bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3299: Harnessing PIKfyve as a therapeutic vulnerability in neuroendocrine prostate cancer
Authors: Zheng Yang , Rogers Kyle Garcia , Kamat Arya Gopal , Yee Sarah Nicole , Mannan Rahul , Jiang Xia , Kannaiyan Rowena , Cao Xuhong , Wang Yuzhuo , Qiao Yuanyuan , Chinnaiyan Arul M. 
Published: March 2024

Abstract
Neuroendocrine prostate cancer (NEPC) represents an aggressive subtype characterized by the independence on androgen receptor (AR) signaling and the acquisition of neuroendocrine features. Despite its rarity among prostate cancer cases, NEPC carries a particularly poor prognosis with limited treatment options. Our prior investigation demonstrated the heightened efficacy of targeting PIKfyve with ESK981 in AR- prostate cancer models, prompting further exploration. In this study, we expanded our investigation to assess the efficacy of ESK981 monotherapy across five NEPC models, encompassing one cell line xenograft and four patient-derived xenografts (PDXs). Our findings revealed consistent tumor inhibition and notable regression in select models. Comparative analysis highlighted the superior effectiveness of ESK981 in NEPC compared to AR+ prostate cancer, as evident through percent tumor growth inhibition (%TGI) assessments. Early evaluations post five days of treatment (PD5) unveiled that PIKfyve inhibition induced apoptotic cell death specifically in NEPC models, confirmed through immunoblotting and TUNEL staining in a time-dependent manner. Intriguingly, PD5 TUNEL positivity correlated with endpoint %TGI, suggesting its potential as a predictor for long-term efficacy. To further delineate the role of PIKfyve in NEPC, we successfully established two novel ex vivo NEPC cell lines from these PDXs, overcoming the constraint of limited publicly accessible NEPC cell lines, and confirmed their NEPC characteristics. Employing a doxycycline-inducible PIKfyve knockdown system in these cells demonstrated significant tumor inhibition in xenograft models, albeit with a lower %TGI compared to ESK981 monotherapy. In conclusion, our results illuminate the preferential cytotoxicity of PIKfyve inhibition in NEPC tumors compared to AR+ prostate cancer, advocating PIKfyve as a compelling therapeutic target. This study provides a strong rationale for advancing ESK981 into clinical trials for NEPC patients, underscoring its potential in addressing this challenging malignancy.
Citation Format: Yang Zheng, Kyle Garcia Rogers, Arya Gopal Kamat, Sarah Nicole Yee, Rahul Mannan, Xia Jiang, Rowena Kannaiyan, Xuhong Cao, Yuzhuo Wang, Yuanyuan Qiao, Arul M. Chinnaiyan. Harnessing PIKfyve as a therapeutic vulnerability in neuroendocrine prostate 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 3299.
Abstract 3331: Preclinical combination of ONC206 with radiotherapy and temozolomide in a GBM mouse orthotopic model
Authors: Zhou Lanlan , Zhang Leiqing , Zhang Jun , Zhang Shengliang , El-Deiry Wafik S. 
Published: March 2024

Abstract
Glioblastoma multiforme (GBM) is the most common form of primary malignant brain tumor in adults. It is also the most aggressive and lethal. Standard of care therapy comprises maximal safe surgical resection followed by adjuvant alkylating agent temozolomide (TMZ) and radiotherapy (RT). There have only been five drugs and one device ever approved by the FDA for the treatment of GBM. The five-year survival rate for GBM patients has shown no notable improvement in the last three decades. We previously reported that the first-in-class imipridone small-molecule Dordaviprone (ONC201) decreases protein chaperone ClpX to unleash mitochondrial protease ClpP activity, integrated stress response and cell death. Preclinical combination of ONC201 (100 mg/kg weekly) with radiotherapy and Temozolomide in a GBM mouse orthotopic model results in reduced tumor burden and prolonged survival. The second generation imipridone ONC206 also activates integrated stress response and decreases ClpX in GBM cells but ONC206 is approximately 20 times more potent than its parent imipridone ONC201. ONC206 0.08 uM in combination with 12.5 uM TMZ and 2 Gy RT reduced the cell viability of GBM cells significantly compared to all single treatments and double treatments. During a short-term treatment of a GBM mouse orthotopic model, ONC206 (50 mg/kg weekly, half of ONC201 doses) synergizes with TMZ and RT to induce more tumor cell apoptosis and inhibits more tumor cell proliferation compared to other groups with single or double treatments. There are two ongoing clinical trials with ONC206: single weekly or multiple-day weekly dose regimens of single-agent, oral ONC206 in patients with recurrent, primary central nervous system (CNS) neoplasms (NCT04541082) and ONC206 alone or in combination with radiation therapy in treating patients with diffuse midline gliomas that is newly diagnosed or has come back (recurrent) or other recurrent primary malignant CNS tumors (NCT04732065). Future studies evaluating the role of immune function, mitochondrial metabolism, dopamine receptors, the ISR and TRAIL pathway in the synergistic effect would support further development of the triple combination regimen of ONC206, TMZ and radiation therapy for GBM clinical trial.
Citation Format: Lanlan Zhou, Leiqing Zhang, Jun Zhang, Shengliang Zhang, Wafik S. El-Deiry. Preclinical combination of ONC206 with radiotherapy and temozolomide in a GBM mouse orthotopic model [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 3331.
Abstract 3344: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA binding proteins
Authors: Kaundal Babita , McGrail Daniel J. , Li Yang , Smith Roger S. , Feng Bin , Dai Hui , Hu Limei , Dennehey Briana , Awasthi Sharad , Mendillo Marc L. , Sood Anil K. , Mills Gordon B. , Lin Shiaw-Yih , Yi S. Stephen , Sahni Nidhi 
Published: March 2024

Abstract
Summary: Defects in homologous recombination DNA repair (HRD) both predispose to cancer development and produce therapeutic vulnerabilities, making it critical to define the spectrum of genetic events that cause HRD. However, we found that mutations in BRCA1/2 and other canonical HR genes only identified 10-20% of tumors that display genomic evidence of HRD. Using a networks-based approach, we discovered that over half of putative genes causing HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA binding protein (RBP)-encoding genes. These putative drivers of HRD were experimentally validated, cross-validated in an independent cohort, and enriched in cancer-associated GWAS loci. Mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD, with implications for basic biology, genetic screening, and therapy stratification.
Citation Format: Babita Kaundal, Daniel J. McGrail, Yang Li, Roger S. Smith, Bin Feng, Hui Dai, Limei Hu, Briana Dennehey, Sharad Awasthi, Marc L. Mendillo, Anil K. Sood, Gordon B. Mills, Shiaw-Yih Lin, S. Stephen Yi, Nidhi Sahni. Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA binding proteins [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 3344.
Abstract 3380: HER2 overexpression induces breast tumorigenesis in a non cell autonomous manner by inducing oxidative stress in the tissue microenvironment
Authors: Gurler Sevim Beyza , Wagstaff Oliver , Dimitrova Lili , Chen Fuhui , Pedley Robert , Weston William , Donaldson Ian , Telfer Brian A. , Novo David , Pavlou Kyriaki , Taylor George , Ou Yaqing , Williams Kaye , Gilmore Andrew , Brennan Keith , Ucar Ahmet 
Published: March 2024

Abstract
Breast cancer is the most common cancer type in the world. Approximately 70% of pre-malignant breast tumours, known as ductal carcinoma in situ (DCIS), and 20% of invasive breast tumours overexpress HER2. Although molecular mechanisms of HER2 function in breast tumour cells have been extensively studied, our knowledge on how HER2 drives breast tumourigenesis at its pre-malignant stage is quite limited. Here, we investigate the HER2-overexpression driven cellular events at the earliest stages of breast tumourigenesis using in vitro, in vivo and ex vivo models. Using mouse models of HER2+ breast cancer and clinical samples of patients with DCIS, we showed that breast cancer stem cells (BCSCs) reside in HER2-negative population of tumour cells and arise from a HER2-negative cell-of-origin. Proteomics and metabolomics analyses of mammary ducts isolated from the MMTV-Neu mice at the pre-cancerous stage showed that HER2/Neu overexpression alters the energy metabolism in mammary epithelial cells in vivo. Furthermore, we have observed an accumulation of reactive oxygen species levels in pre-cancerous mammary ducts, which consequently causes oxidative stress induction and DNA damage in both HER2-positive and HER2-negative epithelial cells. Collectively, our findings indicate that HER2 overexpression in normal mammary epithelia may lead to a genotoxic tissue microenvironment that may consequently result in the accumulation of further somatic mutations in HER2-negative cell populations, which contain BCSCs and their cell-of-origin. Our findings therefore illustrate a novel mechanism explaining the HER2-driven breast tumour initiation and thus provide new avenues of research for developing novel preventive approaches against breast cancer.
Citation Format: Sevim Beyza Gurler, Oliver Wagstaff, Lili Dimitrova, Fuhui Chen, Robert Pedley, William Weston, Ian Donaldson, Brian A. Telfer, David Novo, Kyriaki Pavlou, George Taylor, Yaqing Ou, Kaye Williams, Andrew Gilmore, Keith Brennan, Ahmet Ucar. HER2 overexpression induces breast tumorigenesis in a non cell autonomous manner by inducing oxidative stress in the tissue microenvironment [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 3380.
Abstract 3417: Dissecting tumor microenvironment to predict clinical outcome in prostate cancer
Authors: Bhattacharjee Aritri , Biswas Manjusha , Husain Amjad , Das Asim Kr , Karmakar Sourav Karmakar , Mondal Tapan , Roy Pinaki , Mondal Manas Kr , Sahu Badal Kumar , Murmu Nabendu , Nath Partho , Ghosh Chandra C. , Majumder Pradip Kumar 
Published: March 2024

Abstract
Prostate cancer is one of the major causes of cancer death in males, and its prevalence is particularly high in developed countries such as the United States and Western Europe. However, death rates in developing and underdeveloped countries are greater, presumably, due to a lack of routine clinical check-ups, poor health awareness, inadequate screening resources, and clinical intervention. Much progress has already been made using cutting-edge technologies like whole genome sequencing, RNAseq, phosphoproteomics, and targeted transcriptomic Nanostring profiling, etc. However, understanding of the prostate tumor microenvironment as a whole in clinical samples remains very limited. Here we use the latest genomic, proteomics, and metabolomic tools not only to understand the biology of prostate cancers but also their correlation with patient demography and clinical outcome. We recruited 80 patients from both tertiary research hospitals and clinical centers in the eastern region of India. All of their demographic information is collected along with their clinical outcome. Pathological evaluation revealed only 50 patients with positive Prostate Carcinoma. We performed a detailed analysis using experimental data (from genomic, and proteomic) in a cohort of patients' routine biomarkers (PSA and PSMA), histopathology, and clinical outcome. Our data demonstrate no linear correlation of any of the individual markers or parameters like AR status, PSA, Prostate Specific Acid Phosphatase, Prostate-Specific Membrane Antigen (PSMA), Alpha-methylacyl-CoA racemase (AMACR), Mesothelin, PD-L1, and other potential genomic and proteomic alterations or any histopathological readouts. However, a clear understanding of the relationship between these multiparameter data, disease pathology, and clinical outcomes in a group of patients has been established. The heterogeneity of these individual data for tumor microenvironments will lead us to identify novel biomarkers for the clinical response of targeted drugs, accelerating personalized treatment strategies.
Citation Format: Aritri Bhattacharjee, Manjusha Biswas, Amjad Husain, Asim Kr Das, Sourav Karmakar Karmakar, Tapan Mondal, Pinaki Roy, Manas Kr Mondal, Badal Kumar Sahu, Nabendu Murmu, Partho Nath, Chandra C. Ghosh, Pradip Kumar Majumder. Dissecting tumor microenvironment to predict clinical outcome in prostate 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 3417.
Abstract 3493: Read-level methylation pattern extraction for high-multiplex large-scale targeted NGS assay
Authors: Jin Mingda , Kaneko Masatomo , Cen Steven , Li Hongtao , Guo Wei , Zhou Xinyi , Fujihara Atsuko , Iwata Tsuyoshi , Ramacciotti Lorenzo Storino , Paralkar Divyangi , Cacciamani Giovanni E , Aron Manju , Ukimura Osamu , Gill Inderbir S. , Liang Gangning , Abreu Andre L. , Bhasin Jeffrey , Yang Xiaojing , Jia Xi-Yu 
Published: March 2024

Abstract
The abnormal changes in DNA methylation are linked to the early stages of carcinogenesis. Identifying these epigenetic changes in circulating tumor DNA (ctDNA) can reveal potential biomarkers for the early diagnosis of various cancers. However, analyzing such data poses bioinformatics challenges due to the lack of sensitivity in detecting the low abundance ctDNA signals in biopsy samples, which are often overwhelmed by the complexity of libraries containing hundreds of targeted regions. Read-level methylation analysis holds the promise of more in-depth DNA methylation detection due to the wide coverage and high sensitivity of rare signals. However, this approach is hindered by the absence of a standardized workflow capable of generating interpretable reports suitable for both bench scientists and professional bioinformaticians. Here, we present a bioinformatics workflow that examines next-generation sequencing (NGS) data and characterizes the read-level methylation patterns of amplicons. Compared to other currently available tools, our method is designed to work with high-multiplex, large-scale targeted assays. It effectively eliminates the undesired noise derived from sequencing byproducts such as false CpG calls, dimers, and off-target alignments. Additionally, to accommodate the substantial volume of data generated by state-of-the-art NGS platforms, the workflow enables parallel processing of samples compatible with both cloud-based and on-premises computing resources. This workflow provides a comprehensive per-sample visualization of DNA methylation patterns and reports read-level methylation results in a “pattern-as-a-feature” table. In this table, the occurrence of an amplicon epiallelic haplotype (pattern) for every sample is represented as a “feature column” and is aggregated with all patterns discovered in the experiment. These read-level patterns, along with other information, can be used to develop machine learning algorithms to reiteratively harvest true predictive features and penalize confounding signals in predicting cancer diagnosis.
Citation Format: Mingda Jin, Masatomo Kaneko, Steven Cen, Hongtao Li, Wei Guo, Xinyi Zhou, Atsuko Fujihara, Tsuyoshi Iwata, Lorenzo Storino Ramacciotti, Divyangi Paralkar, Giovanni E Cacciamani, Manju Aron, Osamu Ukimura, Inderbir S. Gill, Gangning Liang, Andre L. Abreu, Jeffrey Bhasin, Xiaojing Yang, Xi-Yu Jia. Read-level methylation pattern extraction for high-multiplex large-scale targeted NGS assay [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 3493.
Abstract 351: Quaratusugene ozeplasmid mediated TUSC2 upregulation in EML4-ALK bearing non-small cell lung carcinoma can induce cellular apoptosis
Authors: Banerjee Ananya , Busette Neeke , Berger Mark S. , Soellner Matthew B. , Qin Angel , Merajver Sofia D. , Merrill Nathan M. 
Published: March 2024

Abstract
Anaplastic Lymphoma Kinase (ALK), a potent oncogenic driver in Non-Small Cell Lung Carcinoma (NSCLC), is found to be rearranged and fused to Echinoderm microtubule-associated protein-like 4 (EML4), contributing to approximately 5% of NSCLC as a distinct clinicopathological subset. Tumors bearing the EML4-ALK fusion are sensitive to ALK Tyrosine Kinase Inhibitors (TKIs), that form the first and second line of treatment for these patients. However, ALK+ lung cancers develop resistance to ALK inhibitors, creating the need for newer treatment strategies in ALK+ NSCLC. Tumor Suppressor Candidate 2 (TUSC2) is a tumor suppressor gene that is known to have low endogenous expression in NSCLC in general but data on TUSC2 in ALK+ lung cancers are not available. Quaratusugene ozeplasmid, developed by Genprex, is an immunogene therapy that upregulates TUSC2 expression in cancer cells by delivering the functional TUSC2 gene. It consists of the TUSC2 gene expressing plasmid encapsulated in non viral lipid nanoparticles. We evaluated TUSC2 expression in 3 ALK+ cell lines, both before and after exposure to quaratusugene ozeplasmid and to a TUSC2-containing plasmid. Controls were non-ALK+ cell lines and transfection with a plasmid containing no insert. Our studies in ALK+ lung cancer reveal that overexpressing TUSC2 using quaratusugene ozeplasmid treatment of ALK+ lung cancer cell lines is able to suppress colony formation by 50%, the effect being more significant than using a TUSC2-containing plasmid. Furthermore, we have observed a robust pro-apoptotic response to TUSC2 expression in ALK+ NSCLC, as both quaratusugene ozeplasmid and TUSC2-containing plasmid induced an increase in caspase 3/7 activity in the cancer cells, accompanied by an increase in cleaved PARP expression. Taken together, our data indicate that overexpression of TUSC2 in ALK+ NSCLC cell lines with quaratusugene ozeplasmid or with TUSC2-containing plasmid is effective in decreasing growth and proliferation through the activation of apoptotic pathways and warrants further investigation as an anti-ALK NSCLC strategy.
Citation Format: Ananya Banerjee, Neeke Busette, Mark S. Berger, Matthew B. Soellner, Angel Qin, Sofia D. Merajver, Nathan M. Merrill. Quaratusugene ozeplasmid mediated TUSC2 upregulation in EML4-ALK bearing non-small cell lung carcinoma can induce cellular apoptosis [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 351.
Abstract 359: The Hippo pathway on breast tumor recurrence &lt;and&gt; collateral vulnerability to ferroptosis
Authors: Lin Chao-Chieh , Chi Jen-Tsan 
Published: March 2024

Abstract
Comparing with primary breast tumors, recurrent breast cancers are generally considered more aggressive and incurable. Therefore, novel molecular strategies are urgently needed to target these type of cancers. Here, we report that murine recurrent breast tumor cells are highly susceptible to ferroptosis, a novel form of cell death. Discoidin Domain Receptor Tyrosine Kinase 2 (DDR2), the receptor for collagen I, is upregulated in ferroptosis-sensitive recurrent tumor cells. Ferroptosis inducer, erastin treatment leads to DDR2 upregulation and phosphorylation, independent of collagen I. Furthermore, DDR2 silencing not only prevent ferroptosis but also abolished the robust cell proliferation of murine recurrent tumor cells. Both the ferroptosis protection and reduction of active cell growth may be compatible with the compromised YAP/TAZ upon DDR2 inhibition. Collectively, these findings suggest the role of DDR2 in recurrent breast tumors to drive aggressive cell growth but at the same time reveals its weakness to YAP/TAZ-mediated ferroptosis, providing potential molecular mechanism to target recurrent breast cancers.
Citation Format: Chao-Chieh Lin, Jen-Tsan Chi. The Hippo pathway on breast tumor recurrence &lt;and&gt; collateral vulnerability to ferroptosis [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 359.
Abstract 3591: Upregulation of CXCL8 is an early step in the oncogenic transition of human thyroid cells by BRAFV600E
Authors: Sarkar Rhitajit , Bolel Priyanka , Klubo-Gwiezdzinska Joanna , Gershengorn Marvin C. 
Published: March 2024

Abstract
Introduction: BRAFV600E is one of the most common oncogenic mutations in human thyroid cancers, especially in papillary thyroid carcinoma (PTC). However, the early molecular changes caused by this mutation have not been studied previously in human thyrocytes in vitro.
Methods: Primary cultures of cells derived from noncancerous thyroid tissue of patients (at least n=3) were infected with BRAFV600E adenovirus to mimic the mutated condition. Changes induced by the infection were measured at early times (&lt;24h). Transcriptome analysis was performed on infected thyrocytes (n=6) to determine the highest differentially expressed genes between the control and infected groups, which were then verified at the gene and protein levels. RNAi downregulation experiments were performed to determine the cross-regulatory function of the genes.
Results: The induction of BRAFV600E mutation, confirmed at the protein level, increased proliferation of the cells, and morphological changes were observed at approximately 24h post-infection. The decreased expression of thyroid-specific genes, viz. TSHR, TG, and TPO were observed after &gt;72h post-introduction of BRAFV600E mutation. Transcriptome and protein expression analysis of BRAFV600E-positive thyrocytes showed the overexpression of chemokines CXCL8 and CXCL12, and upregulation of endothelial cell-specific molecule 1 (ESM1). These molecules are known to be associated with increased neoangiogenesis and proliferation. Functional studies showed that siRNA knockdown of CXCL8 decreased the expressions of CXCL12 and ESM1, whereas knockdown of either CXCL12 or ESM1 did not decrease the expression of CXCL8.
Conclusion: Increased proliferation, de-differentiation, upregulation of chemokines, and endothelial-specific factor are effects associated with BRAFV600E-driven thyroid carcinogenesis. CXCL8 appears to play an important early regulatory role in this process.
Citation Format: Rhitajit Sarkar, Priyanka Bolel, Joanna Klubo-Gwiezdzinska, Marvin C. Gershengorn. Upregulation of CXCL8 is an early step in the oncogenic transition of human thyroid cells by BRAFV600E [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 3591.