4.1 Pathology
The tumor had sheets of atypical cells separated by thick fibrous septae
(Fig. 2A,B). Rare areas of clear cell change were identified (Fig. 2C).
Mitotic activity was prominent. Geographic necrosis, apoptotic debris,
dystrophic calcifications, foci of hemorrhage and hemosiderin deposition
were present. Immunohistochemistry was consistent with the diagnosis
(Fig 2D). Electron microscopy demonstrated primitive intracellular
junctions and rare foci of basal lamina formation, suggesting an element
of epithelial differentiation. Rare primary cilia and abundant
flocculent extracellular material were identified. A Nanostring-based
fusion panel assay identified the YWHAE:NUTM2B fusion.
Molecular
WGTA data revealed somatic alterations in the tumour genome. Whole
genome mutation burden was low at 0.4 mutations/million bases. Somatic
copy number changes were found in a focal region of chromosome 17 and
part of chromosome 10 long arm (Fig. 2E). WGTA data revealed 46
structural variants, including a t(10;17)(q22;p13) translocation
resulting in fusion between exon 5 of YWHAE and exon 2 ofNUTM2B (Fig. 2F). No relevant cancer predisposition germline
findings from 98 reviewed predisposition genes were reported, suggesting
this tumor was a sporadic event, and YWHAE:NUTM2B fusion was likely a
driver.
RNA-seq data revealed multiple expression aberrations indicated from
high expression percentile and overexpression when compared to the
TARGET CCSK cohort (TARGET_CCSK), and GTEx normal tissues
(GTEx_average), respectively. High outlier expression percentile and
overexpression pathways comprised receptor tyrosine kinases (RTKs)
including NTRK3 , RET and KIT , and IGF signaling
genes, namely IGF2 and IGF1R . Genes in MAPK and PI3K/mTor
pathway, NRAS, BRAF, MAPK1, AKT1 and mTOR, showed high
expression percentile compared to TARGET_CCSK. SHH, SMO,
GLI1/2/3, transcription factors of SHH pathway and HES4 from
NOTCH pathway demonstrated high expression percentile and
overexpression. WGTA demonstrated high outlier expression percentile of
cell cycle regulators in phases G1, S and M, indicating heavy
dysregulation: CCND1 , CCND2 , CDK6 , CCNE2 ,CCNA2 , CCNB1 and CDK1 .
BCOR was overexpressed compared to GTEx_average. When compared
to Personalized OncoGenomics (POG) Programs and TCGA sarcomas,BCOR was in the 100th percentile; however,BCOR showed average expression within TARGET CCSK cases, likely
due to it being generally overexpressed in CCSK with either mutually
exclusive changes, YWHAE:NUT2MB fusion or BCOR internal
duplications.11
EZH2 , a gene part of polycomb repressive complex 2, had
overexpression and high outlier percentile when compared to
GTEx_average. TERC and TERT telomerases both showed high
expression percentile and overexpression.
Discussion
Three other cases of YWHAE:NUTM2B fusion in URCS of infancy are
reported, and all were aggressive tumors unresponsive to conventional
chemotherapy.8,9 Our case demonstrated similar
clinical and pathological features.8 As such, this
infant was enrolled into the POG trial (NCT02155621) to describe the
molecular landscape and identify any therapeutically actionable variants
not discovered during routine work up. Targeted therapy was not pursued
due to rapid clinical decline.
Based on WGTA there was limited evidence to support a targeted approach
as most alterations were based on increased RNA expression data. We
found mTOR transcription factors were overexpressed with high outlier
expression profile. Previous literature and experience have clinically
targeted mTOR in pediatric vascular tumors due to administration ease
and limited side effects. Use of mTOR inhibitors had previously reduced
tumor growth both in vivo and in vitro in infantile
hemangiomas and angiosarcomas.12,13 mTOR inhibitors
are also proven efficacious in children with Kaposiform
hemangioendothelioma, where loss of tumor suppressors PTEN and TSC2
leads to abnormally activated mTOR pathway and mTOR-inhibited suppressed
tumor growth.14–17 An mTOR inhibitor could have been
an option in this infant and might be considered in future URCS cases.
The unique YWHAE fusion encodes a 14-3-3-ε protein which interacts with
CDC25 phosphatases, RAF1, and IRS1, suggesting its role in diverse
biochemical activities related to signal transduction (cell division and
insulin sensitivity regulation). Since IGF2 had high outlier
expression in this tumor and correlated with VEGF2 expression in
infantile hemangioma, off-label use of a commercially available IGF-2
inhibitor with pediatric dosing, was considered.18–22Other targets included CDK4/CDK6 inhibitors due to increased expression
of CCND1/CyclinD1 and RTK inhibitors due to high outlier
expression percentile for NTRK3 , RET , and KIT .NTRK3 overexpression is reported in undifferentiated sarcomas
with YWHAE/BCOR genetic modifications but may be a less
efficacious target in a setting of exclusive changes in RNA
expression.6,23–28
Other possibilities with very low level of evidence based on RNA
expression data included targeting EZH2 ; TERT , which
showed increased expression in CCSK; and TERC inhibition in
clinical trials, reporting varied results in myelofibrosis, lung and
breast cancer, and lymphoproliferative disorders (NCT02598661),
(NCT01731951).29–33
Overall, a strongly supported targetable pathway was not identified in
this infant’s tumor, but we described more precisely the genomic profile
of this entity allowing better understanding of the underlying molecular
changes and reinforcing the value of a detailed oncogenomic approach to
confirm conventional cytogenetic findings, detect additional genetic
abnormalities, and suggest alternative therapeutic strategies. Further
clinical and genomic studies are needed to understand how the
YWHAE:NUTM2B fusion drives tumorigenesis and to develop more effective
treatments.