bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3110: An enhanced and cost-efficient method for neoantigen immunogenicity screening method: Double Barcode Neoepitope ScanTM
Authors: Kim Seong Gwang , Jung Min-Ho , Hwang Hyun-Ji , Oh Sejin , Hong Seong-Eui , Paik Soonmyung , Kim Hae-Suk 
Published: March 2024

Abstract
Neoantigens, HLA bound peptides generated by tumor-specific mutations, have emerged as promising targets for cancer immunotherapeutic. However, the significant challenge in neoantigen-based therapies is that the neoantigens are rare and difficult to predict. Therefore, in addition to prediction algorithms, the optimization of validation methods is essential for the reliable selection of highly immunogenic neoepitopes. In this study, we have developed a cost-effective screening method to validate large scale of neoantigen candidates. The DNA library-based methods have been employed for antigen selection and T cell receptor identification. We improved the DNA library-based neoantigen screening method by adding two barcodes to each minigene transcribing multiple neoantigen candidates and pooled synthesis of minigenes. We initially designed the barcodes to allow analysis in a 10 by 10 format for screening of hundreds of neoantigens so that PCR with each barcode result in amplification of ten candidates. The second barcode allowed the deconvolution of immunogenicity results without the need for synthesis of individual peptides. In this method B cell was used as antigen-presenting cell, which were co-transfected with mRNA for a minigene pool, 41BBL, and OX40L after expansion with CD40L/IL4/IL21. The resulting B cells were co-cultured with T cells and T cell responses were evaluated using ELISpot. To validate the method the TESLA consortium reported tetramer positive neoantigens were included in minigene. In results, the neoantigens including each barcode were amplified to form a pool of ten neoantigens as a minigene and confirmed that the neoantigens were equally amplified by nested PCR. The neoantigen pools synthesized as mRNA were transfected for presentation in B cells. The result of the targeting a neoantigen pool containing tetramer-positive neoantigens of the TESLA consortium showed a positive for ELISpot. In conclusion, our optimized screening method, employing the double barcode system, offers a time- and cost-efficient approach for the selection of immunogenic neoantigens without the need for individual peptides. This method will facilitate large-scale screening to identify actual neoantigens with immunogenic potential, contributing to the development of neoantigen-targeted vaccines.
Citation Format: Seong Gwang Kim, Min-Ho Jung, Hyun-Ji Hwang, Sejin Oh, Seong-Eui Hong, Soonmyung Paik, Hae-Suk Kim. An enhanced and cost-efficient method for neoantigen immunogenicity screening method: Double Barcode Neoepitope ScanTM [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3110.
Abstract 3141: LCB02A an antibody drug conjugate (ADC) targeting CLDN18.2 expressing solid tumors
Authors: Baek Eun ji , Chung Chul-Woong , Park Changsik , Jang Taeik , Jeong Yeojin , Lee Sang-Ah 
Published: March 2024

Abstract
Claudin18.2 (CLDN18.2) is an isoform of CLDN18 with very limited expression in gastric epithelial cells in normal tissues, and aberrant overexpression in gastric, pancreatic, esophageal, ovarian, lung, and other solid tumors. This expression pattern presents a significant hurdle in developing an ADC targeting CLDN18.2 due to potential on-target toxicity to the gastrointestinal (GI) tract. LCB02A is an antibody-drug conjugate (ADC) that targets CLDN18.2, composed of a topoisomerase 1 inhibitor (TOPO1i) as payload (DAR4) linked to the CLDN18.2 specific binding PR301839 hClaudin18.2 (CLDN18.2) is an isoform of CLDN18 with very limited expression in gastric epithelial cells in normal tissues, and aberrant overexpression in gastric, pancreatic, esophageal, ovarian, lung, and other solid tumors. This expression pattern presents a significant hurdle in developing an ADC targeting CLDN18.2 due to potential on-target toxicity to the gastrointestinal (GI) tract. LCB02A is an antibody-drug conjugate (ADC) that targets CLDN18.2, composed of a topoisomerase 1 inhibitor (TOPO1i) as payload (DAR4) linked to the CLDN18.2 specific binding PR301839 humanized IgG1 antibody utilizing LegoChem Biosciences’ ConjuAllTM technology. LCB02A showed potent in vitro cytotoxicity in CLDN18.2 expressing gastric and pancreatic cancer cell lines. LCB02A also showed excellent anti-tumor efficacy in various gastric and pancreatic cell line-derived xenograft (CDX) models and patient-derived xenograft (PDX) models. Preliminary toxicity assessment in cynomolgus monkeys (CLDN18.2 cross-reactive species) demonstrated that LCB02A was well tolerated, with repeat doses of up to 60 mg/kg. In conclusion, LCB02A is a promising ADC for the treatment of CLDN18.2 expressing solid tumors including gastric cancer (GC) and pancreatic ductal adenocarcinoma (PDAC). umanized IgG1 antibody utilizing LegoChem Biosciences’ ConjuAllTM technology. LCB02A showed potent in vitro cytotoxicity in CLDN18.2 expressing gastric and pancreatic cancer cell lines. LCB02A also showed excellent anti-tumor efficacy in various gastric and pancreatic cell line-derived xenograft (CDX) models and patient-derived xenograft (PDX) models. Preliminary toxicity assessment in cynomolgus monkeys (CLDN18.2 cross-reactive species) demonstrated that LCB02A was well tolerated, with repeat doses of up to 60 mg/kg. In conclusion, LCB02A is a promising ADC for the treatment of CLDN18.2 expressing solid tumors including gastric cancer (GC) and pancreatic ductal adenocarcinoma (PDAC).
Citation Format: Eun ji Baek, Chul-Woong Chung, Changsik Park, Taeik Jang, Yeojin Jeong, Sang-Ah Lee. LCB02A an antibody drug conjugate (ADC) targeting CLDN18.2 expressing solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3141.
Abstract 3191: Chk1/2 inhibition enhances response to lurbinectedin treatment in small cell lung cancer
Authors: Uruchurtu Ashley Sanchez Sevilla , Roady Tyler , Anderson Agenxnie , El-Deiry Wafik S. 
Published: March 2024

Abstract
Small cell lung cancer (SCLC) remains a significant clinical concern, with only a 7% 5 year survival rate; therefore, there remains an unmet need for efficacious treatments. Lurbinectedin was FDA approved in 2019 to treat platinum-resistant SCLC. Preliminary experiments in SCLC cell lines indicated an increase in intracellular pChk1 when treated with lurbinectedin. Based on these data and our understanding of the role of checkpoint kinases in the DNA damage response (DDR), we hypothesize that the activity of Chk1 is indicative of upregulated DDR activity as a result of double stranded breaks and replicative stress induced by lurbinectedin. In subsequent experiments, we sought to identify the role of Chk1 and Chk2 in the tumor cell response to lurbinectedin by inhibiting their activity using prexasertib (LY2606368, Acrivon Therapeutics). Cell viability experiments indicate decreased tumor cell viability when three SCLC cell lines (H1048, H1105, H1417) are treated with prexasertib as a single agent and in combination with lurbinectedin. Western blot analysis of intracellular proteins from the same SCLC cell lines treated with both drugs demonstrate dose-dependent effects on cell death marker cPARP, DNA damage marker γH2AX, and DDR/cell cycle pathway kinases cdk1 and 2. Ongoing experiments seek to replicate results using alternative Chk1/2 inhibitors, and to explore the effect of lurbinectedin-Chk1/2 inhibitor combination treatment on antitumor immune effector function by in vitro co-culture.
Citation Format: Ashley Sanchez Sevilla Uruchurtu, Tyler Roady, Agenxnie Anderson, Wafik S. El-Deiry. Chk1/2 inhibition enhances response to lurbinectedin treatment in small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3191.
Abstract 3196: Overcoming lung cancer drug resistance: Enhanced cellular delivery using lipid-extracted nanoliposomes
Authors: Alqaryan Mohammed , Allahyani Rashad , Lee Dayeoun , Campbell Robert B. 
Published: March 2024

Abstract
Background: Lung cancer causes substantial cancer deaths in the U.S. Drug resistance remains a major issue. Nanoliposomes demonstrate enhanced drug targeting and resistance-overcoming potential. Incorporating lipid extracts derived from target cells shows improved delivery over conventional nanoliposomes. This study examined the effects of lung cancer cell lipid extract nanoliposomes against target and non-target cell populations from different environments.
Method: Cellular Membrane Lipid-Extracted Nanoliposomes (CLENs) were fabricated with DOPC, DOTAP, ChaGo-K-1 lipid extract, cholesterol, PEG5000, and rhodamine fluorescent label was incorporated for uptake studies. The liposome size was reduced by probe sonication. Particle size and polydispersity index (PDI) were measured by dynamic light scattering. Zeta potential was quantified by laser Doppler micro-electrophoresis. Four cell lines were utilized: ChaGo-K-1 NSCLC target, A549 pulmonary microenvironment control, 4T1 extra-pulmonary control, and normal lung fibroblasts off-target control. All cell lines were cultured in 48-well plates at a seeding density of 10,000 cells/mL and incubated for 24 hours. Freshly prepared CLENs were added to all cell lines and incubated for an additional 24 hours. Cells were washed with PBS, and fluorescence intensity was then quantified and qualified by a microplate reader to measure the cellular uptake of the CLENs.
Results: The mean particle size and PDI of the ChaGo-K-1 CLENs were 117 ± 0.7 nm and 0.216 ±0.009, compared to 126 ± 0.5 nm and 0.195 ± 0.008 for the control, respectively. Both formulations were within the optimal size range for drug delivery and tumor cell penetration. The zeta potential of the ChaGo-K-1 CLENs was -1.75 ± 1.81 mV compared to -1.74 ± 6 mV for the control. Quantification and qualification of cellular uptake using fluorescence intensity measurements revealed a 3.2-fold increase in ChaGo-K-1 CLENs compared to conventional liposomes without ChaGo-K-1 lipid extracts. This demonstrates that the inclusion of the lipid extracts in the CLEN significantly enhanced selectivity and delivery to target cancer cell populations.
Conclusion: Higher uptake occurred with target cells using CLENs with lipid extracts versus standard liposomes. NSCLC-derived CLENs show potential to improve selective delivery and overcome drug resistance. Further, in vivo studies evaluating selective NSCLC tumor accumulation and efficacy enhancement are warranted.
Citation Format: Mohammed Alqaryan, Rashad Allahyani, Dayeoun Lee, Robert B. Campbell. Overcoming lung cancer drug resistance: Enhanced cellular delivery using lipid-extracted nanoliposomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3196.
Abstract 320: Development and automation of a streamlined targeted enrichment method for cancer mutation detection
Authors: Wu Zhong , Baird Michelle , Mechlen Cornelia , Hahn Peter , Shaffer Jonathan M. 
Published: March 2024

Abstract
Next Generation Sequencing (NGS) of DNA is a powerful tool for the detection of genetic variations, including single nucleotide polymorphisms, copy number variation, and small insertions/deletions. Target enrichment technologies enhance DNA sequencing by enabling users to analyze specific regions of interest only, which helps to effectively increase sequencing depth and sample throughput while minimizing cost. However, many targeted DNA library construction workflows are not optimal for routine genetic testing needs due to inconsistent, lengthy workflow. This poses significant challenge to application like cancer mutation profiling that requires detection sensitivity down to 1% or below due to heterogeneous nature of tumor tissue. In addition, high throughput testing with minimal hands on time is desirable with the rapid advance of precision medicine. Magnetic bead separations are commonly used between the individual reactions of targeted DNA library preparation workflows for cleanup and size selection. These bead clean up reactions are not only labor-intensive and tedious procedures but can also greatly contribute to sample-to sample variation especially when employing automated library preparation procedures. With the sophisticated QIAseq Targeted DNA Pro, we developed a novel streamlined targeted DNA workflow that greatly reduces handling variation by replacing the majority of bead clean up steps with enzymatic reactions, which now can be finished in as little as six hours. In combination with the newly developed QIAseq Normalizer kit, the protocol has been successfully implemented on the Hamilton NGS Star liquid handling platform resulting in up to 96 highly uniform, complex and ready-to-sequence libraries that can be effortless generated in one run. This complete automated solution saves researcher up to four hours of hands-on time. When using commercial reference samples, cancer mutations down to 1% were consistently detected with this automated workflow. The presented data demonstrate that this integrated and streamlined workflow does not only provide an automation friendly workflow but also allows to reliably identify low frequent cancer mutations. The applications presented here are for research use only. Not for use in diagnostic procedures.
Citation Format: Zhong Wu, Michelle Baird, Cornelia Mechlen, Peter Hahn, Jonathan M. Shaffer. Development and automation of a streamlined targeted enrichment method for cancer mutation detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 320.
Abstract 3203: Extravasation and metastasis dynamics are cytoplasmically controlled by the epitranscriptome
Authors: Grafinger Olivia R. , Thillainadesan Gobi , Su Boyang , Mo Yulin , Xu Xin , Mar Sara , Sheng Minzhi , Islam Sumaitha Al , Geddes-McAllister Jennifer , Coppolino Marc G. , He Hansen H. , Zheng Gang , Jerzak Katarzyna J. , Leong Hon S. 
Published: March 2024

Abstract
Non-coding RNA (ncRNA) and RNA binding proteins (RBPs) primarily reside in the nucleus to regulate splicing, transcription, and transcript stability. However, their role(s) in the cytoplasm were unclear until now. Evidence now suggests that ncRNAs within the cytoplasm play an important role in cancer invasion. In concert with MT1-MMP, a protease involved in invadopodia formation, long non-coding RNAs (lncRNAs) and RBPs form cytoplasmic complexes with MT1-MMP, which we termed “R-bodies” and are abundant in invasive breast cancer cells. RNA immunoprecipitation sequencing (RIP-seq) of only the cytoplasm identified the RNA at the core of these complexes to be metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a lncRNA which has been previously described as playing a fundamental role in cancer but only within the nucleus. Further investigation revealed that R-body-associated-MALAT1 was m6A-epigenetically marked. Depletion of any component of R-bodies and inhibition of m6A epigenetic marking of MALAT1 halted R-body formation and subsequent cell invasion. Importantly, we demonstrate that this cytoplasmic complex can be functionally targeted using RNA therapy against m6A-MALAT1 as well as drugs which inhibit the methyltransferase responsible for the m6A methylation of MALAT1. The identification of R-bodies has far-reaching implications and links the roles of cytoplasmic ncRNA and RBPs to the progression of disease.
Citation Format: Olivia R. Grafinger, Gobi Thillainadesan, Boyang Su, Yulin Mo, Xin Xu, Sara Mar, Minzhi Sheng, Sumaitha Al Islam, Jennifer Geddes-McAllister, Marc G. Coppolino, Hansen H. He, Gang Zheng, Katarzyna J. Jerzak, Hon S. Leong. Extravasation and metastasis dynamics are cytoplasmically controlled by the epitranscriptome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3203.
Abstract 3225: Profiling the DNA regulome to discover direct inhibitors of the brachyury transcription factor
Authors: Federation Alexander Joel , Gao Yang , McEllin Brian , Gatbonton-Schwager Tonibelle , Gutierrez Andrea , Robbins Julia , Hueffmeier Bodhi , Broderick Erin , Canzani Daniele , Fondrie William , Pino Lindsay 
Published: March 2024

Abstract
Background: The human genome encodes more than 1,600 transcription factors (TFs), along with additional cofactors, chromatin regulators, and structural proteins that collectively execute the regulatory instructions encoded within the nuclear DNA. Dysfunctions of these proteins, collectively known as the Regulome, are known to drive multiple conditions such as cancer, autoimmune conditions, and fibrosis. Despite their importance, many of these proteins are considered undruggable due to challenges in modeling their activity in vitro.
Methods: We have addressed these shortcomings by implementing a live-cell Regulome profiling approach that quantifies the global activity of TFs without the need for cell manipulation or genome engineering, called TF-Scan. The technology coupled rapid, automated purification of the DNA-bound proteome coupled to scalable Data Independent Acquisition (DIA) quantitative mass spectrometry proteomics and machine learning.
Results: We completed a screen of covalent compounds across 8 tissue types to discover hotspot sites on TFs that control their DNA-binding activity. A chordoma cell line was included in this screen. The screen identified compounds capable of binding to and disrupting the activity of several previously undruggable transcription factors, including brachyury. Hit validation and hit-to-lead medicinal chemistry resulted in a covalent chemical probe for brachyury, with activity in cell line models of chordoma.
Conclusion: Phenotypic drug discovery in live, unmodified human cells with systematic regulome profiling enables the discovery of compounds that disrupt previously undruggable targets by multiple mechanisms of action.
Citation Format: Alexander Joel Federation, Yang Gao, Brian McEllin, Tonibelle Gatbonton-Schwager, Andrea Gutierrez, Julia Robbins, Bodhi Hueffmeier, Erin Broderick, Daniele Canzani, William Fondrie, Lindsay Pino. Profiling the DNA regulome to discover direct inhibitors of the brachyury transcription factor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3225.
Abstract 3232: LSD1 inhibition transcriptionally reprograms neuroendocrine prostate cancer exposing unique therapeutic vulnerabilities
Authors: Jasmine Sumer M. , Mandl Adel , Dalrymple Susan L. , Kim Sunghyun , Dias Jennifer , Kleppe Maria , Celatka Cassandra , Tapper Amy , Coleman Ilsa , Nelson Peter , Rienhoff Hugh , Denmeade Samuel R. , Brennen W. Nathaniel 
Published: March 2024

Abstract
Therapeutics have been developed to target castration-resistant prostate cancer (CRPC) classified as adenocarcinoma (CRPC-Adeno). However, an increasing frequency of CRPC-Adeno tumors progress to the highly aggressive and lethal neuroendocrine prostate cancer (NEPC) by acquiring a neuroendocrine (NE) phenotype as a mechanism of therapeutic resistance. This transformation from CRPC-Adeno to NEPC requires distinct epigenetic reprogramming by lysine-specific demethylase 1 (LSD1), which can be exploited for development of novel therapies to target NEPC. LSD1 is upregulated in NEPC and promotes a stem-like transition state through lineage plasticity which enables the cancer cell to undergo NE differentiation. We have shown that LSD1 inhibition reduces the NE program, driving NEPC towards a non-neuroendocrine state through ASCL1 suppression and YAP1 re-expression. This less aggressive non-neuroendocrine state exposes unique vulnerabilities for the development of novel combination therapies to treat this lethal disease.
Citation Format: Sumer M. Jasmine, Adel Mandl, Susan L. Dalrymple, Sunghyun Kim, Jennifer Dias, Maria Kleppe, Cassandra Celatka, Amy Tapper, Ilsa Coleman, Peter Nelson, Hugh Rienhoff, Samuel R. Denmeade, W. Nathaniel Brennen. LSD1 inhibition transcriptionally reprograms neuroendocrine prostate cancer exposing unique therapeutic vulnerabilities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3232.
Abstract 3248: Metabolic rewiring shifts engineered TCR T cell bioenergetics to enhance cytotoxicity
Authors: Pillai Rashmi , Zhang Xiaoyu , Abassi Yama 
Published: March 2024

Abstract
Background: Adoptive T cell-based transfer has shown tremendous success in hematological cancers. However, an important obstacle to using cell and gene therapy for solid tumors is the aggressive tumor microenvironment (TME). To significantly improve prognosis of subjects undergoing immunotherapy, it is essential to incorporate unique methods to drive T cell energy production and metabolism towards empowering T cells to dismantle the suppressive TME. This can promote anti-tumor effects and persistence of the transfused engineered T cells. In the present study we present a simple metabolic preconditioning process that improves T cell performance and bioenergetics.
Methods: Using the Agilent xCELLigence RTCA eSight, and Seahorse XF Analyzer we assessed the killing efficiency, and bioenergetics of engineered T-cells after pretreating with Arginine. Briefly, engineered TCR T-cells against MART-1 were generated by transducing CD3+ T-cells (Hemacare, Seattle, WA) with retrovirus SAMEN-DMF5 with a CD34 marker gene, against MART-1. The TCR T cells were pre-conditioned in 6mM Arginine for 7 days, followed by a killing assay using MART-1 expressing melanoma cell line as target cells (624.38) at the E:T ratio of 5:1. Target melanoma cells, 624.38 cells, were engineered to express a red-fluorescent nuclear protein. The comparison was made with transduced T-cells grown in RPMI (no added amino acid supplementation, and non-transduced T cells. The cytotoxicity assay was assessed using real-time impedance and live cell imaging data collected on xCELLigence RTCA eSight. Concurrently, the metabolic profiling of the engineered T-cells was examined by the XF96 Analyzer.
Results: Supplementing the growth medium with 6 mM Arginine significantly increased the potency of MART-1 engineered T cells (up to 6-fold) and bioenergetic studies revealed increased spare respiratory capacity, basal respiration, and ATP production via mitochondrial respiration.
Conclusions: Arginine pre-conditioning improved TCR T cell potency through metabolic rewiring favoring mitochondrial respiration. For Research Use Only. Not for use in diagnostic procedures RA45236.3483333333
Citation Format: Rashmi Pillai, Xiaoyu Zhang, Yama Abassi. Metabolic rewiring shifts engineered TCR T cell bioenergetics to enhance cytotoxicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3248.