapping to exon 7 of chromosome 18 and other part mapping to exon 3, chromosome 15. The red dotted lines differentiate the 2 chromosomes.

Figure 3.. NUTM1 fusion tumors.

(A) Oncoplot showing a summary of cancers with ZNF::NUTM1 fusions. (B) Kaplan–Meier curve showing overall survival of patients with brain tumors harboring NUTM1 rearrangements (red line) and ZNF::NUTM1 cancers (blue line).