bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1413: Chromosome arm aneuploidies as genetic vulnerabilities of triple-negative breast cancer
Authors: Dandage Rohan , Schwartz Michael , Karam Lynn , Pacis Alain , Hart Traver , Bourque Guillaume , Park Morag , Kuzmin Elena 
Published: June 2023

Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer. It has no approved targeted therapies due to the lack of the expression of key biomarkers, namely Estrogen and Progesterone receptors, and HER2 amplification. As a result, TNBC has the worst prognosis compared to other breast cancer subtypes. We previously showed that chromosome 4p (chr4p) loss is recurrent, correlates with poor prognosis, is an early event in tumor evolution, and confers a proliferative advantage. Here, we propose to leverage chr4p loss as a genetic vulnerability of TNBC by identifying its genetic interactions (GIs) with genes whose inactivation leads to synthetic lethality i.e. loss of viability of chr4p copy loss cells, but not of the chr4p copy neutral cells, or suppression i.e., positive GIs. We first classified breast cancer cell lines with TNBC enriched molecular subtype called basal-like, as chr4p copy loss (9) and chr4p copy neutral (7), using copy number data from CCLE. Associated with chr4p copy loss, the differential expression analysis carried out using CCLE data revealed transcriptomic changes that distinctly cluster the chr4p copy loss and chr4p copy neutral cell lines. We then used the publicly available CRISPR-based genome-wide gene inactivation data from the DepMap project and quantified chr4p loss-associated GIs using multiple scoring methods such as drugZ and MAGeCK. In total, we identified ~200 negative and ~70 positive statistically significant GIs involving genes annotated to biological processes such as translation, metabolism, and others. We have prioritized a subset of them for subsequent experimental validation using CRISPR-Cas9-based gene editing in TNBC cancer cell line models. Alongside, using the publicly available drug sensitivity data obtained from the PRISM project, we identified compounds that impair cell growth in a chr4p loss-specific manner, the strongest of which targeted redox balance. Collectively, the set of GIs, the compound sensitivities, and the computational methods we have generated are unique resources for developing precision oncology therapeutic strategies for TNBC, as well as for other cancers harboring chr4p loss.
Citation Format: Rohan Dandage, Michael Schwartz, Lynn Karam, Alain Pacis, Traver Hart, Guillaume Bourque, Morag Park, Elena Kuzmin. Chromosome arm aneuploidies as genetic vulnerabilities of triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1413.
Abstract 1475: FOXO transcription factors regulate WNT pathway gene expression in GBM
Authors: Keniry Megan , Pintor Shania , Lopez Alma , Flores David 
Published: June 2023

Abstract
Basal-like breast cancer (BBC) and Glioblastoma Multiforme (GBM) are aggressive cancers associated with poor prognosis. BBC and GBM express stem gene expression signatures which are in part driven by FOXO transcription factors. To gain further insight into the impact of FOXO1 in BBC, we treated BT549 cells with the FOXO1 inhibitor AS1842856 and performed RNA Seq. Gene Set Enrichment Analysis (GSEA) with RNA Seq. data indicated that a set of WNT target genes including LEF1 and AXIN2 were robustly induced after 48-hours of AS1842856 treatment. These same genes were also induced in GBM cell lines U87MG, LN18, LN229, A172, and DBTRG upon AS1842856 treatment. RNAi targeting of FOXO1 led to reduced LEF1 gene expression in BT549 and U87MG cells at 18-hour and 24-hour timepoints respectively. CRISPR Cas9-mediated FOXO1 disruption led to reduced expression of canonical WNT target gene LEF1 in U87MG cells.
Citation Format: Megan Keniry, Shania Pintor, Alma Lopez, David Flores. FOXO transcription factors regulate WNT pathway gene expression in GBM [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 1475.
Abstract 1479: FOXA2 induces invasive mucinous adenocarcinoma of the lung in the presence of mutant KRAS
Authors: Maeda Yutaka , Tomoshige Koichi , Stuart William D. , Fink-Baldauf Iris M. , Ito Masaoki , Tsuchiya Tomoshi , Nagayasu Takeshi , Yamatsuji Tomoki , Okada Morihito , Fukazawa Takuya , Guo Minzhe 
Published: June 2023

Abstract
Introduction: The role of the endoderm lineage transcription factor FOXA2 in autochthonous lung tumors has been elusive though the expression of FOXA2 has been reported in human lung cancers. Here, using GEMM (Genetically Engineered Mouse Models) and human lung cancer cell lines, we delineate the role of FOXA2 in lung cancers.
Experimental Procedures: GEMM that carry mutant KRAS or mutant EGFR along with FOXA2 (CCSP-rtTA; tetO-Foxa2; tetO-Kras.G12D or tetO-EGFR.L858R) were developed allowing for lung tumor induction by doxycycline administration. The growth of lung tumors affected by FOXA2 was assessed by microCT and pathologically. FOXA2 downstream genes were also evaluated in vivo by immunohistochemistry of mouse lung sections and in vitro by gain (ectopic lentivirus transduction) and loss (siRNA) of function approaches with human lung cancer cell lines using TaqMan gene expression, RNA-seq, ChIP-seq and CRISPRi analyses. FOXA2 protein expression in human lung cancer specimens was also assessed.
Data: FOXA2 suppressed the growth of EGFR-mutant lung tumors while promoting that of KRAS-mutant lung tumors in GEMM. Notably, half of the KRAS-mutant lung tumors presented invasive mucinous adenocarcinoma of the lung (IMA) with the expression of a master mucous transcription factor SPDEF and the two major IMA mucin genes MUC5AC and MUC5B. In vitro, FOXA2 induced the expression of SPDEF, MUC5AC and MUC5B by directly binding to their loci. H3K27ac was introduced at the enhancer region of MUC5AC (most highly expressed IMA gene) by FOXA2 and the expression of MUC5AC initiated by FOXA2 was enhanced by mutant KRAS. FOXA2 was highly expressed in human IMA compared to normal lung.
Conclusions: FOXA2 induces IMA in the presence of mutant KRAS by directly regulating the expression of mucous genes.
Citation Format: Yutaka Maeda, Koichi Tomoshige, William D. Stuart, Iris M. Fink-Baldauf, Masaoki Ito, Tomoshi Tsuchiya, Takeshi Nagayasu, Tomoki Yamatsuji, Morihito Okada, Takuya Fukazawa, Minzhe Guo. FOXA2 induces invasive mucinous adenocarcinoma of the lung in the presence of mutant KRAS [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 1479.
Abstract 1482: Critical role of OGT-mediated novel NF-κB o-glcNAcylation in pancreatic cancer
Authors: Motolani Aishat , Martin Matthew , Wang Benlian , Jiang Guanglong , Liu Yunlong , Lu Tao 
Published: June 2023

Abstract
Pancreatic ductal adenocarcinoma (PDAC) has one of the highest mortalities of all malignancies, with a mere 5-year survival of ~10%. However, the current first-line treatments have poor patient outcomes, highlighting the urgent need for innovative therapeutics. The nuclear factor κB (NF-κB) is a crucial transcription factor frequently activated constitutively in PDAC. It mediates the transcription of oncogenic and inflammatory genes that facilitate multiple PDAC phenotypes. Thus, a better understanding of the mechanistic underpinnings of NF-κB activation holds substantial promise in PDAC diagnosis and new therapeutics. The purpose of this study is to identify novel regulation of NF-κB, with the aim of providing new diagnostic and therapeutic strategies for PDAC. Here, we report protein O-GlcNAc transferase (OGT) - mediated NF-κB activation through novel serine O-GlcNAcylation of its p65 subunit. We show that overexpression of serine-to-alanine (S-A) mutant at the O-GlcNAcylation site impaired NF-κB nuclear translocation and transcriptional activity in PDAC cells. Moreover, these S-A p65 mutants downregulate NF-κB-target genes important to major cancer hallmarks and inhibit cellular proliferation, migration, and anchorage-independent growth of PDAC cells compared to WT-p65. Interestingly, this modification happens downstream of the inhibitor of NF-κB (IκBα) degradation. Collectively, we have identified OGT-mediated serine O-GlcNAcylation of NF-κB and determined its mechanistic and cellular function in driving PDAC phenotypes. Thus, our study holds great significance as it uncovers a brand-new strategy for PDAC diagnosis and effective therapeutics development.
Citation Format: Aishat Motolani, Matthew Martin, Benlian Wang, Guanglong Jiang, Yunlong Liu, Tao Lu. Critical role of OGT-mediated novel NF-κB o-glcNAcylation in pancreatic 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 1482.
Abstract 1544: MBK-103, a potent novel conjugation platform-based antibody-drug conjugate, changing therapeutic options in folate receptor alpha positive cancer patients
Authors: Viricel Warren , Conilh Louise , Leroy Edouard , Lafay Jean-Guillaume , Brune Frederique , Sadilkova Lenka Kyrych , Dumontet Charles 
Published: June 2023

Abstract
Folate receptor alpha (FOLR1) is a clinically validated target, that is overexpressed extracellularly in numerous solid malignancies with a high unmet medical need. Ovarian, non-small cell lung and breast adenocarcinomas are among indications with the highest frequency of FOLR1-positive patients with one out of two patients showing upregulated topoisomerase I expression. MBK-103, an antibody-drug conjugate targeting FOLR1, is based on Mablink’s novel proprietary hydrophilic drug-linker platform. It is comprised of: (i) an Fc-attenuated humanized IgG1 monoclonal antibody, that selectively binds to FOLR1; (ii) a polysarcosine hydrophobicity masking entity allowing for a high drug-to-antibody ratio (DAR) of 8, while improving the pharmacokinetics and tolerability of the drug; (iii) a proprietary dipeptide cleavable unit and iv) exatecan, a potent topoisomerase I inhibitor. MBK-103 showed excellent ex vivo stability in human plasma enabling a prolonged half-life, similar to that of the unconjugated monoclonal antibody. This led to an increased drug exposure, resulting in a potent antitumor efficacy observed in a collection of more than ten in vivo mouse tumor models with a diverse FOLR1 expression, already at doses as low as 1-3 mg/kg. In addition, the distinct mode of action of exatecan along with the unique characteristics of the proprietary drug-linker platform resulted in the in vivo antitumor potency obtained also in colorectal cancer models, in which tubulin-inhibiting agents exhibit only limited therapeutic effects. The compound was also very well tolerated in cynomolgus monkeys with HNSTD at 50 mg/kg and even when administered repeatedly. High conjugation yields along with 100% homogeneity are major drivers of the successful ongoing manufacturing process with planned IND submission in Q4/2023.
Citation Format: Warren Viricel, Louise Conilh, Edouard Leroy, Jean-Guillaume Lafay, Frederique Brune, Lenka Kyrych Sadilkova, Charles Dumontet. MBK-103, a potent novel conjugation platform-based antibody-drug conjugate, changing therapeutic options in folate receptor alpha positive cancer patients [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 1544.
Abstract 1664: Discovery of a novel and potent TACC3 protein-protein interaction inhibitor targeting highly aggressive cancers
Authors: Sahin Ozgur , Banoglu Erden , Lim Chaemin , Caliskan Burcu , Cruz Emmanuel , Stergiopoulos Sotirios , Vempati Sridhar 
Published: June 2023

Abstract
TACC3 is one of the most oncogenic members of the Transforming Acidic Coiled-Coil Containing (TACC) protein family highly overexpressed in multiple different cancers leading to worse prognosis. TACC3 is a key player in microtubule and centrosomal processes and is considered to have an important role in causing chromosomal instability leading to aggressive cancers. TACC3 also plays important role in DNA damage response mechanisms, hematopoiesis, epigenetics and immune functions by interacting with different protein partners. Inhibition of TACC3 by genomic approaches has shown significant reduction in growth of cancer cells in vitro and in vivo. Given its multiple roles in cancer, TACC3 is an ideal therapeutic target for highly aggressive cancers. Here, using phenotypic screening and rational drug design, we developed AO-252, a novel small molecule TACC3 protein-protein interaction (PPI) inhibitor. Binding assays and kinome screening suggested the specificity of AO-252 to TACC3. AO-252 targets the interactions of TACC3 with its known protein partners e.g., Clathrin/KIFC1, BARD1 and MBD2/HAT complexes regulating mitosis, DNA damage response and epigenetic functions. Gene expression profiling in multiple cell lines further confirmed the various TACC3 pathways affected by AO-252. AO-252 showed low nanomolar potency in &gt;200 cell line panel covering various cancer indications and spared the normal cells. AO-252 showed excellent oral pharmacokinetics and demonstrated strong tumor growth inhibition or regression in multiple xenograft models without any safety concerns. Currently, AO-252 is prepared for IND submission for Q1 2023 and will enter clinic in the first half of 2023 for the treatment of advanced solid tumors including triple-negative breast cancer (TNBC), high-grade serous ovarian carcinoma (HGSOC), and endometrial cancer.
Citation Format: Ozgur Sahin, Erden Banoglu, Chaemin Lim, Burcu Caliskan, Emmanuel Cruz, Sotirios Stergiopoulos, Sridhar Vempati. Discovery of a novel and potent TACC3 protein-protein interaction inhibitor targeting highly aggressive cancers [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 1664.
Abstract 1665: Imipramine enhances the efficacy of lomustine by regulating WNT-β-catenin signaling in glioblastoma
Authors: Venkata Prabhakar Pitta , Rao Arhan , Timilsina Santosh , Subbarayalu Panneerdoss , Brenner Andrew , Sareddy Gangadhara Reddy , Rao Manjeet , Kelly William , Vadlamudi Ratna 
Published: June 2023

Abstract
Background: Glioblastoma (GBM) is one of the most aggressive and difficult-to-treat brain cancers. Surgical excision followed by concurrent temozolomide (TMZ), and radiation therapy are the current standard of care for GBM. Lomustine, another alkylating regimen, has also been approved for the treatment of patients with recurrent GBM in addition to TMZ. However, the primary GBM frequently recur as therapy-resistant relapses resulting in shorter survival of patients. To date, no systemic therapies have shown proven survival benefit in recurrent GBM. In this study, we examined whether FDA approved anti-depressant drug Imipramine serve as the potent option for treating patients with recurrent GBM and to improve efficacy of approved chemotherapy.
Methods: We investigated the anticancer effects of Imipramine using both established and patient-derived GBM cell lines. We tested the effect of Imipramine and Lomustine combination therapy using cell viability, colony formation, migration and apoptosis assays. Mechanistic studies were conducted using RNA-seq, western blotting, RT-PCR and reporter assays. In vivo efficacy of combination therapy was evaluated using orthotopic mouse models.
Results: Our results showed that antidepressant Imipramine blocked the growth of recurrent GBM. Furthermore, Imipramine enhanced the response of Lomustine in therapy resistant GBM cells as a combination therapy and significantly reduced the cell survival and migration, and increased the apoptosis in both established and patient derived GBM cells. Further, our results demonstrated that Imipramine inhibits growth of self-renewing cancer stem cells, which contribute to drug resistance and relapse of GBM. Mechanistic studies revealed that the Imipramine treatment abrogated the WNT-β-catenin signaling, which was confirmed by TOPFLASH reporter assay.
Conclusion: Collectively, the results from our study suggest that Imipramine alone and in combination with Lomustine can be used for treating recurrent GBM. Based on these results, a clinical trial is currently ongoing, where we are testing the efficacy of Imipramine for treating patients with recurrent GBM.
Citation Format: Prabhakar Pitta Venkata, Arhan Rao, Santosh Timilsina, Panneerdoss Subbarayalu, Andrew Brenner, Gangadhara Reddy Sareddy, Manjeet Rao, William Kelly, Ratna Vadlamudi. Imipramine enhances the efficacy of lomustine by regulating WNT-β-catenin signaling in 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 1665.
Abstract 1699: Targeting mercapturic acid pathway transporter in chemoradiotherapy resistant ovarian cancer
Authors: Singhal Sharad S. , Yue Er , Kulkarni Prakash , Horne David , Awasthi Sanjay , Wang Edward , Salgia Ravi 
Published: June 2023

Abstract
Ovarian cancer is the most common and the most lethal malignancies arising in the female reproductive system. Morbidity and mortality associated with ovarian cancer will continue to impact the female population. Although cisplatin centered chemotherapy is the first line anticancer agent for human ovarian cancer, chemoresistance and adverse side effects remain major hurdles to successful treatment. The effective targets for cancer therapy must be desirably expressed differentially in particular cancers as compared with normal cells. Also, there should be an essential dependence of cancer cells on the target compared to non malignant cells. Ideally, the target should be understood in the context of existing biochemical and signaling frameworks known to play a direct role in a particular carcinogenesis or in regulating the response to therapy. In the context of striking chemo radiotherapy resistance of ovarian cancer and the fundamental role of RLIP as an important mercapturic acid pathway transporter that is essential for survival and therapy resistance in cancers, we investigated the role of RLIP in regulating the critical signaling proteins involved in relaying the inputs from multiple upstream survival pathways and mechanisms contributing to chemo radiotherapy resistance in ovarian cancer. Compounds that inhibit, deplete, or downregulate RLIP will function as wide spectrum agents to treat ovarian cancer, independent of common signaling pathway mutations. Here, we demonstrate that RLIP expression is significantly greater in ovarian cancer cells than in non malignant cells, and RLIP is an essential requirement for cancer formation, and its depletion or inhibition will prevent ovarian carcinogenesis as well as metastases. Taken together, the results of our studies provided insights into a novel anticancer effect of RLIP depletion/inhibition on ovarian cancer and might open new therapeutic avenues for the treatment of ovarian cancer. Supported in part by the Department of Defense grant W81XWH 22 1 0331. Funding from the Beckman Research Institute of City of Hope is also acknowledged.
Citation Format: Sharad S. Singhal, Er Yue, Prakash Kulkarni, David Horne, Sanjay Awasthi, Edward Wang, Ravi Salgia. Targeting mercapturic acid pathway transporter in chemoradiotherapy resistant ovarian 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 1699.
Abstract 2028: Using bioinformatic analysis of proteomic data to probe novel drug mechanism of action
Authors: Chen Weining , Woods Nicholas , Qiao Fangfang , Law Henry Chun Hin , Jagadesan Sankarasubramanian , Guda Chittibabu , Bergan Raymond C. 
Published: June 2023

Abstract
Introduction: Metastasis is a major cause of death for patients with solid tumors. Our group has discovered a selective inhibitor of cell motility, KBU2046, that blocks the activation of Raf1 by inhibiting the phosphorylation of ser338 on its activation motif (Nature Communications 2018). To better understand the effect of KBU2046 on human prostate cancer (PCa) cells, we undertook a proteomic analysis. Experimental Procedures: After treatment of PC3 cells with KBU2046 or vehicle (N=3/group), protein expression of whole cell lysate was quantified by Liquid Chromatography/Tandem Mass Spectrometry analysis (LC-MS/MS). In separate experiments (N=4), membrane fractions were isolated, and LC-MS/MS was performed after Tandem Mass Tag (TMT) labeling. Resultant data were analyzed by several complementary bioinformatics tools, including: Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO) term analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Ingenuity Pathway Analysis (IPA), and protein-protein interaction (PPI) network analysis to characterize the proteins that were significantly differentially expressed upon KBU2046 treatment.
Results: Independent bioinformatic analyses of differentially expressed proteins affected by KBU2046 treatment identify significantly enriched processes related to cell motility, inclusive of effects on structural machinery. This constitutes orthogonal confirmation of KBU2046’s known effects on cell motility. Of importance, major effects on cellular energy-generating processes were also identified. This is consistent with prior studies that found changes in motility induce obligatorye changes in cellular energy requirements. Our focused analysis of membrane fractions identified changes in membranous compartments, providing a relevant positive control for bioinformatic analysis, which we confirmed by Western blot. Analytics also pointed to a major role for adhesion proteins in response to KBU2046, consistent with our prior identification of primary effects on cell migration.
Conclusions: These findings provide orthogonal mechanistically relevant support for a novel acting agent. They highlight the ability of proteomics and bioinformatic tools to efficiently probe the mechanism of action and global impact on PCa in response to treatment.
Citation Format: Weining Chen, Nicholas Woods, Fangfang Qiao, Henry Chun Hin Law, Sankarasubramanian Jagadesan, Chittibabu Guda, Raymond C. Bergan. Using bioinformatic analysis of proteomic data to probe novel drug mechanism of action [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 2028.