Structure-Based Design and Synthesis of Potent and Selective KRAS G12D Inhibitors

KRAS G12D mutation has been found in approximately 45% of pancreatic ductal adenocarcinoma (PDAC) cases, making it an attractive therapeutic target. Through structure-based drug design, a series of potent and selective KRAS G12D inhibitors were designed. The lead compound, ERAS-5024, inhibited ERK1/2 phosphorylation and cell proliferation in three-dimensional Cell-Titer Glo assays in AsPC-1 PDAC cells with single-digit nanomolar potency and caused tumor regression in the in vivo efficacy studies. We describe here the details of the design and synthesis program that led to the discovery of ERAS-5024.

The pharmacologic and toxicologic characterization of the potent and selective KRAS G12D inhibitors ERAS-4693 and ERAS-5024

Two potent and selective KRASG12D inhibitors, ERAS-4693 and ERAS-5024, were generated as possible clinical candidates to treat patients harboring G12D mutations in solid tumors. Both molecules exhibited strong anti-tumor activity in the KRASG12D mutant PDAC xenograft mouse models while ERAS-5024 also showed tumor growth inhibition when administered on an intermittent dosing regimen. Acute dose-limiting toxicity consistent with an allergic reaction was observed for both molecules shortly after administration at doses just above those which demonstrated anti-tumor activity, indicative of a narrow therapeutic index. A series of studies were subsequently conducted to identify a common underlying mechanism for the observed toxicity, including CETSA® (Cellular Thermal Shift Assay) as well as several functional off-target screens. Both ERAS-4693 and ERAS-5024 were identified to agonize MRGPRX2 which has been linked to pseudo-allergic reactions. In vivo toxicologic characterization of both molecules included repeat-dose studies in the rat and dog. Dose-limiting toxicities were observed in both species with ERAS-4693 and ERAS-5024 and plasma exposure levels at the maximum tolerated doses were generally below that which caused strong anti-tumor activity, supporting the initial observation of a narrow therapeutic index. Additional overlapping toxicities included a reduction in reticulocytes and clinical pathological changes suggestive of an inflammatory response. Furthermore, increases in plasma histamine were observed in dogs administered ERAS-5024, supporting the hypothesis that MRGPRX2 agonism may be the cause of the pseudo-allergic reaction. This work highlights the importance of balancing both the safety and efficacy of KRASG12D inhibitors as this class of molecules begins to enter clinical development.

Abstract 5255: Effect of STAT3 inhibitors, TTI-101 and SH5-07, against bladder cancer in preclinical 3D tumor models

Bladder cancer (BC) is a lethal genitourinary malignancy associated with frequent recurrence and poor survival due to metastatic potential. Identification of key cancer cell signaling networks and developing promising agents is critical for effectively inhibiting tumor growth and progression. In many cancers, including bladder cancer (BC), signal transducer and activator of transcription 3 (STAT3) has emerged as an important molecular pathway due to its role in promoting proliferation, invasion, and chemoresistance. Thus, developing STAT3 targeting, orally bioavailable small molecule inhibitors may be helpful for the prevention of BC progression and improving the survival rate of patients with muscle invasive BC. Monolayer culture has limitations for drug testing. Therefore, spheroid and organoid culture are used extensively as they may mimic in-vivo drug response more accurately. The aim of our study is to examine the preclinical anticancer efficacy of STAT3 inhibitors [TTI-101 (C188-9) and SH5-07] in 3D (spheroid and tumoroid) invitro models of BC. We optimized the spheroid growth using various BC cell lines [human (J82), rat (NBT-II), and mouse (MB49) BC cells]. Similarly, tumoroids from rat (BBN-induced bladder tumors) and transgenic mice (UPII-SV40T) bladder tumors were developed. These spheroids and tumoroids were treated with various concentrations (0 - 50 μM range) of STAT3 inhibitors and evaluated for their viability [Calcein AM (CA) and EtBr staining], ATP production (CellTiter-Glo™ 3D), and ROS production (MitoSOXTM). Effect of drug treatment on biomarkers of cell proliferation, apoptosis, stemness, STAT3 signaling, and immune modulation was determined using western blotting and immunofluorescence. Treatment with TTI-101 (0 - 50 μM or SH5-07 (0 - 50 μM) for 144 hrs resulted in significant reduction in the spheroids size (39-45% smaller Vs untreated; p<0.0001), along with decreased ATP levels (20%-40%, p<0.05). MitoSOXTM staining suggested that STAT3 inhibitors treatment increased ROS production in BC cells. CA and EtBr staining revealed that TTI-101 and SH5-07 treatment resulted in increased cell death in BC spheroids compared to control. Decreased spheroids and organoids size also correlated with increased apoptotic marker (cleaved caspase-3) along with decreased cyclin D1, PCNA, and pSTAT3 protein expression. Drug treated BC spheroids/tumoroids also showed reduction in CD44 (BC stemness and invasion marker) and induction of cGAS-STING pathway (cGAS, STING, TBK1, and IRF3) in comparison to the control. These findings indicate that STAT3 inhibitors, TTI-101 and SH5-07, could inhibit bladder cancer by suppressing STAT3 pathway activation and therefore warrant further study in vivo. (Supported by P30 CA225520 and Kerley-Cade Endowed Chair)

Citation Format: Surya P. Singh, Gopal Pathuri, Adam Asch, Brian Cholewa, Robert Shoemaker, Chinthalapally V. Rao, Venkateshwar Madka. Effect of STAT3 inhibitors, TTI-101 and SH5-07, against bladder cancer in preclinical 3D tumor models. [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 5255.

Abstract IA007: PREVENT agent development pipeline

The NCI’s PREVENT Cancer Preclinical Drug Development Program is a peer-reviewed program designed to support the preclinical development of promising agents and biomarkers for cancer interception/prevention towards clinical applications. PREVENT is not a grant program but allocates NCI contract resources to advance approved projects in a milestone-driven manner. Results obtained through NCI contract resources are returned to the applicant PIs and used to support further development by the applicants or in partnership with NCI. Resources available to PREVENT Program applicants include preclinical efficacy testing, CGMP manufacturing, GLP pharmacokinetic and IND-enabling toxicology studies, and IND filings. The PREVENT Program is focused on preventive agent development in the areas of Immunoprevention (cancer vaccines and immunomodulatory agents), Chemoprevention (novel mechanisms, anti-inflammatory agents, drug repurposing, toxicity reduction via alternative dosing regimens and agent combinations) and clinically translatable mechanistic biomarkers (pharmacodynamics, immune correlates, and tumor preventive efficacy). Submission deadlines for PREVENT Concept Applications occur twice per year on the second Monday in January and July. Further information can be obtained at the PREVENT Program website: https://prevention.cancer.gov/major-programs/prevent-cancer-preclinical

Citation Format: Mark Stevn Miller, Brian Cholewa, John Clifford, Vignesh Gunasekharan, Altaf Mohammed, Shanker Gupta, Robert Shoemaker, Shizuko Sei. PREVENT agent development pipeline [abstract]. In: Proceedings of the Second Biennial NCI Meeting: Translational Advances in Cancer Prevention Agent Development (TACPAD); 2022 Sep 7-9. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_2): Abstract nr IA007.

Abstract A018: Targeting STAT3 for bladder cancer prevention – in vitro studies using spheroid and organoid models

Signal Transducer and Activator of Transcription 3 (STAT3) is tightly regulated in normal cells to maintain a transiently active state. In contrast, persistent STAT3 activation is frequently observed in bladder cancer (BC) and is associated with poor prognosis and chemoresistance. Hence, developing small molecule inhibitors targeting STAT3 may be helpful for preventing BC progression and improving the survival rate of patients with metastatic BC. Recently, the use of three-dimensional in vitro models in drug development has gained popularity as they closely resemble, to an extent, the in vivo environment in heterogeneity and physiological conditions.

Here we established spheroid and organoid models for bladder cancer and evaluated STAT3 inhibitors (C188-9 and SH5-07) for their anticancer activity in vitro.

Initially, we optimized the spheroid growth from human, rat, and mouse BC cell lines (J82, NBT-II, MB49, respectively) and tumoroid growth from the BBN-rat bladder cancer model. The anticancer efficacy of C188-9 and SH5-07 was evaluated in vitro at various doses (0-50 µM) in the 3D models of BC. Assays were performed to determine spheroid viability (calcein AM (CA) and EtBr staining), ATP and ROS production (MitoSOX™). Protein isolated from control and drug treated spheroids/tumoroids was used to evaluate pharmacodynamic biomarkers of cell proliferation, apoptosis, and STAT3 signaling. We demonstrate that treatment with C188-9 and SH5-07 significantly decreased the spheroids size (39-45% smaller compared to untreated, p<0.0001) along with decreased ATP (20%-40%, p<0.05), and pSTAT3 protein expression in spheroids derived from BC cell lines and rat BC organoids. Further, MitoSOX™ staining showed that STAT3 inhibitor treatment induced mitochondrial mediated ROS generation in BC spheroids. CA and EtBr staining showed that C188-9 and SH5-07 treatment induced cell death in BC spheroids that was also associated with caspase-3 cleavage.

These findings indicate that C188-9 and SH5-07 could suppress the activation of the STAT3 pathway and inhibit the bladder cancer spheroid growth by inducing ROS production and thus warrants further evaluation in vivo. Furthermore, our study provided valuable spheroid and organoid models for evaluating therapeutic candidates in an in vivo-mimic microenvironment, thereby providing great potential for drug testing. (Partly supported by P30CA225520 and Kerley-Cade Endowed Chair)

Citation Format: Surya P Singh, Gopal Pathuri, Adam Asch, Brian Cholewa, Robert Shoemaker, Chinthalapally V. Rao, Venkateshwar Madka. Targeting STAT3 for bladder cancer prevention – in vitro studies using spheroid and organoid models [abstract]. In: Proceedings of the Second Biennial NCI Meeting: Translational Advances in Cancer Prevention Agent Development (TACPAD); 2022 Sep 7-9. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_2): Abstract nr A018.

Abstract 2671: ERAS-601, a potent allosteric inhibitor of SHP2, demonstrates anti-tumor activity in RAS/MAPK-driven tumor models

SHP2 is a non-receptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene. SHP2 transduces upstream receptor tyrosine kinase (RTK) signaling to the RAS/MAPK pathway via its phosphatase-mediated regulation of guanine nucleotide exchange factors (GEFs). The modulation of GEF activity impacts the rate at which KRAS cycles from the inactive GDP-bound state to the active GTP-bound state. ERAS-601 is a potent, selective small molecule allosteric inhibitor of SHP2. ERAS-601 potently inhibits the wild type SHP2 protein with a biochemical IC50 of 4.6 nM. ERAS-601 is a selective SHP2 inhibitor and demonstrates no appreciable inhibition against any off-target kinase or phosphatase across panels of 300 kinases and 12 phosphatases. ERAS-601 inhibits the loading of active GTP-bound oncogenic RAS and inhibits RAS/MAPK pathway signaling as measured by pERK1/2 inhibition and DUSP6 mRNA. ERAS-601 demonstrates anti-proliferative activity across a panel of human cancer cell line models with oncogenic alterations in the RAS/MAPK pathway. In a mouse in vivo study, ERAS-601 achieves substantial systemic exposure and demonstrates inhibition of ERK1/2 phosphorylation and DUSP6 mRNA levels in the NCI-H358 xenograft model. ERAS-601 also inhibits tumor growth in multiple RAS/MAPK-driven CDX and PDX models that harbor EGFR, KRAS, BRAF Class III, and NF1LOF mutations. ERAS-601 is a potent and selective allosteric SHP2 inhibitor that demonstrates anti-tumor activity in vitro and in vivo and is currently being studied as a monotherapy in an ongoing Phase 1 clinical study in patients with advanced or metastatic solid tumors (FLAGSHP-1, NCT04670679).

Citation Format: Leenus Martin, Roopal Patel, Jingchuan Zhang, Jennifer Yang, Robin Nevarez, Taylor Congdon, Les Brail, Robert Shoemaker. ERAS-601, a potent allosteric inhibitor of SHP2, demonstrates anti-tumor activity in RAS/MAPK-driven tumor models [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 2671.

Abstract 2669: ERAS-007 (ERK inhibitor) + ERAS-601 (SHP2 inhibitor) exhibit nonclinical combination activity across KRAS mutated NSCLC, CRC, and PDAC tumor models

KRAS mutations occur in about 25% of all cancers and promote oncogenesis via constitutive activation of the RAS/MAPK pathway. Targeting KRAS mutant tumors by inhibiting individual nodes in the RAS/MAPK pathway, including SHP2, SOS1, KRAS, RAF, MEK, and ERK, has shown early clinical activity, but the rapid emergence of resistance limits the benefit of monotherapy. Resistance is often mediated by reactivation of RAS/MAPK pathway signaling, which can occur by increased activation of upstream of the RAS/MAPK pathway (e.g., EGFR activation) and/or activation of RAS/MAPK pathway nodes (e.g., oncogenic BRAF and MEK mutations). Inhibiting both upstream and downstream RAS/MAPK pathway nodes has the potential to more robustly prevent reactivation relative to inhibition of a single node alone. We are currently exploring the combination of an inhibitor of an upstream node, SHP2, with ERAS-601 and the terminal downstream node, ERK1/2, with ERAS-007 (our first “MAPKlamp”) in nonclinical models. We evaluated this MAPKlamp in NSCLC, CRC, and pancreatic tumor models that harbored KRAS mutations in vitro and in vivo. In 14-day clonogenic assays in KRAS mutant NSCLC, CRC, and PDAC cell lines, this MAPKlamp inhibited colony growth more potently than ERAS-601 or ERAS-007 alone. In KRAS mutant CDX and PDX models, this MAPKlamp’s in vitro activity was observed in vivo where it achieved superior tumor growth inhibition and tumor regression relative to ERAS-601 and ERAS-007 monotherapy. This MAPKlamp showed in vitro and in vivo combination activity in KRAS mutant tumors, and these results support its clinical evaluation in RAS/MAPK pathway-driven tumors.

Citation Format: Leenus Martin, Erin D. Lew, Roopal Patel, Joanne Oh, Jingchuan Zhang, Robin Nevarez, Taylor Congdon, Wei Lin, Les Brail, Robert Shoemaker. ERAS-007 (ERK inhibitor) + ERAS-601 (SHP2 inhibitor) exhibit nonclinical combination activity across KRAS mutated NSCLC, CRC, and PDAC tumor models [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 2669.

Abstract 2675: Discovery of potent CNS-penetrant covalent KRAS G12C inhibitors

The RAS family of GTPases, which include KRAS, NRAS, and HRAS, are key regulators of cellular signaling, acting as molecular switches downstream of receptor tyrosine kinases (RTKs) and as key regulators of the RAS/MAPK pathway. RAS cycles between inactive (GDP) and active (GTP) states to regulate the activity of the RAS/MAPK pathway. In many cancers, activating KRAS mutations enable KRAS to persist in the active GTP-bound state, resulting in hyperactive RAS/MAPK pathway signaling that drives cell growth and survival. The KRAS G12C mutation occurs in 14% of lung adenocarcinoma, a cancer type that frequently metastasizes to the brain (40%). To address the high prevalence of KRAS G12C mutant CNS metastases in lung adenocarcinoma, we are developing CNS-penetrant covalent KRAS G12C inhibitors (“ERAS G12Ci’s”) to treat both CNS and systemic disease. ERAS G12Ci’s rapidly form covalent adducts with the KRAS G12C protein in its inactive GDP state and exhibit low nanomolar IC50’s in a nucleotide exchange assay. ERAS G12Ci’s demonstrate high selectivity in a cell-based proteome selectivity assay and inhibit the growth of RAS Initiative KRAS G12C mutant cells, and not RAS Initiative KRAS WT cells. ERAS G12Ci’s potently inhibit cell proliferation in 3-dimensional Cell-Titer Glo (3D-CTG) assays in KRAS G12C mutant lung and pancreatic cell lines (NCI-H1373, NCI-H2122, and MIA PaCa-2). Mechanistically, ERAS G12Ci’s blocked RAS-RAF complex formation and inhibited ERK1/2 phosphorylation. This in vitro activity translates in vivo where ERAS G12Ci’s induce pharmacodynamic modulation in the pancreatic cancer MIA PaCa-2 model. ERAS G12Ci’s significantly inhibit tumor growth in NCI-H1373 and NCI-H2122 CDX lung adenocarcinoma and MIA PaCa-2 PDAC models. No meaningful body weight loss or clinical adverse events were observed with any of these compounds. Human efflux transporter substrate assessments indicate that ERAS G12Ci’s are either not substrates or weak/modest substrates of P-gp, a crucial efflux transporter that can limit CNS penetration. In rat CNS studies, these inhibitors exhibit good CNS penetration performance as measured by brain-to-plasma partition coefficients, which are comparable to those of approved CNS-active small molecule inhibitors. Daily oral administration demonstrates dose-dependent tumor regression in intracranial and intra-carotid injection (ICA) KRAS G12C CDX models. We are optimizing multiple covalent CNS-penetrant KRAS G12C inhibitors that exhibit both CNS and systemic activity in vivo.

Citation Format: Jae Hyun Bae, Erin D. Lew, Jun Feng, Marcos Gonzalez-Lopez, Joanne Oh, Patrick Fagan, Matt Salie, Nick Isley, Richard Lam, Adriana Irimia, Robin Nevarez, Bingzhen Lin, Taylor Congdon, Jingchuan Zhang, Dawei Xuan, Ping Chen, Jean-Michel Vernier, Robert Shoemaker. Discovery of potent CNS-penetrant covalent KRAS G12C inhibitors [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 2675.

Oral administration of TRAIL-inducing small molecule ONC201/TIC10 prevents intestinal polyposis in the Apc min/+ mouse model

Colorectal cancer (CRC) incidence is rising globally. Hence, preventing this disease is a high priority. With this aim, we determined the CRC prevention potential of the TRAIL-inducing small molecule ONC201/TIC10 using a preclinical model representing high-risk familial adenomatous polyposis (FAP) patients, Apc min/+ mice. Prior to the efficacy study, optimal and non-toxic doses of ONC201 were determined by testing five different doses of ONC201 (0-100 mg/kg body weight (BW); twice weekly by oral gavage) in C57BL/6J mice (n=6/group) for 6 weeks. BW gain, organ weights and histopathology, blood profiling, and the plasma liver enzyme profile suggested no toxicities of ONC201 at doses up to 100 mg/kg BW. For efficacy determination, beginning at six weeks of age, groups of Apc min/+ male and female mice (n≥20) treated with colon carcinogen azoxymethane (AOM) (AOM-Apc min/+) were administered ONC201 (0, 25, and 50 mg/kg BW) as above up to 20 weeks of age. At termination, efficacy was determined by comparing the incidence and multiplicity of intestinal tumors between vehicle- and drug-treated groups. ONC201 showed a strong suppressive effect against the development of both large and small intestinal tumors in male and female mice. Apc min/+ mice treated with ONC201 (50 mg/kg BW) showed >50% less colonic tumor incidence (P<0.0002) than controls. Colonic tumor multiplicity was also significantly reduced by 68% in male mice (0.44 ± 0.11 in treated vs. 1.4 ± 0.14 in controls; P<0.0001) and by 75% in female mice (0.30 ± 0.10 in treated vs. 1.19 ± 0.19 in controls; P<0.0003) with ONC201 treatment (50 mg/kg BW). Small intestinal polyps were reduced by 68% in male mice (11.40 ± 1.19 in treated vs. 36.08 ± 2.62 in controls; P<0.0001) and female mice (9.65 ± 1.15 in treated vs. 29.24 ± 2.51 in controls; P<0.0001). Molecular analysis of the tumors suggested an increase in TRAIL, DR5, cleaved caspases 3/7/8, Fas-associated death domain protein (FADD), and p21 (WAF1) in response to drug treatment. Serum analysis indicated a decrease in pro-inflammatory serum biomarkers, such as IL1β, IL6, TNFα, G-CSF, and GM-CSF, in the ONC201-treated mice compared with controls. Our data demonstrated excellent chemopreventive potential of orally administered ONC201 against intestinal tumorigenesis in the AOM-Apc min/+ mouse model.

Abstract 440: Potentiation of EGFR peptide cancer vaccine by an orally bioavailable glutamine antagonist prodrug JHU-083

Lung cancer is the leading cause of cancer mortality worldwide. More than 85% of lung cancers are non-small cell lung cancer (NSCLC). EGFR mutations occur in 47.9% of Asia-Pacific patients with NSCLC and 19.2% of Western patients. The most common EGFR mutations (&gt;90%) are deletions in exon 19 and/or point mutations in exon 21 (L858R). Th1 helper cellular immunity is critical for immunotherapy-mediated tumor regression. We have previously characterized an MHC-II-restricted EGFR multi-peptide vaccine (two peptides: “SCVRACGADSYEMEEDGVRK” and “VWSYGVTVWELMTFGSKPY”) (EGFR-V) that targets the EGFR protein and decreases EGFR-driven lung tumorigenesis by ~80% in EGFRL858R transgenic mice that were vaccinated before doxycycline-induction of the EGFR protein [1]. However, diminished efficacy was observed when this MHC-II-restricted EGFR multi-peptide vaccine was given two weeks after doxycycline induction of the EGFR protein, suggesting that expression of the EGFR oncoprotein significantly increased the immunosuppressive microenvironment. JHU083, an orally bioavailable glutamine antagonist, has recently been shown to not only inhibit tumor growth but also boost anti-cancer immunity [2]. To determine if JHU083 could potentiate the efficacy of EGFR vaccine in a post-initiation setting, we evaluated in vivo antitumor efficacy of EGFR vaccine combined with JHU083 using an EGFRL858R transgenic mouse model. JHU083 inhibited tumor burden by 31% and EGFR vaccine suppressed tumor burden by 33%, whereas combining JHU083 with anti-EGFR peptide vaccine had an additive effect (54% tumor inhibition). Mechanistically, JHU083 by itself, markedly reduced the immunosuppressive monocytic myeloid-derived suppressor cells (MDSCs) in lung tissues. The combination of JHU083 and the vaccine significantly reduced Tregs in lung tissues. The anti-EGFR vaccine primarily induced expansion of antigen specific antitumor CD4+ effector T cells. Long term administration of JHU-083 did not decrease bodyweight in mice. Together with previous results, these data suggest that JHU083 could be used to reshape the tumor microenvironment toward one that enhances antitumor T cell responses and could further enhance the efficacy of the EGFR anticancer vaccine.

References1.Ebben, J.D., et al., Epidermal growth factor receptor derived peptide vaccination to prevent lung adenocarcinoma formation: An in vivo study in a murine model of EGFR mutant lung cancer. Mol Carcinog, 2016. 55(11): p. 1517-1525.2.Leone, R.D., et al., Glutamine blockade induces divergent metabolic programs to overcome tumor immune evasion. Science, 2019. 366(6468): p. 1013-1021.

Citation Format: Mofei Huang, Jing Pan, Qi Zhang, Shizuko Sei, Robert Shoemaker, Ronald Lubet, Yian Wang, Barbara Slusher, Ming You. Potentiation of EGFR peptide cancer vaccine by an orally bioavailable glutamine antagonist prodrug JHU-083 [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 440.

Abstract 2732: Frameshift neoantigen vaccination prevent Lynch syndrome mouse model intestinal cancer

Microsatellite-unstable (MSI) cancers occurring in the context of Lynch syndrome elicit pronounced tumor-specific immune responses directed against frameshift peptide (FSP) neoantigens, which result from mismatch repair (MMR) deficiency-induced insertion/deletion mutations in coding microsatellites (cMS). We have recently completed a clinical phase I/IIa trial that successfully demonstrated safety and immunogenicity of an FSP neoantigen-based vaccine in MSI colorectal cancer patients (Clinical trial number: NCT01461148). The vaccine was safe and induced robust cellular and humoral immune responses in all vaccinated patients. To further develop a cancer preventive vaccine against MSI cancers in Lynch syndrome, we aimed to establish a preclinical mouse model. A systematic database search was performed to identify cMS sequences in the murine genome. Subsequently, intestinal tumors obtained from Lynch syndrome mice (Msh2flox/flox VpC+/+) were evaluated for mutations affecting these candidate microsatellites. Thirteen candidate cMS were detected that presented with a mutation frequency of 15% or higher. Epitope prediction using the netMHC4.0 algorithm was performed, and ten most promising FSP neoantigens were synthesized. Immunogenicity was evaluated after vaccination of C57BL/6 mice using IFN-gamma ELISpot. Four FSP neoantigens derived from cMS mutations in the genes Nacad, Maz, Xirp1, and Senp6 elicited strong antigen-specific cellular immune responses. CD4-specific T cell responses were detected for Maz, Nacad, and Senp6 and CD8-positive T cells were detected for Xirp1 and Nacad. Vaccination with peptides encoding these four intestinal cancer FSP neoantigens promoted anti-neoantigen immunity, reduced intestinal tumorigenicity and prolonged overall survival (P&lt;0.01). Additionally, NSAIDs, which have chemopreventive efficacy for Lynch syndrome, increase T cell immunity against neoantigens. Mechanistic tumor mutation burden and adaptive immune response studies will be shown. In summary, these data support the further development of vaccination strategies for preventing cancers associated with Lynch syndrome.

Citation Format: Ozkan Gelincik, Hamza Ibrahim, Mine Ozkan, Aysel Ahadova, Shizuko Sei, Robert Shoemaker, Mattias Kloor, Magnus Von Knebel Doeberitz, Steven M. Lipkin. Frameshift neoantigen vaccination prevent Lynch syndrome mouse model intestinal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2732.

Abstract LB-200: A cGMP-grade chimeric papillomavirus candidate vaccine (HPV16 RG1-VLP) confers long term cross-protection compared to a nonavalent hpv vaccine in a pre-clinical papillomavirus animal model

Background: The National Cancer Institute (NCI) PREVENT Cancer Program (PREVENT) is a peer-reviewed R&D pipeline with the core emphasis on preclinical development and clinical translation of novel cancer preventive interventions. One of the latest PREVENT-supported projects include cGMP production and IND enabling studies of a broad spectrum experimental human papillomavirus (HPV) vaccine- HPV16 RG1-VLP. This monovalent chimeric virus-like particle (VLP) displays 360 copies of the highly conserved epitope RG1 (aa 17-36 of minor capsid protein HPV16 L2) in the DE loop of HPV16L1 VLP backbone, and is capable of eliciting broadly neutralizing antibodies that target several clinically relevant HPV genotypes. RG-1 induced cross-neutralizing titers are typically lower than anti-L1 antibodies generated by currently licensed HPV vaccines. Hence, durability of protection has been cited as a cause of concern. Here, using engineering-run cGMP grade HPV16-RG1VLPs formulated with alhdyrogel®, the durability of protection 6 month post-vaccination of HPV16 RG1-VLPs against Gardasil-9®, a licensed HPV vaccine was evaluated using an established papillomavirus disease model.

Methods: New Zealand white rabbits (n=15 per treatment group) were administered three intra-muscular vaccinations of HPV16-RG1 (80 µg), human doses of Gardasil-9®, or no vaccine (adjuvant only). Following vaccination, in vivo protection was assessed against 8 high-risk oncogenic HPVs utilizing methods from an established cottontail rabbit papillomavirus (CRPV) disease model. Within each treatment group, 5 rabbits were challenged two weeks post-final vaccination (at peak serum ELISA titer), while another 5 were challenged six months post-final vaccination to assess durability of protection. The remainder 5 rabbits will be challenged one year post final vaccination.

Results: During the peak-titer period, rabbits vaccinated with monovalent HPV16-RG1VLP were protected from disease development, which was comparable to the protection afforded by Gardasil-9®. Six months after final vaccination, despite lower serum titers, HPV16-RG1VLP immunized rabbits were still protected from disease development with vaccine efficacy comparable to that of Gardasil-9®. And, in some instances, HPV16-RG1VLP vaccine demonstrated a superior cross-protection.

Conclusions: Even as a monovalent formulation, HPV16 RG1 VLP vaccination was able to provide comparable protection against a number of high-risk oncogenic HPV types, including types not covered by Gardasil-9®, even after six months post-vaccination. As a monovalent VLP, HPV16 RG1 VLP holds promise as a broad-spectrum preventative vaccine candidate that could potentially provide broader protection at lower production costs. Studies evaluating protection one-year-post vaccination is currently in progress.

Citation Format: Jiafen Hu, Karla Balogh, Ken Matsui, Huimin Tan, Pola Olczak, George Buchman, Brian Howard, Jonathan White, Michelle Kennedy, Shizuko Sei, Elizabeth Glaze, Sarah Brendle, Christina Schellenbacher, Reinhard Kirnbauer, Richard Roden, Robert Shoemaker, Neil Christensen, Joshua Weiyuan Wang. A cGMP-grade chimeric papillomavirus candidate vaccine (HPV16 RG1-VLP) confers long term cross-protection compared to a nonavalent hpv vaccine in a pre-clinical papillomavirus animal model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-200.

Abstract 5090: Epitope mapping of mouse TERT for vaccine development

Telomerase reverse transcriptase (TERT) is one of two essential components of telomerase, an enzyme complex that generates and maintains telomeres. Telomerase is expressed mainly in embryonic and adult stem cells. Telomere biology has recently been implicated in the pathogenesis of a variety of diseases, and mutations in telomerase components result in a predisposition to solid malignancies. More recent findings show that TERT is not only expressed in late stage primary tumor cells and metastatic cells, but also expressed in incipient cancer stem cells and/or tumor-initiating cells, indicating that TERT has essential roles at every stage of tumorigenesis. However, the clinical benefit of a TERT (hTERT)-targeting vaccine, given as a single agent or in combination with chemotherapeutic agents, has been limited in patients with advanced cancer, possibly due to insufficient epitope coverage as well as tumor-induced immune suppression. Thus, targeting TERT in tumor-initiating cells in early stage lesions may be more effective in preventing cancer development and progression. To develop cancer preventive TERT vaccines, novel immunogenic epitopes must be first identified and evaluated in a relevant preclinical model of tumorigenesis. The goal of this project is to identify the epitopes of mouse TERT with high immunogenicity using MHC I-peptide binding assay by flow cytometry analysis. The in vitro peptide-induced MHC Class I stabilization assay was carried out using RMA/S cell line, which was derived from a Rauscher leukemia virus-induced C57BL/6 T cell lymphoma and is deficient in transporter associated with antigen processing (TAP). Results of screening the overlapping peptide library will be presented.

Funded by NCI Contract No. HHSN261200800001E

Citation Format: Yurong Song, Jason Marshall, Travis Kerr, Ligia Pinto, Shizuko Sei, Robert Shoemaker. Epitope mapping of mouse TERT for vaccine development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5090.

ALK, ROS1, and NTRK Rearrangements in Metastatic Colorectal Cancer

Background

ALK, ROS1, and NTRK fusions occur in 0.2% to 2.4% of colorectal cancers. Pioneer cases of metastatic colorectal cancer (mCRC) patients bearing rearrangements who benefited from anti-ALK, ROS, and TrkA-B-C therapies have been reported previously. Here we aimed at characterizing the clinical and molecular landscape of ALK, ROS1, and NTRK rearranged mCRC.

Methods

Clinical features and molecular characteristics of 27 mCRC patients bearing ALK, ROS1, and NTRK rearranged tumors were compared with those of a cohort of 319 patients not bearing rearrangements by means of Fisher's exact, χ2 test, or Mann-Whitney test as appropriate. Overall survival curves were estimated with the Kaplan-Meier method and compared using the log-rank test. A Cox proportional hazard model was adopted in the multivariable analysis. Deep molecular and immunophenotypic characterizations of rearranged cases, including those described in The Cancer Genome Atlas database, were performed. All statistical tests were two-sided.

Results

Closely recalling the "BRAF history," ALK, ROS1, and NTRK rearrangements more frequently occurred in elderly patients (P = .02) with right-sided tumors (P < .001) and node-spreading (P = .03), RAS wild-type (P < .001), and MSI-high (P < .001) cancers. All patients bearing ALK, ROS1, and NTRK fusions had shorter overall survival (15.6 months, 95% confidence interval [CI] = 0.0 to 20.4 months) than negative patients (33.7 months, 95% CI = 28.3 to 42.1 months), both in the univariate (hazard ratio [HR] = 2.17, 95% CI = 1.03 to 4.57, P < .001) and multivariable models (HR = 2.33, 95% CI = 1.10 to 4.95, P = .02). All four evaluable patients with rearrangements showed primary resistance to anti-epidermal growth factor receptor agents. Frequent association with potentially targetable RNF43 mutations was observed in MSI-high rearranged tumors.

Conclusions

ALK, ROS1, and NTRK rearrangements define a new rare subtype of mCRC with extremely poor prognosis. Primary tumor site, MSI-high, and RAS and BRAF wild-type status may help to identify patients bearing these alterations. While sensitivity to available treatments is limited, targeted strategies inhibiting ALK, ROS, and TrkA-B-C provided encouraging results.

Abstract 717: Mouse model for the development of preventive and therapeutic vaccines against microsatellite-unstable cancers

Microsatellite-unstable (MSI) cancers occurring in the context of Lynch syndrome elicit pronounced tumor-specific immune responses. These immune responses are specifically directed against frameshift peptide (FSP) neoantigens, which result from mismatch repair (MMR) deficiency-induced insertion/deletion mutations in coding microsatellites (cMS). We have recently completed a clinical phase I/IIa trial that successfully demonstrated safety and immunogenicity of an FSP neoantigen-based vaccine in MSI colorectal cancer patients (Clinical trial number: NCT01461148). To further develop a vaccine against MSI cancers in Lynch syndrome, we aimed to establish a preclinical mouse model. A systematic database search was performed to identify cMS sequences in the murine genome. Subsequently, intestinal cancers obtained from Lynch syndrome mice (Msh2flox/flox VpC+/+) were evaluated for mutations affecting these candidate microsatellites. Thirteen candidate cMS were detected that presented with a mutation frequency of 15% or higher. The cMS most frequently affected by frameshift mutations was located in the Nacad gene (75% of tested tumors). Epitope prediction using the netMHC4.0 algorithm was performed, and ten most promising FSP neoantigens were synthesized. Immunogenicity was evaluated after vaccination of C57BL/6 mice using IFN-gamma ELISpot. Four FSP neoantigens derived from cMS mutations in the genes Nacad, Maz, Xirp1, and Senp6 elicited strong antigen-specific cellular immune responses. CD4-specific T cell responses were detected for Maz(-1), Nacad(-1), and Senp(-1), all of which also induced humoral immune responses. CD8-positive T cells were detected for Xirp(-1) and Nacad(-1). Preliminary epitope mapping indicated that there was no cross-reactivity with the respective wild type proteins. Based on mutation data, a vaccine with the four FSP neoantigens has a predicted coverage of up to 75% of intestinal tumors in the Msh2flox/flox VpC+/+ Lynch mouse model. In summary, we have identified 4 immunogenic FSP neoantigens derived from commonly mutated cMS in murine Lynch syndrome colorectal cancers. These results provide the basis for evaluating the concept of cancer-preventive FSP vaccines in a mouse model of Lynch syndrome. This model allows longitudinal monitoring of immune responses and tumor development using different vaccination schemes, adjuvants and combination with chemoprevention.

Citation Format: Matthias Kloor, Mine Oezcan, Aysel Ahadova, Yan Yuan, Peer Bork, Shizuko Sei, Robert Shoemaker, Oezkan Gelincik, Steven Lipkin, Johannes Gebert, Magnus von Knebel Doeberitz. Mouse model for the development of preventive and therapeutic vaccines against microsatellite-unstable cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 717.

Abstract 3771: Mechanistic and pharmacodynamic characterization of the immuno-oncological activity of RXDX-106, a novel TYRO3, AXL, and MER (TAM) inhibitor in clinical development

The TAM family of receptor tyrosine kinases (RTKs) includes TYRO3, AXL, and MER, and is a unique set of molecular targets for cancer immunotherapy. TAM RTKs play a key role in the tumor microenvironment (TME) as negative regulators of innate immune responses and contribute to the evasion of cancer cells from immunosurveillance. RXDX-106 is a novel small molecule TAM inhibitor with single-digit nanomolar kinase inhibition and slow dissociation binding kinetics resulting in potent and durable target inhibition. In preclinical studies, RXDX-106 has demonstrated immune-mediated single agent in vivo activity in multiple syngeneic tumor models and potentiated anti-tumor activity in combination with immune checkpoint inhibitors. To characterize the mechanism of action of and pharmacodynamic responses to RXDX-106 treatment, an integrated approach was employed to explore RXDX-106-mediated immune modulatory effects at the cellular, protein, and transcriptional levels. In syngeneic tumor models, RXDX-106 treatment resulted in the recruitment of both innate and adaptive immune cell subtypes to the TME. Specifically, RXDX-106 treatment resulted in increased immune cell infiltration, macrophage polarization towards an antitumor M1 phenotype, activation of T cell and NK cell function, and modulation of immune markers at both the protein and RNA level, indicative of a pro-inflammatory and anti-tumorigenic effect. Importantly, the immune modulatory effects of RXDX-106 were concordant across platforms. Immune modulation was further characterized in a dose-dependent manner, with increasing immune cell infiltration observed with escalating doses of RXDX-106. In summary, RXDX-106 has the potential to restore and enhance immune function by modulating the local immunosuppressive TME. The unique mechanism of activating both innate and adaptive immunity, and regulating cross-talk between immune cells and tumor cells, supports clinical evaluation of RXDX-106 as an immunomodulatory agent for the treatment of a variety of cancers.

Citation Format: Amanda Albert, Erin D. Lew, Kristen Smith, Elizabeth A. Tindall, Yumi Yokoyama, Amy Diliberto, Heather Ely, Jack Lee, Robin Nevarez, Joanne Oh, Colin Walsh, Jason Christiansen, Gary Li, Robert Shoemaker. Mechanistic and pharmacodynamic characterization of the immuno-oncological activity of RXDX-106, a novel TYRO3, AXL, and MER (TAM) inhibitor in clinical development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3771.

Abstract 52: Antitumor activity of entrectinib, a highly potent pan-TRK, ROS1, and ALK inhibitor, in NTRK-fusion positive acute myeloid leukemia

Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and comprises a heterogeneous group of diseases. A number of recurrent leukemogenic gene mutations or chromosomal rearrangements have been identified and clinically validated in AML. However, nearly 50% of AML patient samples lack any known canonical AML driver mutations. Advances in molecular diagnostics have resulted in the identification of novel and actionable gene mutations or chromosomal rearrangements in a subset of these AML samples. The ETV6-NTRK3 fusion gene is one such rearrangement identified in samples from patients with AML. Fusion of ETV6 to the tyrosine kinase domain of TRKC (encoded by NTRK3) results in constitutive activation of the TRKC kinase, and ETV6-TRKC fusion protein expression has been shown to be sufficient for leukemogenesis. Constitutive activation of TRK family tyrosine kinases has also been detected in a wide range solid tumor and hematologic malignancies including lung, colorectal, salivary gland, sarcoma, thyroid, glioblastoma, melanoma, anaplastic large cell lymphoma, and Philadelphia-like acute lymphoblastic leukemia.

Entrectinib (RXDX-101) is an investigational, orally available, CNS-active, highly potent, and selective kinase inhibitor with low nanomolar potency against TRKA/B/C, ROS1 and ALK kinase activities (encoded by NTRK1/2/3, ROS1, and ALK genes, respectively). In these studies, we have demonstrated sensitivity to entrectinib in AML cell lines with endogenous expression of the ETV6-NTRK3 fusion gene. Entrectinib treatment blocked cell proliferation and induced apoptotic cell death in vitro with sub-nanomolar IC50 values. Phosphorylation of the ETV6-TRKC fusion protein, as well as phosphorylation of known TRKC downstream signaling effectors, was inhibited by entrectinib treatment in a dose-dependent manner. Sensitivity to entrectinib was dependent on expression of the TRKC fusion protein. In xenograft models, entrectinib treatment at clinically relevant doses resulted in tumor regression, which was accompanied by elimination of residual cancer cells from the bone marrow.

The clinical relevance of activated oncogenic tyrosine kinases resulting from chromosomal rearrangements has been validated by the efficacy of selective tyrosine kinase inhibitors. Entrectinib is currently the subject of STARTRK-2, an ongoing global phase 2 basket study enrolling patients across multiple tumor histologies containing TRK, ROS1, or ALK fusions. Our preclinical data demonstrate the potential of entrectinib as an effective treatment for patients with NTRK rearranged acute myeloid leukemia and provide a rationale for the clinical development of entrectinib in molecularly defined hematologic malignancies.

Citation Format: Patrick Fagan, Maria Barrera, Colin Walsh, Danielle Murphy, Ian Silverman, Robert Shoemaker, Ge Wei, Zachary Hornby, Gary Li, Kristen M. Smith. Antitumor activity of entrectinib, a highly potent pan-TRK, ROS1, and ALK inhibitor, in NTRK-fusion positive acute myeloid leukemia [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 52.

Abstract 5110: A novel nucleoside analog therapeutically active against plasma cell malignancies and other ADK-expressing cancers including colon and pancreatic adenocarcinomas

A number of nucleoside analogues are used successfully for the treatment of several cancers, and in particular leukemias and lymphomas, but these have distinct efficacies for different tumor types, and many malignancies do not respond to currently available nucleoside analogues or other forms of chemotherapy. A high throughput screen conducted in our lab to search for inhibitors of primary effusion lymphoma (PEL) identified the nucleoside analog 6-ethylthioinosine (6-ETI) as a potent and selective inhibitor of PEL, a largely incurable malignancy of B cell origin with plasmacytic differentiation. 6-ETI induced necrosis and ATP-depletion accompanied by S-phase arrest, DNA damage and inhibition of DNA synthesis. To understand 6-ETI mechanism of selectivity, RNA-seq analysis of in vitro generated drug-resistant PEL clones revealed inactivating mutations and loss of expression of adenosine kinase (ADK) as the mechanism of resistance. In vitro assays showed that 6-ETI is a pro-drug that gets phosphorylated and activated by adenosine kinase (ADK) into its active form. We found high ADK expression in PEL cell lines and primary specimens of PEL, multiple myeloma (MM) and plasmablastic lymphoma (PBL) patient samples. 6-ETI was effective at killing multiple myeloma cell lines, primary MM specimens, and had a remarkable anti-tumor response in a disseminated multiple myeloma and PEL xenograft mouse models. Thus, ADK expression can serve as a predictive biomarker to help identify patients that are most likely to respond to 6-ETI treatment. To further assess the spectrum of activity and sensitivity of 6-ETI, we examined ADK expression in other cancer subtypes and found that colorectal and pancreatic adenocarcinomas also overexpress ADK and are highly sensitive to killing by 6-ETI at the low nanomolar concentration. We also found high ADK expression in primary colon and pancreatic adenocarcinoma patient specimens. We compared 6-ETI to other FDA-approved purine analogs and failed to find other compounds with similar potency or selectivity profile. Herein, we report the identification of a novel purine analog, 6-ethylthioinosine, as an effective therapeutic with exquisite sensitivity to plasma cell malignancies and other ADK-expressing cancers. We have successfully used RNASeq-based “resistome” analysis to identify its mechanism of specificity and discovered a new biomarker that can potentially impact patient care and the treatment of some of the most aggressive tumors.

Citation Format: Jouliana Sadek, Utthara Nayar, Jonathan Reichel, Jennifer Totonchy, Shizuko Sei, Robert Shoemaker, David Warren, Olivier Elemento, Kenneth Kaye, Ethel Cesarman. A novel nucleoside analog therapeutically active against plasma cell malignancies and other ADK-expressing cancers including colon and pancreatic adenocarcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5110. doi:10.1158/1538-7445.AM2017-5110

Abstract 742: Comprehensive detection of all major classes of MET deregulation by Anchored Multiplex PCR and next-generation sequencing

Introduction: Deregulation of the proto-oncogene, MET, confers an aggressive phenotype in a variety of human cancers, promoting proliferation, invasive growth and angiogenesis. MET deregulation can be driven by gene amplification, overexpression, exon 14 skipping, gene fusions and single nucleotide variants (SNVs), such as kinase-activating point mutations. MET is a target of intensive drug development efforts, although the various mutated forms of MET exhibit unique drug sensitivities. Therefore, detection of these mutations has an important role in the development of drugs targeting MET, and has the potential to guide treatments for cancers driven by MET deregulation.

Next-generation sequencing (NGS) enables comprehensive detection of all mutation types from whole genomes and transcriptomes. However, low detection sensitivity, high input requirement and high costs render these approaches impractical for routine detection of mutations from low-input clinical sample types. We developed a targeted NGS assay based on Anchored Multiplex PCR (AMP™) to detect all types of mutations driving MET deregulation from a single sample.

Methods: AMP only requires a single gene-specific primer for amplification, enabling open-ended capture of DNA and cDNA fragments for NGS-based detection of known and unknown mutations. We developed AMP-based Archer® VariantPlex™ and FusionPlex® library preparation assays to detect mutations from DNA and RNA, respectively. AMP probes were designed to cover the MET gene for detection of copy numbers variants (CNVs) and SNVs from DNA, and known and novel fusions, exon skipping and expression levels from RNA.

Results: We show that the VariantPlex assay enables NGS-based detection of MET amplifications from DNA in concordance with FISH results. Further NGS analysis of RNA from the same sample using the FusionPlex assay revealed the resulting overexpression of MET. We also demonstrate that AMP-enabled open-ended capture of cDNA fragments allows for reliable detection of exon 14 skipping in FFPE samples and in cells, consistent with RT-PCR results. Parallel analysis of DNA from the cell samples revealed splice site mutations that have been previously reported to drive exon 14 skipping. Furthermore, this open-ended capture also permitted identification of a novel GTF2I:MET gene fusion in a patient-derived xenograft model. Finally, we detected an kinase-activating point mutation in MET, p.Y1253D, by analysis of genomic DNA with the VariantPlex NGS assay.

Conclusions: These results show that AMP-based VariantPlex and FusionPlex Assays enable comprehensive detection of multiple mutation types from low-input clinical sample types, such as FFPE specimens. As MET deregulation can be driven by many different genetic aberrations, this allows for NGS-based characterization of MET deregulation from a single sample.

Citation Format: Brian A. Kudlow, Josh Haimes, Marc Bessette, Namitha Manoj, Laura M. Griffin, Danielle Murphy, Robert Shoemaker, Jason Amsbaugh, Joshua Stahl. Comprehensive detection of all major classes of MET deregulation by Anchored Multiplex PCR and next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 742. doi:10.1158/1538-7445.AM2017-742

Abstract 5274: A novel, statistical-based method to determine RNA expression by next-generation sequencing in clinical FFPE samples

Introduction: Next-generation sequencing (NGS) has become a critical diagnostic assay to identify pathologic SNVs, CNVs, and gene rearrangements. However, it has not been routinely used to assess expression levels of target genes that could indicate patient populations responsive to therapeutics. This is largely due to the absence of reliable bioinformatics tools for the assessment of expression levels within RNA assays. We have developed a novel within-sample distribution-based method that assesses the relative extremity of expression for individual genes. Our predominate focus has been on assessing the expression of NTRK1, NTRK2, NTRK3, ROS1, and ALK, however this method can be readily applied to other genes and NGS platforms.

Methods: Within the kinase domain, the expression of a targeted region is represented by the number of unique deduplicated reads for NGS studies and normalized probe expression values (based on spike-in controls) for NanoString studies. A Poisson distribution is used to represent primer expression with the parameters estimated via maximum likelihood. The interquartile range (IQR) of the entirety of the sample's read counts is calculated and only those that do not exceed the third quartile bound by more than 150% of the IQR are considered during parameter estimation. A probability is then assigned to each of the primers based on their read counts. A geometric mean of the individual primer probabilities represents the probability value for the entire gene. Expression values are reported as -log10 (p-value) and cutoffs of 6 and 1 were used to call significant expression for NGS and NanoString platforms, respectively.

Results: The NGS-based approach correctly identified significant expression in all gene rearrangement positive cell lines (n = 11). In cell lines not harboring gene rearrangements, the NGS and NanoString platforms showed 100% concordance in calling significant expression (n = 12). In a gene rearrangement negative FFPE cohort, concordance between NGS and NanoString platforms was 97%-99% for target genes (n = 102). ROS1 and ALK were most commonly found to be significantly expressed in FFPE samples (5% and 2%).

Conclusions: We have developed a statistical-based approach to detecting expression levels for RNA-based NGS assays. This can be applied to cohort studies to not only identify clinical samples that may benefit from targeted kinase inhibitor therapeutics but also correlate with predicted outcome of disease.

Citation Format: Robert Shoemaker, Aaron Berlin, Amy Diliberto, Heather Ely, Marissa Chen, Danielle Murphy, Jason Christiansen, Vince Reuter, Abel Licon. A novel, statistical-based method to determine RNA expression by next-generation sequencing in clinical FFPE samples. [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 5274.

Mesothelin Vaccination for the Prevention of Ovarian Cancer

Survival of ovarian cancer patients with high-grade serous carcinoma (HGSC) remains low. We hypothesized that a tumor antigen-targeted vaccine capable of eliciting a robust cell-mediated immune response may substantially improve women’s health. Mesothelin is a glycosylphosphatidylinisotol (GPI)-anchored, conserved protein that is overexpressed by ovarian, lung and pancreatic cancers. We designed mesothelin vaccines containing cyclic dinucleotide (CDN)-based adjuvants or alum-based adjuvants to trigger CD8 T cell activation. Anti-mesothelin antibody titers were stable or slightly increased after 2 vaccine boosts, and the highest and most stable titers were obtained with CDN-based adjuvants (meso/CDN). In addition, splenocytes from all mice receiving CDN-containing vaccines secreted mesothelin-specific IFNγ. Next, immunized mice were injected orthotopically with luciferase-transduced mouse ovarian cancer cells (ID8). In vivo imaging performed 3 weeks after tumor injections revealed that most of the mice from the groups immunized with Alum-based vaccines (92%) presented a positive signal of bioluminescence, which corresponds to the routine take rate of the ID8 tumors. In contrast, only 1/3 of the mice in the meso/CDN group showed a positive signal compared with 2/3 of the mice immunized with the control CDN-only vaccine. These results suggest that the meso/CDN vaccine regimen delayed tumor establishment. Longer observation of the mice is ongoing to determine whether the vaccination regimen can prevent tumor development. We tentatively conclude that ovarian cancer prevention may be possible through vaccination against mesothelin tumor antigen in combination with adjuvants that trigger cellular immunity.

Abstract A174: RXDX-105 demonstrates potent RET inhibitory activity with therapeutic potential in multiple preclinical models of RET-rearrangement driven cancer

Genomic alterations in RET, encoding the RET (rearranged in transformation) kinase, have been identified as bona fide oncogenic drivers in numerous tumor types. Activating RET point mutations are typically associated with multiple endocrine neoplasia (types A and B) and familial medullary thyroid carcinoma. Although activating RET rearrangements can be found in up to 40% of papillary thyroid cancers, they are only present in up to 2% of non-small cell lung cancers and at lower frequencies in multiple other malignancies. As a result of the relatively low prevalence of molecular alterations in multiple tumor types, diagnostics-driven therapeutic selection strategies are being developed to identify patients with RET alterations. There also remains a clinical need for a potent, selective and safe RET inhibitor that demonstrates robust efficacy in malignancies harboring RET rearrangements and other oncogenic alterations.

RXDX-105 (formerly CEP-32496) is a potent, orally available, small molecule kinase inhibitor that potently binds and antagonizes several known oncogenic driver proteins, including RET, while sparing VEGFR2. RXDX-105 is currently in clinical trial in patients with solid tumors. To evaluate the therapeutic potential of RXDX-105 in malignancies bearing RET alterations, we first assessed the ability of RXDX-105 to antagonize RET activity in vitro. In biochemical and cell based assays, RXDX-105 potently antagonizes the activity of RET-fusion proteins and RET activating point mutations, resulting in a dose dependent inhibition of downstream signaling events and cell proliferation. In vivo, RXDX-105 displays potent and dose dependent anti-tumor activity with significant tumor growth regressions in several patient derived xenograft models harboring RET-rearrangements.

These pre-clinical studies support the inclusion of patients bearing RET alterations in future diagnostics-based clinical trials exploring RXDX-105 efficacy across a variety of tumor types.

Citation Format: James Joseph, Aleksandra Franovic, Anni Schairer, Eric Martin, Ge Wei, Danielle Murphy, Jason Christiansen, Robert Shoemaker, Pratik Multani, Robert Wild, Gang Li. RXDX-105 demonstrates potent RET inhibitory activity with therapeutic potential in multiple preclinical models of RET-rearrangement driven cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A174.

Abstract B177: RXDX-107, a dodecanol alkyl ester of bendamustine, demonstrates improved pharmacokinetic properties and significant anti-tumor efficacy in preclinical models of solid tumors

Bendamustine is an alkylating agent that can form interstrand DNA crosslinks (ICLs) and cause cell death via several pathways, including intrinsic apoptosis. Bendamustine has proven to be a potent and effective treatment for patients with chronic lymphocytic leukemia (CLL) and rituximab-refractory indolent non-Hodgkin's lymphoma (NHL), with additional clinical activity seen in other B-cell malignancies and in multiple myeloma (MM). However, the activity of bendamustine in the treatment of solid tumor malignancies has been less impressive, possibly due to the pharmacokinetic and biodistribution properties of bendamustine.

RXDX-107 is a dodecanol alkyl ester of bendamustine, and the clinical drug product is encapsulated in human serum albumin (HSA) to form nanoparticles. RXDX-107 was designed to improve tissue biodistribution over bendamustine, which may result in superior efficacy and tolerability in patients with solid tumors. In in vitro anti-proliferative studies, RXDX-107 displayed dose-dependent cytotoxicity against multiple solid tumor cell lines, including non-small lung cancer (NSCLC), breast and ovarian cancer. While the IC50s of RXDX-107 were comparable to those of bendamustine, RXDX-107 displayed stronger induction of pH2AX (a biomarker for DNA damage) and more complete cell killing than bendamustine in multiple cell lines. Furthermore, RXDX-107 potently inhibited subcutaneous tumor growth in cell line-derived xenograft (CDX) models of human NSCLC and breast cancer. Importantly, RXDX-107 also showed single agent anti-tumor activities, including tumor regression in multiple patient-derived xenograft (PDX) models of advanced solid tumors, such as breast, lung, and ovarian cancer.

In conclusion, our preclinical data demonstrate potent and broad anti-tumor activity of RXDX-107 across a variety of solid tumor types, and support further clinical development of this novel drug candidate for the treatment of solid tumors.

Citation Format: Leenus Martin, Roopal Patel, Anthony Drager, Renee Roemmele, Bradley McIntyre, Robert McKean, Piyush Patel, Peter Chua, Jerry Cao, Robert Shoemaker, Peter Brown, Pratik Multani, Robert Wild, Ralph Lin, Gang Li. RXDX-107, a dodecanol alkyl ester of bendamustine, demonstrates improved pharmacokinetic properties and significant anti-tumor efficacy in preclinical models of solid tumors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B177.

Abstract A173: Potent anti-tumor activity of entrectinib in patient-derived models harboring oncogenic gene rearrangements of NTRKs

The Trk family of kinases, which include TrkA, TrkB and TrkC, encoded by NTRK1, NTRK2 and NTRK3, respectively, are high affinity receptors for the neurotrophin family of nerve growth factors. Dysregulated kinase activity of Trk family members due to chromosome rearrangements has been shown to be an oncogenic driver in a number of cancer types, including lung, colorectal, salivary gland, papillary thyroid, glioblastoma, melanoma and other tumors. Although the prevalence of such events is relatively low in most tumor types (&lt;2%), the number of new fusion partners and the list of tumor types that are found to harbor these driver fusions have been steadily increasing. The significant unmet medical need and the relatively low frequency of fusion incidents require an integrated therapeutic/diagnostic (Rx/Dx) approach to best serve the patients in need.

Entrectinib (formerly RXDX-101) is an orally available, potent and selective ATP-competitive pan-Trk, ROS1 and ALK inhibitor, with comparable, low nanomolar potency against kinase activity of TrkA, TrkB and TrkC in biochemical and cell based assays. In engineered BaF3 cells expressing clinically identified Trk fusion proteins, with various partners, entrectinib demonstrated potent anti-proliferative activity in the range of 2-5 nM, accompanied by inhibition of Trk phosphorylation and concomitant inactivation of downstream effectors such as PLCγ1, AKT and ERK. The clinical relevance of targeting Trk fusions by entrectinib was further demonstrated by several in vitro and in vivo studies involving patient-derived tumor cells (PDCs) and patient-derived xenografts (PDXs) determined to harbor (by NGS and FISH) and express (by IHC) Trk rearrangements. In 2-dimensional and 3-dimensional proliferation assays, entrectinib effectively inhibited proliferation of PDCs from a CRC patient positive for TPM3-NTRK1 fusion. In another independent study, entrectinib, at exposures significantly lower than clinically achievable levels, caused tumor regression in a PDX derived from a CRC patient positive for LMNA-NTRK1 fusion. All the functional readouts were correlated with changes in target and pathway biomarkers.

In conclusion, our preclinical data demonstrate the potential of entrectinib as an effective treatment for Trk-fusion driven tumors of multiple histologies, which is now being demonstrated in ongoing clinical trials.

Citation Format: Gang Li, Seung Tae Kim, Kyoung-Mee Kim, Jeeyun Lee, Mariangela Russo, Sandra Misale, Alberto Bardelli, Roopal Patel, Nicholas Cam, Ge Wei, Aaron Boomer, Danielle Murphy, Jason Christiansen, Robert Shoemaker, Zachary Hornby, Robert Wild. Potent anti-tumor activity of entrectinib in patient-derived models harboring oncogenic gene rearrangements of NTRKs. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A173.

Acquired Resistance to the TRK Inhibitor Entrectinib in Colorectal Cancer

Entrectinib is a first-in-class pan-TRK kinase inhibitor currently undergoing clinical testing in colorectal cancer and other tumor types. A patient with metastatic colorectal cancer harboring an LMNA-NTRK1 rearrangement displayed a remarkable response to treatment with entrectinib, which was followed by the emergence of resistance. To characterize the molecular bases of the patient's relapse, circulating tumor DNA (ctDNA) was collected longitudinally during treatment, and a tissue biopsy, obtained before entrectinib treatment, was transplanted in mice (xenopatient), which then received the same entrectinib regimen until resistance developed. Genetic profiling of ctDNA and xenopatient samples showed acquisition of two point mutations in the catalytic domain of NTRK1, p.G595R and p.G667C. Biochemical and pharmacologic analysis in multiple preclinical models confirmed that either mutation renders the TRKA kinase insensitive to entrectinib. These findings can be immediately exploited to design next-generation TRKA inhibitors.

SIGNIFICANCE

We provide proof of principle that analyses of xenopatients (avatar) and liquid biopsies allow the identification of drug resistance mechanisms in parallel with clinical treatment of an individual patient. We describe for the first time that p.G595R and p.G667C TRKA mutations drive acquired resistance to entrectinib in colorectal cancers carrying NTRK1 rearrangements.

Abstract 127: Overexpression of neurotrophic tyrosine receptor kinases (NTRKs) as a potential therapeutic target for cancer

Neurotrophic tyrosine receptor kinases (NTRKs), or Tropomyosin receptor kinases (Trks), belong to a family of tyrosine kinases that regulate synaptic strength and plasticity during neural development. Deregulated kinase activity of Trk family members due to chromosomal rearrangements, gene mutations, splice variants and overexpression has been shown to be associated with cancer cell proliferation, survival, invasion and chemo-resistance in a number of cancer types. For example, chromosomal rearrangements involving NTRK1-3 have been reported in lung, colorectal, papillary thyroid, glioblastoma, melanoma and other cancers, and have been demonstrated to function as oncogenic drivers in these tumors. Moreover, overexpression of TrkA, TrkB and/or their corresponding ligands has been observed in a number of solid tumors such as breast, lung, prostate and pancreatic cancers. However, the functional implication of Trk overexpression has not been well defined or fully explored as a potential therapeutic strategy.

To characterize the expression, signaling and function of full-length Trks in cancer, a series of stable cell lines with full-length NTRK genes were established. The engineered cell lines were characterized for Trk expression, Trk phosphorylation and their response to ligand stimulation. Moreover, cell proliferation, cell transformation and growth inhibition by RXDX-101, a clinical stage, potent and selective pan-Trk inhibitor, were assessed. Trk downstream effectors, such as PLCγ, AKT and ERK, were also evaluated in the relevant settings. Furthermore, several cancer cell lines with endogenous overexpression of full-length Trks or rearranged Trks were identified and functionally characterized.

Our studies highlight the similarities and differences between Trk rearrangement and overexpression as potential oncogenic drivers and support further exploration of RXDX-101 in cancers with Trk overexpression.

Citation Format: Ge (Gina) Wei, Nicholas Cam, Roopal Patel, Robert Shoemaker, Robert Wild, Gang Li. Overexpression of neurotrophic tyrosine receptor kinases (NTRKs) as a potential therapeutic target for cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 127. doi:10.1158/1538-7445.AM2015-127

Therapeutic activity of 9-chloro-2-methylellipticinium acetate in an orthotopic model of human brain cancer

A series of ellipticinium derivatives with selective cytotoxicity towards brain tumor cell lines has been identified through in vitro screening against disease-oriented panels of human tumor cell lines. Unfortunately 9-methoxy-2-methylellipticinium, the lead compound of this series, has shown only very limited evidence for in vivo activity when examined in a variety of human tumor xenograft models. This lack of activity has been postulated to be due to metabolism. To address this issue, a derivative was synthesized which was blocked at the theoretically vulnerable 9-position and yet could be shown to retain brain tumor selectivity in vitro. In vivo xenograft testing was performed to assess the therapeutic potential of this second generation compound. To maintain continuity with the in vitro screening data, in vivo experimental therapeutic models were devised employing one of the in vitro sensitive cell lines, the U-251 glioblastoma. Cells were cultivated in vitro and injected into female athymic nude mice for therapeutic studies. The 9-chloro-derivative of the lead compound produced growth delay of subcutaneously implanted tumor cells when. administered by seven-day continuous infusion. Based on this evidence for activity in a systemic chemotherapy mode, further studies were conducted using an orthotopic brain cancer model. In three separate experiments, intracranial implantation of 1x10(7) tumor cells resulted in 100% mortality of control mice with median survival ranging from 15-18.5 days. In all experiments, mice treated by subcutaneous infusion with 9-chloro-2-methylellipticinium acetate showed increases in survival. Statistically significant effects and individual long-term survivors were observed in two experiments; These results provide support for the further preclinical development of 9-chloro-2-methylellipticinium acetate as a candidate for clinical trials against human brain cancer.

An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype

Background

A DNA methylation signature has been characterized that distinguishes rheumatoid arthritis (RA) fibroblast like synoviocytes (FLS) from osteoarthritis (OA) FLS. The presence of epigenetic changes in long-term cultured cells suggest that rheumatoid FLS imprinting might contribute to pathogenic behavior. To understand how differentially methylated genes (DMGs) might participate in the pathogenesis of RA, we evaluated the stability of the RA signature and whether DMGs are enriched in specific pathways and ontology categories.

Methods

To assess the RA methylation signatures the Illumina HumanMethylation450 chip was used to compare methylation levels in RA, OA, and normal (NL) FLS at passage 3, 5, and 7. Then methylation frequencies at CpGs within the signature were compared between passages. To assess the enrichment of DMGs in specific pathways, DMGs were identified as genes that possess significantly differential methylated loci within their promoter regions. These sets of DMGs were then compared to pathway and ontology databases to establish enrichment in specific categories.

Results

Initial studies compared passage 3, 5, and 7 FLS from RA, OA, and NL. The patterns of differential methylation of each individual FLS line were very similar regardless of passage number. Using the most robust analysis, 20 out of 272 KEGG pathways and 43 out of 34,400 GO pathways were significantly altered for RA compared with OA and NL FLS. Most interestingly, we found that the KEGG 'Rheumatoid Arthritis' pathway was consistently the most significantly enriched with differentially methylated loci. Additional pathways involved with innate immunity (Complement and Coagulation, Toll-like Receptors, NOD-like Receptors, and Cytosolic DNA-sensing), cell adhesion (Focal Adhesion, Cell Adhesion Molecule), and cytokines (Cytokine-cytokine Receptor). Taken together, KEGG and GO pathway analysis demonstrates non-random epigenetic imprinting of RA FLS.

Conclusions

The DNA methylation patterns include anomalies in key genes implicated in the pathogenesis of RA and are stable for multiple cell passages. Persistent epigenetic alterations could contribute to the aggressive phenotype of RA synoviocytes and identify potential therapeutic targets that could modulate the pathogenic behavior.

Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells

Human embryonic stem cells (hESCs) hold great promise for regenerative medicine because they can undergo unlimited self-renewal and retain the capability to differentiate into all cell types in the body. Although numerous genes/proteins such as Oct4 and Gata6 have been identified to play critical regulatory roles in self-renewal and differentiation of hESC, the majority of the regulators in these cellular processes and more importantly how these regulators co-operate with each other and/or with epigenetic modifications are still largely unknown. We propose here a systematic approach to integrate genomic and epigenomic data for identification of direct regulatory interactions. This approach allows reconstruction of cell-type-specific transcription networks in embryonic stem cells (ESCs) and fibroblasts at an unprecedented scale. Many links in the reconstructed networks coincide with known regulatory interactions or literature evidence. Systems-level analyses of these networks not only uncover novel regulators for pluripotency and differentiation, but also reveal extensive interplays between transcription factor binding and epigenetic modifications. Especially, we observed poised enhancers characterized by both active (H3K4me1) and repressive (H3K27me3) histone marks that contain enriched Oct4- and Suz12-binding sites. The success of such a systems biology approach is further supported by experimental validation of the predicted interactions.

Library-free methylation sequencing with bisulfite padlock probes

Targeted quantification of DNA methylation allows for interrogation of the most informative loci across many samples quickly and cost-effectively. Here we report improved bisulfite padlock probes (BSPPs) with a design algorithm to generate efficient padlock probes, a library-free protocol that dramatically reduces sample-preparation cost and time and is compatible with automation, and an efficient bioinformatics pipeline to accurately obtain both methylation levels and genotypes from sequencing of bisulfite-converted DNA.

Systematic search for recipes to generate induced pluripotent stem cells

Generation of induced pluripotent stem cells (iPSCs) opens a new avenue in regenerative medicine. One of the major hurdles for therapeutic applications is to improve the efficiency of generating iPSCs and also to avoid the tumorigenicity, which requires searching for new reprogramming recipes. We present a systems biology approach to efficiently evaluate a large number of possible recipes and find those that are most effective at generating iPSCs. We not only recovered several experimentally confirmed recipes but we also suggested new ones that may improve reprogramming efficiency and quality. In addition, our approach allows one to estimate the cell-state landscape, monitor the progress of reprogramming, identify important regulatory transition states, and ultimately understand the mechanisms of iPSC generation.

Converting somatic cells back to the stem cell state (called induced pluripotent stem cells or iPSCs) exemplifies the recent advancement of cellular reprogramming that holds great promise for developing regenerative medicine. Generation of iPSCs is often achieved by overexpressing three to four genes in somatic cells that are critical for regulating pluripotency. Developing optimal reprogramming recipe is a non-trivial task that requires significant effort. We present here a computational method that can facilitate discovery of effective recipes to generate iPSCs with high efficiency and better quality. In addition, our approach provides a new way to estimate the landscape in the cell-state space and monitor the trajectory of cellular reprogramming from a differentiated cell to an iPS cell. This work provides not only practical recipes for iPSC generation but also theoretical understanding of the reprogramming process.

A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention

Deciphering the biological networks underlying complex phenotypic traits, e.g., human disease is undoubtedly crucial to understand the underlying molecular mechanisms and to develop effective therapeutics. Due to the network complexity and the relatively small number of available experiments, data-driven modeling is a great challenge for deducing the functions of genes/proteins in the network and in phenotype formation. We propose a novel knowledge-driven systems biology method that utilizes qualitative knowledge to construct a Dynamic Bayesian network (DBN) to represent the biological network underlying a specific phenotype. Edges in this network depict physical interactions between genes and/or proteins. A qualitative knowledge model first translates typical molecular interactions into constraints when resolving the DBN structure and parameters. Therefore, the uncertainty of the network is restricted to a subset of models which are consistent with the qualitative knowledge. All models satisfying the constraints are considered as candidates for the underlying network. These consistent models are used to perform quantitative inference. By in silico inference, we can predict phenotypic traits upon genetic interventions and perturbing in the network. We applied our method to analyze the puzzling mechanism of breast cancer cell proliferation network and we accurately predicted cancer cell growth rate upon manipulating (anti)cancerous marker genes/proteins.

Capture probability of released males of two Bactrocera species (Diptera: Tephritidae) in detection traps in California

The genus Bactrocera (Diptera: Tephritidae) includes approximately 70 polyphagous species that are major pests of fruit and vegetable crops. Most Bactrocera species have limited geographic distributions, but several species are invasive, and many countries operate continuous trapping programs to detect infestations. In the United States, California maintains approximately 25,000 traps (baited with male lures) specifically for Bactrocera detection distributed over an area of approximately 6,400 km2 (2,500 miles2) in the Los Angeles area. Although prior studies have used male lures to describe movement of Bactrocera males, they do not explicitly relate capture probability with fly distance from lure-baited traps; consequently, they do not address the relative effectiveness of male lures in detecting incipient populations of Bactrocera species. The objective of this study was to measure the distance-dependent capture probability of marked, released males of Bactrocera dorsalis (Hendel) and Bactrocera cucurbitae (Coquillett) (methyl eugenol- and cue lure-responding species, respectively) within the detection trapping grid operating in southern California. These data were then used to compute simple probability estimates for detecting populations of different sizes of the two species. Methyl eugenol was the more powerful attractant, and based on the mark-recapture data, we estimated that B. dorsalis populations with as few as approximately 50 males would always (>99.9%) be detected using the current trap density of five methyl eugenol-baited traps per 2.6 km2 (1 mile2). By contrast, we estimated that certain detection of B. cucurbitae populations would not occur until these contained approximately 350 males. The implications of the results for the California trapping system are discussed, and the findings are compared with mark-release-recapture data obtained for the same two species in Hawaii.

Mediators and dynamics of DNA methylation

As an inherited epigenetic marker occurring mainly on cytosines at CpG dinucleotides, DNA methylation occurs across many higher eukaryotic organisms. Looking at methylation patterns genome-wide classifies cell types uniquely and in several cases discriminates between healthy and cancerous cell types. DNA methylation can occur allele-specifically, which allows the cellular regulatory machinery to recognize each allele separately. Although only a small number of allele specifically methylated (ASM) regions are known, genome-wide experiments show that ASM is prevalent throughout the human genome. These DNA methylation patterns can be modified via DNA demethylation, which is important for induced pluripotent stem reprogramming and primordial germ cells. Recent evidence shows that the protein activation-induced cytidine deaminase plays a critical role in these demethylation events. Many transcription factors mediate DNA methylation patterns. Some transcription factors bind specifically to methylated or unmethylated sequences and other transcription factors protect genomic regions (e.g., promoter regions) from nearby DNA methylation encroachment. Possibly acting as another epigenetic regulatory layer, methylated cytosines are also converted to 5-hydroxyethylcyotines, which is a new modification type whose biological significance has yet been defined.

Abstract 1103: Linkage between endogenous Chk2 activation and p14ARF expression in p53-mutated cells revealed by proteomic and genomic analyses of the NCI60

Chk2 is a multi-substrate kinase involved in the DNA damage response and genomic stability. Chk2 inhibitors are currently being evaluated in cancer models, with the rationale of enhancing the activity of DNA damaging agents in p53-deficient tumors while protecting normal tissues. Part of the ATM-Chk2-p53 axis, Chk2 is overexpressed or activated in various malignant tumors. Here we determined Chk2 copy number, total and single-exon transcriptional levels, and total and activated (pT68) protein across the 60 cell lines of the NCI DTP screen. We correlated these parameters with p53 mutational status, miRNA expression (Agilent miRNA Microarray V2), and performed supervised transcript (Agilent Whole Human Genome Oligo Microarray) class comparison analysis between high and low pT68 Chk2 cell lines using BRB Array Tools 3.8. All the lines used for this purpose were known to be p53-mutated. Our phosphoproteomic analyses demonstrate that a number of cell lines have high endogenous Chk2 activation (ovarian OVCAR3 and OVCAR4, renal RFX-393, lung NCI-H322M, and EKVX, melanoma UACC-62 and −257, leukemia RPMI-8226 and breast BT-549) whereas the wild-type p53 tumors almost invariably show undetectable Chk2 activation. Expression of total Chk2 protein and mRNA were generally positively correlated to each other. Exon array analyses across the NCI-60 suggest exon 3 splicing in almost all Chk2 high expresser cell lines and premature truncation between exons 8 and 10 in the ovarian SKOV3 cells, which could be related to the low level of Chk2 expression in that cell line. One microRNA, hsa-miR-455-3p, showed a highly significant negative correlation with both Chk2 transcript levels and with total protein levels (Spearman's r =-0.48, p &lt; 10-3 and r=-0.35, p &lt; 0.01 respectively) and was predicted to hybridize to Chk2 mRNA by miRBase (www.mirbase.org). Among the 181 probes differentially expressed in cells with highly activated Chk2, 123 mapped to known gene IDs, and 58 were eligible for network analysis with Ingenuity Pathways Analysis 8.0 (Ingenuity Systems Inc.). Functions associated with the networks enriched in genes differentially expressed by high pT68 cells included: cell cycle, cell-to-cell signaling, cell growth and proliferation, cancer. Remarkably, the tumor suppressor CDKN2A (p14ARF) showed a 132-fold difference between the two groups considered (unpaired t test, two-tailed p &lt; 10-7; false discovery rate &lt; 10-7), being highly overexpressed in high pT68 Chk2 cell lines. Several EGFR-Ras-MAPK related genes were downregulated in high pT68 cell lines. Together, these data suggest that Chk2 is part of a multifaceted regulation network in cancer. Although traditionally considered as a low-penetrance tumor suppressor, it clearly plays more complex roles in tumor biology, possibly behaving as an activated oncogene in specific genomic contexts.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1103.

Identification of a Bis-guanylhydrazone [4,4'-Diacetyldiphenylurea-bis(guanylhydrazone); NSC 109555] as a novel chemotype for inhibition of Chk2 kinase

Chk2 is a protein kinase involved in the ATM-dependent checkpoint pathway (http://discover.nci.nih.gov/mim). This pathway is activated by genomic instability and DNA damage and results in either cell cycle arrest, to allow DNA repair to occur, or cell death (apoptosis). Chk2 is activated by ATM-mediated phosphorylation and autophosphorylation and in turn phosphorylates its downstream targets (Cdc25A, Cdc25C, BRCA1, p53, Hdmx, E2F1, PP2A, and PML). Inhibition of Chk2 has been proposed to sensitize p53-deficient cells as well as protect normal tissue after exposure to DNA-damaging agents. We have developed a drug-screening program for specific Chk2 inhibitors using a fluorescence polarization assay, immobilized metal ion affinity-based fluorescence polarization (IMAP). This assay detects the degree of phosphorylation of a fluorescently linked substrate by Chk2. From a screen of over 100,000 compounds from the NCI Developmental Therapeutics Program, we identified a bis-guanylhydrazone [4,4'-diacetyldiphenylureabis(guanylhydrazone); NSC 109555] as a lead compound. In vitro data show the specific inhibition of Chk2 kinase activity by NSC 109555 using in vitro kinase assays and kinase-profiling experiments. NSC 109555 was shown to be a competitive inhibitor of Chk2 with respect to ATP, which was supported by docking of NSC 109555 into the ATP binding pocket of the Chk2 catalytic domain. The potency of NSC 109555 was comparable with that of other known Chk2 inhibitors, such as debromohymenialdisine and 2-arylbenzimidazole. These data define a novel chemotype for the development of potent and selective inhibitors of Chk2. This class of drugs may ultimately be useful in combination with current DNA-damaging agents used in the clinic.

A Three-Dimensional Quantitative Structure-Activity Relationship Study of the Inhibition of the ATPase Activity and the Strand Passing Catalytic Activity of Topoisomerase IIα by Substituted Purine Analogs

Based on the topoisomerase IIalpha catalytic inhibitory activity of a previous hit compound, NSC35866, we screened 40 substituted purines or purine-like compounds from the National Cancer Institute repository for their ability to inhibit the ATPase activity of human topoisomerase IIalpha. Several compounds, including NSC348400, NSC348401 and NSC348402, were inhibitory at submicromolar concentrations. Three-dimensional quantitative structure-activity relationship models using comparative molecular field and comparative molecular similarity indices analyses were constructed using 24 of these compounds. The ability of 10 selected compounds to inhibit the complete DNA strand passage reaction of topoisomerase IIalpha correlated well with their potency as ATPase inhibitors. None of the 40 compounds significantly increased levels of the topoisomerase IIalpha-DNA covalent complex, suggesting that they functioned as catalytic topoisomerase II inhibitors and not as topoisomerase II poisons. Although some of these compounds could antagonize the effect of etoposide on the level of topoisomerase IIalpha-DNA covalent complex formation in vitro, in contrast to NSC35866, they were not capable of antagonizing etoposide-induced cytotoxicity and DNA strand breaks in cells. Two independently selected human SCLC cell lines with reduced topoisomerase IIalpha expression displayed cross-resistance to NSC348400, NBSC348401, and NSC348402, whereas an MDR1 line was fully sensitive. These results suggest that topoisomerase IIalpha is a functional cellular target for most of these substituted purine compounds and that these compounds do not display MDR1 liability.

Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides

The HIV-1 nucleocapsid (NC) protein is a small, basic protein containing two retroviral zinc fingers. It is a highly active nucleic acid chaperone; because of this activity, it plays a crucial role in virus replication as a cofactor during reverse transcription, and is probably important in other steps of the replication cycle as well. We previously reported that NC binds with high-affinity to the repeating sequence d(TG)_n. We have now analyzed the interaction between NC and d(TG)₄ in considerable detail, using surface plasmon resonance (SPR), tryptophan fluorescence quenching (TFQ), fluorescence anisotropy (FA), isothermal titration calorimetry (ITC) and electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). Our results show that the interactions between these two molecules are surprisngly complex: while the K_d for binding of a single d(TG)₄ molecule to NC is only ∼5 nM in 150 mM NaCl, a single NC molecule is capable of interacting with more than one d(TG)₄ molecule, and conversely, more than one NC molecule can bind to a single d(TG)₄ molecule. The strengths of these additional binding reactions are quantitated. The implications of this multivalency for the functions of NC in virus replication are discussed.

Identification of a large cluster of coiled coil-nucleotide binding site--leucine rich repeat-type genes from the Rps1 region containing Phytophthora resistance genes in soybean

Fifteen Rps genes confer resistance against the oomycete pathogen Phytophthora sojae, which causes root and stem rot disease in soybean. We have isolated a disease resistance gene-like sequence from the genomic region containing Rps1-k. Four classes of cDNA of the sequence were isolated from etiolated hypocotyl tissues that express the Rps1-k-encoded Phytophthora resistance. Sequence analyses of a cDNA clone showed that the sequence is a member of the coiled coil-nucleotide binding site-leucine rich repeat (CC-NBS-LRR)-type of disease resistance genes. It showed 36% identity to the recently cloned soybean resistance gene Rpg1-b, which confers resistance against Pseudomonas syringae pv. glycinea, and 56% and 38% sequence identity to putative resistance gene sequences from lotus and Medicago truncatula, respectively. The soybean genome contains about 38 copies of the sequence. Most of these copies are clustered in approximately 600 kb of contiguous DNA of the Rps1-k region. We have identified a recombinant that carries both rps1-k- and Rps1-k-haplotype-specific allelomorphs of two Rps1-k-linked molecular markers. An unequal crossover event presumably led to duplication of alleles for these two physically linked molecular markers. We hypothesize that the unequal crossing over was one of the mechanisms involved in tandem duplication of CC-NBS-LRR sequences in the Rps1-k region.

Rapid screening of chemical inhibitors that block processive DNA synthesis of herpesviruses: potential application to high-throughput screening

Processivity factors associate with DNA polymerases, enabling them to incorporate thousands of nucleotides without dissociating from the template. The processivity factors encoded by each of the herpesviruses are ideal targets for specifically blocking viral replication, particularly since they have unique primary amino acid sequences. Here we provide details of a rapid mechanistic plate assay and its potential application to high-throughput screening of libraries of tens of thousands of chemical compounds to identify inhibitors of processive DNA synthesis. Methods of validation testing are presented.