bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A142: Fragment based discovery of inhibitors of the eIF4E:eIF4G interaction
Authors: Richardson Caroline J , Vincovic Mladen , East Charlotte , Wallis Nicola , Ward George , Woodhead Andrew 
Published: December 2023

Abstract
eIF4E is the rate limiting factor for cap-dependent protein translation, forming an essential part of the translation initiation complex, eIF4F and is a key signalling convergence point for the major oncogenic pathways MAPK and PI3K/AKT/MTOR. eIF4E has been shown to be overexpressed in cancer, which has been associated with poor prognosis and resistance to chemotherapeutics and targeted agents such as mTOR and MAPK inhibitors. eIF4E is therefore a promising target for cancer treatment but has so far been difficult to target with small molecules due to a lack of druggable pockets. Fragment based crystallographic screening is a powerful technique for probing the surface of proteins to identify potentially druggable binding sites. Here, we describe our fragment-based approach and hit optimisation campaign to generate potent compounds binding to eIF4E For the fragment screen, we generated an engineered form of eIF4E, where the N-terminal (residues 1-35) were removed and replaced a short, tethered peptide based on the canonical binding sequence of the eIF4E binding protein 4E-BP1, and screened 1400 fragments using a combination of Xray crystallography and NMR. Several low affinity (mM) fragment hits were identified, binding to both the mRNA cap- binding site and at an additional binding site of unknown functional relevance. Using a combination of biophysical and biochemical assays, subsequent rounds of iterative structure-based drug design of yielded potent lead molecules against both binding sites. For the cap-binding site, lead compounds of low nM potency were generated but due to the polar nature of the binding site, the molecules had very poor permeability properties and did not inhibit cell proliferation. For the non-canonical binding site, lead compounds with potency of 100nM alongside less potent enantiomers were generated which provided useful tools for probing the function of the binding site in vitro. We developed a MSD (Meso-scale discovery) assay to determine that the lead compound and not the inactive enantiomer could disrupt the eIF4E:eIF4G interaction in HeLa cell lysates with an IC50 of 1uM. Using a HeLa extract in vitro translation assay, we could also demonstrate that both the cap site and non-canonical site lead compounds could inhibit cap-dependent but not IRES driven protein translation. This work demonstrates the power of fragment screening to identify novel functional pockets on difficult to drug proteins such as eIF4E.
Citation Format: Caroline J Richardson, Mladen Vincovic, Charlotte East, Nicola Wallis, George Ward, Andrew Woodhead. Fragment based discovery of inhibitors of the eIF4E:eIF4G interaction [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A142.
Abstract A167: Cellular fitness of MYC-driven cancer cells to genetic and pharmacologic perturbations in normoxia, hypoxia and 3D culture
Authors: Yang Jun 
Published: December 2023

Abstract
MYC and hypoxia gene clusters are two most commonly recurring transcriptional programs in a heterogenous tumor. Understanding the cellular fitness of MYC-driven cancer cells in normoxia and hypoxia may lead to identification of cancer cell vulnerabilities. Using genome-wide CRISPR screenings of MYC-driven liver cancer cells cultured in 21% and 1% oxygen in monolayer, and 21% oxygen in 3D spheroid over 4 weeks, we not only identify many targetable essential genes under all three conditions but also context-specific fitness genes and pathways. In parallel, we perform drug screening under three conditions. We find that cells respond to 125 FDA approved oncology drugs in different ways in normoxia, hypoxia and 3D. Our resource study highlights unique epigenetic and metabolic dependency of MYC-driven cancer cells in different tumor environments.
Citation Format: Jun Yang. Cellular fitness of MYC-driven cancer cells to genetic and pharmacologic perturbations in normoxia, hypoxia and 3D culture [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A167.
Abstract A168: T cell receptor-based bispecific molecules targeting KRAS neoantigen cancer driver mutations
Authors: Whale Andrew D , Aleksic Milos , Karuppiah Vijaykumar , Moureau Sylvie , Chillakuri Chandramouli 
Published: December 2023

Abstract
KRAS is the most frequently mutated oncogene. Tumour specific neoantigen peptides derived from KRAS are presented by cell surface human leucocyte antigens (HLA) and form a class of shared, public tumour-specific antigens for T cell receptors (TCR) that are attractive targets for immunotherapy. We have previously reported engineering of a soluble T cell engaging ImmTAC (Immune mobilising monoclonal TCR Against Cancer) molecule, IMC-KRASG12D specific for KRASG12D peptide presented by HLA-A*11:01. IMC-KRASG12D was extensively characterised and demonstrated potent redirection of T cell cytotoxicity towards target KRASG12D presenting cancer cells, while sparing normal cells. Here, we focus on TCRs isolated from healthy donors that specifically recognise KRASG12V peptides presented in the context of HLA-A*11:01 or HLA-A*03:01. The affinity of several TCRs was enhanced by phage display, retaining the remarkable ability to distinguish between KRASG12V and KRASWT peptides. In cell-based assays, ImmTAC molecules containing these TCR mediate T cell activation in response to cells expressing KRASG12V but not KRASWT. Interestingly, although structural, biochemical, and computational approaches can explain the molecular mechanism underlying TCR selectivity for KRASG12D pHLA-A*11complexes, it remains unclear how TCR selectivity to KRASG12V is achieved. These studies demonstrate that affinity enhanced TCR can maintain selectivity for target peptides that differ from self-antigens by only a single amino acid, to enable targeting of public neoantigens.
Citation Format: Andrew D Whale, Milos Aleksic, Vijaykumar Karuppiah, Sylvie Moureau, Chandramouli Chillakuri. T cell receptor-based bispecific molecules targeting KRAS neoantigen cancer driver mutations [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A168.
Abstract B017: Clinical utility of next generation sequencing in advanced colorectal cancer: The earlier the better
Authors: An Ho Jung , Kim Hyunho , Park Hyung Soon , Cho Hyeon-Min , Kye Bong-Hyeon , Yoo Ri Na , Moon Ji-Yeon , Kim Sung Hwan , Lee Jonghoon , Lee Hyo Chun 
Published: December 2023

Abstract
Background. Since next generation sequencing (NGS) was approved in solid tumor in Korea, it has been usually performed when patients were progressed on standard chemotherapy in advanced colorectal cancer (CRC). Recently, new targeted agents have been developed rapidly, so the NGS is recommended as early as possible. In this study, we analyzed NGS results and investigated clinical benefit in advanced CRC.
Patient and method. Between October 2018 to December 2022, NGS data in 85 advanced CRC patients in St. Vincent’s Hospital, Suwon, Korea were retrospectively analyzed.
Results. Seven patients had metachronous, and others had synchronous metastasis. The median age was 58 (34-84), and 59 (69.4%) were male. Fourteen (16.5%) were right-side, 40 (47.1%) were left-side colon, and 30 (35.3%) were rectum. The median time from diagnosis of advanced CRC to NGS was 13 (0-81) months, and median time to death after NGS was 8 (0.3-43.0) months. NGS platform were ‘Oncomine comprehensive assay Plus’ in 71 (83.5%), and the others were various platforms in K-master project. NGS analyses revealed new therapeutic target in 17 (20%): high tumor mutational burden (n = 2), KRAS G12C (n = 4), KRAS (n = 1) or BRAF (n = 2) mutation not routinely screened at initial, BRAF class II mutation (n = 2), Her2/3 mutation (n = 2), and NTRK fusion (n = 1). Among those, two patients with KRAS G12C mutation enrolled in clinical trial of KRAS G12 inhibitor, and one patient with NTRK fusion received NTRK inhibitor (3.5% of total). Among RAS wild type population (n=30), we identified hyperselected patients (n = 18, [60%], absence of either KRAS, NRAS, PTEN, and extracellular domain EGFR mutations, HER2 and MET amplifications, and ALK, RET or NTRK1 fusions by PARADIGM trial), which showed longer survival in cetuximab-treated population (p&lt;0.001). Specific mutation including KRAS, NRAS, BRAF, TP53, or APC did not impact on prognosis. High TMB (≥10Mut/Mb) were associated with longer survival (p = 0.020). For patients with oligometastasis, hyperselected patients (p = 0.062) showed good prognosis.
Conclusion. The NGS results provided additional predictive or prognostic information in advanced CRC patients. Application of NGS as early as possible might help to make a clinical decision.
Citation Format: Ho Jung An, Hyunho Kim, Hyung Soon Park, Hyeon-Min Cho, Bong-Hyeon Kye, Ri Na Yoo, Ji-Yeon Moon, Sung Hwan Kim, Jonghoon Lee, Hyo Chun Lee. Clinical utility of next generation sequencing in advanced colorectal cancer: The earlier the better [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B017.
Abstract B019: RNA transcriptome profiling in microsamples of blood
Authors: Chenchik Alex , Kobzik Lester , Makhanov Mikhail , Diehl Paul 
Published: December 2023

Abstract
Multi-omic analysis of microsamples of lancet-induced blood drops allows frequent capture and quantitation of numerous metabolites, lipids, cytokines, and proteins. Microsample-based transcriptome profiling would facilitate use of RNA biomarkers in diagnosis and treatment of immunotherapy patients, but a suitable method has not been available. We tested a targeted sequencing protocol for this purpose in human blood microsamples. We tested normal blood collected either by phlebotomy into standard vacutainer tubes or by absorption of 30 uL of blood onto a Mitra device pre-treated with an RNA-stabilization reagent. We tested detection of gene expression changes by incubating anti-coagulated blood for 18 hours with endotoxin followed by isolation of identical volumes of blood using a standard method (Qiagen kit) or from Mitra devices air dried for 24 h to mimic a home-use scenario. RNA was extracted from the microsamplers. After RNA purification, a panel of 274 immune/inflammatory genes was quantified by NGS after PCR using targeted primers following the Cellecta DriverMap protocol, which avoids counting of abundant rRNA and mitochondrial sequences. The targeted sequencing results were normalized to counts per million and used to compare results in standard vs microsamples. We found robust detection of gene expression and correlation using the two methods in both unstimulated (r = 0.94) and endotoxin-stimulated blood. The differentially expressed genes (DEGs) identified in both standard and microsample methods showed high overlap with DEGs reported in public datasets in similar experiments. We conclude that RNA transcriptome profiling using targeted sequencing allows sensitive detection of gene expression levels in normal and activated blood samples. Because microsamples can be air-dried and mailed in for analysis, this approach has great promise for simple and repeated monitoring of RNA biomarkers in immunotherapy.
Citation Format: Alex Chenchik, Lester Kobzik, Mikhail Makhanov, Paul Diehl. RNA transcriptome profiling in microsamples of blood [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B019.
Abstract B052: Small molecule RPA inhibitors abrogate the ATR kinase signaling pathway
Authors: Jordan Matthew R , Ainembabazi Diana , VanderVere-Carozza Pamela S , Gavande Navnath S , Pawelczak Katherine S , Turchi John J 
Published: December 2023

Abstract
Replication Protein A (RPA) is the major single-stranded DNA (ssDNA) binding protein in the cell and plays a role in replication, recombination, and the DNA damage response (DDR) and repair. RPA functions to protect ssDNA from degradation and also serves as an interaction hub to recruit replication and DDR machinery. Under normal cellular conditions, RPA protein abundance is in excess to that of the ssDNA generated during S phase replication so as to protect from replication fork collapse and replication catastrophe in the event of elevated levels of replication stress. RPA inhibition is thus a promising cancer therapeutic strategy that targets oncogenic cells with increased replication stress due to rapid cell proliferation, genotoxic stressors, DDR inhibition, etc, and therefore an increased ssDNA burden. We have previously developed the RPA inhibitor (RPAi) NERx329 that disrupts RPA-ssDNA binding and exhibits single agent anti-cancer activity in vitro and in vivo presumably due to chemical RPA exhaustion. When a cell experiences extensive replication stress, elevated levels of RPA-bound ssDNA are recognized by the kinase ataxia telangiectasia and Rad2-related (ATR) through the ATR interacting protein (ATRIP). ATR is then activated through interactions with DNA topoisomerase 2-binding protein 1 (TopBP1) and phosphorylates downstream targets largely to direct the G2/M checkpoint signaling pathway through checkpoint kinase 1 (CHK1). In this work, we biochemically reconstitute this signaling pathway in order to evaluate an RPAi mechanism of action. We utilize a ssDNA substrate that mimics a stalled replication fork and demonstrate the RPA-dependence of ATR activation by monitoring phosphorylation of multiple ATR substrates: RPA, TopBP1, and p53. We then show that RPAi disrupt ATR kinase activity. Collectively, this works describes a novel mechanism of action of RPAi whereby RPA inhibition results in replication catastrophe by blocking the ATR activity and the G2/M checkpoint pathway.
Citation Format: Matthew R Jordan, Diana Ainembabazi, Pamela S VanderVere-Carozza, Navnath S Gavande, Katherine S Pawelczak, John J Turchi. Small molecule RPA inhibitors abrogate the ATR kinase signaling pathway [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B052.
Abstract B060: Dual blockade of BRD4 and the ATR/WEE1 pathway exploits ARID1A loss in clear cell ovarian cancer
Authors: Kinose Yasuto , Xu Haineng , Kumar Sushil , Kim Hyoung , Medvedev Sergey , Wang Xiaolei , George Erin , Shan Xiaoyin , Gitto Sarah , D'Andrea Kurt , Wubbenhorst Bradley , Whicker Margaret , Hallberg Dorothy , Schwartz Lauren , Nathanson Katherine L , Mills Gordon , Velculescu Victor E , Wang Tian-Li , Brown Eric , Drapkin Ronny , Simpkins Fiona 
Published: December 2023

Abstract
Clear Cell Ovarian Cancer (CCOC) is one of the most challenging subtypes of ovarian cancer to treat as advanced stages are often chemo-resistant compared to the more common high-grade serous ovarian cancer (HGSOC). Limited treatment options are available for this devastating disease. Understanding the resistance mechanism and identifying effective therapeutic options for CCOC are clearly needed. Exploiting genetic alterations common in CCOC, such as ARID1A, is a rational strategy for combination therapies. ARID1A, an epigenetic tumor suppressor, is the most common genetic mutation in CCOC, with about 50% of CCOC demonstrating loss of ARID1A. ARID1A regulates the transcription of specific genes (e.g. c-myc) by altering the chromatin structure. We hypothesize that ARID1A loss increases CCOC cell dependency on chromatin remodeling and DNA repair pathways for survival. Through a drug screen, BET inhibitors and DNA damage response inhibitors were the most active monotherapies in ARID1A mutant CCOC. However, monotherapy efficacy needs to be further improved. We demonstrate in our study that the combination of BRD4 inhibitor (BRD4i) with DNA damage response (DDR) inhibitors (ATR or WEE1 inhibitors; e.g. BRD4i-ATRi) were synergistic at low doses leading to decreased survival, and colony formation in an ARID1A dependent manner. Combination BRD4i-ATRi caused significant tumor regression and increased overall survival in ARID1AMUT not ARID1AWT patient-derived xenograft (PDX) models. Combination BRD4i-ATRi significantly increased gH2AX, and decreased RAD51 foci and BRCA1 expression suggesting loss in the ability to repair DNA double-strand-breaks by homologous recombination (HR), more so than with monotherapy in ARID1AMUT cells. These studies demonstrate BRD4i-ATRi is an effective treatment strategy that capitalizes on synthetic lethality with ARID1A loss in CCOC warranting further study.
Citation Format: Yasuto Kinose, Haineng Xu, Sushil Kumar, Hyoung Kim, Sergey Medvedev, Xiaolei Wang, Erin George, Xiaoyin Shan, Sarah Gitto, Kurt D'Andrea, Bradley Wubbenhorst, Margaret Whicker, Dorothy Hallberg, Lauren Schwartz, Katherine L Nathanson, Gordon Mills, Victor E Velculescu, Tian-Li Wang, Eric Brown, Ronny Drapkin, Fiona Simpkins. Dual blockade of BRD4 and the ATR/WEE1 pathway exploits ARID1A loss in clear cell ovarian cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B060.
Abstract B076: Discovery of BBT-176 as fourth generation EGFR tyrosine kinase inhibitor
Authors: Duggirala Krishna Babu , Lee Kwangho 
Published: December 2023

Abstract
Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) improve overall survival rate in patients with EGFR mutated non-small cell lung cancers (NSCLC). However, upon treatment with third-generation EGFR TKIs (Osmertinib) develops C797S resistance[KS1] [u2] in the 20 – 30% of the patients. To date, there is no approved drug for third-generation resistance NSCLC patients. There is an unmet medical need to develop fourth generation EGFR TKIs[KS3] targeting C797S mutation. Extensive structure–activity relationship (SAR) studies led to the discovery of BBT-176 as a reversible fourth generation EGFR TKI. BBT-176 shows promising results with highly potent and anti-cancer efficacy in Osmertinib-resistant in vitro and in vivo cell lines. In mouse models, BBT-176 exhibited potent inhibition of tumor growth, leading to tumor regression in certain cases. Furthermore, promising results were observed in the clinical trial, where two patients with EGFR Del[KS4] 19/T790M/C797S mutations in their blood demonstrated tumor shrinkage and improvements in radiological assessments. BBT-176, a fourth-generation EGFR inhibitor, demonstrates significant preclinical activity against non-small cell lung cancer (NSCLC) that is resistant to current EGFR tyrosine kinase inhibitors (TKIs). This promising compound has shown early signs of clinical efficacy and safety in initial trials.
Citation Format: Krishna Babu Duggirala, Kwangho Lee. Discovery of BBT-176 as fourth generation EGFR tyrosine kinase inhibitor [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B076.
Abstract B081: Aurora kinase A inhibition overcomes adaptive resistance to KRAS G12C inhibitor by G1-checkpoint induced apoptosis in KRAS non-small cell lung cancer
Authors: Li Chendi , Chang Jeremy , Graser Christopher J , Syed Usman M , Nimbalkar Anahita , Shen Yi , Altschuler Steve , Wu Lani , Michor Franziska , Gong Xueqian , Hata Aaron N 
Published: December 2023

Abstract
Cancer cells gain drug-tolerant states and evade therapy. In response to KRAS G12C inhibitor (G12Ci), KRAS mutant non-small cell lung cancer (NSCLC) cells maintain a drug-tolerant state by aurora kinase A (AURKA). AURKA can phosphorylate c-Raf to maintain new KRAS signaling, however, how AURKA becomes activated to cause KRAS G12Ci resistance is unclear. We show here that KRAS G12C + AURKA inhibition cause synthetic lethality in KRAS G12C NSCLC cells. LY3499446 (KRAS G12Ci) and LSN3321213 (aurora kinase A inhibitor) induced apoptosis that is independent of inhibited MAPK reactivation. Using high-content imaging that tracks single-cell fate during treatment, we observed that single-agent KRAS G12Ci induces G1 arrest in a sub-population of cells. Upon co-treatment with G12C + AURKAi, cells that are halted in G1 phase undergo early apoptosis, while those that initially evade G1 arrest and proceed through G2/M undergo apoptosis in subsequent G1. These data suggest the hypothesis that AURKA inhibition may increase the probability of G1 checkpoint-induced apoptosis by facilitating chromosomal misalignment and genomic instability in G2. In summary, we provide pre-clinical rationale for clinical testing of KRAS G12C + AURKA inhibitors. We also suggest a novel mechanism explaining the dependency of KRAS G12C resistant subpopulations on AURKA, leading to the opportunity to investigate the role of genomic instability in conferring KRAS G12Ci adaptive resistance.
Citation Format: Chendi Li, Jeremy Chang, Christopher J Graser, Usman M Syed, Anahita Nimbalkar, Yi Shen, Steve Altschuler, Lani Wu, Franziska Michor, Xueqian Gong, Aaron N Hata. Aurora kinase A inhibition overcomes adaptive resistance to KRAS G12C inhibitor by G1-checkpoint induced apoptosis in KRAS non-small cell lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B081.