bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6393: The Cancer Genomics Cloud enables bioinformatics training in a hybrid educational world
Authors: Ray Manisha , Subramanian Sai Lakshmi , Roberson David , Worman Zelia , Dean Dennis A. , Koc Soner , DiGiovanna Jack , Davis-Dusenbery Brandi 
Published: June 2022

Abstract
The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is an NCI-funded platform that streamlines access to large cancer datasets, bioinformatic tools, and cloud computation for cancer researchers. The attributes of the CGC designed to democratize data analysis also make it ideal for training the next generation of data scientists. During the Covid-19 pandemic, it has become clear that remote/virtual learning is of great importance for workforce development, and that reducing barriers to high quality educational resources is critical for many populations. Here we present our best practices for education of bioinformatics using the CGC, taking advantage of both distributed cloud networks and platform features to enhance learning.
Our best practices methods are focused on a systematic approach that takes the instructor and students through a typical bioinformatics workflow in their field of research. Briefly, the organizational structure of the CGC, known as “projects,'' contains all aspects of an analysis, including data files, tools, and tool settings. Projects have fine-grained permission settings, which allow the owner to securely share their project for viewing or editing. An instructor can generate an example analysis from start to finish then share an entire project with trainees. Both students and instructors have access to the same data on the cloud, so the teacher can pre-populate the projects with specific files, ensuring the same starting point. All members within the project can communicate, including adding notes directly on the results, allowing students to troubleshoot in real time with the teacher. Instructors can manage costs for the whole class through the CGC’s billing system. The CGC also provides Public Projects for self-guided training, where a researcher can learn by example using the data, tools, and completed tasks within the project, including detailed instructions embedded in markdown language.
We have successfully used these methods to train masters students in bioinformatics at Georgetown University for three years, as well as high school students, college students, and current cancer researchers.
This approach to virtual learning of bioinformatics can democratize training for the next generation of data scientists. The FAIR practices built into the CGC enables education across all levels of expertise, empowering users to drive cancer research from any stage of their career.
Citation Format: Manisha Ray, Sai Lakshmi Subramanian, David Roberson, Zelia Worman, Dennis A. Dean, Soner Koc, Jack DiGiovanna, Brandi Davis-Dusenbery. The Cancer Genomics Cloud enables bioinformatics training in a hybrid educational world [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6393.
Abstract 6396: Detection of stemness and EMT in response to radiation in glioblastoma and ovarian cancer cells
Authors: Keniston Aaron , Enciso Alondra , Jung Yeonkyu , Antonissen Ashley , Fuller Ryan , Morcos Ann , Bertucci Antonella , Vazquez Marcello , Unternaehrer Juli 
Published: June 2022

Abstract
Tumor recurrence and metastasis contribute to the poor prognosis of ovarian cancer (OC) and glioblastoma multiforme (GBM). The aggressiveness of GBM and OC during recurrence creates a need to identify potential therapeutic targets. The cancer stem cell (CSC)-like phenotype and epithelial mesenchymal transition (EMT) have been shown to contribute to cancer aggressiveness, which makes CSCs and EMT viable targets for therapeutic intervention. EMT is a normal process during development and wound healing, but its reactivation in cancer cells contributes to metastasis. To detect CSC phenotypes in live cells without the use of antibodies, we are analyzing core stem cell transcription factors in which a SOX2/OCT4 response element, designated as SORE6, regulates a GFP reporter system. Also, to detect EMT we are using a GFP based reporter regulated by Zeb1 3’ UTR, a common EMT marker. Our aim is to detect changes in stemness and EMT in response to proton and photon ionizing radiation (IR). We hypothesize that proton and photon IR have similar effects on aggressiveness in OC and GBM. To investigate this, 2 GBM cancer cell lines, 1 breast cancer cell line, 1 OC cell line, and two patient derived samples were exposed to 0, 1, 2, 4 and 8Gy of 250 MeV proton and 6 MeV photon beams. 72 hours post IR exposure, flow cytometry analysis quantified reporter activity. We found an increase in stemness as radiation dosage increased in most cell lines. Results suggest that proton radiation increases stemness more than photon exposure.
Citation Format: Aaron Keniston, Alondra Enciso, Yeonkyu Jung, Ashley Antonissen, Ryan Fuller, Ann Morcos, Antonella Bertucci, Marcello Vazquez, Juli Unternaehrer. Detection of stemness and EMT in response to radiation in glioblastoma and ovarian cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6396.
Abstract 662: Late CTLA-4 Ig treatment improves antitumor efficacy of immunotherapy
Authors: Mok Stephen , Allison James P. 
Published: June 2022

Abstract
The promising approach of combining immune checkpoint therapies such as anti-CTLA-4 and anti-PD-1 increases antitumor response and overall survival rate relative to single treatments. However, it also increases the frequency and severity of immune-related adverse events (irAEs), such as cardiotoxicity. Our previous results showed that CTLA-4 Ig (abatacept), an inhibitor of T cell costimulation through CD28, can reverse those irAEs in patients with cancer, however, its effect on the antitumor response remains unclear. In the B16F10 melanoma model, we injected mice with CTLA-4 Ig antibody when: 1) mice were first treated with anti-CTLA-4, anti-PD-1, or combination (early time point) and 2) the immunotherapy was finished (late time point). We demonstrated that CTLA-4 Ig at the early time point compromised the antitumor efficacy of the immunotherapy. In contrast, the antitumor efficacy of the immunotherapy was improved if mice were treated with CTLA-4 Ig at the late time point. We also found that the antitumor response induced by CTLA-4 Ig (late) was dependent on CD80/86. Interestingly, the frequency of ICOS+ Foxp3+ Tregs was significantly reduced by CTLA-4 Ig at the late time point. Thus, we treated B16F10 tumors in Foxp3DTR mice with anti-CTLA-4 and then with CTLA-4 Ig (late). The antitumor tumor efficacy was similar between mice treated with or without Diphtheria toxin (DT) at the late time point. This suggests that the improved antitumor efficacy of CTLA-4 Ig at the late time point was Treg dependent. Collectively, we show that CTLA-4 Ig treatment has a differential role throughout the time course of immunotherapy treatments, and this work suggests a potential combination treatment strategy with checkpoint blockade and late CTLA-4 Ig treatment.
Citation Format: Stephen Mok, James P. Allison. Late CTLA-4 Ig treatment improves antitumor efficacy of immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 662.
Abstract 670: Distinct biochemical properties of KRAS Q61H mutant render cancer cells resistant to SHP2 inhibitors
Authors: Gebregiworgis Teklab , Kano Yoshihito , Ohh Michael , Marshall Christopher B. , Ikura Mitsuhiko 
Published: June 2022

Abstract
Recent reports suggest that specific KRAS mutations are associated with either resistance or sensitivity of cancer cells to SHP2 inhibitors (SHP2i). However, a lack of understanding of the underlying mechanism(s) is hindering the clinical advancement of SHP2i therapy for cancer. Here we report that cancer cells that harbor KRAS Q61H mutation (found in about 5% of pancreatic ductal adenocarcinoma tumors) or HEK293 cells that over-express KRAS Q61H are resistant to SHP2i. Our biochemical studies supported by all atom molecular dynamic simulations show that the Q61H mutation impairs intrinsic GTP hydrolysis and impedes stimulation of the GTPase cycle by both SOS1 and RASA1, but has negligible impact on binding to BRAF-RBD. Similar to wild-type KRAS, the Q61H mutant can be phosphorylated by Src at Tyr-32 and Tyr-64, and both site scan be dephosphorylated by SHP2, although SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. In vitro, phosphorylation of KRAS Q61H increased intrinsic nucleotide exchange without affecting its insensitivity to SOS1 and RASA1. Phosphorylation of wild-type and SHP2i-sensitive mutants (e.g., G12V) confers resistance to SOS1/RASA1 activities and impairs binding to BRAF-RBD, thus the constitutive resistance to upstream regulation and uncompromised ability of phosphorylated KRAS Q61H to activate MAPK signaling are distinct properties of this mutant. Decoupling of KRAS Q61H from upstream signaling and impaired intrinsic nucleotide hydrolysis lead to a highly GTP-loaded pool that is insensitive to the suppressive effects of Src phosphorylation. While SHP2 plays multiple roles in stimulating RAS signaling, including promoting the GEF function of SOS1, reducing p120 GAP-mediated inactivation of KRAS, and reversing Src phosphorylation of KRAS, we revealed that none of these are required by KRAS Q61H. These insights provide a mechanistic understanding of oncogenic KRAS mutants that can guide clinical trials of SHP2 inhibitors for patients with pancreatic and other cancers bearing KRAS Q61H.
Citation Format: Teklab Gebregiworgis, Yoshihito Kano, Michael Ohh, Christopher B. Marshall, Mitsuhiko Ikura. Distinct biochemical properties of KRAS Q61H mutant render cancer cells resistant to SHP2 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 670.
Abstract 673: The EMT activator ZEB1 initiates polarized secretion of pro-tumorigenic effector proteins to drive lung adenocarcinoma progression
Authors: Xiao Guan-Yu , Tan Xiaochao , Rodriguez Leticia , Liu Xin , Yu Jiang , Vasquez Mayra , Tran Hai , Russell William , Gibbons Don , Kurie Jonathan 
Published: June 2022

Abstract
There are few effective therapeutic options for metastatic lung adenocarcinomas (LUADs) that lack actionable mutations in receptor tyrosine kinases, and there is an urgent need to develop a better understanding of the biological basis of LUAD growth and metastasis. Our group has developed mouse models of LUAD metastasis and found that LUAD metastasis is epithelial-to-mesenchymal transition (EMT)-dependent. EMT causes cancer cells to switch their axis of polarity from apical-basal to front-rear, which orients organelles and actinbased cytoskeletal structures in ways that facilitate purposeful cancer cell motility and metastasis. The EMT-activating transcription factor ZEB1 silences microRNAs that target key inhibitors of the polarity axis switch. These data support the general belief that EMT-dependent metastasis is a cell-autonomous process. However, our new findings here show that ZEB1 coordinates the components of secretory trafficking machinery, Rab6A and Rab8A, via silencing miR-148a that target these effectors, to drive polarized secretory trafficking toward the leading edge of LUAD cells, to enhance surface exposure of MMP14 so that triggers ECM degradation, accelerates focal adhesion turnover and promotes cancer cell migration. Moreover, the ZEB1-driven secretory trafficking increases the secretions of cytokines and immunomodulation factors, to generate an immunosuppressive tumor microenvironment, and to promote LUAD metastasis. These findings advance a paradigm in which EMT drives LUAD metastasis through a cell non-autonomous mechanism. The novelty rests in our results that demonstrate a transcriptional governance of polarized vesicular transport, providing the potential to target ZEB1-driven secretory pathways for the purpose of blocking metastasis in LUAD.
Citation Format: Guan-Yu Xiao, Xiaochao Tan, Leticia Rodriguez, Xin Liu, Jiang Yu, Mayra Vasquez, Hai Tran, William Russell, Don Gibbons, Jonathan Kurie. The EMT activator ZEB1 initiates polarized secretion of pro-tumorigenic effector proteins to drive lung adenocarcinoma progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 673.
Abstract 74: Single-cell 3D spatial omics for tumor hypoxia
Authors: Wu Yi-Chien , Lee Steve Seung-Young 
Published: June 2022

Abstract
Tumor hypoxia arises from the abnormal vasculature in tumors which limit the oxygen supply to the rapidly growing cancer cells. To acclimate to this deprived microenvironment, cancer cells upregulate hypoxia-inducible factor 1-alpha (HIF-1) signaling pathway priming themselves towards more aggressive and heterogeneous phenotypes. Hence, tumor hypoxia becomes a major obstacle for effective cancer treatment. Deciphering hypoxia-driven tumor heterogeneity within the tumors is essential to understanding cancer biology and developing novel therapeutic strategies. A stronger focus should be directed towards the effect of hypoxia types and levels rather than just the absence or presence of hypoxia since hypoxia is heterogeneous in the three-dimensional (3D) tumor microenvironment (TME). There are acute and chronic types of tumor hypoxia, and the hypoxia levels are also variable, forming unpredictable and irregular 3D hypoxic areas. Although traditional techniques (i.e., single-cell RNA sequencing (scRNA-seq), immunohistochemistry (IHC), and immunofluorescence (IF)) and innovative spatial transcriptomics have been developed and applied for investigating tumor cell heterogeneity. Underlying issue of missing spatial information, limited numbers of the biomarker detection, underrepresentation of 3D tumor structure, or limited analyzed area onto the array chip size exist respectively in these methods.
The objective of this project is to develop a 3D spatial genomics approach with single-cell resolution, named sc3DSG, as an advanced spatial transcriptomic method to study hypoxia-driven cancer cell heterogeneity in 3D. Given that, I developed a 3D cellular fluorescence barcoding method by microscopic photobleaching in tumor macro-sections. The barcodes would maintain a fluorescent footprint of cells in different hypoxic areas upon tissue dissociation. Cells encoded with varied barcodes could be differentiated on flow cytometry and further sorted into separate groups for scRNA-seq. With the optimization with RNA preservation reagent in the workflow, sc3DSG achieves high-quality and high-yield RNA transcript for unbiased transcriptomic analysis. In summary, sc3DSG is an advanced spatial transcriptomic method including a sequential workflow of photobleaching barcoding, tissue dissociation, fluorescence-activated cell sorting (FACS), and scRNA-seq. Sc3DSG enables the study of tissue molecular features without losing spatial information and is a better fit for the study of complex 3D structure like vessels or tumor hypoxia. This approach will unravel hypoxia-driven bimolecular and cellular features by considering the degrees and types of tumor hypoxia.
Citation Format: Yi-Chien Wu, Steve Seung-Young Lee. Single-cell 3D spatial omics for tumor hypoxia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 74.
Abstract 748: Role of LINC01614 in papillary thyroid cancer
Authors: Quaranto Danielle , Carnazza Michelle , DeSouza Nicole , Dadafarin Sina , Moscatello Augustine , Tiwari Raj K. , Geliebter Jan 
Published: June 2022

Abstract
Papillary thyroid cancer (PTC) accounts for the vast majority of thyroid cancer cases (~80%), with a significantly higher prevalence in females, but much more aggressive and with poorer outcomes in males. Despite a high survival rate, disease recurrence and metastasis remain significant issues. Therefore, there is an unmet need for the elucidation and identification of molecular markers associated with PTC, to aid in identifying early-stage disease, as well as patient prognosis and therapeutic approaches. Long intergenic non-coding RNA (lincRNA) molecules comprise the largest subclass of RNA molecules within the human genome, yet the majority of their functions are yet to be identified. Evidence supports that these non-coding RNA molecules play a role in protein and RNA localization and scaffolding - implying a critical role in the fine tuning of gene expression. Recently, lincRNAs have been identified as major players in cancer development and progression. This deems lincRNAs as attractive, specific biomarkers and/or therapeutic targets, making them important aspects for further study. Data from our lab identified LINC01614 as being significantly upregulated (~10-fold increase) in PTC, when compared to normal thyroid tissue. There was also ~30-fold increase in LINC01614 in male PTC when compared to females, highlighting potential sex-related correlation for study. Thus, we are studying LINC01614 as a potential biomarker for diagnosis and prognosis, as well as a target for therapeutic intervention. LINC01614 was found to be upregulated in various thyroid cancer cell lines, with significant upregulation in the TPC1 (~5-fold; RET/PTC rearrangement) and K1 (~2-fold; BRAFV600E) cell lines when compared to the “normal”, immortalized thyroid cancer cell line (Nthy-ori-3-1). To decipher a phenotype for LINC01614 upregulation in PTC, we utilized the CRISPRi technique to decrease its expression in TPC1. The knockdown of LINC01614 resulted in a ~75% reduction in proliferation in TPC1 cells. Studies are underway to investigate the role of LINC01614 in migration, invasion, morphology, and tumorigenicity in TPC1 cells, as well as in the BRAFV600E cells, K1. Exploring the role that lincRNAs have in cancer phenotypes can lead to a plethora of different molecular markers for therapeutic intervention. The mechanisms by which these non-coding molecules regulate the expression of genes and other elements of the cellular milieu can serve as an open revenue for understanding how they impact PTC development and progression.
Citation Format: Danielle Quaranto, Michelle Carnazza, Nicole DeSouza, Sina Dadafarin, Augustine Moscatello, Raj K. Tiwari, Jan Geliebter. Role of LINC01614 in papillary thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 748.
Abstract 75: Highly multiplexed EGFR mutation detection from liquid biopsy samples using the 6-color Crystal Digital PCR™
Authors: Jovelet Cécile , Remy Myrtille , Pata-Merci Noémie , Vasseur Damien , Lacroix Ludovic , Labrador-Rached Claudia , Mallory Allison C. 
Published: June 2022

Abstract
Liquid biopsies are a minimally invasive sampling approach to overcome the heterogeneity of tumors and represent a valuable source of circulating tumor DNA (ctDNA) for oncological biomarker analysis. ctDNA measurements require a highly sensitive and reliable detection technology to quantify often low-level genetic aberrations within a high background of wild-type sequences. Digital PCR emerged as a powerful technology for the next-generation analysis of liquid biopsies. Stilla Technologies' 6-color naica® system is an ultrasensitive, easy-to-use digital PCR platform capable of simultaneously and precisely quantifying high numbers of biomarkers in a single reaction.
Non-small cell lung cancer (NSCLC) is a leading cause of cancer mortality worldwide. Epidermal growth factor receptor (EGFR) is frequently mutated in NSCLC. A handful of anti-EGFR Tyrosine Kinase Inhibitor therapies are approved by the FDA; however, most patients develop resistance over time to these treatments. Both monitoring primary EGFR mutations to predict treatment response and precociously detecting resistance mutations to adapt treatments promptly through ctDNA analysis stand to improve the effectiveness of NSCLC patient management.
Stilla has developed a highly multiplexed 6-color Crystal Digital PCR EGFR kit detecting more than 90% of EGFR mutations described in NSCLC from ctDNA. The assay detects 32 common and rare somatic EGFR mutations in exons 18, 19, 20, and 21, including both activating and resistant mutations.
In this work, we evaluated the sensitivity, precision and specificity of the EGFR 6-color Crystal Digital PCR assay highly specific and sensitive for the detection of EGFR mutations, with a Limit of Detection in a high background of wild-type DNA ranging from 0.30 to 0.46 cp/μL (with observed MAFs ranging from 0.06 to 0.09%). Moreover, a high concordance was observed between those EGFR results obtained for NSCLC ctDNA samples using 6-color Crystal Digital PCR and other technologies. With a rapid time to results and straightforward ctDNA analysis workflow, Crystal Digital PCR on the naica system promises ultrasensitive, highly multiplexed 6-color mutation detection, maximizing the information obtained from precious samples.
Citation Format: Cécile Jovelet, Myrtille Remy, Noémie Pata-Merci, Damien Vasseur, Ludovic Lacroix, Claudia Labrador-Rached, Allison C. Mallory. Highly multiplexed EGFR mutation detection from liquid biopsy samples using the 6-color Crystal Digital PCR™ [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 75.
Abstract 768: Consensus subtypes of hepatocellular carcinoma associated with clinical outcomes
Authors: Lee Ju-Seog , Yim Sun Young , Lee Sung Hwan , Jeong Yun Seong 
Published: June 2022

Abstract
Background & Aims: While many studies revealed transcriptomic subtypes of hepatocellular carcinoma (HCC), they are not translated to the clinic yet due to lack of consensus. We aim to examine consensus of transcriptomic subtypes and uncover their clinical significance.
Methods: We integrated 15 previously established transcriptomic signatures for HCC to uncover consensus subtypes. We also developed and validated a robust predictor of consensus subtype with 100 genes (PICS100). Informatics and statistics approaches were applied to find clinical relevant association of genomic features. Patient derived xenograft (PDX) models were used for testing hypothesis from analysis of transcriptomic data.
Results: We identified 5 clinically and molecularly distinct consensus subtypes. STM (STeM) is characterized by high stem cell features, vascular invasion, and poor prognosis. CIN (Chromosomal INstability) has moderate stem cell features but high genomic instability and low immune activity. IMH (IMmune High) is characterized by high immune activity. BCM (Beta-Catenin with high Male predominance) is characterized by prominent β-catenin activation, low miRNA expression, hypomethylation, and high sensitivity to sorafenib. DLP (Differentiated and Low Proliferation) is differentiated with high HNF4A activity. We also identified potential serum biomarkers that can stratify patients into 5 subtypes.
Conclusions: Five HCC subtypes are associated with potential response to treatments and highly conserved in pre-clinical models, providing a framework for selecting the most appropriate models for preclinical studies of new drugs and potentially for future clinical trials.
Citation Format: Ju-Seog Lee, Sun Young Yim, Sung Hwan Lee, Yun Seong Jeong. Consensus subtypes of hepatocellular carcinoma associated with clinical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 768.