bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 7420: Optimizing proteomic data access and analysis in the cloud: Leveraging Terra's integration with the Proteomic Data Commons
Authors: LaPlante Emily , Huo Bingxing , Mani DR , Thangudu Ratna R. 
Published: March 2024

Abstract
The Proteomic Data Commons (PDC) hosts cancer proteomics data with the goal of making this data available to the public to support development of cancer diagnostics, treatment, and progression tracking. As a part of the Cancer Research Data Commons (CRDC), the Terra platform provides a cloud workbench for the PDC data. FireCloud is a Broad Institute project funded by NCI to empower cancer researchers to access data, run analysis tools and collaborate securely in the cloud. It is powered by Terra, a secure, scalable cloud-native platform developed by the Broad Institute, Microsoft, and Verily, an Alphabet company. It provides batch workflow execution, interactive analysis including data visualization, and ~2,900 publicly available tools with the ability to import more tools from Dockstore.
The integration of PDC and Terra enables researchers to leverage the data navigation and file-level search capabilities on the PDC web browser (pdc.cancer.gov) and export selected data manifests to a Terra workspace. This integrated hand-off specifically allows metadata and cloud links to PDC data in Portable Format for Bioinformatics (PFB) to be transferred to Terra and used in analysis with cloud resources. A featured workspace for Terra-PDC integration includes tools for (i) downloading data files and relevant additional metadata; (ii) organizing the data and metadata for running the FragPipe workflow, a comprehensive collection of tools for reading and processing raw Mass Spec (MS) data; and (iii) implementing a pre-configured FragPipe workflow to process isobarically labeled MS data from Tandem Mass Tag (TMT) or Isobaric tags for relative and absolute quantitation (iTRAQ) experiments using information automatically imported from PDC via the PFB import. The pipelines can also be customized as needed to process any type of raw MS data the PDC supports.
In addition, Terra connects to the NCI Genomic Data Commons (GDC) and hosts The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) datasets allowing users to pull in other data types for co-analysis. As a whole, using the CRDC cloud resources, in conjunction with Terra, allows analysis of data on a massive scale, enabling multi-omic integration spanning the genomic and proteomic commons data, with easy sharing of data and tools.
Citation Format: Emily LaPlante, Bingxing Huo, DR Mani, Ratna R. Thangudu. Optimizing proteomic data access and analysis in the cloud: Leveraging Terra's integration with the Proteomic Data Commons [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 7420.
Abstract 7447: Understanding survivorship: A national survey of post-treatment experiences in Black prostate cancer survivors
Authors: Fullwood Dottington , Lee Daniel , Panagiotou Veronika , Siegel Samantha B. , Molina Mariel , Odedina Folakemi T. 
Published: March 2024

Abstract
Prostate cancer, impacts over 3.1 million survivors, poses persistent challenges in post-treatment care, creating uncertainties regarding the best course of follow-up actions for leading productive lives. Unfortunately, these concerns, especially among ethnically diverse Black men, are frequently overlooked. The post-treatment journey for Black prostate cancer survivors is dependent on how they navigate survivorship to determine how it impacts their quality of life and emotional wellbeing. This study evaluated the post-treatment cancer experience and gauge satisfaction with care among a cohort of Black survivors (n = 45). Utilizing data from the 2023 National Coalition for Cancer Survivorship State of Survivorship Study (n = 1303), conducted between May 9th to June 6th, 2023, the research specifically targets self-identified Black males, constituting 10% of the study population and spanning an age range from 18 to 80 years. Results revealed that oncologists (44%) managed post-treatment care more than primary care physicians (30%). While conversation about follow-up care monitoring cancer tests regularly occurred (68%), while topics such as quality of life (27%), mental and emotional health (21%), and post-treatment survivorship care plans (9%) received minimal attention. Although most survivors felt generally informed about side effects (62% very informed), less than half felt their health care team was very helpful in dealing with them. Symptoms reported by survivors included feeling overly tired (47%), depression, anxiety, and mental health impacts (40%), and uncertainty about the cancer status (34%). Survivors engaging in diverse integrative treatments, including such practices as prayer and exercise, represented 29% and 28%, respectfully. Notably, 80% and 60% of individuals utilizing these modalities reported finding them effective during the post-treatment care phase. The journey from the point of prostate cancer diagnosis to post-treatment can impose a significant mental and physical toll on survivors. To address the emotional and psychological challenges associated with a diagnosis and post-treatment, survivors adopting integrative oncology modalities and exercise prescriptions to cope are crucial. These strategies may help survivors maintain a positive outlook and achieve optimal post-treatment health, with a focus on providing tailored resources that cater to the unique needs of Black survivors.
Citation Format: Dottington Fullwood, Daniel Lee, Veronika Panagiotou, Samantha B. Siegel, Mariel Molina, Folakemi T. Odedina. Understanding survivorship: A national survey of post-treatment experiences in Black prostate cancer survivors [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 7447.
Abstract 7479: Targeting the lipid kinase PIKfyve upregulates surface expression of MHC class I to augment cancer immunotherapy
Authors: Borker Parth , Bao Yi , Qiao Yuanyuan , Chinnaiyan Arul , Choi Jae Eun , Zhang Yuping , Mannan Rahul , Cheng Caleb , He Tongchen , Zheng Yang , Yu Jiali , Gondal Mahnoor , Cruz Gabriel , Grove Sara Sara , Cao Xuhong , Su Fengyun , Wang Rui , Chang Yu , Kryczek Ilona , Cieslik Marcin , Green Michael D. , Zou Weiping 
Published: March 2024

Abstract
The widespread success of cancer immunotherapies suggests a promising future - but has been subverted by unresponsiveness and resistance. Current research has furthered the understanding of immunotherapy resistance through the findings of “hot” (responsive) and “cold” (unresponsive) tumors. Here, we focus on the genetic and pharmacological inhibition of PIKfyve, a lipid kinase regulator of autophagic flux and lysosomal biogenesis. We find that inhibition of PIKfyve results in the upregulation of major histocompatibility complex class I (MHC-I) surface expression in cancer cells (through inhibition of autophagic flux), resulting in increased CD8+ T cell-mediated cancer cell death. These findings were corroborated in multiple syngeneic mouse models, which also displayed increased intratumoral functional CD8+ T cells. In addition, the Pikfyve-depletion antitumor responses are CD8+ T cell and MHC-I dependent - as CD8+ T cell and B2m knockout rescued tumor growth - resulting in improved response to immune checkpoint blockable (ICB), adoptive cell therapy, and a therapeutic vaccine. Further, high PIKfyve expression predicts poor ICB response and is prognostic of poor survival in ICB-treated cohorts. Ultimately, these findings collectively suggest PIKfyve as an effective target to enhance immunotherapies through elevation of MHC-I surface expression in cancer cells, and accordingly, PIKfyve inhibitors have novel potential to increase immunotherapy response in cancer patients.
Citation Format: Parth Borker, Yi Bao, Yuanyuan Qiao, Arul Chinnaiyan, Jae Eun Choi, Yuping Zhang, Rahul Mannan, Caleb Cheng, Tongchen He, Yang Zheng, Jiali Yu, Mahnoor Gondal, Gabriel Cruz, Sara Sara Grove, Xuhong Cao, Fengyun Su, Rui Wang, Yu Chang, Ilona Kryczek, Marcin Cieslik, Michael D. Green, Weiping Zou. Targeting the lipid kinase PIKfyve upregulates surface expression of MHC class I to augment cancer immunotherapy [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 7479.
Abstract 7513: Tumor treating fields (TTFields) can induce immunogenic cell death in GBM resulting in enhanced immune modulation
Authors: Nitta Ryan T. , Lee Si Yeon , Lim Michael , Li Gordon 
Published: March 2024

Abstract
Glioblastoma (GBM) is the most common and aggressive form of malignant primary brain tumors. Despite current standard of care, the overall survival for GBM is ~15 months. While immunotherapy using immune checkpoint inhibitors such as anti-PD-1/PD-L1 have been efficacious for solid malignancies, very little progress has been made in a clinical setting for GBM. This is mainly due to GBM being known as a “cold” and non-immunogenic tumor. It has been previously established that a tumor may become “hot” if the T cell responses can be enhanced by increasing the presentation of tumor-specific antigens to the immune system. Tumor Treating Fields (TTFields) are alternating electric fields in a specific frequency range (100-500 kHz) delivered to the human body through transducer arrays. Treatment with TTFields have been approved and have shown efficacy in GBM. TTFields have induced immunogenic cell death in GBM, which in turn can elicit anti-tumoral immunity by inducing damage-associated molecular patterns (DAMP). These patterns are important for promoting engulfment of lung cancer cells by dendritic cells and recruitment of immune cells. These findings suggest that TTFields may enhance the immune response in GBM by increasing tumor specific antigens. In this study we show in vitro that TTFields enhanced the immune response to GBM. We initially demonstrated that GBM cells (GL261 or CT2A) treated with TTFields (200 kHz) can elicit DAMP emissions as evident by the increase in secretion of ATP and HMGB1 and the enhanced translocation of calreticulin to the cell surface. Additionally, TTFields stimulated the phagocytotic activity of antigen presenting cells (Raw264.7) and increased T-cell early activation (CD69/CD4+, CD69/CD8+) and activity (IFNγ and perforin). Since our findings in vitro indicate TTFields enhanced the immune response to GBM, we studied the therapeutic potential of using TTFields together with anti- PD1 in a syngeneic mouse model. We applied TTFields to GBM cells prior to intracranial injections. While our survival studies are preliminary, our findings suggest that systemic anti-PD1 and TTFields may result in a myeloid and T-cell mediated anti-tumor response and enhanced survival. Our findings indicate that TTFields treatment may help transform GBM into a “hot” tumor thereby making it an attractive target for immunotherapy.
Citation Format: Ryan T. Nitta, Si Yeon Lee, Michael Lim, Gordon Li. Tumor treating fields (TTFields) can induce immunogenic cell death in GBM resulting in enhanced immune modulation [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 7513.
Abstract 7584: The solute transported xCT (SLC7A11) modulates lysosome biogenesis and microRNA trafficking in drug resistant renal cell carcinoma
Authors: Jawadwala Abbas , Rupert Christopher , Adelaiye-Ogala Remi , Pili Roberto , Chintala Sreenivasulu , Orillion Ashley , Elbanna May , Damayanti Nur , Fontane Ilaria Delle 
Published: March 2024

Abstract
Multi-tyrosine kinase inhibitors (TKIs) like sunitinib bind to over 50 kinases and inhibit several receptors such as VEGFR-1, VEGFR-2, and VEGFR-3 receptors, PDGFRa and PDGFRb, RET, cKIT, and FLT3. TKIs are effective drugs for the treatment of renal cell carcinoma (RCC) but intrinsic/acquired resistance remains a major hurdle. One of the proposed models for TKI resistance is drug sequestration by lysosomes. The solute transporter xCT is a cystine/glutamate antiporter that plays a role in the production of antioxidants in cancer cells. Our lab has found that SLC7A11, the gene that encodes xCT, is overexpressed in sunitinib resistant RCC cells. LAMP1 expression was also increased in sunitinib resistant RCC cells, suggesting an upregulation of lysosome biogenesis. The biochemical knock down of SLC7A11 by shRNA showed a decrease in LAMP1 expression, suggesting a decrease in lysosome biogenesis. SEC24D is a key catalytic component of COPII complex involved in formation of exosomes and secretory pathways. Our preliminary data showed that reduction in xCT expression was associated with a decrease in SEC24D protein levels which was associated with a reduction in the extracellular export and, consequently, an increase in intracytoplasmic levels of miRNA 605, a known tumor suppressor. We are currently testing the hypothesis that xCT may modulate lysosomes biogenesis and micro-RNA trafficking in several clear cell and translation renal cell carcinoma models. In summary, a better understanding of the role of xCT in the regulation of intracytoplasmic organelles may lead to the identification of a novel therapeutic strategy to overcome TKI resistance in RCC.
Citation Format: Abbas Jawadwala, Christopher Rupert, Remi Adelaiye-Ogala, Roberto Pili, Sreenivasulu Chintala, Ashley Orillion, May Elbanna, Nur Damayanti, Ilaria Delle Fontane. The solute transported xCT (SLC7A11) modulates lysosome biogenesis and microRNA trafficking in drug resistant renal cell carcinoma [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 7584.
Abstract 7633: CXCR6 positive circulating mucosal-associated invariant T cells play the anti-tumor effect in non-small cell lung caner immunotherapy
Authors: Qu Jingjing , Wu Binggen , Li Yuekang , Shen Qian , Sun Wenjia , Chen Lijun , Zhou Jianya , Zhou Jianying 
Published: March 2024

Abstract
Background: Mucosal-associated invariant T (MAIT) cells is are unconventional innate-like T lymphocytes abundant in human tissues. Recent studies have shown that MAIT cells play important roles in regulating tumor immunity. However, the immune characteristics of MAIT cells in non-small cell lung cancer (NSCLC) and its correlation with ICIs treatment efficacy remain unclear.
Method: In this study, we used single-cell RNA-sequencing (scRNA-seq), flow cytometry and multiplex immunofluorescence to assess the proportion and characteristics of CD8+MAIT cells in metastatic NSCLC patients who respond or not respond to anti-PD-1 therapy.
Results: The proportions of activated and proliferating CD8+ T cells and MAIT cells were significantly higher in responders-derived PBMC or lung tissues prior to anti-PD-1 therapy. Both peripheral and tumor-infiltrating CD8MAIT cells displayed upregulated CXCR6(P&lt;0.05). Besides, CXCR6+CD8MAIT cells from responders had higher expression of cytotoxicity-related genes, like CST7, GNLY, KLRG1, NKG7 and PRF1. Moreover, we found that patients with &gt;1.7% of MAIT among peripheral CD8+ population showed a better response to immunotherapy.
Conclusion: CD8MAIT cells may be considered a predictive biomarker for patients responding to anti-PD-1 therapy in NSCLC. The correlation between CD8MAIT and immunotherapy sensitivity may ascribe to high expression of CXCR6.
Citation Format: Jingjing Qu, Binggen Wu, Yuekang Li, Qian Shen, Wenjia Sun, Lijun Chen, Jianya Zhou, Jianying Zhou. CXCR6 positive circulating mucosal-associated invariant T cells play the anti-tumor effect in non-small cell lung caner immunotherapy [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 7633.
Abstract 7641: Prognostic impact of functional germline mutations in muscle-invasive bladder cancer identified by neural network analysis
Authors: Sonpavde Guru P. , Nassar Amin H. , Ravi Arvind , Sadler Layne 
Published: March 2024

Abstract
Background: An accurate prognostic algorithm based on germline whole exome sequencing (WES) would complement tumor omics as a non-invasive source of biomarkers for guiding cancer patient therapy. In a previous study, we used WES and RNA-seq data from muscle-invasive bladder cancer (MIBC) and normal host cells to train a survival model, wherein we discovered that mutated germline genes accounted for 90% of feature importance. We have since defined a larger cohort to identify key germline biomarkers of overall survival (OS) that may be scalable for application in the clinic.
Methods: 169 patients from The Cancer Genome Atlas (TCGA) with MIBC stages T2-T4 that underwent radical cystectomy (RC) w/o neoadjuvant treatment were eligible. OS at 4 years was the primary clinical endpoint as it is associated with death due to metastatic tumor recurrence. Patients were dichotomized to control survivors who were alive at 4+ years, and cases who died within 4 years but no less than 4 months after RC. 49 qualifying survivors were propensity matched against 49 dead patients by stage, adjuvant treatment, gender, race, and age. The remaining 71 dead patients served as a holdout. Only high (e.g. frameshift) and moderate (e.g. indel) impact germline variants were included. Mutations were weighted for allele frequency (penalize common) and genotype (reward homozygous) before grouping at the gene level. A panel of the 21 most differential genes in stratified patients were selected for neural network training using AIQC. The model forced protective/pathogenic genes to interact and produced individual survival probabilities. Gene importance was determined via permutation.
Results: OS was accurately predicted for 98.2% of patients: 1 FN, 2 FP, 37 TN, 119 TP. The top 3 permuted genes (and related pathways) were: SORL1 (Aβ), KIF27 (hedgehog), CUL7 (p53). The most differential gene was CUL7: 31% of survivors mutated vs 2% of dead.
Conclusion: Neural network analysis identified the promise of germline genetics as an accurate predictor of survival and tumor recurrence in MIBC patients. Upon validation in an external cohort, these biomarkers could be used to inform adjuvant therapy and complement molecular residual disease alongside circulating tumor (ct)-DNA.
Citation Format: Guru P. Sonpavde, Amin H. Nassar, Arvind Ravi, Layne Sadler. Prognostic impact of functional germline mutations in muscle-invasive bladder cancer identified by neural network analysis [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 7641.
Abstract 7653: Role of ITGB2 in patients with luminal B1 breast cancer
Authors: Liu Chun-Yu , Chen Ji-Lin , Tsai Yi-Fang , Chao Ta-Chung , Wang Wan-Lun , Lien Pei-Ju , Hsu Chih-Yi , Lai Jiun-I , Huang Chi-Cheng , Chiu Jen-Hwey , Tseng Ling-Ming 
Published: March 2024

Abstract
Purpose: Luminal-type breast cancers are the most commonly diagnosed in women. Among them, the luminal B1 subtype exhibits higher proliferation rates and a worse prognosis compared to the luminal A subtype. Despite significant advancements in detection and therapies, recurrence still occurs after primary treatment. In this study, our aim is to identify genomic alterations in early recurrent luminal B1 breast cancer.
Experimental Design: In this VGHTPE cohort, we recruited a total of 42 patients diagnosed with stage I-III luminal B1 breast cancer, comprising 15 subjects who experienced recurrence within five years and 27 subjects who did not. Genomic DNA was extracted from formalin-fixed paraffin-embedded samples and subjected to targeted next-generation sequencing. We assessed cell aggressiveness through in vitro transwell migration, invasion, and sphere assays.
Results: Luminal B1 breast cancer patients with advanced stage and poorly differentiated tumors were associated with recurrence within five years. Driver gene mutation analysis revealed that TP53 mutations were present in 46.7% of patients who experienced recurrence within five years, compared to 29.6% in the non-recurrence group. In the analysis of copy number variations, the most common amplifications/gains observed in luminal B1 breast cancer patients were in MCL1, MYC, and KLF6. Remarkably, patients who experienced recurrence within five years showed a higher occurrence of gain in ITGB2, the gene encoding the integrin β chain, compared to those who remained recurrence-free. Patients with ITGB2 amplifications/gains had a shorter 5-year recurrence-free survival compared to those with a neutral status. In vitro studies revealed that the knockdown of ITGB2 suppressed cell migration, invasion, and sphere formation in estrogen receptor-positive HER2-negative breast cancer cells.
Conclusion: Our study has identified ITGB2 amplifications/gains as a potential biomarker for early recurrence in luminal B1 breast cancer.
Citation Format: Chun-Yu Liu, Ji-Lin Chen, Yi-Fang Tsai, Ta-Chung Chao, Wan-Lun Wang, Pei-Ju Lien, Chih-Yi Hsu, Jiun-I Lai, Chi-Cheng Huang, Jen-Hwey Chiu, Ling-Ming Tseng. Role of ITGB2 in patients with luminal B1 breast 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 7653.