PATH-18. INTEGRATING TUMOR MICROENVIRONMENT WITH GENOMIC ABERRATIONS AND TUMOR CLASS IN ADULT GLIAL/GLIONEURONAL TUMORS BY DECONVOLUTION OF BULK METHYLATION DATA

It is increasingly recognized that the tumor microenvironment (TME) plays a critical role in the biology of cancer. To better understand the role of non-neoplastic immune cellular components in CNS tumors, we applied a deconvolution approach to bulk DNA methylation array data using methylCIBERSORT on 450k/850k methylation data from a set (n= 4057) of high- and low-grade glial and glioneuronal tumors. Using the cell type proportion data as input, we used dimension reduction (UMAP) to visualize sample-wise patterns of that emerge from the cell type proportion estimations. In glioblastomas (n= 2076) we identified distinct tumor clusters based on immune cell proportion and, interestingly, TME-based cluster groups demonstrated an association with specific genetic alterations such as EGFR amplification and/or CDKN2A/B homozygous deletion. Among 1178 IDH-mutant gliomas, clustering of tumors according to immune cell proportions led to 2 major subgroups, which largely aligned with 1p/19q co-deletion status. Among the non-codeleted tumors (IDH-mutant astrocytomas, N=734), clustering of immune cell decomposition revealed clusters which showed distinct proportions of a key genomic aberration in these tumors (CDKN2A/B loss). To investigate the possible role of monocyte proportion-relative gene expression and promoter methylation of the immune checkpoint PD-L1 and PD-L2 genes, we used a data subset (n=594) samples with matched gene expression profiles. We observed significantly high positive correlations (R=0.54 and 0.68, respectively) between monocyte proportion and expression of PD-L1 and PD-L2, in line with prior reports that monocytic cells can express these immune markers. Consistent with this, we found high negative correlations (R= -0.51 and -0.61, respectively) between monocytes and promoter methylation of PD-L1 and PD-L2, respectively. Overall, the findings highlight specific roles of the TME in biology and classification of adult CNS tumors, where specific immune cell admixtures correlate with tumor types and genomic aberrations.

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.

Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors

It is recognized that the tumor microenvironment (TME) plays a critical role in the biology of cancer. To better understand the role of immune cell components in CNS tumors, we applied a deconvolution approach to bulk DNA methylation array data in a large set of newly profiled samples (n = 741) as well as samples from external data sources (n = 3311) of methylation-defined glial and glioneuronal tumors. Using the cell-type proportion data as input, we used dimensionality reduction to visualize sample-wise patterns that emerge from the cell type proportion estimations. In IDH-wildtype glioblastomas (n = 2,072), we identified distinct tumor clusters based on immune cell proportion and demonstrated an association with oncogenic alterations such as EGFR amplification and CDKN2A/B homozygous deletion. We also investigated the immune cluster-specific distribution of four malignant cellular states (AC-like, OPC-like, MES-like and NPC-like) in the IDH-wildtype cohort. We identified two major immune-based subgroups of IDH-mutant gliomas, which largely aligned with 1p/19q co-deletion status. Non-codeleted gliomas showed distinct proportions of a key genomic aberration (CDKN2A/B loss) among immune cell-based groups. We also observed significant positive correlations between monocyte proportion and expression of PD-L1 and PD-L2 (R = 0.54 and 0.68, respectively). Overall, the findings highlight specific roles of the TME in biology and classification of CNS tumors, where specific immune cell admixtures correlate with tumor types and genomic alterations.

P14.82 Glioneuronal tumors - a rare tumor entity with diagnostic and therapeutic challenges: report of two cases and review of literature

BACKGROUND The 2007 WHO classification of brain tumors first encompassed two new entities of glioneuronal tumors, including papillary glioneuronal tumors (PGNT) and rosette-forming glioneuronal tumours. The reviewed version of the 2016 WHO classification additionally included diffuse leptomeningeal glioneuronal tumours. The histopathological, genetic, and clinical understanding of glioneuronal tumors is currently evolving, however there are no guidelines for diagnostic and clinical management yet. MATERIAL AND METHODS We report two male patients with glioneuronal tumors and performed a review of literature. RESULTS The first patient was diagnosed with a PGNT (MIB-1 proliferation index = 5%) located in the right parietal lobe at the age of 33 years and received surgical resection. Two years later, the tumor recurred in the same location. A second tumor resection was performed followed by concomitant radiochemotherapy with temozolomide (60/2 Gray). A next-generation sequencing gene panel (Oncomine) confirmed the initial diagnosis of a PGNT. The patient has remained in remission for the past 10 years. The second patient developed complex partial seizures which were first misdiagnosed as anxiety disorder at the age of 26 years. An MRI scan revealed a contrast-enhancing bifrontal cystic lesions 5 years later and he received a gross total tumor resection. The diagnosis of a glioneuronal tumor was made, however molecular pathology and methylation analysis were not able to classify the tumor entity further. There was no evidence of tumor recurrence one year after surgery and he remained seizure-free with antiepileptic treatment. CONCLUSION Glioneuronal tumors encompass rare and heterogenous tumor entities which primarily present in young patients and often show a favorable clinical course. Although the increasing number of reports in the literature have improved our understanding of these tumors, uncertainty remains in diagnostic challenging cases and patients with progressive disease after surgery. The value of next-generation sequencing and the choice of adjuvant treatment modalities have not been systematically evaluated in this patient group.

Papillary glioneuronal tumor growing slowly for 26 years: illustrative case

BACKGROUND Papillary glioneuronal tumors (PGNTs) are classified as a type of World Health Organization grade I mixed neuronal-glial tumor. Most PGNTs involve cystic formations with mural nodules and solid components in the cerebral hemispheres, and PGNTs occur mainly in young adults. The long-term prognosis of PGNTs remains unclear. OBSERVATIONS A 38-year-old male had been diagnosed with an arachnoid cyst associated with epilepsy in a local hospital. The initial magnetic resonance imaging (MRI) study showed the tumor as a heterogeneously enhanced nodule in the left postcentral gyrus. Subsequent MRI studies showed slow growth of the tumor for 26 years. He underwent gross total resection to control his epilepsy. The histopathological findings revealed pseudopapillary structures involving hyalinized blood vessels with a single or pseudostratified layer of cuboidal glial cells with round nuclei and scant cytoplasm. At the periphery of the lesion, Rosenthal fibers and acidophilic granule bodies were observed in the gliotic brain tissue. Immunohistochemically, some interpapillary cells were positive for NeuN. On the basis of these findings, the tumor was diagnosed as a PGNT. LESSONS This PGNT showed slow growth for 26 years. When recognizing a slowly growing tumor in the cerebral hemispheres of relatively young people that is associated with epileptic seizures, PGNT should be considered as a differential diagnosis.

Sustained Tumor Control With MAPK Inhibition in BRAF V600–Mutant Adult Glial and Glioneuronal Tumors

Objective:To assess whether RAF and MEK inhibitors (RAFi/MEKi) can provide long-term clinical benefit in adult patients with BRAF V600-mutant glial and glioneuronal tumors (GGNT), we analyzed tumor response and long-term outcome in a retrospective cohort.Methods:We performed a retrospective search in the institutional databases of six neuroncology departments for adult patients with recurrent or disseminated BRAF V600-mutant GGNT treated with RAFi/MEKi.Results:Twenty-eight adults with recurrent or disseminated BRAF V600-mutant gangliogliomas (n=9), pleomorphic xanthoastrocytomas (n=9), and diffuse gliomas (n=10) were included in the study. At the time treatment with RAFi/MEKi was started, all tumors displayed radiological features of high-grade neoplasms. Thirteen patients received RAFi as single agents [vemurafenib (n=11), dabrafenib (n=2)], and 15 combinations of RAFi/MEKi [vemurafenib+cobimetinib (n=5), dabrafenib+trametinib (n=10)]. Eleven patients achieved a partial or complete response (11/28, 39%), with a median reduction of -78% in their tumor burden. Responders experienced a median increase of 10 points in their Karnofsky Performance Status (KPS) and a median progression-free survival of 18 months, which was longer than achieved with first-line treatment (i.e., 7 months, p=0.047). Responders had better KPS (p=0.018), tended to be younger (p=0.061) and to be treated earlier (p=0.099) compared to non-responders. Five patients were rechallenged with RAFi/MEKi at progression, with novel tumor responses in two. On univariate and multivariate analyses, response to RAFi/MEKi was an independent predictor of overall survival.Conclusions:Our study highlights the clinical benefits of RAFi/MEKi in adult patients with BRAF-mutant GGNT, encourages the systematic screening and rechallenge in responders.

LGG-06. COMPREHENSIVE GENOMIC CHARACTERIZATION AND INTEGRATED CLINICAL ANALYSIS OF LOW-GRADE GLIOMAS IN CHILDREN WITH NEUROFIBROMATOSIS TYPE 1

Background Low-grade gliomas (LGGs) arising in children with neurofibromatosis type 1 (NF1) are usually not biopsied. To identify secondary genetic alterations or molecular features that may contribute to pathogenesis and correlate with clinical behavior, we initiated a comprehensive molecular and clinical analysis of pediatric NF1-LGGs. Methods NF1-LGGs were analysed by whole-genome sequencing (31), targeted gene panel sequencing (9), RNAseq transcriptomal profiling (33) and genome-wide DNA methylation analysis (67). Clinical annotation was available for 48 subjects. Results Most LGGs harbored bi-allelic NF1 inactivation as the sole genetic abnormality, but 11% had additional alterations (FGFR1 mutation, n=3; PIK3CA mutation, n=2; homozygous 9p21 deletion, n=2; MYB:QKI fusion, n=1; SETD2 mutation, n=1; EGFR amplification, n=1). FGFR1 mutation conferred additional growth advantage in multiple complementary murine Nf1 models. 88% of NF1-LGGs resembled sporadic pilocytic astrocytoma (PA) by methylation, higher than that based on histology. Non-PA methylation patterns included low-grade glial/glioneuronal tumors, rosette-forming glioneuronal tumors, MYB/MYBL1-altered glioma, and high-grade astrocytoma with piloid features (2 tumors histologically diagnosed as LGG). In total, 18% of samples were classified as non-PA and/or harbored an additional non-NF1 mutation. Non-PA methylation class tumors were more likely to harbor an additional non-NF1 mutation (p=0.005). 7.7% of optic pathway hypothalamic gliomas (OPHGs) had other mutations or were not classified by methylation as PA, compared with 20.6% of NF1-LGGs arising elsewhere. There was no difference based on age for the presence of an additional non-NF1 mutation or non-PA methylation class. Conclusions Given the overall low occurrence of non-NF1 mutations or non-PA methylation class tumors in this series, routine clinical biopsy of typically-appearing NF1-LGG may not be indicated, particularly for children with OPHG. Biopsy should be considered for non-OPHG tumors refractory to conventional treatment. As additional agents are developed and treatment strategies evolve, the rationale for biopsy of NF1-LGG may become stronger.