NIMG-16. COMPARISON OF A STIR- AND T1-WEIGHTED-BASED RADIOMICS MODEL TO DIFFERENTIATE BETWEEN PLEXIFORM NEUROFIBROMAS AND MALIGNANT PERIPHERAL NERVE SHEATH TUMORS IN NEUROFIBROMATOSIS TYPE 1 (NF1)

BACKGROUND

Plexiform neurofibromas (PNF) and malignant peripheral nerve sheath tumors (MPNST) are best visualized on short TI inversion recovery (STIR) sequences on MRI. However, STIR sequences are not routinely acquired in the clinical setting. T1-weighted pre-contrast (T1W) sequences are more standardly obtained but provide insufficient contrast for tumor identification. We developed a radiomics model based on STIR and T1W sequences to differentiate between NF1-associated PNF and MPNST.

METHODS

Using a 3D quantitative imaging analysis software (3DQI), 68 MPNST and 79 PNF from 134 participants at nine centers were segmented on STIR sequences (if available) or T2 fat-saturated or T1-weighted fat-saturated post-contrast sequences. Tumor regions of interest were co-registered to T1W sequences. Standard pre-processing included N4 bias field correction, intensity normalization (mean 120 SI, SD 80 SI), and resampling (1 mm3 voxel resolution). 107 radiomic features were extracted using PyRadiomics. To classify tumors as PNF or MPNST, we applied the Boruta algorithm and correlation removal for selection of important features. A Random Forest model was built using the top five selected features. The data were divided into a training/validation and test set (7:3 ratio). Five-fold cross-validation was performed and repeated 100 times. Model performance was evaluated using AUC, sensitivity, specificity, accuracy, and 95% CI.

RESULTS

For the STIR-based model, AUC was 0.856 (95% CI 0.727-0.984), sensitivity 0.6, specificity 0.833, and accuracy 0.727 in the test set. For the T1W-based model, AUC was 0.867 (95% CI 0.743-0.990), sensitivity 0.8, specificity 0.79, and accuracy 0.794 in the test set.

CONCLUSIONS

Our radiomics models demonstrate high and comparable performance to distinguish between PNF and MPNST on STIR and T1W sequences. Our inclusion of multicenter MRIs enhances model generalizability. These models can potentially be integrated into the radiologic workflow to help clinicians in the early identification of MPNST or pre-malignant atypical neurofibromas on clinical MRIs.

Abstract 3968: AXL is responsible for much of TKI-mediated adaptive resistance in FLT3/ITD AML cells

FMS-like tyrosine kinase-3 (FLT3) is the most frequently mutated receptor tyrosine kinase (RTK) in acute myeloid leukemia (AML). Internal tandem duplication mutations (ITD) confer a poor prognosis on FLT3/ITD patients, making FLT3/ITD AML susceptible to treatment with tyrosine kinase inhibitors (TKI). However, FLT3 TKI success has been hindered by mechanisms of resistance including adaptive resistance, in which downstream signaling pathways are rapidly reactivated after initial inhibition with targeted therapies. Past work has shown that FLT3/ITD cells undergo adaptive resistance through the reactivation of ERK signaling within 24 hours of sustained FLT3 inhibition. We are interested in finding the mechanisms responsible for this ERK reactivation.

AXL is a RTK that is implicated in acquired resistance for many cancers, including against targeted therapy in FLT3/ITD AML. However, AXL signaling has not been implicated in early adaptive resistance in the context of FLT3/ITD AML. Thus, we sought to determine if AXL plays a role in the ERK reactivation found in TKI-treated AML cells.

To address this, we first treated FLT3/ITD cell lines (Molm14 and MV4;11) with FLT3 TKI for 24 hours and saw an increase in AXL protein and mRNA levels as early as 4 hours after starting treatment. AXL phosphorylation occurred as early as 16 hours, which coincides with the beginning of the ERK phosphorylation (pERK) rebound. Further characterization revealed AXL upregulation, like ERK reactivation, is at least partially serum-dependent and that the ERK reactivation itself is not causing the AXL induction. These results established that TKI-induced AXL activation is associated with the adaptive ERK reactivation.

To determine if AXL signaling actually plays a role in ERK reactivation in FLT3/ITD AML, we inhibited AXL activation using both small-molecule inhibitors (TP-0903 and R428) and selective inhibition (shRNA knockdown and ligand trapping with an AXL chimeric protein) concurrently with FLT3 TKI treatment. Each method of AXL inhibition diminished the pERK rebound, decreased cell proliferation and increased apoptosis of FLT3 TKI-treated FLT3/ITD cells. Combined AXL and FLT3 inhibition also suppressed leukemic cell recovery even after brief treatment exposure. Furthermore, 24-hour FLT3 and AXL TKI treatments of both relapsed and newly-diagnosed FLT3/ITD patient leukemic samples yielded the same upregulation of AXL protein and decreased pERK rebound observed in the cell lines.

In summation, FLT3 TKI treatment causes rapid AXL upregulation resulting in adaptive ERK reactivation. Concurrent FLT3 and AXL inhibition diminishes pERK rebound and sensitives FLT3/ITD cells to TKI treatment. This data suggests that AXL plays a role in adaptive resistance in FLT3/ITD AML, and the addition of AXL inhibition to FLT3 TKI treatment has the potential to improve FLT3/ITD patient outcomes.

Citation Format: Tessa Seale, Li Li, Jaesung Seo, Bao Nguyen, Mark Levis, Christine Pratilas, Donald Small. AXL is responsible for much of TKI-mediated adaptive resistance in FLT3/ITD AML cells [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 3968.

Abstract 2009: Elucidating the mechanistic effect of targeting Ref-1 redox function on MPNST survival signaling using patient-derived xenolines

Malignant Peripheral Nerve Sheath Tumor (MPNST) is a rare soft tissue sarcoma common in patients with NF1 (neurofibromatosis type 1). MPNSTs respond poorly to most chemotherapeutics due to molecular heterogeneity and altered signal transduction pathways. Ref-1 and STAT3 are highly expressed in MPNST patient samples offering druggable pathways. Inhibition of one singular protein, like Ref-1 to block the activity of many important transcription factors (TFs), STAT3, HIF1a, and NFkB is key to improving success in MPNST therapy. Inhibition of both Ref-1 and STAT3 in MPNST lines resulted in decreased proliferation, wound healing, tumor signaling, and deactivation of MPNST survival genes. Further, knockdown of Ref-1 or STAT3 resulted in a concordant decrease in NFkB activity. Ref-1 redox inhibitor, APX3330 that completed Phase I clinical trial (NCT03375086), potently inhibited in vitro growth of a panel of MPNST cells. We have also been developing new more potent analogs of APX3330 for inhibition of Ref-1 redox function and potent cell killing in our panel of MPNST cells. Several of these analogs significantly and potently reduced NFkB and HIF1a activity at concentrations where cell killing was minimal, pointing toward an on-target effect. Based on the role of Ref-1 in transcriptional regulation of MPNST, RNA sequencing after knockdown of Ref-1 was used to determine mechanistic effects on MPNST gene expression. We have identified 443 genes up-regulated and 758 genes down-regulated in two MPNST cell lines with siRef-1. The pathways enriched by the commonly up-regulated genes included RNA polymerase, P53 downstream, glycerophospholipid, and other lipid metabolism pathways; the pathways enriched by the commonly down-regulated genes included cell cycle, adaptive immune response, and VEGF signaling pathways. From this data, we also found that OXPHOS (Oxidative Phosphorylation) pathway genes (like NDUFS2, SURF1, COX15) were down with siRef-1 along with others like AURKA, RNASEH2A, CDC20, GINS4, TIMELESS that were identified in our previous publication to be MPNST survival genes. Based on our published observations that Ref-1 inhibition dramatically affects metabolic pathways, we used OXPHOS deficient and proficient osteosarcoma cells and confirmed the impact of Ref-1 redox activity on metabolism. Furthermore, if we combine Ref-1 inhibition with a-ketoglutarate (aKG) and target the tumor cells’ dependence on aspartate biosynthesis, the tumor cell death was dramatic (p < 0.0001). Two new xenolines were established from patient PDXs and are being validated for growth inhibition and downregulation of MPNST survival genes with Ref-1 knockdown and redox inhibition using APX analogs both in vitro and in vivo. Successful derailing of MPNST survival pathways by targeting Ref-1 redox function is our aim to treat this rare but deadly cancer.

Citation Format: Silpa Gampala, Olivia Babb, Nikkitha Umesh Ganesh, Steven D. Rhodes, Reza M. Saadatzadeh, Kai Pollard, Christine Pratilas, Jing-Ruey Joanna Yeh, Karen E. Pollok, Wade D. Clapp, Mark R. Kelley, Chi Zhang, Melissa L. Fishel. Elucidating the mechanistic effect of targeting Ref-1 redox function on MPNST survival signaling using patient-derived xenolines [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 2009.

Detection of malignant peripheral nerve sheath tumors in patients with neurofibromatosis using aneuploidy and mutation identification in plasma

Malignant peripheral nerve sheath tumors (MPNST) are the deadliest cancer that arises in individuals diagnosed with neurofibromatosis and account for nearly 5% of the 15,000 soft tissue sarcomas diagnosed in the United States each year. Comprised of neoplastic Schwann cells, primary risk factors for developing MPNST include existing plexiform neurofibromas (PN), prior radiotherapy treatment, and expansive germline mutations involving the entire NF1 gene and surrounding genes. PN develop in nearly 30–50% of patients with neurofibromatosis type 1 (NF1) and most often grow rapidly in the first decade of life. One of the most important aspects of clinical care for NF1 patients is monitoring PN for signs of malignant transformation to MPNST that occurs in 10–15% of patients. We perform aneuploidy analysis on ctDNA from 883 ostensibly healthy individuals and 28 patients with neurofibromas, including 7 patients with benign neurofibroma, 9 patients with PN and 12 patients with MPNST. Overall sensitivity for detecting MPNST using genome wide aneuploidy scoring was 33%, and analysis of sub-chromosomal copy number alterations (CNAs) improved sensitivity to 50% while retaining a high specificity of 97%. In addition, we performed mutation analysis on plasma cfDNA for a subset of patients and identified mutations in NF1, NF2, RB1, TP53BP2, and GOLGA2. Given the high throughput and relatively low sequencing coverage required by our assay, liquid biopsy represents a promising technology to identify incipient MPNST.

NIMG-08. A MULTI-CENTER RADIOMICS-BASED MODEL TO DIFFERENTIATE BETWEEN NEUROFIBROMATOSIS TYPE 1-ASSOCIATED PLEXIFORM NEUROFIBROMAS AND MALIGNANT PERIPHERAL NERVE SHEATH TUMORS

BACKGROUND

Several MRI features are proposed to distinguish between plexiform neurofibromas (PNF) and malignant peripheral nerve sheath tumors (MPNST) in neurofibromatosis type 1 (NF1), including tumor size, margins, and degree of heterogeneity. However, most of these features are descriptive in nature, subject to intra-/interrater variability, and based on small single-institution studies. The goal of this study was to identify radiomic features that can differentiate between NF1-associated PNF and MPNST.

METHODS

31 MPNSTs and 24 PNFs from five centers were segmented on short TI inversion recovery sequences using a semi-automated segmentation software (3DQI). Standard pre-processing was performed, including N4 bias field correction, intensity normalization (using a mean of 120 SI and standard deviation of 80 SI), and resampling to 1 mm3 voxel resolution. 1688 radiomic features were extracted from the tumor region of interest using PyRadiomics, an open-source Python radiomics package. To classify tumors as PNF or MPNST, we implemented the Boruta algorithm and correlation removal for selection of important features. A Random Forest model was built using the top ten selected features. Five-fold cross-validation was performed and repeated 100 times. Model performance was evaluated using the area under the ROC curve (AUC), sensitivity, specificity, accuracy, and confidence intervals.

RESULTS

The top ten features included in the model were five intensity features, two shape features, and three texture features. The model demonstrated an AUC of 0.891 (95% CI 0.882-0.899), sensitivity of 0.744, specificity of 0.847, and accuracy of 0.802 (95% CI 0.792-0.813).

CONCLUSIONS

Our machine learning model demonstrated high performance in classifying tumors as either PNF or MPNST in NF1 individuals. Inclusion of additional tumors for model training and testing on an independent dataset are underway. Ultimately, our model may enable improved differentiation between PNF and MPNST compared to descriptive MRI features, permit early patient risk stratification, and improve patient outcomes.

INNV-04. A MULTI-INSTITUTIONAL CLINICAL AND MRI REPOSITORY OF NEUROFIBROMATOSIS TYPE 1-ASSOCIATED PERIPHERAL NERVE SHEATH TUMORS

BACKGROUND

Individuals with neurofibromatosis type 1 (NF1) frequently have peripheral nerve sheath tumors (PNST), including plexiform neurofibromas (PNF), atypical neurofibromas (ANF), and malignant peripheral nerve sheath tumors (MPNST). These tumors reflect a histologic spectrum from benign to malignant. Various clinical and MRI-based features are proposed as risk factors for MPNST development based on small single-institution studies. A major barrier to study these risk factors is collation and annotation of multi-center serial MRIs. To address this, we created a standardized database of clinical data and longitudinal MRIs from NF1-associated PNST from nine international NF1 referral centers.

METHODS

Clinical data from NF1 patients are collected in Research Electronic Data Capture databases housed at Massachusetts General Hospital and Washington University, including demographic information, genotype, disease course, treatment history, and survival. ANF and MPNST require histologic confirmation whereas a diagnosis of PNF can also be made based on clinical/radiographic stability. Longitudinal MRIs predating the histologic diagnosis are uploaded to a HIPAA-compliant cloud-based system.

RESULTS

Data from 200 patients (87 females, 113 males) with 217 tumors (75 PNF, 40 ANF, 102 MPNST) have been collected. 280 regional and 108 whole-body MRIs have been identified. Median age at the time of histologic diagnosis is 30 years (range 5-64). All tumors are histologically confirmed except for 6 PNF which remained stable over time. Median follow-up time is 32 months. Of 147 patients with available survival data, 32 (21.7%) have died from MPNST progression; estimated median overall survival is 20 months.

CONCLUSIONS

In this ongoing work, we have assembled one of the largest systematically annotated clinical and MRI repositories of NF1-associated PNST from pediatric and adult NF1 patients. The data will be accessible to outside researchers which will promote interdisciplinary and multi-center collaborations. Active efforts include the identification of radiomic MRI features to differentiate between PNF and MPNST.

HGG-01. ENTRECTINIB IN RECURRENT OR REFRACTORY SOLID TUMORS INCLUDING PRIMARY CNS TUMORS: UPDATED DATA IN CHILDREN AND ADOLESCENTS

STARTRK-NG (phase 1/2) is evaluating entrectinib, a CNS-penetrant oral, TRK/ROS1/ALK tyrosine kinase inhibitor, in patients <21 years with recurrent/refractory solid tumors, including primary CNS tumors. After determining the recommended dose, 550mg/m²/day, in all-comers, expansion cohorts with gene-fusion-positive CNS/solid tumors (NTRK1/2/3, ROS1) are being enrolled. As of 5Nov2019 (data cut-off), 39 patients (4.9m–20y; median 7y) have been evaluated for response, classified as complete (CR) or partial response (PR), stable (SD) or progressive disease (PD) using RANO (CNS), RECIST (solid tumors), or Curie score (neuroblastoma). Responses in patients with fusion-positive tumors were Investigator-assessed (BICR assessments are ongoing) and occurred at doses ≥400mg/m². Best responses in fusion-positive CNS tumors (n=14) were: 4 CR (GKAP1-NTRK2, ETV6-NTRK3 [n=2], EML1-NTRK2); 5 PR (KANK1-NTRK2, GOPC-ROS1, ETV6-NTRK3, TPR-NTRK1, EEF1G-ROS1); 3 SD (BCR-NTRK2, ARHGEF2-NTRK1, KIF21B-NTRK1); 2 PD (PARP6-NTRK3, EML4-ALK); and in fusion-positive solid tumors (n=8) were: 3 CR (ETV6-NTRK3 [n=2], DCTN1-ALK); 5 PR (EML4-NTRK3, TFG-ROS1 [n=3], KIF5B-ALK). Responses (Investigator-assessed) in non-fusion tumors (n=17) were: 1 CR (ALK F1174L mutation), 3 SD, 10 PD, 3 no data/unevaluable. The objective response rate (CR+PR/total) in patients with fusion-positive tumors was 77% (17/22) versus 6% (1/17) in those with non-fusion tumors. All 39 patients experienced ≥1 adverse event (AE); the most frequent AEs included weight gain and anemia (both 48.7%); increased ALT, increased AST, cough and pyrexia (all 46.2%); increased creatinine and vomiting (both 43.6%); and bone fractures (n=10, in 9 patients). Entrectinib has produced striking, rapid, and durable responses in solid tumors with target gene fusions, especially high-grade CNS neoplasms.

NFB-01. FUNCTIONAL CHARACTERIZATION OF ATRX LOSS IN NF1-ASSOCIATED GLIOMA AND MPNST

To identify the biologic relevance of ATRX loss in NF1-associated gliomagenesis, we studied the effects of Atrx loss using four previously characterized Nf1+/-Trp53+/- murine glioma lines. Lines 130G#3 and 158D#8 (corresponding to grade IV and III gliomas, respectively) displayed preserved ATRX protein expression compared to NIH-3T3 cells. We studied the effects of Atrx knockdown in these two lines in the presence and absence of the TERT inhibitor, BIRBR1532. Using a telomere-specific FISH assay, we identified increased signal intensity after Atrx knockdown, only in the presence of the TERT inhibitor. These features are reminiscent of ALT, although there were no significant alterations in cell growth. Next, we studied the effect of ATRX loss in MPNST lines ST88-14, NF90-8, STS-26T. These cell lines all expressed ATRX and DAXX. However, STS-26T contained a TERT promoter mutation and ST88-14 had a known SNP in the TERT promoter, while NF90-8 had no alterations. ATRX siRNA knockdown showed no significant effects in cell proliferation or apoptosis. However, ATRX knockdown resulted in rare ultra-bright foci, indicative of ALT. Next, we studied the in vitro effect of the ATR inhibitor VE-821 in MPNST cell lines. Only NF90-8 (lacking TERT alterations) demonstrated a decrease in growth after ATRX knockdown and VE-821 treatment. However, ATRX knockdown alone did not affect sensitivity to carboplatin. Our findings further support a role for ATRX loss with subsequent ALT activation in a biologic subset of NF1-associated malignancies, thereby opening an opportunity for therapeutic targeting of these aggressive tumors using specific classes of drugs.

DDRE-13. DECONVOLUTING MECHANISMS OF RESISTANCE TO BRAF INHIBITORS IN BRAF V600E HUMAN GLIOMA

BACKGROUND

While BRAF-targeted therapy can be effective in a subset of patients with glioma, resistance to treatment can emerge over time. The description and validation of mechanisms of resistance in BRAF-mutant glioma are not previously described.

METHODS

Pre- and post- BRAF inhibitor (BRAFi) or BRAFi/MEK inhibitor (MEKi) treated patient samples were obtained under IRB-approved protocols at University of Colorado Denver, UCSF, and Johns Hopkins. Targeted DNA sequencing or whole exome sequencing (WES), and RNA-seq were conducted on paired samples. Functional validation of putative resistance mechanisms was performed using established glioma cell lines with BRAF V600E mutation (DBTRG-5MG, AM38, B76).

RESULTS

Analysis of 15 tissue sample pairs identified point mutations in 15 genes (including CBL, NF1, PTEN, and MAP2K1) and expression changes in RAF1 leading to putative mechanisms of resistance. We performed functional validation of loss of NF1 and CBL as resistance mechanisms and demonstrated growth inhibition and cell death in response to BRAFi with siRNA/sgRNA-mediated knockdown of each gene. Knockdown of CBL resulted in increased EGFR expression and phosphorylation, a possible mechanism for maintaining ERK signaling within the cell. Combination therapy with a MEKi or EGFR inhibitor was able to overcome resistance to BRAFi, in NF1 knockdown and CBL knockdown, respectively. Restoration of wild-type PTEN in B76 cells (PTEN-/-) restored sensitivity to BRAFi. Ingenuity pathway analysis suggested that a switch from BRAF to CRAF dependence mediated resistance in some tumors. Indeed, inhibition of CRAF expression using siRNA in a patient-derived glioma cell line re-sensitized cells to BRAFi.

CONCLUSIONS

Analysis of pre-/post-treatment BRAF mutant glioma sample pairs, primarily from pediatric patients, identified a variety of putative resistance mechanisms, some of which have been validated in vitro. Resistance mechanisms to BRAFi in glioma are varied and may be susceptible to different combinations of targeted therapy, highlighting the importance of a personalized approach.

Abstract A121: Adaptive and acquired signaling response to MEK inhibition in NF1-associated malignant peripheral nerve sheath tumor

Background: About 50% of MPNST arise in patients with neurofibromatosis type 1, and these tumors are among the most difficult types of soft tissue sarcoma to manage. NF1 is a tumor suppressor gene essential for negative regulation of RAS activity and is the most common genetic alteration in MPNST (86%). Despite a number of clinical trials, there has been little improvement in overall patient survival in patients with relapsed disease, and thus novel therapeutic approaches are needed. The concept of pharmacologic MEK inhibition has been applied to models of MPNST. However, the preclinical responses to single agent MEK inhibitor (MEKi) have been partial at best and suggest a need for a better understanding of the role of ERK and other effector pathways. A complex interplay of upstream signaling or parallel pathways may characterize NF1-driven tumorigenesis and inhibiting more than one RAS effector pathway may be necessary for complete anti-tumor effect. Methods: Using a panel of well-characterized MPNST cell lines, levels of NF1, select tumor suppressors and RTKs, and markers of activated ERK and PI3K/AKT signaling were detected by immunoblot. Isoform-specific RAS activity was evaluated using active-Ras immunoprecipitation assay. We determined the sensitivity of MPNST cells to MEKi and identified actionable alterations in signaling that underlie adaptive and acquired resistance by immunoblot analysis. We have developed and characterized novel in vitro models that are resistant to MEKi using proteomic, biochemical, and genetic approaches, in order to identify mechanisms of resistance, providing rationale for combination therapies. The anti-tumor efficacy of combination strategies was further examined in NF1-MPNST models, both in vitro and in vivo. Results: NF1-MPNST demonstrate variable responses to MEKi. Relief of negative feedback and signaling adaptation to MEKi results in compensatory activation of the PDGFRβ/PI3K/AKT axis. Combination of MEKi plus PI3K/mTORki effectively inhibits MPNST cell growth. Additionally, HGF/c-Met signaling is elevated in a MEKi-resistant model; recombinant HGF stimulation or inducible HGF overexpression confer resistance to MEK inhibition in parental cells originally sensitive to MEKi. In support of this observation, inducible shRNA-mediated HGF or MET knockdown restores the sensitivity of MEKi-resistant cells to MEKi; and combination MEKi+METi is active against MEKi resistance. Conclusion: Our ongoing work has begun to unravel the complicated networks which undergo adaptive modeling in response to MEKi. We have identified one mechanism of acquired resistance to MEKi, and found that combination strategies using MEKi+PI3K/mTORi or MEKi+METi may delay or prevent MEKi resistance, which may benefit patients with MPNST harboring NF1 genetic alterations.

Citation Format: Jiawan Wang, Kai Pollard, Christine Pratilas. Adaptive and acquired signaling response to MEK inhibition in NF1-associated malignant peripheral nerve sheath tumor [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A121. doi:10.1158/1535-7163.TARG-19-A121

Abstract B066: Inhibition of farnesyl transferase by tipifarnib leads to isoform specific cell growth inhibition in HRAS-mutated human rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and adolescents. A subset of RMS expresses the characteristic PAX3-FOXO1 or PAX7-FOXO1 translocations, thought to be oncogenic drivers. Among the fusion-negative subset of RMS, a substantial proportion express oncogenic mutations in RAS proteins or other elements of RAS signaling pathways. Activating RAS mutations are disproportionately seen in patients with high-risk RMS and attempts to augment combination chemotherapy have not resulted in improvement in overall survival in this poor prognosis group. Given the common finding of dysregulated RAS signaling, targeting RAS represents an attractive therapeutic approach. RAS family members require posttranslational modification for plasma membrane localization and subsequent downstream signaling. One therapeutic strategy, therefore, includes disruption of RAS protein prenylation, and thereby its membrane localization, via inhibition of farnesyl transferase (FTase). NRAS and KRAS may utilize geranylgeranyltransferase prenylation as a bypass when FTase is inhibited, but HRAS is uniquely dependent on FTase, and therefore, tumor cells with HRAS mutations may be preferentially sensitive to the effects of farnesyltransferase inhibition (FTI). We therefore tested human RMS cell lines harboring mutations in HRAS, KRAS or NRAS, and those wild type (WT) for H-, K-, and N-RAS, and found that only tumor cells with oncogenic HRAS mutations demonstrate growth inhibition and decreased ERK signaling in response to the FTI tipifarnib. Using high-throughput cell proliferation assays, dose dependent cell growth inhibition in response to treatment with tipifarnib is observed in HRAS-mutated RMS cell lines. We observe a reduction in phosphorylated MEK and ERK in HRAS mutated cell lines indicating effective RAS signaling inhibition. Activity of PI3K-mTOR pathway elements p70-S6K and RPS6 are inhibited by tipifarnib in cell lines that demonstrate an antiproliferative response to the compound. In vivo exposure to tipifarnib in HRAS-mutated RMS xenografts results in tumor growth inhibition. Therapeutic strategies targeting RAS protein prenylation may therefore provide an effective approach as an alternative to traditional chemotherapy, while improving outcomes and decreasing toxicities. Based on these data, a genomically-selected clinical trial using tipifarnib to treat pediatric patients with HRAS-mutated tumors, including RMS, would be of interest.

Citation Format: Patience Obasaju, Kai Pollard, Amy Allen, Jiawan Wang, Christine Pratilas. Inhibition of farnesyl transferase by tipifarnib leads to isoform specific cell growth inhibition in HRAS-mutated human rhabdomyosarcoma [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B066. doi:10.1158/1535-7163.TARG-19-B066

Abstract 4785: Signaling adaptation to FLT3 inhibition in FLT3/ITD leukemia results in a reactivation of ERK signaling that can be abrogated with MEK inhibition

The use of FLT3 tyrosine kinase inhibitors (TKIs) for the treatment of FLT3 mutant acute myeloid leukemia (AML) has been explored as a promising strategy for over a decade. However, FLT3 TKIs have thus far shown limited clinical benefit in patients with FLT3/ITD AML. We hypothesized that FLT3/ITD leukemia cells exhibit mechanisms of intrinsic signaling adaptation to FLT3 TKI treatment that are associated with an incomplete biologic response. If true, combined targeted therapeutic approaches that overcome the adaptive resistance to FLT3 inhibition could be used to maximize the efficacy of anti-leukemia treatment for those expressing this mutation.

To evaluate this hypothesis, the FLT3/ITD AML cell lines Molm14 and MV4;11 were treated with FLT3 TKIs for up to 48 hours at concentrations sufficient for maximal FLT3 inhibition and downstream signaling was analyzed by immunoblotting. We identified a rebound in ERK phosphorylation discernible by six hours and continuing for the duration of treatment, despite continued drug presence. This rebound resulted in near baseline levels of phosphorylated ERK (pERK) and was coupled to a rebound in phosphorylation of elements both upstream and downstream of ERK as well as in the expression levels of ERK target genes, suggesting a global reactivation of the signaling cascade. Rebound was sensitive to a reduction in serum, suggesting a growth factor-dependent mechanism.

To explore the consequences of this adaptation, the impact of combinatory targeting of ERK activity using selective small molecule inhibitors of MEK was evaluated. When Molm14 and MV4;11 cells were treated with inhibitors of both FLT3 and MEK in combination, little to no pERK rebound was observed. Additionally, the anti-leukemia effects were more pronounced for the combination compared to either drug alone, both in vitro and in vivo. In vitro, the addition of a MEK inhibitor (PD0325901 or trametinib) to FLT3 TKI (sorafenib) treatment synergistically increased cell death and decreased cell viability. This effect was most pronounced at mid-range sorafenib combined with low dose MEK inhibitor. In vivo, the addition of low-dose PD0325901 to sorafenib treatment resulted in a significant reduction of both peripheral blood and bone marrow blasts in a transplant model (p &lt; 0.05).

Together, these studies reveal that FLT3/ITD leukemia cells demonstrate an adaptive feedback mechanism capable of reactivating ERK signaling in response to FLT3 inhibition. This adaptation limits the efficacy of FLT3 TKI treatment and can be abrogated by the addition of a MEK inhibitor. Our data suggest that the addition of low-dose MEK inhibitor to FLT3 TKI treatment as a means to overcome signaling adaptation may improve outcomes for patients with FLT3/ITD AML.

Citation Format: J. Kyle Bruner, Hayley Ma, Christine Pratilas, Donald Small. Signaling adaptation to FLT3 inhibition in FLT3/ITD leukemia results in a reactivation of ERK signaling that can be abrogated with MEK inhibition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4785.

Abstract C138: Loss of NF1 in melanoma cell lines is associated with active Ras and dependence on MEK even in the absence of BRAF or NRAS mutation

Though two-thirds of cutaneous melanomas harbor activating mutations in the BRAF and NRAS genes, the alterations that drive tumor progression in the roughly 30% of melanoma tumors wild-type for BRAF and NRAS remain largely uncharacterized. The selective RAF inhibitors vemurafenib and dabrafenib inhibit MAPK pathway activity only in BRAF mutant cells, thus their clinical utility is restricted to patients with BRAF mutant tumors. MEK inhibitors, which have broader antitumor activity and have shown promising activity in NRAS mutant melanoma, may be effective in a broader range of MAPK pathway-dependent tumors. We performed a functional and genomic analysis of melanoma cell lines wild-type for BRAF and NRAS to determine whether occult mutations in RAS signaling were present. Elevated RAS-GTP was common in BRAF/NRAS wild-type melanoma cell lines, a subset of which exhibited total loss of NF1 protein expression. The proliferation of NF1-null melanoma cells was dependent upon MEK, though the cellular potency of several allosteric MEK inhibitors that are currently in clinical testing (PD0325901, AZD6244, MEK162 and trametinib) varied widely in NF1-null melanoma cells. The greatest antitumor activity was noted with trametinib, a MEK inhibitor that also blocks RAF mediated phosphorylation of MEK. Notably, alterations in NF1 also co-occurred with RAS and BRAF mutations in both cell lines and human melanomas. In the setting of BRAF co-mutation, loss of NF1 abrogated upstream negative feedback on RAS activation resulting in constitutive expression of RAS-GTP and resistance to RAF but not MEK inhibition. In summary, NF1 loss is a common event in cutaneous melanoma that is associated with RAS activation, MEK dependence and RAF inhibitor resistance.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C138.

Citation Format: Moriah H. Nissan, Christine Pratilas, Alexis Jones, Helen Won, Li Kong, Zhan Yao, Taha Merghoub, Antoni Ribas, Paul Chapman, Rona Yaeger, Barry Taylor, Nikolaus Shultz, Michael F. Berger, Neal Rosen, David B. Solit. Loss of NF1 in melanoma cell lines is associated with active Ras and dependence on MEK even in the absence of BRAF or NRAS mutation. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C138.

Abstract 4630: Feedback dependent suppression of mitogenic signaling and its effect on RAF inhibition in BRAFV600E melanomas

RAF inhibitors have remarkable activity in melanomas harboring BRAFV600E mutations. We previously found that active Ras induces RAF dimers in tumors with wild-type RAF, and, that RAF inhibitors transactivate these dimers. Because BRAFV600E melanomas have enhanced ERK signaling, they are hypothesized to have feedback-mediated suppression of Ras in order to maintain monomeric and inhibitor-sensitive BRAFV600E. To test this hypothesis we evaluated the response of these tumors to RAF inhibitors over time. We found that in the treatment-naive state, BRAFV600E melanomas had suppressed RTK signaling and maintained a low level of Ras-GTP. This occurred through a multifactorial negative feedback process driven by active ERK. In this baseline state, BRAFV600E was sensitive to RAF inhibitors. After treatment with RAF inhibitors, however, inhibition of ERK signaling lead to loss of feedback, a process that restored signaling from RTKs and resulted in Ras activation. In turn, this diminished the effect of RAF inhibitors and lead to a partial, but sustained, reactivation of ERK signaling. In this post-treatment state, ERK signaling was insensitive to RAF inhibitors but sensitive to MEK inhibitors. Targeting the regulatory components of this new steady state, either through co-administration of a MEK inhibitor or a RTK inhibitor along with a RAF inhibitor resulted in improved antitumor activity. These results highlight the need to understand the adaptive response to ERK pathway inhibition in order to design better combinatorial therapies and achieve maximal antitumor effects.

Citation Format: Piro Lito, Christine Pratilas, Eric Joseph, Madhavi Tadi, Ensar Halilovic, Matthew Zubrowski, Alan Huang, Elisa de Stanchina, Sarat Chandarlapaty, Poulikos Poulikakos, Neal Rosen. Feedback dependent suppression of mitogenic signaling and its effect on RAF inhibition in BRAFV600E melanomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4630. doi:10.1158/1538-7445.AM2013-4630

Abstract 1971: Concurrent loss of PTEN and RB is sufficient to confer BRAF independence in melanomas harboring V600E BRAF mutations

BRAF mutations are found in ∼8% of human tumors, with the highest frequency observed in melanoma (40-70%). Supporting its classification as an oncogene, V600E BRAF stimulates ERK signaling, induces proliferation and is capable in model systems of promoting transformation. BRAF mutations are, however, common in nevi suggesting that BRAF mutation alone is insufficient for tumorigenesis. With the goal of identifying concurrent mutations that condition BRAF/MEK dependence in V600E BRAF melanoma, we performed MALDI-TOF mass spectrometry genotyping on a panel of 149 melanoma cell lines. Seventy-nine (53%) harbored BRAF mutations. Proteomic profiling of the class of V600E BRAF mutant cell lines demonstrated significant variability in the expression of PTEN and pAKT. Nine cells lines harboring V600E BRAF mutations were found to express no PTEN protein and high pAKT by immunoblotting. The majority of these cell lines had small (1-2) base-pair insertions or deletions leading to a frame shift and early truncation. Array CGH confirmed focal homozygous deletion of the PTEN gene in three of the models. These deletions were small and in one case detected by the Agilent 1M but not the 244K platform. We have previously reported that mutations of BRAF are associated with enhanced and selective sensitivity to MEK inhibition when compared to either receptor tyrosine kinase-driven cells or cells harboring a RAS mutation. To determine the MAPK pathway dependence of V600E BRAF mutant cell lines as a function of PTEN expression, we used PD0325901, a selective allosteric inhibitor of MEK1/2. All V600E BRAF mutant, PTEN expressing cell lines were sensitive to PD0325901. All but two of the V600E BRAF mutant, PTEN null cells were also dependent upon MEK for proliferation with IC50 values ranging from 1.1 to &gt;500nM. These data suggest that PTEN loss is insufficient to confer resistance to MAPK-pathway inhibition. Further characterization of the two models which displayed complete resistance to MEK inhibition revealed that both harbored concurrent loss of PTEN and RB. These models were also resistant to the selective RAF inhibitor PLX4720. To determine whether loss of RB function was sufficient to confer RAF/MEK-independence in a BRAF mutant, PTEN-null context, we stably infected viral E7 into three MEK-dependent, BRAF mutant, PTEN null models. Infection of E7 led to resistance to MEK-inhibition in all three models. These data suggest that no single mutational event is likely associated with de novo resistance to MEK-inhibition in V600E BRAF mutant melanoma. Loss of PTEN expression and activation of AKT may however be associated with diminished responsiveness to RAF/MEK-inhibition. Further, tumors with concurrent PTEN and RB loss may represent a subset of BRAF mutant patients who derive no clinical benefit from inhibitors of the MAPK pathway such as PLX4032.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1971.

Abstract B87: Genomic complexity and BRAF/MEK-dependence in V600E BRAF mutant melanoma

Constitutive ERK activation, often the result of BRAF mutation, is a common finding in human cancer. BRAF mutations occur in approximately 8% of human tumors, with the highest frequency observed in melanoma (40–70%). Supporting its classification as an oncogene, V600E BRAF stimulates ERK signaling, induces proliferation and is capable in model systems of promoting transformation. BRAF mutations are, however, common in nevi suggesting that BRAF mutation alone is insufficient for tumorigenesis. These observations suggest that additional alterations cooperate with BRAF in promoting melanoma formation and that inhibition of oncogenic BRAF may not be sufficient in many tumors to induce apoptosis in some BRAF mutant melanomas. Prior studies have demonstrated that loss of PTEN is a common event in melanoma and PTEN has been shown to cooperate with BRAF mutation in accelerating invasive melanoma formation in genetic murine models. With the goal of identifying model systems in which to study the the role played by PTEN in promoting tumorigenesis, we performed MALDI-TOF mass spectrometry genotyping on a panel of 116 melanoma cell lines. Seventy-two (62%) harbored BRAF mutations (66 V600E, 3 V600K, 3 in exon 11). Proteomic profiling of the class of V600E BRAF mutant cell lines demonstrated significant variability in the expression of PTEN and pAKT. Nine cells lines harboring V600E BRAF mutations were found to express no PTEN protein and high pAKT by immunoblotting. The majority of these cell lines had small (1–2) base-pair insertions and deletions leading to a frame shift and early truncation. Array CGH confirmed focal homozygous deletion of the PTEN gene in three of the models. These deletions were small and in one case detected by the Agilent 1M but not the 244K platform. We have previously reported that mutations of BRAF are associated with enhanced and selective sensitivity to MEK inhibition when compared to either receptor tyrosine kinase-driven cells or cells harboring a RAS mutation. To determine the MAPK pathway dependence of V600E BRAF mutant cell lines as a function of PTEN expression, we used PD0325901, a selective allosteric inhibitor of MEK1/2. A subset of the V600E BRAF mutant, PTEN null or mutant cells were dependent upon MEK for proliferation with IC50 values ranging from 1.1 to &gt;500nM. These data suggest that PTEN loss is insufficient to confer absolute resistance to MAPK-pathway inhibition. MEK inhibition was, however, cytostatic in all V600E BRAF, PTEN null cell lines whereas MEK inhibition induced significant apoptosis in a subset of V600E BRAF, PTEN wild-type models. PTEN null, BRAF mutant cell lines were sensitive to two selective PI3 kinase inhibitors and the combination of MEK and PI3 kinase inhibition was more effective than either alone in a subset of models. In summary, our data suggest that PTEN is one of several concurrent genetic/epigenetic alterations that condition MEK-dependence in melanoma cell lines harboring V600E BRAF mutations. Given the promising preliminary data with BRAF and MEK selective inhibitors in early stage clinical trials, these data may aid in the identification of those patients most likely to benefit from selective inhibitors of the MAPK pathway.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B87.