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Purpose: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, with high mortality and a lack of targeted therapies. To identify and prioritize druggable targets, we performed genome analysis together with genome-scale siRNA and oncology drug profiling using low-passage tumor cells derived from a patient with treatment-resistant HPV-negative HNSCC.Experimental Design: A tumor cell culture was established and subjected to whole-exome sequencing, RNA sequencing, comparative genome hybridization, and high-throughput phenotyping with a siRNA library covering the druggable genome and an oncology drug library. Secondary screens of candidate target genes were performed on the primary tumor cells and two nontumorigenic keratinocyte cell cultures for validation and to assess cancer specificity. siRNA screens of the kinome on two isogenic pairs of p53-mutated HNSCC cell lines were used to determine generalizability. Clinical utility was addressed by performing drug screens on two additional HNSCC cell cultures derived from patients enrolled in a clinical trial.Results: Many of the identified copy number aberrations and somatic mutations in the primary tumor were typical of HPV(−) HNSCC, but none pointed to obvious therapeutic choices. In contrast, siRNA profiling identified 391 candidate target genes, 35 of which were preferentially lethal to cancer cells, most of which were not genomically altered. Chemotherapies and targeted agents with strong tumor-specific activities corroborated the siRNA profiling results and included drugs that targeted the mitotic spindle, the proteasome, and G2–M kinases WEE1 and CHK1. We also show the feasibility of ex vivo drug profiling for patients enrolled in a clinical trial.Conclusions: High-throughput phenotyping with siRNA and drug libraries using patient-derived tumor cells prioritizes mutated driver genes and identifies novel drug targets not revealed by genomic profiling. Functional profiling is a promising adjunct to DNA sequencing for precision oncology. Clin Cancer Res; 24(12); 2828–43. ©2018 AACR.

Supplementary Table 9

Background: Clinically approved targeted therapies for ovarian cancer patients are currently limited to PARP inhibitors and bevacizumab. To improve treatment outcomes, a precision medicine approach is crucial to match effective drugs to patient-specific genetic features and vulnerabilities. This study aimed to: (1) demonstrate the feasibility of performing high-throughput drug screens on fresh patient organoids using a CLIA-approved assay, (2) assess concordance of responses with genomic and clinical information, and (3) reveal novel biomarkers of response to approved/experimental drugs and insights into ovarian cancer biology. Methods: From 2015 to 2020, 76 ovarian tumor samples were collected from 60 patients. To date, 50 evaluable samples were successfully screened at SEngine Precision Medicine. Drugs tested include a range of chemotherapies and targeted therapies that are FDA-approved or in clinical development, with an average of 61 drugs screened per assay (range: 6-135). Somatic and/or germline DNA sequencing is currently available for 30 samples. Sample collection, screening, and sequencing is ongoing. Results: The cohort included ovarian cancer patients with high grade serous (65%), low grade serous (7%), unknown grade serous (7%), clear cell (7%), carcinosarcoma (5%), stromal (5%), endometrioid (2%) subtypes, and one of unknown pathology. Whole genome mutational analysis of 5 tumor-derived organoids and their original tumors demonstrated a high degree of similarity between the tumor-organoid pairs. We present prospective and retrospective evidence from at least 18 cases that organoid drug screening can accurately predict clinical response to chemotherapy and targeted therapies. We also report a patient with platinum resistant serous carcinoma who responded to ibrutinib treatment after screening identified the drug as having excellent response in this patient's organoids. Three months into treatment, the patient's CA125 level was reduced from 250 to 125U/ml. In samples with available genomic information, we demonstrate high concordance between drug sensitivity and known biomarkers, e.g. 83% of samples with known BRCA1/BRCA2 mutation or high HRDetect showed sensitivity to a PARP inhibitor. Further, organoid screening can identify unique targets for every patient beyond established genomic biomarkers. Subsets of patients responded exceptionally to BET (41%), HDAC (28%), WEE1 (24%), and BTK (11%) inhibitors, indicating potential for these targeted therapies in ovarian cancer. Conclusions: The genomic and histopathological heterogeneity of ovarian cancer points to a need to evolve and prioritize the personalization of treatment. Our data demonstrates the utility of organoid based drug screening to nominate therapeutic options for individual patients with or without known genomic biomarkers. Citation Format: Goldie Lui, Anne Richardson, Payel Chatterjee, Madison Pollastro, Mia Lints, Danielle Peretti, Rachele Rosati, Lauren Appleyard, Grace Durenberger, Robert Diaz, Kay Gurley, Isabella Stork, Adam Whitney, Katannya Kapeli, Hallie Swan, Yasin Memari, Helen Davies, Serena Nik-Zainal, Kalyan Banda, Heidi Gray, Barbara Goff, Elizabeth Swisher, Astrid Margossian, Christopher Kemp, Carla Grandori. Functional drug screening of organoids from ovarian cancer patients demonstrates clinical and genomic concordance and identifies novel therapeutic vulnerabilities [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 534.

The goal of precision medicine is to match the right drug to the right patient. However, every individual cancer carries a unique and complex mosaic of genetic and molecular changes making it difficult to identify the right drug based solely on genomic analysis. We developed a CLIA-certified functional drug assay (PARIS® test) for solid tumors which provides an actionable report of tumor derived organoid sensitivities to targeted, endocrine and chemotherapy agents as a tool for clinical therapeutic decisions. Objectives:1.To establish the concordance between organoid drug sensitivity with well-known genomic or immunohistochemical IHC biomarkers 2.To correlate organoid drug sensitivity with clinical outcomes.Methods: From 2015 to 2020, organoids from 410 tumor samples were subjected to functional testing at SEngine Precision Medicine, including 61 breast tumor samples from 48 patients. Fresh samples of tumor cells from core biopsies, surgical excisions, or from fluids arrived 90%.Conclusions: Organoid based drug testing exhibits strong concordance with genomic or IHC biomarkers and clinical response. In addition, functional testing identifies candidate therapies in patients lacking biomarkers and can nominate variants of unknown significance as candidate biomarkers. This study highlights the utility of functional assays to support clinical decision making in a genetically heterogenous cancer such as breast cancer. Citation Format: Astrid Margossian, Anne Richardson, Madison Pollastro, Michael Churchill, Franz Schaub, Shalini Pereira, Payel Chatterjee, Rachele Rosati, Lauren Appleyard, Grace Durenberger, Alex Federation, G. Adam Whitney, Hallie Swan, Trevor Ainge, Robert Diaz, Natasha Hunter, Eric Gamboa, Chris Kemp, Vijayakrishna Gadi, Carla Grandori. Clinical and genomic correlation of a CLIA certified organoid based functional test in breast cancer patients [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 PS4-01.

Introduction: It is difficult to find targeted therapies that work across the genetically diverse Cholangiocarcinoma (CCA) patient population; genomic sequencing alone has not resulted in substantial changes in treatment choices for this rare cancer. We reasoned that CCA patients would benefit from a highly personalized diagnostic test, where patient-derived tumor organoids are tested with a library of targeted drugs in a high-throughput functional assay. Methods: Seventeen patients with CCA were enrolled in an IRB-approved ongoing study from 2017 to 2019; biopsies were collected from surgical resection and shipped on ice overnight to a CLIA-certified laboratory (SEngine Precision Medicine) for organoid derivation and high throughput drug testing. Tumor organoids were challenged with up to 120 FDA-approved and investigational drugs to obtain 6-dose, 3-log response curves. Drug responses were benchmarked against an in-house database of pan-cancer patients to concurrently assess both sensitivity and the uniqueness of each patient's response. Clinical history and genomic information were collected from each patient for retrospective and prospective analysis. Results: 14/19 (74%) samples were successfully derived from 17 patients and screened. Patient age ranged from 36 to 73 (mean=51). The 120-drug library was adapted based on total viable tumor cells per sample, resulting in average of 71 drugs per screen. Top scoring drugs were Ceritinib, MK2206, Belinostat, Taselisib, AZD4547, Everolimus and Poziotinib. In general, the drug sensitivity highlighted the following pathways: AKT, ALK, FGFR, PI3K and EGFR. Drugs were selected per patient and classified as either good or exceptional response and correlated with mutations in known genomic biomarkers in 7 of 12 drug/target pairs. Retrospective analysis demonstrated 100% concordance (n=3) between ex vivo drug resistance and prior treatments. We observed multiple mutation/drug pairs which showed resistance in our functional screen. We achieved a high success rate and clinically relevant turnaround times, from biopsy to final report generation average 17 days (range 9 to 35). Conclusion: This study shows the feasibility of functional testing of organoids derived from CCA patients in a CLIA-certified diagnostic test. While these results correlate well with genomically predicted drug sensitivities, all patients showed additional drug sensitivities beyond those predicted by genomics offering patients additional potential treatment options. This study highlights the importance of functional data in a genetically heterogenous tumor type such as CCA. Each patient represents a mosaic of drug sensitivities, reflecting unique combinations of genetic and epigenetic alterations, and this test can identify the personalized drug combination for them. Citation Format: Astrid Margossian, Franz X. Schaub, Annie Richardson, Michael Churchill, Rachele Rosati, Alexandra Dullea, G Adam Whitney, Hallie Swan, Robert Diaz, Lauren Appleyard, Vijaykrishna Gadi, Ali Zarrinpar, Milind Javle, Christopher Kemp, Shalini Pereira, Carla Grandori. Organoid based functional test to predict personalized treatment in cholangiocarcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 818.

The pool of targeted therapies is expanding steadily providing novel treatment opportunities. However, the process of expanding indications and including additional cancer types after initial approval is slow. Here we present an in vitro clinical trial platform using the data from the first CLIA-approved Precision Medicine Platform using high-throughput screening (P.A.R.I.S. Assay, SEngine Precision Medicine, Seattle, WA). Briefly, patient-derived tumor cells from biopsies are expanded as living organoids, and functionally evaluated using a high-throughput drug screen. The drug library currently includes FDA approved and experimental drugs. Results are integrated with known genomic information and reported to the clinician to highlight treatment options of an individual patient. Combining this data from multiple patients enables the discovery of novel indications and biomarkers. To date we have acquired data from a wide range of tumor types including hard-to-treat cancers, rare tumor types and tumors from heavily pretreated patients. In addition, we also have collected data from more than 100 patient derived cell lines. Using the data analysis platform developed in R, the drug responses across all patient screens of a given drug can be analyzed to find common indicators of sensitivities. For instance, a BRD4 inhibitor (CPI-203), which was tested on 8 different primary tumor samples, was selectively active in a subset of the patients. Interestingly, most of the responding tumor types are ovarian and breast cancer cases with mutations in BRCA1 or EZH2. However, there are currently no clinical trials investigating the more developed BRD4 inhibitor CPI-0610 for breast or ovarian cancer. Non-responders, on the other hand, are spread between multiple cancer types. The number of patients receiving the P.A.R.I.S. test is steadily increasing and these patient cases contribute to our knowledge base. As this test is used to inform clinicians about potential treatment opportunities, we are also accumulating information on how these patients respond to treatment. Overall, this platform will provide real world data for optimal drug combinations and novel biomarkers to quickly expand indications of existing drugs. Citation Format: Franz X. Schaub, Michael J. Churchill, Hallie A. Swan, Rachele Rosati, Roland M. Watt, Reid C. Shaw, Stephanie A. Murphy, Robert L. Diaz, Shalini C. Pereira, Carla Grandori. Accelerating drug development with a CLIA approved functional test using patient derived organoids [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 582.

Background: Metastatic disease in ovarian cancer is difficult to treat and patients often exhaust standard-of-care regimens. To get a better understanding of potential treatments, genomic data is used in some cases. However, this only points to therapeutic options in a minority of cases highlighting an urgent need to develop assays to identify potential therapies. Current functional tests are limited in the number of tested drugs. Here we present the first CLIA certified high-throughput functional assay employing organoid cultures derived from primary patient specimens to directly aid oncologists for personalized treatment selection (P.A.R.I.S. Assay, SEngine Precision Medicine, Seattle, WA). Experimental Procedures: Organoids are treated for 6 days with a library of 123 clinically relevant drugs. Compounds are evaluated at a multi-dose response curve and ranked by SPM score, which weights both the sensitivity (degree of cell death) and specificity, which compares the patient's tumor cells response to the drug relative to all prior patients. The results are further integrated with genomic data and reported to the clinician to highlight treatment options. SEngine has performed >150 drug screens and established high reproducibility including multiple ovarian cancer cases from either ascites, surgical or core biopsies. Results: Here we present two n-of-one patient studies. Patient 1 is a 48 year old woman with positive family history who was diagnosed with late stage serous ovarian cancer. SEngine generated cancer organoids and performed high-throughput screening with a panel of 123 drugs. Sensitivities to PARP inhibitors prompted SEngine to advise for germline testing which revealed a BRCA1 and TP53 mutation. The cells were also uniquely sensitive to paclitaxel and the combination with carboplatin resulted in remission indicating concordance with clinical data. In addition, highlighting the importance of functional screening, a unique response to a sub-group of EGFR inhibitors was identified, of potential consideration in case of recurrence. The second case also has a family history of ovarian cancer, but no BRCA mutations were detected. Genomic data indicated FGF6 and FGF23 amplification which directly corresponded to a unique sensitivity to one FGFR inhibitor (AZD-4547). The organoids were also resistant to PARP inhibitors, consistent with the absence of BRCA mutations. Impact: We developed a robust ex vivo screening platform to objectively quantify patient specific sensitivity to a panel of 123 oncology drugs. SEngine is compiling a registry capturing clinical data, outcome following the P.A.R.I.S. test as well as genomic data. The power of high throughput technology and organoid isolation will enable the rapid selection of optimal individualized therapies as single agents or in combination. Citation Format: Hallie A. Swan, Rachele Rosati, Caroline Bridgwater, Michael J. Churchill, Roland M. Watt, Reid C. Shaw, Stephanie A. Murphy, Robert L. Diaz, Shalini C. Pereira, Franz X. Schaub, Carla Grandori. Personalized medicine: A CLIA-certified high-throughput drug screening platform for ovarian cancer [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 1619.

In June 2017, SEngine Precision Medicine (Seattle, WA USA) obtained CLIA certification for the first high-complexity and high throughput organotypic chemosensitivity test, P.A.R.I.S., thus opening its doors to oncologists and pharmaceutical companies that may consider personalization of cancer treatments in their practice or in the clinical trial setting. Just as Paris slayed the invulnerable Achilles by aiming specifically at its weaknesses, the PARIS test challenges tumor cells with a library of 137 clinically actionable targeted drugs to identify sensitivity and resistance patterns unique to each individual cancer in an unbiased manner. Here we will present an overview of the approach that has led to CLIA certification, including novel cell culture techniques and analysis metrics. We will also highlight insights gained by comparative analysis across a multitude of cancer samples. SEngine has derived and expanded primary cancer cells from a cohort of over 100 patient derived specimens. Patients include many who have been heavily pre-treated with prior chemotherapy and several with rare cancers, including adrenocortical carcinoma, neuroblastoma, leiomyosarcoma and cholangiocarcinoma. Standard operating procedures have been established for transport of specimens as well as primary cultures in three dimensional organotypic conditions. Our analysis pipeline evaluates the multi-dose response of a given patient's tumor to each drug in our library and compares those responses to all prior patients. This establishes not only functional sensitivity but also the uniqueness of the patient's response. We calculate the SPM score, a proprietary ranking metric weighing both the sensitivity and uniqueness of the response. The results from the P.A.R.I.S. test are highly reproducible (Spearman rank correlation coefficients: 0.95, 0.88 technical and biological replicates respectively). We perform bi-annual proficiency validation of our platform with another CLIA-certified laboratory. Ten samples tested demonstrated greater than 75% concordance between responses. The data obtained are visualized by an in-house application suite (SEngine Medicine APP), consisting of interactive charts, statistical analysis, and reactive reports which can be shared with oncologists and investigators. A cohort of 50 samples was employed to demonstrate sensitivities or resistances concordant with those predicted by the patient's genomic aberrations and/or prior clinical responses.In summary, we envision that the P.A.R.I.S. test will be essential for patient's selection while developing novel targeted drugs, providing crucial functional information much needed to decode the complexity of individual cancer genomics. Citation Format: Hallie A. Swan, Michael J. Churchill, Rachele Rosati, Franz X. Schaub, Reid C. Shaw, Roland M. Watt, Eduardo Mendez, Christopher J. Kemp, Vijayakrishna K. Gadi, Stephanie A. Murphy, Brady Bernard, Robert L. Diaz, Shalini C. Pereira, Carla Grandori. Personalization of cancer treatments with a CLIA-certified high-complexity and high-throughput drug sensitivity test [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 1605.

Goal: Neuroblastoma (NBL) is the second most frequent pediatric solid tumor. We have seen an increase in survival for children with NBL, however treatment still consists of many cycles of chemotherapy and radiation. We reasoned, that in vitro high throughput drug screening (HTDS) of patient derived organoids using a library of targeted therapies, would highlight novel targeted and personalized treatment options. Methods: We optimized an in vitro 3D culture for high-risk NBL samples, initially established as patient derived xenografts (PDX) and screened a total of 10 patient samples with genomic information using two different drug libraries: Informer Set (320 drugs) compiled by the Cancer Target Discovery and Development network which is focused on cancer pathways and SEngine Library (123 drugs) focused on clinically relevant therapies. The screen was performed in a 384 well-format and cell viability was measured. Organoids were characterized by immunohistochemistry and genomic and pathway alterations were confirmed. Results: Here we highlighted unique results from 4 cases. The first sample showed sensitivities to CDK inhibitors in concordance with amplification of CDK4. However, for this patient additional drug sensitivities were not directly linked to a genetic alteration, such as AZD7762 (CHK inhibitor) and MK-1775 (WEE1 inhibitor) indicating sensitivities in the cell-cycle checkpoints, and an exceptional response to Enzalutamide, an androgen receptor antagonist. The second case had unique sensitivities to IGF1R and Insulin Receptor inhibitors (Linsitinib and BMS-754807) indicating a specific addiction to this growth-factors/survival signal. The third sample had multiple sensitivities linked to genomic alterations, such as Dabrafenib, concordant with the presence of a BRAF activating mutation. In addition, sensitivity to Alisertib was detected as previously reported for MYCN amplified NBL, but this was not true for other MYCN amplified cases. Interestingly, this third sample also showed profound sensitivities to PARP inhibitors, most likely related to a mutation in the BRP1 gene a BRCA1 interacting protein gene. The fourth case showed a strong sensitivity to nutlin-3 (MDM2 inhibitor) and Oxaliplatin. Conclusion: A newly established NBL 3D patient organoid culture system coupled with personalized HTDS and genomic analysis offers an effective platform for the discovery of novel personalized therapies and drug combinations tailored to individual patients. In this NBL cohort, we discovered both drugs predicted by the patient-specific genomic alterations, as well as novel patient-specific drug sensitivities without a known genomic marker. More in depth genomic analysis is underway, but epigenetic alterations could explain these exceptional responses. In summary, this investigational study of 10 NBL highlights the need of personalization of targeted therapies in NBL. Citation Format: Rachele Rosati, Hallie A. Swan, Laura Scolaro, Kateryna Krytska, John M. Maris, Franz X. Schaub, Carla Grandori. Patient derived organoids to guide personalized neuroblastoma treatment [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 2625.

Recurrent metastatic breast cancer is difficult to treat and patients often exhaust standard-of-care regimens. P.A.R.I.S. is a CLIA certified high throughput chemosensitivity test developed by SEngine Precision Medicine. (Seattle, WA USA) Tumor cells derived from patient breast tissue are expanded as mammospheres, and challenged with a library of 123 clinically actionable, targeted drugs. These results are integrated with patient genomic data and reported to the oncologist to prioritize treatment options. To date, we have performed over 100 such drug screens using low passage patient-derived tumor cells in 70 independent replicate pairs. Of 18 viable primary breast tumor samples received to date, we have successfully derived organotypic cultures in 13 cases. (72%) Of these, 7 were challenged to the full 123 agent library. Three of the seven cases were HER2 positive and demonstrated clear sensitivity to HER2 kinase inhibitors. Overall, patients can be separated into two groups, characterized by families of drug sensitivities. Patients in group one respond preferentially to inhibitors of signaling pathways such as IGF1R, ALK, FGFR and EGFR. Patients in the second group responded to therapies targeting epigenetic modifiers, cell cycle control and apoptosis. Presented here is a premenopausal female, diagnosed in 2010 as pT2N0M0 (stage IIA), ER+ PR+ HER2+. This patient underwent surgery and received adjuvant chemotherapy, followed by tamoxifen. Upon progression to metastatic disease, biopsy of her recurrent lesion showed loss of ER and PR expression, but remained positive for HER-2 amplification. Sequencing of this biopsy exposed a PIK3CA G106R mutation and amplification of unknown significance. Tumor cells were isolated from ascites, cultured and the P.A.R.I.S. test was performed. Patient derived tumor cells were sensitive to HER2 targeting agents, concordant with the patient's HER2 amplification. Of these, the non-reversible inhibitor neratinib exhibited a significantly enhanced effect and achieved maximum growth inhibition of 80% over the duration of the assay. Two different AKT inhibitors, afuresertib and AZD5363, demonstrated activity in the patient cells consistent with the activating PIK3CA mutation. Also consistent with the loss of ER/PR expression, the patient derived tumor cells no longer responded to anti-estrogen therapies nor to chemotherapies the patient had been refractory to prior: cyclophosphamide, docetaxel, doxorubicin, gemcitabine, and paclitaxel.The PARIS assay is a robust ex vivo screening platform to objectively quantify patient specific sensitivities to a panel of 123 clinically actionable oncology drugs. We show here concordance with both genomic data and prior treatments the patient received in the course of disease however the same approach may be used to successfully identify unique sensitivities in the absence of established biomarkers. Citation Format: Michael J. Churchill, Franz X. Schaub, Hallie A. Swan, Rachele Rosati, Fengting Yan, Reid C. Shaw, Kay E. Gurley, Robert L. Diaz, Shalini C. Pereira, Carla Grandori, Christopher J. Kemp, Vijayakrishna K. Gadi. Patient derived tumor organoids identify actionable targets in heavily pretreated metastatic breast cancer patients [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 1603.