Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Current treatment approaches for renal cell carcinoma (RCC) face challenges in achieving durable tumor responses due to tumor heterogeneity and drug resistance. Combination therapies that leverage tumor molecular profiles could offer an avenue for enhancing treatment efficacy and addressing the limitations of current therapies. To identify effective strategies for treating RCC, we selected ten drugs guided by tumor biology to test in six RCC patient-derived xenograft (PDX) models. The multitargeted tyrosine kinase inhibitor (TKI) cabozantinib and mTORC1/2 inhibitor sapanisertib emerged as the most effective drugs, particularly when combined. The combination demonstrated favorable tolerability and inhibited tumor growth or induced tumor regression in all models, including two from patients who experienced treatment failure with FDA-approved TKI and immunotherapy combinations. In cabozantinib-treated samples, imaging analysis revealed a significant reduction in vascular density, and single-nucleus RNA sequencing (snRNA-seq) analysis indicated a decreased proportion of endothelial cells in the tumors. SnRNA-seq data further identified a tumor subpopulation enriched with cell-cycle activity that exhibited heightened sensitivity to the cabozantinib and sapanisertib combination. Conversely, activation of the epithelial-mesenchymal transition pathway, detected at the protein level, was associated with drug resistance in residual tumors following combination treatment. The combination effectively restrained ERK phosphorylation and reduced expression of ERK downstream transcription factors and their target genes implicated in cell-cycle control and apoptosis. This study highlights the potential of the cabozantinib plus sapanisertib combination as a promising treatment approach for patients with RCC, particularly those whose tumors progressed on immune checkpoint inhibitors and other TKIs.

SIGNIFICANCE

The molecular-guided therapeutic strategy of combining cabozantinib and sapanisertib restrains ERK activity to effectively suppress growth of renal cell carcinomas, including those unresponsive to immune checkpoint inhibitors.

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment

Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.

Abstract PS4-13: Irreversible inhibition of HER2 activating mutations with neratinib enhances the pre-clinical efficacy of trastuzumab emtansine and trastuzumab deruxtecan

Background: HER2 activating mutations occur in 2-5% of metastatic breast cancer (MBC) patients, and three phase II or basket clinical trials have shown that the irreversible pan-HER tyrosine kinase inhibitor, neratinib, has good single agent efficacy for HER2 mutated MBC patients. Current trials are combining neratinib with other targeted therapies to increase response rate and progression free survival for these patients. Methods: We established patient derived xenografts (PDX) and organoids from two patients with HER2 mutated, non-amplified MBC and used them to test neratinib with the antibody drug conjugates (ADC’s), trastuzumab emtansine (T-DM1) and trastuzumab deruxtecan (T-DXd), both in 3D culture and in vivo. Real time, in vivo uptake of these ADC’s was visualized with a near infrared fluorophore. Results: PDX lines WHIM51 and WHIM64 were established from ER+, HER2 non-amplified MBC patients that had HER2 activating mutations. WHIM51 has HER2 exon 20 insertion mutation at amino acid 776 (ERBB2 A775_G776insYVMA) and WHIM64 has a HER2 L869R missense mutation, both of which are located in the HER2 tyrosine kinase domain. Both of these HER2 mutations have been previously characterized and are known activating mutations. Organoids were established from both PDX’s and were grown in 3D culture. Drug combination testing of neratinib with T-DM1 in 3D culture showed strong synergy and the mechanism was explored. We demonstrate that neratinib and other irreversible HER2 inhibitors increase the endocytic uptake of T-DM1, but this effect does not occur with the reversible HER2 inhibitors, tucatinib and lapatinib. Real time, in vivo uptake of T-DM1 was measured by labeling the ADC with a near infrared fluorophore and we observed statistically significant increase in T-DM1 uptake with neratinib pre-treatment. Combining neratinib with T-DM1 increased apoptosis at day 3 post-treatment and enhanced tumor shrinkage. With the FDA approval of T-DXd at the end of 2019, we hypothesized that this same mechanism may apply to neratinib combined with T-DXd. We have tested both the combinations of neratinib + T-DXd and neratinib + T-DM1 in vivo in both HER2 mutant PDX’s and observed statistically significant tumor regression with the neratinib + ADC combinations as compared to either T-DXd or T-DM1 on its own. Conclusions: Neratinib increases the endocytosis of trastuzumab emtansine (T-DM1) and trastuzumab deruxtecan (T-DXd), thereby increasing tumor cell kill and causing greater tumor regression in HER2 mutated MBC. These data provide preclinical justification for trials of neratinib plus HER2 ADCs including T-DXd or T-DM1 in HER2 mutant or HER2+ MBC. Further, this mechanism of neratinib stimulated HER2 endocytosis may also apply to HER2 low MBC.

Citation Format: Ron Bose, Shunqiang Li, Tina M. Primeau, Maureen K. Highkin, Ashley R. Tipton, Nagalaxmi Vemalapally, Xuefeng Gao, Gail Sudlow, Irmina Diala, Yu Tao, Jingqin Luo, Ian Hagemann, Chieh-Yu Lin, Richard P. Bryce, Alshad S. Lalani, Samuel Achilefu, Cynthia X. Ma. Irreversible inhibition of HER2 activating mutations with neratinib enhances the pre-clinical efficacy of trastuzumab emtansine and trastuzumab deruxtecan [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-13.

Abstract 4527: Patient-derived organoids and xenografts identify neratinib plus HER2 antibody drug conjugate as a synergistic drug combination for HER2 mutated, nonamplified metastatic breast cancer

HER2 activating mutations are a novel, druggable genomic alteration in metastatic breast cancer (MBC). These HER2 mutations are predominantly found in HER2 gene amplification negative, hormone receptor positive breast cancers. We have previously demonstrated that HER2 mutations can be potently inhibited by the second generation, irreversible pan-HER tyrosine kinase inhibitor, neratinib (Bose et al., Cancer Discovery 2013). Further, we performed a phase II clinical trial to treat HER2 mutated MBC and we found that neratinib monotherapy produced a clinical benefit rate of 31% and progression free survival (PFS) of 16 weeks in a heavily pre-treated patient population (Ma et al., Clin. Can. Res. 2017). A second clinical trial, the SUMMIT trial (Hyman et al., Nature 2018), similarly showed a response rate of 32% and median PFS of 3.5 months for neratinib monotherapy for HER2 mutated, metastatic breast cancer. The objective of the current study is to explore novel combination strategies to improve the efficacy of neratinib in HER2 mutated breast cancer. In order to accelerate progress on testing multiple drug combinations, we developed organoids from two patient-derived xenografts (PDX’s) of HER2 mutated, ER positive metastatic breast cancer from our institution. We found that the ex vivoculture of these patient-derived organoids provides a platform to rapidly perform drug screens and drug combination testing on a scale that cannot be matched by other existing experimental platforms for patient-derived samples. The drug sensitivity of these organoids cultured ex vivo recapitulates the data previously obtained with transfected cell lines and in vivo experiments using PDX’s. Further, multiple drug combinations can be tested on these organoids in just two weeks, which is much shorter than the four to six months required for the corresponding slow-growing ER positive, breast cancer PDX’s that they are derived from. Strong, single agent activity was seen with neratinib, the HER2 antibody drug conjugate (ADC) ado-trastuzumab emtansine (T-DM1), and the chemotherapy drug vinorelbine. Therefore, we tested combinations of neratinib plus the HER2 ADC and neratinib plus vinorelbine on these patient derived organoids. Neratinib plus HER2 ADC showed a strong drug synergy in both HER2 mutated organoids, as judged by the Loewe model of drug synergy. Prior publications suggest that the mechanism of action of neratinib in this combination is by increasing HER2 ubiquitylation and endocytic degradation, which will increase the uptake of the ADC that binds to HER2. We are now performing 384 well drug screens with these HER2 mutated, ER positive metastatic breast cancer organoids, and the results of the screens will be shown in our presentation.

Citation Format: Shunqiang Li, Highkin Maureen, Tina M. Primeau, Stephanie L. Pratt, Irmina Diala, Richard E. Cutler, Grace Mann, Alshad S. Lalani, Cynthia X. Ma, Ron Bose. Patient-derived organoids and xenografts identify neratinib plus HER2 antibody drug conjugate as a synergistic drug combination for HER2 mutated, nonamplified metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4527.

Abstract 2173: Testing neratinib-containing drug combination regimens on HER2 mutated non-amplified, ER+ breast cancer patient-derived xenografts

Introduction: HER2 activating mutations are a novel, druggable genomic alteration in metastatic breast cancer (MBC). These HER2 mutations are predominantly found in HER2 gene amplification negative, hormone receptor positive breast cancers. We have previously demonstrated that HER2 mutations can be potently inhibited by the second generation, irreversible pan-HER tyrosine kinase inhibitor, neratinib (Bose et al., Cancer Discovery 2013). Further, we performed a phase II clinical trial to treat HER2 mutated MBC and we found that neratinib monotherapy produced a clinical benefit rate of 31% and progression free survival of 16 weeks in a heavily pre-treated patient population (Ma et al., Clinical Cancer Research 2017). The objective of the current pre-clinical study is to develop combination strategies to improve the anti-tumor activity of neratinib in HER2 mutated breast cancer. As ER and CDK4/6 signaling activation are known resistance mechanisms to HER2 targeted agents in HER2 positive breast cancer, we hypothesized that neratinib in combination with agents that target ER (fulvestrant) or CDK4/6 (palbociclib) will induce synergistic anti-tumor effect in HER2 mutated MBC. In addition, we hypothesized that dual HER2 targeting (with trastuzumab) or in combination with chemotherapy agents (vinorelbine), may be more effective than neratinib alone. Since these partnering agents are well established in the treatment of breast cancer and are without overlapping toxicities with neratinib, rapid clinical translation is possible for the treatment of patients with HER2 mutated, ER+ MBC.

Description of our Human-in-Mouse Patient Derived Xenografts (PDX): We developed two HER2 mutated breast cancer PDX lines. Both lines come from HER2 mutation positive, HER2 gene amplification negative, ER+ MBC patients. PDX-51 has a HER2 exon 20 insertion mutation (ERBB2 G776insYVMA), a PIK3CA H1047R mutation and is wild-type for TP53. PDX-64 has a HER2 kinase domain missense mutation (ERBB2 L869R) and is wild-type for both PIK3CA and TP53. Both PDX lines are grown in female NSG strain mice without any exogenous estrogen supplementation.

Results: We tested combinations of neratinib with fulvestrant, palbociclib, trastuzumab, or vinorelbine for their anti-tumor activity and effects on cell proliferation and survival pathway signaling activities, including ER, CDK4/6 and HER2 pathways, in vivo. We will present data on the efficacy of these drug combinations. Tumor size measurements and reverse phase protein array (RPPA) data on the treated PDX lines will be shown.

Citation Format: Shunqiang Li, Tina M. Primeau, Stephanie L. Pratt, Katherine R. Harrill, Francesca Avogadri-Connors, Alshad S. Lalani, Cynthia X. Ma, Ron Bose. Testing neratinib-containing drug combination regimens on HER2 mutated non-amplified, ER+ breast cancer patient-derived xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2173.

A single peptide-MHC complex positively selects a diverse and specific CD8 T cell repertoire

Pathogen recognition by T cells is dependent on their exquisite specificity for self-major histocompatibility complex (MHC) molecules presenting a bound peptide. Although this specificity results from positive and negative selection of developing T cells in the thymus, the relative contribution of these two processes remains controversial. To address the relation between the selecting peptide-MHC complex and the specificity of mature T cells, we generated transgenic mice that express a single peptide-MHC class I complex. We demonstrate that positive selection of CD8 T cells in these mice results in an MHC-specific repertoire. Although selection on a single complex is peptide promiscuous, mature T cells are highly peptide specific. Thus, positive selection imparts MHC and peptide specificity on the peripheral CD8 T cell repertoire.

Mucopolysaccharidosis I cats mount a cytotoxic T lymphocyte response after neonatal gene therapy that can be blocked with CTLA4-Ig

Although gene therapy has reduced manifestations of genetic diseases, immune responses can abrogate the effect. One approach to inducing tolerance is to perform gene transfer in newborns when the immune system is immature. We demonstrate here that the dose of retroviral vector (RV) is important in mice, as mucopolysaccharidosis I (MPS I) mice that received neonatal intravenous gene therapy with a high dose of a canine alpha-L-iduronidase (cIDUA)-expressing RV had stable expression, while those that received a low dose did not. It was unclear, however, if neonatal transfer with any dose could induce tolerance in large animals. Therefore, newborn MPS I cats were injected intravenously with the RV expressing cIDUA. Although this resulted in high serum IDUA activity due to secretion by transduced cells, expression fell due to a CTL response. Cats that transiently received the immunosuppressive agent CTLA4-Ig did not develop a CTL response. In contrast, MPS I dogs, which can respond immunologically to canine IDUA, had stable serum IDUA activity after neonatal gene therapy. We conclude that cats, but not dogs, mount a potent CTL response to canine IDUA after neonatal gene therapy, which can be prevented with transient CTLA4-Ig.