Oncology Therapeutic Development Research Articles

Prediction of therapeutic response and cancer outcomes in solid tumours via in silico clinical trials.

e13603 Background: Oncology therapeutic development has high failure rates with substantial costs. Advances in technology, including molecular characterisations of cancer and computational power, provide the opportunity to better model therapeutic response for existing and emerging therapies. Methods: Concr adapted Bayesian statistical principles used by astrophysicists to effectively integrate multi-dimensional data (genomic & transcriptomic) for accurate modelling of cancer biology. Our proprietary computational framework was applied to predict clinical response and survival through construction of digital twins and in silico simulations of clinical trials. Predicted log odds ratios (LOR) were generated for drug response and compared to published data from 8 suitable historical clinical trials. Three distinct models underpin this framework: Drug Efficacy, Treatment Response & Overall Survival (OS). Three publicly available datasets were used for training: Cancer Therapeutic Response Portal ( in vitro dose-response data), Cancer Cell Line Encyclopaedia and TCGA. Results: For all 8 clinical studies, the digital twin model accurately simulated both trial arms, compared drug efficacy across arms and predicted which treatment was most active. Unblinded evaluation: Our model accurately predicted gemcitabine would have greater clinical benefit than 5-FU (LOR -0.10, P <0.0001) in metastatic pancreatic cancer. In advanced breast cancer, the model predicted docetaxel had a higher response rate than doxorubicin, and carboplatin response rates were similar to docetaxel in BRCA wild-type patients. In platinum-sensitive recurrent ovarian cancer, the model predicted cisplatin-based combination had a higher response rate than paclitaxel. Blinded evaluation: Using data for paclitaxel, the model correctly predicted that nab-paclitaxel+gemcitabine response rates were higher than gemcitabine in metastatic pancreatic cancer (predicted LOR -0.090, p = <0.001). In all 3 early breast cancer studies, predictions mirrored clinical trial results, adjuvant ECF > CMF, adjuvant TC > AC and adjuvant tamoxifen was superior to capecitabine. The underlying pan-tumour Overall Survival model used a Random Survival Forest approach, trained on 23 cancers with predictive accuracy of 0.78 AUC ROC and C-index 0.71. To enable cohort enrichment for drug response, the model segmented patient cohorts into treatment responder and non-responder. Using this approach, the log odds increased for drug response rate for 16 of the 19 different cancers and 14 of the different 17 drugs. Conclusions: Our digital twin model represents transformative technology for clinical trial simulation with strong potential for accelerating and de-risking clinical drug development, and utility for synthetic control arms.

An NGS-based assay for accurate detection and quantification of immune gene expression in mouse tumor models.

Tumor microenvironment (TME) is a complex dynamic system with many tumor-interacting components including tumor-infiltrating leukocytes (TILs), cancer associated fibroblasts, blood vessels, and other stromal constituents. It intrinsically affects tumor development and pharmacology of oncology therapeutics, particularly immune-oncology (IO) treatments. Accurate measurement of TME is therefore of great importance for understanding the tumor immunity, identifying IO treatment mechanisms, developing predictive biomarkers, and ultimately, improving the treatment of cancer. Here, we introduce a mouse-IO NGS-based (NGSmIO) assay for accurately detecting and quantifying the mRNA expression of 1080 TME related genes in mouse tumor models. The NGSmIO panel was shown to be superior to the commonly used microarray approach by hosting 300 more relevant genes to better characterize various lineage of immune cells, exhibits improved mRNA and protein expression correlation to flow cytometry, shows stronger correlation with mRNA expression than RNAseq with 10x higher sequencing depth, and demonstrates higher sensitivity in measuring low-expressed genes. We describe two studies; firstly, detecting the pharmacodynamic change of interferon-γ expression levels upon anti-PD-1: anti-CD4 combination treatment in MC38 and Hepa 1-6 tumors; and secondly, benchmarking baseline TILs in 14 syngeneic tumors using transcript level expression of lineage specific genes, which demonstrate effective and robust applications of the NGSmIO panel.

Aligning Germline Cancer Predisposition With Tumor-Based Next-Generation Sequencing for Modern Oncology Diagnosis, Interception, and Therapeutic Development.

In the era of precision medicine, genomic interrogation for identification of both germline and somatic genetic alterations has become increasingly important. While such germline testing was usually undertaken via a phenotype-driven single-gene approach, with the advent of next-generation sequencing (NGS) technologies, the widespread utilization of multigene panels, often agnostic of cancer phenotype, has become a commonplace in many different cancer types. At the same time, somatic tumor testing in oncology performed for the purpose of guiding therapeutic decisions for targeted therapies has also rapidly expanded, recently starting to incorporate not just patients with recurrent or metastatic cancer but even patients with early-stage disease. An integrated approach may be the best approach for the optimal management of patients with different cancers. The lack of complete congruence between germline and somatic NGS tests does not minimize the power or importance of either, but highlights the need to understand their limitations so as not to overlook an important finding or omission. NGS tests built to more uniformly and comprehensively evaluate both the germline and tumor simultaneously are urgently required and are in development. In this article, we discuss approaches to somatic and germline analyses in patients with cancer and the knowledge gained from integration of tumor-normal sequencing. We also detail strategies for the incorporation of genomic analysis into oncology care delivery models and the important emergence of poly(ADP-ribose) polymerase and other DNA Damage Response inhibitors in the clinic for patients with cancer with germline and somatic BRCA1 and BRCA2 mutations.

A novel heterophilic graph diffusion convolutional network for identifying cancer driver genes.

Identifying cancer driver genes plays a curial role in the development of precision oncology and cancer therapeutics. Although a plethora of methods have been developed to tackle this problem, the complex cancer mechanisms and intricate interactions between genes still make the identification of cancer driver genes challenging. In this work, we propose a novel machine learning method of heterophilic graph diffusion convolutional networks (called HGDCs) to boost cancer-driver gene identification. Specifically, HGDC first introduces graph diffusion to generate an auxiliary network for capturing the structurally similar nodes in a biomolecular network. Then, HGDC designs an improved message aggregation and propagation scheme to adapt to the heterophilic setting of biomolecular networks, alleviating the problem of driver gene features being smoothed by its neighboring dissimilar genes. Finally, HGDC uses a layer-wise attention classifier to predict the probability of one gene being a cancer driver gene. In the comparison experiments with other existing state-of-the-art methods, our HGDC achieves outstanding performance in identifying cancer driver genes. The experimental results demonstrate that HGDC not only effectively identifies well-known driver genes on different networks but also novel candidate cancer genes. Moreover, HGDC can effectively prioritize cancer driver genes for individual patients. Particularly, HGDC can identify patient-specific additional driver genes, which work together with the well-known driver genes to cooperatively promote tumorigenesis.

Exploration of the inhibition action of TPGS on tumor cells and its combined use with chemotherapy drugs

D-alpha-tocopheryl polyethylene glycol 1000 succinate (TPGS) is a commonly used nonionic surfactant used as a pharmaceutical carrier in different drug delivery systems. TPGS can reverse P-glycoprotein (P-gp)-mediated multidrug resistance (MDR) and also has anticancer activities. It suggests that when designing antitumor drug preparation, it’s necessary to take into account the antitumor activity of TPGS. Our in vivo studies showed that TPGS exerted the strongest cytotoxicity in MCF-7-ADR cells when compared with seven other tumor cell lines. The further study revealed TPGS caused apoptosis and blocked MCF-7 cell growth in G2/M phase. Mechanistic insights suggested that TPGS increased intracellular calcium ion concentrations, leading to apoptosis via the mitochondrial pathway. Furthermore, two in vivo experiments were performed. One was TPGS, and DOX solution was administered by tail vein injection on MCF-7-ADR tumor bearing nude mice. The other was temperature sensitive TPGS gel (TPGS-TG) was administered by intratumoral injection on MCF-7-ADR tumor bearing nude mice combined with paclitaxel albumin nanoparticles (Abraxane®) administered by tail vein injection. The findings confirmed that TPGS could play its role in anti-tumor to reduce the toxicity of chemotherapeutic drugs and improve the efficiency of drug-resistant tumors, thereby enhancing the development of safe oncology therapeutics.

297 (PB077) - CAR T cells in marginal zone lymphoma (MZL) models with acquired resistance to PI3K and BTK inhibitors

Background. MZLs are characterized by an indolent course with median survival over 10 years. However, relapses/progressions are common and if they occur during the during the first 2 years, they heavily impact the median survival. Among the 23 relapsed/refractoryMZL patients treated with the anti-CD19 CAR-T cells axicabtagene ciloleucel (Axi-Cel), the overall response rate was 83% with 73% of complete responses (Jacobson, Lancet Onc 2022; Neelapu, ASH2021). We previously presented MZL-derived models with secondary resistance to BTK/PI3K inhibitors, observing, in some of the resistant cells, an increase in CD19 levels and higher sensitivity to the anti-CD19 loncastuximab tesirine antibody drug conjugate (Arribas, ASH2019, ENA2019, Haematologica 2022). Here, we tested CAR-T cells with costimulatory receptors CD28 or 4-1BB (28z CAR-T and BBz CAR-T), representative of Axi-Cel and tisagenlecleucel (Tisa-Cel), respectively, in these models. Methods: CD19-specific 28z CAR-T and BBz CAR-T produced from 4 healthy donors with retroviral vectors. Transduction efficacy evaluated by protein L staining. MZL models of secondary resistance to PI3K/BTK inhibitors and their parental cells cocultured for 48 h with CAR-T cells (1:1 E: T ratio) after adjusting for transduction efficacy. CAR-T cell-mediated cytotoxicity (CX) calculated as percentage of cell death compared to tumor cells cultured alone. CD19 expression determined by flow cytometry (protein) and RNA-Seq (RNA). Results. We first tested 28z CAR-T and BBz CAR-T against the VL51 cell line and in the 2 derivatives, resistant to various PI3K inhibitors and ibrutinib, respectively. Median CX against parental was 24% and 29% with 28z or BBz CAR-T, respectively. CX was significantly increased against PI3K resistant cells, with a median CX of 62% after coculture with 28z CAR-T and 55% with BBz CAR T cells. Ibrutinib resistant VL51 cells displayed an even higher sensitivity to CAR-T cell killing, with a median CX of 68% after co-culture with 28z CAR-T and 79% with BBz CAR-T cells. Differently from VL51, both parental Karpas1718 and PI3K resistant derivative were equally sensitive to CAR-T cells, with a median 28z CAR-T CX of 72% against parental and 72% against PI3K resistant Karpas1718. Similar results were observed after coculture with BBz CAR-T cells (median CX 67% against parental and 66% against PI3K resistant Karpas1718). The results agreed with CD19 levels, higher in Karpas1718 (parental and derivative) and in the resistant VL-51 derivatives than in parental VL51. Conclusions: Anti-CD19 28z and BBz CAR-T showed maintained or even increased in vitro antitumor activity in MZL models after acquisition of secondary resistance to PI3K/BTK inhibitors. The data support exploring CD19 directed therapeutic modalities for MZL patients. FS, FB: co-senior authors. Work supported by Barletta and Henriette Meyer Foundations. Conflict of interest: Advisory Board: Gilead, AbbVie, Janssen, AstraZeneca, MSD, BMS/ Celgene, Roche, Mei Pharma, Astra Zeneca, Celltrion Healthcare, Incyte, Kite/Gilead. Corporate-sponsored Research: Celgene, Roche, Janssen, Acerta, ADC Therapeutics, Bayer AG, Cellestia, CTI Life Sciences, EMD Serono, Helsinn, ImmunoGen, Menarini Ricerche, NEOMED Therapeutics 1, Nordic Nanovector ASA, Oncology Therapeutic Development, PIQUR Therapeutics AG, Gilead, AbbVie, Janssen.

Pan-cancer proteomic map of 949 human cell lines.

SummaryThe proteome provides unique insights into disease biology beyond the genome and transcriptome. A lack of large proteomic datasets has restricted the identification of new cancer biomarkers. Here, proteomes of 949 cancer cell lines across 28 tissue types are analyzed by mass spectrometry. Deploying a workflow to quantify 8,498 proteins, these data capture evidence of cell-type and post-transcriptional modifications. Integrating multi-omics, drug response, and CRISPR-Cas9 gene essentiality screens with a deep learning-based pipeline reveals thousands of protein biomarkers of cancer vulnerabilities that are not significant at the transcript level. The power of the proteome to predict drug response is very similar to that of the transcriptome. Further, random downsampling to only 1,500 proteins has limited impact on predictive power, consistent with protein networks being highly connected and co-regulated. This pan-cancer proteomic map (ProCan-DepMapSanger) is a comprehensive resource available at https://cellmodelpassports.sanger.ac.uk.

Abstract 1612: Comparative oncology analysis of canine cancer by tumor and liquid biopsy testing for biomarker and therapeutic discovery in humans and dogs

Abstract Human and canine cancers share a high level of homology. Characterizing their respective genomic landscapes can expand the knowledge base of comparative oncology and support biomarker discovery and therapeutic development for the benefit of both species. Genomic profiling via tumor biopsy infers risk to the patient in both human and veterinary medicine and is often complicated by tumor heterogeneity. Blood-based liquid biopsy has been shown to open new opportunities to profile the cancer genome noninvasively in both species. The goal of this study was to benchmark the occurrence of homologous genomic variants in a variety of canine cancers that have a counterpart in humans, including lymphoma (B-cell and T-cell), soft-tissue sarcoma, osteosarcoma, and melanoma, among others, utilizing tumor and liquid biopsy profiling. The study was performed in a prospective cohort of over 300 client-owned dogs that received a confirmed cancer diagnosis either at the time of enrollment or after sample collection. A blood sample was collected prior to biopsy or surgical resection of the tumor to evaluate the use of liquid biopsy to noninvasively profile the cancer genome. Tumor tissue samples were collected at the time of surgical resection. In a subset of the subjects, blood samples were collected 3 to 30 days following surgical removal of the tumor, and longitudinally during cancer therapy and monitoring. The Cancer Gene Census (CGC) and COSMIC databases were interrogated, and a high degree of homology (>90%) between human and canine oncogenes and tumor suppressor genes was observed. A custom panel was designed encompassing 95 of the top 100 human DNA single nucleotide variants from COSMIC that had a canine orthologue, and targeted sequencing was performed on all tissue and blood samples. A large number of these variants—many of which are actionable in human cancer— were detected in the tumor samples and pre-surgical plasma samples. In some patients, tumor-derived variants were detected in the post-surgical plasma that confirmed the presence of residual disease after surgery. As disease progressed, an increase in the variant allele fraction (VAF) of the tumor-derived mutations was observed and tracked with the patient’s clinical course. Additionally, the presence of variants that may be targetable by human cancer drugs were identified in a subset of patients. These findings demonstrate the potential of liquid biopsy to characterize the genomic landscape of canine cancers at diagnosis and throughout treatment, similar to observations reported in human cancers. This builds the foundation for comparative oncology to translate the knowledge of precision medicine between humans and dogs, to facilitate biomarker discovery, and to track emergence of potential actionable biomarkers in various therapeutic contexts to the benefit of both species. Citation Format: Ilya Chorny, Kristina M. Kruglyak, John A. Tynan, Gilberto E. Hernandez, Prachi Nakashe, Susan Hicks, Rita Motalli-Pepio, Lisa McLennan, Lauren E. Holtvoigt, Jill M. Rafalko, Jason Chibuk, Angela L. McCleary-Wheeler, Andi Flory, Daniel S. Grosu, Dana W. Tsui. Comparative oncology analysis of canine cancer by tumor and liquid biopsy testing for biomarker and therapeutic discovery in humans and dogs [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 1612.

Early Drug Discovery and Development of Novel Cancer Therapeutics Targeting DNA Polymerase Eta (POLH).

Polymerase eta (or Pol η or POLH) is a specialized DNA polymerase that is able to bypass certain blocking lesions, such as those generated by ultraviolet radiation (UVR) or cisplatin, and is deployed to replication foci for translesion synthesis as part of the DNA damage response (DDR). Inherited defects in the gene encoding POLH (a.k.a., XPV) are associated with the rare, sun-sensitive, cancer-prone disorder, xeroderma pigmentosum, owing to the enzyme’s ability to accurately bypass UVR-induced thymine dimers. In standard-of-care cancer therapies involving platinum-based clinical agents, e.g., cisplatin or oxaliplatin, POLH can bypass platinum-DNA adducts, negating benefits of the treatment and enabling drug resistance. POLH inhibition can sensitize cells to platinum-based chemotherapies, and the polymerase has also been implicated in resistance to nucleoside analogs, such as gemcitabine. POLH overexpression has been linked to the development of chemoresistance in several cancers, including lung, ovarian, and bladder. Co-inhibition of POLH and the ATR serine/threonine kinase, another DDR protein, causes synthetic lethality in a range of cancers, reinforcing that POLH is an emerging target for the development of novel oncology therapeutics. Using a fragment-based drug discovery approach in combination with an optimized crystallization screen, we have solved the first X-ray crystal structures of small novel drug-like compounds, i.e., fragments, bound to POLH, as starting points for the design of POLH inhibitors. The intrinsic molecular resolution afforded by the method can be quickly exploited in fragment growth and elaboration as well as analog scoping and scaffold hopping using medicinal and computational chemistry to advance hits to lead. An initial small round of medicinal chemistry has resulted in inhibitors with a range of functional activity in an in vitro biochemical assay, leading to the rapid identification of an inhibitor to advance to subsequent rounds of chemistry to generate a lead compound. Importantly, our chemical matter is different from the traditional nucleoside analog-based approaches for targeting DNA polymerases.

With Our Powers Combined: Exploring PARP Inhibitors and Immunotherapy.

The use of poly(ADP-ribose) polymerase inhibitors and immune checkpoint inhibitor therapies has seen substantial clinical success in oncology therapeutic development. Although multiple agents within these classes have achieved regulatory approval globally-in several malignancies in early and advanced stages-drug resistance remains an issue. Building on preclinical evidence, several early trials and late-phase studies are underway. This review explores the therapeutic potential of combination poly(ADP-ribose) polymerase inhibitors and immune checkpoint inhibitor therapy in solid tumors, including the scientific and therapeutic rationale, available clinical evidence, and considerations for future trial and biomarker development across different malignancies using ovarian and other solid cancer subtypes as key examples.

Biology, technology and a bit of serendipity: an interview with Shiva Malek.

Biology, technology and a bit of serendipity: an interview with Shiva Malek.

Billion dollar deals end 2020 for big pharma

A string of billion dollar deals, many focused on the development of oncology therapeutics, rounded off an extraordinary year. A string of billion dollar deals, many focused on the development of oncology therapeutics, rounded off an extraordinary year.

The Dual Cell Cycle Kinase Inhibitor JNJ-7706621 Reverses Resistance to CD37 Targeted Radioimmunotherapy in Activated B Cell like Diffuse Large B Cell Lymphoma Cell Lines

The CD37 targeting radioimmunoconjugate 177Lu-lilotomab satetraxetan (Betalutin®) is currently being evaluated as monotherapy in a clinical phase 2b trial for patients with follicular lymphoma (FL) and in a phase 1 trial for patients with diffuse large B-cell lymphoma (DLBCL), as well as in a phase 1b trial in combination with rituximab for patients with relapsed/refractory FL. Herein we have investigated the effect of 177Lu-lilotomab satetraxetan in seven activated B-cell like (ABC) DLBCL cell lines. Although the radioimmunoconjugate showed anti-tumor activity, primary resistance was observed in a subset of cell lines: U-2932 and RIVA. Both cell lines are representative for TP53 deficient Double Expressor (DE) DLBCL. Importantly, resistance was not a consequence of reduced binding of the radioimmunoconjugate to cell surface expressed CD37. Thus, we set out to identify drugs able to overcome the resistance to 177Lu-lilotomab satetraxetan in both resistant ABC-DLBCL cell lines. We performed a viability-based screen combining 177Lu-lilotomab satetraxetan with the 384-compound Cambridge Cancer Compound Library. Drug combinations were scored using Bliss and Chou-Talalay algorithms. We identified and characterized the dual-specific CDK1/2 and AURA/B kinase inhibitor JNJ-7706621 as compound able to revert the resistance to radioimmunotherapy (RIT), alongside topoisomerase and histone deacetylases (HDAC) inhibitors. Kinetic studies of the effect of mono- and combination therapy of U-2932 and RIVA cells with JNJ-7706621 and 177Lu-lilotomab satetraxetan are suggestive of a model in which radiation damage induced G2-arrested lymphoma cells eventually enter mitosis (repair or escape) and mitotic entry, progression and exit are impaired by JNJ-7706621 mediated inhibition of CDK1/2 and AURKA/B. Extended residence-time of cells in mitosis due to chromosome condensation and congression defects as well as spindle and mid-spindle assembly failure is likely pivotal for the increased sensitivity to persistent 177Lu-lilotomab satetraxetan deposited DNA damage, ultimately promoting cytokinesis failure (multinucleation, aneuploidy, increased cell size) and cell death. In conclusion, CD37-targeting 177Lu-lilotomab satetraxetan RIT showed activity in several ABC-DLBCL lymphoma cell lines. CD37-independent RIT-resistance was identified in two cell lines representative of aggressive DE ABC-DLBCLs with inactive TP53, and reversed by subsequent inhibition of CDK1/2 and AURKA/B by JNJ-7706621. These findings may be of potential relevance for ongoing clinical trials of 177Lu-lilotomab satetraxetan in relapsed, ASCT-non-eligible DLBCL, and may also be more generally applicable to other 177Lu-based RITs and alternative radionuclide utilizing targeted therapies. Future pre-clinical investigations are required to elucidate the potential application of CDK1/2 and AURKA/B inhibitors as a strategy to revert RIT resistance in TP53 deficient cancers. Disclosures Rødland: Nordic Nanovector ASA: Patents & Royalties, Research Funding. Melhus:Nordic Nanovector ASA: Employment, Equity Ownership, Patents & Royalties. Generalov:Nordic Nanovector ASA: Employment, Equity Ownership, Patents & Royalties. Bertoni:Nordic Nanovector ASA: Research Funding; Oncology Therapeutic Development: Research Funding; PIQUR Therapeutics AG: Other: travel grant, Research Funding; HTG: Other: Expert Statements ; Amgen: Other: travel grants; Astra Zeneca: Other: travel grants; Jazz Pharmaceuticals: Other: travel grants; NEOMED Therapeutics 1: Research Funding; Acerta: Research Funding; ADC Therapeutics: Research Funding; Bayer AG: Research Funding; Cellestia: Research Funding; CTI Life Sciences: Research Funding; EMD Serono: Research Funding; Helsinn: Consultancy, Research Funding; ImmunoGen: Research Funding; Menarini Ricerche: Consultancy, Research Funding. Dahle:Nordic Nanovector ASA: Employment, Equity Ownership, Patents & Royalties. Syljuåsen:Nordic Nanovector ASA: Patents & Royalties, Research Funding. Patzke:Nordic Nanovector ASA: Employment, Patents & Royalties.

Inhibition of PIM Kinases Targets Synthetic Vulnerabilities and Enhances Antigen Presentation in B-Cell Lymphoma

The PIM kinases are highly expressed in activated B-cell (ABC) diffuse large B-cell lymphoma (DLBCL). Oncogenic cooperation between PIMs and MYC has been demonstrated. Transgenic mice co-expressing Em-PIM and Em-MYC showed accelerated lymphomagenesis. Conversely, knockdown of PIMs dramatically decreased cMYC levels and lowered tumor incidence. Based on these preclinical data, a treatment strategy aiming at disrupting the oncogenic cooperation between PIMs and MYC may improve the outcome of DLBCL. Therefore, we treated a panel of DLBCL cell lines with increasing dose of the clinically relevant pan-PIM inhibitor (PIMi) AZD1208 (from 0.1 to 10μM) for 48 hours (Hrs), which resulted in a dose-dependent growth inhibition with a stronger efficacy in ABC DLBCL cell lines. (Figure 1A)The analysis of a CRISPR loss-of-function screening in three ABC (LY3, TMD8, HBL1) and three GCB (SUDHL-4, Pfeiffer, BJAB) DLBCL cell lines (Reddy et al, 2017) showed that PIM2 silencing led to significantly decreased viability irrespective of cell-of-origin (Figure 1B), suggesting that this oncogene is essential for cell proliferation in DLBCLs. To identify the genes through which PIMs drive the lymphoma phenotype we performed gene expression profiling using 4 ABC DLBCL cell lines (RIVA, TMD8, SUDHL-2, U2932) treated with either DMSO or AZD1208 at 1μM for 4, 8 and 12 Hrs. We observed induction of 3,439 genes whereas 2,473 genes were downregulated. (Figure 1C) Gene pathway analysis showed that AZD1208 led to downregulation of genes regulated by MYC, including its known downstream p53 and NFKB target genes. On the other hand, AZD1208 treatment broadly induced MHC class II and antigen presentation genes as well as PI3K/AKT, cell cycle and glutaminase genes. (Figure 1D) Using a high-throughput screening approach, we found that the inhibitors of cell cycle (such as the BCL2 inhibitor venetoclax/ABT199 and the PLK4 inhibitor CFI-400945) and of glutaminase (CB839) enhanced the antiproliferative effect of AZD1208, whereas combinations with the PI3K/AKT/mTOR inhibitors had negligible synergistic effect. (Figure 1E) In conclusion, our study revealed previously unknown mechanisms of action of PIM inhibitors and provides a framework for future combination strategies. Disclosures Younes: Xynomics: Consultancy; Biopath: Consultancy; Genentech: Research Funding; AstraZeneca: Research Funding; Syndax: Research Funding; BMS: Research Funding; HCM: Consultancy; Celgene: Consultancy, Honoraria; Epizyme: Consultancy, Honoraria; Takeda: Honoraria; Roche: Consultancy, Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Curis: Honoraria, Research Funding; Merck: Honoraria, Research Funding; Abbvie: Honoraria; Pharmacyclics: Research Funding. Bertoni:Nordic Nanovector ASA: Research Funding; Acerta: Research Funding; ADC Therapeutics: Research Funding; Bayer AG: Research Funding; Cellestia: Research Funding; CTI Life Sciences: Research Funding; EMD Serono: Research Funding; Helsinn: Consultancy, Research Funding; ImmunoGen: Research Funding; Menarini Ricerche: Consultancy, Research Funding; NEOMED Therapeutics 1: Research Funding; Oncology Therapeutic Development: Research Funding; PIQUR Therapeutics AG: Other: travel grant, Research Funding; HTG: Other: Expert Statements ; Amgen: Other: travel grants; Astra Zeneca: Other: travel grants; Jazz Pharmaceuticals: Other: travel grants.

Secreted Factors Determine Resistance to Idelalisib in Marginal Zone Lymphoma Models of Resistance

Background . PI3Kδ is expressed in B-cells and has a central role in the B-cell receptor signaling in B-cell derived malignancies. Idelalisib was the first-in-class PI3Kδ inhibitors and several second-generation compounds are undergoing clinical investigation as single agents and in combinations. To identify modalities to overcome the resistance that develops to this class of agents, we have developed two idelalisib-resistant models derived from splenic marginal zone lymphoma (SMZL) cell lines. Materials and Methods. Cells were kept under idelalisib (IC90) until acquisition of resistance (RES) or with no drug (parental, PAR). Stable resistance was confirmed by MTT assay after 2-weeks of drug-free culture. Multi-drug resistance phenotype was ruled out. Cells underwent transcriptome and miRNA profiling by RNA-Seq, whole exome sequencing (WES), lipidomics profiling, pharmacological screening (348 compounds), and FACS analysis. Cytokines and growth factor secretion was performed by ELISA. Results. Two RES models were obtained from VL51 and Karpas1718 with 7-10 fold times higher IC50s than PAR counterparts. In both models, conditioned media from RES cells transferred the resistance in the PAR cells. While WES did not identify somatic mutations associated with resistance, RNA-Seq and lipidomics analyses showed that the two cell lines had developed resistance activating different modalities. The VL51 RES model showed an enrichment in BCR-TLR-NFkB (TLR4, CD19, SYK), IL6-STAT3 (IL6, CD44), chemokines (CXCL10, CXCR4, CXCR3) and PDGFR (PDGFRA, PRKCE) signatures, paired with increased p-AKT and p-BTK levels, decreased cardiolipins and sphingomyelins levels, and increased levels of specific triacylglycerols and glycerophosphocholines. In particular, there was an over-expression of surface expression of PDGFRA and secretion of IL6 in the medium. Silencing of both IL6and PDGFRA by siRNAs reverted the resistance, while the silencing of the individual genes had only a partial effect. These data were paired with the acquired sensitivity to the PDGFR inhibitor masitinib, identified in the pharmacologic screening. In the Karpas1718 model, we observed an increased p-AKT activity with an enrichment for B-cell activation signatures (RAG1, RAG2, TCL1A), proliferation (E2F2, MKI67), ERBB signaling (HBEGF, NRG2, ERRB4), increased levels of some triacylglycerols and repressed levels for specific glycerophosphocholines. HBEGF secretion was confirmed by ELISA. The addition of recombinant HBEGF to the medium induced resistance in the PAR cells. Combination with the pan ERBB inhibitor lapatinib was beneficial in the K1718 RES. Recombinant HBEGF also induced resistance to the BTK inhibitor ibrutinib in the PAR cells and in the mantle cell lymphoma SP-53 cell line. Specific members of the let-7 family of miRNAs were repressed in the RES lines derived from both cell lines, indicating the involvement of miRNA deregulation in the mechanism of resistance. Indeed, let-7 members are known to directly target IL6-STAT3 and cytokine signaling cascade, as well PI3K-AKT network. In solid tumors, let-7 members are also expressed at low levels in tumors with constitutive active ERBB signaling, in accordance with the activation of ERBB pathway and p-AKT we observed in our Karpas1718model. Experiments with a LIN28B inhibitor are now on-going. Finally, we validated the findings across a panel of 34 B-cell lymphoma cell lines, in which IL6, PDGFRA, HBEGF and LIN28 expression levels were negatively correlated with idelalisib sensitivity, while the latter was positively correlated with let-7 levels (P <0.05). Conclusions. We developed two distinct models derived from MZL of secondary resistance to the PI3Kδ inhibitor idelalisib. We identified treatments that might overcome resistance to idelalisib and are worth of further investigations. The two models, driven by different biologic processes, will allow the evaluation of further alternative therapeutic approaches. Disclosures Stathis: PharmaMar: Other: Renumeration; ADC Therapeutics: Other: Institutional research funding; Abbvie: Other: Renumeration; Bayer: Other: Institutional research funding; Novartis: Other: Institutional research funding; MEI-Pharma: Other: Institutional research funding; Roche: Other: Institutional research funding; Pfizer: Other: Institutional research funding; Merck: Other: Institutional research funding. Stuessi:Gilead: Speakers Bureau. Zucca:Gilead: Honoraria, Other: travel grant. Rossi:Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Honoraria, Other: Scientific advisory board; Janseen: Honoraria, Other: Scientific advisory board; Roche: Honoraria, Other: Scientific advisory board; Astra Zeneca: Honoraria, Other: Scientific advisory board. Bertoni:Nordic Nanovector ASA: Research Funding; Acerta: Research Funding; Jazz Pharmaceuticals: Other: travel grants; ADC Therapeutics: Research Funding; Bayer AG: Research Funding; Cellestia: Research Funding; CTI Life Sciences: Research Funding; EMD Serono: Research Funding; Helsinn: Consultancy, Research Funding; ImmunoGen: Research Funding; Menarini Ricerche: Consultancy, Research Funding; NEOMED Therapeutics 1: Research Funding; Oncology Therapeutic Development: Research Funding; PIQUR Therapeutics AG: Other: travel grant, Research Funding; HTG: Other: Expert Statements ; Amgen: Other: travel grants; Astra Zeneca: Other: travel grants.

Discovery and optimization of covalent Bcl-xL antagonists.

Over the last ten years, targeted covalent inhibition has become a key discipline within medicinal chemistry research, most notably in the development of oncology therapeutics. One area where this approach is underrepresented, however, is in targeting protein-protein interactions. This is primarily because these hydrophobic interfaces lack appropriately located cysteine residues to allow for standard conjugate addition chemistry. Herein, we report our development of the first covalent inhibitors of the antiapoptotic protein B-cell lymphoma extra-large (Bcl-xL), utilizing a sulfonyl fluoride (SF) warhead to selectively covalently modify tyrosine 101 of the BH3 domain-binding groove. These compounds display time-dependent inhibition in a biochemical assay and are cellularly active (U266B1). In addition, compound 7 was further elaborated to generate a chemical-biology probe molecule, which may find utility in understanding the intricacies of Bcl-xL biology.

Preliminary Safety and Efficacy Results with an Intermittent Schedule of the PI3kδ Inhibitor ME-401 Alone or in Combination with Rituximab for B-Cell Malignancies

Preliminary Safety and Efficacy Results with an Intermittent Schedule of the PI3kδ Inhibitor ME-401 Alone or in Combination with Rituximab for B-Cell Malignancies

Targeting Both BET and Crebbp/EP300 Proteins with the Novel Dual Inhibitor NEO2734 Leads to More Preclinical Anti-Tumor Activity in Diffuse Large B Cell Lymphomathan with Single BET or Crebbp/EP300 Inhibitors

Background: Lymphoma cells have frequent deregulation of their epigenome. The Bromodomain (BRD) and Extra-Terminal domain (BET) proteins are key regulators of the transcription process (Stathis & Bertoni, Cancer Discovery 2018). The acetyltransferases cyclic AMP response element binding protein (CREB)-binding protein (CBP) and the E1A interacting protein of 300 kDa (EP300 or P300) are highly homologous BRD-containing transcriptional co-activators and their genes are often mutated in diffuse large B cell lymphoma (DLBCL) (Pasqualucci et al, Nature 2011; Morin et al, Nature 2011). Targeting the individual classes of proteins is a new therapeutic approach, as shown especially by BET inhibitors with both preclinical and early clinical anti-lymphoma activity (Stathis & Bertoni, Cancer Discovery 2018). NEO2734 (Epigene Therapeutics Inc) is a novel oral dual inhibitor of BET and CREBBP/EP300 proteins with pre-clinical activity in a spectrum of solid tumors (Giles et al, ESMO 2018). Here, we present the first data exploring its anti-tumor activity in DLBCL models.Methods: Lymphoma cell lines were exposed to increasing doses of compounds for 72h. Cell proliferation was measured by using the MTT assay.Results: Twenty-seven DLBCL cell lines were exposed to NEO2734. The compound showed anti-tumor activity with a median IC50 of 157 nM (95% C.I., 135-214). Cell lines derived from activated B-cell-like DLBCL (ABC DLBCL) (n.=7) were more sensitive than the ones derived from germinal center B-cell (GCB) DLBCL (n.=20) (P = 0.04). No difference were observed based on MYC gene status (translocation: yes, n=8; no, n.=13), BCL2 gene status (translocation: yes, n=12; no, n.=6), TP53 gene status (inactive: yes, n=14; no, n.=6), double hit MYC/BCL2 (yes, n.=6; no, n.=14), CREBBP gene status (mutated, n.=10; wild type, n.=16), or EP300 gene status (mutated, n.=5; wild type, n.=20).As comparison, all the cell lines were also exposed to a BET inhibitor (birabresib, OTX015) (Boi et al, Clinical Cancer Res 2015) and to a CREBBP/EP300 inhibitor (CBP30) (Hammitzsch et al, PNAS 2015). The median IC50 values of the two molecules were 237 nM (95% C.I., 171-344) and 5.5 μM (95% C.I., 4.2-8.3 μM), respectively. The data obtained for birabresib were in agreement with what we had previously reported (Boi et al, Clinical Cancer Res 2015). The three compounds presented a similar pattern of anti-proliferative activity across all the cell lines (NEO2734 and birabresib: R2 =0.84, P < 0.001; NEO2734 and CBP30, R2 = 0.73, P < 0.001; birabresib and CBP30, R2 = 0.73, P < 0.001) but with different degrees of IC50. Both NEO2734 and birabresib were more potent than CBP30 (P <0.0001). The novel dual inhibitor was more potent than birabresib (P=0.0182) and the difference was even bigger considering the compounds' IC90 (P = 0.0025): median values were 1.1 μM (95% C.I., 735 nM - 2.7 μM) and 20 μM (95% C.I., 2 - 30 μM) for the dual inhibitor and for the BET inhibitor, respectively.Conclusions: The novel dual BET and CREBBP/EP300 inhibitor NEO2734 showed strong in vitro anti-tumor activity across a large panel of DLBCL cell lines and it appeared more potent than single BET or CREBBP/EP300 inhibitors. DisclosuresZucca:Celltrion: Consultancy; AstraZeneca: Consultancy. Stathis:Oncology Therapeutic Development: Research Funding. Giles:Actuate Therapeutics Inc: Employment, Equity Ownership.

Enhancing value of clinical pharmacodynamics in oncology drug development: An alliance between quantitative pharmacology and translational science.

Clinical pharmacodynamic evaluation is a key component of the "pharmacologic audit trail" in oncology drug development. We posit that its value can and should be greatly enhanced via application of a robust quantitative pharmacology framework informed by biologically mechanistic considerations. Herein, we illustrate examples of intersectional blindspots across the disciplines of quantitative pharmacology and translational science and offer a roadmap aimed at enhancing the caliber of clinical pharmacodynamic research in the development of oncology therapeutics.

Abstract 789: Leveraging transcriptomic and genomic data to better select models for preclinical oncology therapeutic development to identify cell lines most similar to patient tumors

Abstract Cancer cell lines represent the front line of new compound testing, and results from these experiments often decide which compounds go on for further testing. Genomic context plays a critical role in drug response and now genomic data for tumors and cell lines are widely available. However, cell lines are often chosen based on ease of access, literature prevalence, and ease of culture. We combined gene expression and CNV/mutation profiling from four pancreatic cancer tumor datasets (GSE21501, GSE28735, ICGC, TCGA,) and three pancreatic cancer cell line datasets (Klijn et al, Collisson et al, and CCLE) to identify which cell lines best match patient tumors. CNV comparison revealed that popular cell lines do not always have the best CNV correlation with tumors: when comparing pancreatic cancer tumors to cell lines, the citations of the top five cell lines by CNV correlation were less than 10% of the pancreatic cancer cell line total. Next we filtered for driver mutations including SMAD4 and CDKN2A using mutation scoring algorithms and clustered tumors and cell lines. We found that many cell lines with few citation counts clustered readily amongst tumors (such as L33). Leveraging the hypothesis that different hits in the same pathway can have a similar downstream effect, we combined CNV, expression and mutation data and clustered cell lines together with tumors based on overall aberrations in MSigDB cancer pathways. L33 and YAPC clustered near tumors while the majority of other cell lines clustered together. To identify coexpressed gene clusters, we ran WGCNA individually in all seven datasets and discovered modules consistent in cell line and tumor datasets using iGraph. One of the most interesting modules (interferon regulated genes) is expressed highly in the majority of tumors profiled. About half of cell lines also express this module highly, suggesting that they may be more ideal models for high interferon expression tumors than other cell lines. Here we present evidence demonstrating that certain cell lines mimic pancreatic tumor genomes more closely while others represent patterns of genomic features not commonly observed in vivo. We also show that certain biologically relevant tumor subtypes may be better represented by some cell lines than others. Our analysis highlights the emerging role of genomics in advancing the clinical success of therapeutic trials. Citation Format: Yoonjeong Cha, Adam Labradorf, Joseph Perez-Rogers, Brian Haas, Andrew Lysaght, Brian Weiner, Fadi Towfic, Kevin Fowler, Benjamin Zeskind, Sarah Kolitz, Badri Vardarajan, Maxim Artyomov, Rebecca L. Kusko. Leveraging transcriptomic and genomic data to better select models for preclinical oncology therapeutic development to identify cell lines most similar to patient tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 789.