bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B019: Stearoyl-CoA desaturase is a synthetic lethal target in SMAD4-deficient cancers
Authors: Lu Alvin Z. , Fenoglio Silvia , Wu Hsin-Jung , Chen Yingnan P. 
Published: June 2024

Abstract
Mothers against decapentaplegic homolog 4, or SMAD4, is a member of the SMAD family of transcription factors that mediate TGF-β signal transduction. SMAD4 loss of function mutation or deletion is found in about 30% of PDAC and 15% of COAD and EAC patients, and it is associated with their poor prognosis. Over the past two decades, its tumor suppressor role has been elucidated, and the loss of SMAD4 is sufficient to promote tumorigenesis in multiple GEM models. To identify novel therapeutic vulnerabilities for SMAD4-deficient cancers, a CRISPR dropout screening approach was employed in SMAD4 isogenic PDAC models. We identified stearoyl-CoA desaturase, SCD, as a synthetic lethal target in SMAD4-deficient context. SCD is critical for de novo lipid biogenesis and catalyzes the rate-limiting step in the production of monounsaturated fatty acid. Genetic and pharmacologic studies in vitro confirmed this synthetic lethal relationship. Additionally, drug-anchored CRISPR dropout screening and RNA expression profiling demonstrated that accumulation of saturated fatty acid in response to SCD inhibition drives cytotoxicity in SMAD4-deficient cells. Mouse studies with CRISPR-based knockout of SCD and a well-characterized SCD inhibitor (A939572) demonstrated anti-tumor efficacy in SMAD4-mutant xenograft models. However, compared to genetic KO of SCD the pharmacological inhibitor was less effective at inhibiting tumor proliferation in vivo. Together, these data identify SCD as a selective vulnerability in SMAD4-mutant cancers.
Citation Format: Alvin Z. Lu, Silvia Fenoglio, Hsin-Jung Wu, Yingnan P. Chen. Stearoyl-CoA desaturase is a synthetic lethal target in SMAD4-deficient cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B019.
Abstract B028: Expression of NOTCH1 in head and neck tumours at selected hospitals in Ghana
Authors: Barnes Precious , Saahene Roland Osei 
Published: June 2024

Abstract
Head and neck tumors (HNT) are of paranasal sinuses origin (the salivary glands and the upper aerodigestive tract). It constitutes the sixth most common tumors. Studies have shown that, factors such as tobacco and alcohol intake and viral infections may increase the relative risk to the tumor. Notch1 pathways are frequently altered in many tumors, however, the clinical significance of NOTCH1dysregulation in head and neck tumors is poorly understood. METHOD: The aim of this study was to investigate the expression NOTCH1 in head and neck tumor and also to elucidate the various anatomical pattern of the head and neck tumors in selected hospitals in Ghana. NOTCH1 expression were analyzed using quantitative real-time PCR (qRT-PCR) and immunohistochemical staining on tissue samples from a consecutive series of head and neck tumor patients resections over a four-year period. RESULTS: The percentage of low expression of Notch1 were 71.4% in the malignant tissue (n=98) and 76.9% (n=52) in the benign tissue. The anatomical site with high of low expression of the NOTCH1 was found in oral cavity (37.1%) followed by respiratory (27.1%) followed by mandible (14.3%). CONCLUSION: There were low expression of NOTCH1 in head and neck tumour tissues suggesting that NOTCH1may be a tumor suppressor gene. We further propose that, NOTCH1 offers a potential tool as a target molecule in the development of therapies for head and neck tumors.
Citation Format: Precious Barnes, Roland Osei Saahene. Expression of NOTCH1 in head and neck tumours at selected hospitals in Ghana [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B028.
Abstract IA005: Therapeutic vulnerabilities of cohesin-mutant myeloid malignancies
Authors: Tothova Zuzana 
Published: June 2024

Abstract
Splicing modulation is a promising treatment strategy pursued to date only in splicing-factor mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in myeloid malignancies, including 15-20% of myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. I will discuss our recent findings identifying cohesin mutations as biomarkers of sensitivity to drugs targeting splicing-factor SF3B1 (H3B-8800 and E-7107) and describe the mechanism by which drug-induced alterations in splicing of DNA repair genes, such as BRCA1 and BRCA2, underlie this sensitivity. We have demonstrated that treatment of cohesin-mutant cells with SF3B1 modulators results in impaired DNA damage response, accumulation of DNA damage, and increased sensitivity to PARP inhibitors and a panel of chemotherapeutic agents in vitro and in vivo, using AML cell lines and patient-derived xenograft models. Furthermore, we identified RAD51 foci formation as a predictive biomarker of sensitivity to SF3B1 splicing modulation alone or followed by sequential treatment with PARP inhibition and chemotherapy, and have identified additional non-cohesin mutant subtypes of MDS/AML and ovarian and breast cancer which are sensitive to this therapeutic approach. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS/AML and we propose this as broader strategy for therapeutic targeting of other DNA damage-repair deficient cancers.
Citation Format: Zuzana Tothova. Therapeutic vulnerabilities of cohesin-mutant myeloid malignancies [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA005.
Abstract PR005: CX-5461 sensitizes DNA damage repair-proficient castrate-resistant prostate cancer to PARP inhibition
Authors: Lawrence Mitchell G. , Porter Laura H. , Choo Nicholas , Sanij Elaine , Taylor Renea , Pearson Richard , Simpson Kaylene J. , Hannan Ross D. , Sandhu Shahneen , Furic Luc 
Published: June 2024

Abstract
Monotherapy with PARP inhibitors is effective for the subset of castrate-resistant prostate cancer (CRPC) with defects in homologous recombination (HR) DNA repair. New treatments are required for the remaining tumors, and an emerging strategy is to combine PARP inhibitors with other therapies that induce DNA damage. Here we tested whether PARP inhibitors are effective for HR-proficient CRPC, including androgen receptor (AR)-null tumors, when used in combination with CX-5461, a small molecule that inhibits RNA polymerase I transcription and activates the DNA damage response, and has antitumor activity in early phase I trials. The combination of CX-5461 and talazoparib significantly decreased in vivo growth of patient-derived xenografts of HR-proficient CRPC, including AR-positive, AR-null, and neuroendocrine tumors. CX-5461 and talazoparib synergistically inhibited the growth of organoids and cell lines, and significantly increased the levels of DNA damage. Decreased tumor growth after combination therapy was maintained for 2 weeks without treatment, significantly increasing host survival. Therefore, combination treatment with CX-5461 and talazoparib is effective for HR-proficient tumors that are not suitable for monotherapy with PARP inhibitors, including AR-null CRPC. This expands the spectrum of CRPC that is sensitive to PARP inhibition. We have recently initiated a clinical trial combining CX-5461 with talazoparib in mCRPC patients (REPAIR trial, NCT05425862) to explore this combination in both HR proficient and deficient settings.
Citation Format: Mitchell G. Lawrence, Laura H. Porter, Nicholas Choo, Elaine Sanij, Renea Taylor, Richard Pearson, Kaylene J. Simpson, Ross D. Hannan, Shahneen Sandhu, Luc Furic. CX-5461 sensitizes DNA damage repair-proficient castrate-resistant prostate cancer to PARP inhibition [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR005.
Abstract PR008: Targeting mechanisms of dosage compensation to selectively kill aneuploid cancer cells
Authors: Okada Hajime , Sdeor Eran , Karmon Miriam , Levanon Erez , Ben-David Uri 
Published: June 2024

Abstract
Aneuploidy is an abnormal chromosome composition and a general hallmark of human cancer. Aneuploidy causes detrimental cellular stresses, but cancer cells evolve to cope with these stresses. Consequently, targeting such mitigation mechanisms is a promising potential therapeutic strategy. As an abnormal dosage of gene products from altered chromosomes can cause RNA and proteotoxic stress, dosage compensation (DC) of imbalanced gene products was reported to mitigate these stresses in aneuploid cells. However, the mechanisms that regulate DC remain elusive. To address these mechanisms, we focused on the role(s) of stress granules (SGs) and RNA binding proteins (RBPs) in aneuploid cancer cells. Our recent study revealed that aneuploid cancer cells preferentially depend on RNA and protein metabolism, and need to attenuate translation in order to cope with proteotoxic stress (Ippolito & Zerbib et al. bioRxiv 2023). In yeast, it has been previously reported that Ssd1, one of the RBPs localized in P-bodies, is indispensable to tolerating aneuploidy stress. Based on these findings, we set out to explore SGs as potential regulators of gene expression in aneuploid cancer cells. As expected, we revealed that SGs emerged in cells under acute aneuploidy stress induced by chromosome mis-segregation. These results imply that SGs are formed in cells during and right after aneuploidization, potentially as a way to mediate DC and ameliorate aneuploidy-induced cellular stress. To gain further insight into RNA regulation in aneuploid cells, we analyzed the essentiality of RBPs across cancer cell lines. We found that the RNA-editing enzyme ADAR, a suppressor of SG formation, is preferentially essential in aneuploid cancer cells. Remarkably, ADAR disruption synergized with acute aneuploidy stress to induce SGs, and ADAR exhibited increased RNA editing activity following chromosome mis-segregation. Our results suggest that SGs and their suppressor ADAR might contribute to ameliorating acute aneuploidy-induced stress. We are currently investigating the target RNAs regulated by SGs and ADAR and examining their functional role(s) in DC, with the goal of uncovering potential synthetic lethalities associated with aneuploidy in cancer cells.
Citation Format: Hajime Okada, Eran Sdeor, Miriam Karmon, Erez Levanon, Uri Ben-David. Targeting mechanisms of dosage compensation to selectively kill aneuploid cancer cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR008.
Abstract PR010: CDK12 loss promotes prostate cancer development while exposing vulnerabilities to paralog-based synthetic lethality
Authors: Tien Jean C. , Chang Yu , Zhang Yuping , Chou Jonathan , Cheng Yunhui , Wang Xiaoju , Yang Jianzhang , Mannan Rahul , Shah Palak , Wang Xiao-Ming , Todd Abbey , Eyunni Sanjana , Cheng Caleb , Cao Xuhong , Bao Yi , Neiswender James , Brough Rachel , Pettitt Stephen , Labanca Estefania , Wang Yuzhuo , Cieslik Marcin , Lord Christopher J. , Ding Ke , Chinnaiyan Arul M. 
Published: June 2024

Abstract
Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration-resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development—either alone, or in the context of other genetic alterations—and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions and robust T cell infiltration in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with Trp53 inactivation but negatively associated with Pten inactivation—akin to what is observed in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent Trp53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic Cdk12 and Trp53 loss allografts represent a new syngeneic model for the study of androgen receptor (AR)-positive, luminal prostate cancer. Notably, Cdk12/Trp53 loss prostate tumors are sensitive to immune checkpoint blockade. Cdk12-null organoids (either with or without Trp53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fidetumor suppressor gene with impact on tumor progression and lends support to paralog-based synthetic lethality as a promising strategy for treating CDK12-mutant mCRPC.
Citation Format: Jean C. Tien, Yu Chang, Yuping Zhang, Jonathan Chou, Yunhui Cheng, Xiaoju Wang, Jianzhang Yang, Rahul Mannan, Palak Shah, Xiao-Ming Wang, Abbey Todd, Sanjana Eyunni, Caleb Cheng, Xuhong Cao, Yi Bao, James Neiswender, Rachel Brough, Stephen Pettitt, Estefania Labanca, Yuzhuo Wang, Marcin Cieslik, Christopher J. Lord, Ke Ding, Arul M. Chinnaiyan. CDK12 loss promotes prostate cancer development while exposing vulnerabilities to paralog-based synthetic lethality [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR010.
Abstract PR015: Discovery of LY4050784 (FHD-909), a selective BRM (SMARCA2) ATPase inhibitor for the treatment of BRG1(SMARCA4) mutant cancers
Authors: Lee Janice Y. , Brooks Nathan , Antonakos Brandon , Perria Bryan , Langan Candace , Jones Bonita D. , Flack Robert Stephen , Li Zhifang , Terry David , Wallace Ross , Bondi Robert , Sis Gereint , Baracani Ronee , McVean Maralee , Kolakowski Gabrielle , Osimboni Dayo , Wilson Kevin 
Published: June 2024

Abstract
BRM (SMARCA2) and BRG1 (SMARCA4) are highly homologous ATPases that are members of the BAF (also known as the mSWI/SNF) chromatin remodeling complex. BRM and BRG1 are mutually exclusive enzymatic subunits of BAF complexes, and functional genomic screens have shown a synthetic lethal relationship between the two genes. BRG1 is frequently mutated in cancer, including in approximately 10% of non-small cell lung carcinomas. Selective inhibition of BRM is a mechanism by which BRG1-mutated cancer cell growth would be affected by losing BRM function, while normal tissues should be spared as they still express functional BRG1. Given that the ATPase domains of BRM and BRG1 are 92% identical, the identification of selective enzymatic inhibitors of BRM has been challenging. Here, we report the discovery of a novel, highly potent compound that selectively inhibits BRM over BRG1 and that also possesses excellent oral pharmacokinetics. LY4050784 (aka FHD-909) inhibits BRM in cell-based transcriptional and proliferation assays and is greater than 30-fold selective over BRG1. It is also selective against other helicases and does not show any significant activity in off-target screening panels. Dosing of mice carrying BRG1-mutant xenografts causes target gene modulation that is correlated with compound exposure. Treatment of A549 and RERF-LC-AI xenografts with LY4050784 led to tumor growth inhibition of 87% and 96%, respectively, at well-tolerated doses, and significant tumor growth inhibition, including regression, was also achieved in BRG1-mutant models NCI-2126 and NCI-1793. The results suggest that our compound has first-in-class potential as a potent and selective BRM ATPase inhibitor for the treatment of BRG1-mutated cancers, and we are planning to file an IND in Q2 of 2024.
Citation Format: Janice Y. Lee, Nathan Brooks, Brandon Antonakos, Bryan Perria, Candace Langan, Bonita D. Jones, Robert Stephen Flack, Zhifang Li, David Terry, Ross Wallace, Robert Bondi, Gereint Sis, Ronee Baracani, Maralee McVean, Gabrielle Kolakowski, Dayo Osimboni, Kevin Wilson. Discovery of LY4050784 (FHD-909), a selective BRM (SMARCA2) ATPase inhibitor for the treatment of BRG1(SMARCA4) mutant cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR015.
Epigenetic Induction of Cancer-Testis Antigens and Endogenous Retroviruses at Single-Cell Level Enhances Immune Recognition and Response in Glioma
Authors: Lai Thomas J. , Sun Lu , Li Kevin , Prins Terry J. , Treger Janet , Li Tie , Sun Matthew Z. , Nathanson David A. , Liau Linda M. , Lai Albert , Prins Robert M. , Everson Richard G. 
Published: June 2024

Abstract

Glioblastoma (GBM) is the most common malignant primary brain tumor and remains incurable. Previous work has shown that systemic administration of Decitabine (DAC) induces sufficient expression of cancer-testis antigens (CTA) in GBM for targeting by adoptive T-cell therapy in vivo. However, the mechanisms by which DAC enhances immunogenicity in GBM remain to be elucidated. Using New York esophageal squamous cell carcinoma 1 (NY-ESO-1) as a representative inducible CTA, we demonstrate in patient tissue, immortalized glioma cells, and primary patient-derived gliomaspheres that basal CTA expression is restricted by promoter hypermethylation in gliomas. DAC treatment of glioma cells specifically inhibits DNA methylation silencing to render NY-ESO-1 and other CTA into inducible tumor antigens at single-cell resolution. Functionally, NY-ESO-1 T-cell receptor–engineered effector cell targeting of DAC-induced antigen in primary glioma cells promotes specific and polyfunctional T-cell cytokine profiles. In addition to induction of CTA, DAC concomitantly reactivates tumor-intrinsic human endogenous retroviruses, interferon response signatures, and MHC-I. Overall, we demonstrate that DAC induces targetable tumor antigen and enhances T-cell functionality against GBM, ultimately contributing to the improvement of targeted immune therapies in glioma.

Significance:
This study dissects the tumor-intrinsic epigenetic and transcriptional mechanisms underlying enhanced T-cell functionality targeting decitabine-induced cancer-testis antigens in glioma. Our findings demonstrate concomitant induction of tumor antigens, reactivation of human endogenous retroviruses, and stimulation of interferon signaling as a mechanistic rationale to epigenetically prime human gliomas to immunotherapeutic targeting.
Multiple focal pulvinar projection fields in the macaque cortex
Authors: Froesel Mathilda , Clavagnier Simon , Goudard Quentin , Zhu Qi , Vanduffel Wim , Hamed Suliann Ben 
Published: June 2024

Abstract
The pulvinar, the largest nucleus of the thalamus, is functionally heterogeneous and involved in multiple cognitive functions. It has been proposed to act as a functional hub of cortical processes due to its extensive reciprocal connectivity with the cortex. However, its role in cognition is not fully understood yet. Here, we posit that an improved understanding of its functional connectivity with the cortex is needed to better capture the cognitive functions of this nucleus. To address this question, we characterize the pulvino-cortical functional connectivity along the ventro-dorsal, antero-posterior, and medio-lateral axes, using awake resting-state data from 10 adult macaques. We first report two global cortical functional connectivity gradients along the antero-posterior and ventro-dorsal pulvinar gradients that match remarkably well the structural connectivity gradients described by anatomical approaches. In addition to these global gradients, multiple local cortical pulvinar projection fields can be identified at the sulci level such as in the lateral sulcus (LS), the intraparietal sulcus (IPS), the principal sulci (PS), and the anterior cingulate cortex (ACC). For most sulci, we show that functional pulvino-cortical projection fields follow the major anatomical axis of these different sulci (e.g., the ventro-dorsal axis for the LS and the antero-posterior axis for the IPS). Other sulci, such as the superior temporal sulcus, the posterior cingulate cortex, or the central sulcus, display multiple projection fields from the pulvinar. Although substantial inter-individual differences exist, the general functional connectivity patterns are remarkably consistent across hemispheres and individuals. Overall, we propose that these multiple pulvinar projection fields correspond to a fundamental principle of pulvino-cortical connectivity and that a better understanding of this connectional organization will shed light on the function of pulvino-cortical interactions and the role of the pulvinar in cognition at large.
GPT-based normative models of brain sMRI correlate with dimensional psychopathology
Authors: Mendes Sergio Leonardo , Pinaya Walter Hugo Lopez , Pan Pedro Mario , Gadelha Ary , Belangero Sintia , Jackowski Andrea Parolin , Rohde Luis Augusto , Miguel Euripedes Constantino , Sato João Ricardo 
Published: June 2024

Abstract
Generative Pre-trained Transformer (GPT) models have been widely used for language tasks with surprising results. Furthermore, neuroimaging studies using deep generative normative modeling show promise in detecting brain abnormalities from brain structural MRI (sMRI). Meanwhile, psychiatric disorders are typically diagnosed through clinical assessment, which is particularly challenging in children and adolescents who present early symptoms or are in the early stages of the disease. Brain biomarkers research may contribute to the complex task of disentangling typical neurodevelopment from emergent psychiatric disorders. Here, we investigate whether a GPT-based normative architecture can detect psychiatric symptoms and disorders from brain sMRI of youths. The studied datasets contain measures of dimensional psychopathology: Brazilian High-Risk Cohort Study (BHRCS, n = 737) and Adolescent Brain Cognitive Development (ABCD, n = 11,031), and scores and diagnostic of psychiatric disorders: Attention Deficit Hyperactivity Disorder (ADHD-200, n = 922) and Autism Brain Imaging Data Exchange II (ABIDE-II, n = 580). We examined the associations of all brain regions with: the Child Behavior Checklist (CBCL) symptom groups, ADHD scores, and Autism Spectrum Disorder (ASD) diagnosis. Results showed the whole-brain typicality likelihood as correlated with social problems (ABCD test set) and ASD diagnosis (ABIDE-II dataset). Analysis by brain regions linked different areas to several CBCL scales, ADHD scores, and ASD diagnostic. This is the first successful study assessing all dimensional groups of CBCL symptoms, from all brain regions, based exclusively on sMRI. The normative models based on GPT are promising to investigate the gap between the phenotypes of psychiatric conditions and their neurobiological substrates.