bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4482: Development of small molecule inhibitors of lipocalin 2 for the treatment of aggressive cancers
Authors: Flores-Colón Marienid , Peña-Vázquez Cristal A. , Hernández-O'Farril Eliud , Vázquez-Quiñones Luis E. , Vivas-Mejía Pablo E. 
Published: March 2024

Abstract
Lipocalin-2 (LCN2), a secreted protein pivotal in iron homeostasis, immune responses, siderophore transport, and epithelial cell differentiation. LCN2 is highly abundant in aggressive forms of many cancers including breast, pancreatic, ovarian, and esophageal cancer. Elevated LCN2 levels in aggressive tumors correlate with heightened cancer cell motility, proliferation, angiogenesis, invasion, and metastasis. After the protein folds it makes a barrel structure which encloses a three-calyx pocket that can bind and transport molecules. A first generation of small molecule inhibitors (SMIs) targeting LCN2 demonstrated efficacy in attenuating the proliferative capacity of Inflammatory breast cancer (IBC) cells. IBC stands as a rare and highly aggressive variant, accounting for 1 to 5% of all BC cases, with 20-30% presenting as de novo metastatic disease. In the previous studies the concentration of LCN2 inhibitors to reduce cell proliferation in 50% was around 10 µM. In pursuit of better LCN2 SMIs, we conducted in-silico analysis using a library of 369,000 ligands. Through the High-Performance Computer Facility at UPR Río Piedras, we employed AutoDock Vina for virtual screening, targeting the LCN2-calyx with Lys134 as the central coordinate. Docking protocols, predicting binding affinities, identified 8,162 out of 327,638 ligands that have been docked already with values below -9.6 kcal/mol for further consideration. The next phase involves subjecting these potential inhibitors to the SwissADME tool for a comprehensive evaluation of absorption, distribution, metabolism, and excretion parameters, as well as pharmacokinetics, drug-likeness, and medicinal chemistry considerations. The parameters to be evaluated are the Lipinski rules, which states that an orally active drug may have a maximum of one violation and the pann-assay interference compounds (PAINS) alerts tool, a source of false positives for biologically active compounds. The top candidates, exhibit binding affinities within the range of -11.5 to -12.2. After SwissADME filtering, we will re-rank the ligand list, identifying 30 commercially available candidates for subsequent cell viability assays in SUM149 (TNBC) and SUM190 (HER2+) cell lines. This multifaceted approach integrates computational methodologies with rigorous experimental validation, paving the way for potential therapeutic interventions in IBC treatment.
Citation Format: Marienid Flores-Colón, Cristal A. Peña-Vázquez, Eliud Hernández-O'Farril, Luis E. Vázquez-Quiñones, Pablo E. Vivas-Mejía. Development of small molecule inhibitors of lipocalin 2 for the treatment of aggressive cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4482.
Abstract 4501: First reported PIM kinase degraders: Design, profiling & optimization
Authors: Legros Celine , Ratcliffe Paul , Porkolab Vanessa , Modugno Michele , Mirguet Olivier 
Published: March 2024

Abstract
The PIM serine/threonine kinases (PIM1/PIM2/PIM3) are downstream effectors of ABL, JAK2 and Flt-3 oncogenes and are required for tumorigenesis. Overexpression has been reported in hematological and solid tumors, myeloma, lymphoma, leukemia and adenocarcinoma. The first generation of PIM inhibitors to make it to the clinic, including SGI-1776, AZD1208 and PIM447, are known to be pan-PIM inhibitors, while the aim of this project was to identify novel & selective PIM3 inhibitors. To this end, several Hit-finding approaches were employed to rapidly generate novel chemical matter, which were then assessed for their activity against PIM3 using a robust ADP-Glo™ assay. In parallel to this Hit-findings activity, we used AZD1208 scaffold as a starting point to generate PIM3 bifunctional protein degraders and designed a specific screening cascade in order to profile such modalities. The PIM degrader library, synthetized using Automated Robotics Lab, was characterized using ADP-Glo assays. It was then screened on our binding and activity kinase platforms, KINOMEscan® and KinaseProfiler™, and then fully profiled including ternary complex formation with biophysics and in vitro Safety Pharmacology Profiling Panels. One example is the AZD1208 derivate degrader, i.e. EC108154-1, which showed nanomolar range affinity for PIM3 and the E3-ligase CRBN-DDB1, and its affinity range was also confirmed with the ternary complex in SPR and MST-TRIC. This comprehensive screening cascade ensures an in-depth characterization and optimization of protein degraders, with the possibility of monitoring the ternary complex formation with biophysics methods. It is a good illustration of how this combination of tests can be instrumental in selecting the best degraders to progress to the next step of drug discovery.
Citation Format: Celine Legros, Paul Ratcliffe, Vanessa Porkolab, Michele Modugno, Olivier Mirguet. First reported PIM kinase degraders: Design, profiling & optimization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4501.
Abstract 4525: Discovery of a highly potent and selective PARP1 inhibitor with superior PK and safety profiles
Authors: Wei Yi , Li Wenming , Li Zehui , Li Manhua , Kang Kai , Wen Zhiming , Yin Tinggui , Yu Kuo-Long , Zhao Genshi , Yuan Hongbin 
Published: March 2024

Abstract
PARP inhibitors have been an effective treatment option for cancers deficient in homologous recombination repair, such as ovarian, breast, prostate, and pancreatic cancers, particularly those harboring BRCA mutations. However, their severe overlapping hematological and gastrointestinal toxicities have limited their clinical use, especially in the combination therapies with other anti-cancer agents. More recently, studies have shown that inhibiting PARP1 mainly drives anti-tumor activity while inhibiting PARP2 contributes to the hematological toxicity such as anemia due to its essential role in the survival of hematopoietic stem and progenitor cells. Thus, there is an urgent need for developing a selective PARP1 inhibitor. In this study, we report the discovery and characterization of a unique PARP1 inhibitor, ACE-86225106. This molecule is highly selective at inhibiting PARP1 over PARP2 as demonstrated in biochemical (72x) and DNA-trapping (131x) assays. It demonstrates potent anti-proliferative activities against BRCA mutant cancer cell lines (IC50 = 1-9 nM) but not against BRCA wild type cancer cells (IC50 &gt;30,000 nM). As compared to the BRCA mutant cancer cells, this molecule is much less active at inhibiting the differentiation of CD34+ hematopoietic stem cells (IC50 ≈ 450-1,400 nM), i.e.: erythroid, myeloid and megakaryocyte. The results of these studies show that ACE-86225106 is a highly potent and selective PARP1 inhibitor. This molecule has a unique PK profile characterized by its long half-life and low volume of distribution. As such, it demonstrates robust efficacy at low dose (1 mg/kg) with a less frequent dosing schedule (once a week). Importantly, there was no significant body weight loss observed in the treatment group even at much higher doses (10 mg/kg), but there was a significant body weight gain. The GLP toxicology studies have confirmed its superior safety profile as the maximum recommended safe starting first-in-human dose was &gt;5-fold higher than the predicted human efficacious dose. Taken together, ACE-86225106 is a highly potent, selective PARP1 inhibitor with excellent PK and safety profile and expected to have a better safety profile, deeper and more durable clinical responses, and broader utility in the clinic as a preferred combination partner with other anti-cancer therapies. A phase 1 clinical trial to evaluate its safety, PK, and clinical utility is to begin in early 2024.
Citation Format: Yi Wei, Wenming Li, Zehui Li, Manhua Li, Kai Kang, Zhiming Wen, Tinggui Yin, Kuo-Long Yu, Genshi Zhao, Hongbin Yuan. Discovery of a highly potent and selective PARP1 inhibitor with superior PK and safety profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4525.
Abstract 4557: Overexpressed CPAP promotes cancer stemness and enhances chemo-resistance in HCC
Authors: Hung Liang-Yi 
Published: March 2024

Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and is highly resistant to chemotherapy and targeted therapy. It was reported that HCC cancer stem cells (CSCs) are involved in chemo-drug resistance by regulating multidrug resistance (MDR) gene expression, such as ABC transporters. Our previous reports indicated that CPAP, a centrosomal protein, can promote HCC progression by up-regulating NF-κB and STAT3 transcriptional activities. Here, we demonstrated that overexpressed CPAP can increase cancer stemness features and CSCs-derived sorafenib resistance in HCC by up-regulating the transcriptional activities of NF-κB and β-catenin. Importantly, CPAP stably expressed HCC spheroids are significantly resistance to sorafenib in vitro and in vivo. Our results suggested that CD24 and ABCG2 are two potential downstream effectors in CPAP overexpressed HCC. CPAP can transcriptionally up-regulate CD24 and ABCG2 expression via Wnt/β-catenin and NF-κB signaling pathways, respectively; high CPAP/ABCG2/CD24 expression levels are negatively correlated with disease-specific survival rates in HCC patients. Combined treatment with sorafenib and Wnt/β-catenin pathway inhibitor PRI-724 significantly inhibited CPAP-overexpressing Hep3B spheroids-derived tumor growth in a xenograft mouse model. Our study highlights the oncogenic role of CPAP in promoting CSCs-induced sorafenib resistance in HCC and provides insights into potential therapeutic strategies.
Citation Format: Liang-Yi Hung. Overexpressed CPAP promotes cancer stemness and enhances chemo-resistance in HCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4557.
Abstract 4579: DNMT1 determines the sensitivity of Class I HDAC inhibitor Psammaplin A to induce apoptosis and DNA damage in hematological malignant cells
Authors: Bao Yu , Liu Dan , Wu Zi , He Yumei , Gong Ping , Waxman Samuel , Jing Yongkui 
Published: March 2024

Abstract
Histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) are overexpressed in cancer cells associated with dysregulated gene expression and tumor progression. DNMT1 partnered with Class I HDAC as complex to inhibit gene transcription. Several pan-HDAC inhibitors have been approved for T-cell lymphoma with evident side effects. More selective HDAC inhibitors need to be developed. Psammaplin A (PsA), a symmetrical bromotyrosine-derived disulfide dimer isolated from the Psammaplysilla sponge, is a selective Class I HDAC inhibitor. We tested its cell growth inhibition and apoptosis induction in 12 hematological malignant cell lines with 8 lines sensitive (more than 50% growth inhibition at 1 μM) and 4 lines insensitive (less than 20% growth inhibition at 1 μM). PsA induces acetylation of H3, but not α-tubulin, supporting the Class I HDAC inhibition selection. In the sensitive cell lines, PsA induces apoptosis with down-regulation of c-Flip and upregulation of NOXA as well as DNA damage detected by γ-H2A.X. RNA sequence analysis results confirm the regulation of PsA on NOXA, c-Flip and p21 gene expression. The four insensitive cell lines express high levels of DNMT1 with resistance to apoptosis induction. Silencing DNMT1 with siRNA sensitizes PsA-induced apoptosis with induction of NOXA and γ-H2A.X. Azacytidine, the DNMT1 degrader, in combination with PsA induce synergistic cell growth inhibition and apoptosis in vitro. PsA (20 mg/kg) plus Azacytidine (2.5 mg/kg) synergistically inhibit tumor growth in insensitive mantle cell lymphoma Jeko-1 xenografts, without detected toxic signs in organ pathological analysis. We find a new mechanism of DNMT1 controlling the sensitivity of Class I HDAC inhibitor PsA and provide a rationale of PsA with azacytidine for combination therapy.
Citation Format: Yu Bao, Dan Liu, Zi Wu, Yumei He, Ping Gong, Samuel Waxman, Yongkui Jing. DNMT1 determines the sensitivity of Class I HDAC inhibitor Psammaplin A to induce apoptosis and DNA damage in hematological malignant cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4579.
Abstract 4585: Discovery of ETS-006, a highly potent YAP/TEADs PPI inhibitor with broad anti-tumor activity as a single agent
Authors: Lu Jiajun , Gao Ming , Du Wenpei , Fan Xiaofei , Li Jinping , Wang Mengya , Feng Lijian , Li Yingjie , Yao Jiaqi , Lu Jiting , Cui Wenqi , Zheng Qiangang , Zhu Jidong 
Published: March 2024

Abstract
The transcription co-activators YAP, pairing with the TEAD family of transcription factors, serve as essential effectors of the conserved Hippo signaling pathway. Hippo kinase cascade controls YAP nuclear entry and binding with TEADs by modulating its phosphorylation and stability. Overexpression and activation of YAP/TAZ are frequently observed in a variety of cancers. It has been well established that YAP aberration contributes to cancer development, metastasis, immunosurveillance escape and drug resistance. Disruption of YAP/TEADs PPI is an effective approach to inhibit YAP transcriptional activity. We previously have reported the identification of YAP/TEADs PPI hit compound through the fragment-based screen and advanced the hit to lead compound ETS-003. Here we reported the preclinical candidate of YAP/TEADs PPI inhibitor ETS-006 with much more potent anti-tumor activity and favorable safety profile. Compared to TEAD palmitoylation inhibitor, ETS-006 could completely disrupt the interaction of YAP/TEADs, resulting in a more profound downregulation of YAP target gene expression. ETS-006 demonstrated more robust anti-tumor activity than the competitor’s YAP/TEADs PPI inhibitor in MPM CDX model with favorable ADME properties. Notably, ETS-006 showed promising efficacy across multiple solid tumor types, including head and neck squamous cell carcinoma, osteosarcoma, and triple-negative breast cancer with urgent unmet clinical needs. In conclusion, ETS-006 is a highly potent and orally available YAP/TEADs PPI inhibitor with broad anti-tumor activity as a single agent.
Citation Format: Jiajun Lu, Ming Gao, Wenpei Du, Xiaofei Fan, Jinping Li, Mengya Wang, Lijian Feng, Yingjie Li, Jiaqi Yao, Jiting Lu, Wenqi Cui, Qiangang Zheng, Jidong Zhu. Discovery of ETS-006, a highly potent YAP/TEADs PPI inhibitor with broad anti-tumor activity as a single agent [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4585.
Abstract 4633: Differentiation driver gene HOXD4 as a potential prognostic indicator and therapeutic target in anaplastic thyroid cancer
Authors: Kopec Kaci , Jarboe Tara , DeSouza Nicole R. , Islam Humayun K. , Geliebter Jan , Tiwari Raj K. 
Published: March 2024

Abstract
Anaplastic thyroid cancer (ATC) is always diagnosed as stage IV with a 5 year survival rate of less than 3% due to its aggressive metastatic phenotype. ATC lacks differentiation and loses its thyroid-like functions making it a difficult cancer to treat due to its lack of targetable genetic lesions and unresponsiveness to conventional treatments. Therefore, we investigated genes that had aberrant expression in ATC in relation to differentiation. Using NCBI Gene expression omnibus (GSE33630, GSE85457), which provides publicly available transcriptomic datasets, and bioinformatics software, GEO2R, we found that Homeobox D4 (HOXD4) has 12.5FC higher expression in ATC vs. normal tissue (p=0.000552) and 4.36FC higher in ATC vs. papillary thyroid cancer (PTC) in human patients (p=6.69e-08). HOXD4 is a transcription factor that plays a crucial role in cell differentiation and has been associated with a worse prognosis in cancers such as ovarian serous carcinoma. As loss of differentiation is essential to ATC’s refractory nature and therapeutic resistance, we are exploring modulation of differentiation by all-trans retinoic acid (ATRA). ATRA was used to induce differentiation in ATC cell line T238 therefore abrogating the aggressive phenotype of this cancer. T238 treated with ATRA had a 26% decrease in proliferation at 24 hours, 46% at 48 hours, and 87% at 72 hours measured using a trypan blue exclusion assay. T238 treated with ATRA also had a 44% decrease in migratory capacity at 24 hours and 24% at 48 hours measured by a cell scratch wound assay. Immortalized normal thyroid cell line NTHY-ori-3-1 did not have a significant decrease in either proliferation or migratory capacity when treated with ATRA. T238 cells treated with ATRA for 24 hours had a 30% decrease in HOXD4 protein levels. Lastly, immunohistochemistry staining of HOXD4 in human patient tissue samples confirmed the over-expression of HOXD4 in ATC (19.5% staining) vs. normal tissue (2.5%) and PTC (7.5%). Overall, we hypothesize that the aberrant expression of HOXD4 in ATC plays a crucial role in the aggressive metastatic phenotype and therefore differentiation agents such as ATRA can target this biomarker to modulate the ATC phenotype. Therefore, HOXD4 can be used as a potential prognostic indicator for early detection of ATC. Future studies will involve CRISPRi based knockdown of HOXD4 in vitro and validation of these results in animal in vivo models.
Citation Format: Kaci Kopec, Tara Jarboe, Nicole R. DeSouza, Humayun K. Islam, Jan Geliebter, Raj K. Tiwari. Differentiation driver gene HOXD4 as a potential prognostic indicator and therapeutic target in anaplastic thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4633.
Abstract 4636: Genome-wide drug anchor screens identify CAAP1 and AKAP17A as regulators of PRMT5 inhibitor sensitivity
Authors: Yoda Satoshi , Tonini Matthew R. , Nicolson Hilary E. , Poleretzky Samuel , Fenoglio Silvia , Lombardo Steven , Grove Lauren , Meier Samuel R. , Choi Ashley , Yu Yi , Cottrell Kevin M. , Maxwell John P. , Teng  , Andersen Jannik N. , Briggs Kimberly J. 
Published: March 2024

Abstract
MTA-cooperative PRMT5 inhibitors are an emerging treatment option for patients with one of the 10-15% of all human cancers harboring MTAP homozygous deletion. To identify potential regulators of sensitivity to PRMT5 inhibitors, we performed genome-wide CRISPR knockout screens in the presence and absence of an MTA-cooperative PRMT5 inhibitor. Knockout of CAAP1 and AKAP17A were among the strongest sensitizing hits across multiple MTAP-deleted cancer cell lines representing different histologies. Strikingly, the CAAP1 gene co-localizes with MTAP and CDKN2A on chromosome 9p21. Co-deletion of CAAP1 is reported in 20 percent of MTAP-deleted cancers in the TCGA PanCancer Atlas. CAAP1 or AKAP17A knockout in MTAP-deleted cancer cell lines sensitized the cells to PRMT5 inhibitors including the clinical stage MTA-cooperative inhibitors, TNG908 and TNG462, and the non-MTA-cooperative inhibitor, GSK3326595. Moreover, we discovered that CAAP1 and AKAP17A protein levels are interdependent, as knockout of either gene caused decreased protein levels for the other. Consistent with this finding, CAAP1 reconstitution in CAAP1-deleted cell lines led to increased AKAP17A levels. Endogenous CAAP1 and AKAP17A protein levels are positively correlated across a panel of cancer cell lines and MTAP-deleted patient-derived xenograft models. Consistent with a previous report (Ni et al., 2023), exogenous CAAP1 and AKAP17A co-immunoprecipitation studies suggest that the proteins form a protein complex. AKAP17A and CAAP1 are not well-characterized proteins, but PRMT5 inhibitors induce global alternative splicing events (ASEs) in cancer cells, and based on preliminary studies a possible function for the CAAP1/AKAP17A complex could be to mitigate ASEs induced by PRMT5 inhibition. Collectively, these data indicate that CAAP1 and AKAP17A exist interdependently and mediate sensitivity to PRMT5 inhibitors. The colocalization and 20 percent incidence of CAAP1 deletion in the setting of MTAP deletion may suggest that such patients will have improved responses to PRMT5-targeted therapy. S. Yoda and M. R. Tonini contributed equally.
Citation Format: Satoshi Yoda, Matthew R. Tonini, Hilary E. Nicolson, Samuel Poleretzky, Silvia Fenoglio, Steven Lombardo, Lauren Grove, Samuel R. Meier, Ashley Choi, Yi Yu, Kevin M. Cottrell, John P. Maxwell, Teng, Jannik N. Andersen, Kimberly J. Briggs. Genome-wide drug anchor screens identify CAAP1 and AKAP17A as regulators of PRMT5 inhibitor sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4636.