<p>Genomic comparison across the different metastatic sites compared to the matched primary. A. Genomic alterations across metastatic sites compared to matched primary B. Copy number variations across metastatic sites compared to matched primary</p>
<p>Genomic comparison across the different metastatic sites compared to the matched primary. A. Genomic alterations across metastatic sites compared to matched primary B. Copy number variations across metastatic sites compared to matched primary</p>
<div><p>The development of novel therapies for brain metastases is an unmet need. Brain metastases may have unique molecular features that could be explored as therapeutic targets. A better understanding of the drug sensitivity of live cells coupled to molecular analyses will lead to a rational prioritization of therapeutic candidates. We evaluated the molecular profiles of 12 breast cancer brain metastases (BCBM) and matched primary breast tumors to identify potential therapeutic targets. We established six novel patient-derived xenograft (PDX) from BCBM from patients undergoing clinically indicated surgical resection of BCBM and used the PDXs as a drug screening platform to interrogate potential molecular targets. Many of the alterations were conserved in brain metastases compared with the matched primary. We observed differential expressions in the immune-related and metabolism pathways. The PDXs from BCBM captured the potentially targetable molecular alterations in the source brain metastases tumor. The alterations in the PI3K pathway were the most predictive for drug efficacy in the PDXs. The PDXs were also treated with a panel of over 350 drugs and demonstrated high sensitivity to histone deacetylase and proteasome inhibitors. Our study revealed significant differences between the paired BCBM and primary breast tumors with the pathways involved in metabolisms and immune functions. While molecular targeted drug therapy based on genomic profiling of tumors is currently evaluated in clinical trials for patients with brain metastases, a functional precision medicine strategy may complement such an approach by expanding potential therapeutic options, even for BCBM without known targetable molecular alterations.</p>Significance:<p>Examining genomic alterations and differentially expressed pathways in brain metastases may inform future therapeutic strategies. This study supports genomically-guided therapy for BCBM and further investigation into incorporating real-time functional evaluation will increase confidence in efficacy estimations during drug development and predictive biomarker assessment for BCBM.</p></div>
<p>Volcano plot of differentially expressed genes comparing the paired brain metastases and primary breast tumor (Group A). The downregulated and the upregulated genes in the brain metastases samples compared with the matched primary breast tumor samples are color coded as blue (down) and red (up).</p>
Abstract Introduction: Bladder cancer (BC) is the most frequent urinary system cancer in the US. Neoadjuvant chemotherapy before cystectomy for muscle-invasive BC is standard management, though the absolute survival benefit is small, with many patients progressing during chemotherapy. Identifying therapies with a high probability of specific activity against each patient’s tumor remains a critical need. Methods: Following informed consent, from patients undergoing a transurethral resection of bladder tumor or cystectomy, 1+ gram of tumor was procured and divided between DNA/RNA sequencing, organoid drug-screening, and single-cell sequencing of cells surviving chemotherapy. Tissue was dissociated, filtered, and resuspended in organoid media for minimal passaging and drug screening. Drugs were tested at the maximum plasma concentration (Cmax) in human trials, so to provide physiologic relevance. When material was sufficient, cells were additionally tested using dose response. Cmax screening results were normalized to control such that a value of “100” indicated no difference in organoid viability compared to control, and a value of 0 indicated complete response. The number of drugs screened was dependent upon tissue available, with up to 34 drugs screened at Cmax and 9 drugs screened in dose response format. Results: Thus far, >100 patient-derived organoids have undergone collection and development with ~ 2/3 samples collected resulting in organoid development and drug screening. RNA sequencing and GSEA enriched pathways across organoids was compared to other published datasets, noting high levels of correlation between our organoid models and in particular, the Cancer Cell Line Encyclopedia urethral lines. Moreover, analysis of subtype and mutation/copy number data further indicate that our organoid dataset is representative of the full spectrum of disease. RNA sequencing and subtyping of cultured organoids compared to patient tissue indicate that organoid models are representative of patient tissue and do not undergo subtype shifts in our short-term 3D cultures. Our drug screening results highlight the large spectrum of response to chemotherapies that in fact, clinically benefit only a small proportion of patients in the neoadjuvant setting. Crucially, we identify promising targeted therapies to consider for patients who progress following resection and adjuvant chemotherapy. Conclusions: Rapid organoid development, characterization, and drug screening allows for the prediction of therapeutic response in ~10 days following sample collection. Use of this technique on tissue provided during disease work-up may further guide selection of effective therapeutic agents in patients with bladder cancer. This would overall minimize the morbidity of standard of care therapies and could be used to identify alternative therapeutics for patients who progress on standard therapies. Citation Format: Nathan M. Merrill, Liwei Bao, Xu Cheng, Nathalie Vandecan, Zhaoping Qin, Albert Liu, Athena Apfel, Laura Goo, Lila Tudrick, Armand Bankhead III, Phil Palmbos, Samuel Kaffenberger, Khaled Hafez, Jeffrey Montgomery, Todd Morgan, Ajjai Alva, Aaron Udager, Matthew Soellner, Sofia Merajver. Functional assays of drug sensitivity in real-time from patient material for precision oncology in bladder cancer [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 3072.
Abstract Introduction: Activating EGFR mutations are characteristic of inverted sinonasal papillomas (ISP) and ISP-associated sinonasal carcinomas (SNC). Using standard 2D culture models, our group has shown that targeting EGFR activity in ISP-associated SNC effectively inhibits cellular proliferation in vitro. Targeting EGFR in pre-clinical models that are more representative of in vivo patient responses is a critical next step. Methods: High-throughput drug screening was conducted using a 3D in vitro culture model for two ISP-associated SNC cell lines (SCCNC4 and UM-SCC-112) using a library of >800 curated small molecule inhibitors including inhibitors of EGFR, PI3K/AKT/mTOR (P/A/M), and Bcl-2. Viability was assessed and drug sensitivity scores were calculated. Dual combinations (inhibition of EGFR and P/A/M or Bcl-2) and triple combinations (inhibition of EGFR, P/A/M, and Bcl-2) for select drugs were tested for synergistic killing using the Chou-Talalay and Bliss methods. Treatment-associated transcriptomic changes were monitored using whole-transcriptome RNAseq. Finally, patient-derived organoids (PDOs) from primary sinonasal papilloma or carcinoma tissue were utilized ex vivo for short-term drug screening with EGFR, P/A/M, and/or Bcl-2 inhibitors at maximum human plasma concentration (Cmax) format. Results: Drug screening demonstrated that ISP-associated SNC cell lines are highly resistant to a diversity of standard and targeted therapeutic agents. Indeed, these cell lines demonstrated poorer responses than other highly resistant tumor types previously analyzed by our group, including triple-negative breast cancer and bladder cancer. Our data demonstrated that EGFR inhibition alone does not effectively kill ISP-associated SNC cells in 3D culture; however, dual and triple combinations of EGFR and P/A/M and/or Bcl-2 inhibitors showed synergistic killing. Finally, sinonasal papilloma and carcinoma PDOs showed partial responses to selected EGFR inhibitors in 3D ex vivo culture. Conclusions: While EGFR inhibitors effectively inhibit cellular proliferation in ISP-associated SNC cell lines in 2D culture, drug screening in 3D culture and using PDO material - more representative models of in vivo patient responses - show that EGFR inhibition alone is insufficient to completely eliminate these tumor cells, suggesting that EGFR inhibitors alone are unlikely to generate significant clinical responses for patients with ISP or associated SNCs. However, combining targeting of the P/A/M and/or Bcl-2 pathways revealed synergistic killing of ISP-associated SNC cell lines. Taken together, these data demonstrate that compensatory oncogenic and/or anti-apoptotic pathways must be targeted to potentiate EGFR inhibition for successful treatment of ISP and associated SNCs. Citation Format: Athena M. Apfel, Zhaoping Qin, Albert Liu, Matthew B. Soellner, Sofia D. Merajver, Aaron M. Udager, Nathan M. Merrill. EGFR inhibition in combination with PI3K/AKT/mTOR and/or Bcl-2 inhibition is a promising novel therapeutic approach for inverted sinonasal papillomas and associated sinonasal carcinomas [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 4012.
