Alterations In NF1 Research Articles

52 (PB042) - The RAF/MEK clamp VS-6766 shows strong anti-tumor activity across multiple MAPK pathway alterations, with a preferential effect on KRAS G12V

Background: KRAS is the most frequently mutated RAS/RAF family member (mutated in 15% of cancers), followed by BRAF (5%) and NRAS (3%). Several BRAF and MEK inhibitors (MEKi) are approved for BRAF V600E cancers, and the G12C inhibitor sotorasib is approved for KRAS G12C non-small cell lung cancer (NSCLC). However, there is still a need for agents targeting other RAS/RAF mutations (mt), including KRAS G12 V which is mutated in ∼7%, ∼9% and ∼19% of NSCLC, colorectal and pancreatic cancers, respectively. VS-6766 is a unique RAF/MEK clamp that potently inhibits MEK kinase activity and induces a dominant negative RAF-MEK complex preventing phosphorylation of MEK by ARAF, BRAF and CRAF. This unique mechanism allows VS-6766 to block MEK signaling without the compensatory re-activation of MEK that appears to limit the efficacy of MEKi. Material and Methods: In vitro assays were performed to evaluate the anti-proliferative activity of VS-6766 in human tumor cell lines with MAPK pathway alterations and in RAS-less mouse embryonic fibroblasts (MEFs) stably transfected with various KRAS variants. The anti-tumor activity of VS-6766 was assessed in genetically engineered mouse models (GEMM) of KRAS G12 V/Trp53 KO and KRAS G12C/Trp53 KO NSCLC. Results: VS-6766 showed strong anti-proliferative potency across tumor cell lines carrying KRAS, BRAF, CRAF, NRAS or NF1 alterations. Among KRAS mt cell lines, the anti-proliferative potency of VS-6766 differed by KRAS variant, with greatest potency observed with G12 V > G12C > G12D, which is consistent with G12 V signaling through CRAF/MEK/ERK and G12D signaling more through PI3 K/AKT/mTOR. Similarly, in MEFs stably transfected with different KRAS variants, VS-6766 showed best potency with KRAS G12 V and G12C, and least potency with G12D and KRAS wildtype. Accordingly, in the KRAS G12 V NSCLC GEMM model, previously shown to be CRAF-dependent, VS-6766 monotherapy induced stronger tumor regression than in a corresponding G12C NSCLC GEMM model. Strikingly, the combination of VS-6766 with FAK inhibition conferred tumor regressions in 87% (27/31) and 71% (36/51) of all tumors in the KRAS G12 V and KRAS G12C NSCLC models, respectively. Clinically, objective responses to VS-6766 monotherapy occurred mainly in patients with KRAS G12 V with 4 out of the 7 responders bearing KRAS G12 V (Guo, 2020). In KRAS mt NSCLC patients treated with VS-6766 in combination with the FAK inhibitor defactinib, a G12 V preference was also observed with confirmed responses in 2/2 patients with KRAS G12 V and tumor reduction in 4/6 patients with KRAS G12C (Krebs, 2021). Conclusions: These data support the ongoing registration-directed study evaluating VS-6766 ± defactinib for patients with KRAS G12 V NSCLC (NCT04620330), as well as the clinical combinations of VS-6766 with the KRAS G12C inhibitors sotorasib (NCT05074810) or adagrasib (NCT05375994) for KRAS G12C NSCLC. No conflict of interest.

1011P MET and NF2 alterations confer early resistance to first-line alectinib treatment in ALK-rearranged non-small cell lung cancer

The second-generation anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitor (TKI), alectinib, has shown impressive efficacy in naïve ALK-rearranged advanced non-small-cell lung cancer (NSCLC). However, why tumors develop early resistance to the drug is incompletely understood.

A diagnostic approach to paratesticular lesions with tubulopapillary architecture: a series of 16 serous borderline tumors/low-grade serous carcinoma and 14 well-differentiated papillary mesothelial tumors and mesothelioma

As there is limited literature on paratesticular tumors of müllerian and mesothelial origin, we reviewed archived cases of serous borderline tumors (n=15), low-grade serous carcinoma (n=1), well-differentiated papillary mesothelial tumors (WDPMTs; n=2), and mesothelioma (n=12), for relevant clinicopathologic features. Molecular profiling data from the American Association for Cancer Research (AACR) GENIE registry was accessed for 8 additional patients with testicular mesothelioma. For tumors of mesothelial origin, the median age at surgical excision was 62 years, the median size was 4.5cm, and they consistently exhibited positivity for mesothelial markers (CK5/6, calretinin, WT1, and D2-40). Recurrent alterations of the NF2 gene were identified in 3 of 8patients (38%), and alterations of BAP1 and CDKN2A were relatively infrequent. While one patient with WDPMT had a recurrence, a second patient with WDPMT progressed to a biphasic mesothelioma 2 years after initial resection. For tumors of müllerian origin, the median age at surgical excision was 45 years, the median size was 2.5cm, and these exhibited consistent positivity for ER, WT1, and PAX8. Although no recurrences were documented in patients with serous borderline tumors, a single patient with a low-grade serous carcinoma developed widely metastatic disease and died of disease-related complications. Our study emphasizes the need for close clinical follow-up in patients with WDPMT and highlights the prognostic significance of documenting invasive behavior in tumors of müllerian origin as they can have an aggressive clinical course. Finally, our results suggest that NF2 alterations may play an important role in the pathogenesis of testicular mesothelioma.

Abstract 5165: The genomic landscape and prognostic implications of somatic alterations in patients (pts) with ER+, HER2-, PIK3CA mutated (mut) advanced breast cancer treated with taselisib and fulvestrant

Abstract Background: Mutations in PIK3CA, encoding the catalytic subunit p110α of PI3K, are present in ~40% of ER+/HER- BC. Taselisib (TAS) is a potent and selective β-sparing PI3K inhibitor that improves outcomes in combination with endocrine therapy in pts with PIK3CAmut advanced breast cancer (aBC). To better understand the molecular alterations associated with response to PI3K inhibition, we profiled the genomic landscape of ctDNA collected from PIK3CAmut, ER+, HER2- aBC pts immediately prior to treatment (tx) with TAS or placebo (PBO) plus fulvestrant (FUL). Methods: Pts were enrolled as part of a phase III randomized study of TAS or PBO plus FUL in ER+, HER2- PIK3CAmut aBC (SANDPIPER, NCT02340221). Pre-tx ctDNA samples from 508 pts underwent comprehensive genomic profiling using the FoundationOne Liquid NGS assay at Foundation Medicine, Inc.; the 339 pts with PIK3CAmut ctDNA were further analyzed herein. The top mutated genes were analyzed for prognostic value against investigator-assessed progression-free survival (PFS) for both tx regimens using Cox proportional hazards regression modeling. As analysis was exploratory, no adjustments were made for multiple testing. Results: The top altered genes were TP53 (44%), ESR1 (37%), CDH1 (17%), FGFR1 (12%), NF1 (11%), CHEK2 (10%), and PTEN (9%). In pts treated with PBO+FUL, alterations in PTEN (HR 2.8; 95% CI 1.4-5.7; p=0.0107) and TP53 (HR 2.0; 95% CI 1.3-3.1; p=0.0025) were associated with a worse prognosis compared to pts with no mutation detected (NMD) in these genes. In pts treated with TAS+FUL, alterations in FGFR1 (HR 2.4; 95% CI 1.5-3.7; p=0.0006), TP53 (HR 1.9; 95% CI 1.4-2.6; p=0.0001) and PTEN (HR 1.8; 95% CI 1.1-2.8; p=0.0265) were associated with a worse prognosis compared to pts with NMD in these genes. Alterations in ESR1, CDH1, or CHEK2 were not associated with prognosis (p≥0.05) in either tx arm. A trend towards worse prognosis was observed in pts with NF1 altered ctDNA treated with PBO+FUL (HR 2.1; 95% CI 1.1-4.1; p=0.0527), which was not observed in pts treated with TAS+FUL (HR 0.97; 95% CI 0.57-1.65; p=0.901). Within the NF1-altered subgroup, a significant PFS difference was observed between TAS- vs PBO-treated pts (HR 0.28; 95% CI 0.11-0.67; p=0.0058; median 5.65 vs 1.94 months, respectively). Conclusions: We report that the most frequently mutated genes identified are consistent with previous studies in pts with ER+, HER2- aBC. This analysis shows that alterations in TP53 and PTEN were associated with poor prognosis in both tx arms, and FGFR1 alterations were associated with a poor prognosis in TAS+FUL treated pts. Further, NF1 alterations were associated with a poor prognosis in PBO+FUL treated pts, an association that was not observed with TAS+FUL. These findings may inform future rational combination strategies for the clinical development of PI3K inhibitors. Citation Format: Jessica W. Chen, Susan Dent, William Jacot, Javier Cortés, Ian E. Krop, Thomas J. Stout, Frauke Schimmoller, Heidi M. Savage, Katherine E. Hutchinson, Timothy R. Wilson. The genomic landscape and prognostic implications of somatic alterations in patients (pts) with ER+, HER2-, PIK3CA mutated (mut) advanced breast cancer treated with taselisib and fulvestrant [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5165.

Abstract 5772: Differences in clinical actionability by comparing mutational landscape of young and old breast cancer patients

Abstract Background: Early-onset breast cancer (BC) is associated with poor prognosis, which is also characterized by high recurrence risk, distant metastases and advanced stages at the time of diagnosis. While germline mutations in BRCA1/2 are known to underlie a subset of early-onset BC cases, the clinical and genetic characteristics in other young BC patients remain to be explored. Method: We profiled primary lesions from 440 Chinese female BC patients by using a 425-cancer-gene panel. The population was sub-divided into young (≤40 years old) and old (>40 years old) BC patients according to ages at diagnosis. Young and old BC patients were compared for their associations with genomic aberrations, with focus on existing BC targetable alterations, including those in the ERBB2 gene and PI3K and homologous recombination repair (HRR) pathways. Results: 137 (31.1%) patients presented with BC at a young age (median age=35 [18-40]) and 303 (68.9%) with BC diagnosed at an older age (median age=53 [41-82]) in our study cohort. TP53 (young, 61.3%; old, 67%), PIK3CA (33.6% and 41.3%), and GATA3 (9.5% and 8.3%) were among the top frequently altered genes in both subgroups. A total of 70 patients carried pathogenic germline mutations. Of these, 57.3% were alterations in the HRR pathway genes, including BRCA1/2, WRN, BLM, and PALB2, etc, with comparable frequencies in young and old patients. Germline BRCA1/2 mutations were detected in nine (6.6%) and 23 (7.6%) of the young and old patients, respectively. Somatic BRCA1/2 mutational frequencies were also comparable between young (8.8%) and old (9.9%) patients. Overall, somatic alterations in HRR pathway genes were detected in 32.1% young and 40.6% old BC patients. While similar frequencies of ERBB2 amplification (14.6% vs. 18.2%; P= 0.41) were detected in young and old BC patients, older patients carried more ERBB2 mutations (1.5% vs. 7.3%, P= 0.01). Interestingly, the highest rate of ERBB2 amplification was observed in the 20-30 years age group. Alterations in NF1 (10.6% vs. 3.6%, P=0.02) and PKHD1 (6.9% vs. 2.2%, P=0.04) were more frequent in older patients. Alterations in the PI3K pathway genes were more enriched in the older BC patients with overall mutational frequencies of 55.5% and 68.6% (P=0.01) in young and old subgroups, respectively. Finally, we observed an age-dependent increase in tumor mutational burden. Conclusion: BC in young and old patients exhibited different genomic characteristics that could be taken into consideration for treatment recommendations. Citation Format: Jiaqi Liu, Ziqi Jia, Gang Liu, Xiang Wang, Qi Meng, Sha Wang, Yang Shao. Differences in clinical actionability by comparing mutational landscape of young and old breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5772.

Abstract 1245: Comprehensive analysis of non-small cell lung cancer identifies molecular genotype-immunophenotype associations and candidate biomarkers predictive of response to immunotherapy

Abstract Lung cancer has the second highest incidence and leads cancer mortality worldwide, being Non-Small Cell Lung Cancer (NSCLC) the most prevalent subtype. Immunotherapy with checkpoint blockers has shown outstanding benefits in a subset of NSCLC patients, which are not accurately identified due to the lack of robust biomarkers of response. We hypothesize that specific molecular alterations of NSCLC tumor cells impact the immune microenvironment. Defining this association could improve the prediction of response to immunotherapy. This work aims to identify a multiparametric biomarker signature. We studied 178 tumor samples from a cohort of early stage NSCLC with complete clinical annotation. We analyzed their molecular aberrations, calculated their Tumor Mutational Burden and described their immune landscape by immunohistochemistry and a dedicated RNAseq panel. We defined novel subgroups of NSCLC tumors with specific immune, molecular and clinical features, showing an association between their molecular genotype and immune phenotype. Based on these data, subgroups were proposed as pro-immunogenic, pro-tumorigenic or mixed. Adenocarcinomas clustered in 4 groups. The pro-tumorigenic group had a significant higher proportion of alterations in ARID1A, FGF10, ROS1, TP53. One pro-immunogenic group had a significant higher proportion of MET alterations and lower proportion of EGFR alterations. An immune mixed group significantly accrued never smokers and had no alterations in FGF10. Squamous cell carcinomas clustered in 4 groups. The pro-tumorigenic group had a significant higher proportion of alterations in CCND1, FGF3, FGF10, FGF19, NOTCH1, PIK3CA, PIK3CB, TFRC. A pro-immunogenic group had a significant higher infiltration of T CD4+, T CD8+ and B cells and a higher overall survival. Another pro-immunogenic group had a significant absence of MYCN and NF1 alterations. Taken together we identified a set of candidate predictive biomarkers of response to immunotherapy in NSCLC. Genes overexpressed in pro-immunogenic tumors are related to adaptive immune response stimulation (CD28, FCRLA, JCHAIN, LY9, MS4A1, SLAMF7, TNFRSF9, TNFRSF17), antigen presentation (CD1C, CD1D, HLA-A), apoptosis (FAS), immune chemotaxis (CCL20, CCR4, CCR6), and immune regulation (CD53, PDCD1, SH2D1A, ZAP70). On the other hand, genes upregulated in pro-tumorigenic tumors are involved in angiogenesis (VEGFA), cell cycle regulation (BUB1, CCNB2, FOXM1, MAD2L1, TOP2A), cell growth/survival (IGF1R), DNA replication/repair (KIAA0101) and iron metabolism (HMBS, TFRC). These findings are being validated by Digital Spatial Profiling in a cohort of patients with advanced stage NSCLC that were treated with checkpoint blockers. If confirmed, these results could remarkably improve patient selection and the benefit upon immunotherapy. Citation Format: Javier Ramos-Paradas, David Gomez-Sanchez, Aranzazu Rosado, Alvaro Conrado Ucero, Nuria Carrizo, Ana Belen Enguita, Maria Teresa Muñoz, Esther Conde, Luis Paz-Ares, Eva Maria Garrido-Martin. Comprehensive analysis of non-small cell lung cancer identifies molecular genotype-immunophenotype associations and candidate biomarkers predictive of response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1245.

Abstract LB516: MDM2/MDM4 amplification and CDKN2A deletion in melanoma brain metastases and GBM may have implications for targeted therapeutics and immunotherapy

Abstract Melanoma has a five-year survival rate of 27% for distant metastatic disease, and there remains a paucity of targeted therapies for metastatic disease and biomarkers that predict metastasis to specific sites. We analyzed 1081 primary melanoma samples and 358 metastatic melanoma samples and found that metastatic disease is enriched for amplifications in both MDM2 and MDM4 compared to primary disease, and these amplifications are associated with a lower probability of overall survival. Two additional negative regulators of TP53, namely USP7 and PPM1D, are enriched for alterations in metastatic melanoma compared to primary melanoma. MDM4 amplifications are associated with a higher rate of metastasis to the brain, liver, and lungs, while MDM2 amplifications are associated with a higher rate of metastasis to the brain, liver, and adrenal glands. These findings suggest that patients with metastatic melanoma show an enhanced dysregulation of the TP53 pathway compared to primary disease; though still under ongoing preclinical evaluation to assess therapeutic implications, we propose that patients with metastatic melanoma and TP53 wild-type status may be more likely to benefit from MDM2, MDM4, USP7, and PPM1D inhibitors, both alone and in combination, compared to those with primary disease. Additionally, we found that patients with MDM2 alterations were more likely to have a deep deletion in CDKN2A, alterations that are also associated with a higher rate of metastasis to the brain. We found that patients with a CDKN2A deep deletion had a statistically significant higher rate of alterations in TTN, MUC16, LRP1B, NF1, and SERPINB4, alterations that have all been previously associated with a favorable response to immune checkpoint inhibitors in melanoma. We therefore propose that CDKN2A deletion may serve as a biomarker to predict response to immunotherapy in melanoma. Moreover, given prior documented cases of patients diagnosed with both melanoma and glioblastoma multiforme (GBM), we found that GBM displays the highest rate of deep deletions in CDKN2A (54.39%) across all cancer types screened. We analyzed 619 GBM samples and found that 9.16% display an MDM2 amplification and 9.52% display an MDM4 amplification. Given the genomic similarities between melanoma and glioblastoma, we suggest that patients with melanoma or GBM and amplifications in MDM2/4 and CDKN2A deletions may need the development of combinations of targeted inhibitors of MDM2/4, CDK’s and immunotherapy. We are currently pursuing these translational directions. Citation Format: Taylor E. Arnoff, Wafik S. El-Deiry. MDM2/MDM4 amplification and CDKN2A deletion in melanoma brain metastases and GBM may have implications for targeted therapeutics and immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB516.

SURG-03. Durability of an Early Management Strategy Facilitating Endoscopic Removal of Recurrent Choroid Plexus Carcinoma

BACKGROUND: Choroid plexus carcinoma (CPC) is a rare, primarily intraventricular neoplasm with a dismal prognosis. Extent of surgical removal is correlated with improved outcomes but is frequently limited due to tumor vascularity and size. Information related to surgical management and molecular drivers of tumor recurrence is currently limited. Here we characterize a case of multiply recurrent CPC treated solely with sequential endoscopic tumor removals over a 10-year period and highlight its genomic properties. METHODS: We performed a retrospective review of a 16-year-old female treated for CPC with local and distal recurrences undergoing repeat excision with minimally invasive neuro-endoscopy. We describe technical nuances associated with neuro-endoscopic intervention, mean hospital stay, complications, and perioperative MRI. Whole exome sequencing (WES), targeted sequencing, and methylation profiling results over time are reviewed. RESULTS: Five years after standard treatment, the patient was evaluated for a distant intraventricular recurrence. A total endoscopic resection was performed given the local, non-disseminated recurrence pattern. WES results included NF1, PER1, and GLI3 mutations as well as FGFR3 gain, and was negative for TP53 alterations. Repeat sequencing on a recurrence 4 years later showed persistent NF1 and FGFR3 alterations. Methylation profiling was consistent with “plexus tumor, subclass pediatric B”. Overall, short-term surveillance neuroimaging detected four isolated recurrences, all treated with complete endoscopic resections at 5 years, 6.5 years, 9 years, and 10 years after initial CPC diagnosis. Mean hospital stay for all recurrences was 1 day with no complications from treatment. CONCLUSION: We describe a patient with 4 isolated recurrences of CPC over a decade, each treated with complete endoscopic removal, and identify an unusual set of molecular alterations that persisted over time. These outcomes support a strategy encompassing frequent neuroimaging surveillance to facilitate a minimally invasive endoscopic surgical approach at early detection and relatively low tumor mutagenicity.

Utility of liquid biopsy (LB)-based comprehensive genomic profiling (CGP) of circulating tumor DNA (ctDNA) in lymphomas and plasma cell neoplasms.

e19543 Background: LB-based CGP of ctDNA can facilitate the molecular evaluation of lymphoid and plasma cell neoplasms (PCNs), especially when traditional CGP is infeasible due to insufficient tumor in the blood or tissue or when tissue biopsy itself cannot be performed. Methods: Retrospective study of LB samples from patients reported to have lymphomas or PCNs tested using hybrid-capture next-generation sequencing using the FoundationOne Liquid CDx (targeting 324 genes), FoundationOne Liquid (70 genes), or FoundationACT (62 genes) assays during routine clinical care between 5/2016 and 9/2021. Results: Among 48,459 unique patient samples submitted for CGP, 133 were from lymphomas or PCNs: 69 non-Hodgkin lymphoma (NHL), 32 PCN, 16 diffuse large B-cell lymphoma (DLBCL), and 16 classic Hodgkin lymphoma (cHL) cases. The median cell-free DNA yield was 72.7 ng (interquartile range [IQR]: 46.0-157.0), well above the minimum quantity needed for analysis. Reportable pathogenic genomic alterations were detected in 67.7% (90/133) of cases. The median maximum somatic allele frequency (MSAF) was 3.8% (IQR: 1.1-19.6%), with no statistically significant differences noted between DLBCL (8.2%), NHL (5.6%), cHL (1.7%), and PCNs (1.4%) ( P= 0.13, Kruskal-Wallis test). In all, 322 pathogenic short variants and 3 pathogenic rearrangements were detected (median variant allele frequency [VAF]: 0.6%, IQR: 0.3-2.6%, range: 0.09-81.8%). One hundred ninety-seven had VAFs < 1.0%, indicating excellent sensitivity. NHLs exhibited pathogenic alterations in TP53 (53.2% of cases in which pathogenic alterations were identified), KMT2D (14.9%), NF1 (10.6%), MYD88 (8.5%), BCL2 (6.4%), BRAF (6.4%), EZH2 (6.4%), NRAS (6.4%), BTK (4.3%, all of which were C481X ibrutinib resistance mutations in cases of chronic lymphocytic leukemia detected at VAFs ranging from 0.18-5.5%), KRAS (4.3%), RB1 (4.3%), and TNFAIP3 (4.3%), among others. PCNs exhibited pathogenic alterations in TP53 (54.6%), KRAS (18.2%), NF1 (13.6%), PTPN11 (13.6%), BRAF (9.1%), NRAS (9.1%), MAP2K1 (4.6%), and RB1 (4.6%), among others. DLBCLs exhibited pathogenic alterations in TP53 (63.6%), MYD88 (27.3%), CCND2/3 (9.1%), EZH2 (9.1%), and KMT2D (9.1%), among others. CD274 (PD-L1) and PDCD1LG2 (PD-L2) amplification and IGH- PAX5 and IGH- MYC fusions were also detected in individual cases of DLBCL. cHLs exhibited pathogenic alterations in TP53 (40.0%), ATM (20.0%), BCOR (10.0%), KRAS (10.0%), MYD88 (10.0%), and PDCD1LG2 (PD-L2) (10.0%), among others. Conclusions: LB identified clinically actionable genomic alterations in lymphomas and PCNs and may be used when traditional CGP of tumor biopsy specimens cannot be performed. Given its low limit of detection, LB may also allow for minimally invasive dynamic monitoring of response to therapy.

Rosette-forming glioneuronal tumours are midline, FGFR1-mutated tumours.

Rosette-forming glioneuronal tumour (RGNT) is a rare central nervous system (CNS) World Health Organization (WHO) grade 1 brain neoplasm. According to the WHO 2021, essential diagnostic criteria are a 'biphasic histomorphology with neurocytic and a glial component, and uniform neurocytes forming rosettes and/or perivascular pseudorosettes associated with synaptophysin expression' and/or DNA methylation profile of RGNT whereas 'FGFR1 mutation with co-occurring PIK3CA and/or NF1 mutation' are desirable criteria. We report a series of 46 cases fulfilling the essential pathological diagnostic criteria for RGNT. FGFR1 and PIK3CA hotspot mutations were searched for by multiplexed digital PCR in all cases, whereas DNA methylation profiling and/or PIK3R1 and NF1 alterations were analysed in a subset of cases. Three groups were observed. The first one included 21 intracranial midline tumours demonstrating FGFR1 mutation associated with PIK3CA or PIK3R1 (n =19) or NF1 (n =1) or PIK3CA and NF1 (n =1) mutation. By DNA methylation profiling, eight cases were classified as RGNT (they demonstrated FGFR1 and PIK3CA or PIK3R1 mutations). Group 2 comprised 11 cases associated with one single FGFR1 mutation. Group 3 included six cases classified as low-grade glioma (LGG) other than RGNT (one-sixth showed FGFR1 mutation and one a FGFR1 and NF1 mutation) and eight cases without FGFR1 mutation. Groups 2 and 3 were enriched in lateral and spinal cases. We suggest adding FGFR1 mutation and intracranial midline location as essential diagnostic criteria. When DNA methylation profiling is not available, a RGNT diagnosis remains certain in cases demonstrating characteristic pathological features and FGFR1 mutation associated with either PIK3CA or PIK3R1 mutation.

Evaluation of ctDNA alterations in mCRPC patients with germline pathogenic mutations.

177 Background: Germline alterations are found in approximately 12-17% of CRPC patients. Similarly, evaluating tumoral changes with circulating tumor DNA (ctDNA) has become an increasingly useful tool for understanding mechanisms underpinning disease progression. In this study, we evaluated both germline and somatic genetic changes in patients with mCRPC. Methods: Patients included had germline screening and ctDNA analyzed with the Guardant 360 assay. All patients were CRPC at the time of Guardant testing. Germline alterations were classified as pathogenic/likely-pathogenic or not pathogenic. Only ctDNA alterations with an alleleic fraction greater than 0.5% were included in analyses. Additional evaluation of CRPC status, treatment history, family history and other clinical covariates are ongoing. Chi-square and Fischer’s Exact tests were used for comparison of cohorts. Results: A total of 168 Caucasian CRPC patients had Guardant 360 testing at time of progression and germline testing between 2015-2021. 61% (n = 102/168) of patients have previously had treatment with abiraterone, 49% (n = 82/168) have had Enzalutamide and 40% (n = 68/168) have had treatment with taxanes. 12% (n = 20/168) of CRPC patients had a pathogenic/likely-pathogenic (P/LPv) germline alteration, 46% (n = 77/168) had a germline variant of unknown significance (VUS), 42% (n = 71/168) were germline negative. CRPC patients with pathogenic germline mutations were significantly more likely to have subsequent somatic alterations in BRCA2 (OR = 5.05, 95% C.I. (1.11, 23.01), p = 0.055), NF1 (OR = 7.89, 95% C.I. (2.15, 28.10), p = 0.004), and TP53 (OR = 3.52, 95% C.I. (1.28, 9.68), p = 0.015). In TP53, among germline positive patients, 45% (n = 9/20) had TP53 alterations compared to 30% (n = 45/148) of germline negative patients. Conclusions: Germline positive (P/LPv) CRPC patients were significantly more likely to have somatic alterations in BRCA2, NF1, and TP53. Understanding the totality of genetic changes, both germline and acquired somatic alterations is essential as the arsenal of targeted treatment for CRPC continues to expand. Additional studies including longitudinal assessment genetic changes and clinical correlates will be necessary to evaluate these findings in the context of treatment outcomes and disease progression.

Abstract PD14-04: Circulating tumor DNA characterization of invasive lobular carcinoma in patients with metastatic breast cancer

Abstract Background:Invasive lobular carcinoma (ILC) is the second most common histology of breast cancer, accounting for approximately 10-15% of cases. Prior studies have demonstrated that loss of E-cadherin, as well as alterations in tissue including CDH1, FOXA1, TBX3 and PTEN loss, that were more commonly observed in Luminal A ILC, while GATA3 was more commonly observed in invasive ductal carcinoma (IDC) (Ciriello et al., Cell 2015). However, data regarding the characterization of circulating tumor DNA (ctDNA) in patients (pts) with metastatic ILC are limited. We hypothesized that there would be distinct mutational profiles between pts with metastatic ILC and IDC that could be characterized using ctDNA. Methods:This retrospective cohort study included de-identified clinical, pathological, and ctDNA data from pts with metastatic breast cancer (MBC) combined under a data use agreement and approved by the institutional review boards of three sites: Washington University in St. Louis (MO), Northwestern University (Chicago, IL), and Massachusetts General Hospital (Boston, MA). All pts included in the study had ctDNA testing per standard of care with plasma-based genotyping performed by Guardant360 (Redwood City, CA) between 2015-2020. Histological classification (ILC vs. IDC) was defined based on review of pathology reports from the primary tumor or from breast biopsies of de novo MBC, and additional clinical and pathological variables were obtained via electronic medical record review. Single nucleotide variants (SNVs) were annotated using OncoKB and ClinVar and only pathogenic variants were included. Mutational profiles were compared across histologic subtypes using Fisher’s exact test to assess differences in alteration frequency across subtypes. Multivariable analysis was performed. Results:A total of 994 pts with MBC underwent ctDNA testing and were included in the analysis. 10.7% of pts had ILC (N=106) and 89.3% had IDC (N=888). 89.4% of ILC cases were categorized as hormone-receptor positive (HR+) compared with 67.1% of IDC cases. Pts with ILC had a lower frequency of triple-negative (6.7% vs. 17.7%) and HER2 positive (3.9% vs. 15.2%) breast cancer compared with IDC. Pts with ILC had a significantly higher number of pathogenic SNVs compared with IDC (mean 4.45 vs. 2.77; P=0.0037). In contrast, pts with ILC had a significantly lower number of copy number alterations as compared to pts with IDC (mean 0.40 vs. 1.03; P=0.0017). No differences were observed in mutant allele frequency between pts with ILC and IDC. The 5 most common alterations observed in pts with ILC were the following: PIK3CA, TP53, ESR1, ERBB2, and ARID1A. Alterations in AR, BRAF, CDH1, ERBB2, FGFR2, IDH2, KRAS, NF1, PIK3CA, SMAD4, and TERT were significantly higher in ILC than IDC (all P<0.05). In contrast, mutations in GATA3, and amplifications in ERBB2 and MYC were significantly more common in pts with IDC (all P<0.05). In multivariable analysis, mutations in BRAF, CDH1, ERBB2, IDH2, TERT remained significantly higher in ILC, while amplification of MYC was significantly higher in IDC (all P<0.05). After restricting the analysis to pts with HR+ HER2 negative MBC, the following genes were significant in multivariate analysis: CDH1 and ERBB2 for pts with ILC and MYC amplification for pts with IDC (all P<0.05). Discussion:In this large, multi-institutional dataset, pts with metastatic ILC were characterized by a significantly higher number of SNVs in ctDNA compared to pts with IDC, suggesting higher mutational burden. We report several alterations that were significantly different in ILC vs. IDC. These results demonstrate the ctDNA profile of pts with ILC, and future studies should explore serial plasma-based genotyping to track ILC evolution to develop targeted precision medicine based therapeutic approaches for this unique subset of pts with MBC. Citation Format: Andrew A Davis, Lorenzo Gerratana, Katherine Clifton, Marko Velimirovic, Whitney L Hensing, Ami N Shah, Paolo D’Amico, Carolina Reduzzi, Qiang Zhang, Charles S Dai, Elyssa N Denault, Nusayba A Bagegni, Mateusz Opyrchal, Foluso O Ademuyiwa, Ron Bose, William J Gradishar, Amir Behdad, Cynthia X Ma, Aditya Bardia, Massimo Cristofanilli. Circulating tumor DNA characterization of invasive lobular carcinoma in patients with metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD14-04.

Molecular alterations associated with improved outcome in patients with glioblastoma treated with Tumor-Treating Fields.

BackgroundThe genomic and overall biologic landscape of glioblastoma (GB) has become clearer over the past 2 decades, as predictive and prognostic biomarkers of both de novo and transformed forms of GB have been identified. The oral chemotherapeutic agent temozolomide (TMZ) has been integral to standard-of-care treatment for nearly 2 decades. More recently, the use of non-pharmacologic interventions, such as application of alternating electric fields, called Tumor-Treating Fields (TTFields), has emerged as a complementary treatment option that increases overall survival (OS) in patients with newly diagnosed GB. The genomic factors associated with improved or lack of response to TTFields are unknown.MethodsWe performed comprehensive genomic analysis of GB tumors resected from 55 patients who went on to receive treatment using TTFields, and compared results to 57 patients who received standard treatment without TTFields.ResultsWe found that molecular driver alterations in NF1, and wild-type PIK3CA and epidermal growth factor receptor (EGFR), were associated with increased benefit from TTFields as measured by progression-free survival (PFS) and OS. There were no differences when stratified by TP53 status. When NF1, PIK3CA, and EGFR status were combined as a Molecular Survival Score, the combination of the 3 factors significantly correlated with improved OS and PFS in TTFields-treated patients compared to patients not treated with TTFields.ConclusionsThese results shed light on potential driver and passenger mutations in GB that can be validated as predictive biomarkers of response to TTFields treatment, and provide an objective and testable genomic-based approach to assessing response.

Molecular Analysis of Luminal Androgen Receptor Reveals Activated Pathways and Potential Therapeutic Targets in Breast Cancer.

Triple-negative breast cancers represent 15% of all mammary malignancies and encompass several entities with different genomic characteristics. Among these, luminal androgen receptor (LAR) tumors express the androgen receptor (AR) and are characterized by a genomic profile which resembles luminal breast cancers. Moreover, LAR malignancies are usually enriched in PIK3CA, KMTC, CDH, NF1, and AKT1 alterations. Still, molecular features, clinical behavior and prognosis of this variant remain controversial, while identification of effective treatments represents an unmet medical need. Additionally, the predictive role of the AR is unclear. We performed an extensive next generation sequencing analysis using a commercially available panel in a cohort of patients with LAR breast cancer followed at two local Institutions. We next employed bioinformatic tools to identify signaling pathways involved in LAR pathogenesis and looked for potentially targetable alterations. Eight patients were included in the study. In our cohort we found 26 known genetic alterations (KGAs) in 15 genes and 64 variants of unknown significance (VUS) in 59 genes. The most frequent KGAs were single nucleotide variants in PIK3CA, HER2, PTEN and TP53. Among VUS, CBFB, EP300, GRP124, MAP3K1, RANBP2 and TSC2 represented recurrently altered genes. We identified five signaling pathways (MAPK, PI3K/AKT, TP53, apoptosis and angiogenesis) involved in the pathogenesis of LAR breast cancer. Several alterations, including those in PIK3CA, ERBB2 and PI3K/AKT/mTOR signaling, were potentially targetable. Our findings confirm a role for PI3K/AKT/mTOR signaling in the pathogenesis of LAR breast cancers and indicate that targeting this pathway, along with ERBB2 mutations, may represent an additional therapeutic strategy which deserves further exploration in larger studies.

IDH-wild type glioblastomas featuring at least 30% giant cells are characterized by frequent RB1 and NF1 alterations and hypermutation

Giant cell glioblastoma (GC-GBM) is a rare variant of IDH-wt GBM histologically characterized by the presence of numerous multinucleated giant cells and molecularly considered a hybrid between IDH-wt and IDH-mutant GBM. The lack of an objective definition, specifying the percentage of giant cells required for this diagnosis, may account for the absence of a definite molecular profile of this variant. This study aimed to clarify the molecular landscape of GC-GBM, exploring the mutations and copy number variations of 458 cancer-related genes, tumor mutational burden (TMB), and microsatellite instability (MSI) in 39 GBMs dichotomized into having 30–49% (15 cases) or ≥ 50% (24 cases) GCs. The type and prevalence of the genetic alterations in this series was not associated with the GCs content (< 50% or ≥ 50%). Most cases (82% and 51.2%) had impairment in TP53/MDM2 and PTEN/PI3K pathways, but a high proportion also featured TERT promoter mutations (61.5%) and RB1 (25.6%) or NF1 (25.6%) alterations. EGFR amplification was detected in 18% cases in association with a shorter overall survival (P = 0.004). Sixteen (41%) cases had a TMB > 10 mut/Mb, including two (5%) that harbored MSI and one with a POLE mutation. The frequency of RB1 and NF1 alterations and TMB counts were significantly higher compared to 567 IDH wild type (P < 0.0001; P = 0.0003; P < 0.0001) and 26 IDH-mutant (P < 0.0001; P = 0.0227; P < 0.0001) GBMs in the TCGA PanCancer Atlas cohort. These findings demonstrate that the molecular landscape of GBMs with at least 30% giant cells is dominated by the impairment of TP53/MDM2 and PTEN/PI3K pathways, and additionally characterized by frequent RB1 alterations and hypermutation and by EGFR amplification in more aggressive cases. The high frequency of hypermutated cases suggests that GC-GBMs might be candidates for immune check-point inhibitors clinical trials.

Malignant Melanoma With Neuroendocrine Differentiation: A Case Report and Literature Review

BackgroundMelanoma has a wide range of histologic variants and cytomorphologic features that make its diagnosis challenging. Melanoma can also rarely have neuroendocrine markers adding further diagnostic uncertainty particularly given that unrelated tumor types, such as prostate cancer, can also display focal neuroendocrine differentiations.Case presentationOur patient is a 74-year-old Caucasian man found to have a lung mass. Initial biopsy revealed typical microscopic morphology and neuroendocrine differentiation consistent with small cell carcinoma. Despite standard chemoradiation treatment, the patient continued to progress with new metastasis in the brain, liver and bone. Subsequent chest wall biopsy revealed golden-brown pigment associated with melanin. Further tumor immunohistochemistry revealed extensive neuroendocrine differentiation with CD56, synaptophysin, and INSM1, as well as strong immunoreactivity for melanocyte markers including SOX10, S100, PRAME, and MITF, consistent with metastatic melanoma with neuroendocrine differentiation. Genomic testing revealed increased tumor mutational burden and alterations in NF1, BRAF, CDKN2A/B, TERT. The patient was transitioned to checkpoint inhibitor therapy with nivolumab and ipilimumab and had resolution of his intracranial mass and decrease in size of other metastatic lesions.ConclusionOften the combination of anatomic findings such as a lung mass, typical microscopic morphology, and confirmation of neuroendocrine differentiation correctly identifies a patient with small cell carcinoma. However, in a patient who fails to respond to treatment, a broader immunohistochemical workup along with molecular testing with additional tissue may be warranted.

Clinicopathological and genomic characterization of BCORL1-driven high-grade endometrial stromal sarcomas

BCORL1 is a transcriptional corepressor homologous to BCOR. We describe 12 BCORL1-altered uterine sarcomas with striking resemblance to BCOR-altered endometrial stromal sarcoma (BCOR-ESS), including 5 with BCORL1 rearrangements (JAZF1-BCORL1, EP300-BCORL1, or internal BCORL1 rearrangement), 5 with inactivating BCORL1 mutations (T513fs*22, P600fs*1, R945*, R1196*, or R1265fs*4) and 2 with homozygous BCORL1 deletion. The median patient age was 57.5 years (range 33–79). An association with aggressive clinical behavior was identified. Diagnoses assigned prior to genomic testing varied: 7 tumors were previously diagnosed as ESS, 2 as high-grade uterine sarcomas, 2 as myxoid uterine leiomyosarcomas, and 1 as a uterine spindle cell neoplasm consistent with leiomyosarcoma. Tumors harbored frequent gelatinous, mucomyxoid-like appearance by gross examination and unique histology with morphological overlap with BCOR-ESS. Key microscopic features included (1) a spindle cell appearance, most often with at least focal myxoid stroma, (2) variable amounts of hypocellular fibromyxoid spindle areas with lower grade atypia and/or (3) variable amounts of epithelioid areas with higher grade atypia. Specifically, spindle and epithelioid components were present in 100 and 75% of sarcomas, respectively; myxoid stroma was identified in 83%, collagen plaques or fibrosis in 50%, and high-grade nuclear atypia was present in 42%. Like BCOR-ESS, 50% of BCORL1-altered sarcomas exhibited CDK4 amplification or CDKN2A loss. In contrast, 33% harbored NF1 alterations, while 25% had other alterations in the NF2-mTOR pathway, expanding potential therapeutic targets. In conclusion, inactivating BCORL1 genomic alterations may define a distinct subset of high-grade endometrial stromal sarcomas with biological overlap with BCOR-ESS, both of which may mimic myxoid leiomyosarcomas.

NF1-mutated melanomas reveal distinct clinical characteristics depending on tumour origin and respond favourably to immune checkpoint inhibitors

BackgroundNF1-mutated tumours represent a small subset (10–15%) of melanomas, not sufficiently analysed in large clinical cohorts. This study investigated the largest multicentre collection of NF1-mutated melanomas to date. MethodsThis study analysed a multicentre tumour tissue sample cohort from 266 patients with NF1-mutated melanoma. Targeted next-generation sequencing of the TERT promoter and 29 relevant melanoma genes was performed. Survival was compared with NF1 wild-type cohorts from the Tissue Registry in Melanoma project (n = 432). ResultsMost NF1-mutated melanoma arose in the head-and-neck region of patients >60 years. NF1 alterations were frequently inactivating, primarily non-sense, less frequently truncating mutations. Non-inactivating NF1 mutations more frequently co-occurred with activating BRAF and RAS mutations. NF1-mutated tumours had higher numbers of gene mutations and UV signature C>T and CC>TT transitions than BRAF, RAS and triple wild-type melanomas. NF1-mutated acral and mucosal melanomas harboured a different mutation signature and were frequent in women (69% and 83%, respectively), differing from non-acral cutaneous NF1-mutated melanomas (men 73%, women 27%). Overall survival in stage IV disease was comparable for patients with NF1-mutated or wild-type melanoma. However, in patients receiving first-line immune checkpoint inhibitor treatment, better median overall survival (mOS) was observed for NF1-mutated than wild-type tumours (mOS = not reached vs mOS = 25.82, p = 0.0154, n = 80 and 432, respectively). ConclusionsCutaneous, acral and mucosal NF1-mutated melanomas vary in clinical and genetic characteristics and demonstrate a favourable outcome on immune checkpoint inhibition therapy.

Malignant Melanoma of the Genitourinary System

Abstract Introduction/Objective Malignant melanoma (MM) of mucosal membranes (excluding anus and head and neck) is a rare but aggressive disease with poor outcome. There is little information available on the development mechanism, risk factors, and management of this tumor, mainly due to the low number of cases. Methods/Case Report We performed a comprehensive literature review on mucosal MM (between 1970-2020). We identified 52 papers reporting 242 patients with primary genitourinary melanomas (limited to urothelium, vagina and cervix). A comprehensive review of the demographics, stage, treatment and survival was performed. Results (if a Case Study enter NA) The demographics are provided in Table 1. In 204 cases, lesions were located in the urothelium (urethra: 202, bladder: 2) followed by 34 in the vagina and 4 in uterine cervix. None of the cases had any other known primary source of MM. Molecular studies in a subset of cases revealed alterations in c-KIT, NRAS, BRAF (non-V600E and V600E), TP53 and NF1 (Table 2). Tumor stage was provided in a few (n=10) cases (stage 1=1, stage 2=1, stage 3=3 &amp; stage 4=5). 3 patients had distant metastasis (brain, retroperitoneal and inguinal lymph nodes). Treatment data was available in 178 cases. 177 patients were managed by surgery. In addition to surgery, 10 received chemotherapy, 7 received immunotherapy and chemotherapy, 2 received chemoradiation, 1 received immunotherapy and 1 received radiotherapy. In 43 patients, the treatment regimen was not provided. The outcome was available in 178 cases (range of follow up between 3-97 months), showing 15 deaths of disease. Median survival based on available information in 28 patients was 82% (5-year survival). Table 1 legend: Demographics of genitourinary malignant melanoma cases. Table 2 legend: Frequency of molecular alterations in genitourinary malignant melanoma. Conclusion Similarities in genetic signatures of mucosal and skin MM suggest similar mechanism of development; however, unlike skin melanoma, there is less BRAF mutation and more of PI3K/AKT/mTOR pathway alterations in mucosal MM. Prolonged administration of chemotherapy (i.e., methotrexate) and immune-modulating agents (i.e., natalizumab) may be a risk factor. In light of absence of a definite adjuvant therapy, tumor stage at the time of diagnosis and proper surgical removal have central role in the prognosis and survival of patients.

Molecular profiling of pediatric meningiomas shows tumor characteristics distinct from adult meningiomas

In contrast to adults, meningiomas are uncommon tumors in childhood and adolescence. Whether adult and pediatric meningiomas differ on a molecular level is unclear. Here we report detailed genomic analyses of 37 pediatric meningiomas by sequencing and DNA methylation profiling. Histologically, the series was dominated by meningioma subtypes with aggressive behavior, with 70% of patients suffering from WHO grade II or III meningiomas. The most frequent cytogenetic aberrations were loss of chromosomes 22 (23/37 [62%]), 1 (9/37 [24%]), 18 (7/37 [19%]), and 14 (5/37 [14%]). Tumors with NF2 alterations exhibited overall increased chromosomal instability. Unsupervised clustering of DNA methylation profiles revealed separation into three groups: designated group 1 composed of clear cell and papillary meningiomas, whereas group 2A comprised predominantly atypical meningiomas and group 2B enriched for rare high-grade subtypes (rhabdoid, chordoid). Meningiomas from NF2 patients clustered exclusively within groups 1 and 2A. When compared with a dataset of 105 adult meningiomas, the pediatric meningiomas largely grouped separately. Targeted panel DNA sequencing of 34 tumors revealed frequent NF2 alterations, while other typical alterations found in adult non-NF2 tumors were absent. These data demonstrate that pediatric meningiomas are characterized by molecular features distinct from adult tumors.