bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB186: Rapid photoinhibition of the autophagy pathway
Authors: Mondal Payel , Cyril Amanda , Towers Christina 
Published: April 2024

Abstract
Autophagy is a highly regulated and conserved cellular recycling process that is activated under stress conditions. Although cancer cells are known to rely on autophagy for survival, recent studies indicate that when the nutrient recycling process is blocked, a few rare cancer cells still can circumvent autophagy inhibition and maintain their aggressive growth rate. To understand the autophagy inhibition adaptation mechanism, we have developed a novel optogenetic autophagy inhibition tool (ASAP) that can rapidly and reversibly block the autophagy pathway in response to blue light. Our preliminary data shows ASAP releases a mutant autophagy inhibitory protein from the plasma membrane within 5 minutes of blue light exposure, blocks autophagosome-lysosome fusion, and induces LC3-II protein accumulation. In comparison, bafilomycin, a known autophagosome-lysosome fusion inhibitor, takes 4-hours to reproduce similar inhibitory effects as ASAP. Additionally, unlike bafilomycin, ASAP-induced autophagy inhibition is reversible within 2-6 hours. As light-induced autophagy inhibition has not been previously tested, our system brings a novelty to the conventional genetic and pharmacological approaches of autophagy inhibition. We will utilize the novel ASAP tool to understand the rapid changes in cellular proteomics and signaling events that dictate autophagy inhibition adaptation in cancer cells. We will perform tandem mass tag (TMT) based total proteomics and phospho-proteomics screen to visualize the temporal kinetics of protein turnover rates and changes in cell-signaling pathways following rapid autophagy inhibition. Additionally, our optogenetic tool will be applied in vivo in C. elegans to rapidly block autophagy and answer key questions of the spatial and temporal roles of autophagy in aging.
Citation Format: Payel Mondal, Amanda Cyril, Christina Towers. Rapid photoinhibition of the autophagy pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB186.
Abstract LB204: EHMT1 mediates cellular motility in embryonal rhabdomyosarcoma by activating SOX8 expression
Authors: Das Dipanwita , Bajaj Upasana , Yu Leung Jia , Rashi Nurul Fateha Binti Abdul , Tergaonkar Vinay , Taneja Reshma 
Published: April 2024

Abstract
Embryonal Rhabdomyosarcoma (ERMS) stands as the prevailing subtype of Rhabdomyosarcoma (RMS), the most prevalent pediatric soft tissue sarcoma. With a survival rate below 20% in the metastatic stage, RMS lacks targeted drug therapies, emphasizing the need for novel treatment avenues. Genomic analyses have unveiled a low incidence of somatic mutations in RMS, highlighting the substantial role of epigenetic modifiers in oncogenesis.This investigation focuses on EHMT1's involvement in ERMS oncogenesis. Our findings illuminate EHMT1 as a pivotal contributor to the migratory and invasive capabilities of ERMS cells, both in vitro and in vivo. Transcriptomic analysis following EHMT1 depletion unveils significant alterations in pathways crucial for cell migration and invasion. Specifically, the transcription factor SOX8, essential for cellular motility, experiences a substantial reduction upon EHMT1 loss. Notably, the phenotypic effects of EHMT1 loss are mirrored upon SOX8 depletion.Further RNA-Sequencing of SOX8-depleted cells exposes the downregulation of multiple integrin genes. Mechanistically, we delineate EHMT1's role in the upregulation of SOX8 through the regulation of BRD4 expression, influencing its occupancy at the promoter. This study unravels a novel EHMT1-SOX8 axis as a key driver of metastasis in ERMS, providing valuable insights for potential therapeutic interventions in this challenging clinical landscape.
Citation Format: Dipanwita Das, Upasana Bajaj, Jia Yu Leung, Nurul Fateha Binti Abdul Rashi, Vinay Tergaonkar, Reshma Taneja. EHMT1 mediates cellular motility in embryonal rhabdomyosarcoma by activating SOX8 expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB204.
Abstract LB223: The molecular landscape of injury-induced mammary epithelial cell fate switching
Authors: Martín Queralt Vallmajó , Lytle Nikki K. , Murali Divya , Srinivasan Sumana , Ma Zhibo , Mukund Kavitha , Dravis Christopher , Zamora Liliana , Peterson Ana , Khramtsova Galina , Olopade Funmi , Subramaniam Shankar , Wahl Geoffrey M. 
Published: April 2024

Abstract
The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes to cancer progression, treatment resistance, and ultimately cancer death. Tissue injury and microenvironmental changes can cause adult differentiated cells to acquire a plastic “developmentally unstable hybrid cell state” (DUHCS) enabling transdifferentiation into other cell types to effect repair. Yet, the relevant mechanisms that enable cell state reprogramming to arise remain under-explored. Here, we used CRISPR mediated homologous recombination to generate mice in which the mammary basal and luminal cells could be distinguished by their expression of Krt14-mClover-NLS or Krt18-tdTomato-NLS, respectively. We used this novel system to identify mammary epithelial cells undergoing cell state transitions in real time. Using a transplantation paradigm, we found that transplanted basal cells rapidly exhibited a DUHCS resembling mammary embryonic progenitors expressing Sox11, a tightly regulated differentiation factor shut off before birth. We discovered that Sox11 is also expressed in many murine models of TNBC and in single cell transcriptomes from untreated human BRCA1 mutant TNBCs. This suggests that Sox11-expressing cells might be developmentally plastic intermediates in TNBC malignant progression. In a preliminary cohort of patient-derived xenografts from TNBC patients diagnosed at different stages, we detected SOX11-expressing cells in earlier but not in advanced stages. Re-expression of Sox11 in TNBC is consistent with TNBCs being transcriptomically related to fetal mammary stem cells and p53 dysfunction resulting in enhanced cellular plasticity. Taken together, these studies highlight a role for mammary epithelial cell state reprogramming in early breast tumorigenesis, and reveals actionable steps to mitigate tumor heterogeneity by halting tumor progression.
Citation Format: Queralt Vallmajó Martín, Nikki K. Lytle, Divya Murali, Sumana Srinivasan, Zhibo Ma, Kavitha Mukund, Christopher Dravis, Liliana Zamora, Ana Peterson, Galina Khramtsova, Funmi Olopade, Shankar Subramaniam, Geoffrey M. Wahl. The molecular landscape of injury-induced mammary epithelial cell fate switching [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB223.
Abstract LB246: Deep learning framework for patient recurrence and genetic marker prediction in diffuse glioma
Authors: Lin Ko-Hong , Zhang Kai , Lee Dung-Fang , Jiang Xiaoqian 
Published: April 2024

Abstract
Investigation of important molecular features of glioma patients may reveal driving mechanisms of patient recurrence and treatment failures in glioma. Applying various deep learning techniques enables the integration and systematic comparison of multi-omics features, allowing robust marker prediction and patient stratification. We extracted mutation and copy number variation data from the Glioma Longitudinal Analysis (GLASS) Consortium, consisting of 628 primary or recurrent samples. To achieve the patient recurrence classification task, we designed a transformer-based model that learns the genomic profiles and predicts patient recurrence status. Our model outperforms traditional machine learning models, including support vector machine (SVM), logistic regression, and decision trees, for up to 34% and 40% improvement of AUROC and AUPRC, respectively. Including mutational features alone can achieve the best prediction performance, while copy number variations are less informative in predicting patient recurrence status. Our approach is an early attempt that employs deep learning for dissecting the contribution of diverse genomic profiles on glioma recurrence and might provide insights into developing novel therapies for treating glioma.
Citation Format: Ko-Hong Lin, Kai Zhang, Dung-Fang Lee, Xiaoqian Jiang. Deep learning framework for patient recurrence and genetic marker prediction in diffuse glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB246.
Abstract LB247: TCPAplus: An LLM-empowered chatbot for analyzing a large protein expression atlas of human cancers
Authors: Liu Wei , Liu Jun , Tang Yitao , Liu Chaozhong , Song Meiyi , Ju Zhenlin , Kumar Shweth V. , Lu Yiling , Akbani Rehan , Mills Gordon , Liang Han 
Published: April 2024

Abstract
We present a comprehensive functional proteomics resource comprising nearly 9,000 samples from The Cancer Genome Atlas and Cancer Cell Line Encyclopedia, using ~500 high-quality antibodies through reverse phase protein arrays. To enhance its utility, we have developed an analytical chatbot harnessing advanced large language models. This intuitive platform empowers researchers to effortlessly query protein-centered cancer omics data, conduct related analyses, and visualize results using natural language, significantly easing the translation from intricate proteogenomic data to valuable biological insights.
Citation Format: Wei Liu, Jun Liu, Yitao Tang, Chaozhong Liu, Meiyi Song, Zhenlin Ju, Shweth V. Kumar, Yiling Lu, Rehan Akbani, Gordon Mills, Han Liang. TCPAplus: An LLM-empowered chatbot for analyzing a large protein expression atlas of human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB247.
Abstract LB253: Crafted experiments to evaluate feature selection methods for single cell RNA-seq data
Authors: Liu Siyao , Corcoran David , Garcia-Recio Susana , Perou Charles , Marron J.S. 
Published: April 2024

Abstract
Single-cell RNA sequencing (scRNA-seq) technologies have revolutionized our understanding of cellular compositions and tumor behavior at the single-cell level, and have been widely used in many biomedical applications, such as identifying and characterizing novel cell types/states. While numerous computational methods have been developed for analyzing scRNA-seq data, benchmarking various analytical methods remains a key challenge for two reasons. First, there is a lack of ground truth datasets where unambiguous cell type identities are known using external information. Second, simulation of scRNA-seq data tends to be overly artificial and simplistic, which may not well mimic the underlying biological complexity as well as high level of technical variability. Here, we propose the use of crafted experiments, a new approach based upon perturbing signals in a real dataset for comparing different scRNA-seq analytical methodologies. We demonstrate the effectiveness of crafted experiments in the context of a novel univariate distribution-oriented suite of feature selection methods, called GOF (Goodness of Fit). We show that GOF more frequently selects features that robustly identify crafted artificial clusters in crafted experiments and achieves similar performance compared to the field standard method using real datasets. Importantly, we show the use of crafted experiments for identifying the contexts in which each method performs the best. Crafted experiments offer valuable comparisons of scRNA-seq analysis methods, and the crafted datasets generated from this study provide a useful resource for the single-cell community.
Citation Format: Siyao Liu, David Corcoran, Susana Garcia-Recio, Charles Perou, J.S. Marron. Crafted experiments to evaluate feature selection methods for single cell RNA-seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB253.
Abstract LB258: ZDHHC20 is a potential target for overcoming ABCB1-mediated multidrug resisance (MDR) in cancer
Authors: Ji Ning , Peng Xin , Liu Yi-nan , Yang Yuqi , Chen Zhe-Sheng , Kong Dexin , Li Yueguo 
Published: April 2024

Abstract
ABCB1-mediated multidrug resistance (MDR) in cancer cells is an increasingly important cause of anticancer drug treatment failure. The occurrence of MDR in cancer reduces the effectiveness of antitumor drugs, which results in poor quality of life and increased mortality of patients, and creates a heavy burden for the patient's family and society. Hence, the reversal of ABCB1-mediated MDR in cancer is a highly urgent clinical need. Although reversal agents targeting ABCB1 have been developed and partially tested in clinical trials, their main mechanism limits to inhibit the function of ABCB1 efflux pumps, which lacks tumor tissue specificity and has poor clinical effects, and the development of ABCB1-based resistance reversal strategies has entered a bottleneck. ABCB1 mediates tumor MDR through drug efflux and lysosomal segregation, and intervention in the plasma membrane/lysosomal membrane localization of ABCB1 is a potential strategy to reverse drug resistance. Palmitoylation, as a post-translational lipid modification, plays an important role in protein anchoring, transport, and functional regulation, and is highly relevant to human tumors. In the present study, palmitoylation modification was first identified as a key post-translational lipid modification of ABCB1. ABCB1 is palmitoylated in its cytoplasmic domain, which is further stabilized by blocking its ubiquitination, consequently suppressing ABCB1 degradation by lysosomes. We identified palmitoyltransferase ZDHHC20 (DHHC20) as the main acetyltransferase required for the palmitoylation of ABCB1, and show that the inhibition of ABCB1 palmitoylation via 2-bromopalmitate (2-BP), or the silencing of DHHC20, decreases ABCB1 expression and overcomes MDR in vitro as well as in mice bearing SW620/Ad300 resistance cells. Moreover, Cysteine residues C787 was identified as the main palmitoylation cite in human ABCB1. Database and RNAseq analyses revealed that ZDHHC20 is highly expressed in tumor tissues and tumor MDR cells, which makes it a potential tumor tissue-specific target for overcoming ABCB1-mediated MDR in cancer. Our results firstly identified the novel post-translational modification (palmitoylation) of ABCB1 and provide a new research direction and theoretical basis for breaking through the bottleneck of the development of reversal agents for ABCB1-mediated MDR in cancer.
Citation Format: Ning Ji, Xin Peng, Yi-nan Liu, Yuqi Yang, Zhe-Sheng Chen, Dexin Kong, Yueguo Li. ZDHHC20 is a potential target for overcoming ABCB1-mediated multidrug resisance (MDR) in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB258.
Abstract LB275: Reactivation of mitotic arrest upon targeting TACC3 restores immunogenic cell death and T-DM1 response in HER2-positive breast cancer
Authors: Saatci Ozge , Gedik Mustafa Emre , Oberholtzer Nathaniel , Uner Meral , Akbulut Ozge , Cetin Metin , Aras Mertkaya , Ibis Kubra , Caliskan Burcu , Banoglu Erden , Wiemann Stefan , Uner Aysegul , Aksoy Sercan , Mehrotra Shikhar , Sahin Ozgur 
Published: April 2024

Abstract
Immunogenic cell death (ICD) is a specific form of cell death that is characterized by the release of danger-associated molecular patterns (DAMPs), such as cell surface exposure of calreticulin, ATP and HMGB1 release, and can be induced by several different anti-cancer therapies. This, in turn, evokes a strong anti-tumor immune response, leading to reduced tumor growth. Despite being the first and one of the most successful antibody-drug conjugates (ADCs) approved for refractory HER2-positive breast cancer, little is known if response and resistance to trastuzumab emtansine (T-DM1) involves ICD modulation that can be leveraged to enhance T-DM1 response. Here we report that T-DM1 induces spindle assembly checkpoint (SAC)-dependent ICD in sensitive cells, mediated by its payload by inducing eIF2α phosphorylation, surface exposure of calreticulin, ATP and HMGB1 release, and secretion of ICD-related cytokines, all of which are lost in resistance. Accordingly, ICD-related gene signatures correlate with clinical response to T-DM1-containing therapy in pre-treatment samples, and increased infiltration of anti-tumor CD8+ T cells is correlated with better T-DM1 response in post-treatment samples. We found that transforming acidic coiled-coil containing 3 (TACC3) is overexpressed in T-DM1 resistant cells, and that T-DM1 responsive patients have reduced TACC3 protein while the non-responders exhibited increased TACC3 expression during T-DM1 treatment. Notably, genetic or pharmacological inhibition of TACC3 revives T-DM1-induced SAC activation and induction of ICD markers in vitro. TACC3 inhibition elicits ICD in vivo as shown by vaccination assay. It also potentiates T-DM1 in the human HER2-overexpressing MMTV-huHER2#5 (Fo5) transgenic model by activating ICD markers, release of cytokines and inducing dendritic cell (DC) maturation and enhancing infiltration of cytotoxic T cells. Together, our results show that ICD is a key mechanism of action of T-DM1 which is lost in resistance, and that targeting TACC3 restores T-DM1-mediated ICD and overcomes resistance.
Citation Format: Ozge Saatci, Mustafa Emre Gedik, Nathaniel Oberholtzer, Meral Uner, Ozge Akbulut, Metin Cetin, Mertkaya Aras, Kubra Ibis, Burcu Caliskan, Erden Banoglu, Stefan Wiemann, Aysegul Uner, Sercan Aksoy, Shikhar Mehrotra, Ozgur Sahin. Reactivation of mitotic arrest upon targeting TACC3 restores immunogenic cell death and T-DM1 response in HER2-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB275.
Abstract LB296: Human CYP1B1 enhances cancer progression through induction of Sp1 via DNMT-mediated epigenetic regulation of miR-375
Authors: Chun Young-Jin , Kwon Yeo-Jung , Kwon Tae-Uk 
Published: April 2024

Abstract
Human cytochrome P450 1B1 (CYP1B1) is a major catalytic enzyme for metabolism of 17β-estradiol (E2) to catechol estrogens, mainly carcinogenic metabolite 4-hydroxyestradiol (4-OHE2). To identify the unknown molecular mechanism for cancer progression induced by CYP1B1, we studied the role of CYP1B1 in human tumor cells, MCF-7, MDA-MB-231, and HeLa cells. Suppression of CYP1B1 by shRNA significantly reduced cancer cell viability and invasion. Clinical data from cancer patients showed that high level of CYP1B1 expression resulted in relatively lower survival rate. Interestingly, overexpression of CYP1B1 markedly activated Wnt/β-catenin signaling and EMT process, and suppression of specificity protein 1 (Sp1) by siRNA, an well-known transcription factor, demolished the promoting effects of CYP1B1 on cancer progression. To investigate the correlation between CYP1B1 and Sp1, we analyzed the clinical data from breast and cervical cancer patients and the results showed the positive correlation between two genes. Furthermore, TMS (tetramethoxystilbene), a specific CYP1B1 inhibitor, diminished the induction of Sp1 by CYP1B1, and 4-OHE2 exceedingly promoted the expression level of Sp1. Surprisingly, miR-375, known as an oncogenic microRNA, substantially decreased by 4-OHE2 and CYP1B1 overexpression in CYP1B1-transgenic (TG) mice. Methylation specific assay revealed that CYP1B1 suppressed miR-375 expression through induction of hyper-methylation on pre-miR-375. In addition, epigenetic regulation of miR-375 by CYP1B1 was executed via induction of DNA methyltransferases (DNMTs), DNMT1, 3a, and 3b. Enhanced expression level of Sp1 by 4-OHE2 was significantly deteriorated by 5-aza-dC, a DNMT inhibitor. Taken together, our data suggest that CYP1B1 enhances cancer progression through induction of cancer cell proliferation and invasion via DNMT-mediated epigenetic regulation of miR-375 and further promotion of Sp1 expression.
Citation Format: Young-Jin Chun, Yeo-Jung Kwon, Tae-Uk Kwon. Human CYP1B1 enhances cancer progression through induction of Sp1 via DNMT-mediated epigenetic regulation of miR-375 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB296.