NF1 Loss Research Articles

Runx1/3-driven adaptive endoplasmic reticulum stress pathways contribute to neurofibromagenesis.

Neurofibromatosis type 1 (NF1) patients are predisposed to develop plexiform neurofibromas (PNFs). Three endoplasmic reticulum (ER) stress response pathways restore cellular homeostasis. The unfolded protein response (UPR) sensors contribute to tumor initiation in many cancers. We found that all three UPR pathways were activated in mouse and human PNFs, with protein kinase RNA [PKR]-like ER kinase (PERK) the most highly expressed. We tested if neurofibroma cells adapt to ER stress, leading to their growth. Pharmacological or genetic inhibition of PERK reduced mouse neurofibroma-sphere number, and genetic inhibition in PERK in Schwann cell precursors (SCPs) decreased tumor-like lesion numbers in a cell transplantation model. Further, in a PNF mouse model, deletion of PERK in Schwann cells (SCs) and SCPs reduced tumor size, number, and increased survival. Mechanistically, loss of Nf1 activated PERK-eIF2α-ATF4 signaling and increased ATF4 downstream target gene p21 translocation from nucleus to cytoplasm. This nucleus-cytoplasm translocation was mediated by exportin-1. Runx transcriptionally activated ribosome gene expression and increased protein synthesis to allow SCs to adapt to ER stress and tumor formation. We propose that targeting proteostasis might provide cytotoxic and/or potentially durable novel therapy for PNFs.

Loss of Nf1 and Ink4a/Arf Are Associated with Sex-Dependent Growth Differences in a Mouse Model of Embryonal Rhabdomyosarcoma.

Rhabdomyosarcoma (RMS) is an aggressive form of cancer that accounts for half of all pediatric soft tissue sarcomas. Little progress has been made in improving survival outcomes over the past three decades. Mouse models of rhabdomyosarcoma are a critical component of translational research aimed at understanding tumor biology and developing new, improved therapies. Though several models exist, many common mutations found in human rhabdomyosarcoma tumors remain unmodeled and understudied. This study describes a new model of embryonal rhabdomyosarcoma driven by the loss of Nf1 and Ink4a/Arf, two mutations commonly found in patient tumors. We find that this new model is histologically similar to other previously-published rhabdomyosarcoma models, although it substantially differs in the time required for tumor onset and in tumor growth kinetics. We also observe unique sex-dependent phenotypes in both primary and newly-developed orthotopic syngeneic allograft tumors that are not present in previous models. Using in vitro and in vivo studies, we examined the response to vincristine, a component of the standard-of-care chemotherapy for RMS. The findings from this study provide valuable insight into a new mouse model of rhabdomyosarcoma that addresses an ongoing need for patient-relevant animal models to further translational research.

YAP/TAZ activation predicts clinical outcomes in mesothelioma and is conserved in in vitro model of driver mutations.

The Hippo signalling pathway is dysregulated across a wide range of cancer types and, although driver mutations that directly affect the core Hippo components are rare, a handful is found within pleural mesothelioma (PM). PM is a deadly disease of the lining of the lung caused by asbestos exposure. By pooling the largest-scale clinical datasets publicly available, we here interrogate associations between the most prevalent driver mutations within PM and Hippo pathway disruption in patients, while assessing correlations with a variety of clinical markers. This analysis reveals a consistent worse outcome in patients exhibiting transcriptional markers of YAP/TAZ activation, pointing to the potential of leveraging Hippo pathway transcriptional activation status as a metric by which patients may be meaningfully stratified. Preclinical models recapitulating disease are transformative in order to develop new therapeutic strategies. We here establish an isogenic cell-line model of PM, which represents the most frequently mutated genes and which faithfully recapitulates the molecular features of clinical PM. This preclinical model is developed to probe the molecular basis by which the Hippo pathway and key driver mutations affect cancer initiation and progression. Implementing this approach, we reveal the role of NF2 as a mechanosensory component of the Hippo pathway in mesothelial cells. Cellular NF2 loss upon physiological stiffnesses analogous to the tumour niche drive YAP/TAZ-dependent anchorage-independent growth. Consequently, the development and characterisation of this cellular model provide a unique resource to obtain molecular insights into the disease and progress new drug discovery programs together with future stratification of PM patients.

Next-generation sequencing shows the genomic features of ovarian clear cell cancer and compares the genetic architectures of high-grade serous ovarian cancer and clear cell carcinoma in ovarian and endometrial tissues.

Ovarian clear cell carcinoma (OCCC) is a special histological type of epithelial ovarian cancer (EOC) that is not derived from epithelial cells of the ovarian or fallopian tube as the most common type of ovarian cancer, high-grade serous ovarian carcinoma (HGSOC), but is closely related to endometriosis and similar to endometrial clear cell carcinoma (ECCC) at morphologic and phenotypic features. However, limited data was shown in OCCC genomic features and compared with that in OCCC, HGSOC and ECCC. Herein, we utilized next-generation sequencing analysis of a panel of 1,021 genes to profile the mutational alterations in 34 OCCC and compared them to those from HGSOC (402 cases) and ECCC (30 cases). In result, the ARID1A and PIK3CA are high-frequency mutations of OCCC. Clonal architectures showed that all the mutations of genes occur in the later stage in the OCCC progress, whereas KRAS mutation is the earlier event compared with mutation of ARID1A or PIK3CA, which usually occurs in a group of ARID1A or PIK3CA mutations. The mutation frequency of main driver genes is similar between OCCC and ECCC, while TP53 is the main mutation in HGSOC and ECCC. Shared mutational signatures between OCCC and ECCC tissues with commonly observed a C>T change indicated a common carcinogens-exposed between these two carcinomas, but HGSOC and ECCC have common and distinct mutational signatures across cohorts respectively. In addition, we identified some novel CNV gains in NF1, ASXL1, TCF7L2, CREBBP and LRP1B and loss in ATM, FANCM, RB1 and FLT in OCCC. Our study offered a new perspective for OCCC tumorigenesis from two organs, the ovary and uterus, at genomic architectures and revealed novel CNV events for helping to provide theoretical support for OCCC treatment.

Multi-institution analysis of tumor mutational burden and outcomes in pediatric central nervous system tumor patients.

Pediatric central nervous system (CNS) tumors are the leading cause of pediatric cancer mortality. Research addressing genomic biomarkers and clinical outcomes is needed to inform therapeutic decision-making. We conducted a retrospective analysis of pediatric patients (age <21) diagnosed with a primary CNS tumor at four upstate New York hospitals from 2008 to 2021. Clinical and histopathologic data were identified from each patient, including genomic analysis of somatic mutations and tumor mutational burden (TMB) where available. These variables were each compared with overall survival using Cox regression analyses. Multivariable analysis was conducted to identify patient characteristics that may independently predict survival. We identified 119 patients. Common tumor types included low-grade glioma (N=51), high-grade glioma (N=29), and medulloblastoma (N=11). Common driver mutations included TP53 inactivation (N=16), BRAF-KIAA1549 fusion (N=16), FGFR1 amplification (N=12), BRAF V600E mutation (N=12), NF1 loss (N=12), and H3F3A K28M mutation (N=6). Median TMB was one mutation/megabase (mut/Mb, range=0-132). Overall survival was 79.9%. Variables associated with poorer survival on univariable analysis were higher TMB (p=.002, HR 4.97), high-grade tumors (p=.009, HR 84.3), and high-grade glioma histology (p=.021, HR 3.14). Multivariable analyses further identified TMB (p=.011, HR 4.46) and high-grade histology (p=.015, HR 5.28) as independently predictive of worse survival. Tumor progression was more common in high-TMB (N=15, 44%) than in low-TMB tumors (N=19, 35%). High TMB is correlated with higher rates of progression and death as compared to low-TMB tumors. These findings may help identify patients who may benefit from alternative treatments, such as immunotherapies.

Abstract A007: Integrative multiomic analysis reveals NOTCH signaling is derepressed by loss of PRC2 in malignant peripheral nerve sheath tumors

Abstract Neurofibromatosis Type 1 syndrome (NF1) is a cancer predisposition syndrome caused by inheritance of one loss of function allele of the NF1 gene. NF1 patients can develop malignant peripheral nerve sheath tumors (MPNST), a deadly soft tissue sarcoma. MPNSTs develop after somatic loss of the wild-type NF1 allele, resulting in an increase in Ras-GTP activated signaling. This malignant transformation is still not completely understood, but loss of TP53 or CDKN2A/2B function and the polycomb repressor complex 2 (PRC2) are common events during the transition to MPNST. SUZ12, EED and EZH2 are core components of PRC2, which is responsible for trimethylation of Histone H3 at lysine 27 (H3K27me3), a repressive epigenetic mark that silences genes through formation of heterochromatin. We hypothesized loss of PRC2 has direct and indirect effects on gene expression resulting in MPNSTs. PRC2 loss may result in altered topologically associated domains, which can affect access of promoters by distal enhancers. Altered gene expression leads to deregulation of cell differentiation and proliferation controls, promoting the transition to MPNSTs. The purpose of this study is to identify epigenomic vulnerabilities of MPNSTs using multi-omics to elucidate more effective treatments. We have engineered NF1-deficient human Schwann cells with or without concomitant loss of function SUZ12 or EED mutations. We found major epigenomic changes in the histone code of SUZ12 mutants including complete loss of H3K27me3 with concomitant gain in H3K27 acetylation. SUZ12-deficient cells also become hypersensitive to histone deacetylase inhibitors. RNA sequencing has revealed many differentially expressed genes when SUZ12 and NF1 are lost in our engineered cell lines. Preliminary results show 92 differentially expressed genes that are common to PRC2-deficient MPNSTs and engineered cell lines. 824 genes are common between our engineered cell lines where 686 of these are derepressed when SUZ12 or EED are lost with NF1. We also identified an increase in differentially expressed genes when PRC2 is lost with NF1 versus NF1 loss alone. Comparing these to genes expressed in MPNST patient samples, we have identified potential drivers of MPNST generation. Pathway enrichment analysis on differentially expressed genes indicates many upregulated cancer related pathways when PRC2 is lost. We found NOTCH and Sonic Hedgehog signaling are common to all comparisons. NOTCH signaling has been implicated in Schwann cell development. These are currently being validated via Western blot. Proteomics data will also be compared to the findings. Citation Format: Minu Bhunia, Christopher M. Stehn, Mahathi Madala, Kyle Williams, Alex Larsson, Tyler Jubenville, Suganth Suppiah, Gelareh Zadeh. Integrative multiomic analysis reveals NOTCH signaling is derepressed by loss of PRC2 in malignant peripheral nerve sheath tumors. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A007.

Loss of NF1 in Melanoma Confers Sensitivity to SYK Kinase Inhibition.

A kinase inhibitor screen identifies SYK as a targetable vulnerability in melanoma cells with NF1 loss of function.

DDDR-06. NEUROFIBROMATOSIS TUMOR SUPPRESSORS COOPERATIVELY DRIVE TUMOR DE-DIFFERENTIATION AND MEK INHIBITOR RESISTANCE IN PERIPHERAL NERVOUS SYSTEM TUMORS

Abstract Schwann cell derived tumors comprising schwannomas, neurofibromas, and malignant peripheral nerve sheath tumors (MPNSTs) are the most common cancers of the peripheral nervous system and often arise in patients with neurofibromatosis type-1 (NF-1) or type-2 (NF-2). NF-1 is caused by loss of NF1, a negative regulator of Ras signaling, and NF-2 is caused by loss of NF2, a pleiotropic tumor suppressor with numerous functions including inhibition of PAK signaling. However, whether functional interactions exist between the NF1 and NF2 tumor suppressors remain unclear. More broadly, there are currently no effective molecular therapies for patients with Schwann cell tumors beyond the MEK inhibitor selumetinib to treat neurofibromas in patients with NF-1. Here, we integrate DNA methylation profiling, whole exome sequencing, bulk and single-cell RNA sequencing, biochemistry, and pharmacology across human samples, cell lines, and mouse xenografts to identify cellular de-differentiation as a driver of malignant transformation and selumetinib resistance. Single nuclear RNA-sequencing of human neurofibromas (n = 3) or MPNSTs (n = 3) revealed a total of 13 cell types with increased proliferating, de-differentiated tumor cell populations in MPNST samples. Single cell RNA-sequencing of MPNST mouse xenografts revealed persistence of de-differentiated cell populations in selumetinib treated samples compared to vehicle control, suggesting cellular de-differentiation underlies treatment resistance. A genome-wide CRISPRi screen for mediators of selumetinib response in NF1 deficient neurofibroma cells revealed NF2 loss drives selumetinib resistance. Consistently, NF2 suppression in NF1 deficient neurofibroma cells caused Schwann cell de-differentiation and activation of PAK, a serine threonine kinase. Translationally, a small molecule PAK inhibitor in combination with selumetinib formed an effective therapy in mouse MPNST xenografts. In sum, we elucidate a paradigm of de-differentiation driving malignant transformation and treatment resistance in Schwann cell tumors, uncovering a functional link between the NF1 and NF2 tumor suppressors that sheds light on a novel therapeutic vulnerability.

PATH-28. DIFFERENCES IN METHYLATION PROFILES BETWEEN LONG-TERM SURVIVORS AND SHORT-TERM SURVIVORS OF IDH WILD-TYPE GLIOBLASTOMA

Abstract INTRODUCTION Patients with glioblastomas (GBM) have an overall survival (OS) of approximately 15 months. However, approximately 5% of patients survive much longer, with an OS of &amp;gt; 5 years. This study examines the differences in methylation profiles between long-term survivors ( &amp;gt; 5 years, LTS) and short-term survivors (&amp;lt; 1 year, STS) with an isocitrate dehydrogenase (IDH) wild-type GBM. METHODS In a multicenter retrospective analysis, we identified 25 long-term survivors with a histologically confirmed GBM. These were age and sex-matched to a short-term survivor. The methylation profiles of all 50 samples were analyzed with EPIC 850k, classified according to the DKFZ methylation classifier, and the methylation profiles of all IDH wild-type LTS vs STS were compared. RESULTS After methylation profiling, 16/25 LTS and 23/25 STS were confirmed to be IDH wild-type GBMs, all with copy number gains of chromosome 7 and loss of chromosome 10. There were no significant differences between tumour purity or GBM subtype between LTS and STS. LTS had significantly increased MGMT promoter methylation (p = 0.01), and higher FGFR3-TACC3 (p = 0.03), compared to STS. STS had significantly more often a CDKN2A/B loss (p = 0.01) and higher levels of NF1 (p = 0.02), compared to LTS. There were no significant CpGs identified between LTS vs STS at an adjusted p-value of 0.05. Unadjusted analyses identified key pathways and biological processes involved in both LTS and STS. The top pathway in LTS was the Hippo signaling pathway and the Wnt pathway. The top pathway in STS was GPCR ligand binding and cell-cell signaling. CONCLUSION A small group of patients with IDH wild-type GBM survive more than 5 years. While there are few differences in the global methylation profiles of long-term survivors compared to short-term survivors, our study highlights potential pathways involved in aggressive and senescent GBMs.

EPCO-40. INFRATENTORIAL NF2 MUTANT SPORADIC MENINGIOMAS DIFFER FROM THOSE IN SUPRATENTORIAL LOCATIONS AND ARE MORE BENIGN

Abstract INTRODUCTION Approximately 50% of sporadic meningiomas, which originate throughout the neuroaxis, harbor bi-alleic NF2 loss. We sought to determine whether NF2 mutant meningiomas originating from different intracranial locations relative to the tentorium differ with regards to their genomic profile and clinical behavior. METHODS Clinical and whole exome sequencing data (WES) for all patients who underwent resection of NF2 mutant meningiomas and consented to WES were reviewed and analyzed. RESULTS 258 NF2 mutant meningiomas were included and subdivided into supra- (sNF2) versus infra-tentorial (iNF2) groups (230 versus 28, respectively). Supratentorial location was significantly associated with genomically unstable tumors (percent genome altered median 12% vs. 1%, p&amp;lt; 0.001) and were more likely to harbor the more aggressive feature of chromosome 1p deletion (31.4% vs. 8.3%, p= 0.036). These malignant genomic features correlated with an increased incidence of high risk clinical features, including higher-grade (i.e. WHO Grade II/III) (48.9% vs. 7.14%, p &amp;lt; 0.001) and elevated Ki-67 (58.9% vs. 16.6%, p&amp;lt; 0.01), as well as larger volume (median 26.21 cm3 vs. 9.84 cm3, p&amp;lt; 0.001) and edema (65.8% vs. 25.9%, p= 0.001) in sNF2 meningiomas as compared with iNF2 tumors, respectively. Not surprisingly, although there was no difference in extent of resection between the groups (gross total resection (GTR), 96.26% vs. 96.15%, p= 0.45), patients with sNF2 tumors had more associated deaths (14.6% vs. 0%, p= 0.03) and a marginally shorter overall survival (p= 0.061). GTR was associated with longer progression-free survival (p= 0.037). CONCLUSION Within the homogeneous group of somatic NF2 mutated meningiomas, infratentorial tumors are seemingly more benign in their genomic make-up and clinical manifestation as compared to ones located in the supratentorial location. While GTR is useful to both groups in preventing recurrence, this benefit may be especially important in the clinically and genomically higher risk sNF2 tumors.

PSAT023 Not Every Pain Is a Gain! A Rare Case of Adrenal Leiomyosarcoma.

Abstract Introduction Adrenal leiomyosarcoma (AL) is a rare malignant tumor, representing only 0.1% to 0.2% of all retroperitoneal soft tissue sarcomas in adults (1). A young male's acute abdominal and back pain led to an unusual diagnosis of AL. Case Presentation A 38-year-old male patient with no past medical history presented with a history of right sided abdominal pain of several months duration radiating to the back and significant weight loss. His vital signs were stable; however, he appeared mildly distressed and had tenderness on deep palpation in the right mid-upper quadrant. An abdominal sonogram showed a hypoechoic mass between the liver and the right kidney with no evidence of acute cholecystitis. A CT scan of the abdomen with IV contrast showed a lobulated mass invading the right adrenal gland, measuring 5.4×4.3×5.1 cm, with a post-contrast density measurement of 30 Hounsfield units. Laboratory tests showed plasma renin of 1.8 (upper limit of normal ULN 4.3 ng/ml/h), aldosterone of 8.6 (ULN 21 ng/dl), plasma metanephrine of &amp;lt;0.2 (ULN 0.50 nmol/l), and plasma normetanephrine of 0.49 (ULN 0.90 nmol/l). Additionally, his cortisol level after dexamethasone suppression was 0.9 (ULN 22.4 ug/dl). He underwent a right-sided laparoscopic adrenalectomy. The histopathological testing returned as a high-grade undifferentiated malignant neoplasm consistent with leiomyosarcoma. The IHC stains showed positive staining for SMA, CD10, and GATA3. He underwent whole-body PET/CT that showed multiple hypermetabolic abnormalities, including the right adrenalectomy bed, with a possible tumor invading the right upper renal pole. Systemic chemotherapy with doxorubicin and dacarbazine was initiated. Foundation panel testing showed NF1 loss on exons 2-3, CDKN2A/B CDKN2A rearrangement on exon 2, and TP53 loss on exons 1-4. He has received two rounds of chemotherapy, with no evidence of disease progression. Discussion Adrenal leiomyosarcoma usually originates from the smooth muscle cells of the adrenal or adjacent vascular structures. The tumor is asymptomatic until it enlarges and compresses the surrounding structures. Currently, there are about 50 reported valid cases (2) with no reports of NF-1 exon loss to our knowledge. The primary treatment is radical surgery with or without adjuvant chemotherapy and radiotherapy. Foundation panel testing showing NF-1 and TP53 exon loss may guide future targeted therapy. References 1-Fatema Jabarkhel, Henri Puttonen, Lina Hansson, Andreas Muth, Oskar Ragnarsson, Primary Adrenal Leiomyosarcoma: Clinical, Radiological, and Histopathological Characteristics, Journal of the Endocrine Society, Volume 4, Issue 6, June 2020. 2-Bahador Oshidari, Amir Zamani, Hooman Bahrami-Motlagh, Elena Jamali, Setareh Mahmoodi, Manoochehr Ebrahimian, Primary leiomyosarcoma of the adrenal; a case report, International Journal of Surgery Case Reports, Volume 90, 2022, 106707. Presentation: Saturday, June 11, 2022 1:00 p.m. - 3:00 p.m.

Multiple Nf1 Schwann cell populations reprogram the plexiform neurofibroma tumor microenvironment.

To define alterations early in tumor formation, we studied nerve tumors in neurofibromatosis 1 (NF1), a tumor predisposition syndrome. Affected individuals develop neurofibromas, benign tumors driven by NF1 loss in Schwann cells (SCs). By comparing normal nerve cells to plexiform neurofibroma (PN) cells using single-cell and bulk RNA sequencing, we identified changes in 5 SC populations, including a de novo SC progenitor-like (SCP-like) population. Long after Nf1 loss, SC populations developed PN-specific expression of Dcn, Postn, and Cd74, with sustained expression of the injury response gene Postn and showed dramatic expansion of immune and stromal cell populations; in corresponding human PNs, the immune and stromal cells comprised 90% of cells. Comparisons between injury-related and tumor monocytes/macrophages support early monocyte recruitment and aberrant macrophage differentiation. Cross-species analysis verified each SC population and unique conserved patterns of predicted cell-cell communication in each SC population. This analysis identified PROS1-AXL, FGF-FGFR, and MIF-CD74 and its effector pathway NF-κB as deregulated in NF1 SC populations, including SCP-like cells predicted to influence other types of SCs, stromal cells, and/or immune cells in mouse and human. These findings highlight remarkable changes in multiple types of SCs and identify therapeutic targets for PN.

Identifying selection signatures for litter size in Guangxi Bama Xiang pigs.

Litter size is an important economic trait in pig production. However, the genetic mechanisms underlying varying litter size in Guangxi Bama Xiang pigs remain unknown. To identify selection signatures for litter size in Guangxi Bama Xiang pigs, we obtained 297 Illumina PorcineSNP50 BeadChip array data and the average born number (ABN) from parity one to nine in Guangxi Bama Xiang pigs. Fixation index (Fst) methods were used to identify the selection signature of the litter size, and three phenotypic gradient differential population pairs (according to the ABN) in individuals were used to reduce the false positives of signature selections. Single nucleotide polymorphisms (SNPs) were identified in the VEGFA promoter and exons. The general linear model was used to analyse the differences in distinct genotypes after they were typed using three-round multiplex PCR technology. Finally, the transcriptome factor and CpG island in the VEGFA promoter were predicted. A total of 328, 328 and 317 significant loci were identified in the 1st, 2nd and 3rd population pairs, respectively. After removing the false positives, 25 SNPs were defined as the selection signatures in relation to litter size. Ten (VEGFA, USP49, USP25, SRPK1, SLC26A8, RPL10A, PPARD, MAPK14, HMGA1 and CHRDL2) out of 52 genes in the selection regions were annotated as the candidate genes of litter size, respectively, VEGFA. There were no SNPs in the VEGFA exon region, but we obtained three SNPs (rs786889605, rs343769603 and rs323942424) in the VEGFA promoter regions. The ABN in CC was significantly higher than that in TT in rs786889605, and the ABN in TT was significantly lower than that in GG in rs323942424. Meanwhile, the mutation of the VEGFA promoter result in the loss of Sp1 and NF-1 and the formation of Oct-1. In summary, we obtained ten candidate genes, and two mutations in the VEGFA promoter that could be important potential molecular biomarkers for litter size in Bama Xiang pigs.

Human induced pluripotent stem cell engineering establishes a humanized mouse platform for pediatric low-grade glioma modeling

A major obstacle to identifying improved treatments for pediatric low-grade brain tumors (gliomas) is the inability to reproducibly generate human xenografts. To surmount this barrier, we leveraged human induced pluripotent stem cell (hiPSC) engineering to generate low-grade gliomas (LGGs) harboring the two most common pediatric pilocytic astrocytoma-associated molecular alterations, NF1 loss and KIAA1549:BRAF fusion. Herein, we identified that hiPSC-derived neuroglial progenitor populations (neural progenitors, glial restricted progenitors and oligodendrocyte progenitors), but not terminally differentiated astrocytes, give rise to tumors retaining LGG histologic features for at least 6 months in vivo. Additionally, we demonstrated that hiPSC-LGG xenograft formation requires the absence of CD4 T cell-mediated induction of astrocytic Cxcl10 expression. Genetic Cxcl10 ablation is both necessary and sufficient for human LGG xenograft development, which additionally enables the successful long-term growth of patient-derived pediatric LGGs in vivo. Lastly, MEK inhibitor (PD0325901) treatment increased hiPSC-LGG cell apoptosis and reduced proliferation both in vitro and in vivo. Collectively, this study establishes a tractable experimental humanized platform to elucidate the pathogenesis of and potential therapeutic opportunities for childhood brain tumors.

Concurrent inhibition of FAK/SRC and MEK overcomes MEK inhibitor resistance in Neurofibromatosis Type I related malignant peripheral nerve sheath tumors.

Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft-tissue sarcomas which lack effective drugs. Loss of the RAS GTPase-activating protein NF1 and subsequent overactivation of mitogen-activated protein kinase kinase (MAPK) signaling exist nearly uniformly in MPNST, making MAPK inhibition a promising therapeutic intervention. However, the efficacy of MEK inhibitor (MEKi) monotherapy was limited in MPNST and the relative mechanisms remained largely unexplored. In this study, we generated three MEKi-resistant cell models and investigated the mechanisms of MEKi resistance using high-throughput transcriptomic sequencing. We discovered that cell apoptosis and cell cycle arrest induced by MEKi were rescued in MEKi-resistant cells and the upregulation of LAMA4/ITGB1/FAK/SRC signaling conferred resistance to MEKi. In addition, concurrent inhibition of MAPK signaling and FAK/SRC cascade could sensitize MPNST cells to MEKi. Our findings provide potential solutions to overcome MEKi resistance and effective combination therapeutic strategies for treating MPNSTs.

Modern views on the recurrence of meningiomas

Meningiomas are common tumors of the central nervous system. Grade I meningiomas are generally considered to be "benign". However, a certain percentage of these tumors have a more aggressive course, similar to malignant tumors. Numerous observations have shown that even in the case of radical removal of the tumor, the latter recur within the next 10 years. Recent molecular studies have shed new light on meningioma subtypes, their behavior, the prospect of new treatment, and prognostic features for patients. The study of V.E. Clark et al. found a number of mutations in NF2 meningiomas, namely TRAF7 (tumor necrosis factor receptor 7 factor), KLF4 (Kruppel-like factor 4c), AKT1 and SMO. The pattern between the type of mutation and the tumor location was established: posterior cranial fossa, parasagittal area, falx, torculae and intraventricular sections - loss of NF2 or chromosome 22, olfactory groove and middle cranial fossa - KLF4 / TRAF7, olfactory groove, - PIK3CA, middle parts of the anterior cranial fossa and middle cranial fossa - AKT1 / POLR2, olfactory groove - SMO. The selection criteria in the study, which analyzed data from 469 meningiomas of a known molecular subgroup, were the degree of resection, postoperative irradiation, postoperative neuroimaging and time to recurrence (if present). Molecular subgroups of meningiomas had different clinical manifestations during the two years of follow-up, with several aggressive subgroups (NF2, PI3K, HH, TRAF7) recurring at an average rate 22 times faster than less aggressive tumors (KLF4, POLR2A, SMARCB1). PI3K-activated meningiomas recurred earlier than tumors in other groups. The potentially more aggressive group of meningiomas with HH, NF2, and TRAF7 mutations demonstrated a high recurrence rate after 60 months of follow-up (35.3, 43.7, and 36.4%, respectively), whereas most tumor recurrences with PI3K mutations were reported within the first 24 months (75,0%). Classification of meningiomas by genomic mutations is a promising tool. Its introduction into clinical practice will make it possible to predict the aggressiveness of meningiomas and the risk of their recurrence, which will help to give a more accurate prognosis for patients and develop effective therapeutic methods for these tumors.

Abstract 1168: From clinical mutational data to a novel lung cancer mouse model -NF1inactivation cooperates withRASA1inactivation to drive non-small cell lung cancer (NSCLC)

Abstract 11% of non-small cell lung cancer (NSCLC) patients harbor NF1 mutations. The enrichment of NF1 mutations in lung adenocarcinoma (LUAD) cases that otherwise lack activated oncogene mutations indicates that NF1 loss may play a necessary role in the activation of the RAS pathway. However, conditional, biallelic loss of Nf1 in the mouse lung is insufficient for LUAD initiation over 2 years, indicating additional genetic or epigenetic events cooperate with Nf1 loss in lung tumorigenesis. To better understand NF1 mutant lung cancers, we analyzed a lung cancer dataset with 47227 patients’ genomic mutation data from Foundation Medicine (FMI) and found that NF1 mutations (5270 patients) are associated with a higher mutational burden compared to NF1 wild type lung cancer patients in the lung cancer patients’ clinical database. We then analyzed the AACR GENIE non-small cell lung cancer datasets for genes mutated concurrently with NF1 mutation. We found that NF1 mutation statistically significantly cooccurs with RASA1 (p &amp;lt;0.001 for concurrency) and with TP53 mutations in the non-small lung cancer dataset. NF1-mutated samples lack other key driver oncogene mutations such as EGFR (p &amp;lt;0.001 for mutual exclusivity). To functionally validate our findings of genetic cooperativity, we conditionally deleted the two key GAPs: Nf1 and Rasa1 (with Trp53) in vivo. Deletion of both Nf1 and Rasa1 but neither the Nf1 or Rasa1 deletion alone lead to LUAD when combined with Trp53 deletion. Our new mouse model provides a unique tool for our ongoing effort to understand the mechanism of Nf1 &amp; Rasa1 tumor initiation in the lung and will aid preclinical investigations of targeted therapies. Citation Format: Lin Song, Thaidy Y. Rodriguez, Adam Olshen, Eric Collisson. From clinical mutational data to a novel lung cancer mouse model -NF1inactivation cooperates withRASA1inactivation to drive non-small cell lung cancer (NSCLC) [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 1168.

Abstract 373: Silver nanoparticles are selectively cytotoxic to neurofibromin 1 deficient peripheral nerve sheath tumors

Abstract Neurofibromatosis type 1 (NF1) is the most common neurogenic disorder affecting 1 in every 3,000 people worldwide. NF1 is defined by heterozygous loss-of-function of the neurofibromin 1 gene (NF1). NF1 patients develop neurofibromas with near complete penetrance. These neurofibromas include peripheral nerve sheath tumors (PNSTs) such as plexiform neurofibromas (pNFs) and malignant PNSTs (MPNSTs). Current standard of care shows incomplete penetrance limiting clinical utility. Therefore, treatments to selectively and safely remove PNST cells would be advantageous. Biallelic loss of functional NF1 is the major driving force in the development of PNSTs. NF1 is a tumor suppressor gene responsible for suppressing Ras activity. Loss of NF1 increases Ras activity and subsequently increases intracellular reactive oxygen species (ROS). We and other groups have demonstrated that systemically administrable silver nanoparticles (AgNPs) are cytotoxic to a variety of cancers. We further showed that AgNP-mediated cytotoxicity is dependent upon intracellular ROS which induces rapid ionization (activation) of Ag0 to cytotoxic Ag+. Therefore, AgNPs represent a rational cancer-selective therapy for NF1-deficient PNSTs as these cells are enriched for ROS relative to non-cancerous cells. In this study, we found that AgNPs are significantly (~5-fold) more cytotoxic to NF1-null MPNST cells relative to tumor cell of origin Schwann cells and ~7-fold more cytotoxic to pNF cells relative to patient matched Schwann cells. Sporadic NF1 wild-type MPNST cells were not sensitive to AgNP. We further explored the relationship between oxidative stress and AgNP-mediated cytotoxicity in PNSTs. We found that co-administration of oxidative stress inducing cumene hydroperoxide with AgNP augments the cytotoxicity of AgNP in otherwise AgNP-tolerant cells (Schwann cells, NF1-wildtype MPNSTs). Importantly, either agent alone only showed modest cytotoxicity. As NF1 gene expression levels correlated with AgNP-sensitivity, we further studied this possible interaction by reintroducing NF1 into NF1-null MPNST. Remarkably, NF1 restoration decreased sensitivity to AgNP. This change is unique to AgNP as there was no altered sensitivity to standard of care chemotherapy doxorubicin. Conversely, knockdown of NF1 expression in Schwann cells increased sensitivity to AgNP with no corresponding change in sensitivity to pNF standard of care MEK inhibitor selumetinib. In conclusion, our work provides evidence that a therapeutic window exists for the safe use of AgNPs as a precision medicine to treat NF1-null PNSTs. Citation Format: Garrett Alewine, Adithya Ghantae, Christina Mamrega, Jerrica L. Knight, Bashnona Attiah, Robert A. Coover, Cale D. Fahrenholtz. Silver nanoparticles are selectively cytotoxic to neurofibromin 1 deficient peripheral nerve sheath tumors [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 373.

Abstract 2975: RAS precision medicine transatlantic partnership: Exploration of RAS and NF1 co-mutations in NSCLC

Abstract Background: RAS is the most commonly mutated oncogene in cancer, with KRAS mutated in ~30% of non-small cell lung cancer (NSCLC). RAS is a small GTPase cycling between GTP-bound ‘ON’ state and GDP-bound ‘OFF’ state. KRAS oncoproteins cycle between these states via hydrolysis and nucleotide exchange with the aid of GAPs, including NF1, and GEFs. Given the ’inactive state’ inhibition of recently developed KRAS G12C inhibitors on the GDP-bound state, this has highlighted the continued reliance of KRAS-mutants upon cycling, and the potential for mutants to retain dependence upon upstream influences, including NF1, for pathogenicity. Methods: 474 patients with advanced RAS- and/or NF1-mutant NSCLC were retrospectively identified from four tertiary cancer centers between 2008 -2021. DNA from archival FFPE samples, serum or combination underwent targeted NGS panels to identify mutations. Molecular, clinical, pathological and treatment outcome data were collected. Online resources including cBioPortal and Project Achilles were used to assess the functional role of any findings. Results: KRAS mutations were identified in 416/474 patients and NF1-mutations in 63/474 patients, eight of whom harbored two NF1-mutations. 24/63 (38%) of NF1-mutant cancers had a concomitant KRAS-mutation. We identified that KRAS G13D was more prevalent in NF1 mutant cancers vs. NF1 wildtype (NF1 MT: 6/24, 25%; vs. NF1 WT: 4/281, 1.4%; p&amp;lt;0.0001). KRAS G12C was identified in 11/24 (45.8%) of the double mutants vs. 109/282 (38.7%) of the NF1 WT patients (p=0.52). Those with G13D/NF1 co-mutation had a predicted pathogenic NF1-mutation in 5/6 (83%) of cases. Functional analysis of NF1 KO in G13D mutant lung cancer cell lines identified that NF1 was more essential in G13D mutant cell lines, with median Chronos score -0.26 G13D vs. -0.04 G12C (p=0.02). mRNA expression data identified a range of mRNA expression Z-scores relative to all samples for NF1-mutant cancers, ranging from lowest expression at -4.54 to +1.63, median -0.51. A higher mRNA expression was identified for NF1 missense mutations of unknown significance compared to truncating mutations with likely pathogenic, loss of function. Conclusions: These results highlight the co-mutational landscape of KRAS G13D with NF1 in NSCLC, suggesting functional importance conferred by NF1 loss, and highlight NF1 mutations as an additional pathogenic even when combined with KRAS mutation. The genomic landscape of KRAS and NF1 mutant NSCLC will be explored further through Whole Genome Sequencing data from the 100,000 Genomes Project (Genomics England). Citation Format: Helen M. Adderley, Mihaela Aldea, Jaqueline Aredo, Mathew Carter, Matthew Church, Pantelis Nicola, Jamie Weaver, Aisha Ghaus, Damien Vasseur, Matthew Krebs, Nicola Steele, Fiona Blackhall, Heather Wakelee, Benjamin Besse, Colin Lindsay. RAS precision medicine transatlantic partnership: Exploration of RAS and NF1 co-mutations in NSCLC [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 2975.

Abstract 2196: Oncogenic context drives the landscape of tumor suppression in lung cancer

Abstract Cooperative interactions between genomic alterations in oncogenes and tumor suppressors are a hallmark of cancer. While molecular characterization of tens of thousands of primary tumors has solidified estimates of how frequently specific genomic alterations occur, identifying genetic interactions from co-mutation rates alone remains limited by the vast number of possible combinations as well as inherent biases and confounding effects. Conversely, genetically engineered mouse models can reliably uncover causal effects of specific genetic alterations but are not sufficiently high throughput to generate broad insights into the interplay between genetic alterations in tumors. Therefore, how the effects of one alteration on tumor growth change in the context of other alterations remains largely unknown. We previously addressed these technical limitations by combining CRISPR/Cas9-mediated gene editing, tumor barcoding, and ultra-deep barcode sequencing methods with genetically engineered mouse models of human lung cancer, which together enable multiplexing of tumor genotypes in individual mice and precise, high-throughput quantification of in vivo tumor fitness. Here, we leverage this platform to systematically quantify the growth effects of over 45 known and putative tumor suppressor gene alterations across different common oncogenic point mutations in Kras and Braf. While the set of genes we identified as tumor suppressive in KrasG12D- and KrasG12C-driven lung cancers was largely consistent, inactivation of those genes typically resulted in larger tumor growth advantages in the KrasG12D model. Inactivation of most genes in BrafV600E-driven lung tumors had a strikingly different growth effect than in tumors with either Kras variant, and effects were generally far less pronounced in the BrafV600E context. Interestingly, loss of genes upstream of Braf within the Ras pathway often had strong effects in the KrasG12D or KrasG12C models—loss of Nf1, a negative regulator of Kras, or loss of the wildtype Kras allele enhanced oncogenic Kras-driven tumor growth, while loss of Shp2, a positive regulator of Kras, was mildly detrimental—but had little or no effects in the BrafV600E model. We assessed translatability of our experimental cause-and-effect data through comparisons to correlative data from publicly available human lung cancer genomics databases, and found that genetic interactions predicted by our models and gene co-mutation rates in patient tumors largely align. Together, these findings underscore the need for a contextual understanding of the ways in which tumors are influenced by their genetics and highlight the utility of high-throughput, quantitative autochthonous mouse models in pursuing this endeavor. Citation Format: Ian Winters, Lily Blair, Lafia Sebastian, Gabriel Grenot, Edwin Apilado, Wensheng Nie, Vy Tran, Ian Lai, Gregory Wall, Dmitri Petrov, Monte Winslow, Joseph Juan, Michael Rosen. Oncogenic context drives the landscape of tumor suppression in lung cancer [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 2196.