Kinase-Impaired BTK Mutations Are Susceptible to Clinical-Stage BTK and IKZF1/3 Degrader NX-2127

INTRODUCTION: Bruton’s tyrosine kinase (BTK) is a nonreceptor kinase in the B cell receptor (BCR) signaling cascade critical for B cell survival. As such, chronic lymphocytic leukemia (CLL) and other B cell cancers are sensitive to inhibition of BTK. Covalent and noncovalent inhibitors of BTK have revolutionized the treatment of these cancers. Therefore, understanding mechanisms by which acquired mutation in BTK confer drug resistance and developing new therapies to overcome resistance are critically important. RATIONALE: We recently discovered BTK mutations that confer resistance across covalent and noncovalent BTK inhibitors. In this study, we found that a group of these mutants impair BTK kinase activity despite still enabling downstream BCR signaling. We therefore set out to understand the nonenzymatic functions of BTK and explored targeted protein degradation to overcome the oncogenic scaffold function of mutant BTK. This effort included evaluation of BTK degradation in patients with CLL treated in a phase 1 clinical trial of NX-2127, a first-in-class BTK degrader (NCT04830137). RESULTS: BTK enzymatic activity assays revealed that drug resistance mutations in BTK fall into two distinct groups: kinase proficient and kinase impaired. Immunoprecipitation mass spectrometry of kinase-impaired BTK L528W (Leu528→Trp) revealed a scaffold function of BTK with downstream signaling and survival dependent on surrogate kinases that bind to kinase-impaired BTK proteoforms. To target the nonenzymatic functions of BTK, we developed NX-2127, a heterobifunctional molecule that engages the ubiquitin-proteasome system to simultaneously bind both BTK and the cereblon E3 ubiquitin ligase complex, inducing polyubiquitination and proteasome-dependent degradation of IKZF1/3 and all recurrent drug-resistant forms of mutant BTK. The activity of NX-2127 on BTK degradation was further demonstrated in patients with CLL treated in a phase 1 clinical trial of NX-2127, where \u3e80% BTK degradation was achieved and clinical responses were also seen in 79% of evaluable patients, independent of mutant BTK genotypes. CONCLUSION: We identified that BTK inhibitor resistance mutations fall into two distinct functional categories. Kinase-impaired BTK mutants disable BTK kinase activity while promoting physical interactions with other kinases to sustain downstream BCR signaling. This scaffold function of BTK was disrupted by NX-2127, a potent BTK degrader, which showed promising responses for patients with relapsed and refractory CLL, independently of mutant BTK functional category

Mechanisms of Resistance to Noncovalent Bruton's Tyrosine Kinase Inhibitors

BackgroundCovalent (irreversible) Bruton's tyrosine kinase (BTK) inhibitors have transformed the treatment of multiple B-cell cancers, especially chronic lymphocytic leukemia (CLL). However, resistance can arise through multiple mechanisms, including acquired mutations in BTK at residue C481, the binding site of covalent BTK inhibitors. Noncovalent (reversible) BTK inhibitors overcome this mechanism and other sources of resistance, but the mechanisms of resistance to these therapies are currently not well understood.MethodsWe performed genomic analyses of pretreatment specimens as well as specimens obtained at the time of disease progression from patients with CLL who had been treated with the noncovalent BTK inhibitor pirtobrutinib. Structural modeling, BTK-binding assays, and cell-based assays were conducted to study mutations that confer resistance to noncovalent BTK inhibitors.ResultsAmong 55 treated patients, we identified 9 patients with relapsed or refractory CLL and acquired mechanisms of genetic resistance to pirtobrutinib. We found mutations (V416L, A428D, M437R, T474I, and L528W) that were clustered in the kinase domain of BTK and that conferred resistance to both noncovalent BTK inhibitors and certain covalent BTK inhibitors. Mutations in BTK or phospholipase C gamma 2 (PLCγ2), a signaling molecule and downstream substrate of BTK, were found in all 9 patients. Transcriptional activation reflecting B-cell-receptor signaling persisted despite continued therapy with noncovalent BTK inhibitors.ConclusionsResistance to noncovalent BTK inhibitors arose through on-target BTK mutations and downstream PLCγ2 mutations that allowed escape from BTK inhibition. A proportion of these mutations also conferred resistance across clinically approved covalent BTK inhibitors. These data suggested new mechanisms of genomic escape from established covalent and novel noncovalent BTK inhibitors. (Funded by the American Society of Hematology and others.)

Abstract 1341: Inhibiting the nuclear exporter XPO1 and the antiapoptotic factor BCL2 is synergistic in XPO1 and SF3B1 mutant hematologic malignancies

Abstract Mutations in the nuclear exporter XPO1 and the spliceosomal protein SF3B1 are bona fide cancer drivers and occur across a spectrum of hematologic cancers, specifically in chronic lymphocytic leukemia (CLL), myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Selinexor is a potent, XPO1 inhibitor that was recently approved in diffuse large B-cell lymphoma and is being tested in MDS and AML. The BCL2 inhibitor, venetoclax, is approved for use in CLL and has also shown to be effective in myeloid malignancies. XPO1 inhibition exerts its antineoplastic effects by blocking key tumorigenic pathways, such as NFκB, and decreasing the anti-apoptotic protein MCL1. We therefore hypothesized that combining selinexor and venetoclax would have potential synergy and could be used to target hematologic malignancies bearing XPO1 and SF3B1 mutations. We first determined whether XPO1 and SF3B1 mutant cell lines showed differential response to either selinexor or venetoclax monotherapy. Five lymphoma cell lines; 3 diffuse large B-cell lymphoma (SU-DHL-6, SU-DHL-16, FARAGE) and 2 classical Hodgkin lymphoma (L428 and SUP-HD1), were used based on the presence or absence of XPO1 mutations. SUDHL-16 and SUP-HD1 are heterozygous for the XPO1 E571K hotspot mutation while SUDHL-6, FARAGE and SUP-HD1 are wildtype. These cell lines were used to assess sensitivity to Selinexor or Venetoclax using the CellTiter Glo assay. The XPO1 mutant cells showed increased sensitivity to selinexor (IC50 = 16-35nM vs 41-231nM). Additionally, the XPO1 mutant cell lines showed increased sensitivity to single-agent venetoclax (XPO1 mutant IC50 = 2-13nM vs 5-2853nM). SF3B1 K666N mutant K562 and Nalm-6 cells also showed increased sensitivity to selinexor compared to wildtype cells (IC50 =116-190nM vs 212-1405nM), as well as to venetoclax as compared to wildtype (IC50 =149nM-1.28 μM vs 1.26-1.4μM). Next, we tested the synergy of the combination of these drugs in the XPO1 and SF3B1 mutant cell lines. Increasing concentrations of the individual drugs were applied to each individual cell line in a 6x6 matrix and the Bliss Independence model was used to calculate synergy of the combination. As hypothesized, the combination of Selinexor and venetoclax showed synergy in both the XPO1 and SF3B1 mutant cell lines (synergy scores 4.5-16.5). Western blots of treated wildtype versus mutant cells showed decreased levels of p65 and MCL1 with selinexor (but not venetoclax) that was enhanced with combination therapy, specifically in mutant cell lines. In conclusion, inhibiting the nuclear exporter XPO1 and the anti-apoptotic factor BCL2 is synergistic in both XPO1 and SF3B1 mutant cells. This combination is highly promising as an all oral regimen for hematologic malignancies bearing these mutations. Further, preclinical testing in in vivo using XPO1 and SF3B1 mutant and wildtype mice is ongoing. Citation Format: Tulasigeri M. Totiger, Sana Chaudhry, Jumana Afaghani, Justin Taylor. Inhibiting the nuclear exporter XPO1 and the antiapoptotic factor BCL2 is synergistic in XPO1 and SF3B1 mutant hematologic malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1341

Lung Inflammation Predictors in Combined Immune Checkpoint-Inhibitor and Radiation Therapy—Proof-of-Concept Animal Study

Purpose: Combined radiotherapy (RT) and immune checkpoint-inhibitor (ICI) therapy can act synergistically to enhance tumor response beyond what either treatment can achieve alone. Alongside the revolutionary impact of ICIs on cancer therapy, life-threatening potential side effects, such as checkpoint-inhibitor-induced (CIP) pneumonitis, remain underreported and unpredictable. In this preclinical study, we hypothesized that routinely collected data such as imaging, blood counts, and blood cytokine levels can be utilized to build a model that predicts lung inflammation associated with combined RT/ICI therapy. Materials and Methods: This proof-of-concept investigational work was performed on Lewis lung carcinoma in a syngeneic murine model. Nineteen mice were used, four as untreated controls and the rest subjected to RT/ICI therapy. Tumors were implanted subcutaneously in both flanks and upon reaching volumes of ~200 mm3 the animals were imaged with both CT and MRI and blood was collected. Quantitative radiomics features were extracted from imaging of both lungs. The animals then received RT to the right flank tumor only with a regimen of three 8 Gy fractions (one fraction per day over 3 days) with PD-1 inhibitor administration delivered intraperitoneally after each daily RT fraction. Tumor volume evolution was followed until tumors reached the maximum size allowed by the Institutional Animal Care and Use Committee (IACUC). The animals were sacrificed, and lung tissues harvested for immunohistochemistry evaluation. Tissue biomarkers of lung inflammation (CD45) were tallied, and binary logistic regression analyses were performed to create models predictive of lung inflammation, incorporating pretreatment CT/MRI radiomics, blood counts, and blood cytokines. Results: The treated animal cohort was dichotomized by the median value of CD45 infiltration in the lungs. Four pretreatment radiomics features (3 CT features and 1 MRI feature) together with pre-treatment neutrophil-to-lymphocyte (NLR) ratio and pre-treatment granulocyte-macrophage colony-stimulating factor (GM-CSF) level correlated with dichotomized CD45 infiltration. Predictive models were created by combining radiomics with NLR and GM-CSF. Receiver operating characteristic (ROC) analyses of two-fold internal cross-validation indicated that the predictive model incorporating MR radiomics had an average area under the curve (AUC) of 0.834, while the model incorporating CT radiomics had an AUC of 0.787. Conclusions: Model building using quantitative imaging data, blood counts, and blood cytokines resulted in lung inflammation prediction models justifying the study hypothesis. The models yielded very-good-to-excellent AUCs of more than 0.78 on internal cross-validation analyses

Establishing Correlations between Breast Tumor Response to Radio-Immunotherapy and Radiomics from Multi-Parametric Imaging: An Animal Study

Triple-negative breast cancer (TNBC), which is a type of invasive breast cancer, is characterized by severe disease progression, poor prognosis, high recurrence rate, and short survival. We sought to gain new insight into TNBC by applying computed tomography (CT) and magnetic resonance (MR) quantitative imaging (radiomics) approaches to predict the outcome of radio-immunotherapy treatments in a syngeneic subcutaneous murine breast tumor model. Five Athymic Nude mice were implanted with breast cancer cell lines (4T1) tumors on the right flank. The animals were CT- and MRI-imaged, tumors were contoured, and radiomics features were extracted. All animals were treated with radiotherapy (RT), followed by the administration of PD1 inhibitor. Approximately 10 days later, the animals were sacrificed, tumor volumes were measured, and histopathology evaluation was performed through Ki-67 staining. Linear regression modeling between radiomics and Ki-67 results was performed to establish a correlation between quantitative imaging and post-treatment histochemistry. There was no correlation between tumor volumes and Ki-67 values. Multiple CT- and MRI-derived features, however, correlated with histopathology with correlation coefficients greater than 0.8. MRI imaging helps in tumor delineation as well as an additional orthogonal imaging modality for quantitative imaging purposes. This is the first investigation correlating simultaneously CT- and MRI-derived radiomics to histopathology outcomes of combined radio-immunotherapy treatments in a preclinical setting applied to treatment naïve tumors. The findings indicate that imaging can guide discrimination between responding and non-responding tumors for the combined RT and ImT treatment regimen in TNBC

Establishing Correlations between Breast Tumor Response to Radio-Immunotherapy and Radiomics from Multi-Parametric Imaging: An Animal Study

Triple-negative breast cancer (TNBC), which is a type of invasive breast cancer, is characterized by severe disease progression, poor prognosis, high recurrence rate, and short survival. We sought to gain new insight into TNBC by applying computed tomography (CT) and magnetic resonance (MR) quantitative imaging (radiomics) approaches to predict the outcome of radio-immunotherapy treatments in a syngeneic subcutaneous murine breast tumor model. Five Athymic Nude mice were implanted with breast cancer cell lines (4T1) tumors on the right flank. The animals were CT- and MRI-imaged, tumors were contoured, and radiomics features were extracted. All animals were treated with radiotherapy (RT), followed by the administration of PD1 inhibitor. Approximately 10 days later, the animals were sacrificed, tumor volumes were measured, and histopathology evaluation was performed through Ki-67 staining. Linear regression modeling between radiomics and Ki-67 results was performed to establish a correlation between quantitative imaging and post-treatment histochemistry. There was no correlation between tumor volumes and Ki-67 values. Multiple CT- and MRI-derived features, however, correlated with histopathology with correlation coefficients greater than 0.8. MRI imaging helps in tumor delineation as well as an additional orthogonal imaging modality for quantitative imaging purposes. This is the first investigation correlating simultaneously CT- and MRI-derived radiomics to histopathology outcomes of combined radio-immunotherapy treatments in a preclinical setting applied to treatment naïve tumors. The findings indicate that imaging can guide discrimination between responding and non-responding tumors for the combined RT and ImT treatment regimen in TNBC

Toward prediction of abscopal effect in radioimmunotherapy: Pre-clinical investigation

Immunotherapy (IT) and radiotherapy (RT) can act synergistically, enhancing antitumor response beyond what either treatment can achieve separately. Anecdotal reports suggest that these results are in part due to the induction of an abscopal effect on non-irradiated lesions. Systematic data on incidence of the abscopal effect are scarce, while the existence and the identification of predictive signatures or this phenomenon are lacking. The purpose of this pre-clinical investigational work is to shed more light on the subject by identifying several imaging features and blood counts, which can be utilized to build a predictive binary logistic model. This proof-of-principle study was performed on Lewis Lung Carcinoma in a syngeneic, subcutaneous murine model. Nineteen mice were used: four as control and the rest were subjected to combined RT plus IT regimen. Tumors were implanted on both flanks and after reaching volume of ~200 mm3 the animals were CT and MRI imaged and blood was collected. Quantitative imaging features (radiomics) were extracted for both flanks. Subsequently, the treated animals received radiation (only to the right flank) in three 8 Gy fractions followed by PD-1 inhibitor administrations. Tumor volumes were followed and animals exhibiting identical of better tumor growth delay on the non-irradiated (left) flank as compared to the irradiated flank were identified as experiencing an abscopal effect. Binary logistic regression analysis was performed to create models for CT and MRI radiomics and blood counts, which are predictive of the abscopal effect. Four of the treated animals experienced an abscopal effect. Three CT and two MRI radiomics features together with the pre-treatment neutrophil-to-lymphocyte (NLR) ratio correlated with the abscopal effect. Predictive models were created by combining the radiomics with NLR. ROC analyses indicated that the CT model had AUC of 0.846, while the MRI model had AUC of 0.946. The combination of CT and MRI radiomics with blood counts resulted in models with AUCs of 1 on the modeling dataset. Application of the models to the validation dataset exhibited AUCs above 0.84, indicating very good predictive power of the combination between quantitative imaging and blood counts

Targeted Therapy Development in Acute Myeloid Leukemia

Therapeutic developments targeting acute myeloid leukemia (AML) have been in the pipeline for five decades and have recently resulted in the approval of multiple targeted therapies. However, there remains an unmet need for molecular treatments that can deliver long-term remissions and cure for this heterogeneous disease. Previously, a wide range of small molecule drugs were developed to target sub-types of AML, mainly in the relapsed and refractory setting; however, drug resistance has derailed the long-term efficacy of these as monotherapies. Recently, the small molecule venetoclax was introduced in combination with azacitidine, which has improved the response rates and the overall survival in older adults with AML compared to those of chemotherapy. However, this regimen is still limited by cytotoxicity and is not curative. Therefore, there is high demand for therapies that target specific abnormalities in AML while sparing normal cells and eliminating leukemia-initiating cells. Despite this, the urgent need to develop these therapies has been hampered by the complexities of this heterogeneous disease, spurring the development of innovative therapies that target different mechanisms of leukemogenesis. This review comprehensively addresses the development of novel targeted therapies and the translational perspective for acute myeloid leukemia, including the development of selective and non-selective drugs

Abstract 3218: Combination drug screen identifies novel epigenetic therapies to enhance menin inhibitor efficacy in KMT2A rearranged and NPM1 mutant AML

Abstract Background: Acute myeloid leukemia (AML) with KMT2A-rearrangements have a poor prognosis and so there is an urgent need for novel therapies. Menin inhibitors have shown promising anti-leukemic effects in KMT2A-rearranged and NPM1-mutated AML. However, the efficacy of menin inhibitors as single agents may be limited by the development of resistance mutations. Combining menin inhibitors with other epigenetic drugs may present a strategy to enhance their therapeutic potential. In this study, we performed a combination drug screen using an epigenetic drug library in KMT2A-rearranged (MV4;11) and NPM1-mutant (OCI-AML3) AML cell lines to identify synergistic therapies that can be used in conjunction with menin inhibitors. Methods: During assay optimization, MV4;11 and OCI-AML3 cells were treated with the menin inhibitor DSP-5336, and their viability was assessed. Quality control metrics were applied with Z’ values consistently greater than 0.5 for all assay plates and then the cells were subjected to a small molecule compound library screen containing a set of 932 epigenetic drugs. The screening process included a systematic evaluation of each drug's effect on cell viability in combination with the DSP-5336. Results: The combination drug screen demonstrated robust performance in both MV4;11 and OCI-AML3 cell lines, with reliable quality control metrics. Among the epigenetic drugs tested, five compounds were identified as potential hits that synergistically enhanced the efficacy of DSP-5336 across both cell lines.The five identified compounds exhibited enhanced anti-leukemic effects when combined with the menin inhibitor in either one of the cell lines. The targets of these drugs varied, including histone deacetylases, histone acetyltransferases and BRD4 inhibition, suggesting many alternate mechanisms of action involving epigenetic modulation. Remarkably, one of the 5 hits C301-3161, a KAT2A inhibitor, showed limited activity in either cell line alone but increased cell killing with DSP-5336 in both cell lines, highlighting its potential as a specific therapeutic for combining with DSP-5336 in AML patients. Conclusions: Our findings suggest combining menin inhibitors with other epigenetic drugs may improve AML treatment outcomes. The combination drug screen successfully identified four novel compounds that synergistically enhance menin inhibitor efficacy in both KMT2A-rearranged and NPM1-mutant AML cell lines. These compounds hold significant promise as potential therapeutic candidates for further investigation. Future studies should focus on elucidating the underlying mechanisms of action for each hit and evaluating their effects in preclinical animal models. Ultimately, this research may pave the way for the development of innovative combination therapeutic strategies for AML patients with KMT2A-rearragned and NPM1-mutant AML. Citation Format: Tulasigeri M. Totiger, Sana Chaudhry, Skye Montoya, Maurizio Affer, Anya K. Sondhi, Alexandra Chirino, Claude-Henry Volmar, Shaun Brothers, Justin Watts, Justin Taylor. Combination drug screen identifies novel epigenetic therapies to enhance menin inhibitor efficacy in KMT2A rearranged and NPM1 mutant AML [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 3218