On-target Resistance Research Articles

Multidrug tolerance conferred by loss-of-function mutations in anti-sigma factor RshA of Mycobacterium abscessus.

Low-level drug resistance in noncanonical pathways can constitute steppingstones toward acquisition of high-level on-target resistance mutations in the clinic. To capture these intermediate steps in Mycobacterium abscessus (Mab), we performed classic mutant selection experiments with moxifloxacin at twofold its minimum inhibitory concentration (MIC) on solid medium. We found that low-level resistance emerged reproducibly as loss-of-function mutations in RshA (MAB_3542c), an anti-sigma factor that negatively regulates activity of SigH, which orchestrates a response to oxidative stress in mycobacteria. Since oxidative stress is generated in response to many antibiotics, we went on to show that deletion of rshA confers low to moderate resistance-by measure of MIC-to a dozen agents recommended or evaluated for the treatment of Mab pulmonary infections. Interestingly, this moderate resistance was associated with a wide range of drug tolerance, up to 1,000-fold increased survival of a ΔrshA Mab mutant upon exposure to several β-lactams and DNA gyrase inhibitors. Consistent with the putative involvement of the SigH regulon, we showed that addition of the transcription inhibitor rifabutin (RBT) abrogated the high-tolerance phenotype of ΔrshA to representatives of the β-lactam and DNA gyrase inhibitor classes. In a survey of 10,000 whole Mab genome sequences, we identified several loss-of-function mutations in rshA as well as non-synonymous polymorphisms in two cysteine residues critical for interactions with SigH. Thus, the multidrug multiform resistance phenotype we have uncovered may not only constitute a step toward canonical resistance acquisition during treatment but also contribute directly to treatment failure.

Deciphering resistance mechanisms in cancer: final report of MATCH-R study with a focus on molecular drivers and PDX development

BackgroundUnderstanding the resistance mechanisms of tumor is crucial for advancing cancer therapies. The prospective MATCH-R trial (NCT02517892), led by Gustave Roussy, aimed to characterize resistance mechanisms to cancer treatments through molecular analysis of fresh tumor biopsies. This report presents the genomic data analysis of the MATCH-R study conducted from 2015 to 2022 and focuses on targeted therapies.MethodsThe study included resistant metastatic patients (pts) who accepted an image-guided tumor biopsy. After evaluation of tumor content (TC) in frozen tissue biopsies, targeted NGS (10 < TC < 30%) or Whole Exome Sequencing and RNA sequencing (TC > 30%) were performed before and/or after the anticancer therapy.Patient-derived xenografts (PDX) were established by implanting tumor fragments into NOD scid gamma mice and amplified up to five passages.ResultsA total of 1,120 biopsies were collected from 857 pts with the most frequent tumor types being lung (38.8%), digestive (16.3%) and prostate (14.1%) cancer. Molecular targetable driver were identified in 30.9% (n = 265/857) of the patients, with EGFR (41.5%), FGFR2/3 (15.5%), ALK (11.7%), BRAF (6.8%), and KRAS (5.7%) being the most common altered genes. Furthermore, 66.0% (n = 175/265) had a biopsy at progression on targeted therapy. Among resistant cases, 41.1% (n = 72/175) had no identified molecular mechanism, 32.0% (n = 56/175) showed on-target resistance, and 25.1% (n = 44/175) exhibited a by-pass resistance mechanism. Molecular profiling of the 44 patients with by-pass resistance identified 51 variants, with KRAS (13.7%), PIK3CA (11.8%), PTEN (11.8%), NF2 (7.8%), AKT1 (5.9%), and NF1 (5.9%) being the most altered genes. Treatment was tailored for 45% of the patients with a resistance mechanism identified leading to an 11 months median extension of clinical benefit.A total of 341 biopsies were implanted in mice, successfully establishing 136 PDX models achieving a 39.9% success rate. PDX models are available for EGFR (n = 31), FGFR2/3 (n = 26), KRAS (n = 18), ALK (n = 16), BRAF (n = 6) and NTRK (n = 2) driven cancers. These models closely recapitulate the biology of the original tumors in term of molecular alterations and pharmacological status, and served as valuable models to validate overcoming treatment strategies.ConclusionThe MATCH-R study highlights the feasibility of on purpose image guided tumor biopsies and PDX establishment to characterize resistance mechanisms and guide personalized therapies to improve outcomes in pre-treated metastatic patients.Graphical

Repotrectinib: Redefining the therapeutic landscape for patients with ROS1 fusion-driven non-small cell lung cancer.

The ROS1 proto-oncogene encodes a receptor tyrosine kinase with structural homology to other oncogenic drivers, including ALK and TRKA-B-C. The FDA-approved tyrosine kinase inhibitors (TKIs) crizotinib and entrectinib have demonstrated efficacy in treating ROS1 fusion-positive NSCLC. However, limitations such as poor blood-brain barrier penetration and acquired resistance, particularly the ROS1 G2032R solvent-front mutation, hinder treatment durability. Repotrectinib, a next-generation macrocyclic TKI, was rationally designed to overcome on-target resistance mutations and improve brain distribution through its low molecular weight. In the TRIDENT-1 clinical trial, repotrectinib demonstrated significant efficacy in both TKI-naïve and TKI-pretreated patients with ROS1-rearranged NSCLC, including those with CNS metastases and G2032R resistance mutations. In the TKI-naïve cohort (n = 71), 79% of patients achieved an objective response, with a median progression-free survival (PFS) of 35.7 months, surpassing all previously approved ROS1 TKIs. In patients who had received one prior ROS1 TKI but were chemotherapy-naïve (n = 56), objective responses were observed in 38%, and median PFS was 9.0 months. The safety profile of repotrectinib was consistent with earlier-generation ROS1 TKIs and common adverse events included anemia, neurotoxicity, increased creatine kinase levels, and weight gain. These findings underscore the potential of repotrectinib to address unmet needs in ROS1-rearranged NSCLC, offering durable responses and improved intracranial activity. Future research should prioritize developing next-generation, selective ROS1 inhibitors to reduce Trk-mediated toxicities and improve treatment tolerance.

RET Inhibitors in RET Fusion-Positive Lung Cancers: Past, Present, and Future.

While activating RET fusions are identified in various cancers, lung cancer represents the most common RET fusion-positive tumor. The clinical drug development of RET inhibitors in RET fusion-positive lung cancers naturally began after RET fusions were first identified in patient tumor samples in 2011, and thereafter paralleled drug development in RET fusion-positive thyroid cancers. Multikinase inhibitors were initially tested with limited efficacy and substantial toxicity. RET inhibitors were then designed with improved selectivity, central nervous system penetrance, and activity against RET fusions and most RET mutations, including resistance mutations. Owing their success to these rationally designed features, the first-generation selective RET tyrosine kinase inhibitors (TKIs) had higher response rates, more durable disease control, and an improved safety profile compared to the multikinase inhibitors. This led to lung and thyroid cancer, and later tumor-agnostic regulatory approvals. While next-generation RET TKIs were designed to abrogate uncommon on-target (e.g., solvent front mutation) resistance to selpercatinib and pralsetinib, many of these drugs lacked the selectivity of the first-generation TKIs, raising the question of what the future holds for drug development in RET-dependent cancers.

Zurletrectinib is a next-generation TRK inhibitor with strong intracranial activity against NTRK fusion-positive tumours with on-target resistance to first-generation agents

BackgroundWhile NTRK fusion-positive cancers can be exquisitely sensitive to first-generation TRK inhibitors, resistance inevitably occurs, mediated in many cases by acquired NTRK mutations. Next-generation inhibitors (e.g., selitrectinib, repotrectinib) maintain activity against these TRK mutant tumors; however, there are no next-generation TRK inhibitors approved by the FDA and select trials have stopped treating patients. Thus, the identification of novel, potent and specific next-generation TRK inhibitors is a high priority.MethodsIn silico modeling and in vitro kinase assays were performed on TRK wild type (WT) and TRK mutant kinases. Cell viability and clonogenic assays as well as western blots were performed on human primary and murine engineered NTRK fusion-positive TRK WT and mutant cell models. Finally, zurletrectinib was tested in vivo in human xenografts and murine orthotopic glioma models harboring TRK-resistant mutations.ResultsIn vitro kinase and in cell-based assays showed that zurletrectinib, while displaying similar potency against TRKA, TRKB, and TRKC WT kinases, was more active than other FDA approved or clinically tested 1st- (larotrectinib) and next-generation (selitrectinib and repotrectinib) TRK inhibitors against most TRK inhibitor resistance mutations (13 out of 18). Similarly, zurletrectinib inhibited tumor growth in vivo in sub-cute xenograft models derived from NTRK fusion-positive cells at a dose 30 times lower when compared to selitrectinib. Computational modeling suggests this stronger activity to be the consequence of augmented binding affinity of zurletrectinib for TRK kinases. When compared to selitrectinib and repotrectinib, zurletrectinib showed increased brain penetration in rats 0.5 and 2 h following a single oral administration. Consistently, zurletrectinib significantly improved the survival of mice harboring orthotopic NTRK fusion-positive, TRK-mutant gliomas (median survival = 41.5, 66.5, and 104 days for selitrectinib, repotrectinib, and zurletrectinib respectively; P < 0.05).ConclusionOur data identifies zurletrectinib as a novel, highly potent next-generation TRK inhibitor with stronger in vivo brain penetration and intracranial activity than other next-generation agents.

Mechanisms of Resistance to Targeted Therapies in AML

The treatment of acute myeloid leukemia (AML) has historically relied on cytotoxic chemotherapy, but modern understanding of AML biology has paved the way for new treatments that target the molecular pathways that drive AML, in particular FLT3, IDH1/IDH2, and BCL2. Many of these targeted therapies are effective, but responses are typically short-lived and resistance remains a ubiquitous clinical problem. Understanding the mechanisms of resistance to targeted therapy is essential to continue improving AML therapy. Recent studies have shed new light on the ways in which AML evades targeted inhibition, including on-target resistance mutations, mutations in parallel molecular pathways, and plasticity in cellular state. In this review, we outline the mechanisms of resistance to commonly used targeted therapies in AML and discuss ideas to overcome the urgent problem of resistance.

Integrated PBPK-EO modeling of osimertinib to predict plasma concentrations and intracranial EGFR engagement in patients with brain metastases

The purpose of this study was to develop and validate a physiologically based pharmacokinetic (PBPK) model combined with an EGFR occupancy (EO) model for osimertinib (OSI) to predict plasma trough concentration (Ctrough) and the intracranial time-course of EGFR (T790M and L858R mutants) engagement in patient populations. The PBPK model was also used to investigate the key factors affecting OSI pharmacokinetics (PK) and intracranial EGFR engagement, analyze resistance to the target mutation C797S, and determine optimal dosing regimens when used alone and in drug-drug interactions (DDIs). A population PBPK-EO model of OSI was developed using physicochemical, biochemical, binding kinetic, and physiological properties, and then validated using nine clinical PK studies, observed EO study, and two clinical DDI studies. The PBPK-EO model demonstrated good consistency with observed data, with most prediction-to-observation ratios falling within the range of 0.7 to 1.3 for plasma AUC, Cmax, Ctrough and intracranial free concentration. The simulated time-course of C797S occupancy by the PBPK model was much lower than T790M and L858R occupancy, providing an explanation for OSI on-target resistance to the C797S mutation. The PBPK model identified ABCB1 CLint,u, albumin level, and EGFR expression as key factors affecting plasma Ctrough and intracranial EO for OSI. Additionally, PBPK-EO simulations indicated that the optimal dosing regimen for OSI in patients with brain metastases is either 80 mg once daily (OD) or 160 mg OD, or 40 mg or 80 mg twice daily (BID). When used concomitantly with CYP enzyme perpetrators, the PBPK-EO model suggested appropriate dosing regimens of 80 mg OD with fluvoxamine (FLUV) itraconazole (ITR) or fluvoxamine (FLUC) for co-administration and an increase to 160 mg OD with rifampicin (RIF) or efavirenz (EFA). In conclusion, the PBPK-EO model has been shown to be capable of simulating the pharmacokinetic concentration–time profiles and the time-course of EGFR engagement for OSI, as well as determining the optimum dosing in various clinical situations.

Serial Cell-Free DNA Sequencing in ROS1 Fusion-Positive Lung Cancers During Treatment With Entrectinib.

Patients with metastatic ROS1 fusion-positive non-small cell lung cancer (NSCLC) are effectively treated with entrectinib, a multikinase inhibitor. Whether serial targeted gene panel sequencing of cell-free DNA (cfDNA) can identify response and progression along with mechanisms of acquired resistance to entrectinib is underexplored. In patients with ROS1 fusion-positive NSCLC, coclinical trial plasma samples were collected before treatment, after two cycles, and after progression on entrectinib (global phase II clinical trial, ClinicalTrials.gov identifier: NCT02568267). Samples underwent cfDNA analysis using MSK-ACCESS. Variant allele frequencies of detectable alterations were correlated with objective response per RECIST v1.1 criteria. Twelve patients were included, with best response as partial response (n = 9, 75%), stable disease (n = 2, 17%), and progressive disease (PD; n = 1, 8%). A ROS1 fusion was variably detected in cfDNA; however, patients without a ROS1 fusion in cfDNA had no other somatic alterations detected, indicative of possible low cfDNA shedding. Clearance of the enrolling ROS1 fusion or concurrent non-ROS1 alterations (TP53, CDH1, NF1, or ARID1A mutations) was observed in response to entrectinib therapy. Radiologic PD was accompanied by redemonstration of a ROS1 fusion or non-ROS1 alterations. On-target resistance was rare; only one patient acquired ROS1 G2032R at the time of progression. Several patients acquired new off-target likely oncogenic alterations, including a truncating alteration in NF1. Serial cfDNA monitoring may complement radiographic assessments as determinants of response and resistance to entrectinib in ROS1 fusion-positive lung cancers in addition to detecting putative resistance mechanisms on progression.

What is a bad ALK? A scoping review of molecular markers of poor prognosis.

e20530 Background: Patients with non-small cell lung cancer (NSCLC) with anaplastic lymphoma kinase ( ALK) rearrangements derive a significant and durable clinical benefit from tyrosine kinase inhibitors (TKI). However, a portion of patients have progressive disease as their best response and progress to death much earlier than expected which is termed primary resistance. This scoping review aims to summarize the known molecular mechanisms that underlie this lethal ALK phenotype. Methods: We performed a systematic scoping review from scientific databases such as Ovid Medline, Ovid Embase, and Cochrane Central Register of Controlled Trials. Data was extracted from the database inception to March 13, 2023. Studies included molecular markers of poor prognosis, with a focus on TP53, variant 3 re-arrangements, and reports of poor clinical response to TKIs (defined as progression-free survival less than 3 months on 1st line TKI or overall survival less than 2 years from exposure to 1st line TKI). 2nd generation and 3rd generation ALK TKI clinical trial data were also included. Results: A total of 4360 studies were screened and 136 studies were included. Numerous studies implicated the negative prognostic role of variant 3 likely mediated through the acquisition of on-target resistance mutations compared to other variants. TP53 mutations were also associated with a worse prognosis and implicated with greater chromosomal instability and mutational burden. Furthermore, reports of both variant 3 and TP53 mutations together were associated with even worse survival suggesting both molecular mechanisms combined can confer primary resistance phenotype. Other mediators of primary resistance included aberrations in cell cycle regulators such as CDKN2A/B loss, mutations in cell signalling pathways such as the PI3K/ AKT/mTOR pathway, deficiencies in DNA repair mechanisms, and uncommon fusion partners. Consistent with these prior studies, comprehensive genomic analysis from clinical trial data of 2nd generation and 3rd generation TKIs was unable to identify a singular genomic signature that underlies this lethal phenotype. However, a general trend from the literature suggested that the combination of multiple aberrations is likely necessary to confer a primary resistance phenotype, though the relative contribution of each somatic mutation likely will vary. Conclusions: This scoping review highlights that in NSCLC, the lethal ALK phenotype is likely composed of a heterogeneous population of various combinations of poor prognostic factors including variant 3, mutations in cell cycle regulators and other aberrations in cell signalling pathways. There remains an unmet need for a genomic assay to integrate all these various molecular markers to predict the lethal ALK phenotype.

Osimertinib, platinum, etoposide as initial treatment for patients with EGFR mutant lung cancers with TP53 and RB1 alterations.

8565 Background: EGFR-mutant lung adenocarcinomas (EGFR+LC) transform to small cell lung cancer (SCLC) in up to 14% of cases, which creates an aggressive disease phenotype that is treated like de novo small lung cancer with platinum/etoposide chemotherapy. Transformed EGFR+LC molecularly mimic de novo small cell lung cancers and harbor TP53and RB1 loss. We hypothesized that if small cell directed chemotherapy is utilized prior to histologic transformation in EGFR/TP53/RB1 mutant LC, we may eradicate any pre-existing small cell clones, prevent small cell histologic transformation, and improve patient outcomes. Methods: We administered osimertinib, platinum, and etoposide in patients with newly diagnosed EGFR+LC with TP53and RB1alterations. Patients received 3 months of osimertinib induction, then 4 cycles of osimertinib, platinum and etoposide followed by osimertinib until progression. Objective response rate (ORR), progression-free survival (PFS), overall survival (OS), and safety were assessed. Patients were required to have an on-treatment biopsy prior to initiation of chemotherapy upon which single cell RNA sequencing (scRNAseq) was performed. All patients had pre-treatment and post-progression biopsies that underwent next-generation sequencing. Patients were evaluated for acquired resistance (classified as on-target, off-target, transformation, and unknown). Among patients that transformed, markers of SCLC (ASCL1, NEUROD1, POU2F3, YAP1, synaptophysin, chromogranin, and Ki-67) were analyzed. Results: Eleven patients were enrolled [median age 58 years old range (49-81), 45% female, 73% EGFRexon 19 deletions and 27% EGFR L858R]. Three patients received cisplatin/etoposide, six patients carboplatin/etoposide, and two patients progressed two months on induction osimertinib before they could start chemotherapy. The ORR was 82%, median PFS 15.6 months and median OS was 37.9 months. All patients retained EGFR, TP53, and RB1mutations on post-treatment biopsy. Acquired on-target resistance mechanisms were identified in 9% of patients ( EGFR C797S), off-target in 9% of patients ( CDKN2A), and small cell transformation in 46% of patients. Among the transformed patients, all had high Ki-67 (70-95%) and 80% were positive for synaptophysin and chromogranin. 40% of cases were ASCL1-dominant, 40% were NEUROD1-dominant, and 20% were unknown. Additionally, we utilized copy number inference and CytoTrace to identify subclones within pre-transformed EGFR+LC that potentially harbor features of early plasticity. Further scRNAseq and whole exome sequencing data are forthcoming. Conclusions: In patients with EGFR+LCs with concurrent TP53and RB1alterations, osimertinib plus platinum and etoposide demonstrated activity and no new safety signals were seen. Early addition of small cell directed chemotherapy did not prevent histologic transformation. Clinical trial information: NCT03567642 .

Abstract GS03-10: Allosteric PI3K-alpha inhibition overcomes on-target resistance to orthosteric inhibitors mediated by secondary PIK3CA mutations

Abstract Background: PIK3CA mutations occur in ~40% of HR-positive breast cancers, where alpelisib, an orthosteric PI3Kα inhibitor, is FDA-approved in combination with fulvestrant. Although prior studies have identified potential resistance mechanisms, such as PTEN loss, clinical acquired resistance to orthosteric PI3Kα inhibitors and the role of next-generation allosteric PI3Kα inhibitors remain poorly understood. Methods: To identify on-target and off-target alterations potentially mediating resistance to PI3Kα inhibitors, we used a targeted next-generation sequencing assay (Guardant360; Guardant Health) to analyze ctDNA in serially collected plasma samples from 32 patients with PIK3CA-mutated advanced HR-positive, HER2-negative breast cancer treated with alpelisib and inavolisib. In addition, we performed whole exome sequencing (WES) of 100 tissue samples collected from 8 autopsy series from patients with metastatic, PIK3CA-mutant HR-positive, HER2-negative breast cancer previously treated with PI3Kα inhibitors. Acquired alterations were prioritized through a combination of structural modeling and free-energy perturbation simulation and validated in genomically engineered PIK3CA mutant breast cancer cell lines T47D (PIK3CA H1047R-mutant) or MCF7 (PIK3CA E545K-mutant). Results: We observed that 50% of patients acquire genomic alterations within the PI3K-pathway, including PTEN loss and activating AKT1 mutations. Notably, while secondary PIK3CA mutations were previously reported to increase sensitivity to PI3Ka-inhibitors, we identified emergent secondary resistance mutations in PIK3CA that alter the inhibitor binding pocket including PIK3CA Q859K and PIK3CA W780R. Some mutations had differential effects on PI3Ka-selective vs. pan-PI3K inhibitors, but resistance induced by all mutations could be overcome by the novel allosteric pan-mutant-selective PI3Ka-inhibitor RLY-2608. Conclusion: In one of the largest patient cohorts analyzed to date, this study defines the clinical landscape of acquired resistance to PI3Ka inhibitors. Genomic alterations within the PI3K pathway represent a major mode of resistance and identify a novel class of secondary PIK3CA resistance mutations that can be overcome by an allosteric PI3Ka inhibitor. Together, these findings provide insights to guide strategies to overcome resistance in PIK3CA-mutated cancers. Citation Format: Andreas Varkaris, Ferran Fece de la Cruz, Elizabeth Martin, Bryanna Nordern, Nicholas Chevalier, Ignaty Leshchiner, Anastasia Stavridi, Janice Kim, Alkistis Papatheodoridi, Hakan Gunaydin, Brian Danysh, Laxmi Parida, Ioannis Sanidas, Yongli Ji, Kayao Lau, Gerburg Wulf, Aditya Bardia, Laura Spring, Steven Isakoff, Jochen Lennerz, Levi Pierce, Ermira Pazolli, Gad Getz, Ryan Corcoran, Dejan Juric. Allosteric PI3K-alpha inhibition overcomes on-target resistance to orthosteric inhibitors mediated by secondary PIK3CA mutations [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr GS03-10.

Structure-Based Optimization of Pyrazinamide-Containing Macrocyclic Derivatives as Fms-like Tyrosine Kinase 3 (FLT3) Inhibitors to Overcome Clinical Mutations.

Secondary mutations in Fms-like tyrosine kinase 3-tyrosine kinase domain (FLT3-TKD) (e.g., D835Y and F691L) have become a major on-target resistance mechanism of FLT3 inhibitors, which present a significant clinical challenge. To date, no effective drugs have been approved to simultaneously overcome clinical resistance caused by these two mutants. Thus, a series of pyrazinamide macrocyclic compounds were first designed and evaluated to overcome the secondary mutations of FLT3. The representative 8v exhibited potent inhibitory activities against FLT3D835Y and FLT3D835Y/F691L with IC50 values of 1.5 and 9.7 nM, respectively. 8v also strongly suppressed the proliferation against Ba/F3 cells transfected with FLT3-ITD, FLT3-ITD-D835Y, FLT3-ITD-F691L, FLT3-ITD-D835Y-F691L, and MV4-11 acute myeloid leukemia (AML) cell lines with IC50 values of 12.2, 10.5, 24.6, 16.9, and 6.8 nM, respectively. Furthermore, 8v demonstrated ideal anticancer efficacy in a Ba/F3-FLT3-ITD-D835Y xenograft model. The results suggested that 8v can serve as a promising macrocycle-based FLT3 inhibitor for the treatment of AML.

LTK mutations responsible for resistance to lorlatinib in non-small cell lung cancer harboring CLIP1-LTK fusion

The CLIP1-LTK fusion was recently discovered as a novel oncogenic driver in non-small cell lung cancer (NSCLC). Lorlatinib, a third-generation ALK inhibitor, exhibited a dramatic clinical response in a NSCLC patient harboring CLIP1-LTK fusion. However, it is expected that acquired resistance will inevitably develop, particularly by LTK mutations, as observed in NSCLC induced by oncogenic tyrosine kinases treated with corresponding tyrosine kinase inhibitors (TKIs). In this study, we evaluate eight LTK mutations corresponding to ALK mutations that lead to on-target resistance to lorlatinib. All LTK mutations show resistance to lorlatinib with the L650F mutation being the highest. In vitro and in vivo analyses demonstrate that gilteritinib can overcome the L650F-mediated resistance to lorlatinib. In silico analysis suggests that introduction of the L650F mutation may attenuate lorlatinib-LTK binding. Our study provides preclinical evaluations of potential on-target resistance mutations to lorlatinib, and a novel strategy to overcome the resistance.

Abstract 6511: BPI-520105, a highly potent, CNS-penetrant 4th generation EGFR inhibitor overcoming major EGFR resistance mutations in NSCLC

Abstract EGFR activating mutations are prevalent in 10-50% of NSCLC patients. The most common EGFR mutations, L858R (L) and Del19 (D), initially respond to first-, second-, or third-generation (1G, 2G and 3G) EGFR-TKIs. However, on-target resistance, primarily by T790M (T) and C797X(C), inevitably emerges post-treatment and leads to disease progression. Different treatment sequence give rise to different complex mutations. In patients resistant to the 3G TKI osimertinib, double mutations L858R/C797X or Del19/C797X (LC or DC) were observed at a frequency of up to 12% after first-line osimertinib, and triple mutations L858R/T790M/C797S or Del19/T790M/C797S (LTC or DTC) were up to 20% after second-line osimertinib. There are no approved targeted therapy options for these complex resistant mutations. In this study, we developed BPI-520105, a 4th generation EGFR inhibitor capable of targeting all aforementioned major forms of EGFR activating and resistance mutations in NSCLC. It might be an optimal way to address this urgent medical need. In vitro, BPI-520105 potently inhibited the activity of a variety of EGFR kinases, as well as inhibited the proliferation and EGFR phosphorylation in cell lines bearing relative mutations, including single (D, L), double (DT, LT, and DC, LC) and triple (LTC, DTC) mutations. Meanwhile, BPI-520105 exhibited relative weakness towards wild type EGFR and IGF1R, demonstrating good selectivity in kinase and cell-based assays. Despite being a reversible EGFR inhibitor, BPI-520105 sustained the inhibition of pEGFR and pERK for up to 24 hours in the western blot assay. In vivo, oral administration of BPI-520105 displayed significant dose-dependent antitumor effect in multiple EGFR mutant xenograft models, including HCC827 (D), NCI-H1975 (LT), BaF3-EGFR-LC/DC, and BaF3-EGFR-LTC models. Remarkably, BPI-520105 significantly prolonged the lifespan of mice with brain orthotropic BaF3-EGFR-DTC-Luc2 allografts, demonstrating its activity towards brain metastasis. Additionally, BPI-520105 exhibited favorable ADME properties, with high oral exposure across various preclinical species. In summary, BPI-520105 is a highly potent, CNS-penetrant, wide type sparing, and orally bioavailable 4th generation EGFR inhibitor, holding promise for the treatment of NSCLC patients with resistance mutations post 3G progression or even at front line. Citation Format: Jing Guo, Lijia Liu, Xiangyong Liu, Bang Fu, Guangcan Bai, Changyong Qiu, Wei Ren, Xiaodong Song, Guolong Du, Xiao Sun, Yongchun Zhang, Weidong Cai, Pingping Wang, Haibo Chen, Xiaoyun Liu, Zhengyao Zou, Jiayu Zhao, Xuepeng Jv, Hong Lan, Lieming Ding, Jiabing Wang. BPI-520105, a highly potent, CNS-penetrant 4th generation EGFR inhibitor overcoming major EGFR resistance mutations in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6511.

Mechanisms of Resistance to Tyrosine Kinase Inhibitors in ROS1 Fusion-Positive Nonsmall Cell Lung Cancer.

ROS1 fusion-positive (ROS1+) nonsmall cell lung cancer (NSCLC) patients are highly sensitive to tyrosine kinase inhibitor (TKI) treatments. However, acquired TKI resistance remains the major hurdle preventing patients from experiencing prolonged benefits. 107 advanced or metastatic ROS1+ NSCLC patients who progressed on crizotinib and lorlatinib were recruited. Tissue and plasma samples were collected at baseline (N = 50), postcrizotinib (N = 91), and postlorlatinib (N = 21), which were all subject to the 139-gene targeted next-generation DNA sequencing. Molecular dynamics modeling was performed to investigate the effects of ROS1 mutations on binding to different TKIs. In patients with postcrizotinib and postlorlatinib samples, an accumulation of on- and off-target resistance alterations after multiple TKI treatments was observed. ROS1 G2032R and MET amplification were the most common on-target and off-target alterations, respectively. Patients with CD74-ROS1 and SLC34A2-ROS1 had longer progression-free survival (PFS) (P < 0.001) and higher rates of resistance mutations (on-target, P = 0.001; off-target, P = 0.077) than other ROS1 fusion variants following crizotinib treatment. Ten distinct on-target resistance mutations were detected after TKI therapies, of which 4 were previously unreported (ROS1 L2010M, G1957A, D1988N, L1982V). Molecular dynamics simulations showed that all 4 mutations were refractory to crizotinib, while G1957A, D1988N, and L1982V were potentially sensitive to lorlatinib and entrectinib. This study provided a comprehensive portrait of TKI-resistance mechanisms in ROS1+ NSCLC patients. Using in silico simulations of TKI activity, novel secondary mutations that may confer TKI resistance were identified and may support clinical therapeutic decision-making.

Discovery of a Novel Potent EGFR Inhibitor Against EGFR Activating Mutations and On-Target Resistance in NSCLC.

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) serve as the standard first-line therapy for EGFR-mutated non-small cell lung cancer (NSCLC). Despite the sustained clinical benefits achieved through optimal EGFR-TKI treatments, including the third-generation EGFR-TKI osimertinib, resistance inevitably develops. Currently, there are no targeted therapeutic options available postprogression on osimertinib. Here, we assessed the preclinical efficacy of BI-4732, a novel fourth-generation EGFR-TKI, using patient-derived preclinical models reflecting various clinical scenarios. The antitumor activity of BI-4732 was evaluated using Ba/F3 cells and patient-derived cell/organoid/xenograft models with diverse EGFR mutations. Intracranial antitumor activity of BI-4732 was evaluated in a brain-metastasis mouse model. We demonstrated the remarkable antitumor efficacy of BI-4732 as a single agent in various patient-derived models with EGFR_C797S-mediated osimertinib resistance. Moreover, BI-4732 exhibited activity comparable to osimertinib in inhibiting EGFR-activating (E19del and L858R) and T790M mutations. In a combination treatment strategy with osimertinib, BI-4732 exhibited a synergistic effect at significantly lower concentrations than those used in monotherapy. Importantly, BI-4732 displayed potent antitumor activity in an intracranial model, with low efflux at the blood-brain barrier. Our findings highlight the potential of BI-4732, a selective EGFR-TKI with high blood-brain barrier penetration, targeting a broad range of EGFR mutations, including C797S, warranting clinical development.

Selective RET Inhibitors (SRIs) in Cancer: A Journey from Multi-Kinase Inhibitors to the Next Generation of SRIs.

RET is a receptor tyrosine kinase that plays an important role in the development of neurons and kidneys. The gene encoding the rearranged-during-transfection (RET) receptor tyrosine kinase was first discovered in the 1980s. Activating RET mutations and rearrangements have since been identified as actionable drivers of oncogenesis in numerous cancer types and are most prevalent in thyroid and non-small-cell lung cancer. Following the modest success of repurposed RET-active multikinase inhibitors, the first selective RET inhibitors (SRIs), selpercatinib and pralsetinib, received regulatory approval in 2020. Now, thousands of patients with RET-altered cancers have benefited from first-generation SRIs, with impressive deep and durable responses. However, following prolonged treatment with these SRIs, a number of acquired on-target resistance mutations have been identified together with other non-RET-dependent resistance mechanisms. Today, the focus is on how we can further evolve and improve the treatment of RET-altered tumors with next-generation SRIs, and a number of candidate drugs are in development. The ideal next-generation SRIs will be active against on-target acquired resistance alterations, including those that emerge in the CNS, and will have improved safety and tolerability relative to first-generation SRIs. In this review, we will provide an update on these candidates and their potential to meet the unmet clinical need for patients who progress on first-generation SRIs.

Abstract IA006: Clinical activity of lirafugratinib (RLY-4008), a highly selective FGFR2 inhibitor, in patients with advanced FGFR2-altered solid tumors: The ReFocus study

Abstract Background: Oncogenic FGFR2 alterations (fusions/rearrangements [f/r], amplifications, mutations) drive multiple solid tumors. Pan-FGFR inhibitors have validated FGFR2 as an actionable target in cholangiocarcinoma (CCA), however, activity has been limited by off-isoform toxicity and on-target resistance. Lirafugratinib (RLY-4008), the first highly selective FGFR2 inhibitor, was studied in ReFocus, an ongoing Phase I/II study (NCT04526106) in advanced FGFR2-altered solid tumor patients (pts). Previously, we defined the RP2D, confirmed the selective mechanism that minimizes off-isoform toxicity (FGFR1-hyperphosphatemia; FGFR4-diarrhea), and reported efficacy in CCA pts with FGFR2 f/r. Here, we report initial efficacy and safety from pts with solid tumors other than CCA treated at the RP2D. Methods: Pts with advanced solid tumors and FGFR2 alterations identified per local testing enrolled and received lirafugratinib orally. Key objectives were investigator-assessed objective response rate (ORR), duration of response (DOR), and safety. Efficacy was analyzed in pts with measurable disease, no prior FGFRi therapy and an opportunity for ³1 post-baseline imaging assessment. Safety was analyzed in all pts. Results: As of 09May23, 98 pts with solid tumors other than CCA (21 tumor types) were enrolled and treated at the RP2D. Fifty-three percent of pts had ³3 prior therapies; 19% had prior FGFRi therapy. Median treatment exposure was 8.3 weeks (range: 0.1–55.7). Of 79 FGFRi-naïve pts, 61 were evaluable; 18 unevaluable (1 nonmeasurable; 17 ongoing pending imaging). Twenty had f/r with an ORR of 40% (8/20, 7 confirmed/5 ongoing) and DOR from 8-50+ weeks. Twenty-seven had amplification with an ORR of 33% (9/27, 7 confirmed/5 ongoing) and DOR from 8-32+ weeks. Pts with breast (n=7), lung (n=3), and pancreatic (n=5) cancer with FGFR2 f/r or amplification had confirmed ORRs of 43%, 67%, and 40%, respectively. Response varied by mutation with ORR 14.3% (2 [N549K; C382R]/14; both confirmed, 1 ongoing) with DOR each of 40+ weeks. Most common treatment-related adverse events (TRAEs, all grades; grade 3) were stomatitis (50%; 10%), nail toxicities (44%; 4%), and palmar-plantar erythema (45%; 5%). Typical off-isoform TRAEs for pan-FGFR inhibitors were uncommon, including hyperphosphatemia (16%; 0%) and diarrhea (9%; 1%). One percent of pts discontinued treatment because of TRAEs. No grade 4/5 TRAEs were observed. Conclusion: Beyond CCA, lirafugratinib demonstrates promising initial efficacy in multiple tumor types with diverse FGFR2 alterations including f/r, amplification, and select mutations. Together with lirafugratinib’s differentiated safety profile (minimal off-isoform toxicity), these efficacy data validate FGFR2 as a tumor agnostic target sensitive to selective FGFR2 inhibition. Pivotal development across solid tumors continues in Phase 2 of ReFocus. Additional/updated data will be presented at the conference. Citation Format: Alison M Schram, Vivek Subbiah, Chih-Yi (Andy) Liao, Victor Moreno, Roda Desamparados, Mariano Ponz-Sarvise, Efrat Dotan, Philippe Alexandre Cassier, Irene Moreno, Andreas Varkaris, Richard D Kim, Elena Garralda, Frans Opdam, David Tai, Antoine Italiano, Do-Youn Oh, Lipika Goyal, Elisa Fontana, Jia Liu, Myrto Boukovala, Francois Ghiringelli, Mitesh J Borad, Hani Babiker, Zhaohui Jin, Michael Millward, Jeffrey Yachnin, Suneel Deepak Kamath, Jermaine M. Coward, Changhoon Yoo, Robin Kate Kelley, Vaibhav Sahai, John Bridgewater, Christoph Springfield, Vaia Florou, Anthony El-Khoueiry, Ferry Eskens, Bruce Lin, Scott Paulson, Giuseppe Curigliano, Meredith Murphy, Alicia Deary, Fabien Ricard, Kai Yu Jen, Florence (Tianhui) Ramirez, Rick E. Blakesley, Oleg Schmidt-Kittler, Brenton G. Mar, Joon Oh Park, Antoine Hollebecque. Clinical activity of lirafugratinib (RLY-4008), a highly selective FGFR2 inhibitor, in patients with advanced FGFR2-altered solid tumors: The ReFocus study [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr IA006.

Abstract B167: Preclinical characterization of THE-349, a mutant-selective, CNS-active, fourth-generation EGFR inhibitor to overcome T790M- and C797S-mediated resistance in NSCLC

Abstract Background: EGFR activating mutations are observed in 10-50% of NSCLC patients. Although the common mutations (L858R [L] and exon 19 deletions [D]) are initially sensitive to first-, second-, and third-generation EGFR inhibitors (e.g., erlotinib [1G], afatinib [2G], and osimertinib [3G], respectively), on-target resistance is observed in a substantial percentage of patients, with T790M (T) and C797S (C) observed most frequently (post-1G/2G and post-3G, respectively). Furthermore, EGFR mutational heterogeneity can increase during treatment with existing inhibitors, inhibition of wild type (WT) EGFR leads to dose-limiting toxicities, and tumors commonly metastasize to the brain. We have designed THE-349 to be a fourth-generation EGFR inhibitor with potent activity against all 8 major single- (L, D), double- (LT, DT, LC, DC), and triple- (LTC, DTC) mutant variants, selectivity over WT EGFR, and activity in the CNS. Methods: Kinome selectivity was evaluated biochemically against a panel of 412 kinases. In vitro potency was determined by assessing effects (IC50s) on human and BaF3 cell lines expressing WT or mutant forms of EGFR. Efficacy studies were conducted using engineered BaF3 cell lines, a luciferase-tagged human NSCLC cell line, and a patient-derived xenograft (PDX) model dosed orally, once-daily at levels that did not exceed the maximum tolerated dose (40 mg/kg THE-349 and 25 mg/kg osimertinib). Results:THE-349 potently inhibited the biochemical activity of all major EGFR mutant variants (IC50s &amp;lt;2 nM) with a high degree of kinome selectivity. In engineered BaF3 cells in vitro, THE-349 potently inhibited viability of all 8 major EGFR mutant variants (L, LT, LC, LTC, D, DT, DC, and DTC), with IC50s &amp;lt;6 nM and with ≥10-fold selectivity over WT EGFR. Similarly, THE-349 demonstrated robust anti-tumor activity against the same 8 EGFR variants in vivo, in all cases inducing deep tumor regressions (&amp;gt;80% TR) in mice implanted with engineered BaF3 cells. In a PDX model from an osimertinib-resistant tumor containing D and DTC variants, THE-349 induced deep and sustained regressions (99% TR) through 56 days of dosing, and tumor regrowth that occurred during a subsequent 5-week dosing holiday was reversed (88% TR) upon redosing with THE-349. In an intracranial tumor model using a triple-mutant (LTC) NSCLC cell line, THE-349 significantly prolonged median survival (from 42.5 to 71.5 days), while osimertinib had no effect. THE-349 has a favorable ADME profile and promising safety profile in IND-enabling toxicology studies. Conclusion: THE-349 is a fourth-generation, CNS-active, mutant-selective EGFR inhibitor that has potent, single-agent activity against all major classes of EGFR activating and resistance mutations. A phase 1 clinical trial of THE-349 is planned. Citation Format: Sen Zhang, Sara Nadworny, Wei-Sheng Huang, Adam Talbot, Emily Ye, Narayana Narasimhan, William C Shakespeare, Victor M Rivera. Preclinical characterization of THE-349, a mutant-selective, CNS-active, fourth-generation EGFR inhibitor to overcome T790M- and C797S-mediated resistance in NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B167.

Abstract B157: Preclinical evaluation of the blood-brain barrier permeability and intracranial efficacy of the next-generation RET inhibitor Vepafestinib

Abstract Background. Drug resistance and central nervous system (CNS) metastasis often hampers response to precision therapy for RET-rearranged solid tumors. Vepafestinib (Vepa) is a clinical-stage, potent and selective RET tyrosine-kinase inhibitor (TKI) with proven activity against on-target resistance mutations that arise post first-generation RET TKI. Here, we utilized an array of structural and pharmacokinetic methods to determine blood-brain barrier (BBB) permeability of vepa compared with other RET TKIs. Furthermore, we correlate BBB penetrability of RET inhibitors with in vivo efficacy in preclinical models of RET-rearranged intracranial solid tumors. Methods. RET inhibitors were generated by rational chemical design to identify agents which penetrate BBB more effectively than currently approved RET TKIs, and with reduced efflux transporter susceptibility. Transcellular transport assays were conducted in LLC-PK1 and MDCK II cells expressing P-gp and BCRP, respectively. Brain penetrability was assessed by total (Kp) and unbound (Kp,uu) brain:plasma concentration ratios in male Balb/c mice and microdialysis studies in freely-moving male Wistar rats. Models of CNS metastasis were generated by implanting cells labelled with luciferase into the cerebellum of mice. Studies were conducted in comparison with selpercatinib (Selp), pralsetinib (Pral) and TPX-0046. Results. Assessment of Kp and Kp,uu parameters of analogs revealed an excellent structure-activity relationship where modification at the 6-position of the pyrrolopyrimidine core resulted in improved BBB penetrability. The analog with the most favorable physiochemical and biological properties was Vepa. Vepa showed poor susceptibility to P-gp and BCRP-mediated efflux and better CNS penetrability (Kp,uu: 1.3) and retention than Sel, Pral and TPX-0046. The ratio of the observed concentrations of Vepa in microdialysates from the prefrontal cortex, cerebrospinal fluid (CSF) and plasma free fraction was approximately 1:1:1; these ratios were maintained from 2h to 6.5h after Vepaadministration (up to 8h for CSF). Importantly, Vepa was more effective than Selp at causing regression of intracranial xenograft tumors of RET fusion-driven malignancies (lung adenocarcinoma and sarcoma), thus extending survival of tumor-bearing animals. Common first-generation RET TKI resistance mutations at the solvent front (G810A/C/S/R), gatekeeper (V804L/M), hinge (Y806C) and roof (L730Q/R) regions remained sensitive to Vepa. Vepa was more selective than Selp, Pral and TPX-0046, inhibiting only RET when profiled against a panel of 256 kinases. In contrast, Selp, Pral and TPX-0045 also inhibited VEGFR2, and 4, 11 and 39 additional kinases, respectively. Conclusions. Vepafestinib is a structurally distinct and specific RET inhibitor, with superior brain penetration and retention kinetics. It is more effective than selpercatinib in controlling CNS disease. Vepafestinib is currently undergoing phase 1 and 2 clinical trial for patients with advanced solid tumors with RET alterations (margaRET, NCT04683250). Citation Format: Igor Odintsov, Kentaro Wakayama, Tom Zhang, Satoru Iguchi, Masanori Kato, Allan JW Lui, Inna Khodos, Morana Vojnic, Claudio Giuliano, Annalisa Bonifacio, Monika A Davare, Elisa de Stanchina, Emanuela Lovati, Marc Ladanyi, Isao Miyazaki, Romel Somwar. Preclinical evaluation of the blood-brain barrier permeability and intracranial efficacy of the next-generation RET inhibitor Vepafestinib [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B157.