Panel Of Patient-derived Xenografts Research Articles

Pre-clinical modeling of navtemadlin pharmacokinetics (PK), pharmacodynamics (PD), and efficacy in glioblastoma, IDH-wildtype.

2012 Background: Navtemadlin (nvtm) is a potent, selective, orally available small molecule inhibitor of murine double minute 2 homologue (MDM2), which has completed a Ph 0 surgical window of opportunity study in glioblastoma, IDH-wildtype (GBM; Lee SNO 2022). To optimally interpret the clinical data, an extensive evaluation of nvtm PK, PD, and efficacy was performed in GBM patient derived xenografts (PDXs). Methods: Response to nvtm +/- radiotherapy (RT) was characterized in vitro and in vivo across a panel of GBM PDXs with various TP53 and MDM2 alterations. Efficacy, PK, and PD were evaluated in flank or orthotopic PDX models. p53 pathway activation was evaluated by qPCR, Western blot, and IHC. Nvtm brain penetration was evaluated in immunodeficient abcb1a/b-/- (P-glycoprotein; P-gp), abcg2-/- (BCRP), or double-knockout mice. Binding was assessed by rapid equilibrium dialysis, and nvtm concentrations by LC/MS-MS and MALDI-MSI. Results: Nvtm decreased in vitro viability of TP53WT GBM PDX explant cultures with IC50s <100 nM, but was ineffective in TP53-mutant GBM. In flank PDX models, nvtm (100 mg/kg daily for 4 weeks) delayed tumor regrowth by 1.9 to 4.8-fold in TP53 WT PDXs without MDM2amplification (n=9 models), and more markedly by 20.1 to 29.4-fold in MDM2amplified models (n=4; 2 PDXs did not recur). In a flank PDX dose-response study, nvtm delayed the growth of MDM2amplified GBM108 at 25 mg/kg vs. placebo (61 vs. 11 days; p=0.014; mean intra-tumoral nvtm = 590 nM). In contrast, growth of MDM2 non-amplified GBM14 was delayed only at 100 mg/kg (37 vs. 15 days; p=0.082; mean intra-tumoral nvtm = 2990 nM). In both flank models, p53 target gene upregulation was similar between 25 and 100 mg/kg and did not correlate with regrowth. Nvtm was highly bound (fraction unbound = 0.090 in culture media and 0.014 in GBM tissue homogenate). In mice after oral dosing, distribution to CNS was limited by P-gp, with a brain to plasma ratio of 0.009 and unbound ratio of 0.005, whereas BCRP deficiency did not affect CNS distribution. With orthotopic GBM108, nvtm efficacy was evaluated in nude vs. efflux-deficient mice. In nude mice, nvtm was ineffective at doses up to 100 mg/kg; however, in efflux deficient mice, the mean intra-tumoral nvtm level at 25 mg/kg was similar to flank tumors (690 nM) and survival was significantly extended (134 vs. 62 days, p=0.0002) with additional benefit at 100 mg/kg (>300 vs. 62 days, p=0.002). Conclusions: Nvtm showed significant efficacy in TP53 WT GBM flank PDX models but efficacy in orthotopic PDX was highly dependent on CNS penetration. Targeting nvtm levels based on the in vitroIC50 may significantly underestimate the in vivo effective concentration . In vivo studies showed lower intra-tumoral nvtm levels are required to significantly inhibit growth of MDM2amplified compared with non-amplified tumors.

Abstract C079: Targeting cancer stem cell OXPHOS with tailored ruthenium complexes as a new approach to treat pancreatic cancer

Abstract Background and aims: Annual world-wide cancer-related fatalities remain high for pancreatic ductal adenocarcinoma (PDAC), largely due to the presence of “stem-like” tumor cells known as cancer stem cells (CSCs). Previous studies by our group have shown that oxidative phosphorylation (OXPHOS) is the main pathway by which pancreatic CSCs meet their energetic requirements; therefore, OXPHOS represents an Achille’s heel of these highly tumorigenic cells. Methods: The anti-CSC activity of a ruthenium complex featuring bipyridine and terpyridine ligands and one coordination labile position (Ru1) was evaluated across primary PDAC cultures and 8 patient-derived xenografts (PDXs). RNAseq analysis followed by mitochondria-specific molecular assays were used to determine the mechanism of action. Results: We show that Ru1 is capable of inhibiting CSC OXPHOS function in vitro, and more importantly, it presents excellent anti-cancer activity, with low toxicity, across a large panel of PDXs. Mechanistic studies suggest that this activity stems from Ru1 binding to the D-loop region of the mitochondrial DNA of CSCs, inhibiting OXPHOS complex-associated transcription, leading to reduced mitochondrial oxygen consumption, membrane potential, and ATP production, all of which are necessary for PaCSCs that heavily depend on mitochondrial respiration. Conclusion Overall, the coordination complex Ru1 represents not only an exciting new anti-cancer agent, but also a molecular tool to dissect the role of OXPHOS in CSCs. Results indicating that the compound is non-toxic and highly effective in vivo are extremely exciting, and have allowed us to uncover an unprecedented approach to fight PDAC based on targeting CSC OXPHOS. Citation Format: Bruno Jr Sainz, Sonia Alcalá, Lara Villarino, Laura Ruíz-Cañas, José Couceiro, Miguel Martínez-Calvo, Adrián Palencia-Campos, Diego Navarro, Pablo Cabezas-Sainz, Alfonso Cordero-Barreal, Juan A. Rubiolo, Cristina González-Páramos, Alfredo Carrato, Patrick C. Hermann, Laura Sánchez, Susana Torrente, Miguel Ángel Fernández-Moreno, José L. Mascareñas. Targeting cancer stem cell OXPHOS with tailored ruthenium complexes as a new approach to treat pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C079.

Idasanutlin and Navitoclax Induce a Synergistic p53-Dependent Apoptotic Cell Death in T-Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with a five-year event-free survival rate that declines with age. Existing therapies for T-ALL, particularly in adults, are intensive and poorly tolerated, with high rates of of treatment-related morbidity and mortality and a high frequency of relapse. In T-ALL, activating Notch pathway mutations are common and thought to induce transformation in part through activation of c-Myc. Typically, increased expression of c-Myc induces apoptosis through the p19(ARF)-Mdm2-p53 tumor suppressor pathway. Unsurprisingly, over 70% of T-ALL cases have inactivating mutations in CDKN2A (p19Arf). However, greater than 95% of primary and 75% of relapsed T-ALL cases maintain wild type p53. We hypothesized that MDM2 inhibition would lead to T-ALL cell apoptosis by bypassing the loss of ARF. We reported in a previous ASH abstract initial studies evaluating the MDM2 inhibitor idasanutlin in the context of T-ALL. We observed that T-ALL patient-derived xenograft (PDX) lines treated in vitro showed modest induction of apoptosis. Additionally, we observed upregulation of pro-apoptotic p53 target genes including Bax and Puma1, leading us to hypothesize that inhibition of pro-survival BH3 domain proteins Bcl-2, Bcl-xL, and Bcl-W by navitoclax (ABT-263) would synergize to enhance apoptosis. In vitro treatment of a panel of PDX lines with combined therapy led to robust cell death with strong induction of pro-apoptotic p53 targets in all lines. In vivo, we assessed the response of four T-ALL xenografts to dual treatment. All showed a significant reduction of tumor burden compared to the most efficacious single therapy and evidence of synergy in all tested lines, as evaluated by a modified Bliss Independence test analyzing average daily change in tumor burden. Overall survival was significantly increased in the combination treatment group. We report here further mechanistic characterization of idasanutlin and navitoclax dual therapy in the context of T-ALL, as well as several therapeutically-oriented comparisons. While our initial studies used navitoclax due to prior work showing that T-ALL frequently expresses and is dependent on Bcl-xL ( Chonghaile et al., 2014), navitoclax can cause a dose-limiting thrombocytopenia due to on-target Bcl-xL inhibition in circulating platelets. Therefore, we treated our PDX panel with a dose matrix of idasanutlin with navitoclax or venetoclax, which lacks Bcl-xL activity. We observed that the navitoclax combination showed strong evidence of synergic activity, as measured by zero interaction potency (ZIP) score ( Yadav et al., 2015). Idasanutlin and navitoclax combination therapy had global ZIP scores suggesting an additive effect in 1 line and strongly synergic activity in the remaining 4 lines. Venetoclax showed an additive benefit in 3 lines, but was only synergistic in 1 of 5 lines tested. These results underscore the importance of Bcl-xL targeting in T-ALL and support further investigation of whether combination treatment with idasanutlin permits a more tolerable navitoclax dosing regimen. We also evaluated ruxolitinib in combination with idasanutlin, as recent work has shown overlapping responses to inhibitors of Jak/Stat or Bcl-2 ( Yuan et al. 2022). While we observed moderate activity of ruxolitinib monotherapy, combination with idasanutlin was additive against one and synergistic in none of the tested lines. To confirm the p53-dependence of idasanutlin dual therapy, we engineered p53 knockout T-ALL cell lines and observed strong induction of apoptosis and p53 target genes in wildtype cells, which was entirely abrogated in p53 LOF lines. Additionally, we performed RNA-seq on PDX cells treated with single or dual therapy to mechanistically characterize transcriptional responses to the drug combination. We observed minimal changes in navitoclax-only treated cells at the RNA level, consistent with its on-target post-transcriptional regulation of apoptotic induction. Idasanutlin and combination therapy samples clustered closely in PCA analysis, with p53 response a strongly-induced pathway, as expected. Our data suggest that the rational combination of idasanutlin and navitoclax is highly active against T-ALL, with greater synergic opportunity compared to other available idasanutlin combination treatments, through induction of a p53-dependent apoptotic cell death.

Abstract B004: Genomic loss of TP53 impairs AR-targeted activity in metastatic prostate cancer

Abstract Background: Metastatic prostate cancer (mPC) is notable for a spectrum of recurrent genomic alterations, some associated with overall prognosis and others predicting response to specific therapeutics. Standard mPC interventions are designed to suppress the signaling program regulated by the androgen receptor (AR). These include androgen deprivation therapy (ADT) to reduce AR ligand levels and AR signaling inhibitors (ARSI) that directly impair AR function. While ADT and ARSI produce clinical responses in most patients, the duration and depth of response vary greatly. In addition, specific recurring genomic alterations are associated with shorter responses after ADT and ARSI therapy. Among these are mutations and/or genomic copy loss involving key tumor suppressor genes, including PTEN, RB1 and TP53. However, the mechanistic contribution of TP53 loss to AR signaling and resistance to AR pathway-directed therapy remains unresolved. Methods: Isogenic prostate cancer cell lines with intact and TP53 deletions were constructed using CRISPR/Cas9. The transcriptome profiles were determined by RNA-seq, and ChIP-seq was used to determine the chromatin landscapes of AR localization. In addition, we performed ATAC-seq to assess chromatin accessibility. Finally, to further validate the findings, we comprehensively analyzed AR-regulated gene expression and AR cistromes across a panel of patient-derived xenograft (PDX) models and clinical cohorts of mPC patient samples with respect to TP53 status. Results: Compared to TP53-wild-type (WT) cells, the transcriptional results of isogenic knockout TP53 lines showed impaired AR canonical activity. However, the downregulated AR response pathway is not caused by reduced levels of AR transcript or protein levels. Additionally, a similar trend was also found while comparing TP53-WT PDX models with TP53-loss models. We found that the loss of TP53 can shift the chromatin binding of AR, and the altered AR binding sites correlated with genes involved in neurogenesis pathways, which provide a potential mechanism of how the loss of TP53 might impact AR signaling and promote ADT and ARSI treatment resistance. We also identified additional AR chromatin binding sites that were enriched due to the loss of TP53. The targets potentially regulated by these sites are involved in multiple pathways, including cell morphogenesis involved in differentiation and response to the endogenous stimulus. Conclusions and Future Directions: Overall, the results indicate that in addition to altering DNA damage and repair pathways and contributing to cancer progression, genetic loss of TP53 in mPC may directly impair ADT and ARSI therapies, partially through alteration of AR chromatin activity. In addition, the AR cistrome reprogramming resulting from TP53 loss could also affect other pathways that could be exploited to overcome ARSI treatment resistance. Citation Format: Wanting Han, Michael D. Nyquist, Ilsa Coleman, Navonil De Sarkar, Lisa Ang, Eva Corey, Peter S. Nelson. Genomic loss of TP53 impairs AR-targeted activity in metastatic prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B004.

Abstract 4677: A preclinical platform of breast cancer PDX and derived cellular models as a tool for pharmacological screening and functional studies

Abstract Despite considerable progress in understanding the biology and genetics of breast cancer, the development of effective therapies needs physiological and predictive preclinical models. In this context, breast cancer (BC) patient-derived xenograft (PDX) models have become a standard tool as they reproduce the biology of tumors of origin, in term of histology, genotype and response to chemotherapy. They have proven their relevance in the study of pathways leading to the development and progression of cancer, to the mechanisms linked to tumor resistance and to the identification of novel effective therapies. We present a preclinical platform of over 60 fully characterized BC PDX models and their in vitro cell derivatives for preclinical evaluation of new treatment modalities. Our platform consists of a PDX collection of 43 TNBC, 6 ER+, 4 HER2+, 6 Luminal B models (ER+ HER2+) and 14 cellular models derived from these PDXs, representing the variety of BC. PDX models were obtained by transplantation of post-surgery tumor specimens either by grafting of tumor fragments in the interscapular region of nude mice or by injection of tumor cells into the fat pad of NOD-Scid mice. Molecular analyses were done included gene expression, gene copy number, whole exome sequencing and IHC markers staining. In vivo drug efficacy assays were performed with standards of care as single agent or in combinations. This PDX panel mostly reflects the molecular heterogeneity of breast cancer and reproduce accurately the molecular and drug response profile of human tumors. It provides an invaluable tool for translational research. It is widely used to performed standard drug evaluation but also “Mouse Clinical Trials” (MCT) in vivo screens to provide more predictive preclinical data on single-agent or combination drug efficacy. Engrafted on highly immunodeficient mice humanized with human PBMCs or CD34+ cells, these PDX models allow bispecific T-Cell engager antibody testing or immune-checkpoint inhibitors evaluation. In addition to these PDX panel, we derived cellular models (PDXDCs) to offer a time- and cost-effective preclinical screening tool. PDXDCs were obtained from dissociated PDX tumors cultured under different media and matrix conditions. They were characterized by comparison with the parental PDX by Short Tandem Repeat (STR) profiling before performing a master bank. WES and RNASeq molecular analyses were done and in vitro drug sensitivity was compared with their parental PDX in vivo drug response. Overall, the results show that this PDXDC panel reproduced in vitro the in vivo drug response profile of the original PDXs with various therapies. This BC PDX panel and in vitro cell derivatives provide a powerful preclinical platform to improve our knowledge on BC biology and to rapidly evaluate response to new treatments and translate this knowledge to the clinic. Citation Format: Delphine Nicolle, Aurore Gorce, Marie Tavernier, Elisabetta Marangoni, Didier Decaudin, Christophe Ginestier, Emmanuelle Charafe-Jaufret, Judith Passildas, Nina Robin, Robert Clarke, Erwan Corcuff, Anaïs Joachim, Bernard Malissen, Ana Zarubica, Hervé Luche, Jean-Gabriel Judde, Olivier Déas. A preclinical platform of breast cancer PDX and derived cellular models as a tool for pharmacological screening and functional studies. [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 4677.

Abstract 4010: Inhibition of PERK by HC-5404 sensitizes clear cell renal cell carcinoma tumor models to anti-angiogenic tyrosine kinase inhibitors

Abstract Anti-angiogenic agents form the backbone of standard of care for advanced clear cell renal cell carcinoma (ccRCC), but their clinical impact is limited by primary and secondary resistance mechanisms that remain a critical problem. Furthermore, the approvals for VEGFR-targeting receptor tyrosine kinase inhibitors (VEGFR-TKIs), cabozantinib in second-line, and tivozanib in third-line RCC patients were based on modest objective response rates and median progression-free survival. There is an urgent need for novel mechanisms that target adaptive tumor responses that drive resistance to these agents, as well as combination drug partners that improve outcomes for patients. As part of their mechanism, VEGFR-TKIs induce oxygen- and nutrient-deprivation that drives ER stress. Tumors can evade deleterious ER stress by activating PERK branch of the integrated stress response, which arrests global translation and restores homeostasis. We hypothesized that inhibiting PERK would enhance the anti-tumor activity of VEGFR-TKIs in vivo and tested this using HC-5404, a potent and selective PERK inhibitor currently in Ph1 clinical testing (NCT04834778). Here, we present preclinical evidence that supports combining HC-5404 with VEGFR-TKIs in ccRCC. We demonstrate that axitinib, cabozantinib, lenvatinib, and sunitinib all activate PERK in 786-O ccRCC xenografts in a dose-responsive manner. The addition of HC-5404 significantly enhanced the tumor growth inhibition (TGI) of VEGFR-TKIs across multiple ccRCC tumor models, resulting in tumor stasis or regression in combination groups. Expression profiling and IHC analysis of tumor sections revealed that HC-5404 enhanced the anti-angiogenic effects of axitinib and lenvatinib in 786-O tumors, highlighting the protective role of PERK in response to anti-angiogenics. To evaluate whether the combination treatments could benefit a diverse patient population, sensitivity to HC-5404 and axitinib was evaluated across a panel of patient-derived xenograft (PDX) models. This experiment confirmed widespread responsiveness to the combination treatment that in some cases achieved >50% tumor regression. As tumor progression on VEGFR-TKIs limits the success of these agents in the clinic, we evaluated the effect of adding HC-5404 to tumors that have previously progressed on axitinib. In this study, 786-O xenografts were treated with axitinib for 2-weeks and non-responders were rerandomized into groups of either single agent or combination of HC-5404 and axitinib. The combination treatment significantly improved TGI relative to either monotherapy, resulting in tumor regression of ~20%. Taken together, these findings highlight that by disrupting an adaptive stress response evoked by VEGFR-TKIs, HC-5404 presents a clinical opportunity to enhance the anti-tumor effects of well-established standard of care therapies in ccRCC. Citation Format: Michael E. Stokes, Veronica Calvo, Crissy Dudgeon, Sho Fujisawa, Sharon Huang, Leyi Shen, Nupur Ballal, Joe McGinley, David Liu, Mark J. Mulvihill, Alan C. Rigby, Nandita Bose, Eric S. Lightcap, David Surguladze. Inhibition of PERK by HC-5404 sensitizes clear cell renal cell carcinoma tumor models to anti-angiogenic tyrosine kinase inhibitors. [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 4010.

Abstract 6212: Inhibition of ATM-dependent checkpoint control and DNA double-strand break repair enhances the efficacy of ATR inhibitors

Abstract Ataxia telangiectasia and Rad3 related (ATR) and ataxia telangiectasia mutated (ATM) protein kinases play key roles in the DNA damage response (DDR) by responding to replication stress and double-strand DNA breaks respectively to pause the cell cycle and promote DNA repair. ATR kinase inhibition in cancer cells disrupts cell cycle control and causes unrepaired DNA lesions and cytotoxicity. Accordingly, several ATR inhibitors (ATRi) are in clinical development as monotherapies and in combination with DNA damaging chemotherapies and poly(ADP-ribose) polymerase (PARP) inhibitors. Here we show that while treatment of cancer cells with an ATRi inhibits the ATR pathway, it simultaneously activates the ATM signaling pathway as shown by increased levels of p-ATM, p-CHK2, p-KAP1 and p-p53. In p53 wild-type cancer cells, ATR inhibition causes an ATM-mediated G1 cell cycle arrest which diminishes the DNA lesions and cytotoxic effects of ATR inhibition. Combination of an ATRi with a selective ATM inhibitor (ATMi) synergistically potentiated efficacy in cancer cells in vitro and increased efficacy in vivo at doses that did not show overt toxicities. In a panel of patient-derived xenograft (PDX) models of triple-negative breast cancer treated with an ATRi/ATMi combination, substantial improvement in efficacy was observed. Thus, activation of the ATM pathway by an ATRi acts as a compensatory resistance pathway for ATR inhibition. These results suggest a novel and efficacious combination approach for cancer therapy by dual inhibition of these two key DDR kinases. Citation Format: Audrey Turchick, Astrid Zimmermann, Li-Ya Chiu, Heike Dahmen, Brian Elenbaas, Frank T. Zenke, Andree Blaukat, Lyubomir T. Vassilev. Inhibition of ATM-dependent checkpoint control and DNA double-strand break repair enhances the efficacy of ATR inhibitors. [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 6212.

Abstract 1533: ZW220, a novel NaPi2b-targeting antibody drug conjugate bearing a topoisomerase 1 inhibitor payload

Abstract Background: NaPi2b is a multi-pass transmembrane sodium-dependent phosphate transport protein encoded by the gene SLC34A2. NaPi2b is involved in normal phosphate homeostasis and its expression is found in the lung, liver, and small intestine. NaPi2b is highly expressed in ovarian carcinomas, lung adenocarcinomas, and colorectal carcinomas. ZW220 is an antibody-drug conjugate (ADC) targeting human NaPi2b, wherein a humanized IgG1 antibody is conjugated to novel camptothecin-based topoisomerase I inhibitor, ZD06519. The drug linker in ZW220 is comprised of a maleimide anchor and a glycyl glycyl phenylalanyl glycine (GGFG)-aminomethyl (AM) cleavable sequence. Materials and Methods: A series of in vitro and in vivo studies were conducted to interrogate the mechanism of action and the therapeutic potential of ZW220. The binding, internalization, potency, and bystander effect of ZW220 were evaluated in vitro using endogenous NaPi2b-expressing ovarian and lung cancer cell lines. In vivo, the anti-tumor activity of ZW220 was evaluated in a panel of cell line derived xenograft (CDX) models and ovarian patient derived xenograft (PDX) models featuring a range of NaPi2b expression. The pharmacokinetic (PK) profile of ZW220 was determined in Tg32 mice, a transgenic mouse expressing human neonatal Fc receptor (hFcRn). Results: ZW220 antibody exhibited cross-reactivity to human and cynomolgus monkey NaPi2b, nanomolar binding affinity and rapid internalization in NaPi2b-expressing cell lines in vitro. ZW220 elicited target-specific, sub-nanomolar cytotoxicity in two-dimensional monolayer and three-dimensional tumor spheroid models and demonstrated bystander-mediated cell killing in cancer cell co-culture assays. The treatment of a panel of ovarian PDXs with a single dose of 6 mg/kg of ZW220 resulted in robust tumor growth inhibition. ZW220 demonstrated a favourable PK profile in Tg32 mice, with comparable half-life to its parental unconjugated antibody. These results support the potential of ZW220 as a novel therapeutic agent which may help address unmet medical need in patients with NaPi2b-expressing tumors. Citation Format: Andrea Hernandez Rojas, Jodi Wong, Dunja Urosev, Sam Lawn, Kaylee Wu, Saki Konomura, Manuel Lasalle, Diego A. Alonzo, Luying Yang, Mark Petersen, Lemlem T. Degefie, Araba P. Sagoe-Wagner, Sohyeong Kang, Chi Wing Cheng, Raffaele Colombo, Daya Siddappa, Stuart D. Barnscher, Jamie R. Rich. ZW220, a novel NaPi2b-targeting antibody drug conjugate bearing a topoisomerase 1 inhibitor payload [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 1533.

Integrative Multi-OMICs Identifies Therapeutic Response Biomarkers and Confirms Fidelity of Clinically Annotated, Serially Passaged Patient-Derived Xenografts Established from Primary and Metastatic Pediatric and AYA Solid Tumors.

Establishment of clinically annotated, molecularly characterized, patient-derived xenografts (PDXs) from treatment-naïve and pretreated patients provides a platform to test precision genomics-guided therapies. An integrated multi-OMICS pipeline was developed to identify cancer-associated pathways and evaluate stability of molecular signatures in a panel of pediatric and AYA PDXs following serial passaging in mice. Original solid tumor samples and their corresponding PDXs were evaluated by whole-genome sequencing, RNA-seq, immunoblotting, pathway enrichment analyses, and the drug−gene interaction database to identify as well as cross-validate actionable targets in patients with sarcomas or Wilms tumors. While some divergence between original tumor and the respective PDX was evident, majority of alterations were not functionally impactful, and oncogenic pathway activation was maintained following serial passaging. CDK4/6 and BETs were prioritized as biomarkers of therapeutic response in osteosarcoma PDXs with pertinent molecular signatures. Inhibition of CDK4/6 or BETs decreased osteosarcoma PDX growth (two-way ANOVA, p < 0.05) confirming mechanistic involvement in growth. Linking patient treatment history with molecular and efficacy data in PDX will provide a strong rationale for targeted therapy and improve our understanding of which therapy is most beneficial in patients at diagnosis and in those already exposed to therapy.

Abstract 1539: LKB1 down-modulation by miR-17 biologically and clinically mirrors LKB1-mutated NSCLC

Abstract Introduction: In non-small cell lung cancer (NSCLC) LKB1 mutations combined with KRAS hyperactivation define a poor responsive, aggressive and disseminating phenotype. We recently unveiled the vulnerability of KRAS/LKB1 co-mutated (KL) patient-derived xenografts (PDXs) to metabolic stress-based treatments, and a clinical trial to test the efficacy of metformin and fasting-mimicking diet on KL NSCLC is currently ongoing in our Institute. Besides inactivating mutations, LKB1 functionality may be impaired by post-translation regulation. Because miR-17 is a potential epigenetic regulator of LKB1,we hypothesized that wild-type LKB1 (LKB1WT) NSCLC with high miR-17 expression may biologically and clinically mirror LKB1 mutated tumors. Methods: NSCLC cell lines with different combinations of KRAS mutation and LKB1 deletion were selected, together with a panel of PDXs with high (LKB1WT/miR-17 high) or low (LKB1WT/miR-17 low) miR-17 expression. Taking advantage of series of NSCLC patients and PDXs, we retrospectively evaluated LKB1 and miR-17 expression levels in tumor tissue specimens. In addition, the TCGA dataset was interrogated for miR-17 expression and potential correlation with lung cancer clinical features. Results: Direct targeting of miR-17 to LKB1 3’UTR was confirmed by luciferase reporter assay. We found that miR-17 overexpression in LKB1WT cell lines functionally impaired the LKB1/AMPK pathway, and prompted apoptotic response to metformin. Of note, LKB1WT/miR-17 high PDXs tumor cells showed a similar behavior upon metformin treatment. A retrospective analysis in patients with NSCLC revealed an inverse correlation between miR-17 and LKB1 expression, and highlighted a prognostic role of miR-17 expression in LKB1WT patients, further confirmed by TCGA data analysis. Conclusions: We validated miR-17 as epigenetic regulator of LKB1 expression in NSCLC tumors. We propose a miR-17 expression score potentially exploitable to discriminate LKB1WT NSCLC patients with impaired LKB1 expression and poor outcome, eligible for energy-stress-based treatments. Citation Format: Cristina Borzi, Monica Ganzinelli, Elisa Caiola, Marika Colombo, Giovanni Centonze, Mattia Boeri, Laura Caleca, Ugo Pastorino, Mirko Marabese, Massimo Milione, Massimo Broggini, Marina C. Garassino, Gabriella Sozzi, Massimo Moro. LKB1 down-modulation by miR-17 biologically and clinically mirrors LKB1-mutated NSCLC [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 1539.

Abstract 4001: Evaluation of novel therapeutics using the Mayo Clinic GBM Patient-Derived Xenograft (PDX) collection

Abstract The Mayo Clinic collection of patient-derived xenograft (PDXs) has been developed from the direct implantation of glioblastoma (GBM) samples into immunodeficient mice. Over 105 models have been extensively characterized with regards to histology, invasion, flank and orthotopic growth rates, and molecular profiling. Evaluation of orthotopic tumors demonstrated infiltration of tumor cells into the brain parenchymal in 90% of models with contralateral hemisphere involvement in 64%. Extensive molecular profiling confirmed the PDX collection captures the genetic heterogeneity of GBM, with the majority of typical molecular alterations seen at a frequency similar to the TCGA including gain of chromosome 7 and loss of chromosome 10. TERT promoter mutations (86%) and homozygous deletion of CDKN2A (70%) were the most frequent. Additional alterations in the p53 pathway included TP53 mutations (36%) and MDM2/4 amplification (10%/2%). IDH mutations were found in three models while MGMT promoter methylation was observed in 45% of PDXs. The available molecular sequencing results are viewable on cBioPortal. These genetically diverse models are extremely useful for biomarker discovery and efficacy evaluations. Using an innovative 1x1x1 PDX preclinical trial design, we are establishing a workflow to evaluate control and drug treatment in an individual animal across PDX lines in the flank. As our first use of this strategy, a small molecule MDM2 inhibitor was evaluated in 17 PDX lines with variable MDM2 and TP53 statuses. Tumors harboring MDM2 amplification without TP53 mutation (n=5) showed profound response, with 4 PDXs showing a complete response that lasted &amp;gt;150 days. Response in TP53 wild-type tumors lacking MDM2 amplification was variable, with a 1.9 to 4.8 fold longer time to endpoint (mean 3; median 2.7). A more traditionally powered intracranial efficacy study performed with one MDM2 amplified (GBM108) and two non-amplified (GBM14, GBM10) PDX lines confirmed these findings of reduced and more variable response to therapy in MDM2 non-amplified TP53 wild-type tumors. Future studies will aim to examine novel biomarkers indicative of therapeutic response to better understand molecular features associated with MDM2 inhibitor efficacy. With over 20 years of experience, our group has extensive expertise in development of clinically relevant study designs focused on examining efficacy, tolerability, and pharmacokinetic/pharmacodynamic assessments. Our diverse collection of clinically relevant GBM PDX models provides a highly sought-after resource which has been utilized by the pharmaceutical community with 58 working relationships to date (26 contracts, 32 collaborations). Through these collaborations, we aim to expand the use of our highly characterized GBM PDX panel for biomarker discovery using similar strategies. Citation Format: Danielle M. Burgenske, Ann C. Mladek, Shulan Tian, Mark A. Schroeder, Zeng Hu, Brett L. Carlson, Paul A. Decker, Jeanette E. Eckel-Passow, Rachael Vaubel, Jann N. Sarkaria. Evaluation of novel therapeutics using the Mayo Clinic GBM Patient-Derived Xenograft (PDX) collection [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 4001.

Abstract 3115: Establishment and characterization of patient-derived breast cancer models for cancer studies

Abstract BACKGROUND: Despite the progress and development of targeted agents and Immunotherapeutics, breast cancer is still the leading cause of death among women worldwide. At present, targeted therapy for breast cancers include endocrine blockage therapy for estrogen receptor positive (ER+) tumors and trastuzumab or lapatinib for HER2 positive (HER2+) tumors and CDK inhibitors for HER negative (HER-) tumors as well as PARP inhibitors for BRCA1/2 mutations. There is still a high unmet need for triple negative breast cancer (TNBC) and relapsed breast cancers with specific mutations. Breast cancer is a highly heterogeneous disease and reliable breast cancer models are needed to develop new clinical therapies and better reflect tumor biology. Patient-derived xenograft (PDX) models have been widely used for understanding tumor characteristics and represent human heterogeneity more faithfully and thus are suitable for mouse clinical studies for predicting drug efficacy in the clinic. Here we report the establishment and characterization of a panel of breast cancer (BC) PDX for preclinical research. METHODS: Tumor samples from patients’ breast tumor or metastastic lesion obtained via surgery, biopsy, or pleural effusions/ascites were engrafted subcutaneously in immunodeficient mice to establish PDX models. The models were classified and characterized by histopathology, immunohistochemistry (IHC), and breast cancer specific biomarkers such as estrogen receptor (ER), progesterone receptor (PR) and HER2. Genomic analysis of these models was performed by next generation sequencing (NGS). In these breast cancer models, the effects of estrogen on tumor growth and targeted endocrine therapy such as Fulvestrant were evaluated. The change of tumor volume over time was used to determine the growth rate and response to treatment in mice. RESULTS: A series of BC PDX models derived from primary patient breast tumor or metastatic lesions were successfully established and characterized. Key characteristics of parental tumors, such as histopathology, clinical markers, gene expression and copy number, as well as estrogen dependence was retained. The IHC data indicated various expression levels of ER, PR and HER2 across the panel, with TNBC being the dominant subtype. ESR1 mutation, which may play an important role in BC progression and endocrine therapy resistance, was also identified in an estrogen-independent model. In vivo, these models showed distinct tumor growth rates and different pharmacodynamic responses to standard of care agents. For example, ESR1 mutant model was responsive to Fulvestrant. CONCLUSIONS: The established BC PDX panel represent a range or ER/PR/HER2 expression status from primary and advanced cancer providing a series of preclinical models for breast cancer research and potential for mouse clinical trial enrollment. Citation Format: Leilei Chen, Xueying Yang, Likun Zhang, Xiaobo Chen, Henry Q.X. Li, Jingjing Wang. Establishment and characterization of patient-derived breast cancer models for cancer studies [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 3115.

Abstract P5-08-12: Efficacy of futibatinib, an irreversible fibroblast growth factor receptor (FGFR) inhibitor, in breast cancer models with FGFR alterations

Abstract Purpose: Several FGFR alterations have been found in breast cancer, however, their role as a therapeutic target in breast has been controversial. Futibatinib (TAS-120; Taiho) is a novel, selective pan-FGFR inhibitor which irreversibly binds to and inhibits FGFR1-4 at nanomolar concentrations. We sought to determine the efficacy of futibatinib in breast cancer models with differing FGFR alterations. Experimental Design: In vivo, antitumor efficacy was evaluated by tumor growth curves and event-free survival in a panel of patient-derived xenografts (PDXs) from breast cancer patients with different FGFR1-4 alterations. Genomic alterations in the PDXs were characterized by next generation sequencing. Correlation of FGFR gene expression in matched patient tumors and PDXs was analyzed by RNA sequencing. In vitro, FGFR2 Y375C mutant and FGFR2-BICC1 fusion expressing MCF10A cell lines were generated, and effect on cell proliferation, colony formation assay, and cell signaling was assessed with and without futibatinib. Frequency of FGFR mutations and FGFR2 amplification was compiled from internal and public databases. Results: Breast cancer PDXs varied in their expression of FGFR1-4. FGFR gene expression significantly correlated between matched patient tumors and PDXs derived from them, however, PDXs had higher levels of FGFR3 and FGFR4 expression compared to patient samples. Futibatinib inhibited tumor growth in three of 10 PDX models, with tumor stabilization in a FGFR2 amplified model and prolonged tumor regression (more than 110 days) in a PDX bearing a FGFR2 Y375C mutation. In vitro, expression of FGFR2 Y375C, as well as FGFR2-BICC fusion in normal-like MCF10A cells enhanced growth, colony formation ability and FGFR signaling. Cells expressing FGFR2 Y375C as well as FGFR2-BICC fusions were more sensitive to futibatinib. In the five breast cancer genomic series we analyzed, FGFR2 mutations and amplifications were found in 1.1%-2.6% and 1.4%-2.5%, respectively. Conclusions: Futibatinib had single agent activity of selected breast cancer PDX models. FGFR2 activating mutations and amplification may represent rare but promising therapeutic targets to FGFR inhibition. Citation Format: Turcin Saridogan, Argun Akcakanat, Ming Zhao, Kurt W. Evans, Erkan Yuca, Stephen Scott, Bryce P. Kirby, Xiaofeng Zheng, Senthil Damodaran, Funda Meric-Bernstam. Efficacy of futibatinib, an irreversible fibroblast growth factor receptor (FGFR) inhibitor, in breast cancer models with FGFR alterations [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-08-12.

Abstract P086: Identification of pharmacodynamic and sensitivity biomarkers for TACH101, a pan-inhibitor of KDM4 histone lysine demethylase

Abstract Background: TACH101 is a novel, selective and potent inhibitor of KDM4 in development for advanced cancers. KDM4 plays a key role in epigenetic regulation by removing methyl marks on histone H3K9 and H3K36. Overexpression of KDM4 leads to dysregulation of transcription, cell cycle, and DNA replication/repair processes and has been associated with many cancer types. Methods: Candidate pharmacodynamic (PD) and sensitivity biomarkers for TACH101 were evaluated in vitro and in vivo using cancer cell lines, mouse xenograft models, gene microarrays, ChIP-seq, and ChIP-qPCR. Results: Evaluation of differential gene expression from tumor tissue identified several candidates as potential PD markers for TACH101 activity. In particular, direct binding of KDM4 to Protein Phosphatase 1 Regulatory subunit 10 (PPP1R10 or PNUTS) was confirmed by ChIP-seq in cell lines from esophageal (KYSE-150), breast (MDA-MB-231) and lymphoma (OCI-Ly19) cancers. TACH101 treatment caused 86% repression of PNUTS mRNA, as well as a 51% increase in H3K9me3, a mark of repressed transcription. A 78% decrease in H3K36me3 at the PNUTS gene was also observed. PNUTS as a target of KDM4 was validated via ChIP-qPCR in xenograft tumors of KYSE-150, OCI-Ly19 and SU-60 (colorectal). In vivo, maximum inhibition of PNUTS was reached at 8 hours post TACH101 administration, when TACH101 concentration was 100-200 nM in tumors. In addition, extensive bioinformatics analysis using &amp;gt;300 cancer cell lines showed that cell lines with MSI-high (MSI-H) status tended to be more sensitive to TACH101 in vitro. This association was found with other markers of MSI-H status such as MMR gene mutations, MLH1 methylation status, and overall mutation frequency. To further test this association, TACH101 was evaluated in a panel of patient-derived xenograft (PDX) and organoid models. The results showed a strong correlation of TACH101 sensitivity with MSI-H status (IC50 ranges 1-150 nM). Conclusions: Candidate PD biomarkers of TACH101 activity for clinical evaluation have been identified and further studies are ongoing to explore current and additional markers. In addition, MSI-H status was associated with increased sensitivity to TACH101, which may be useful for enriching for select patient populations in clinical studies. Citation Format: Frank Perabo, Sanghee Yoo, Chandtip Chandhasin, Joselyn Del Rosario, Young K. Chen, Ellen Filvaroff, Jeffrey A. Stafford, Stephen Quake, Michael F. Clarke. Identification of pharmacodynamic and sensitivity biomarkers for TACH101, a pan-inhibitor of KDM4 histone lysine demethylase [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P086.

EXTH-51. DEVELOPMENT OF A NOVEL GENE THERAPY APPROACH TARGETING GLIOBLASTOMA FOLLOWING ARTIFICIAL INTELLIGENCE (AI)-DIRECTED IDENTIFICATION OF THE GBM STATE

Abstract BACKGROUND Profound heterogeneity has severely hampered therapeutic advancements in GBM. Remarkably, however, GBM exhibits broad clinical and histopathologic overlaps suggesting the presence of a common state. The GBM state embodies network restructuring forced by founding mutations and perpetuated in subclones of GBM stem-like cells (GSCs). Successful targeting of the GBM state promises to circumvent the heterogeneity. METHODS To decipher the GBM state, we applied NETZEN, an AI suite integrating a deep neural network with gene network-based ranking, to first generate the reference GBM gene network from TCGA’s entire GBM RNAseq collection, and then identify the altered master regulatory gene subnetwork in GBM using a dataset containing &amp;gt;30 diverse patient-derived GSC lines and their paired differentiated cells, 6 astrocyte and 3 neuronal precursor cell lines. To develop a gene therapy against the GBM state, we screened a rAAV capsid library through GBM patient-derived xenografts (PDX) to identify variants with specific tropism for GBM cells that can deliver targeting constructs intratumorally. RESULTS We discovered a putative GBM state anchored by developmentally restricted master regulators. To validate its critical role, we deconstructed it using shRNA in a panel of PDX and uniformly observed improved tumor control and survival compared to controls (p&amp;lt; 0.05 in all lines). More notably, when the core GBM state was forcibly reconstructed in astrocytes, transformation into GSC-like cells occurred, as measured by single-cell analysis, neurosphere formation, and most importantly, development of lethal infiltrating brain tumors in 15/15 mice. Finally, selected novel rAAV capsids with 10-40-fold higher specificity for GBM cells were utilized in a shRNA-based rAAV platform to target key master regulators of the validated GBM state. CONCLUSIONS The GBM state is established by a developmental master regulator subnetwork permitting the creation of a first-of-its-kind, heterogeneity-agnostic GBM therapy. This AI-directed R&amp;D program can be expanded to target other tumors.

Abstract 3008: Characterization of a panel of orthotopic bioluminescent patient-derived models for drug discovery

Abstract Background: Cancer is a complicated disease featuring geographic, genetic and immunological diversity. The tumor microenvironment (TME) is an essential part of tumor development, influencing tumor growth, metastasis and also therapeutic response. Patient-derived xenografts (PDX) and PDX-derived organoids (PDXO) are widely-used preclinically for drug evaluation with the prominent advantage of largely maintaining the histo- and molecular- pathology of the original tumor. Over decades of studies using PDX models, we found limitations in monitoring the orthotopic and metastatic pattern of cancer. With the development of gene engineering technologies (particularly for luciferase labeling), we now present the transduction of patient-derived models with firefly luciferase, to enable real-time monitoring of tumor burden in mice following orthotopic engraftment of either PDX tumor cells or PDXO in vivo. Methods: A panel of PDX cell slurry or PDXO cultures were transduced with lentiviral vectors carrying both the firefly luciferase gene as well as GFP. Mixed pools or GFP-sorted cells were used for in vivo validation. Bioluminescent PDX or PDXO were orthotopically and subcutaneously engrafted into immunodeficient mice. Real-time tumor growth and metastasis were monitored using the IVIS® Spectrum In Vivo Imaging System. Results: We have established a series of luciferase-labeled PDXO from different cancer types, including liver, ovarian, pancreatic and lung cancer and characterized their growth following orthotopic implantation. We have also established a series of luciferase-labeled PDX models from non-epithelial origin, including brain tumors, osteosarcoma and lymphomas. All of the models were confirmed with GFP signaling in vitro and showed significant luciferase signaling and growth in vivo. A mixed pool of bioluminescent PDXs or PDXOs presented heterogenous luciferase signals in tumors, while single clones or cell sorting by GFP or selected passage in vivo improved the consistency of the bioluminescent signal. Conclusions: PDX models are widely used as preclinical tools for clinical predictivity, however their application in orthotopic/metastatic modeling has been challenging due to the limitation in labelling PDXs for real-time monitoring. With the development of gene engineering technology in vitro and bioluminescent imaging (BLI) in vivo, we have developed and characterized a large panel of bioluminescent PDX and PDXO models from a range of different cancer types for real-time monitoring of orthotopic engrafted tumors in an organ-specific location to represent the TME, and the potential metastatic spread. Citation Format: Jessie Jingjing Wang, Jun Zhou, Ling Chen, Rongyun Zhou, Xiaoxi Xu, Henry Q. X. Li, Davy Xuesong Ouyang. Characterization of a panel of orthotopic bioluminescent patient-derived models for drug discovery [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 3008.

Abstract 4106: High throughput chemical profiling of chemoresistant triple negative breast cancer

Abstract Triple-negative breast cancer (TNBC) makes up approximately 10-20% of all breast cancers, is characterized by a lack of targeted therapies, and in approximately 40-50% of cases a significant residual cancer burden remains after neoadjuvant chemotherapy, thus presenting a need to identify actionable targets in both treatment naive and resistant settings. To address the unmet treatment needs of chemo-resistant patients, our multi-institutional collaborative of clinical oncologists and basic researchers are assembling a panel of patient-derived xenograft (PDX) models of TNBC as part of an ongoing IRB-approved clinical trial at MD Anderson Cancer Center (ARTEMIS; NCT02276443). PDX models are generated from serial fine needle aspirates of primary TNBC from patients (1) prior to treatment, and in non-responding tumors (2) after four cycles of Adriamycin plus cyclophosphamide (AC), and (3) after a 3-month course of targeted therapy. We first developed a standardized intake procedure that simultaneously optimized cell seeding densities in 384-well plates, tested multiple cell culturing medias, determined baseline phenotypic characteristics, and established robust assay controls. After optimization, we performed high-throughput drug screens with a panel of 634 mechanistically annotated chemical probes that are FDA approved, late stage investigational or mechanistic probes. A bioluminescent reporter quantifying the amount of ATP (CellTiter Glo, Promega) was used as a surrogate readout of cell viability, which is well suited for the majority of PDX cultures that grew as non-adherent multi-cellular aggregates as well as being integrable into larger datasets run in a similar format. Screening assays are performed with 3-4 technical replicates over a three log concentration range (10.0, 1.0, 0.1 uM). The effectiveness of each drug is summarized as an area under the fitted concentration-response curve, simultaneously capturing alterations in potency and efficacy. In total, we have tested 21 PDX models isolated from 14 unique patients using this strategy. From these data, we show that PDX models generated from individual patients have unique pharmacologic profiles with little correspondence to molecularly defined sub-classifications, which may suggest the need for the development of an actionable sub-classification strategy to better stratify patients. Despite the significant heterogeneity across pharmacologic profiles, we identified a consolidated set of drugs targeting specific epigenetic processes and protein homeostasis that have increased activity in a subset of chemo-resistant samples. We are currently collecting orthogonal data including next-generation sequencing and transcriptomics to further elucidate the mechanism of these targets and identify potential biomarkers. Citation Format: Reid Trenton Powell, Abena Redwood, Lei Guo, Shirong Cai, Yizheng Tu, Yan Jiang, Xuan Liu, Xinhui Zhou, Clifford Stephan, Peter Davies, Jeffrey T. Chang, Stacey Moulder, William F. Symmans, Helen Piwnica-Worms. High throughput chemical profiling of chemoresistant triple negative breast cancer [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 4106.

SKP2 My Lou, My Darling.

Myxofibrosarcoma and undifferentiated pleomorphic sarcoma (UPS) lack specific molecular underpinnings, show high rates of metastasis, and display limited responsiveness to current therapies, making them challenging cancers both to treat and to study. It has been noted that MFS and UPS frequently lose function of the tumor suppressor genes RB1 and TP53 In this issue of Cancer Research, Li and colleagues demonstrate that proliferation in RB1- and TP53-deficient MFS and UPS depends on SKP2; inhibiting SKP2 with the neddylation inhibitor, pevonedistat, halts tumor growth in a panel of patient-derived xenografts. This renders the oncogenic protein SKP2 a promising therapeutic target.See related article by Li et al., p. 2461.

Abstract A03: Predictors of HPV-related head and neck cancer progression identified through patient-derived models

Abstract Purpose/Objectives: Therapeutic innovation for human papilloma virus-related (HPV+) head and neck squamous cell carcinomas (HNSCCs) is hindered by both inadequate biomarkers and a paucity of experimental models. To address these limitations, this study aimed to establish the first well-characterized panel of patient-derived xenografts (PDXs) and organoids from HPV+ HNSCCs, which typically grow poorly outside humans. The models were hypothesized to retain molecular hallmarks of HPV+ HNSCC that are lost in cell lines. In addition, genotype-phenotype correlations in the models were hypothesized to offer prognostic utility for patients. Materials/Methods: Whole-exome sequencing was performed on 20 HNSCC PDXs, including nine new HPV+ PDXs. Results were compared against the known genetic profiles of human HPV+ HNSCCs and their derivative cell lines. Genetic traits of the PDXs were subsequently evaluated relative to their growth properties and the outcomes of their patients of origin. Genotype-phenotype associations in the models were then tested for prognostic utility across multiple published patient cohorts. Results: Despite low engraftment rates, HPV+ PDXs retained multiple molecular features of HPV+ HNSCC lost in cell lines, including PIK3CA mutations, TRAF3 deletion, and absence of EGFR amplifications. Selective engraftment notably enriched for NOTCH1 mutants, thus providing new models for this negatively prognostic feature in HPV+ HNSCC. Observation of high tumor mutational burden (TMB) in faster-growing models facilitated detection of a novel association between TMB and local progression in both HPV+ and HPV- patients. Whereas TMB’s prognostic utility was limited to early stage HPV- tumors, outcomes prediction for HPV+ cases was served by features of an HPV+ PDX from an outlier case with lethal outcome. Reduced E7 and p16INK4A levels found in this PDX led to detection of similar profiles among recurrent HPV+ HNSCCs in two patient cohorts. Further analysis of the same cohorts revealed lower E2F target gene expression downstream of reduced E7 levels to be predictive of recurrence and mortality. Conclusions: Our PDXs are the first models systematically shown to retain the distinguishing genetic hallmarks of HPV+ HNSCC lost in cancer cell lines. Beyond bridging the critical gap in experimental models, these materials revealed novel applications for quantifying TMB and viral oncogene effects in biomarker development. Our findings suggest that E2F target transcript levels allow discrimination of HPV+ HNSCC patients at risk of treatment failure. Emerging evidence that low E2F target expression in poor-prognosis cases is part of a wider decrease in the viral imprint upon host gene expression holds promise for development of molecular risk stratifiers with clinical utility. Citation Format: Nicole D. Facompre, Pavithra Rajagopalan, Varun Sahu, Frederico O. Gleber-Netto, Joseph A. Califano, Curtis R. Pickering, Phyllis A. Gimotty, Devraj Basu. Predictors of HPV-related head and neck cancer progression identified through patient-derived models [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr A03.

Effective targeting of NAMPT in patient-derived xenograft models of high-risk pediatric acute lymphoblastic leukemia.

The prognosis for children diagnosed with high-risk acute lymphoblastic leukemia (ALL) remains suboptimal, and more potent and less toxic treatments are urgently needed. We investigated the efficacy of a novel nicotinamide phosphoribosyltransferase inhibitor, OT-82, against a panel of patient-derived xenografts (PDXs) established from high-risk and poor outcome pediatric ALL cases. OT-82 was well-tolerated and demonstrated impressive single agent in vivo efficacy, achieving significant leukemia growth delay in 95% (20/21) and disease regression in 86% (18/21) of PDXs. In addition, OT-82 enhanced the efficacy of the established drugs cytarabine and dasatinib and, as a single agent, showed similar efficacy as an induction-type regimen combining three drugs used to treat pediatric ALL. OT-82 exerted its antileukemic action by depleting NAD+ and ATP, inhibiting the NAD+-requiring DNA damage repair enzyme PARP-1, increasing mitochondrial ROS levels and inducing DNA damage, culminating in apoptosis induction. OT-82 sensitivity was associated with the occurrence of mutations in major DNA damage response genes, while OT-82 resistance was characterized by high expression levels of CD38. In conclusion, our study provides evidence that OT-82, as a single agent, and in combination with established drugs, is a promising new therapeutic strategy for a broad spectrum of high-risk pediatric ALL for which improved therapies are urgently needed.