High-throughput Drug Sensitivity Research Articles

Replication Stress is an Actionable Genetic Vulnerability in Desmoplastic Small Round Cell Tumors.

Desmoplastic small round cell tumor (DSRCT) is an aggressive sarcoma subtype that is driven by the EWS-WT1 chimeric transcription factor. The prognosis for DSRCT is poor, and major advances in treating DSCRT have not occurred for over two decades. To identify effective therapeutic approaches to target DSRCT, we conducted a high-throughput drug sensitivity screen in a DSRCT cell line assessing chemosensitivity profiles for 79 small-molecule inhibitors. DSRCT cells were sensitive to PARP and ATR inhibitors (PARPi, ATRi), as monotherapies and in combination. These effects were recapitulated using multiple clinical PARPi and ATRi in three biologically distinct, clinically-relevant models of DSRCT, including cell lines, a patient-derived xenograft (PDX)-derived organoid model, and a cell line-derived xenograft mouse model. Mechanistically, exposure to a combination of PARPi and ATRi caused increased DNA damage, G2/M checkpoint activation, micronuclei accumulation, replication stress, and R-loop formation. EWS-WT1 silencing abrogated these phenotypes and was epistatic with exogenous expression of the R-loop resolution enzyme RNase H1 in reversing the sensitivity to PARPi and ATRi monotherapies. The combination of PARPi and ATRi also induced EWS-WT1-dependent cell-autonomous activation of the cGAS/STING innate immune pathway and cell surface expression of PD-L1. Taken together, these findings point towards a role for EWS-WT1 in generating R-loop-dependent replication stress that leads to a targetable vulnerability, providing a rationale for the clinical assessment of PARPi and ATRi in DSRCT.

Application of high-throughput drug sensitivity testing in children with relapsed and refractory acute leukemia

To explore the current application of high-throughput drug sensitivity (HDS) testing in children with relapsed and refractory acute leukemia (RR-AL) and analyze the feasibility of salvage treatment plans. A retrospective collection of clinical data from children with RR-AL who underwent HDS testing at the Department of Children's Hematology and Oncology of the First Affiliated Hospital of Zhengzhou University from November 2021 to October 2023 was conducted, followed by an analysis of drug sensitivity results and treatment outcomes. A total of 17 children with RR-AL underwent HDS testing, including 7 cases of relapsed refractory acute myeloid leukemia and 10 cases of relapsed refractory acute lymphoblastic leukemia. The detection rate of highly sensitive chemotherapy drugs/regimens was 53% (9/17), while the detection rate of moderately sensitive chemotherapy drugs/regimens was 100% (17/17). Among the 17 RR-AL patients with highly and moderately sensitive chemotherapy drugs and regimens, the MOACD regimen (mitoxantrone + vincristine + cytarabine + cyclophosphamide + dexamethasone) accounted for 100%, with the highest inhibition rate for single-agent mitoxantrone (94%, 16/17), and the highest inhibition rate for targeted therapy being bortezomib (94%, 16/17). Nine patients adjusted their chemotherapy based on HDS testing results, with 4 undergoing hematopoietic stem cell transplantation. Four patients achieved disease-free survival, while 5 died. Eight patients received empirical chemotherapy, with 2 undergoing hematopoietic stem cell transplantation; 4 achieved disease-free survival, while 4 died. HDS testing can identify highly sensitive drugs/regimens for children with RR-AL, improving the rate of re-remission and creating conditions for subsequent hematopoietic stem cell transplantation.

Clinical utility and accessibility of functional precision medicine for relapsed/refractory pediatric and adult cancers.

1551 Background: Pediatric and adult patients with rare, relapsed, or refractory cancers often have few treatment options. Precision medicine approaches are often the first strategy used to identify salvage therapy options when standard treatments fail. Despite the significant clinical benefit to advanced cancer patients, multiple genomics precision medicine trials have revealed important constraints for patients that lack treatments matched to mutations or biomarkers and have highlighted challenges in drug accessibility associated with novel targeted therapies identified through genomics precision medicine. Current clinical findings from large-scale studies demonstrate ~10% of cancer patients receive clinical benefit from genomics-guided therapies - in part due to limited insight into the complex relationship between tumor molecular characteristics and patient response. Methods: We implemented a functional precision medicine (FPM) approach combining genomic tumor profiling with high-throughput drug sensitivity testing (DST) of FDA-approved agents on patient-derived tumor cells to identify treatment options when standard-of-care is exhausted. Clinical utility and benefit of this program was investigated via a clinical trial (NCT03860376) at Nicklaus Children’s Hospital in Miami, FL. Results: We were returned DST data on 21 of 24 patients DST (median = 102 agents per sample) and genomic profiling on 20 of 24 patients. DST turnaround time was significantly below the 14 days required for clinical use (median = 10 days, p = 0.0012). FPM recommendations were returned to 19 (76%) patients, of which 14 patients underwent therapeutic intervention. Six patients received FPM-guided treatments, and five (83%) patients experienced a >1.3-fold improved progression-free survival over their previous therapy, significantly above the rate from physician’s choice (p = 0.0104). We subsequently opened pan-cancer FPM clinical studies for adults (n = 36 patients) and children (n = 65 patients). A key objective in these trials is optimizing our DST protocol for tissue samples of various sizes. Here, we report preliminary efforts to optimize our DST approach for tissue samples from resections, core biopsies, and fine-needle biopsies from primary and metastatic lesions. Conclusions: The findings from our feasibility study illustrate the potential for FPM to positively impact clinical care for pediatric/adolescent patients with relapsed/refractory cancers, and have supported initiation of currently enrolling clinical studies. An NIMHD-funded expansion cohort now enrolling at Nicklaus Children’s Hospital (NCT05857969, n = 65 patients), and a rare/relapsed/refractory adult patient cohort at Cleveland Clinic Florida (NCT06024603, n = 36 patients). These studies aim to further investigate the impact on clinical outcomes through the use of FPM to recommend treatment options. Clinical trial information: NCT06024603 , NCT05857969 , NCT04956198 , NCT03860376 .

Biomarker development from functional precision medicine datasets via explainable machine learning.

10061 Background: Genomics precision medicine, deployed via tumor panel sequencing, now assists in deploying targeted therapies to cancer patients. Numerous clinical trials have investigated the utility and benefit of genomics precision medicine in multiple cancer indications. Current large-scale studies report actionability rates from ~35% to ~60%, although clinical benefit rates have been shown to be closer to 10%. While this has positively impacted patients in need, the gap between actionability and benefit remains a clinical challenge attributed to multiple factors including the complex, multi-factorial relationship between molecular status and response to therapy. These differences go beyond simple disease states and may be reflective of multiple clinically relevant features including age, sex, and race/ethnicity. Methods: We implemented a functional precision medicine (FPM) program where patients with advanced pediatric cancers were prospectively profiled via high-throughput drug sensitivity testing (DST) of FDA-approved agents on patient-derived tumor cells as well as genomics testing. The objective was to investigate the clinical utility and benefit of FPM guidance in the treatment of pediatric cancer and elucidate the relationship between molecular status of patients’ diseases and treatment responses. We generated DST data (n = 21 patients) and genomic profiling data (n = 20 patients) on pediatric cancer patients in Miami, FL, as well as post-hoc whole exome and transcriptome sequencing data (n = 13 patients) and investigated three specific relationships. Results: We analyzed the relationship between racial/ethnic background and functional response to anti-cancer agents, determining potential differences in response to therapeutic classes. Next, we examined relationships between functional response and cancer type, identifying an unanticipated lack of clustering between disease indications in patients with advanced pediatric cancers. Finally, we applied an explainable machine learning (xML) framework to the functional genomic dataset to develop multi-omics biomarker hypotheses for the chemotherapy agent idarubicin, pinpointing a potential multi-cancer relationship between response to idarubicin and known disease mechanisms in acute myeloid leukemia (AML), the sole indication where idarubicin is approved. We further present additional proof-of-concept studies generating biomarker hypotheses via xML, demonstrating a framework for development of multi-omics biomarkers. Conclusions: We are now expanding our pan-pediatric cancer functional genomics dataset through an NIMHD-funded expansion cohort (NCT05857969, n = 65 patients) to further investigate multi-omics relationships between functional and molecular characteristics and understand the role of race/ethnicity in the complex relationship.

Andrographolide inhibits Burkitt’s lymphoma by binding JUN and CASP3 proteins

BackgroundBurkitt’s lymphoma, one of the most common subtypes of pediatric malignant lymphoma, is notorious for its swift onset, aggressive proliferation, pronounced invasiveness, and marked malignancy. The therapeutic landscape for Burkitt’s lymphoma currently falls short of providing universally effective and tolerable solutions. Andrographolide, a primary active component of Andrographis paniculata, is renowned for its properties of heat-clearing, detoxification, inflammation reduction, and pain relief. It is predominantly used in treating bacterial and viral infections of the upper respiratory tract, as well as dysentery. Various reports highlight the antitumor effects of andrographolide. Yet, its specific impact and the underlying mechanism of action on Burkitt’s lymphoma remain an uncharted area of research.MethodWe employed network pharmacology to pinpoint the targets of andrographolide’s action on Burkitt’s lymphoma and the associated pathways. We then evaluated the impact of andrographolide on Burkitt’s lymphoma using both in vitro and in vivo patient-derived xenograft (PDX) models. Concurrently, we confirmed the molecular targets of andrographolide in Burkitt’s lymphoma through immunofluorescence assays.ResultUtilizing network pharmacology, we identified 15 relevant targets, 60 interrelationships between these targets, and numerous associated signaling pathways for andrographolide’s action on Burkitt’s lymphoma. In vitro efficacy tests using High-throughput Drug Sensitivity Testing and in vivo PDX model evaluations revealed that andrographolide effectively curtailed the growth of Burkitt’s lymphoma. Moreover, we observed a increased in the expression of JUN (c-Jun) and CASP3 (Caspase 3) proteins in Burkitt’s lymphoma cells treated with andrographolide.ConclusionAndrographolide inhibits the growth of Burkitt’s lymphoma by inhibiting JUN and CASP3 proteins.

High-Throughput Screens Identify NEDD8 Inhibition As a Strategy to Augment Natural Killer Cell Cytotoxicity Against Blood Cancers

Natural killer (NK) cell-based therapies are amongst the emerging immunotherapeutic approaches that aim to target malignant cells refractory to standard therapies. Currently used strategies to augment the NK cell anti-cancer function of NK cells include cytokine treatments and the use of feeder expansion protocols for culturing NK cells. Recent studies have indicated that NK cell cytotoxicity and function may also be enhanced by certain anti-cancer drugs. However, the effects of the hundreds of available oncology drugs on NK cell function have not been systematically evaluated. Here, we perform large-scale high-throughput testing of NK cell-drug combinations using co-culture models with diverse blood cancer cells, identifying the NEDD8-activating enzyme inhibitor pevonedistat as a promising candidate for augmenting NK cell anti-cancer responses. To identify oncology drugs synergizing with NK cell-based immunotherapy, we established a high-throughput drug sensitivity and resistance testing (DSRT) platform to investigate effects of 527 approved drugs and investigational compounds on NK cell cytotoxicity against blood cancer cell lines. Overall, 10 cell lines, including acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphoblastic leukemia (ALL), diffuse large B-cell lymphoma (DLBCL), and multiple myeloma (MM), were screened in combination with primary expanded NK cells. Target cells were treated for 24 hours with drugs at five different concentrations both with and without NK cells. In NK cell co-culture, an effector-target (ET) cell ratio at which half of the target cells were killed was selected for experiments. Most effective compounds were then selected for further testing using multiplexed single-cell RNA sequencing (scRNA-seq) and analysis of secreted cytokines (Figure 1). Overall, the results from our DSRT platform demonstrated varying effects of different drug classes on NK cell cytotoxicity against blood cancer cell lines. In general, 5-10% of drugs had NK cell cytotoxicity-enhancing effects, 30-40% inhibited NK function and 35-50% of drugs had no effect. Similarities in results between cell lines highlighted the dependence of NK cell-drug synergistic effects on disease pathobiology. Across multiple disease models, pevonedistat (MLN4924), a selective NEDD8 activating enzyme inhibitor that has been studied as treatment for relapsed/refractory AML, showed strong synergistic effects with NK cells. For example, in OCI-AML-3 (AML), pevonedistat alone showed no effect on target cell viability, but in combination with NK cells at a 1:4 ET ratio, it resulted in 98% target cell killing at 100 nM. Similar effects were also seen in MM1.S (MM), although a higher concentration (10000 nM) of pevonedistat was required (Figure 2). Results from scRNA-seq after combination treatment with NK cells and pevonedistat revealed distinct transcriptomic changes in both NK cells and target cells when compared to controls. In both NK cells and target cells, pevonedistat caused upregulation of TXN, TALDO1, TXNRD1, NQO1, SRXN1 and SLC7A11,collectively indicating effects on the NRF2 signaling pathway. The upregulation of these genes correlated with the tested concentration of pevonedistat, with notably higher expression when treated with 1000 nM pevonedistat compared to 100 nM. Changes were also observed in the secretion of cytokines detected from the cell culture media, where concentrations of IL-1β, IL-2, IL-6, IL-8, IL-10, IFN-γ and TNF-α all increased up to 300% compared to controls. In HEL (AML) and LAMA-84 (CML), where pevonedistat had only minor effects on NK cell cytotoxicity, the expression TNF and TNFRSF1B at baseline and after pevonedistat treatment were notably lower, when compared to cell lines where the combination therapy led to stronger responses. This suggests a possible mechanism for pevonedistat-NK cell synergy, given that previous reports have demonstrated a synergy between pevonedistat and TNF-α to activate apoptosis. In conclusion, we discovered a cell context-specific synergy between pevonedistat and NK cells, which increased NK cell cytotoxicity against malignant cells in vitro. In addition, our results demonstrate the potential of using a high-throughput platform for studying NK cell-drug interactions against malignant cells, while aiming to improve treatment for hematological malignancies through combination immunotherapies.

HDS screening with patient-derived primary cells guided individualized therapy for esophageal squamous cell carcinoma-in vivo and vitro.

To analyze and evaluate the role of the High-throughput Drug Sensitivity (HDS) screening strategy in identifying highly sensitive drugs against esophageal squamous cell carcinoma (ESCC). A total of 80 patients with progressive ESCC were randomly divided into the observation (40 cases) and the control groups (40 cases). In the observation group, primary ESCC cells were isolated from the tumor tissues with a gastroscope, and drug sensitivity screening was performed on cells derived from the 40 ESCC cases using the HDS method, followed by verification in a patient-derived tumor xenograft (PDX) mouse model. Finally, the differences in the therapeutic efficacy (levels of CEA, CYFRA21-1, SCCA after chemotherapy and the rates of overall survival, local progression, and distant metastasis at 12 months and 18 months time points after chemotherapy) were compared between the observation group (Screened drug-treated) and the control group (Paclitaxel combined with cisplatin regimen-treated). Forty ESCC patients were screened for nine different high-sensitive chemotherapeutics, with the majority showing sensitivity to Bortezomib. Experiments on animal models revealed that the tumor tissue mass of PDX mice treated with the HDS-screened drug was significantly lower than that of the Paclitaxel-treated mice (p < 0.05), and the therapeutic efficacy of the observation group was better than the control group (p < 0.05). HDS screening technology can be beneficial in screening high-efficacy anticancer drugs for advanced-stage ESCC patients, thereby minimizing adverse drug toxicity in critically ill patients. Moreover, this study provides a new avenue for treating advanced ESCC patients with improved outcomes.

Abstract B034: Determination of KRAS- and ERK-regulated phosphoproteomes in KRAS-mutant cancers

Abstract Direct inhibitors of mutationally activated KRAS are currently under intense preclinical and clinical development, with one KRASG12C mutant-selective inhibitor approved. However, treatment-associated resistance to KRASG12C inhibitors has been reported, with ~60% of relapsed patients acquiring mutations in signaling components both upstream and downstream, and at the level of RAS itself, that led to reactivation of RAF-MEK-ERK and PI3K-AKT effector pathways. Unexpectedly, we found that ectopic expression of constitutively activated MEK1, ERK1 or ERK2, but not AKT1, drove near-complete resistance to direct inhibitors of KRASG12C or KRASG12D in KRAS-mutant pancreatic ductal adenocarcinoma (PDAC). Despite comprehensive studies, how ERK supports KRAS-dependent cancer growth remains poorly understood. Therefore, we focused on delineating the ERK-dependent phosphoproteome. We treated a panel of six KRAS-mutant PDAC cell lines acutely (1 h) and long-term (24 h) with the highly selective ERK1/2 inhibitor SCH772984. Our proteomics analyses identified 5,117 phosphosites on 2,252 proteins significantly dysregulated by ERK inhibition. We first compared our PDAC ERK phosphoproteome with a recent compendium of published direct/indirect ERK substrates identified in non-PDAC cells and found, surprisingly, only 12% overlap. Thus, our dataset substaintially extends the complexity of ERK-regulated phosphoproteins, in part, reflecting a pancreatic cancer selective profile. To elucidate the kinase network that drives our PDAC ERK-dependent phosphoproteome, we utilized our newly described global atlas of kinase-substrate specificities and reported kinase-substrate interaction datasets. This revealed a highly dynamic kinome dominated by ERK at 1 h, then dominated by ERK-regulation of CDK1-6 cell cycle components and RHO GTPase signaling. Next, we established the subcellular distribution of the PDAC ERK phosphoproteome, then evaluated data from DepMap, and found enrichment of nuclear ERK substrates that displayed strong dependencies in PDAC. We also determined the KRASG12C-regulated phosphoproteome in pancreatic, lung, and colorectal cancer cells using the KRASG12C selective inhibitor MRTX1257. We used our global atlas of kinase-motif specificities and ERK-regulated phosphoproteome to determine KRAS-regulated signaling pathways in KRASG12C mutant cancers. We found a high correlation between KRAS- and ERK-regulated phosphorylations, primarily driven by CDK substrates. However, we also noted key differences, principally in DNA damage response pathways not identified in our ERK-regulated phosphoproteome. Finally, we performed a high-throughput drug sensitivity and resistance screen of (DSRT) comprised of &amp;gt;500 clinically actionable drugs in combination with a KRASG12C inhibitor, and found ERK inhibitors as top hits. In summary, our studies establish a comprehensive profile of KRAS-ERK signaling output that may define new therapeutic targets for targeting KRAS- and ERK-dependent cancer growth. Citation Format: Jennifer E. Klomp, Jeff A. Klomp, Nathaniel J. Diehl, Cole A. Edwards, Kristina Drizyte-Miller, Priya S. Hibshman, Runying Yang, Alexis J. Morales, Khalilah E. Taylor, Mariaelena Pierobon, Emanuel F. Petricoin III, Johnson L. Jared, Emily M. Huntsman, Tomer M. Yaron, Markus Vähä-Koskela, Laura E. Herring, Alex W. Prevatte, Natalie K. Barker, Lee M. Graves, Wennerberg Krister, Lewis C. Cantley, James G. Christensen, Adrienne D. Cox, Channing J. Der, Clint A. Stalnecker. Determination of KRAS- and ERK-regulated phosphoproteomes in KRAS-mutant cancers [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr B034.

PRR15 deficiency facilitates malignant progression by mediating PI3K/Akt signaling and predicts clinical prognosis in triple-negative rather than non-triple-negative breast cancer

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast neoplasms with a higher risk of recurrence and metastasis than non-TNBC. Nevertheless, the factors responsible for the differences in the malignant behavior between TNBC and non-TNBC are not fully explored. Proline rich 15 (PRR15) is a protein involved in the progression of several tumor types, but its mechanisms are still controversial. Therefore, this study aimed to investigate the biological role and clinical applications of PRR15 on TNBC. PRR15 gene was differentially expressed between TNBC and non-TNBC patients, previously described as an oncogenic factor in breast cancer. However, our results showed a decreased expression of PRR15 that portended a favorable prognosis in TNBC rather than non-TNBC. PRR15 knockdown facilitated the proliferation, migration, and invasive ability of TNBC cells in vitro and in vivo, which was abolished by PRR15 restoration, without remarkable effects on non-TNBC. High-throughput drug sensitivity revealed that PI3K/Akt signaling was involved in the aggressive properties of PRR15 silencing, which was confirmed by the PI3K/Akt signaling activation in the tumors of PRR15Low patients, and PI3K inhibitor reversed the metastatic capacity of TNBC in mice. The reduced PRR15 expression in TNBC patients was positively correlated with more aggressive clinicopathological characteristics, enhanced metastasis, and poor disease-free survival. Collectively, PRR15 down-regulation promotes malignant progression through the PI3K/Akt signaling in TNBC rather than in non-TNBC, affects the response of TNBC cells to antitumor agents, and is a promising indicator of disease outcomes in TNBC.

Abstract 2912: High-throughput screening and single-cell transcriptomics identify synergies between oncology drugs and natural killer cell immunotherapy

Abstract Background &amp; Objective: Natural killer (NK) cell-based immunotherapies are emerging therapeutic approaches that aim to target malignant cells resistant to conventional treatments and T cell-based immunotherapies. Existing oncology drugs may enhance the anti-cancer function of NK cells, although large-scale high-throughput testing of NK cell-drug combinations has not been previously attempted. Our objective was to evaluate the potential of approved and investigational oncology drugs to synergize with NK cell-based immunotherapy in acute myeloid leukemia (AML), with the aim to discover both potentiating and inhibiting compounds. Methods: A high-throughput drug sensitivity and resistance screen including 528 oncology drugs was combined with expanded NK cells to evaluate their cytotoxicity against luciferase-expressing AML cells (MOLM-14). The most prominent drugs were investigated further with single-cell RNA sequencing to reveal underlying biological mechanisms. Results: Overall, 191 drugs had an inhibitory effect on cytotoxicity, 294 had no effect, and 43 had an enhancing effect. The most notable NK cell cytotoxicity-potentiating drugs were pevonedistat (NEDD8 inhibitor), daporinad (NAMPT inhibitor), and JAK inhibitors. These drugs also induced distinct changes in NK and target cell transcriptional profiles. When combined with NK cells, pevonedistat and daporinad induced an upregulation of HLA-E and CXCL10 in target cells. In addition, MYC and FLT3 proto-oncogenes were downregulated in target cells when combining NK cells with pevonedistat. Moreover, in NK cells, daporinad induced dysregulated expression of genes related to NK cell effector functions such as TYROBP, TXNIP and KLRC1. Treatment with JAK inhibitors downregulated MHC I expression on target cells, providing a putative mechanism for increased NK cell activity. Validation of key hits is ongoing in additional AML cell lines. Conclusion: We discovered novel drugs with both potentiating and inhibiting effects on NK cell cytotoxicity against AML cells in vitro. Our results demonstrate the potential of using a high-throughput framework for studying NK cell-drug interactions against malignant cells, while aiming to improve treatment for AML and other malignancies through combination immunotherapies. Citation Format: Jonas O. Bouhlal, Petra Nygren, Essi Laajala, Aleksandr Ianevski, Jay Klievink, Hanna Lähteenmäki, Khalid Saeed, Dean Lee, Tero Aittokallio, Olli Dufva, Satu Mustjoki. High-throughput screening and single-cell transcriptomics identify synergies between oncology drugs and natural killer cell immunotherapy [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 2912.

Abstract 3399: Tumor organoid based drug sensitivity testing in ovarian cancer identifies exceptional responders to targeted therapies

Abstract Background: Over 50% of patients with ovarian cancer (OVCA) succumb to their disease within five years from diagnosis, highlighting the need for new approaches to identify therapeutic options. The PARIS® test is a CLIA certified organoid based high throughput drug sensitivity assay that can be used by oncologists to select personalized treatments. In this study our objectives were to: 1) demonstrate the feasibility of organoid based drug testing in the clinical setting; 2) highlight the clinical utility and the predictive value of the PARIS® test; and 3) identify new therapeutic options for OVCA patients. Methods: 93 patients, with a median age at diagnosis of 55 years (range 25-82) were selected as eligible for the PARIS® test at the discretion of the oncologists. The cohort included 74.1% high grade serous tumors, 6.9% low grade serous tumors, 6.0% clear cell carcinomas, 3.4% granulosa cell tumors, 2.5% Mullerian tumors, 1.7% carcinosarcomas and 2.5% fallopian tumors. 16.1% of patients were treatment naïve and 83.9% received one or more previous lines of treatment. 116 patient derived tumor organoids (PDTOs) were derived from surgical excisions, biopsies, or body fluids and subjected to functional testing with a panel of chemo- and targeted therapies that are FDA-approved or in clinical development. Drug responses were evaluated using a proprietary score ranking drugs from exceptional responses to no response. The median turnaround time from biopsy to report delivery was 19 days. Results: The success rate for deriving OVCA organoids was 92%; 81.0% of samples demonstrated exceptional/good response to at least one drug. PDTO drug sensitivities were highly concordant with both retrospective and prospective clinical response. Drugs that frequently showed exceptional/good responses included WEE1 inhibitors (28.4%), HDAC inhibitors (25.0%), and Pan-DNMT inhibitors (11.2%). Further, 12.9% of cases showed responses to the BTK/EGFR inhibitor ibrutinib and 23.3% to HER2 inhibitors lapatinib and neratinib. Two patients with advanced stage, recurrent low grade serous ovarian cancer showed exceptional and durable clinical responses to PARIS® guided treatments, ibrutinib and lapatinib, respectively. Conclusions: This study demonstrates the utility of organoid based drug testing to identify potentially effective drugs and to guide treatment choice for patients with ovarian cancer. Tumor organoid based personalized treatments lead to extraordinary responses in several patients, including a patient in hospice care who responded to ibrutinib monotherapy and is still alive after 27 months. Citation Format: Amanda M. Prechtl, Marwah Al-Aloosi, Payel Chatterjee, Rachele Rosati, Samantha Velazquez, Lauren Appleyard, Grace Durenberger, Cristina Cordero, Robert Diaz, Hallie Swan, Brady Bernard, Siddhartha Mukherjee, Barbara Goff, Elizabeth Swisher, Heidi Gray, Kalyan Banda, Christopher Kemp, Carla Grandori. Tumor organoid based drug sensitivity testing in ovarian cancer identifies exceptional responders to targeted therapies [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 3399.

Abstract 5507: A potential combinatorial treatment strategy to overcome olaparib resistance in high-grade ovarian cancer

Abstract PARP1 inhibitors have evolved the treatment of BRCA1/2-mutated high-grade serous ovarian cancer. However, its resistance is frequently observed. In our initial combinatorial drug screening, OSU-03012 (AR-12) appeared as a promising drug to be combined with PARP inhibitor Olaparib in multiple ovarian cancer cell lines, regardless of BRCA mutation status. OSU-03012 is designed as an orphan drug with anti-microbial activity. It has also shown cell-context-dependent anti-cancer activity. Using imaging-based high-throughput drug sensitivity analysis, we found that OSU-03012 and BX-912, while both classified as 3-Phosphoinositide Dependent Protein Kinase 1 (PDK-1) inhibitors, not only differed in their synergistic effect together with Olaparib, also caused distinct phenotypic changes in ovarian cancer cells. Cell senescence was observed in BX-912 but not OSU-03012 treatment, alone or together with Olaparib. Recently, dihydroorotate dehydrogenase (DHODH) has been identified as a secondary target of OSU-03012, which explains its anti-cancer activity by regulating nucleotide metabolism and thus affecting DNA repair. However, in our study, OSU-03012 did not similarly affect cell viability and phenotype on ovarian cancer cell lines as a DHODH inhibitor BAY2402234. Interestingly, compared to BX-912 and BAY2402234, OSU-03012 showed higher selectivity on ovarian cancer cell lines over normal epithelial carrying BRCA and TP53 mutations; it also exhibited reduced toxicity on a human fibroblast cell line. We are further clarifying the putative targets of OSU-03012 using thermal proteome profiling. To investigate the molecular evidence of OSU-03012 for treating ovarian cancer, we performed a differential gene expression analysis using Genomics of Drug Sensitivity in Cancer (GDSC) database. All ovarian cancer cell lines included in GDSC drug screening are classified as Olaparib- or OSU-03012-sensitive/insensitive, based on the respective IC50 threshold. We found that OSU-03012 sensitivity is positively associated with several known genes regulating ovarian cancer progression, such as LUM and COL3A1, as well as genes (e.g., PTPRZ1) that are associated with Olaparib insensitivity in this analysis. Interestingly, angiogenesis signatures were found to be enriched in both Olaparib and OSU-03012-sensitive cancer cell lines. We are currently establishing a cancer-vascular cell system in a microfluidic setting to study how such combinatorial drug treatment would connect to tumor microenvironment remodeling. Altogether, we identified a potential non-cancer drug for ovarian cancer treatment and to overcome Olaparib resistance. A multidisciplinary approach highlights the importance of drug target profiling and sensitivity signatures scoring to improve treatment stratification. Citation Format: Jie Bao, Eva Daniela Mendoza Ortiz, Jessica Agudelo, Roman Filimonov, Anniina Färkkilä, Jing Tang. A potential combinatorial treatment strategy to overcome olaparib resistance in high-grade ovarian cancer. [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 5507.

Novel therapeutic approaches for pleural mesothelioma identified by functional ex vivo drug sensitivity testing

ObjectivesPleural mesothelioma (PM) is an aggressive malignancy with limited treatment options. The first-line therapy has remained unchanged for two decades and consists of pemetrexed in combination with cisplatin. Immune-checkpoint inhibitors (nivolumab plus ipilimumab) have high response rates, resulting in recent updates in treatment recommendations by the U.S. Food and Drug Administration. However, the overall benefits of combination treatment are modest, suggesting that other targeted therapy options should be investigated. Materials and MethodsWe employed high-throughput drug sensitivity and resistance testing on five established PM cell lines using 527 cancer drugs in a 2D setting. Drugs of the greatest potential (n = 19) were selected for further testing in primary cell models derived from pleural effusions of seven PM patients. ResultsAll established and primary patient-derived PM cell models were sensitive to the mTOR inhibitor AZD8055. Furthermore, another mTOR inhibitor (temsirolimus) showed efficacy in most of the primary patient-derived cells, although a less robust effect was observed when compared with the established cell lines. Most of the established cell lines and all patient-derived primary cells exhibited sensitivity to the PI3K/mTOR/DNA-PK inhibitor LY3023414. The Chk1 inhibitor prexasertib showed activity in 4/5 (80%) of the established cell lines and in 2/7 (29%) of the patient-derived primary cell lines. The BET family inhibitor JQ1 showed activity in four patient-derived cell models and in one established cell line. ConclusionmTOR and Chk1 pathways had promising results with established mesothelioma cell lines in an ex vivo setting. In patient-derived primary cells, drugs targeting mTOR pathway in particular showed efficacy. These findings may inform novel treatment strategies for PM.

Abstract P4-08-17: Repurposing proteasome inhibitors for improved treatment of triple-negative breast cancer

Abstract Background: The de novo drug development process is expensive and challenging, with a high risk of failure. Drug repurposing can ideally identify novel therapeutic indications for FDA-approved drugs with pre-existing pre-clinical and clinical evidence. Both aspirin and tamoxifen drugs are good examples of successful drug repurposing in oncology. Although proteasome inhibitors such as bortezomib and carfilzomib are currently only used to treat multiple myeloma and basal cell lymphoma, we and others have shown that triple-negative breast cancer (TNBC) is particularly sensitive to proteasome inhibition. TNBC is an aggressive form of breast cancer with an urgent need for novel treatment options. Here, we evaluate the potency of proteasome inhibitors and other clinically relevant chemotherapeutic agents on TNBC cell lines. Methods: We performed a high-throughput drug sensitivity screen with eight cell lines representing the four TNBC subtypes (basal-like 1: HCC70 and MDA-MB-468; basal-like 2: HCC1806 and MDA-MB-436; mesenchymal-like: BT-549 and HCC38; luminal androgen receptor: CAL-148 and MDA-MB-435) and MCF-7 as control (estrogen and progesterone receptor-positive) exposed to 18 drugs (11 proteasome inhibitors, 2 mitosis inhibitors, 2 topoisomerase inhibitors, and 3 platinum agents) for 24 hours. Drug potency was determined using the IC50, GR50, GRmax drug metrics. IDACombo was then used to predict efficacious drug combinations, followed by calculation of synergistic drug combinations with SynergyFinder. Results: TNBC cell lines were generally more sensitive to proteasome inhibitors with significantly reduced cell viability than clinically relevant drugs, e.g. paclitaxel. Although the potency of different proteasome inhibitors varied, the most potent proteasome inhibitors included bortezomib, carfilzomib, delanzomib, epoxomicin, and MLN-2238. According to the GR50 values, HCC38 (range, 8.2-382.7 nM) and MDA-MB-468 (range, 10.8-110.6 nM) were most sensitive to proteasome inhibition, whereas the least sensitive TNBC cell lines were HCC1806 (range, 289.9-Inf nM) and BT-549 (range, 101.0-Inf nM). Using the drug sensitivity screening results for single drugs, IDACombo predicted potent drug combinations for different combinations of bortezomib, carboplatin, carfilzomib, delanzomib, docetaxel, doxorubicin, epirubicin, epoxomicin, MLN-2238, MLN-9708, and nedaplatin. Conclusions: In summary, some proteasome inhibitors (e.g. bortezomib) had a substantial impact on TNBC cell survival. These findings indicate that proteasome inhibitors, together with other forms of chemotherapy, may be further explored as a novel complement treatment for TNBC. Citation Format: Peter Larsson, Daniella Pettersson, Maxim Olsson, Eva Forssell-Aronsson, Anikó Kovács, Per Karlsson, Khalil Helou, Toshima Z. Parris. Repurposing proteasome inhibitors for improved treatment of triple-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-08-17.

Feasibility of high-throughput drug sensitivity screening (HDS)-guided treatment for children with refractory or relapsed acute myeloid leukemia.

Relapsed/refractory (rel/ref) acute myeloid leukemia (AML) has a very high mortality rate. At present, hematopoietic stem cell transplantation (HSCT) is the most effective treatment for rel/ref AML. The remission of the primary disease before HSCT is crucial for the transplantation to be effective. Therefore, it is critical to choose a suitable type of chemotherapy before HSCT. Here, we recorded the outcomes of high-throughput drug sensitivity screening (HDS) in children with rel/ref AML. Thirty-seven pediatric rel/ref AML patients who received HDS from September 2017 until July 2021 were analyzed retrospectively. Most of the patients (24 patients, 64.9%) had adverse cytogenetics. Two patients had rel/ref AML with central nervous system leukemia. The complete remission (CR) rate was 67.6%. Eight patients developed IV grade bone marrow suppression. Twenty-three patients (62.2%) underwent HSCT. The 3-year overall survival (OS) and EFS rates were 45.9% and 43.2%, respectively. Infection in the myelosuppression stage was the main cause of death. The outcome of HDS was superior to the commonly reported rates. These results suggest that HDS may be a novel treatment option for pediatric patients with rel/ref AML, and it is a promising transitional regimen prior to HSCT.

Multiomics characterization implicates PTK7 in ovarian cancer EMT and cell plasticity and offers strategies for therapeutic intervention

Most patients with ovarian cancer (OC) are diagnosed at a late stage when there are very few therapeutic options and a poor prognosis. This is due to the lack of clearly defined underlying mechanisms or an oncogenic addiction that can be targeted pharmacologically, unlike other types of cancer. Here, we identified protein tyrosine kinase 7 (PTK7) as a potential new therapeutic target in OC following a multiomics approach using genetic and pharmacological interventions. We performed proteomics analyses upon PTK7 knockdown in OC cells and identified novel downstream effectors such as synuclein-γ (SNCG), SALL2, and PP1γ, and these findings were corroborated in ex vivo primary samples using PTK7 monoclonal antibody cofetuzumab. Our phosphoproteomics analyses demonstrated that PTK7 modulates cell adhesion and Rho-GTPase signaling to sustain epithelial-mesenchymal transition (EMT) and cell plasticity, which was confirmed by high-content image analysis of 3D models. Furthermore, using high-throughput drug sensitivity testing (525 drugs) we show that targeting PTK7 exhibited synergistic activity with chemotherapeutic agent paclitaxel, CHK1/2 inhibitor prexasertib, and PLK1 inhibitor GSK461364, among others, in OC cells and ex vivo primary samples. Taken together, our study provides unique insight into the function of PTK7, which helps to define its role in mediating aberrant Wnt signaling in ovarian cancer.

Application of High-Efficiency Cell Expansion and High-Throughput Drug Sensitivity Screening for Leukemia Treatment.

This study is to assess the clinical value of in vitro primary cell high-efficiency expansion and high-throughput drug sensitivity screening (HEHDS) system in leukemia, and we evaluated a cohort of 121 patients with acute myeloid leukemia (AML) and 27 patients with acute lymphoblastic leukemia (ALL) using HEHDS. Bone marrow aspirates were collected from patients with leukemia. Purified leukemic cancer cells were obtained, cultured, and screened with a panel of 247 FDA-approved compounds by HEHDS technology. Ninety-six patients received HEHDS-guided therapy while 52 patients who were subjected to physician directed therapy served as controls. ALL patients who received treatment guided by HEHDS showed higher rate of complete remission (CR) than that of patients in the non-HEHDS group (90.91% vs. 56.25%). Similarly, AML patients received HEHDS-guided therapy were found to have greater CR rate, when compared with patients who received physician-directed therapy (45.88% vs. 25%). There was a significantly higher rate of CR in HEHDS-guided therapy group compared to the non-HEHDS group. The application of HEHDS could be beneficial for leukemia treatment.

Gambogic acid suppresses nasopharyngeal carcinoma via rewiring molecular network of cancer malignancy and immunosurveillance.

Nasopharyngeal carcinoma (NPC) is a malignant tumor highly prevalent in Southeast Asia. The distant metastasis and disease recurrence are still unsolved clinical problems. In recent years, traditional Chinese medicine (TCM) monomers have become significantly attractive due to their advantages. Using high throughput drug sensitivity screening, we identified gambogic acid (GA) as a common TCM monomer displaying multiple anti-NPC effects. GA could effectively inhibit the proliferation of low differentiated cells and highly metastatic cells in NPC via inducing apoptosis and G2/M cell cycle arrest. In addition, GA obviously repressed the abilities of cell clone, migration, invasion, angiogenesis and represented satisfied synergistic effects combined with chemotherapy. Importantly, we found the elevated immune checkpoint CD47 stimulated after chemotherapy was dramatically impaired by GA treatment. Mechanically, the network pharmacology analyses unraveled that the oncogenic signaling pathways including STATs were rewired by GA treatment. Taken together, our study reveals a molecular basis and provides a rationale for GA application as the treatment regime in NPC therapy in future.

Correlation between Immunohistochemical Markers in Hepatocellular Carcinoma Cells and In Vitro High-Throughput Drug Sensitivity Screening.

Aim This study analyzed the correlation between immunohistochemical markers in hepatocellular carcinoma cells and the results of in vitro high-throughput drug sensitivity screening, to provide a reference for individualized drug treatment in patients with liver cancer. Methods Seventy-four patients with hepatocellular carcinoma were included in this study from December 2019 to June 2021, and their liver cancer cells were used for in vitro high-throughput drug sensitivity screening. According to the screening results, the patients were divided into relatively sensitive and insensitive groups, and the correlations between sensitivity and immunohistochemistry results were analyzed statistically. Results Alpha-fetoprotein (AFP)-positive liver cancer cells were significantly more sensitive to gemcitabine than AFP-negative cells (χ2 = 6.102, P=0.014). AFP was also positively correlated with sensitivity of liver cancer cells to three combined regimens containing oxaliplatin (L-OHP) and epirubicin (EPI) : L-OHP + EPI + irinotecan + 5-fluorouracil (5-FU), L-OHP + irinotecan + EPI, and L-OHP + EPI (χ2 = 8.168, P=0.004, χ2 = 5.705, P=0.017, and χ2 = 8.275, P=0.004, respectively). Conclusion Gemcitabine and L-OHP + EPI + irinotecan + 5-FU, L-OHP + EPI, and L-OHP + irinotecan + EPI were more effective against AFP-positive compared with AFP-negative liver cancer cells according to in vitro high-throughput drug sensitivity screening. These results may guide the selection of personalized drug treatments for patients with advanced liver cancer in the future but still need further clinical studies to confirm.

High-throughput ex vivo drug testing identifies potential drugs and drug combinations for NRAS-positive malignant melanoma

Therapy options for patients with metastatic melanoma (MM) have considerably improved over the past decade. However, many patients still need effective therapy after unsuccessful immunotherapy, especially patients with BRAF-negative tumors who lack the option of targeted treatment second line. Therefore, the elucidation of efficient and personalized therapy options for these patients is required. In this study, three patient-derived cancer cells (PDCs) were established from NRAS Q61-positive MM patients. The response of PDCs and five established melanoma cell lines (two NRAS-positive, one wild type, and two BRAF V600-positive) was evaluated toward a panel of 527 oncology drugs using high-throughput drug sensitivity and resistance testing. The PDCs and cell lines displayed strong responses to MAPK inhibitors, as expected. Additionally, the PDCs and cell lines were responsive to PI3K/mTOR, mTOR, and PLK1 inhibitors among other effective drugs currently undergoing clinical trials. Combinations with a MEK inhibitor were tested with other targeted agents to identify effective synergies. MEK inhibitor showed synergy with multikinase inhibitor ponatinib, ABL inhibitor nilotinib, PI3K/mTOR inhibitor pictilisib, and pan-RAF inhibitor LY3009120. The application of the patients’ cancer cells for functional drug testing ex vivo is one step further in the process of identifying potential agents and agent combinations to personalize treatment for patients with MM. Our preliminary study results suggest that this approach has the potential for larger-scale drug testing and personalized treatment applications in our expansion trial. Our results show that drug sensitivity and resistance testing may be implementable in the treatment planning of patients with MM.