bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6572: A lung cancer cell line explorer
Authors: Cai Ling , Girard Luc , DeBerardinis Ralph , Xiao Guanghua , Minna John , Xie Yang 
Published: April 2023

Abstract
Over 300 lung cancer cell lines have been established in the past few decades with clinical annotations. Efforts from multiple institutions comprehensively profiled these cell lines for their genetic and epigenetic variations, gene and protein expression, metabolism, and functional liabilities. These data provide an unprecedented opportunity to accelerate lung cancer research. We developed a lung cancer cell line explorer at https://lccl.shinyapps.io/LCCL/ integrating over 35 datasets. We also incorporated engineered features such as pathway enrichment scores from copy number-denoised transcriptomic data and neuroendocrine scores. Our web application allows users to 1) query and download the processed datasets, 2) assess data reproducibility across studies, 3) review genomic abnormalities, 4) perform ad hoc bivariate analyses with the option to add filtering or coloring by a third feature, 5) generate heatmaps and correlation maps, 6) perform global association test to screen for significant association between a feature of interest and all features from a dataset of interest, and 7) upload their own datasets to be analyzed in conjunction with our in-house datasets. In summary, this online tool will greatly facilitate the utilization of high-dimensional datasets that characterize lung cancer cell lines.
Citation Format: Ling Cai, Luc Girard, Ralph DeBerardinis, Guanghua Xiao, John Minna, Yang Xie. A lung cancer cell line explorer [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 6572.
Abstract 6591: A universal atlas of cellular and oncogenic phenotypes
Authors: Weistuch Corey , Murgas Kevin , Dill Ken , Norton Larry , Deasy Joseph , Tannenbaum Allen 
Published: April 2023

Abstract
Tumors and healthy tissues exhibit gene expression variability in many of the same pathways. We propose that these commonalities result from a performance trade-off between universal cellular phenotypes; each phenotype is defined by an orthogonal gene expression profile identified using unsupervised dimensionality reduction. Using two publicly available RNA-seq datasets (n=54 normal tissues; n=1504 cancer cell lines), we show that both healthy and cancerous cells occupy a trade-off between five canonical phenotypes: OxPhos, Warburg, Fibroblastic, Immune, and Growth. Each cell is assigned a phenotype score that, as we demonstrate, predicts differential drug sensitivities and mutational signatures, even among cancers of the same tissue type. Since these phenotype scores are defined using only healthy tissues, they can be generally applied to other diseases as well.
Citation Format: Corey Weistuch, Kevin Murgas, Ken Dill, Larry Norton, Joseph Deasy, Allen Tannenbaum. A universal atlas of cellular and oncogenic phenotypes [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 6591.
Abstract 6690: Monitoring response and resistance to EGFR inhibition with circulating tumor DNA in a non-small cell lung cancer patient-derived xenograft
Authors: Do Long H. , Pippa Raffaella , Andrews Warren , Chien Yuan , Sperry Jantzen , Nakashima Jonathan 
Published: April 2023

Abstract
Circulating tumor DNA (ctDNA) has been shown as a clinically relevant biomarker for non-invasive monitoring of therapy response, disease burden and disease progression in cancer patients. Patient-derived xenografts (PDX) are essential translational models used for evaluating therapeutic response and identifying novel biomarkers, but analysis of ctDNA in these models remains understudied. Here, we report the use of ctDNA for the monitoring of therapeutic response and secondary resistance of a Non-Small Cell Lung Cancer PDX treated with EGFR inhibitors. We demonstrate measurable ctDNA changes correlate with disease burden and therapeutic response. Altogether, the isolation of ctDNA from PDX models is a robust methodology for interrogating therapeutic efficacy, response, and resistance in a preclinical setting that can be translated as a viable biomarker for non-invasive monitoring in patients.
Citation Format: Long H. Do, Raffaella Pippa, Warren Andrews, Yuan Chien, Jantzen Sperry, Jonathan Nakashima. Monitoring response and resistance to EGFR inhibition with circulating tumor DNA in a non-small cell lung cancer patient-derived xenograft. [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 6690.
Abstract 76: Reprogramming of the preinvasive breast microenvironment identified by spatial nucleus barcoding
Authors: Wang Kaile , Xiao Zhenna , Lin Yiyun , Wei Runmin , Ye Jie , Ye Rui , Hu Min , Bai Shanshan , Sei Emi , Thennavan Aatish , Lim Bora , Futreal Andrew , Thompson Alastair , Krishnamurthy Savitri , Navin Nicholas 
Published: April 2023

Abstract
Ductal-carcinoma-in-situ (DCIS) is the most common early-stage breast cancer and a non-obligate precursor to invasive breast cancer. However our understanding of the spatial microenvironment and the reprogramming of cell types in DCIS remains limited. To address this question, we developed a Spatial Nucleus Barcoding (SNuBar) method that utilizes a single oligonucleotide adaptor to preserve spatial information followed by performing single nucleus RNA sequencing. We validated the accuracy and scalability of SNuBar in cell lines and applied this method to investigate the spatial microenvironment of 4 normal breast tissues, 7 normal adjacent DCIS tissues, and 8 DCIS cancers. The analysis of single cells isolated from 596 macrodissected spatial regions identified 13 major cell types and 43 cell states, that co-localized in different combinations across four main topographic areas. Spatial analysis revealed that vascular and myoepithelial cells were reprogrammed in localized zones near the premalignant cells, while fibroblasts, T-cells and myeloid cells were reprogrammed across broader fields. Our data shows that many diverse cell types are reprogrammed in spatially-defined areas in the DCIS microenvironment, relative to the normal breast tissue regions.
Citation Format: Kaile Wang, Zhenna Xiao, Yiyun Lin, Runmin Wei, Jie Ye, Rui Ye, Min Hu, Shanshan Bai, Emi Sei, Aatish Thennavan, Bora Lim, Andrew Futreal, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin. Reprogramming of the preinvasive breast microenvironment identified by spatial nucleus barcoding [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 76.
Abstract 82: Role of MSC-derived CXCL1 in bone-metastatic prostate cancer
Authors: Johnson Catherine S. , Costanzo-Garvey Diane , Alsamraae Massar , Frieling Jeremy S. , Cook Leah M. 
Published: April 2023

Abstract
In 2022, the American Cancer Society estimates that over 34,000 men will die of PCa, largely due to metastatic PCa. Up to 90% of advanced prostate cancers metastasize to bone, and there are currently no curative therapies for bone metastatic prostate cancer (BM-PCa). BM-PCa cells interact with bone-forming osteoblasts and bone-resorbing osteoclasts to induce aberrant bone remodeling, which leads to skeletal related adverse events such as increased risk of fractures, bone pain, and poor quality of life. Mesenchymal stem cells (MSCs) are multipotent stem cells that can differentiate into osteoblasts. Cook lab data show BM-PCa cells interact with MSCs and promote MSC differentiation into osteoblasts. Microarray analysis of MSC gene expression changes in response to BM-PCa show significant upregulation of CXCL8. To determine the importance of MSC-derived CXCL8 to BM-PCa, CXCL1 (the murine homolog of CXCL8) was genetically deleted in murine MSCs. While CXCL1 knock out (KO) had no significant impact on MSC proliferation, loss of CXCL1 decreased MSC migration, which suggests upregulation of MSC CXCL1 by BM-PCa cells functions to increase MSC migration into the tumor microenvironment. Additionally, CXCL1 KO MSCs have altered osteoblastic differentiation, whereas adipogenic differentiation was unchanged. RNA sequencing of MSCs stably expressing CXCL1-targeted shRNAs compared to scrambled controls show extensive gene expression changes, including altered expression of multiple osteogenic genes. In vivo data show intratibial co-injection of CXCL1 KO MSCs with murine RM1 BM-PCa cells in an immunocompetent mouse model increases tumor burden compared with co-injection of wildtype MSCs and BM-PCa cells, indicating a role for MSC-derived CXCL1 in suppressing BM-PCa tumor growth in bone. This project shows for the first time the importance of CXCL1 in MSC migration, osteogenesis, gene expression, suppression of BM-PCa progression in bone and tumor-induced bone remodeling.
Citation Format: Catherine S. Johnson, Diane Costanzo-Garvey, Massar Alsamraae, Jeremy S. Frieling, Leah M. Cook. Role of MSC-derived CXCL1 in bone-metastatic prostate 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 82.
Abstract 826: Illuminating cancer cells with a novel nano fluorescent NIR probe for bioimaging
Authors: Chauhan Neeraj , Cabrera Marco , Chowdhury Pallabita , Nagesh Prashanth K. , Dhasmana Anupam , Jaggi Meena , Chauhan Subhash C. , Yallapu Murali M. 
Published: April 2023

Abstract
Background: Adequate bioimaging is crucial in cancer management in many ways including screening, detection, characterization, staging and grading, therapy response, surgical guidance, and margins assessment. Indocyanine green (ICG) is one of the FDA-approved near infra-red fluorescent (NIRF) probe for cancer imaging and image-guided surgery in clinical setting. However, limitations of ICG includes poor photostability, high concentration toxicity, short circulation time, and poor cancer cell specificity. To overcome these hurdles, we engineered a nanoconstruct composed of poly(vinyl pyrrolidone) (PVP)-indocyanine green that is cloaked self-assembled with tannic acid (termed as ICG-Glow NPs) for the cancer cells/tissues specific targeting.
Methods: Pursuing the novel nanotherapy approach, our lab has developed PVP-TA based ICG (PVT-ICG) fluorescent nanoparticles via self-assembly process. Our optimized PVT-ICG nanoformulation was further characterized for its physicochemical properties. An IVIS imaging system was further used to measure NIR fluorescence of novel PVT-ICG. Moreover, Human cancer (Breast, Pancreatic, Liver and Prostate) tissue microarrays (TMAs) were histochemically stained to assess cancer cell targeting/specificity of PVT-ICG.
Results: PVT-ICG indicated particle size and surface charge ideal for cancer cell/tissue delivery. PVT-ICG, further, demonstrated improved photostability and fluorescent intensity. Additionally, TMA studies exhibited enhanced internalization and cancer targeting/specificity of PVT-ICG nanoparticles compared to free ICG dye in all cancers.
Conclusion: Collectively, our findings suggest that this NIR fluorescent probe PVT-ICG has great potential for becoming a novel and safe imaging modality for various types of cancer cells and tumors which can result in early cancer diagnosis leading to improved disease management.
Citation Format: Neeraj Chauhan, Marco Cabrera, Pallabita Chowdhury, Prashanth K. Nagesh, Anupam Dhasmana, Meena Jaggi, Subhash C. Chauhan, Murali M. Yallapu. Illuminating cancer cells with a novel nano fluorescent NIR probe for bioimaging [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 826.
Abstract 85: Senescent cells promote breast cancer tumorigenesis
Authors: Ye Jiayu (Jennifer) , Delgado Ana Paula , Ren Qihao , Powers Robert S. , Stewart Sheila A. 
Published: April 2023

Abstract
Age is the largest risk factor for breast cancer development. While numerous changes arise with age, we posit that the accumulation of p16INKA4 (p16)+ senescent stromal cells—which express cytokines, chemokines, and enzymes together recognized as senescence-associated secretory phenotype (SASP)—promote cancer progression. Indeed, high p16 positivity in stroma strongly correlates with breast cancer recurrence. To investigate how senescent stroma impact tumorigenesis, we crossed MMTV-PyMT (PyMT) mice that spontaneously develop mammary tumors to INK-ATTAC (INK) mice, which allows selective elimination of p16+ cells. Depletion of p16+ stroma in PyMT/INK mice led to a significantly delayed tumor onset and changes in tumor-infiltrating immune cells, both of which could be recapitulated by treating PyMT mice with a senolytic drug. scRNA-seq analyses of murine and human tumor samples revealed that senescence is restricted to a specific cancer associated fibroblasts (CAF) subpopulation that expresses numerous immune and extracellular matrix SASP factors that could impact T cells and Natural Killer (NK) cells. We refer to these cells as senescent CAFs (senCAFs). To assess the impact of senCAFs on T and NK cells’ anti-tumor effect, we depleted each population and found that the elimination of senCAFs no longer restricted tumor development in the absence of NK cells. We thus focused on addressing how senCAFs modulate NK cell function. Together our data highlight how senescent CAFs contribute to mammary gland tumorigenesis by modifying tumor microenvironment.
Citation Format: Jiayu (Jennifer) Ye, Ana Paula Delgado, Qihao Ren, Robert S. Powers, Sheila A. Stewart. Senescent cells promote breast cancer tumorigenesis [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 85.
Abstract 904: Optimizing CAR T therapy via metabolic engineering for the treatment of glioblastoma
Authors: Ghosh Tanya , Chakraborty Avirup , Jin Linchun , Feier Diana , Silver Aryeh , Rahman Maryam , Flores Catherine , Sarkisian Matthew , Huang Jianping , Mitchell Duane A. , Deleyrolle Loic P. 
Published: April 2023

Abstract
Glioblastoma represent a great challenge and current therapies are negligibly effective, with disease recurrence being inevitable. T cell therapy has emerged as a viable treatment for brain malignancies. While promising, the efficacy of this approach is often limited by a complex immunosuppressive tumor microenvironment. These complexities mean that more sophisticated T cell products are required. The brain tumor microenvironment provides local restraints via metabolic competition suppressing antitumor immunity, specifically inhibiting infiltration and effector functions of host and adoptively transferred tumor-reactive T cells. The objective of this project is to test new treatments to reverse immune dysfunction in brain cancer through the regulation of T cell metabolic signaling. We propose that modulating glucose signaling can potentiate T cell anti-tumor activity. The glucose signaling pathway of T cells was modulated through overexpression of glucose transporters and the function of metabolically modified T cells was investigated using murine and human models. We revealed a competition for glucose between T cells and tumor cells, with tumor cells imposing glucose restriction mediating T cell hyporesponsiveness. Overexpression of glucose transporters such as Glut1 and Glut3 enhanced T cell glucose utilization and provided a survival/growth advantage and greater activation, specifically in glucose-restricted conditions. We established that glucose transporter overexpression improves intratumoral infiltration and expansion of adoptively transferred CAR T cells, resulting in improved survival. Our study integrates fundamental concepts of tumor and immune metabolism in the design of immunotherapy and confirms that immunometabolism represents a viable target for new cancer therapy to treat brain tumors.
Citation Format: Tanya Ghosh, Avirup Chakraborty, Linchun Jin, Diana Feier, Aryeh Silver, Maryam Rahman, Catherine Flores, Matthew Sarkisian, Jianping Huang, Duane A. Mitchell, Loic P. Deleyrolle. Optimizing CAR T therapy via metabolic engineering for the treatment of glioblastoma [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 904.
Data Supplement from SMAD4 Suppresses AURKA-Induced Metastatic Phenotypes via Degradation of AURKA in a TGFβ-Independent Manner
Authors: Jia Lina , Lee Hun Seok , Wu Chun Fu , Kundu Juthika , Park Sang Gyu , Kim Ryong Nam , Wang Li-Hui , Erkin Özgür Cem , Choi Jong-Sun , Chae Seoung Wan , Yang Ho Bin , Choi Yoon-La , Shin Young Kee 
Published: April 2023

<p>Supplementary Figure 1B . AGS, SW480, and HeLa cells were pretreated with control siRNA (lane 1 and 2) or AURKA siRNA (10 nM, lane 3 and 4) for 48 h, and transfected with the plasmid encoding 6Myc-SMAD4 or empty vector. Cells were collected 24 h after transfection and subjected to cell migration and invasion assay (n=3). Data were presented as means {plus minus}SD obtained from three independent experiments (*P<0.05, Ã¢?Â P<0.01, Ã¢?Â¡P<0.001, compared to the control group).</p>
Sources of Drag in Estuarine Meanders: Momentum Redistribution, Bottom Stress Enhancement, and Bend-Scale Form Drag
Authors: Bo Tong , Ralston David K. , Geyer W. Rockwell 
Published: April 2023

Abstract
Curvature can create secondary circulation and flow separation in tidal channels, and both have important consequences for the along-channel momentum budget. The North River is a sinuous estuary where drag is observed to be higher than expected, and a numerical model is used to investigate the influence of curvature-induced processes on the momentum distribution and drag. The hydrodynamic drag is greatly increased in channel bends compared to that for straight channel flows. Drag coefficients are calculated using several approaches to identify the different factors contributing to the drag increase. Flow separation creates low-pressure recirculation zones on the lee side of the bends and results in form drag. Form drag is the dominant source of the increase in total drag during flood tides and is less of a factor during ebb tides. During both floods and ebbs, curvature-induced secondary circulation transports higher-momentum fluid to the lower water column through vertical and lateral advection. Consequently, the streamwise velocity profile deviates from the classic log profile and vertical shear becomes more concentrated near the bed. This redistribution by the lateral circulation causes an overall increase in bottom friction and contributes to the increased drag. Additionally, spatial variations in the depth-averaged velocity field due to the curvature-induced flow are nonlinearly correlated with the bathymetric structure, leading to increased bottom friction. In addition to affecting the tidal flow, the redistributed momentum and altered bottom shear stress have clear implications for channel morphodynamics.
DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
Authors: Maansson Christoffer Trier , Andersen Emma Roger , Ulhoi Maiken Parm , Meldgaard Peter , Sorensen Boe Sandahl 
Published: April 2023

Abstract
Background
EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools.

Results
We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts.

Conclusion
Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics.
Survey on the management of childhood epilepsy among general practitioners in the area of Marrakech
Authors: Lahmini Widad , Gyamfi Samuel Opoku , Bourrous Mounir 
Published: April 2023

Abstract
Background
Epilepsy is a common chronic neurological disorder in the pediatric population and its evolution can be fatal. It represents a major public health problem as well as an economic burden for the families of affected children, health systems and the overall economies of countries. This further accentuates the role that general practitioners can play in the management of childhood epilepsy in the face of the persistent lack of neurologists and neuro-pediatricians in our country.

Methods
In order to assess the knowledge and therapeutic habits of general practitioners, we carried out a descriptive and cross-sectional study with general practitioners practicing in the two healthcare sectors: public and private, and in two settings: urban and rural, during the year 2018. The data was collected through a pre-established survey.

Results
In total, 155 general practitioners responded to the survey. For 85.2% of physicians, the diagnosis of childhood epilepsy was based on interrogation, physical examination, and EEG. While brain imaging would be systematic regardless of the type of epilepsy for 45.2% of doctors. Only 6 doctors (3.9%) had knowledge of the latest classifications of the “ILAE”. For treatment, the majority of physicians (65.5%) adopted first-line monotherapy with valproate in leading position. Almost half of the doctors (48.4%) found that education of parents and children was always necessary. None of the GPs interviewed in our series assessed the academic impact of epilepsy. Only 32% of doctors had received continuing education on epilepsy.

Conclusion
The data from our study demonstrates that continuing education on the management of childhood epilepsy and the greater involvement of general practitioners were essential elements in improving care.