Genome-Wide DNA Methylation Profiling as Frontline Diagnostics for Central Nervous System Embryonal Tumors in Hong Kong

This paper examines the link between CNS tumor biology and heterogeneity and the use of genome-wide DNA methylation profiling as a clinical diagnostic platform. CNS tumors are the most common solid tumors in children, and their prognosis remains poor. This study retrospectively analyzed pediatric patients with CNS embryonal tumors in Hong Kong between 1999 and 2017, using data from the territory-wide registry and available formalin-fixed paraffin-embedded tumor tissue. After processing archival tumor tissue via DNA extraction, quantification, and methylation profiling, the data were analyzed by using the web-based DKFZ classifier (Molecular Neuropathology (MNP) 2.0 v11b4) and t-SNE analysis. Methylation profiles were deemed informative in 85 samples. Epigenetic data allowed molecular subgrouping and confirmed diagnosis in 65 samples, verified histologic diagnosis in 8, and suggested an alternative diagnosis in 12. This study demonstrates the potential of DNA methylation profiling in characterizing pediatric CNS embryonal tumors in a large cohort from Hong Kong, which should enable regional and international collaboration in future pediatric neuro-oncology research.

HGG-37. A case ofETV6-NTRK3 fusion driven infantile hemispheric glioma (IHG) with acquired drug resistance against first- and second-generation NTRK-inhibitors

A 3-month-old girl had left cerebral infantile hemispheric glioma (IHG), H3 wild type (wt), Grade IV (WHO2020) with diffuse leptomeningeal and spinal metastasis. Craniotomies were performed twice which achieved partial resection. Histopathology revealed high grade glioma, Ki67 30-40%, mitosis and widespread necrosis. IHC showed H3wt, IDH-, and retained INI-1. RNAseq found ETV6-NTRK3 fusion. She was treated per Baby POG-9233, however after 3 cycles, there was mixed response (static for primary, partial response for metastasis). She had severe developmental delay, right hemiparesis and dysphagia. Aiming for better disease control and potential resectability, we switched to first-generation NTRK-inhibitor, Larotrectinib. MRI at 3 months showed significant interval reduction in tumour size, then became static at 6 months. She was stable with gradual neurological improvement until 10 months after Larotrectinib, there was worsening neurology and imaging confirmed tumour progression with haemorrhage. Craniotomy was performed for haemostasis and tumour debulking. Histopathology showed same IHG with ETV6-NTRK3 fusion. Targeted panel sequencing found NTRK3 p.Gly623Arg mutation, a solvent-front substitution responsible for acquired resistance to first-generation TRK-inhibitors. BRAFV600E and MET amplification were not detected. Larotrectinib was switched to second-generation NTRK-inhibitor, Selitrectinib. MRI at 1 month showed post-operative changes, but disease progressed at 3 months and in an accelerated manner over the course of 10 days while on therapy. Choice of conventional chemotherapy and radiotherapy were discussed, but the girl deteriorated rapidly and deceased (3 months from start of Selitrectinib, 19 months from diagnosis). CONCLUSION: IHG is aggressive with challenging surgery and medical treatment. The use of small molecular inhibitor requires careful consideration, i.e. treatment effect, toxicity and potential acquired drug resistance as showed in this case. For unresectable tumour, it may be inevitable as we also reported a similar case with ROS1 fusion. Access to newer novel agents is difficult while therapeutic effect is uncertain.

PATH-10. Nanopore sequencing reveals novel ALK fusion with interposed element in a neonate with hemispheric glioma

Here we describe the clinical course and unique molecular findings in a female neonate with infantile hemispheric glioma (IHG). The patient presented at the age of 17 days with macrocephaly and suboptimal weight gain. MRI brain revealed an 8.5cm mass over the right frontal region with significant mass effect and entrapment of ventricles. Urgent ventriculoperitoneal shunt insertion and biopsy of the highly vascular lesion was performed. Pathology was compatible with glioblastoma multiforme. Methylation profiling classified the sample as inflammatory tumor tissue (MNP v11b4), while panel RNA-sequencing revealed a fusion event between HMBOX1 and ALK which has not been described in primary CNS tumors. Long-read sequencing with the Nanopore system further revealed complex genomic rearrangement involving an interposed genomic fragment from a third chromosome with validation by Sanger sequencing. Based on an integrated diagnosis of IHG, the patient went on to receive neoadjuvant chemotherapy per the CNS-14 protocol (cyclophosphamide, carboplatin, etoposide) with significant tumor shrinkage. Near total removal of the lesion was achieved after 4 cycles of chemotherapy and adjuvant treatment with 4 additional cycles was given. The patient tolerated therapy well other than self-limiting transaminitis. At the end of treatment, the patient enjoyed intact neurology and satisfactory developmental progress. Our case report illustrates the value a multi-pronged approach to characterizing rare pediatric CNS tumors. The precise delineation of breakpoints in fusion-driven tumors might be of value in the design of cfDNA-based assays. (APYL and CTLC contributed equally to the submission)

Case Report: Primary Thoracic Low-Grade Fibromyxoid Sarcoma in a Young Girl Presenting With Mediastinal Mass Syndrome

Low-grade fibromyxoid sarcomas (LGFMSs) are typically adult-onset tumors that arise from the extremities. Here, we report an exceptional case of primary thoracic LGFMS in an 8-year-old girl that resulted in mediastinal syndrome. In reporting this case, we discuss the clinical challenges, role of molecular profiling and review reported cases of pediatric thoracic LGFMSs.

Incidence and Outcomes of CNS Tumors in Chinese Children: Comparative Analysis With the Surveillance, Epidemiology, and End Results Program

PURPOSE

Despite being the most common pediatric solid tumors, incidence and outcome of CNS tumors in Chinese children have not been systematically reported. We addressed this knowledge gap by comparing the epidemiology of pediatric CNS tumors in Hong Kong and the United States.

PATIENTS AND METHODS

Data between 1999 and 2016 from a population-based cancer registry in Hong Kong, China, on patients < 18 years old with CNS tumors (Hong Kong cohort) and from the US SEER Program (Asian/Pacific Islander and all ethnicities) were compared. Incidence and overall survival (OS) by histology were evaluated.

RESULTS

During the study period, 526 children were newly diagnosed with CNS tumors in Hong Kong (crude incidence rate, 2.47 per 100,000; 95% CI, 2.26 to 2.69). Adjusted incidences were significantly lower in the Hong Kong (2.51; 95% CI, 2.30 to 2.74) than in the SEER (Asian/Pacific Islander: 3.26; 95% CI, 2.97 to 3.57; P < .001; all ethnicities: 4.10 per 100,000; 95% CI, 3.99 to 4.22; P < .001) cohorts. Incidences of germ cell tumors (0.57 v 0.24; P < .001) were significantly higher, but those of glial and neuronal tumors (0.94 v 2.61; P < .001), ependymomas (0.18 v 0.31; P = .005), and choroid plexus tumors (0.08 v 0.16; P = .045) were significantly lower in Hong Kong compared with SEER (all ethnicities) cohorts. Compared with the SEER (Asian/Pacific Islander) cohort, histology-specific incidences were similar except for a lower incidence of glial and neuronal tumors in Hong Kong (0.94 v 1.74; P < .001). Among cohorts, OS differed only for patients with glial and neuronal tumors (5-year OS: Hong Kong, 52.5%; SEER [Asian/Pacific Islander], 73.6%; SEER [all ethnicities], 79.9%; P < .001).

CONCLUSION

We identified important ethnic differences in the epidemiology of CNS tumors in Chinese children. These results will inform the development of pediatric neuro-oncology services in China and aid further etiologic studies.

GERM-03. CLINICAL FEATURES AND OUTCOME OF CHILDREN WITH INTRACRANIAL NON-GERMINOMATOUS GERM CELL TUMORS: A POPULATION-BASED STUDY IN HONG KONG

The incidence of central nervous system non-germinomatous germ cell tumor (NGGCT) is four times higher in Chinese children than in the Western population. Reports on the outcome of Asian patients are nonetheless limited. Here we aim to summarize the experience of treating pediatric NGGCT in Hong Kong. Leveraging a population-wide pediatric oncology database, Chinese children with NGGCT diagnosed from 2002–2020 (n=43) were retrospectively studied. The diagnoses of NGGCT were made either with elevation in tumor markers (AFP/hCG; n=19), or by histology with/without concomitant raise in tumor markers (n=24). Most patients were treated with a combination of chemotherapy (cisplatin/etoposide/bleomycin, carboplatin/etoposide or carboplatin/etoposide/ifosfamide) and radiation (craniospinal+boost, whole ventricular+boost, or focal). The male:female ratio was 37:6, and the median age of diagnosis was 11.2 years. Primary tumor locations were pineal in 18, sellar/suprasellar in 12, basal ganglial in 9, supratentorial in 3 and posterior fossa in 1. Three had metastasis. Among the patients diagnosed by histology (n=24), 12 had mixed GCT, 8 had malignant/immature teratoma, 3 had embryonal carcinoma, and 1 had yolk sac tumor. With a median follow-up of 8 years, 8 patients progressed (local=7, distant=1), and 9 patients died (progression=5, palliative treatment for congenital tumors=2, sepsis=1, procedural complication=1). The respective 5-year PFS and OS were 74.9±6.9% and 82.2±6.1%. In multivariate analysis, high serum hCG level and no radiation use were significantly associated with inferior PFS. Outcome did not differ according to chemotherapeutic reagents used or radiation fields. Four patients had growing teratoma syndrome. Long-term neuroendocrine sequalae were common. In conclusion, children with NGGCT had reasonable outcome after multi-modal therapy in Hong Kong. Effort should be made to minimize tumor and treatment-related toxicities. The role of tumor markers for risk-stratification within NGGCT needs to be further interrogated.

OMIC-07. FEASIBILITY AND UTILITY OF EPIGENOMIC PROFILING FOR CHILDHOOD CNS TUMORS IN HONG KONG

Genome-wide DNA methylation profiling has emerged as an important diagnostic tool that complements histopathology for CNS tumors in children and adults. Literature describing its application in Asian countries is nonetheless limited. Herein, we report the feasibility and utility of adopting such platform for children diagnosed with CNS tumors in Hong Kong. A multi-institutional cohort (n=94, 97% of Chinese ethnicity) with CNS embryonal or high grade neuroepithelial tumors (HGNET) diagnosed in Hong Kong from 1996–2020 was assembled based on tissue availability. DNA was extracted from FFPE tumor material (median 301ng, range 13-1000ng), bisulfite converted and profiled with the Infinium Methylation EPIC BeadChip kit. Raw data were analyzed on the German Cancer Research Center MNP 2.0 classifier and through unsupervised dimensionality-reduction analysis (t-SNE) referencing a published CNS tumor reference dataset (GSE90496). The radio-histologic diagnosis included medulloblastoma (n=65), ATRT (n=9), pineal parenchymal tumors (n=7), ETMR (n=5), CNS-PNET (n=4) and other embryonal tumors/HGNETs (n=4). Methylation class could be assigned based on results from MNP 2.0 (calibrated score ≥ 0.9) in 62 patients (66%, including 2 clustering with control) and t-SNE in 22 (23%), while no-match was encountered in 10 (11%). Methylation-based analysis allowed confirmation of diagnosis and assignment of molecular subgroup in 64 patients (68%), confirmation of histologic diagnosis alone in 5 (5%) and resulted in revision/reassignment of diagnosis in 13 (14%). Among medulloblastoma samples that were assigned molecular tumor classes (n=57), 8 clustered with WNT-activated medulloblastoma, 13 with SHH-activated medulloblastoma, 10 with Group 3 medulloblastoma, 21 with Group 4 medulloblastoma, and 5 with non-medulloblastoma entities (high-grade gliomas=3, ETMR=1, ATRT=1). In conclusion, epigenomic profiling allowed refinement of disease classification for pediatric CNS tumors. Availability of such methodology in Asia sets the stage for international collaborations in molecularly-driven trials.

LINC-20. INFANT BRAIN TUMOURS IN HONG KONG

OBJECTIVES

To review the clinical features, pathology and survivals of infants with brain tumours.

METHODS

A retrospective review of the clinical findings, pathology, treatment and survival outcome in infants with brain tumours.

RESULTS

From 1999 to 2018, there were 507 children (<18 years) who were diagnosed to have brain tumours in Hong Kong. The patients were treated in five public hospitals. The clinical data were collected by the Hong Kong Paediatric Haematology and Oncology Study Group, and were cross-checked with the data of the Hong Kong Cancer Registry. In this group of patients, there were 36 infants (birth to 365 days of age) i.e. 7.1% of the whole group. Both benign and malignant brain tumours were included, while non-neoplastic lesions were excluded. On average, there was 1.89 cases per year. The pathology of the tumours were astrocytoma (n= 8), medulloblastoma (n=6), germ cell tumour (n=6), PNET (n=5), ATRT (n=4), choroid plexus tumours (n=3), ependymoma (n=2), craniopharyngioma (n= 1) and ganglioglioma (n= 1). These infants were treated according to their clinical conditions and prognosis, with operation, chemotherapy or both. Radiotherapy was withheld or postponed to older age. Some patients only received palliative care due to the poor neurological status or prognosis. The overall survivals of children younger than 18 years old vs infants were 67.3% (±2.3) vs 50.5%(±9.2) respectively, while the event free survivals were 64.4% (±2.4) and 43.5% (±8.8) at 10-years respectively.

CONCLUSION

Infants with brain tumours have different pathology and inferior outcome.