Comprehensive profiling of mRNA splicing indicates that GC content signals altered cassette exon inclusion in Ewing sarcoma

ABSTRACT Ewing sarcoma (EwS) is a small round blue cell tumor and is the second most frequent pediatric bone cancer. 85% of EwS tumors express the fusion oncoprotein EWS-FLI1, the product of a t(11;22) reciprocal translocation. Prior work has indicated that transcription regulation alone does not fully describe the oncogenic capacity of EWS-FLI1, nor does it provide an effective means to stratify patient tumors. Research using EwS cell lines and patient samples has suggested that EWS-FLI1 also disrupts mRNA biogenesis. In this work we both describe the underlying characteristics of mRNA that are aberrantly spliced in EwS tumor samples as well as catalogue mRNA splicing events across other pediatric tumor types. Here, we also use short- and long-read sequencing to identify cis-factors that contribute to splicing profiles we observe in Ewing sarcoma. Our analysis suggests that GC content upstream of cassette exons is a defining factor of mRNA splicing in EwS. We also describe specific splicing events that discriminate EwS tumor samples from the assumed cell of origin, human mesenchymal stem cells derived from bone marrow (hMSC-BM). Finally, we identify specific splicing factors PCBP2, RBMX, and SRSF9 by motif enrichment and confirm findings from tumor samples in EwS cell lines.

CTNI-58. EFFICACY AND SAFETY OF LAROTRECTINIB IN ADULT AND PEDIATRIC PATIENTS WITH TROPOMYOSIN RECEPTOR KINASE (TRK) FUSION-POSITIVE PRIMARY CENTRAL NERVOUS SYSTEM (CNS) TUMORS

BACKGROUND NTRK gene fusions are oncogenic drivers in various CNS and non-CNS tumors. Larotrectinib is a first-in-class, highly selective TRK inhibitor approved for patients with TRK fusion cancer, with a 75% objective response rate (ORR) in 206 evaluable patients with various non-CNS cancers (Hong et al, ASCO 2021). We report data on patients with TRK fusion-positive primary CNS tumors. METHODS Patients with TRK fusion-positive primary CNS tumors in 2 clinical trials (NCT02637687, NCT02576431) were identified. Objective responses were investigator-assessed. RESULTS As of July 2020, 33 patients with TRK fusion-positive primary CNS tumors were identified (19 high-grade gliomas [HGG], 8 low-grade gliomas [LGG], 2 glioneuronal tumors, 2 neuroepithelial tumors, 1 CNS neuroblastoma, 1 small round blue cell tumor). Median age was 8.9 years (range 1.3-79.0). Patients were heavily pre-treated, with 45% having ≥ 2 prior systemic therapies. ORR was 30% (95% CI 16-49): 3 complete responses (all pediatric), 7 partial responses, 20 stable disease, and 3 progressive disease. ORR in patients with HGG and LGG were 26% (95% CI 9-51) and 38% (95% CI 9-76), respectively. Median time to response was 1.9 months. Responses were seen regardless of the number of prior systemic therapies. The 24-week disease control rate was 73% (95% CI 54-87). Median PFS was 18.3 months (95% CI 6.7-not estimable [NE]) and median overall survival (OS) was not reached (95% CI 16.9-NE) at a median follow-up of 16.5 months; 12-month OS rate was 85% (95% CI 71-99). Treatment duration ranged from 1.2 to 31.3+ months. Grade 3-4 treatment-related adverse events (TRAEs) occurred in 3 patients (9%). There were no treatment discontinuations due to TRAEs. CONCLUSIONS In patients with TRK fusion-positive CNS tumors, larotrectinib demonstrated rapid and durable responses, high disease control rate, and favorable safety regardless of age or number of prior systemic therapies.

Primary primitive neuroectodermal tumor of the adrenal gland: A unique tumor at an unusual site

Ewing sarcoma/Primitive Neuroectodermal Tumor (ES/PNET) is a malignant small round blue cell tumor of neuroectodermal origin that affects bones and soft tissue in children and young adults. ES/PNET is very uncommon in parenchymal organs. We report a case of primary adrenal PNET in a young female having pregnancy induced persistent hypertension. She underwent right adrenalectomy for a large adrenal mass. On histopathology, it was typical malignant round cell tumor (MRCT). Immunohistochemistry confirmed the diagnosis of ES/PNET with expression of CD99, FLI-1 and NKX2.2. Until now, only 38 cases of primary adrenal ES/PNET have been reported in the English literature with just 5 cases from India. Adrenal ES/PNET can be mistaken with other MRCTs like Non-Hodgkin lymphoma and neuroblastoma. Since the biology, treatment and prognosis of these tumors is entirely different, we emphasize that pathologists must be aware of this possibility and try to differentiate them using ancillary techniques.

RARE-10. PRIMARY INTRACRANIAL EWING SARCOMA IN A 12 MONTH OLD MALE

Background Ewing sarcoma (EWS) is a rare type of pediatric bone and soft tissue tumor that accounts for approximately 1% of all pediatric malignancies. It most commonly occurs in the long bones or axial skeleton, and rarely includes extraosseous sites or intracranial involvement. Reports of primary intracranial EWS are minimal. Pediatric intracranial EWS is even more rare with less than 15 cases reported. Case Description We describe the case of primary intracranial EWS in a 12 month old male. The patient’s initial MRI showed a large heterogeneous supratentorial cystic and solid mass centered in the right parietal region measuring 9.1cm x10.3cm x 7.6cm. No distant metastases were detected. The patient underwent surgical resection and pathology was consistent with a small round blue cell tumor. Further pathological evaluation revealed presence of EWSR1-FLI1 fusion and was negative for CD99, GFAP, synaptophysin, Olig2, desmin, and CAM5.2. Stains for INI1 and BRG1 were retained. The patient was treated with adjuvant chemotherapy and focal proton beam radiation (as per AEWS0031). Conclusion Primary intracranial Ewing Sarcoma is a rare pediatric brain tumor and, to our knowledge, this would be the youngest reported case to date. This case demonstrates the successful application of a sarcoma-based regimen to a primary intracranial EWS tumor with no evidence of residual tumor on MRI at 8 months into treatment. Future studies should be directed at understanding the biology of these rare tumors and optimizing treatment approaches.

A Rare Presentation of Ewing Sarcoma as Supraclavicular Swelling in an Adolescent Male – A Case Report

Supraclavicular swellings can have numerous differential diagnosis ranging from infections to malignancy, in almost all age groups. Here we present a case of 15 year old boy who presented with left supraclavicular swelling and clinically diagnosed as a case of Tuberculosis, underwent FNAC which was suggestive of Small Round Blue Cell Tumor favouring Ewing sarcoma. Later, trucut biopsy of the swelling confirmed the diagnosis of Ewing sarcoma. Ewing sarcoma is one of the most common primary malignancy of bone in children but can also arise from extraskeletal region like soft tissue.

Desmoplastic Infantile Astrocytoma and Desmoplastic Infantile Ganglioglioma – not so infantile anymore

DIA and DIG are rare, infantile, supratentorial neoplasms that usually occur in children before 2years of age and are exceedingly rare in older age groups. They appear as hypodense, cystic masseswith solid components showing dural attachment on neuroimaging. They are characterized byreticulin-rich spindle cell stroma containing connective tissue due to meningeal involvement,microscopically. These tumors have potential for misdiagnosis because they contain varyingproportions of neoplastic glial, neuronal and poorly differentiated cells, which causes them to have a“small round blue cell tumor” like appearance, though they have a good prognosis if correctlydiagnosed. The current study report two cases diagnosed at our institution that had very latepresentation with varying complaints which challenged the normally believed dictum of these tumorsbeing entirely infantile.

Ectopic ACTH Syndrome and Hypothyroidism Due to Right Renal Small Round Blue Cell Tumor: A Case Report

Background: Small round blue cell malignancies are rare and highly aggressive tumors that are commonly located in the soft tissues or axial bones of the bone or trunk and are particularly rare in the kidney. The common cause of ectopic ACTH syndrome is pulmonary neuroendocrine tumors, such as small cell carcinomas and carcinoid tumors. Here, we present an unusual case of ectopic ACTH syndrome and hypothyroidism caused by small round blue cell tumor of the right kidney.Case presentation: A 19-year-old girl presented with a history of right lumbar pain and discomfort for 2 months, aggravated for 2 days. Abdominal contrast-enhanced computed tomography and computed tomography angiography showed right suprarenal pole occupancy with subepithelial hemorrhage. Preoperative hormone levels including plasma total cortisol (PTC), adrenocorticotrophic hormone (ACTH) and thyroid hormone measurements were abnormal, indicating that the patient had Cushing syndrome and hypothyroidism. The patient underwent right radical nephrectomy. Histopathological analysis revealed a renal small round blue cell tumor (consistent with a primitive neuroectodermal tumor), with positive immunohistochemistry for CD99 and Ki67 (about 10%) and molecular pathology for EWSR1 gene fusions. PTC, ACTH and thyroid hormone returned to normal after surgery.Conclusions: We report a rare ectopic ACTH syndrome and hypothyroidism due to renal small round blue cell tumor. The clinical manifestation of renal small round blue cell tumor is non-specific and the diagnosis relies on pathological morphology, immunohistochemistry and fusion gene detection. At present, surgery combined with radiotherapy and chemotherapy is used in the treatment, but the prognosis is still not optimistic.

Highly aggressive undifferentiated small round blue cell tumor of foot with unique SMARCA1, KAT6A and NAV3 mutations

ABSTRACT Malignancies characterized histologically by high-grade monotonous small round blue cells (SRBCs) belong to a heterogeneous group of neoplasms often referred to as Ewing family of tumors. The most common molecular confirmation of these neoplasms is by fusions between EWSR1 gene on chromosome 22 and the ETS family of transcription factors, including FLI1 gene (11q24) and the ERG (21q22), that are implicated in the development of different tissues as well as cancer progression. In this article, we present a case of highly aggressive extraskeletal SRBC tumor involving the foot of a 24-year-old male with sole molecular findings of mutations in KAT6A, NAV3 and SMARCA1 genes with high expression of soft tissue markers (COL1A1, COL1A2, COL3A1) and MYC mRNA. To our knowledge, this unique mutational pattern has not previously been described in SRBCs.