bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6582: A path to sustainability for the National Cancer Institute's Cancer Research Data Commons
Authors: Klenk Juergen A. , Maggio Angela , Singh Bhavani S. , Byrne Erin N. , Kim Erika , Davidsen Tanja M. 
Published: April 2023

Abstract
Purpose: The volume of data produced by the biomedical research community continues to grow rapidly. Efficient collection, curation, and sharing of these data are expected to enable researchers to synthesize larger datasets and apply novel methods to discover new patterns for diagnosis, treatment, and care of disease. Consequently, data platforms that support these functionalities have become an important instrument for the biomedical research community. The National Cancer Institute’s (NCI’s) Cancer Research Data Commons (CRDC) is a data platform for the cancer research community that provides cloud-based, secure storage and analytic tools for cancer data, including genomics, proteomics, imaging, and clinical trial data. CRDC has been funded by multiple sources, including the Beau Biden Cancer Moonshot program. Achieving long-term sustainability of the CRDC program is the focus of our study.
Methods: We applied a Financial Operations (FinOps) framework to map all costs to functionalities provided by the CRDC, including processes such as data intake, storage, compute, user support, and project management. We established a comprehensive financial baseline for the operations of the CRDC, identified opportunities for optimization across multiple dimensions (people, processes, technology), projected future costs based on trends for cancer data, and evaluated sustainability under defined funding scenarios.
Results: We identified 15 recommendations for optimization of the CRDC, including automation and centralization of core services (e.g., intake, curation, indexing), optimization of storage (e.g., compression, archiving), and harmonization of common services across the CRDC components (e.g., common architecture, governance). If implemented, we could demonstrate that these recommendations offer a path to long-term sustainability of the CRDC program under a variety of funding scenarios.
Conclusion: Data platforms such as the CRDC will see rapid increases in operational costs due to the growing data volumes and demand from researchers. Optimizing governance and operational frameworks will result in efficiency gains that can ensure long-term sustainability. Taking these steps will be critical to provide the necessary infrastructure to advance the field of data-driven biomedical research.
Citation Format: Juergen A. Klenk, Angela Maggio, Bhavani S. Singh, Erin N. Byrne, Erika Kim, Tanja M. Davidsen. A path to sustainability for the National Cancer Institute's Cancer Research Data Commons. [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 6582.
Abstract 66: Galectin-1 mediated chronic tumoral-STING activation promotes metastasisthrough MDSC recruitment
Authors: Nambiar Dhanya K. , Viswanathan Vignesh Vignesh , Cao Hongbin , Zhang Weiruo , Guan Li , Chamoli Manish , Holmes Brittany , Kong Christina , Hildebrand Rachel , Koong Amanda , Eyben Rie , Giaccia Amato , Li Lingyin , Engleman Edgar , Le Quynh Thu 
Published: April 2023

Abstract
Tumor cells alter the immune microenvironment to facilitate metastatic progression. Galectin-1 (Gal1) is a known modulator of tumor growth and progression in multiple cancer types including head and neck cancer (HNC). However, its contribution to the regulation of metastasis is poorly understood. Through this study we report a previously unknown role for Gal1 in modulating the STING pathway to regulate metastasis. The cGAS-STING pathway has paradoxical roles in cancer depending on the kinetics and strength of its induction, with chronic STING activation being linked to immune suppression and tumor progression while acute activation being associated with immune activation. However, little is known about the pathways that promote chronic STING activation. Using HNC and lung cancer models, we show that Gal-1 enhances STING protein stability, leading to sustained NF-κΒ activation and heightened chemokine-driven recruitment of myeloid derived suppressor cells (MDSCs). We show that Gal1-STING connection fosters the establishment of pre-metastatic niche through polymorphonuclear MDSCs (PMN-MDSCs), which modify the local lung microenvironment to support metastatic spread. Notably, RNA sequencing of MDSCs isolated from pre-metastatic lungs indicate the role of PMN-MDSCs in remodeling collagen and the extracellular matrix in the pre-metastatic compartment. Our findings reveal an unexpected role of STING activation in metastatic progression of HNC and lung cancer models and establish Gal1 as an endogenous positive regulator of STING.
Citation Format: Dhanya K. Nambiar, Vignesh Vignesh Viswanathan, Hongbin Cao, Weiruo Zhang, Li Guan, Manish Chamoli, Brittany Holmes, Christina Kong, Rachel Hildebrand, Amanda Koong, Rie Eyben, Amato Giaccia, Lingyin Li, Edgar Engleman, Quynh Thu Le. Galectin-1 mediated chronic tumoral-STING activation promotes metastasisthrough MDSC recruitment [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 66.
Abstract 6665: A spatiotemporal cell atlas of human gastric malignancy reveals mechanisms underlying metastasis and immunotherapy response
Authors: Luo Yikai , Kang Muxing , Liu Wei , Jiao Shiping , Wang Lie , Chen Jian , Liang Han 
Published: April 2023

Abstract
Cellular heterogeneity in the tumor immune microenvironment (TIME) of gastric cancer (GC) is progressively molded in pre- and early-malignant lesions and has a profound impact on disease progression and responses to therapeutics, in particular those based on immune checkpoint blockade (ICB). To date, no study has been conducted to characterize the single-cell kinetics of tumor-infiltrating immune populations in gastric cancer patients treated with ICB. Here, we generated for the first time single-cell RNA sequencing (scRNA-seq) and TCR sequencing (scTCR-seq) profiles of ICB-treated primary GC tumors, as well as liver and ovary metastases. When integrated with public scRNA-seq datasets, our data capture a full trajectory of GC malignancy comprising more than 300,000 cells derived from 73 samples. We further performed bulk TCR-seq, cytometry by time of flight (CyTOF), and multiplex immunofluorescence (mxIF) on independent GC samples to orthogonally validate the key observations from the scRNA-seq cohort and unbiasedly search for more in-depth and spatial-relationship-focused features of ICB-responsive immune populations. Built upon this multi-omic atlas of GC cell states, we identified remarkable transformation of the abundance and clonal dynamics of distinct immune populations and their population-specific transcriptional programs. Most importantly, we observed the rejuvenation of exhausted CD8+ T cells induced by anti-PD-1 treatment, which is associated with the enhanced immunogenicity of gastric cancer cells. In addition, we found the enrichment of NK-like terminally differentiated CD8+ T cells in metastases independent of migration destinations. Our single-cell ICB-perturbed spatiotemporal GC landscape reveals how neoadjuvant checkpoint blockade induces local and systemic tumor immunity. As a cellular and molecular reference, it also enables high-resolution interpretation of future single-cell omics data in gastric cancer that may be masked by de novo analysis.
Citation Format: Yikai Luo, Muxing Kang, Wei Liu, Shiping Jiao, Lie Wang, Jian Chen, Han Liang. A spatiotemporal cell atlas of human gastric malignancy reveals mechanisms underlying metastasis and immunotherapy response [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 6665.
Abstract 6669: Antigen features are associated with response and survival after neoadjuvant chemo-immunotherapy for muscle-invasive bladder cancer
Authors: Beckabir Wolfgang , Vensko Steven , Wilkinson Alec , Atassi Gatphan , Zhou Mi , Fowler Kenneth , Flick Leah , Wang Hsing-Hui , Woodcock Mark , McKinnon Karen , Serody Jonathan , Rose Tracy , Milowsky Matthew , Kim William , Vincent Benjamin 
Published: April 2023

Abstract
In the Phase II LCCC1520 trial, neoadjuvant chemo-immunotherapy (pembrolizumab with gemcitabine plus cisplatin) induced response in 22 of 39 muscle-invasive bladder cancer patients[1]. In this correlative analysis, we identify molecular features associated with response and survival. Associations of molecular subtype, TMB, and antigen presentation and immune checkpoint gene expression with response and survival were evaluated pre-and post-treatment. Neoantigens were predicted in 4 immuno-oncology data sets (LCCC1520, IMvigor210 cohorts 1[2] and 2[3], and Hugo[4]) using Landscape of Effective Neoantigens Software[5]. Effective neoantigen count (ENC) was calculated by binning predicted neoantigens by expression, binding affinity, binding stability, and tumor PD-1 and PD-L1 expression, then identifying the bin in which neoantigen count was most strongly associated with response in the discovery set. Using elastic net modeling with 10-fold cross-validation, survival was predicted from immune gene signature expression, clinical variables, TMB and ENC. Response was associated with pre-treatment molecular subtype and immune checkpoint expression. Pre-treatment ENC was associated with response in Hugo (discovery set, p = 0.020) and the three validation sets (p = 0.011, 0.042, 0.049). The final elastic net model (Cox P-H p = 5.6e-5) predicted survival significantly better than TMB (p = 0.055) or ENC (p = 0.141) alone. Post-treatment antigen presentation gene expression was associated with survival among non-responders. We identify pre-and post-treatment features associated with response and survival in the LCCC1520 trial and propose that tumor antigen presentation is a major driver of neoadjuvant chemo-immunotherapy outcomes. [1] Rose JCO 2022 [2] Balar Lancet 2017 [3] Mariathasan Nature 2018 [4] Hugo Cell 2016 [5] Vensko bioRxiv 2022
Citation Format: Wolfgang Beckabir, Steven Vensko, Alec Wilkinson, Gatphan Atassi, Mi Zhou, Kenneth Fowler, Leah Flick, Hsing-Hui Wang, Mark Woodcock, Karen McKinnon, Jonathan Serody, Tracy Rose, Matthew Milowsky, William Kim, Benjamin Vincent. Antigen features are associated with response and survival after neoadjuvant chemo-immunotherapy for muscle-invasive bladder cancer [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 6669.
Abstract 6701: 6-color Crystal Digital PCR for the high-plex detection of 10 ESR1 mutations in breast cancer
Authors: Smilkou Stavroula , Ntzifa Aliki , Stergiopoulou Dimitra , Blache Quentin , Remy Myrtille , Jovelet Cecile , Mallory Allison , Lianidou Evi 
Published: April 2023

Abstract
Introduction. ESR1 mutations have emerged as a key mechanism of resistance to endocrine therapy in estrogen-receptor-positive (ER+) breast cancer, thus detection of ESR1 mutations is crucial to monitor during patient treatment. We evaluated a novel 12plex breast cancer assay for the detection of 10 ESR1 mutations and AKT1 E17K in plasma cell-free DNA (cfDNA) using 6-color Crystal Digital PCRTM (naica® system, Stilla Technologies, France). We further compared the results with our previously reported ESR1 NAPA assay for D538G, Y537S, Y537C and Y537N mutations (Stergiopoulou et al, Cancers, 2021).
Patients and Methods. Using the 6-color Crystal Digital PCRTM breast cancer 12plex assay, we analyzed 35 plasma cfDNA samples from ER+ breast cancer patients and 10 plasma cfDNA from healthy donors (HD). We also analyzed the same cfDNA samples using the ESR1 NAPA assay.
Results. The Stilla 6-color breast cancer assay revealed in 5/35 (14,3%) ER+ cfDNA samples the AKT1_E17K and ESR1 D538G mutations. ESR1 D538G was detected in 4/35 ER+ cfDNA samples with the ESR1 NAPA assay. Direct comparison between Crystal Digital PCR™ and the ESR1 NAPA assay revealed a high concordance (97.1%) for 34/35 samples tested, for the detection of the D538G mutation, and with a higher sensitivity for the Stilla 6-color breast cancer assay. The ESR1 mutations Y537S, Y537C and Y537N were not detected by either method in any of the plasma-cfDNA samples. No AKT1 E17K or ESR1 mutations were detected in cfDNA from HD plasma.
Conclusions. The naica® system 12plex ESR1 assay is quantitative, highly sensitive and easy to perform using plasma-cfDNA samples. The use of highly multiplexed Crystal Digital PCR™ shows great promise for clinical utility for ER+ breast cancer patient monitoring.
Key words: Circulating tumor DNA; Crystal Digital PCR™, ESR1 mutations; liquid biopsy; mutation monitoring, 6-color multiplexing;
Citation Format: Stavroula Smilkou, Aliki Ntzifa, Dimitra Stergiopoulou, Quentin Blache, Myrtille Remy, Cecile Jovelet, Allison Mallory, Evi Lianidou. 6-color Crystal Digital PCR for the high-plex detection of 10 ESR1 mutations in breast cancer [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 6701.
Abstract 788: Novel multiplex methylation-specific qPCR strategy for early CRC detection
Authors: Bao Yun , Wang Heng , Vu Peter , Zhao Grace , Lin Shengrong 
Published: April 2023

Abstract
Colorectal cancer (CRC) can be cured if detected early. Analysis of abnormalities in cfDNA methylation is an emerging and powerful strategy for early cancer detection. Recently, targeted methylation NGS methods have shown encouraging performance in CRC detection, but their high cost and complicated workflow can be challenging for many clinical settings. At the same time, the alternative, single methylation biomarker PCR assays, demonstrate limited sensitivity and specificity. An accurate, accessible and affordable assay ideal for clinical applications requires an easily scalable set-up and a set of high quality biomarkers providing sufficient predictive power. We aim to develop an assay fulfilling the CMS definitive performance guideline of LBx CRC screening – at least 74% sensitivity and 90% specificity.
Here we report the development of a novel multiplex methylation-specific qPCR (MMS-qPCR) strategy for early CRC detection. Previously, we established detailed methylation profiles of our proprietary CRC targeted methylation sequencing panel with 560 biomarkers, based on more than 500 plasma samples of both healthy controls and CRC patients of various stages. We selected 9 biomarkers that are both highly sensitive and specific for CRC. These 9 markers show methylation signatures prevalent in patients and have very low noise in healthy controls. Along with one reference gene, the 9 CRC hypermethylated biomarkers can be multiplexed and analyzed in a single methylation-specific qPCR reaction. Analytical sensitivity and specificity were determined using a model system where hypermethylated DNA molecules were spiked into normal cell free DNA background at various percentages. With 10 ng of input, we can detect a single copy of the hypermethylated genome, achieving 0.006% limit of detection. Plasma samples from 10 stage I and 11 stage II CRC patients as well as 104 age-matched control subjects were subjected to the PCR analysis to yield a specificity of 96% and detection rate of 50% for stage I and 81% for stage II. The total turnaround time for analysis was &lt;4 hours including DNA isolation, bisulfite conversion and qPCR analysis.
The MMS-qPCR described here provides an accurate, accessible, and affordable liquid biopsy assay for the early detection of CRC. The same development strategy can also be applied to many other cancer types.
Citation Format: Yun Bao, Heng Wang, Peter Vu, Grace Zhao, Shengrong Lin. Novel multiplex methylation-specific qPCR strategy for early CRC detection [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 788.
Abstract 824: Statistical optimization of stable Quercetin nanoparticles for tumor targeting
Authors: Hassan Nourhan Khaled , El-labbad Eman , jagal Jayalakshmi , Haider Mohamed , El-sayed Ibrahim 
Published: April 2023

Abstract
Quercetin is a well-known flavonoid with a significant in vitro anticancer effect and low toxicity profile. Despite of that, its clinical use is still limited because of its low solubility, bioavailability, and instability in physiological conditions. The aim of this study was to develop and optimize stable quercetin nanoparticles targeting tumor cells within the body. Quercetin nanoparticles were synthesized using solvent emulsification technique using zein, beta-cyclodextrin, and pectin at different concentrations. The prepared formulations were optimized using factorial response surface analysis. The stability of the optimized quercetin nanoparticles in conditioned media, obtained from subculture of colorectal cancer cell line HCT-116, was compared to the stability of the free drug powder over 24 h. Moreover, the cytotoxic effect of Quercetin powder and the optimized Quercetin nanoparticles were evaluated against two colorectal cancer lines (HT-29, and HCT116), using MTT assay, under normoxic conditions. Annexin-V/FITC apoptotic assay was used to detect the number of cells that underwent apoptosis using flow cytometry. The optimized formulation was composed of 10 mg of zein and 31.35 mg beta-cyclodextrin, with no pectin. It had particle size of 221 nm, polydispersity index of 0.115, zetapotential of 7.65 mV. The stability of the optimized quercetin nanoparticles in the conditioned media of HCT-116 was significantly higher than the free drug powder over 24 h. In HT-29, the optimized nanoparticles and the free drug had IC50 of 29.33 µM and 60.78 µM, respectively. In HCT-116, optimized nanoparticle and the free drug had IC50’s 31.11 µM and 59.20 µM, respectively. The flow cytometric analysis after annexin-V/FITC staining showed that treatment with the optimized quercetin nanoparticles significantly induced total apoptosis in the two colorectal cancer lines (HT-29 and HCT 116) when compared to the free drug and plain nanoparticles. In conclusion, the optimized quercetin nanoparticles were found to be capable of increasing drug stability in physiological fluids as well as increasing its cytotoxic effect in two colorectal cancer cell lines by apoptosis induction when compared to the drug in powder form as well as plain nanoparticles.
Citation Format: Nourhan Khaled Hassan, Eman El-labbad, Jayalakshmi jagal, Mohamed Haider, Ibrahim El-sayed. Statistical optimization of stable Quercetin nanoparticles for tumor targeting [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 824.
Abstract 838: Development of cationic polypeptide-based adjuvants for cancer immunotherapy
Authors: Lee DaeYong , Huntoon Kristin , Jiang Wen , Kim Betty 
Published: April 2023

Abstract
Stimulation of intracellular DNA sensors plays a crucial role in regulating innate immunity as well as bridging to adaptive immune responses. Although delivery of agonists can activate such innate immune sensors, their intracellular delivery are generally challenging due to vulnerability to enzymatic degradation, low water solubility, or electrostatic repulsions. To overcome the hurdles, we developed a synthetic cationic helical polypeptide that stimulated toll-like receptor 9 (TLR9) and cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) axes by triggering mitochondrial DNA release preferentially in APCs. We revealed that systemic administration of this polypeptide-based adjuvant generated pro-inflammatory responses in APCs, and subsequently primed cytotoxic T cells. Furthermore, the polypeptide treatment with immune checkpoint blockade (anti-programmed cell death protein 1: anti-PD1) synergistically improved tumor suppression and increase animal survival of breast tumor-bearing mice. Taken together, this study suggests that the multi-potent cationic polypeptide stimulated multiple innate immune sensors, thus providing a promising therapeutic strategy to generate meaningful anti-tumor effects.
Citation Format: DaeYong Lee, Kristin Huntoon, Wen Jiang, Betty Kim. Development of cationic polypeptide-based adjuvants for cancer immunotherapy [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 838.
Abstract 876: Sequencing a new broadly-consented tumor/normal cell line for a Genome in a Bottle Benchmark
Authors: Rosen Gail , Wagner Justin , Liss Andrew , Zook Justin 
Published: April 2023

Abstract
Here, we describe analyses towards the first tumor/normal benchmark from the Genome in a Bottle (GIAB) consortium using new cell lines from a broadly-consented pancreatic ductal adenocarcinoma patient. This effort builds on the widely-used germline variant benchmarks for seven normal DNA reference materials. GIAB benchmarks are designed to reliably identify false positive and false negative variant calls, and are formed by combining multiple sequencing technologies and variant callers. To combine technologies and variant callers, we first understand their strengths and weaknesses for different variant types and repetitive regions. In this initial work on the new tumor/normal cell line, we have analyzed sequencing from HiC for copy number and structural variant analysis and 100to150x PCR-free Illumina WGS from normal and tumor cells for small variants. Preliminary HiC results identified substantial aneuploidy common in pancreatic tumors, with ~15 large inversions and translocations and 16 chromosomes with extensive loss of heterozygosity due to missing &gt;30% of one copy. The tumor contains the common G12V mutation in KRAS, and interestingly the ~2Mbp region containing this mutation is likely triplicated. About 300 (76% of) SNVs and 10,000 (69% of) small indels agree between mutect2 and strelka2 with default filtering. After excluding difficult regions, 95% of SNVs and 94% of small indels agree, with remaining disagreements caused by systematic sequencing errors, alignment errors, low frequency, and proximity to germline variants. Examining discordant SNVs indifficult regions, most are erroneous somatic variants inregions with loss of heterozygosity that also have mapping errors due to segmental duplications, sequences missing from GRCh38, and/or tandem repeats. After excluding difficult regions, we also found that somatic SNVs fell in 4 primary classes: ~5100 in most cells in diploid regions, ~2100 in most cells in haploid regions, ~760 in only some cells in diploid regions, and ~450 in only some cells in haploid regions. GIAB plans to perform PacBioHiFi and ultra long ONT sequencing to generate phased assemblies for the normal and tumor, and is forming an open working group to develop the first authoritative benchmarks from publicly available, broadly-consented tumor-normal cell lines.
Citation Format: Gail Rosen, Justin Wagner, Andrew Liss, Justin Zook. Sequencing a new broadly-consented tumor/normal cell line for a Genome in a Bottle Benchmark [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 876.