bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3409: Design and characterization of highly potent and selective CDK9 heterobifunctional degraders
Authors: Toure Mohammed A. , Motoyama Keisuke , Richters André , Koehler Angela N. 
Published: April 2023

Abstract
Cyclin-dependent kinase 9 (CDK9) has long been considered an attractive therapeutic target for modulating transcription in cancers of high unmet clinical need. CDK9 coordinates signaling events that regulate RNA polymerase II (Pol II) pause-release state and is considered an important co-factor for oncogenic transcription factors that drive transcription in an addictive manner. CDK9 modulation offers an approach for attenuating transcriptional dysregulation driven by amplified or overexpressed transcription factors, such as c-MYC. However, targeting CDK9 in the clinic has proven very challenging. This stems from the often highly intolerable cytotoxic effects likely due to off-target effects. Targeted protein degradation offers a novel approach for engineering enhanced selectivity and mitigating other liabilities of the conventional inhibition-driven approach that have been applied to date. Here, we present the design and characterization of a focused library of highly selective CDK9 degrader molecules with rapid kinetics and potency (half-degrading concentration of &lt;1nM). We carry out transcriptional and phosphoproteomics profiling to comprehensively characterize the downstream effects and cellular adaptations resulting from CDK9 degradation. We gain new insights into adaptive responses to CDK9 modulation and the biological contexts most responsive for therapeutic application.
Citation Format: Mohammed A. Toure, Keisuke Motoyama, André Richters, Angela N. Koehler. Design and characterization of highly potent and selective CDK9 heterobifunctional degraders [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 3409.
Abstract 3450: Discovery and preclinical study of novel BTK degrader HZ-Q1070
Authors: Liu Xingguo , Zhou Yubo , Wu Yizhe , Luo Xiaomin , Xie Jiangfeng , Jin Xinxin , Li Jia , Zhou Xinglu 
Published: April 2023

Abstract
Introduction: Bruton's tyrosine kinase (BTK) is a clinical validated target for B cell lymphoma and autoimmune diseases. However, acquired resistance, which is the result of BTK C481S mutation, has been observed in patients. So reversible BTK inhibitors are developed to overcome acquired resistance of covalent BTK inhibitors. In order to achieve adequate efficacy, reversible BTK inhibitors require much higher exposure which may lead to higher risk of adverse effect. Proteolysis-targeting chimera (PROTAC) is a novel drug discovery strategy and achieve sustained target degradation though a catalytic mechanism of action. Comparing with traditional small molecule inhibitor, PROTAC has shown great advantages in overcoming acquired resistance, since potent and sustained active site occupation is no longer required. Here, we have identified a novel BTK-PROTAC HZ-Q1070 based on our DaTProD® platform, which is set up to promote the druggability research of PROTAC. After a series of evaluations, HZ-Q1070 has been validated as a promising pre-clinical candidate for further clinical development.
Results: 1. HZ-Q1070 can effectively degrade BTK in cancer cell lines with DC50 &lt; 0.05 nM. In vitro cancer cell growth inhibition assay, it completely suppressed the cell proliferation of a panel of lymphoma cell lines with IC50 &lt; 0.05 nM, such as Mino, OCI-ly10 and TMD8. 2. At the same time, HZ-Q1070 catalyzes the mutated BTK degradation (C481S/C481Y/C481F/T474M) and potently inhibits growth of BTK inhibitor-resistant tumor cell lines. 3. In proteomic analysis assay, HZ-Q1070 can selectively degrade BTK. 4. HZ-Q1070 has been engineered to avoid Aiolos and Ikaros degradation and therefore does not show IMiD activity. 5. Mechanistic investigation of indicates that HZ-Q1070 can function through the ubiquitin-proteasome system (UPS). 6. In the PK/PD experiments, HZ-Q1070 shows excellent pharmacokinetic properties and BTK degradation activity in vivo. 7. HZ-Q1070 demonstrates robust tumor growth inhibition in TMD8 and Mino xenograft mouse model. Doses as low as 3 mg/kg demonstrates a significant inhibitory effect.
Conclusion: In summary, HZ-Q1070 is a potent and highly selective BTK degrader against both BTK-WT and multiple BTK inhibitors-resistant mutations. In vivo, HZ-Q1070 exhibits excellent pharmacokinetic properties, BTK degradation activity and robust tumor growth inhibition in TMD8 and Mino mouse xenograft tumor model. These findings support further clinical development of HZ-Q1070 for the treatment of B cell malignancies.
Citation Format: Xingguo Liu, Yubo Zhou, Yizhe Wu, Xiaomin Luo, Jiangfeng Xie, Xinxin Jin, Jia Li, Xinglu Zhou. Discovery and preclinical study of novel BTK degrader HZ-Q1070 [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 3450.
Abstract 3451: XS-04: A first-in-class dual IRAK4/BTK inhibitor for the treatment of hematological malignancies
Authors: Zhao Chunyan , Wang Jianfei , Liu Aiguo , Gao Xin , Teng Yanfen , Liu Lei , Zhang Yang , Yu Xiaohong 
Published: April 2023

Abstract
Bruton's tyrosine kinase (BTK), a critical mediator of B-cell receptor (BCR) signaling, is a validated therapeutic target found across multiple B-cell cancers. Though initially responding to treatment with a BTK inhibitor, many patients with chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), or Waldenström macroglobulinemia (WM) eventually progressed and clinical responses to BTK inhibitors are often poor in diffuse large B-cell lymphoma (DLBCL) patients. These highlight the need to understand the resistance mechanisms and improve responses to BTK inhibitors. The serine/threonine protein kinase IRAK4 is a key modulator of MYD88, which is found to be mutated in various aggressive B-cell lymphomas, including DLBCL. As BCR signaling and MYD88 signaling converge downstream on NF-kB activation, which plays an essential role in proliferation and survival of lymphoma cells, blockade of the two signaling pathways presents a potential therapeutic strategy. Here, we investigated the pharmacokinetic properties and anti-tumor activity of XS-04, a first-in-class dual inhibitor targeting both IRAK4 and BTK, using preclinical models of DLBCL subtypes, including tumors resistant to BTK inhibitors. XS-04 showed potent inhibition of IRAK4 and BTK kinases, with IC50 values of 0.2 and 2.9 nM, respectively. Favorable pharmacokinetic properties were also seen across multiple non-clinical species. Using in vitro anti-proliferative assays, we found that XS-04 inhibited proliferation of various DLBCL cell lines with IC50s of 30 to 40 nM. Mechanistically, XS-04 suppressed NF-kB activity in DLBCL cells and in vivo xenograft tumors, as indicated by decreased phosphorylation of IkBa. Oral dosing of XS-04 in TMD8 xenograft model led to a dose-dependent inhibition of tumor growth, which was comparable to the inhibition shown by a combination of BTK and IRAK4 inhibitors. In addition, XS-04 treatment resulted in tumor regression in a patient-derived ibrutinib-resistant MCL xenograft model, without significant changes in body weight. XS-04, a first-in-class IRAK4/BTK dual inhibitor, shows broad anti-tumor activity across preclinical models of DLBCL subtypes, including tumors resistant to BTK inhibitors. These results support XS-04 as a therapeutic candidate for the treatment of hematological malignancies. An IND submission is planned for 2023.
Citation Format: Chunyan Zhao, Jianfei Wang, Aiguo Liu, Xin Gao, Yanfen Teng, Lei Liu, Yang Zhang, Xiaohong Yu. XS-04: A first-in-class dual IRAK4/BTK inhibitor for the treatment of hematological malignancies [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 3451.
Abstract 3529: EWSR1-WT1 isoform selectivity, DNA binding, and druggable targets: unpacking the biology of desmoplastic small round cell tumor
Authors: Magrath Justin W. , Goldberg Ilon A. , Hartono Alifiani B. , Lee Sean B. 
Published: April 2023

Abstract
Desmoplastic small round cell tumor (DSRCT) is a rare pediatric cancer caused by the EWSR1-WT1 fusion gene. No targeted therapies have been established and multimodal therapy is ineffective with a 5-year survival rate of 15-25%. Many questions about the biology of DSRCT remain unanswered including the critical genes regulated by the EWSR1-WT1 fusion gene, the role of the - and +KTS fusion gene isoforms produced by alternative splicing, and the relationship between EWSR1-WT1 binding and gene expression alterations. To address these questions, we established four doxycycline-inducible DSRCT cell lines that selectively knockdown the expression of EWSR1-WT1. RNA-seq analysis on these cell lines with or without EWSR1-WT1 knockdown identified commonly altered genes and pathways. To illuminate the role of the EWSR1-WT1 -KTS and +KTS isoforms, the -KTS, +KTS, or both isoforms were overexpressed in a mesothelial cell line, a hypothesized cell of origin for DSRCT. Remarkably, different gene expression alterations were observed between the -KTS and +KTS isoforms. While overexpression of the -KTS isoform upregulated 765 genes and downregulated 366 genes, overexpression of the +KTS isoform upregulated 203 genes and downregulated 25 genes. Gene set enrichment analysis showed EWSR1-WT1 regulated gene signatures are recapitulated by overexpression of the -KTS isoform or both +/-KTS isoforms, but not the +KTS isoform alone, suggesting the -KTS isoform predominantly regulates gene expression in DSRCT. To interrogate the influence of direct and indirect gene regulation by EWSR1-WT1, ChIP-seq and CUT&RUN data were integrated into our RNA-seq analysis. Across each of our four DSRCT cell lines, approximately 25% of EWSR1-WT1 bound peaks led to upregulation, 10% led to downregulation, and 65% led to no gene expression alteration. EWSR1-WT1 binding accounted for 33% of EWSR1-WT1 commonly upregulated genes but only 4.2% of commonly downregulated genes. Upregulated EWSR1-WT1 bound genes were more likely to be bound in the promoter or first intron and coincide with Znf263 or Hoxb4 motifs. To evaluate the functional role of EWSR1-WT1 targets in DSRCT biology, a screen of the 24 druggable EWSR1-WT1 targets was conducted and a number of novel and known target genes were identified as important for DSRCT survival. Current work is verifying these targets with gene knockdown and evaluating their function in vivo.
Citation Format: Justin W. Magrath, Ilon A. Goldberg, Alifiani B. Hartono, Sean B. Lee. EWSR1-WT1 isoform selectivity, DNA binding, and druggable targets: unpacking the biology of desmoplastic small round cell tumor. [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 3529.
Abstract 3558: Role of FLI portion of EWS::FLI in transcription regulation via modulation of chromatin 3D landscape in Ewing sarcoma
Authors: Bayanjargal Ariunaa , Taslim Cenny , Crow Jesse , Selich-Anderson Julia , Lessnick Stephen L. 
Published: April 2023

Abstract
Ewing sarcoma is an aggressive bone-associated tumor currently treated with dose-intense chemotherapy, radiation, and surgery and it affects adolescents and young adults. The hallmark of Ewing sarcoma is a translocated fusion transcription factor named EWS::FLI that drives the oncogenic process. We hypothesize that FLI portion of EWS::FLI containing a crucial alpha-helix plays a novel role in transcription regulation of thousands of genes by modulating chromatin looping. The hypothesis is based on recent evidences from our lab: an alpha-helix immediately downstream of DNA binding domain as an important player in regulating transcriptional activity and that EWS::FLI has a substantial role in shaping the chromatin landscape of Ewing sarcoma cells. The objective of this study is to elucidate the mechanism underlying transcriptional regulation by FLI. We utilized knockdown/rescue experiments in which EWS::FLI was depleted with shRNA and replaced with constructs containing the ETS DNA Binding Domain (DBD) alone or DBD+ (DBD and 4th alpha-helix). The binding pattern and transcriptional regulation were assessed with CUT&Tag and RNA-Seq respectively. The extent of roles each of these construct play in organization, structure, and function of chromatin are being assessed using Micro-C technique, a variation of Hi-C with improved resolution, higher signal-to-noise ratio and more information on chromatin domain boundaries and chromatin looping. The DNA binding and genomic localization of EWS::FLI was unaltered by the deletion surrounding the DNA binding domain (which contains a 4th alpha-helix) in A673 and TTC466 cells. Despite this similarity in genomic localization and binding, the transcriptional output driven by EWS::FLI was significantly diminished by the deletion. With this current study, we hope to understand if the flanking region neighboring the DNA binding domain contributes to the chromatin architecture remodeling function of EWS::FLI and whether this function could be attributed to the transcriptional output differences in the DBD and DBD+ conditions.
Citation Format: Ariunaa Bayanjargal, Cenny Taslim, Jesse Crow, Julia Selich-Anderson, Stephen L. Lessnick. Role of FLI portion of EWS::FLI in transcription regulation via modulation of chromatin 3D landscape in Ewing sarcoma. [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 3558.
Abstract 356: Targeting differential metabolism in an aged model of cancer cachexia
Authors: Dasgupta Aneesha , Schmitt Rebecca E. , Schneider Jessica Z. , Kono Tatsuyoshi , Lee Chih-Chun , Evans-Molina Carmella , Doles Jason D. 
Published: April 2023

Abstract
Cancer cachexia is a multifactorial syndrome entailing muscle and fat wasting, inflammation, and metabolic dysfunction. Pancreatic cancer has the highest incidence of cachexia at around 80%. However, there are no FDA approved therapy for cachexia in the clinic yet. This is mostly because of the failure of preclinical therapies to demonstrate success in the clinic. Most preclinical studies utilize 6-8 week old mice which roughly corresponds to a human age of ~ 20 years. However, the median age of diagnosis of pancreatic cancer is ~70 years. Given widespread physiology, microenvironment, and metabolism differences in young and aged skeletal muscle, we sought to study cancer cachexia in mice aged to &gt;78 weeks, which corresponds to a human age of greater than 60 years. Our previously published study reported little difference in tumor growth or survival between the two cohorts, yet significant alterations in the muscle transcriptome. Building on this work, we show significant differences in the muscle metabolome of young/aged control and tumor bearing mice. Notably, histamine was higher in aged versus young control mice and even higher in the aged tumor-bearing cohort. We show higher activity of histamine decarboxylase (HDC), the enzyme that converts histidine to histamine in the muscles of aged tumor-bearing mice. Addition of cancer conditioned-media (CM) to C2C12 myotubes was able to induce histamine production and HDC activity in vitro, which demonstrates the ability of muscle cells to induce histamine independent of mast cells. We further show that addition of histamine to myotubes is sufficient to increase atrophy-associated markers. Inhibition of HDC activity by α-fluoromethylhistidine (FMH) in the in vitro model of cachexia protected against myotube thinning. Finally, we treated tumor-bearing aged mice with FMH and observed a) decreased histamine in the muscles 2) decreased HDC activity in the muscles 3) decreased muscle wasting, 4) decreased atrophy markers. Together, we present a novel wasting-associated metabolic pathway and corresponding therapeutic avenue for cancer cachexia that may have been overlooked if not for the use of a more-age-appropriate model of pancreatic cancer.
Citation Format: Aneesha Dasgupta, Rebecca E. Schmitt, Jessica Z. Schneider, Tatsuyoshi Kono, Chih-Chun Lee, Carmella Evans-Molina, Jason D. Doles. Targeting differential metabolism in an aged model of cancer cachexia [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 356.
Abstract 3602: The metastasis-suppressive function of intracellular galectin-3 in melanoma
Authors: Mohammed Norhan B. B. , Dimitroff Charles J. 
Published: April 2023

Abstract
Melanoma is a relatively rare skin cancer. However, it accounts for most of all skin cancer-related deaths worldwide. Once melanoma spreads to distant sites, it confers a poor prognosis characterized by resistance to therapy and high mortality rate. Hence, a favorable clinical outcome is strongly correlated with early diagnosis. Despite the ongoing research to identify novel diagnostic, prognostic, and therapeutic targets for metastatic melanoma (MM), a reliable serum marker to predict whether melanoma is vulnerable to metastasize or has already metastasized is still lacking. Galectin-3 (Gal-3), a ß-galactoside-binding protein, is widely expressed by many human epithelial and immune cells. High extracellular Gal-3 expression levels have been reported to be positively correlated with late-stage disease in melanoma patients, where it is theorized to bind surface glycosylated proteins to promote melanoma cell invasion and metastasis. Gal-3 is also expressed intracellularly where it participates in the regulation of many biological processes. However, intrinsic Gal-3 levels within the melanoma cell and its relationship to melanoma progression is still poorly understood. Using The Cancer Genome Atlas (TCGA) database, we analyzed the Gal-3 expression profiles of 471 tumor samples obtained from melanoma patients. To our surprise, TCGA data analysis has shown significantly higher expression of Gal-3 in primary melanoma samples compared to metastatic melanoma. We hypothesize that intracellular Gal-3 potentially negatively regulates primary melanoma progression to metastatic disease. Using several human melanoma cell lines silenced for Gal-3 expression, we investigated the corresponding malignancy-associated activities of these cells. Our results revealed that Gal-3 silencing in melanoma cells potentiated melanoma migration, invasion, and colony formation, compared with mock controls, suggesting that intracellular Gal-3 could interfere with melanoma metastatic activity. Moreover, loss of Gal-3 boosted the activation of the PI3K/AKT and MAPK signaling pathways and upregulated nuclear factor of activated T cells (NFAT1) expression and its pro-metastatic downstream target genes. Importantly, this study illuminates the apparent opposing roles of Gal-3 in melanoma progression, with intracellular Gal-3 potentially serving as a metastasis-suppressive molecule. Moreover, these studies reveal the potential of analyzing melanoma cell-intrinsic levels of Gal-3 to better predict metastatic potential and clinical outcome in melanoma patients.
Citation Format: Norhan B. B. Mohammed, Charles J. Dimitroff. The metastasis-suppressive function of intracellular galectin-3 in melanoma. [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 3602.
Abstract 3615: Targeting tumor-brain crosstalk in invasive brain metastases
Authors: Mourcos Caitlyn , Maritan Sarah M. , Annis Matthew G. , Kruck Georgia , Nowakowski Alexander , Lazaratos Anna-Maria , Petrecca Kevin , Siegel Peter 
Published: April 2023

Abstract
Background: An estimated 20-40% of cancer patients develop brain metastases (BrM), mostly those affected by lung cancer, breast cancer or melanoma. Unfortunately, these patients suffer from poor outcomes and diminished quality of life. Few BrM treatment options beyond local therapy exist and this is often a short-term solution as 60% of resected BrM recur within 1 year. Our group discovered that patient prognosis is linked to BrM invasiveness, with highly invasive (HI) BrM more likely to recur, compared to minimally invasive (MI) BrM. This has presented us the opportunity to investigate exploitable biological mechanisms driving HI BrM. For instance, invasive signaling can be driven by microenvironmental proteins such as growth and immunological factors (cytokines) secreted by surrounding brain or cancer cells, through inter-cellular or self-feeding autocrine loops.
Hypothesis: Considering the influence of secreted factors on cancer invasion and the brain microenvironment, I hypothesize that secretory profiling of BrM and brain parenchymal cells will be mechanistically insightful and help identify potential targetable drivers of BrM invasion.
Results: To identify BrM invasion-related tumor- and brain-derived factors, I performed human- and mouse-specific high throughput Enzyme-Linked Immunosorbent Assay (ELISA)-based screens on conditioned media from mouse brain slices harboring intracranial MI or HI BrM patient-derived xenografts (PDX). This secretome screen reveals distinct MI and HI secretory profiles for melanoma, breast cancer and lung cancer BrMs and several HI BrM-derived factors of interest have been identified. Such factors are important to investigate as possible drivers of invasiveness in BrM through functional studies.
Conclusion: BrM patients currently face a bleak prognosis, with few treatment options and a median survival of only 8-16 months. Considering the clinical availability of targeted therapies including inhibitors for growth factor-binding tyrosine kinases, antibody-drug conjugates, and immunotherapy, this project will help elucidate the cancer-brain crosstalk which may be exploited therapeutically with existing drugs in patients with frequently recurring HI BrM. ADDIN
Citation Format: Caitlyn Mourcos, Sarah M. Maritan, Matthew G. Annis, Georgia Kruck, Alexander Nowakowski, Anna-Maria Lazaratos, Kevin Petrecca, Peter Siegel. Targeting tumor-brain crosstalk in invasive brain metastases. [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 3615.