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[4-(4-Methyl-2-(4-(trifluoromethyl)phenyl)thiazole-5-yl)pyrimidine-2-amine] (JNJ-2482272), under investigation as an anti-inflammatory agent, was orally administered to rats once daily at 60 mg/kg for 6 consecutive days. Despite high plasma exposure after single administration (C

BackgroundP21-activated kinase 4 (PAK4) is a serine/threonine protein kinase that is mostly expressed in tumor and stroma cells. PAK4 activates tumor WNT/β-catenin pathway and regulates cellular morphology, motility, EMT, cell proliferation and survival. Recent studies also showed that PAK4 can actively exclude T cells from tumors, suggesting that therapeutic inhibition of PAK4 can increase T cell infiltration in tumor microenvironment and overcome resistance to checkpoint inhibitor immunotherapy.1MethodsWe generated PAK4 knockout (KO) clones in human and mouse tumor cells to validate its biology in vitro and in vivo. We also performed pharmacological evaluation of PAK4 inhibition using Pfizer compounds (referred to as 'PAK4i compounds' below) for their potential tumor-intrinsic and immune-regulatory roles.ResultsNanostring, qPCR and RNASeq analysis showed that PAK4 depletion led to increase of cytokine expression in tumor, including conventional dendritic cell (cDC)- recruiting chemokine CCL4, and type I IFN / ISG pathway genes that are associated with MHC upregulation such as CXCL10. In addition, PAK4 KO sensitizes B16F10 tumors to anti-PD-1 treatment and increases infiltration of cDC and T cells in the tumor microenvironment.We also showed that small molecule PAK4i compounds induced more potent cancer cell growth inhibition over treated normal PBMCs. PAK4i compounds also increased immune-activating and decreased immune exclusion genes in B16F10 cells and tumor explants in vitro. Although PAK4 target engagement is demonstrated by CETSA assay, the compound potency on modulating PAK4 downstream Wnt/ β-catenin pathway is low, suggesting that the aforementioned phenotypic changes induced by PAK4i compounds may be partially attributed to other off-target effects.ConclusionsCollectively, our data suggests that genetic depletion or pharmacological inhibition of PAK4 may induce immune-activating cytokine production in tumor cells, revert immune cell exclusion in tumor microenvironment, and synergize with checkpoint blockade therapies. However, further optimization on these PAK4i compounds is needed to improve its specificity on modulating PAK4 enzyme activities.ReferenceAbril-Rodriguez G, Torrejon DY, Liu W, Zaretsky JM, Nowicki TS, Tsoi J, Puig-Saus C, Baselga-Carretero I, Medina E, Quist MJ, Garcia AJ, Senapedis W, Baloglu E, Kalbasi A, Cheung-Lau G, Berent-Maoz B, Comin-Anduix B, Hu-Lieskovan S, CWang CY, Grasso CS & Ribas A. PAK4 inhibition improves PD-1 blockade immunotherapy. Nat Cancer 2020;1:46–58.Ethics ApprovalAll animal studies were conducted in accordance with protocols approved by the Institutional Animal Care and Use Committee of Pfizer. Approved protocol # LAJ-2019-01347

Background Ultra-deep next-generation sequencing of circulating tumor DNA (ctDNA) holds great promise as a tool for the early detection of cancer and for monitoring disease progression and therapeutic responses. However, the low abundance of ctDNA in the bloodstream coupled with technical errors introduced during library construction and sequencing complicates mutation detection. Results To achieve high accuracy of variant calling via better distinguishing low-frequency ctDNA mutations from background errors, we introduce TNER (Tri-Nucleotide Error Reducer), a novel background error suppression method that provides a robust estimation of background noise to reduce sequencing errors. The results on both simulated data and real data from healthy subjects demonstrate that the proposed algorithm consistently outperforms a current, state-of-the-art, position-specific error polishing model, particularly when the sample size of healthy subjects is small. Conclusions TNER significantly enhances the specificity of downstream ctDNA mutation detection without sacrificing sensitivity. The tool is publicly available at https://github.com/ctDNA/TNER. Electronic supplementary material The online version of this article (10.1186/s12859-018-2428-3) contains supplementary material, which is available to authorized users.

Background: CDK4/6 inhibition combined with endocrine therapy (ET) is now the standard of care for advanced hormone receptor (HR) positive breast cancer patients (pts). Previous ctDNA analysis of paired pre-treatment (pre-T) and end of treatment (EoT) plasma samples from the PALOMA-3 trial of the CDK4/6 inhibitor P with/without F demonstrated that acquired PIK3CA, ESR1, RB1 and rare growth factor receptor mutations (mut) likely contribute to resistance (Turner et al, ASCO 2018, Abstract 1001). We now report results from an extended ctDNA analysis of paired PALOMA-3 plasma samples using hybridization capture-based, next-generation sequencing (NGS) assay covering 87 breast cancer, HR signaling, and cell cycle-related genes. Methods: Pre-/post-menopausal pts whose disease progressed after prior ET (N=521) were randomized 2:1 to receive F 500 mg + P (125 mg/d, 3 wk on/1 wk off) or placebo. Cell-free DNA extracted from paired plasma samples (n=194) was analyzed with a custom 87-gene NGS assay, to identify single nucleotide variants and copy number amplification (CNA), with molecular barcoding, high NGS coverage (10,000-20,000 reads per nucleotide position), and background error correction. Differences in ctDNA mut frequencies detected in P+F compared to F alone were assessed and their association to clinical outcome estimated. Results: Blinded assay qualification and droplet digital PCR validation suggested a mut detection frequency cutoff at 0.3%. A high coefficient of correlation with previously presented data was observed for ESR1 and PIK3CA variants (r=0.94 and 0.97, respectively), with acquisition of PIK3CA and ESR1 mutations at EoT in P+F and F groups. Gene level mut analysis of EoT plasma revealed no significant difference between P+F vs F alone (Table), although there was an increase in RB1 mutations in P+F consistent with previous data. Other acquired muts at EoT (SMAD4, NOTCH2, and CDKN1B) were observed at low frequencies. Muts in CDK4 and CDK6 were rarely observed (< 1% of pts), regardless of treatment arm. Detected Variants, Frequency, n (%) P+FF GenePre-TEoTPre-TEoTPre-T pvalEoT pvalPIK3CA47(37)51(40)19(28)22(33)0.2660.352ESR136(28)45(35)19(28)24(36)11TP5330(24)33(26)23(34)25(37)0.1280.137RB12(2)9(7)2(3)2(3)NA0.336PTEN5(4)7(6)3(4)3(4)11AKT17(6)7(6)2(3)2(3)0.7210.721 Conclusions: Our results corroborate the previously reported results demonstrating that genomic profiles of treatment resistant cancer are similar between P + F and F therapy. Expanded analysis of cell-cycle genes identified no new recurrently mutated genes, and confirmed that RB1 mutations are selected at low frequency after P+F treatment. Alterations in cell cycle genes may not be a common mechanism of resistance to CDK4/6 inhibitors in HR+ HER2- advanced breast cancer. Sponsor: Pfizer Citation Format: O'Leary B, Lira ME, Huang S, Deng S, Xie T, Kinong JK, Hardwick J, Rejto P, Liu Y, Huang X, Huang Bartlett C, André F, Loibl S, DeMichele A, Cristofanilli M, Turner NC. Longitudinal ctDNA sequencing using an expanded genomic panel in the PALOMA3 trial of palbociclib plus fulvestrant [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD2-02.

Liquid biopsies have the potential to revolutionize the way physicians select personalized anti-cancer therapies, monitor patient responses to treatment, and characterize acquired resistance to cancer drugs. New tests that use a simple peripheral blood draw offer snapshots of a patient‘s total tumor DNA mutation profile and are attractive because of their minimally-invasive modality and because they integrate information from both primary and metastatic disease. Currently, most plasma cell-free DNA (cfDNA) mutation detection tests used in clinical research detect known hotspot mutations in a limited number of genes. Technologies that interrogate multi-gene panels in cfDNA are advancing, but commercially-available options suitable for clinical use are limited, come at a high cost, and are not customizable. We designed and developed a customized, next generation sequencing-based, liquid biopsy assay capable of detecting somatic mutations in 87 breast cancer genes involved in cell cycle and estrogen receptor signaling. Targeted regions (147 Kb) were enriched using hybrid capture resulting in an average capture specificity and uniformity of 65.93% and 96.38%, respectively. When tested on cfDNA from healthy donors (n=14), we demonstrated a level of specificity >99.99%. Analytical sensitivity of 0.1% was established on HapMap and reference mutant cell line DNA. Using a pool of HapMap genomic DNA (n=10), 96% (48/50) of SNPs with expected allele frequency of 0.1% were detected. In reference mutant cell line DNA with 1% or 0.1% mutant allele frequencies, we were able to reliably detect all mutations present at 1% and mutations at 0.1% in 50% of the cases. Assay validation on plasma cfDNA with matching tumor from ER+, HER2- breast cancer patients will be presented. In conclusion, we developed a highly sensitive and specific liquid biopsy assay to interrogate 87 breast cancer-related genes. The high level of specificity and sensitivity makes the test ideal not only for detecting known cancer gene hotspot mutations but also for detection of novel gene mutations that may arise during treatment as a result of acquired drug resistance. Citation Format: Maruja E. Lira, Tao Xie, Shibing Deng, Jennifer Kinong, Jingjin Gao, Zhou Zhu, Nathan Lee, Paul Rejto, Jadwiga Bienkowska, James Hardwick, Kai Wang, Stephen Huang. Liquid biopsy testing allows highly-sensitive detection of plasma cfDNA mutations in 87 breast cancer-related genes [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 2749. doi:10.1158/1538-7445.AM2017-2749