Mechanisms Of Inhibitor Resistance Research Articles

Resistance mechanisms of EGFR tyrosine kinase inhibitors, in EGFR exon 20 insertion-mutant lung cancer

BackgroundMobocertinib, an EGFR exon 20 insertion (Ex20ins)–specific tyrosine kinase inhibitor has been used for treatment of advanced/metastatic EGFR Ex20ins-mutant non-small cell lung cancer (NSCLC). However, resistance mechanisms to EGFR Ex20ins-specific inhibitors and the efficacy of subsequent amivantamab treatment is unknown. MethodsTo investigate resistance mechanisms, tissue and cfDNA samples were collected before treatment initiation and upon development of resistance from NSCLC patients with EGFR Ex20ins mutations received mobocertinib, poziotinib, and amivantamab treatments. Genetic alterations were analyzed using whole-genome and targeted sequencing, and in vitro resistant cell lines were generated for validation. ResultsEGFR amplification (n = 6, including 2 broad copy number gain) and EGFR secondary mutation (n = 3) were observed at the resistance of mobocertinib. One patient had both EGFR secondary mutation and high EGFR focal amplification. In vitro models harboring EGFR alterations were constructed to validate resistance mechanisms and identify overcoming strategies to resistance. Acquired EGFR-dependent alterations were found to mediate resistance to mobocertinib in patients and in vitro models. Furthermore, two of six patients who received sequential amivantamab followed by an EGFR tyrosine kinase inhibitor had MET amplification and showed partial response. ConclusionsOur study revealed EGFR-dependent and -independent mechanisms of mobocertinib resistance in patients with advanced EGFR Ex20ins-mutant NSCLC.

Interrogating the tumor microenvironment (TME) in patients (pts) with head and neck mucosal squamous cell carcinoma (HNmSCC) treated with programmed death-1 (PD-1) inhibitors.

6048 Background: Survival in recurrent/metastatic HNmSCC remain poor. PD-1 inhibitors have become standard of care, demonstrating improved overall survival and toxicity when compared to chemotherapy and targeted therapy. Biomarkers such as PD-Ligand(L)1 combined proportion score (CPS) remain rudimentary, with CPS >20 showing a response rate of only 23% to pembrolizumab (KEYNOTE-048). We used high-dimensional imaging mass cytometry (IMC) to explore predictive biomarkers in HNmSCC pts receiving PD-1 inhibitor-based therapy. Methods: We retrospectively analysed 27 formalin-fixed paraffin embedded tissue samples from 24 pts prior to receiving PD-1 inhibitor-based therapy between May 2016 – April 2021. Clinicopathological characteristics including PD-L1, p16 status, prior treatment and survival data were collected. Pts were classified into responders (RES, Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 complete response (CR) or partial response (PR), stable disease (SD) >6 months (mths)) and non-responders (non-RES, RECIST SD <6 mths or disease progression (PD)). An antibody panel (n = 40) was created to interrogate specific components of interest within the TME and was analysed by IMC using the HyperionTM Imaging System. Results: Of the 24 patients, 16/24 were male and median age 57.6 year. 8 pts were RES (RECIST CR, n = 1; PR, n = 3; SD > 6 mths, n = 4) and 14 pts were non-RES (RECIST SD < 6 mths, n = 1; PD, n = 11; clinical PD, n = 4). Four patients underwent rapid clinical disease progression prior to progress imaging and were categorised as non-RES. At time of data cut off on January 2024, and 23/24 pts had progressed on treatment. The cellular landscape within the TME was similar, irrespective of the location of the primary and p16 status. However, distinct immune profiles were observed between RES vs non-RES: RES showed higher infiltrates of CD4+ T cells, B cells, PD-1+ CD8+ T cells (P < 0.05) and both central memory and effector memory T cell subsets (p < 0.01). In contrast, non-RES showed high frequencies of CD44+ NK cells. Key cell interactions within the TME identified proliferating malignant squamous cells closely interacting with CD8+ T cells, CD4+ Tregs and endothelial cell in RES but not interacting in non-RES. Further spatial regional analysis identified a distinct tissue architecture with hallmarks of Tertiary Lymphoid-like Structures (TLS), present in higher proportions in RES. RES pts with TLS proportions >20% (n = 3) had a progression free survival of 80.3 mths, 26.8 mths and NE (unrelated death at 15.6 mths). Conclusions: The findings of this study identify mechanisms of PD-1 inhibitor response and resistance in HNmSCC pts, providing a unique opportunity to guide combination strategies and improve outcome.

Phase II trial of regorafenib in metastatic medullary thyroid carcinoma (MTC) and radioactive iodine refractory differentiated thyroid carcinoma (RAIR DTC).

6109 Background: Multi-kinase inhibitors show activity in both MTC & RAIR DTC. However, therapeutic options are limited after disease becomes refractory to one or two lines of standard of care therapies. We report here results of an investigator-initiated phase II clinical trial evaluating regorafenib in this population (NCT02657551). Methods: Patients with MTC (disease progression within 6-12 months, mo, prior to study registration) and RAIR DTC (progression within 12 mo) were enrolled regardless of prior lines of therapy. Regorafenib (each cycle 3 weeks ON/1 week OFF) was started at 80 mg daily, with planned escalation after 1 & 2 weeks to 120 mg daily & 160 mg daily, respectively, in absence of significant treatment-related adverse events (TRAEs). The highest tolerated dose was continued from cycle 2 onwards until progression. The primary endpoints were proportion progression-free at 10 months in MTC & overall response rate (ORR) by RECIST v1.1 in RAIR DTC. Simon two-stage design was utilized; MTC: <2 in 8 progression-free in first stage stops for futility, stage 2: enroll 13, >6/21 provides 81% power for proportion >20%; DTC: <3 in 9 in response in first stage stops for futility; stage 2: enroll 11, >7/20 provides 81% power for ORR >25%. Results: 17 patients (8 MTC, 9 DTC) were enrolled between April 2016 and October 2022. Among MTC, median (range) age was 54.7y (48.1, 62.8), 25% female. Among DTC, median age (range) was 62.8y (44.3, 75.8), 55.6% female. In MTC group, the proportion progression-free at 10 months was 12.5% (95% CI 0.3%, 52.7%) & did not meet the criteria to continue into 2nd stage. ORR in MTC group was 12.5% (95% CI 0.3%, 52.7%). In DTC group, ORR was 11.1% (95% CI 0.3%, 48.2%), & did not meet the criteria to continue into 2nd stage. No patients were receiving treatment at cutoff. Patients with MTC and DTC with objective responses (1 each) had received one (vandetanib) & no prior systemic therapy, respectively. The most common reason for discontinuation was disease progression in MTC (4, 50%) & DTC (5, 55.6%). Grade 3-4 TRAEs were observed in 8/17 (47.1%), most frequent were diarrhea, hypophosphatemia, & hypertension (each grade 3: 2, 11.7%). There were no treatment-related deaths. Median progression-free survival (PFS) in MTC & DTC were 5.3 (95% CI 3.6, 20.1) & 11.0 (95% CI 1.2, 24.0) mo, respectively. Median overall survival (OS) in MTC & DTC were 16.1 (95% CI 5.2, NA) and 20.1 (95% CI 1.6, NA) mo, respectively. Conclusions: Regorafenib clinical trial did not reach its primary endpoints in MTC and DTC. Analyses are planned to investigate impact of prior VEGFR inhibitor exposure, biomarkers and resistance mechanisms. Clinical trial information: NCT02657551 . [Table: see text]

Identification of BRAF Inhibitor Resistance-associated lncRNAs Using Genome-scale CRISPR-Cas9 Transcriptional Activation Screening.

Approximately 50% of melanomas harbor the BRAF V600E mutation and targeted therapies using BRAF inhibitors improve patient outcomes. Nonetheless, resistance to BRAF inhibitors develops rapidly and remains a challenge in melanoma treatment. In this study, we attempted to isolate long noncoding RNAs (lncRNAs) involved in BRAF inhibitor resistance using a comprehensive screening method. We used a CRISPR-Cas9 synergistic activation mediator (SAM) protein complex in a genome-scale transcriptional activation assay to screen for candidate lncRNA genes related to BRAF inhibitor resistance. Correlation analysis was performed between expression levels of isolated lncRNA genes and IC50 of dabrafenib in a BRAF-mutated melanoma cell line. Next, online databases were used to construct the lncRNA-miRNA-mRNA regulatory network. Finally, we evaluated the significance of the expression levels of these lncRNAs and mRNAs as biomarkers using clinical specimens. We isolated three BRAF inhibitor resistance-associated lncRNA genes, namely SNHG16, NDUFV2-AS1, and LINC01502. We constructed a lncRNA-miRNA-mRNA network of 13 nodes consisting of three lncRNAs, six miRNAs, and four mRNAs. The lncRNAs and target mRNAs from each regulatory axis significantly and positively correlated with each other. Finally, Kaplan-Meier analysis showed that higher expression levels of MITF, which was up-regulated by LINC01502, were significantly associated with worse prognosis in BRAF V600E-mutated melanoma. The identification of these BRAF inhibitor resistance-associated lncRNA genes at the genomic scale and the establishment of the lncRNA-miRNA-mRNA regulatory network provides new insights into the underlying mechanisms of BRAF inhibitor resistance in melanoma.

Acquired resistance to immunotherapy and chemoradiation in MYC amplified head and neck cancer

The proto-oncogene MYC encodes a nuclear transcription factor that has an important role in a variety of cellular processes, such as cell cycle progression, proliferation, metabolism, adhesion, apoptosis, and therapeutic resistance. MYC amplification is consistently observed in aggressive forms of several solid malignancies and correlates with poor prognosis and distant metastases. While the tumorigenic effects of MYC in patients with head and neck squamous cell carcinoma (HNSCC) are well known, the molecular mechanisms by which the amplification of this gene may confer treatment resistance, especially to immune checkpoint inhibitors, remains under-investigated. Here we present a unique case of a patient with recurrent/metastatic (R/M) HNSCC who, despite initial response to nivolumab-based treatment, developed rapidly progressive metastatic disease after the acquisition of MYC amplification. We conducted comparative transcriptomic analysis of this patient’s tumor at baseline and upon progression to interrogate potential molecular processes through which MYC may confer resistance to immunotherapy and/or chemoradiation and used TCGA-HNSC dataset and an institutional cohort to further explore clinicopathologic features and key molecular networks associated with MYC amplification in HNSCC. This study highlights MYC amplification as a potential mechanism of immune checkpoint inhibitor resistance and suggest its use as a predictive biomarker and potential therapeutic target in R/M HNSCC.

New Directions for Advanced Targeting Strategies of EGFR Signaling in Cancer.

Epidermal growth factor (EGF)-EGF receptor (EGFR) signaling studies paved the way for a basic understanding of growth factor and oncogene signaling pathways and the development of tyrosine kinase inhibitors (TKIs). Due to resistance mutations and the activation of alternative pathways when cancer cells escape TKIs, highly diverse cell populations form in recurrent tumors through mechanisms that have not yet been fully elucidated. In this review, we summarize recent advances in EGFR basic research on signaling networks and intracellular trafficking that may clarify the novel mechanisms of inhibitor resistance, discuss recent clinical developments in EGFR-targeted cancer therapy, and offer novel strategies for cancer drug development.

The fungicide pyraclostrobin affects gene expression by altering the DNA methylation pattern in Magnaporthe oryzae.

Rice blast disease caused by Magnaporthe oryzae has long been the main cause of rice (Oryza sativa L.) yield reduction worldwide. The quinone external inhibitor pyraclostrobin is widely used as a fungicide to effectively control the spread of pathogenic fungi, including M. oryzae. However, M. oryzae can develop resistance through multiple levels of mutation, such as target protein cytb mutation G143A/S, leading to a decrease in the effectiveness of the biocide after a period of application. Therefore, uncovering the possible mutational mechanisms from multiple perspectives will further provide feasible targets for drug development. In this work, we determined the gene expression changes in M. oryzae in response to pyraclostrobin stress and their relationship with DNA methylation by transcriptome and methylome. The results showed that under pyraclostrobin treatment, endoplasmic reticulum (ER)-associated and ubiquitin-mediated proteolysis were enhanced, suggesting that more aberrant proteins may be generated that need to be cleared. DNA replication and repair processes were inhibited. Glutathione metabolism was enhanced, while lipid metabolism was impaired. The number of alternative splicing events increased. These changes may be related to the elevated methylation levels of cytosine and adenine in gene bodies. Both hypermethylation and hypomethylation of differentially methylated genes (DMGs) mainly occurred in exons and promoters. Some DMGs and differentially expressed genes (DEGs) were annotated to the same pathways by GO and KEGG, including protein processing in the ER, ubiquitin-mediated proteolysis, RNA transport and glutathione metabolism, suggesting that pyraclostrobin may affect gene expression by altering the methylation patterns of cytosine and adenine. Our results revealed that 5mC and 6mA in the gene body are associated with gene expression and contribute to adversity adaptation in M. oryzae. This enriched the understanding for potential mechanism of quinone inhibitor resistance, which will facilitate the development of feasible strategies for maintaining the high efficacy of this kind of fungicide.

Activated NAD+ biosynthesis pathway induces olaparib resistance in BRCA1 knockout pancreatic cancer cells.

PARP inhibitors have been developed as anti-cancer agents based on synthetic lethality in homologous recombination deficient cancer cells. However, resistance to PARP inhibitors such as olaparib remains a problem in clinical use, and the mechanisms of resistance are not fully understood. To investigate mechanisms of PARP inhibitor resistance, we established a BRCA1 knockout clone derived from the pancreatic cancer MIA PaCa-2 cells, which we termed C1 cells, and subsequently isolated an olaparib-resistant C1/OLA cells. We then performed RNA-sequencing and pathway analysis on olaparib-treated C1 and C1/OLA cells. Our results revealed activation of cell signaling pathway related to NAD+ metabolism in the olaparib-resistant C1/OLA cells, with increased expression of genes encoding the NAD+ biosynthetic enzymes NAMPT and NMNAT2. Moreover, intracellular NAD+ levels were significantly higher in C1/OLA cells than in the non-olaparib-resistant C1 cells. Upregulation of intracellular NAD+ levels by the addition of nicotinamide also induced resistance to olaparib and talazoparib in C1 cells. Taken together, our findings suggest that upregulation of intracellular NAD+ is one of the factors underlying the acquisition of PARP inhibitor resistance.

KRAS: Biology, Inhibition, and Mechanisms of Inhibitor Resistance.

KRAS is a small GTPase that is among the most commonly mutated oncogenes in cancer. Here, we discuss KRAS biology, therapeutic avenues to target it, and mechanisms of resistance that tumors employ in response to KRAS inhibition. Several strategies are under investigation for inhibiting oncogenic KRAS, including small molecule compounds targeting specific KRAS mutations, pan-KRAS inhibitors, PROTACs, siRNAs, PNAs, and mutant KRAS-specific immunostimulatory strategies. A central challenge to therapeutic effectiveness is the frequent development of resistance to these treatments. Direct resistance mechanisms can involve KRAS mutations that reduce drug efficacy or copy number alterations that increase the expression of mutant KRAS. Indirect resistance mechanisms arise from mutations that can rescue mutant KRAS-dependent cells either by reactivating the same signaling or via alternative pathways. Further, non-mutational forms of resistance can take the form of epigenetic marks, transcriptional reprogramming, or alterations within the tumor microenvironment. As the possible strategies to inhibit KRAS expand, understanding the nuances of resistance mechanisms is paramount to the development of both enhanced therapeutics and innovative drug combinations.

Abstract 5833: Genomic mechanisms of RET inhibitor resistance in RET-fusion positive NSCLC

Abstract RET fusions are a driver oncogene detected in 1-2% of non-small cell lung cancer (NSCLC) cases. Currently, two selective RET inhibitors (RETi), selpercatinib and pralsetinib have received FDA approval for RET fusion-positive NSCLC. However, RET fusions are highly heterogeneous and the impact of specific fusion partners and breakpoints on RETi sensitivity is not well understood. Moreover, most patients eventually develop resistance to RETi, and secondary RET mutations are thought to be a key mechanism of acquired resistance. Thus, we aimed to identify RET-dependent mechanism of RETi resistance in effort to improve treatment options and clinical outcomes. We engineered a panel of Ba/F3 cells expressing various RET fusion partners and breakpoints observed in clinical cases of NSCLC and evaluated their drug sensitivity profile against a panel of RETi including selpercatinib, pralsetinib, TPX-0046, lovatinib, zeteletinib and ponatinib. We determined that individual RET fusions impart distinct sensitivities to RETi. For example, cells expressing KIF-RET (K22, R12) were sensitive to selpercatinib and pralsetinib but less sensitive to ponatinib, whereas cells expressing KIF-RET (K15, R12) were highly sensitive to selpercatinib, pralsetinib, and ponatinib. Moreover, using RET-fusion positive NSCLCs, we observed that the RETi sensitivity profile of human cell lines was similar to that observed using Ba/F3 models. To identify potential resistance mutations, we utilized the LentiMutate approach. In KIF5B-RET (K15, R12) expressing cells, we identified G810S as being associated with resistance to both selpercatinib and pralsetinib, a finding consistent with previous reports and clinical observations. In addition, we identified Y806H/N, V804M/E, and M918T as being associtated with selpercatinib-resistance and L730I/V, E732K, and Y806H/N as being associated with pralsetinib-resistance. We next constructed Ba/F3 cells expressing KIF5B-RET in combination with each secondary mutation and evaluated RETi sensitivity. G810S and Y806N conferred resistance to selpercatinib and pralsetinib, as well as to RET-targeting multi-kinase inhibitors. V804M/E mutations conferred resistance to selpercatinib but not pralsetinib, whereas L730I/V and E732K mutations conferred resistance to pralsetinib but not selpercatinib, demonstrating RETi-specific resistance mutations. Cells expressing G810S secondary mutations were resistant to selpercatinib and pralsetinib, but sensitive to zeteletinib. Collectively, we show that individual RET fusion variants have distinct drug sensitivity profiles and that secondary resistance mutations are non-overlapping between RETi. The comprehensive characterization of RET-dependent mechanisms of resistance to RETi may provide therapeutic guidance for treating RET-fusion driven NSCLC and provide structural insights that can guide the development of new therapeutic regimens. Citation Format: Ximeng Liu, Monique Nilsson, Tomohiro Takehara, Junqin He, Xiaofang Huo, Ashwani Kumar, John Heymach, Ralf Kittler. Genomic mechanisms of RET inhibitor resistance in RET-fusion positive 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 5833.

Abstract 1669: KRAS G12X mutants display differential preferences in downstream effector binding

Abstract KRAS is among the most frequently mutated oncogenic driver proteins in human cancers including lung, colorectal, and pancreatic cancers. Activating KRAS mutants cause increased cell proliferation through direct binding and overactivation of effector proteins. Effector activation preference is driver mutation specific, as KRAS G12D and G12C purportedly bind both RAF and PI3K, whereas G12R has been reported to bind RAF but not PI3K. The mechanisms of effector binding of G12S action are under-investigated. Furthermore, most KRAS mutations remain clinically untreatable, as clinically approved KRAS inhibitors (KRASi) are currently limited to specifically targeting G12C. While experimental non-G12C inhibitors are being developed, resistance mechanisms to non-G12C mutations—including G12D/R/S/V—remain relatively understudied. We set out to characterize the binding efficiency of KRAS to RAF1 and the PI3K subunit p110α, and to understand how isoforms differ in inhibitor resistance strategies. Our findings suggest that significant variances in KRAS mutation-specific effector binding preference exist and are cell line dependent. We performed proximity ligation based immunofluorescence assays (PLA) on an isogenic panel of human colorectal SW48 KRAS cells with G12C/D/R/S/V or wildtype. SW48 cells with G12S significantly prefer the KRAS-RAF1 mode of binding over otherwise isogenic WT cells, and G12V homologs prefer PI3K. Our findings suggest that in this model, G12R cells have no specific preference of one binding mode over the other. We hypothesize that G12 chemistry drives effector binding preference and that G12X inhibitor resistant cell cultures will demonstrate variant mechanisms of resistance in line with their preferred binding partner. Ongoing studies will further characterize understudied RAS isoform biology and evaluate the links between isoform chemistry and mechanisms of inhibitor resistance. These studies will expand our mechanistic knowledge of the interplay between G12X chemistry and adaptive resistance in human cancer. Citation Format: Leonard J. Ash, Ottavia Bourdain, Dennis Lam, Shlomo S. Pallas, Andrew L. Wolfe. KRAS G12X mutants display differential preferences in downstream effector binding [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 1669.

Abstract 1943: Discovery and characterization of potential drivers of resistance to the KRAS G12D inhibitor, MRTX1133, in cancer cell line models

Abstract Introduction: KRASG12D is the most common KRAS mutation and is present in approximately 34% of pancreatic cancer, 10-12% of colorectal cancer, 4% of lung adenocarcinoma and in a number of other cancer types. We previously identified MRTX1133, a potent, selective, and non-covalent KRASG12D inhibitor. The advancement of MRTX1133 to clinical trials warrants continued study of the role of the KRASG12D mutation in cancer pathogenesis and progression. Methods: Previous pharmacodynamic and pharmacogenomic profiling in sensitive and partially resistant models identified mechanisms implicated in limiting the anti-tumor response including signaling pathways that induce feedback reactivation and/or bypass KRAS dependence. Thus, cell lines (GP2D and SNU-1033, colorectal cancer; HPAC and AsPC-1, pancreatic cancer) were utilized to study acquired resistance to MRTX1133 following continuous treatment at increasing concentrations over time. These cell lines were confirmed to be stably resistant as determined by evaluation of response to MRTX1133 in vitro and in vivo. These cell lines were extensively profiled to determine underlying mechanisms of resistance utilizing molecular profiling strategies as well as drug combination screens to interrogate pathways that could circumvent resistance. Results: In one of the four generated cell lines with acquired resistance, evidence of secondary KRAS mutations Y96N and H95Q were confirmed by RNAseq and are likely drivers of resistance in this cell line and are consistent with known mechanisms of KRASG12C inhibitor resistance. The three other MRTX1133 resistant cell lines did not show evidence of secondary KRAS mutations and were further evaluated for mechanisms that bypass KRAS dependence. Combinations of MRTX1133 with therapies that target pathways including upstream RTK signaling, mTOR, or AKT broadly enhanced the anti-tumor activity of MRTX1133 in both in vitro cell viability and in vivo efficacy studies in the resistant cell lines. Conclusion: Collectively, these data provide early insight onto potential mechanisms of resistance to selective KRASG12D inhibitors and demonstrate the importance of developing rational combination strategies designed to address drug resistance. In addition, these studies provide a catalogue of potentially druggable vulnerabilities that complement KRAS blockade. Citation Format: Xousaen M. Helu, Ellie Griffiths, Andrew Calinisan, Allan Hebbert, Larry Yan, Natalie Hoffman, David Trinh, Laura Hover, Julio Fernandez-Banet, David M. Briere, Ella Lifset, Peter Olson, James G. Christensen, Jill Hallin. Discovery and characterization of potential drivers of resistance to the KRAS G12D inhibitor, MRTX1133, in cancer cell line models [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 1943.

Abstract 5857: Trastuzumab deruxtecan resistance can be mediated by payload resistance or secondary extracellular ERBB2 mutations but sensitivity to HER2 tyrosine kinase inhibitors is maintained

Abstract Among NSCLC patients, the most common HER2 mutation is the exon 20 insertion mutation, Y772dupYVMA, which accounts for over 40% of all HER2 mutations in lung cancer. Trastuzumab deruxtecan (T-DXd), a HER2 antibody-drug conjugate (ADC), received FDA approval for the treatment of HER2 mutant NSCLC yielding a confirmed objective response of 52% and a median duration of response of greater than 9 months. Unfortunately, patients that initially respond to T-DXd will eventually acquire resistance, and the mechanisms of resistance as well as effective targeting strategies to overcome resistance are not yet elucidated. We generated Ba/F3 cells expressing the HER2 YVMA insertion mutation with acquired resistance to T-DXd by culturing cells in T-DXd until resistance occurred. T-DXd resistant cells retained expression of HER2, but were resistant to the payload, deruxtecan, as well as other topoisomerase inhibitors. T-DXd resistant cells exhibited loss of topoisomerase I, a previously reported mechanism of topoisomerase inhibitor resistance. In parallel, we generated a PDX model of acquired T-DXd resistance and observed sustained expression of HER2 but loss of TOP1 in resistant tumors. T-DXd resistant cell lines were sensitive to payloads with alternate mechanisms of action including maytansine and likewise retained sensitivity to the HER2 ADC trastuzumab emtansine (T-DM1) which utilizes DM1 as a payload. Given that T-DXd resistant cells retained HER2 expression, we assessed whether they were sensitive to HER2 tyrosine kinase inhibitors (TKI). T-DXd resistant cells remained highly sensitive to HER2 TKIs including poziotinib, afatinib, BI-4142, and BI-1622. To investigate whether genomic alterations of HER2 could facilitate HER2 ADC resistance, we utilized the LentiMutate approach which employs an error-prone HIV-1 reverse transcriptase to produce a high frequency of mutations to identify resistance-associated mutations in cells treated with a HER2 ADC. Sequencing analysis revealed that resistant cells had an enrichment in point mutations within HER2 domain IV (D582N, F595C/S, E580K, C623Y), which includes the binding site of trastuzumab. To validate the impact of these mutations on HER2 ADC resistance, we generated cells expressing a HER2 exon 20 insertion in combination with the observed domain IV mutations. D582N and F695C/S co-mutations conferred resistance to T-DXd and T-DM1 but not to HER2 TKIs. These data demonstrate that resistance to T-DXd can be mediated by loss of sensitivity to the ADC payload in which case ADCs bearing payloads with alternate mechanisms of action as well as HER2 TKIs retain anti-tumor cell activity. Moreover, resistance to trastuzumab-based ADCs can also be mediated by secondary mutations within domain IV of HER2. However, these resistance mutations do not diminish HER2 TKI activity. Citation Format: Monique B. Nilsson, Xiuning Le, Junqin He, Xiaoxing Yu, Xiaofang Huo, Ashwani Kumar, Alissa Poteete, Qian Huang, Ralf Kittler, John Heymach. Trastuzumab deruxtecan resistance can be mediated by payload resistance or secondary extracellular ERBB2 mutations but sensitivity to HER2 tyrosine kinase inhibitors is maintained [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 5857.

Abstract 1663: Single-cell signaling analysis reveals that major vault protein facilitates RasG12C inhibitor resistance

Abstract Covalent inhibitors of RasG12C are the first clinically-approved drugs for targeting mutant Ras-driven cancers. However, the rapid development of clinical resistance to current Ras G12C inhibitors is common. It has been demonstrated that a subpopulation of cancer cells facilitate drug resistance but the mechanistic basis of this heterogenous response is not well understood. Here, we utilized recently developed Ras sensors to profile the environment of active Ras and to measure the activity of endogenous Ras to pair structure (Ras signalosome) to function (Ras activity), respectively, at a single-cell level. With this approach, we found that a subpopulation of KRasG12C cells treated with RasG12C-GDP inhibitors underwent oncogenic signaling and metabolic changes driven by WT Ras at the golgi and mutant Ras at mitochondria, respectively. Our Ras sensors identified Major Vault Protein (MVP) as a mediator of Ras activation at both subcellular locations by scaffolding Ras signaling pathway components and metabolite channels. We found that recently developed RasG12C-GTP inhibitors also led to MVP-mediated WT Ras signaling at the golgi, demonstrating that this a general mechanism of RasG12C inhibitor resistance. Overall, single-cell analyses enabled the discovery of a RasG12C inhibitor-resistant subpopulation driven by MVP, providing insight into the complex and heterogenous rewiring that confers drug resistance in cancer. Citation Format: Jason Z. Zhang, Shao-En Ong, David Baker, Dustin J. Maly. Single-cell signaling analysis reveals that major vault protein facilitates RasG12C inhibitor resistance [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 1663.

Abstract 4539: ZM-2311 a novel and highly potent Polθ inhibitor demonstrates synergistically anti-tumor activities in combination with different therapeutics

Abstract Homologous recombination (HR) is a high-fidelity DNA double-strand break (DSB) repair pathway, and its dysfunction leads to cell genome instability and can result in tumorigenesis. In the situation of HR deficiency, DNA polymerase theta (Polθ) mediated microhomology-mediated end joining (MMEJ) is up-regulated to serve as a backup pathway for DSB repair. Several studies have proved that the inhibition of Polθ causes synthetic lethality with HR deficiency, and Polθ emerges as a potential DNA damage repair (DDR) target for the treatment of HR deficient tumors. In addition, there is evidence showing that the depletion of Polθ improves the sensitivity of some other DDR-related targeted therapies, chemotherapy, and radiotherapy. Here we identify a novel small molecular Polθ inhibitor, ZM-2311, which inhibits Polθ activity with an IC50 of 24 nM, and strongly inhibits cellular MMEJ pathway with a single nanomolar IC50. ZM-2311 illustrates a robust potency against tumor growth in a MDA-MB-436 SHLD2-/- xenograft model, suggesting potential monotherapy application in BRCA1 mutation patients with TP53BP1/Shieldin complex deficiency. Besides monotherapy, ZM-2311 elicits strong synergetic anti-proliferation activities in combination with PARP inhibitors on BRCA2-/- DLD-1 and endogenous HR deficient tumor cells in vitro and in vivo. Tumor regression is observed even at a low dosage, indicating a high potency of ZM-2311. As reversion mutation of HR genes such as BRCA1/2 mediated by the MMEJ pathway is reported to be a mechanism of PARP inhibitor resistance, ZM-2311 is evaluated and demonstrates its potential to overcome the resistance to PARP inhibitors. Furthermore, the combination of ZM-2311 with other DDR agents, such as ATR inhibitors, induces fatal DNA damage to HR deficient cells. Considering a low risk of hematotoxicity of Polθ inhibition, ZM-2311 may provide a new combination option for DDR agents. Besides, ZM-2311 was assessed in combination with different therapies respectively which functionally induce DNA damage, such as radiotherapy and chemotherapy. ZM-2311 renders tumor cells more sensitive to radiotherapy in both HR deficient cells and proficient cells in vitro, accompanying with the upregulation of Polθ expression after radiotherapy and an enhanced phosphorylation level of H2AX in the combination treatment. Similarly, ZM-2311 also achieves a robust synergetic effect in combination with chemotherapy in cell lines with different HR statuses. These results indicate a potential application expansion of ZM-2311 to HR-proficient tumors, which is expected to bring better efficacy and reduced hematotoxicity. Taken together, ZM-2311 has proved to be a highly potent Polθ inhibitor and has promising combination potential with multiple therapy strategies. Citation Format: Feng Zhou, Lu Liu, Lei Jiang, Shuo Qian, Liting Xue, Mengying Li, Zhengtao Li, Zhen Li, Jian Li, Renhong Tang. ZM-2311 a novel and highly potent Polθ inhibitor demonstrates synergistically anti-tumor activities in combination with different therapeutics [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 4539.

Adipose Stromal Cell-Derived Cancer-Associated Fibroblasts Suppress FGFR Inhibitor Efficacy.

Cancer aggressiveness has been linked with obesity, and studies have shown that adipose tissue can enhance cancer progression. In this issue of Cancer Research, Hosni and colleagues discover a paracrine mechanism mediated by adipocyte precursor cells through which urothelial carcinomas become resistant to erdafitinib, a recently approved therapy inhibiting fibroblast growth factor receptors (FGFR). They identified neuregulin 1 (NRG1) secreted by adipocyte precursor cells as an activator of HER3 signaling that enables resistance. The NRG1-mediated FGFR inhibitor resistance was amenable to intervention with pertuzumab, an antibody blocking the NRG1/HER3 axis. To investigate the nature of the resistance-associated NRG1-expressing cells in human patients, the authors analyzed published single-cell RNA sequencing data and observed that such cells appear in a cluster assigned as inflammatory cancer-associated fibroblasts (iCAF). Notably, the gene signature corresponding to these CAFs is highly similar to that shared by adipose stromal cells (ASC) in fat tissue and fibro-adipogenic progenitors (FAP) in skeletal muscle of cancer-free individuals. Because fibroblasts with the ASC/FAP signature are enriched in various carcinomas, it is possible that the paracrine signaling conferred by NRG1 is a pan-cancer mechanism of FGFR inhibitor resistance and tumor aggressiveness. See related article by Hosni et al., p. 725.

Glutamine metabolism and VEGF analysis to elucidate and overcome the mechanism of tyrosine kinase inhibitor resistance in renal cell carcinoma.

Glutamine metabolism and VEGF analysis to elucidate and overcome the mechanism of tyrosine kinase inhibitor resistance in renal cell carcinoma.

Single-cell genomics analysis reveals complex genetic interactions in an in vivo model of acquired BRAF inhibitor resistance.

The evolution of therapeutic resistance is a major obstacle to the success of targeted oncology drugs. While both inter- and intratumoral heterogeneity limit our ability to detect resistant subpopulations that pre-exist or emerge during treatment, our ability to analyze tumors with single-cell resolution is limited. Here, we utilized a cell-based transposon mutagenesis method to identify mechanisms of BRAF inhibitor resistance in a model of cutaneous melanoma. This screen identified overexpression of NEDD4L and VGLL3 as significant drivers of BRAF inhibitor resistance in vivo. In addition, we describe a novel single-cell genomics profiling method to genotype thousands of individual cells within tumors driven by transposon mutagenesis. This approach revealed a surprising genetic diversity among xenograft tumors and identified recurrent co-occurring mutations that emerge within distinct tumor subclones. Taken together, these observations reveal an unappreciated genetic complexity that drives BRAF inhibitor resistance.

Other Driver Genes as Resistance Mechanisms of ALK Inhibitors in ALK-Rearranged Lung Adenocarcinoma

Other Driver Genes as Resistance Mechanisms of ALK Inhibitors in ALK-Rearranged Lung Adenocarcinoma

Mechanisms of tyrosine kinase inhibitor resistance in renal cell carcinoma.

Renal cell carcinoma (RCC), the most prevalent type of kidney cancer, is a significant cause of cancer morbidity and mortality worldwide. Antiangiogenic tyrosine kinase inhibitors (TKIs), in combination with immune checkpoint inhibitors (ICIs), are among the first-line treatment options for patients with advanced RCC. These therapies target the vascular endothelial growth factor receptor (VEGFR) tyrosine kinase pathway and other kinases crucial to cancer proliferation, survival, and metastasis. TKIs have yielded substantial improvements in progression-free survival (PFS) and overall survival (OS) for patients with advanced RCC. However, nearly all patients eventually progress on these drugs as resistance develops. This review provides an overview of TKI resistance in RCC and explores different mechanisms of resistance, including upregulation of alternative proangiogenic pathways, epithelial-mesenchymal transition (EMT), decreased intracellular drug concentrations due to efflux pumps and lysosomal sequestration, alterations in the tumor microenvironment including bone marrow-derived cells (BMDCs) and tumor-associated fibroblasts (TAFs), and genetic factors such as single nucleotide polymorphisms (SNPs). A comprehensive understanding of these mechanisms opens the door to the development of innovative therapeutic approaches that can effectively overcome TKI resistance, thereby improving outcomes for patients with advanced RCC.