Raghunathan, Aditya

Abstract Background DNA methylation profiling can be used to robustly predict postsurgical outcomes and response to radiotherapy (RT) for meningioma patients. To allow for seamless integration of these complementary models into clinical practice, a practical framework is needed. Methods We leveraged a cohort of nearly 2000 surgically-treated meningiomas with DNA methylation profiling and clinical outcomes data. Existing methylation-based prediction models were dichotomized to yield four risk groups: low and high recurrent risk, each with RT sensitive and resistant subgroups. Risk groups were correlated with progression-free survival in the context of existing biomarkers including extent of resection and WHO grade. Results We first demonstrated that all risk groups benefit from gross total resection. All “high-risk, RT sensitive” tumors (n = 306, 15.7%) also benefited from adjuvant RT: after GTR, median PFS increased from 4.68 (4.13-9.48) years to not reached (P = .003); after subtotal resection (STR), from 2.12 (1.59-3.02) to 4.09 (3.41-not reached) years (P = .004). “Low-risk, RT sensitive cases” (n = 1207, 61.8%) also benefited from RT after STR (median PFS 7.39 (6.66-12.8) vs. 16.53 (10.35-not reached) years, P = .03), suggesting that RT be considered in these patients. Neither “low-risk RT resistant” (n = 84, 4.3%) nor “high-risk RT resistant” (n = 356, 18.2%) cases benefited from RT, and the latter group was associated with universally poor outcomes. Conclusions We identify methylation-defined risk groups of meningioma for which additional benefit is gained from adjuvant RT, leading to a clinical decision-making framework for straightforward integration of molecular models into clinical practice.

Abstract MGMT is primarily inactivated via promoter methylation, but MGMT homozygous deletion (hmzdel) has been rarely reported as an alternative inactivating mechanism. Although functionally similar to a methylated MGMT promoter, MGMT hmzdel is associated with an unmethylated MGMT promoter test result reflecting the MGMT promoter status of the non-neoplastic cells invariably present in any tumor specimen. Thus, patients whose tumors have MGMT hmzdel (and unmethylated MGMT promoter) would be inaccurately predicted to lack benefit from alkylating chemotherapy based on MGMT promoter methylation testing alone. To evaluate the impact of this clinical scenario, we estimated the frequency and distribution of MGMT hmzdel in routine clinical testing of CNS tumors. Among 12,424 CNS tumors (3,044 with provided diagnosis of glioblastoma) tested using Oncoscan chromosomal microarray (2015-2025), 10 tumors (0.08%) had MGMT hmzdel: 8 with entire gene hmzdel and 2 with partial gene hmzdel favored to be inactivating (RNA-sequencing underway to exclude possibility of activating rearrangements). All tumors were supratentorial and non-midline. Median age at diagnosis was 58.5 years (range, 34-81), with 3:2 male:female. Of the 10 cases, 9 (of 3,044; 0.3%) had integrated diagnosis of glioblastoma, IDH-wildtype; the remaining case was a recurrent astrocytoma, IDH-mutant, CNS WHO grade 4. All 10 cases had loss of chromosome 10q and a highly unmethylated MGMT promoter by droplet digital PCR testing of downstream CpG sites 75-80/84-87, with median fraction abundance of 0.19% (range, 0-0.85). In summary, MGMT hmzdel only occurred in high-grade adult-type diffuse astrocytic gliomas, and is a rare potential pitfall for MGMT promoter methylation testing leading to inaccurate patient stratification. It is critical that laboratories performing routine CNS tumor copy number testing include MGMT in the curated list of reportable genes, and that clinicians be aware of this rare clinical scenario to accurately stratify patients despite misleading MGMT promoter test results.

Abstract BACKGROUND The majority of pituitary neuroendocrine tumors (PitNETs) are effectively managed with medical therapy, surgery, and/or radiation therapy; however, a subset of pituitary adenomas exhibit aggressive behavior. Temozolomide is thought to be an effective treatment option for patients with PitNETs. METHODS We identified and retrospectively reviewed 11 patients with pituitary tumors treated with temozolomide. We then conducted a review of the literature, combining 114 previously published cases with our cohort. RESULTS 125 cases were identified with diagnoses of pituitary adenomas (n=45), aggressive pituitary tumors (n=61), and pituitary carcinoma (n=19) treated with temozolomide. 79 patients were male (68.1%) with a median age of 47.5 (range 9-72). A variety of tumor types were represented: 50 corticotroph adenomas (40.7%), 37 prolactinomas (30.1%), 22 hormone nonfunctioning adenomas (17.9%), 8 somatotroph adenomas (6.5%), 6 other functioning adenomas (4.9%), and 2 cases where the functional status was not mentioned. Median treatment duration was 9 cycles (n=91, 150-200 mg/m2 days 1-5, 28-day cycles; n=2, 75 mg/m2, days 1-21, 28-day cycles; n=1, 75 mg/m2 daily). 27 patients received concurrent therapy with a dopamine agonist/somatostatin analogue (n=10), other chemotherapy agent (n=9) or radiotherapy (n=8). Radiographic responses included stable disease (n=40), partial response (n=35), complete response (n=8), and progressive disease (n=30). Hormonal responses included complete response (n=13), partial response (n=32), and no response (n=16). 22 patients (47.8%; out of 46 patients where progression/recurrence was assessed) experienced progression/recurrence following temozolomide initiation with a median progression free survival (PFS) of 24 months. There was no significant association between MGMT methylation status and radiological or hormonal response. No unexpected toxicities were observed. CONCLUSION In this cohort, temozolomide was well-tolerated with a median PFS of 24 months. MGMT methylation status did not predict temozolomide response. Temozolomide is an option with a survival benefit for patients with PitNETs.

Abstract WSD0922-Fu is an oral, CNS-penetrant, small molecule EGFR inhibitor which potently inhibits EGFR aberrations specific to non-small cell lung cancer (NSCLC) and glioblastoma (GBM). MC1914 (NCT04197934) is a first-in-human phase 1 trial in patients with EGFR aberrant recurrent GBM and NSCLC. After determining the maximum tolerated dose, adults with recurrent GBM were treated in two expansion cohorts: (a) non-surgical cohort (6/12 patients thus far): EGFRvIII mutation, first recurrence; food-effect study included (b) surgical cohort (6/6 patients), any EGFR mutation, any recurrence; window-of-opportunity study (WOO) included. Among these 12 patients, median age = 60 years; 50% female; 58% ECOG 0). All patients received prior radiation and temozolomide. After the WOO or food-effect study, patients were dosed at 120 mg BID (5 days on, 2 days off), and escalated to 160 mg BID (5 days on, 2 days off) based on tolerability. Common adverse events (>40%) are comparable to other EGFR inhibitors (acneiform rash, diarrhea, fatigue, xerosis, pruritis). Treatment-related grade 3+ adverse events were limited to lymphopenia (n = 1). WSD0922-Fu exposure in the fed state exceeded the fasted state (median plasma Cmax and AUC0-24h are 1.6x and 1.3x, respectively) with a delayed Tmax (6.0 vs 1.8 hours). For the WOO, time between last dose administered to tumor collection ranged between 4 - 13.5 hours. Median tumor WSD0922-Fu concentration was 0.76 µg/g; estimated median unbound tumor concentration was 24.9 ng/g and within expectations for pharmacodynamic effect. Median brain/plasma ratio = 0.59; median unbound brain/unbound plasma = 0.88. Enrollment to the non-surgical cohort is ongoing, so formal efficacy data remain immature. However, examples of clinical efficacy will be shown along with data on recurrence patterns. Phase 2 clinical trial development is in progress.

Abstract The WHO 2021 classification of central nervous system tumors incorporated molecular markers to better define diffuse glioma subgroups. We analyzed array-based copy number, targeted next-generation sequencing, germline genotyping, and Illumina EPIC array methylation data from 404 primary IDH-mutant astrocytomas to further understand the relationship between copy number and outcomes. Loss of chromosome arm 13q was associated with poor overall survival after adjusting for age, sex, tumor grade, and treatment status (hazard ratio [HR]=2.04 (95% confidence interval: 1.25-3.33), p=0.004). Chromosome 13q loss was also significantly associated with the total number of copy number alterations (p<0.001). Loss of arm 11p was associated with poor survival in the adjusted analysis (HR=2.29 (1.38-3.79), p=0.001). Unsupervised clustering of the raw copy number data identified 12 clusters, where each cluster was defined by distinct copy number alteration(s). Clusters that contained 13q loss exhibited worse overall survival compared to other clusters. The clusters were significantly associated with age at diagnosis (p=0.015), tumor grade (p<0.001) and copy number complexity (p<0.001). The clusters with a high proportion of grade 4 tumors and with the highest complexity had the poorest overall survival. These findings highlight the prognostic relevance of chromosome 13q and 11p losses in IDH-mutant astrocytomas and support the integration of additional copy number alterations into molecular classification frameworks of IDH-mutant astrocytomas to improve risk stratification and patient management.

Abstract To propose a novel entity of possible intraosseous pseudoprogression in clival chordoma following proton radiation therapy (PRT). A total of 38 consecutive patients who underwent surgical resection followed by PRT for clival chordoma between January 2015 and December 2023 were analyzed retrospectively. Follow-up magnetic resonance imaging (MRI) suggesting recurrence or progression was evaluated for validity. Apparent diffusion coefficient (ADC) and tumor-to-brainstem signal intensity ratio on contrast-enhanced T1-weighted imaging (Rce) were assessed. Pseudoprogression was defined as (1) MRI signs of recurrence or progression with no pathological confirmation despite obtaining a specimen, or (2) MRI signs of recurrence or regression with spontaneous resolution/regression. Of the 11 patients with MRI findings suggestive of recurrence or progression, 3 were diagnosed with recurrence, 5 with progression, and 3 with pseudoprogression. Patients with pseudoprogression were significantly younger than those with progression (p = 0.04), and all were female. The median time to recurrence, progression, and pseudoprogression was 31, 29, and 21 months, respectively. The three pseudoprogression cases were managed with gross-total resection followed by stereotactic radiosurgery, extensive biopsy, and observation, respectively. Although statistical significance was not reached, ADC (p = 0.33) and Rce (p = 0.13) tended to be higher in pseudoprogression cases. After PRT for clival chordoma, intraosseous pseudoprogression should be considered in the differential diagnosis, particularly in relatively young female patients, although the role of ADC and Rce on MRI remains inconclusive. Multidisciplinary teams managing chordomas should take this into account when determining the aggressiveness of treatment in such cases.