On-target Mutations Research Articles

Abstract 6403: A self-replicating RNA precision medicine approach to overcoming resistance to endocrine therapy in ER+BC

Abstract Drug resistance remains the major driving factor behind the clinical failure of targeted therapeutics. Current oncology precision medicine approaches rely on targeting known acquired resistance mutations, such as EGFR T790M or ALK/ROS mutations in NSCLC with 2nd and 3rd generation molecules designed to overcome or prevent resistance. These next generation targeted therapeutic approaches have increasingly long and complex drug development timelines and burdensome toxicities from off target effects (e.g. wild-type receptor targeting) or drug-drug interactions (DDI). The toxicities limit tolerability, compliance and combinability of different targeted therapeutics. RNA-based immunotherapy approaches offer an increasingly attractive alternative to next generation small molecule targeted therapeutics approaches: (1) RNA-based approaches only require a known acquired resistance sequence, (2) drug development timelines, cost and complexity can be meaningfully condensed, and (3) multiple acquired resistance mutations can be targeted with the same candidate. RBI-1000 is a candidate using a novel type of self-replicating RNA (srRNA) to generate robust immunity directed against acquired resistance mutations that develop in ER+ breast cancer (ER+ BC) in response to endocrine therapy. RBI-1000 includes on-target mutations within the estrogen receptor ligand binding domain, and bypass mutations either in the form of activating mutations in the PI3K kinase domain or amplifications of HER2/HER3. Here, we demonstrate that this srRNA encapsulated in a lipid nanoparticle primes polyfunctional CD4 and CD8 T cells leading to tumor growth inhibition and improved survival in a mouse model expressing the targeted acquired resistance mutation. Priming of T cells against acquired mutations is also confirmed in human HLA-transgenic mice. The immune cell-mediated elimination of clones expressing the acquired resistance mutations is predicted to prolong endocrine control of ER+BC, in an analogous manner to small molecule or monoclonal antibody targeted therapies, but with a more favorable dosing and adverse event profile due to precise immunologic targeting and no DDI. Citation Format: Zelanna Goldberg, Christian Maine, Gabrielle P. Dailey, Christine Domingo, Gaelle Picarda, Hunter Little, Annie Chou, Jessica Sparks, Darina Spasova, Shigeki Miyake-Stoner, Zachary C. Hartman, Christopher A. Rabiola, Erika J. Crosby, Herbert K. Lyerly, Nathaniel Wang, Parinaz Aliahmad. A self-replicating RNA precision medicine approach to overcoming resistance to endocrine therapy in ER+BC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6403.

A Closer Look at EGFR Inhibitor Resistance in Non-Small Cell Lung Cancer through the Lens of Precision Medicine

The development of EGFR small-molecule inhibitors has provided significant benefit for the affected patient population. Unfortunately, current inhibitors are no curative therapy, and their development has been driven by on-target mutations that interfere with binding and thus inhibitory activity. Genomic studies have revealed that, in addition to these on-target mutations, there are also multiple off-target mechanisms of EGFR inhibitor resistance and novel therapeutics that can overcome these challenges are sought. Resistance to competitive 1st-generation and covalent 2nd- and 3rd-generation EGFR inhibitors is overall more complex than initially thought, and novel 4th-generation allosteric inhibitors are expected to suffer from a similar fate. Additional nongenetic mechanisms of resistance are significant and can include up to 50% of the escape pathways. These potential targets have gained recent interest and are usually not part of cancer panels that look for alterations in resistant patient specimen. We discuss the duality between genetic and nongenetic EGFR inhibitor drug resistance and summarize current team medicine approaches, wherein clinical developments, hand in hand with drug development research, drive potential opportunities for combination therapy.

First in human (FIH) phase 1/1b study evaluating KIN-3248, a next-generation, irreversible pan-FGFR inhibitor (FGFRi), in patients (pts) with advanced urothelial carcinoma (UC) and other solid tumors harboring FGFR2 and/or FGFR3 gene alterations.

TPS593 Background: FGFR1-4 gene alterations are infrequent across solid tumors though preclinical and clinical evidence indicate activating alterations drive oncogenesis and tumor growth. They can be found in up to 20% of patients with UC and up to 35% of upper tract UC. Reversible FGFRi are approved for the treatment of pts with locally advanced or metastatic urothelial carcinoma (UC) with susceptible FGFR2 or FGFR3 genetic alterations (erdafitinib) or metastatic CCA harboring FGFR2 gene fusions or rearrangements (pemigatinib and infigratinib). A critical limitation of current clinical-stage FGFRi is the emergence of secondary, on-target resistance mutations (mutn) that reduce duration of response, and indeed, about 70% of CCA patients pre-treated with FGFRi exhibit secondary FGFR2 kinase domain resistance mutn at the time of relapse. KIN-3248 is a next-generation, selective, irreversible, small molecule pan-FGFRi, structurally designed to inhibit primary FGFR oncogenic alterations as well as secondary kinase domain mutn associated with disease progression. Preclinically, KIN-3248 has favorable pharmaceutical properties, is well-tolerated with continuous, daily oral administration in GLP toxicology studies and is efficacious against primary FGFR2 and FGFR3 oncogenic driver alterations as well as secondary FGFR2 resistance mutn (e.g., gatekeeper and molecular brake) in human cancer cell and PDX models. Methods: This is a FIH, multicenter, non-randomized Ph1 study of KIN-3248 in adult pts with advanced and metastatic solid tumors (AMST) harboring FGFR2 and/or FGFR3 gene alterations. KIN-3248 is given PO QD continuously in 28-day cycles until drug intolerance or disease progression. Part A is a dose-escalation assessing single agent KIN-3248 via a BOIN design to determine the MTD/RP2D. Part B will evaluate a selected dose of KIN-3248 in 3 cohorts of pts (UC, CCA, or other AMST), each driven by specified FGFR alterations—FGFRi-naïve and -pretreated pts are eligible in both parts. Enrollment criteria include ECOG PS 0-1, intact organ function, prior receipt of standard treatment or medical judgment that such is not appropriate. Pts may have measurable or evaluable disease. Key exclusion criteria include known active brain metastases and active/uncontrolled HBV/HCV. Planned sample size is ~120 pts. Primary endpoints are safety/tolerability (Part A), and preliminary antitumor activity: objective response rate, disease control rate, duration of response, & duration of stable disease (Part B). Secondary objectives include pharmacokinetic and pharmacodynamic assessments including measures of FGFR pathway modulation. The study is actively enrolling patients in the US and globally. Clinical trial information: NCT05242822 .

First in human (FIH) phase 1/1b study evaluating KIN-3248, a next-generation, irreversible pan-FGFR inhibitor (FGFRi), in patients (pts) with advanced cholangiocarcinoma (CCA) and other solid tumors harboring FGFR2 and/or FGFR3 gene alterations.

TPS637 Background: FGFR1-4 gene alterations are infrequent across solid tumors though preclinical and clinical evidence indicate activating alterations drive oncogenesis and tumor growth. Pharmacological inhibition of FGFR1-4 leads to tumor shrinkage and disease control. Reversible FGFRi are approved for the treatment of pts with locally advanced or metastatic CCA harboring FGFR2 gene fusions or rearrangements (pemigatinib and infigratinib) or metastatic urothelial carcinoma (UC) with susceptible FGFR2 or FGFR3 genetic alterations (erdafitinib). A critical limitation of current clinical-stage FGFRi is the emergence of secondary, on-target resistance mutations (mutn) that reduce duration of response, and indeed, about 70% of CCA patients treated with either reversible or irreversible FGFRi exhibit secondary FGFR2 kinase domain resistance mutn at the time of relapse. KIN-3248 is a next-generation, selective, irreversible, small molecule pan-FGFRi, structurally designed to inhibit primary FGFR oncogenic alterations as well as secondary kinase domain mutn associated with disease progression. Preclinically, KIN-3248 has favorable pharmaceutical properties, is well-tolerated with continuous, daily oral administration in GLP toxicology studies and is efficacious against primary FGFR2 and FGFR3 oncogenic driver alterations as well as secondary FGFR2 resistance mutn (e.g., gatekeeper and molecular brake) in human cancer cell and PDX models. Methods: This is a FIH, multicenter, non-randomized Ph1 study of KIN-3248 in adult pts with advanced and metastatic solid tumors (AMST) harboring FGFR2 and/or FGFR3 gene alterations. KIN-3248 is given PO QD continuously in 28-day cycles until drug intolerance or disease progression. Part A is a dose-escalation assessing single agent KIN-3248 via a BOIN design to determine the MTD/RP2D; Part B will evaluate a selected dose of KIN-3248 in 3 cohorts of pts (CCA, UC, or other AMST), each driven by specified FGFR alterations—FGFRi-naïve and -pretreated pts are eligible in both parts. Enrollment criteria include ECOG PS 0-1, intact organ function, prior receipt of standard treatment or medical judgment that such is not appropriate. Pts may have measurable or evaluable disease. Key exclusion criteria include known active brain metastases and active/uncontrolled HBV/HCV. Planned sample size is ~120 pts. Primary endpoints are safety/tolerability (Part A), and preliminary antitumor activity: objective response rate, disease control rate, duration of response, and duration of stable disease (Part B). Secondary objectives include pharmacokinetic and pharmacodynamic assessments including measures of FGFR pathway modulation. The study is actively enrolling patients in the US and globally. Clinical trial information: NCT05242822 .

Application of a Spacer-nick Gene-targeting Approach to Repair Disease-causing Mutations with Increased Safety.

The CRISPR/Cas9 system is a powerful tool for gene repair that holds great potential for gene therapy to cure monogenic diseases. Despite intensive improvement, the safety of this system remains a major clinical concern. In contrast to Cas9 nuclease, Cas9 nickases with a pair of short-distance (38-68 bp) PAM-out single-guide RNAs (sgRNAs) preserve gene repair efficiency while strongly reducing off-target effects. However, this approach still leads to efficient unwanted on-target mutations that may cause tumorigenesis or abnormal hematopoiesis. We establish a precise and safe spacer-nick gene repair approach that combines Cas9D10A nickase with a pair of PAM-out sgRNAs at a distance of 200-350 bp. In combination with adeno-associated virus (AAV) serotype 6 donor templates, this approach leads to efficient gene repair with minimal unintended on- and off-target mutations in human hematopoietic stem and progenitor cells (HSPCs). Here, we provide detailed protocols to use the spacer-nick approach for gene repair and to assess the safety of this system in human HSPCs. The spacer-nick approach enables efficient gene correction for repair of disease-causing mutations with increased safety and suitability for gene therapy. Graphical overview.

Gene Editing Profiles in 94 CRISPR-Cas9 Expressing T0 Transgenic Tobacco Lines Reveal High Frequencies of Chimeric Editing of the Target Gene.

Chimeric editing is often reported in gene editing. To assess how the general chimeric editing is, we created a transgenic tobacco line carrying a marker, beta-glucuronidase gene (gusA), introduced a CRISPR-Cas9 editing vector into the transgenic tobacco line for knocking out gusA, and then investigated the gusA editing efficiencies in T0 and subsequent generations. The editing vector carried a Cas9 gene, which was driven by the cauliflower mosaic virus 35S promoter, and two guide RNAs, gRNA1 and gRNA2, which were driven by Arabidopsis U6 (AtU6) and U3 (AtU3) promoter, respectively. The two gRNAs were designed to knock out a 42-nucleotide fragment of the coding region of gusA. The editing vector was transformed into gusA-containing tobacco leaves using Agrobacterium tumefaciens-mediated transformation and hygromycin selection. Hygromycin-resistant, independent T0 transgenic lines were used to evaluate gusA-editing efficiencies through histochemical GUS assays, polymerase chain reactions (PCR), and next-generation sequencing of PCR amplicons. Profiles of targeted sequences of 94 T0 transgenic lines revealed that these lines were regenerated from non-edited cells where subsequent editing occurred and created chimeric-edited cells in these lines during or after regeneration. Two of them had the target fragment of 42 bp pairs of nucleotides removed. Detail analysis showed that on-target mutations at the AtU6-gRNA1 site and the AtU3-gRNA2 site were found in 4.3% and 77.7% of T0 transgenic lines, respectively. To overcome the issue of extremely low editing efficiencies in T0 lines, we conducted a second round of shoot induction from the chimeric line(s) to enhance the success of obtaining lines with all or most cells edited. The mutation profiles in T0 transgenic lines provide valuable information to understand gene editing in plant cells with constitutively expressed CRISPR-Cas9 and gRNAs.

Elvn-001, a Next Generation ATP-Competitive ABL1 Tyrosine Kinase Inhibitor for the Treatment of Chronic Myeloid Leukemia

Of the six small-molecule ABL1 tyrosine kinase inhibitors (TKIs) that have received FDA-approval for the treatment of BCR-ABL1-driven Chronic Myeloid Leukemia (CML), five (Imatinib, Nilotinib, Dasatinib, Ponatinib, Bosutinib) target the ATP-binding site in the kinase domain. While each of these TKIs provides added value to the arsenal of treatments for CML, these agents suffer from selectivity issues, inhibiting a number of off-target kinases that drive an array of dose-limiting toxicities (DLTs) which constrain their ability to fully engage ABL1 and drive maximal efficacy. In addition, the emergence of on-target resistance against these TKIs, such as the highly prevalent T315I mutation at the gatekeeper position of the active site, is common and represents a significant clinical challenge. The recently approved ABL1 TKI Asciminib is an allosteric inhibitor that interacts with the unique myristoyl binding pocket of ABL1 and therefore possesses high kinome selectivity and an improved tolerability profile. Despite its unique binding mode, clinical activity against the T315I mutant requires a dose five times higher than that approved for the broader third-line or greater patient population, which leads to issues with tolerance. In addition, emergent on-target resistance remains a challenge, particularly with respect to mutations within the myristoyl pocket as well as select active site mutants. Here we report the discovery of ELVN-001, a potent ATP-competitive small-molecule ABL1 TKI which, unlike the majority of currently approved ABL1 TKIs, is highly selective in both biochemical and cell-based assays versus the kinome in general as well as the key off-target kinases KDR, c-KIT, PDGFR and SRC, which are associated with a variety of DLTs including myelosuppression, edema, pleural effusions, hypertension, and certain cardiovascular events. ELVN-001 exhibited potent pharmacodynamic (phosphorylated CRKL) and anti-proliferative activity in vitro against BCR-ABL1-driven CML cell lines with comparable or superior activity to the approved therapies. Evaluation of ELVN-001 against Ba/F3 cell lines expressing a panel of clinically relevant BCR-ABL1 TKI-resistant mutants demonstrated activity of ELVN-001 against many of these mutants, including T315I as well as two myristoyl pocket mutants (A334P, P465S) which are highly resistant to asciminib. Cell-based mutagenesis screens using Ba/F3 BCR-ABL1 cells confirmed a concentration-dependent reduction in outgrowth of resistant clones, which generally narrowed to a select subset of P-loop mutations. Consistent with previously reported findings for ponatinib, while ELVN-001 showed little to no activity against cells expressing a subset of T315I-inclusive BCR-ABL1 compound mutants, the addition of Asciminib resulted in varying degrees of re-sensitizing these mutants to ELVN-001. Importantly, ELVN-001 possessed a favorable absorption, distribution, metabolism, elimination, and toxicity profile, as determined from both in vitro and in vivo studies, that readily translated into favorable pharmacokinetic properties in all preclinical species evaluated. Accordingly, administration of doses of ELVN-001 corresponding to well-tolerated free drug exposures in rats and non-human primates readily translated to mouse in vivo tumor xenograft models of efficacy, including a model of T315I CML. These anti-tumor activities also compared favorably to currently approved therapies when evaluated head-to-head in these studies. Together, these findings support ELVN-001 as an extremely selective, novel ATP-competitive inhibitor of ABL1 kinase with superior pharmacokinetic and tolerability properties compared to currently approved TKIs and which retains activity against T315I and other key on-target resistance mutations, warranting its further investigation in patients with TKI-resistant/intolerant CML.

Establishment and Characterization of Mouse Models with Primary and Acquired BTK Inhibitor Resistance

Background: The second-generation Bruton's tyrosine kinase (BTK) inhibitor acalabrutinib is effective for treatment of patients with chronic lymphocytic leukemia (CLL), including high-risk and relapsed patients. Resistance to BTK inhibitors can develop not only due to on-target mutations, but also by bypassing the BTK signaling pathway. Mouse models represent useful tools in studying mechanisms of resistance as well as testing the efficacy of alternative therapy options to overcome resistance. Eµ-TCL1-transgenic (TCL1-tg) mice have the advantage of immunocompetence and resemble the human CD49d-high CLL cohort (Szenes et al., 2020). Transplantation of tumors from these mice to wild-type recipients allows acceleration of pathophysiology, selection of specific tumor clones, and more efficient testing of drug combinations. Here, we developed acalabrutinib resistance models by serial transplantation and long-term administration of the drug in drinking water, characterized these models, and compared molecular resistance signatures with those of human patient samples. Methods: Models were developed starting from four primary TCL1-tg mice at overt disease with tumor burden in spleen ranging up to 95% of lymphocytes. Serial retransplantation to wild-type C57BL/6J recipients for two to four rounds and acalabrutinib therapy pressure resulted in several drug resistant pedigrees. Mice were sacrificed at end-stage disease and tumor burden in spleen, bone marrow and blood was analyzed by flow cytometry using anti-CD5/CD19 antibodies. Purified leukemic cells were subjected to RNA-seq, real-time quantitative PCR and mutational analyses. Results: Three response patterns were identified in recipient mice: a) sustained sensitivity (models were stopped after 23 weeks of treatment), b) acquired resistance (with initial response followed by development of resistance under continuous therapy pressure and c) retransplantation-induced resistance in a case of an aggressive tumor clone that was responding to acalabrutinib in the parental mouse. The sensitive models displayed a 63% reduction in spleen weight upon treatment and a concomitant 65% reduction in blood tumor burden. In acquired or primary resistant mice, spleen weight and tumor burden was not significantly different from that of untreated mice, with blood tumor burden in the magnitude of 100,000 leukemic cells/µl and spleen tumor burden of 500-1000 million leukemic cells. Resistance could not be attributed to the mutational landscape of BTK and PLCγ2. Mutations in p53, Myc, Notch1, Atm, and Sf3b1 were detected but found to be intrinsic in individual ancestors and further present in the follow-up transplantations. RNA-seq analysis revealed 863 differentially expressed genes in mice with acquired resistance to acalabrutinib (compared to untreated, Figure 1) and 114 shared differentially expressed genes in mice with acquired or transplantation-based resistance. Gene set enrichment analysis demonstrated the presence of MAPK signaling and NF-kB signaling gene signatures within the resistant tumors. In particular, acquired resistance was accompanied by changes in the B cell receptor downstream components. We also compared the murine 863 gene signature to human samples from acalabrutinib resistant patients (progression on drug versus baseline) and found 13 genes are differently expressed in both, human and mouse. Validation for this gene expression data is ongoing and updated results will be presented. Conclusion: We have developed novel TCL1-tg based murine models of acalabrutinib resistance. Our models provide well-characterized tools to study primary as well as acquired BTK inhibitor resistance and allow the current testing of potential new therapeutic approaches to overcome resistance. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

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In This Issue

Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 in Komagataella phaffii: A Budding Yeast in Distress.

The industrially important non-conventional yeast Komagataella phaffii suffers from low rates of homologous recombination, making site specific genetic engineering tedious. Therefore, genome editing using CRISPR/Cas represents a simple and efficient alternative. To characterize on- and off-target mutations caused by CRISPR/Cas9 followed by non-homologous end joining repair, we chose a diverse set of CRISPR/Cas targets and conducted whole genome sequencing on 146 CRISPR/Cas9 engineered single colonies. We compared the outcomes of single target CRISPR transformations to double target experiments. Furthermore, we examined the extent of possible large deletions by targeting a large genomic region, which is likely to be non-essential. The analysis of on-target mutations showed an unexpectedly high number of large deletions and chromosomal rearrangements at the CRISPR target loci. We also observed an increase of on-target structural variants in double target experiments as compared to single target experiments. Targeting of two loci within a putatively non-essential region led to a truncation of chromosome 3 at the target locus in multiple cases, causing the deletion of 20 genes and several ribosomal DNA repeats. The identified de novo off-target mutations were rare and randomly distributed, with no apparent connection to unspecific CRISPR/Cas9 off-target binding sites.

Developments and challenges of FLT3 inhibitors in acute myeloid leukemia.

FLT3 mutations are one of the most common genetic alterations in acute myeloid leukemia (AML) and are identified in approximately one-third of newly diagnosed patients. Aberrant FLT3 receptor signaling has important implications for the biology and clinical management of AML. In recent years, targeting FLT3 has been a part of every course of treatment in FLT3-ITD/TKD-mutated AML and contributes to substantially prolonged survival. At the same time, wide application of next-generation sequencing (NGS) technology has revealed a series of non-canonical FLT3 mutations, including point mutations and small insertions/deletions. Some of these mutations may be able to influence downstream phosphorylation and sensitivity to FLT3 inhibitors, while the correlation with clinical outcomes remains unclear. Exploration of FLT3-targeted therapy has made substantial progress, but resistance to FLT3 inhibitors has become a pressing issue. The mechanisms underlying FLT3 inhibitor tolerance can be roughly divided into primary resistance and secondary resistance. Primary resistance is related to abnormalities in signaling factors, such as FL, CXCL12, and FGF2, and secondary resistance mainly involves on-target mutations and off-target aberrations. To overcome this problem, novel agents such as FF-10101 have shown promising potential. Multitarget strategies directed at FLT3 and anomalous signaling factors simultaneously are in active clinical development and show promising results.

Abstract A04: Targeted protein degradation as a strategy to overcome non-covalent BTK inhibitor resistance in lymphoma

Abstract Bruton’s tyrosine kinase (BTK) is a target for multiple generations of covalent (irreversible) and non-covalent (reversible) inhibitors due to its critical role in the proliferation and survival of B-cell malignancies. Similar to drug resistance mechanisms in other cancers, resistance to covalent BTK inhibitors (BTKi) in chronic lymphocytic leukemia (CLL), such as ibrutinib, arise through on-target BTK mutations at the BTK C481 residue (the binding site of ibrutinib), which allow escape from BTK inhibition. Non-covalent BTKi represent a new avenue to overcome resistance to the clinically approved covalent BTKi; however, we have recently discovered mechanisms of resistance to non-covalent BTK inhibition in patients with CLL (Wang, Xi, Thompson, Montoya et al NEJM 2022). We used bulk and single cell genomic analyses that identified a series of acquired BTK mutations in a cohort of CLL patients that relapsed on the phase I/II clinical trial of pirtobrutinib. We discovered mutations (BTK V416L, A428D, M437R, T474I, L528W) that occur at critical residues within the catalytic kinase domain of BTK and conferred resistance to both non-covalent and covalent BTKis. Based on structural models of BTK, we observed that these mutations physically impede drug binding, and disrupt the normal kinase activity of BTK but can, upon B-cell receptor stimulation, sustain AKT, ERK, and NF𝜅B signaling as well intracellular Ca2+ release in the presence of pirtobrutinib. In addition, CITE-seq analyses of 53,722 cells from this cohort identified pre-existing leukemic and immune cell states associated with development of resistance in patients. These findings identify novel mechanisms to engender clinical resistance to non-covalent BTKis, including contribution of the immune microenvironment to response to BTK inhibition. Together our data suggest that mutations at the BTK kinase domain may alter conformation of BTK’s non-kinase protein interaction domains thus allowing BTK to be used as a scaffold for other signaling molecules to phosphorylate phospholipase C gamma 2 (PLC𝛾2), the direct downstream target of BTK. We have performed mass spectrometry phosphoproteomics to evaluate potential signaling molecules that are active and could bypass BTK in catalytically inactive BTK mutant cells. Given the above, we decided to target BTK’s non-kinase function by investigating targeted protein degraders of BTK using BTK-degrading protein targeting chimeras (PROTACS). The immediate advantages of using protein degraders are (1) Binding may occur at any site of the target protein, and (2) PROTACS can act catalytically to bind to and degrade multiple target proteins. Our studies have shown that several of the BTK mutants that engendered clinical resistance to covalent and non-covalent BTKi are sensitive to these degraders, elucidating an exciting alternative therapeutic approach for patients who become resistant to BTKi therapies. We are continuing to test the efficacy of BTK PROTAC degraders in overcoming acquired resistance mechanisms in CLL as well as other B-cell lymphomas. Citation Format: Skye Montoya, Eric Wang, Jessie Bourcier, Sana Chaudhry, Tulasigeri Totiger, Alejandro Pardo, Gabriel Pardo, Maurizio Affer, Jacob Jahn, Anthony Mato, Omar Abdel-Wahab, Justin Taylor. Targeted protein degradation as a strategy to overcome non-covalent BTK inhibitor resistance in lymphoma [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A04.

EP08.02-019 Phase 1/2 Study of BLU-701, a Highly Selective EGFR Inhibitor, in Patients With EGFR-Mutant Non-Small Cell Lung Cancer

Third-generation tyrosine kinase inhibitors (TKIs), such as osimertinib, are highly effective in front-line metastatic EGFR-mutated (EGFRm) non-small cell lung cancer (NSCLC), but treatment resistance can ultimately occur, including the emergence of the on-target C797X mutation for which there are no approved TKIs. BLU-701 is an investigational, reversible, central nervous system (CNS)-penetrant, wildtype-sparing oral TKI with nanomolar potency on common activating (exon 19 deletion and L858R) and C797X resistance mutations.

Diverse mutational landscapes in human lymphocytes

The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

Discovery of BLU-945, a Reversible, Potent, and Wild-Type-Sparing Next-Generation EGFR Mutant Inhibitor for Treatment-Resistant Non-Small-Cell Lung Cancer.

While epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have changed the treatment landscape for EGFR mutant (L858R and ex19del)-driven non-small-cell lung cancer (NSCLC), most patients will eventually develop resistance to TKIs. In the case of first- and second-generation TKIs, up to 60% of patients will develop an EGFR T790M mutation, while third-generation irreversible TKIs, like osimertinib, lead to C797S as the primary on-target resistance mutation. The development of reversible inhibitors of these resistance mutants is often hampered by poor selectivity against wild-type EGFR, resulting in potentially dose-limiting toxicities and a sub-optimal profile for use in combinations. BLU-945 (compound 30) is a potent, reversible, wild-type-sparing inhibitor of EGFR+/T790M and EGFR+/T790M/C797S resistance mutants that maintains activity against the sensitizing mutations, especially L858R. Pre-clinical efficacy and safety studies supported progression of BLU-945 into clinical studies, and it is currently in phase 1/2 clinical trials for treatment-resistant EGFR-driven NSCLC.

Abstract LB565: Efficacy of a highly potent and selective KIT V654A inhibitor for treatment of imatinib resistant GIST

Abstract Gastrointestinal stromal tumor (GIST) is the most common type of sarcoma, with approximately 5,000 patients diagnosed per year in the US. Approximately 80% of patients with GIST present with mutations in the c-KIT oncogene at exon 9 or 11, which leads to constitutive, ligand-independent activation of the KIT receptor tyrosine kinase. For patients with metastatic GIST, frontline therapy with imatinib is effective, with a response rate of approximately 51-54% and median progression-free survival (PFS) of 19-23 months, in a molecularly unselected population. Other agents are approved for advanced GIST, without molecular selection, after progression on imatinib, including sunitinib, regorafenib, and ripretinib; however, response rates are less than 10% with PFS of approximately 5-6 months. Notably, patients who progress on imatinib and other tyrosine kinase inhibitors may develop a variety of on-target resistance mutations in the KIT oncogene, such as those in exon 17 (including at amino acids D816 and D820, activation loop mutation), exon 13 (V654A, ATP-binding region mutation), and less frequently in exon 14 (T670I, gatekeeper mutation). Several KIT inhibitors have been developed to potently target the exon 17 resistance mutations (avapritinib and ripretinib); however, there remains an important medical need in 2nd- and 3rd-line therapy in a molecularly unselected population of imatinib-resistant GIST. This suggests more broad-spectrum KIT inhibition is likely required, a hypothesis supported by the observation of large inter- and intra-patient heterogeneity of KIT secondary mutations across hundreds of samples obtained from patients with GIST treated with avapritinib. Sequencing data from the NAVIGATOR phase 1 trial (NCT02508532) revealed that patients with KIT mutant GIST and with the KIT V654A secondary resistance mutation had a poor response to treatment with avapritinib. To address this, we developed a highly potent and selective inhibitor of KIT V654A. This inhibitor showed dose-dependent modulation of downstream pharmacodynamic markers and induced tumor regression in a mastocytoma xenograft model driven by an exon 11 plus 13 V654A resistance mutation. Importantly, this inhibitor was generally well-tolerated and showed high selectivity over wild-type KIT. These findings suggest this novel KIT inhibitor has the potential to be used as a single agent or combination therapy for patients with imatinib-resistant GIST harboring the KIT V654A mutation. Citation Format: Alexandra R. Grassian, Joseph Kim, Omar Ahmad, Kevin Barvian, Alison Davis, Tom Dineen, Wei Hu, Ebby Job, Ludivine Moine, Kate Newberry, Maria Roche, Doug Shorten, Yeon Sook Choi, Francis Wolenski, Sebastian Bauer, Cesar Serrano, Jonathan Trent, Suzanne George. Efficacy of a highly potent and selective KIT V654A inhibitor for treatment of imatinib resistant GIST [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 LB565.

Abstract 1106: Detection of MET alterations at the DNA, RNA and protein levels in NSCLC patients progressing on ALK and ROS1 targeted therapies

Abstract Background: ALK and ROS1 fusion-positive NSCLC patients derive clinical benefit from tyrosine kinase inhibitors (TKIs) but ultimately relapse. Acquired resistance mechanisms include on-target secondary mutations or copy number gains and activation of bypass signaling. Although MET amplification has been described as a bypass resistance mechanism to ALK and ROS1 inhibitors, there are limited data on MET gene and protein overexpression. Aims: (i) detection of MET alterations at the DNA, mRNA and protein levels in ALK and ROS1 fusion-positive NSCLC patients progressing on TKIs, and (ii) establishment of primary cultures using samples from those patients. Methods: MET alterations were studied in 12 patients after progression on TKIs, 10 ALK and 2 ROS1 fusion-positive. Informed consent was obtained from all patients. NGS and FISH were used to detect resistance mutations and amplifications. MET mRNA expression levels were determined by nCounter. Total and phospho-MET levels were assessed by IHC and Western blotting. Results: A total of 21 samples were available from the 12 patients, including tumor biopsies (n=5), plasma (n=10), pleural effusions (n=3) and cerebrospinal fluids (n=3). MET alterations were detected in 4 patients, 3 ALK fusion-positive progressing on lorlatinib and one ROS1 fusion-positive patient progressing on crizotinib. The 3 ALK fusion-positive patients had MET amplification detected in liquid biopsy (n=2) or tumor tissue (n=1), collected after progression on lorlatinib. In the patient with tissue biopsy available, the increased MET copy number was in line with the presence of MET protein and RNA overexpression. MET amplification was not present on the pre-treatment biopsy available for one of the 3 patients. In primary cultures established from pleural effusion samples of 2 ALK fusion-positive patients, MET amplification was maintained, particularly if the cells were cultured in presence of an ALK TKI. Although the ROS1 fusion-positive patient had no MET amplification after progression on crizotinib, MET and phospho-MET upregulation were detected by IHC. These alterations were also present in primary culture that could be established from a pleural effusion sample of the patient. Conclusions: We found MET alterations in 4 out of 12 (33%) fusion-positive patients after progression on TKIs. Three of them had MET amplification and one MET protein overexpression in the absence of MET copy number gain. Despite the small size of the cohort, our results suggest that testing not only at the DNA but also at the RNA and protein levels, discovers amplification-negative patients with MET alterations who may derive benefit from a MET targeted therapy. Finally, our findings highlight the potential of pleural effusion as a source of material for the establishment of primary cultures. Citation Format: Núria Jordana-Ariza, Nadine Reischmann, Carlos Esparré, Ruth Román, Cristina Aguado-Esteban, Silvia García-Román, Christopher Stroh, Andrés Aguilar Aguilar, Rafael Rosell, Niki Karachaliou, Miguel A. Molina-Vila. Detection of MET alterations at the DNA, RNA and protein levels in NSCLC patients progressing on ALK and ROS1 targeted therapies [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 1106.

Foretinib can overcome common on-target resistance mutations after capmatinib/tepotinib treatment in NSCLCs with MET exon 14 skipping mutation

BackgroundCapmatinib and tepotinib are guideline-recommended front-line treatments for non-small-cell lung cancer (NSCLC) patients with MET exon 14 skipping mutations (METex14). However, the emergence of acquired resistance to capmatinib/tepotinib is almost inevitable partially due to D1228X or Y1230X secondary mutations of the MET. In this study, we explored agents that are active against both D1228X and Y1230X MET to propose an ideal sequential treatment after capmatinib/tepotinib treatment failure in NSCLC patients with METex14.MethodsThe inhibitory effects of 300 drugs, including 33 MET-TKIs, were screened in Ba/F3 cells carrying METex14 plus MET D1228A/Y secondary mutations. The screen revealed four-candidate type II MET-TKIs (altiratinib, CEP-40783, foretinib and sitravatinib). Therefore, we performed further growth inhibitory assays using these four MET-TKIs plus cabozantinib and merestinib in Ba/F3 cells carrying MET D1228A/E/G/H/N/V/Y or Y1230C/D/H/N/S secondary mutations. We also performed analyses using Hs746t cell models carrying METex14 (with mutant allele amplification) with/without D1228X or Y1230X in vitro and in vivo to confirm the findings. Furthermore, molecular dynamics (MD) simulations were carried out to examine differences in binding between type II MET-TKIs.ResultsAll 6 type II MET-TKIs were active against Y1230X secondary mutations. However, among these 6 agents, only foretinib showed potent activity against D1228X secondary mutations of the MET in the Ba/F3 cell and Hs746t in vitro model and Hs746t in vivo model, and CEP-40783 and altiratinib demonstrated some activity. MD analysis suggested that the long tail of foretinib plays an important role in binding D1228X MET through interaction with a residue at the solvent front (G1163). Tertiary G1163X mutations, together with L1195F/I and F1200I/L, occurred as acquired resistance mechanisms to the second-line treatment foretinib in Ba/F3 cell models.ConclusionsThe type II MET-TKI foretinib may be an appropriate second-line treatment for NSCLCs carrying METex14 after campatinib/tepotinib treatment failure by secondary mutations at residue D1228 or Y1230.

Precise CRISPR-Cas-mediated gene repair with minimal off-target and unintended on-target mutations in human hematopoietic stem cells.

While CRISPR-Cas9 is key for the development of gene therapy, its potential off-target mutations are still a major concern. Here, we establish a “spacer-nick” gene correction approach that combines the Cas9D10A nickase with a pair of PAM-out sgRNAs at a distance of 200 to 350 bp. In combination with adeno-associated virus (AAV) serotype 6 template delivery, our approach led to efficient HDR in human hematopoietic stem and progenitor cells (HSPCs including long-term HSCs) and T cells, with minimal NHEJ-mediated on-target mutations. Using spacer-nick, we developed an approach to repair disease-causing mutations occurring in the HBB, ELANE, IL7R, and PRF1 genes. We achieved gene correction efficiencies of 20 to 50% with minimal NHEJ-mediated on-target mutations. On the basis of in-depth off-target assessment, frequent unintended genetic alterations induced by classical CRISPR-Cas9 were significantly reduced or absent in the HSPCs treated with spacer-nick. Thus, the spacer-nick gene correction approach provides improved safety and suitability for gene therapy.

Design and rationale of a first-in-human (FIH) phase 1/1b study evaluating KIN-3248, a next-generation, irreversible (irrev), pan-FGFR inhibitor (FGFRi), in adult patients with solid tumors harboring FGFR2 and/or FGFR3 gene alterations (NCT05242822).

TPS9601 Background: FGFR1-4 gene alterations are observed in approximately 7% of all human cancers. There are currently 3 FDA-approved, reversible FGFRi for treatment of patients w/previously treated, locally advanced or metastatic (met) cholangiocarcinoma (CCA) harboring FGFR2 gene fusions/rearrangements (pemigatinib and infigratinib) or met urothelial carcinoma (UC) w/susceptible FGFR2 or FGFR3 genetic alterations (erdafitinib). A major limitation of approved and clinical-stage FGFRi is emergence of secondary, on-target resistance mutations (mutn) that reduce duration of response. Up to 67% of CCA patients treated with either reversible or irrev FGFRi exhibit secondary FGFR2 kinase domain resistance mutn at the time of relapse. KIN-3248 is a next-generation, selective, irrev, small molecule pan-FGFRi, structurally designed to inhibit primary FGFR oncogenic alterations as well as secondary kinase domain mutn associated w/disease progression. Preclinically, KIN-3248 has favorable pharmaceutical properties, is well-tolerated with continuous, daily oral administration in 28d GLP toxicology studies in rats and beagle dogs and is efficacious against primary FGFR2 and FGFR3 oncogenic driver alterations as well as secondary FGFR2 resistance mutn (e.g., gatekeeper and molecular brake) in human cancer cell and PDX models in vitro and in vivo. Methods: This is a FIH, multicenter, non-randomized Ph1 study of KIN-3248 in adult pts with advanced & metastatic solid tumors (AMST) harboring FGFR2 and/or FGFR3 gene alterations. KIN-3248 is given po qd continuously in 28-day cycles until drug intolerance or disease progression. Planned sample size is approx. 120 pts: Part A is a dose-escalation to MTD for pts w/AMST having either FGFR2 and/or FGFR3 alterations. Part A assesses single agent KIN-3248; Part B will evaluate a selected dose of KIN-3248 in 3 cohorts of pts (ICC, UC, or other AMST), each driven by specified FGFR alterations. Standard Ph1 enrollment criteria are required (ECOG PS 0-1, normal organ function, prior receipt of standard treatment or medical judgment that such is not appropriate). Pts may have measurable or evaluable disease. Key exclusion criteria include known active brain metastases and active/uncontrolled HBV/HCV. FGFRi-naïve & -pretreated patients are both eligible. Primary endpoints are safety/tolerability (Part A), and preliminary antitumor activity: objective response rate, disease control rate, duration of response, & duration of stable disease (Part B). Secondary objectives include pharmacokinetic and pharmacodynamic assessments including measures of FGFR pathway modulation. Enrollment is expected to commence in April 2022. Clinical trial information: NCT05242822.