bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6963: Cysteinyl leukotriene receptors promote melanoma progression and metastasis
Authors: Sabu Kattuman Emma Elizabeth , Teegala Lakshminarayan Reddy , Darzi Somayeh , Paruchuri Sailaja 
Published: March 2024

Abstract
Background: Cysteinyl leukotrienes (cys-LTs; LTC4, LTD4, LTE4) are pro-inflammatory mediators mainly produced by hematopoietic cells, which enhance inflammation through their receptors, CysLT1R and CysLT2R. They play a pivotal role in the development of chronic asthma in humans. Recent association of inflammation with cancer has led to immense interest on the role of cysteinyl leukotrienes in cancer progression and metastasis. However, the exact molecular mechanisms regarding how these inflammatory mediators regulate the tumor proliferation and metastasis remain unexplored. A thorough investigation of these precise molecular mechanisms and identification of the specific receptor/s responsible can aid in understanding the therapeutic potential of these receptors in various cancers like melanoma. Since the inhibitors of these receptors are already FDA approved for the treatment of asthma, our goal is to repurpose these drugs to treat melanoma progression.
Objective: To determine the mechanistic aspects of how CysLTRs regulate melanoma tumor initiation, progression, and metastasis.
Methods: Protein expression by western blotting and ELISA, transcript expression by qPCR, viability, and proliferation by XTT and BrDU, migration using trans-well assay, tumor growth and metastasis were confirmed through in vivo experiments.
Results & Conclusion: B16F10 melanoma cells express high CysLT1R compared to CysLT2R and produce endogenous cys-LTs that function in an autocrine signaling pattern. Further, cys-LTs mediated the activation of several signaling proteins such as ERK, p38, AKT, and CREB that are important for melanoma survival and proliferation. Moreover, treatment with CysLTR antagonists significantly reduced melanoma cell proliferation, survival, and migration. Accordingly, we observed a significant reduction in the melanoma tumor volume in vivo in both Cysltr1−/- and Cysltr2−/− mice compared to the WT mice. Interestingly, angiogenesis was significantly reduced in Cysltr2−/- mice but not in Cysltr1−/−.Therefore, we speculate that while both receptors play a crucial role in tumor proliferation in vivo, CysLT2R is the main driver of angiogenesis and metastasis. Therefore, targeting both these receptors using their specific antagonists can offer potential therapy for melanoma progression and metastasis.
Citation Format: Emma Elizabeth Sabu Kattuman, Lakshminarayan Reddy Teegala, Somayeh Darzi, Sailaja Paruchuri. Cysteinyl leukotriene receptors promote melanoma progression and metastasis [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 6963.
Abstract 7025: Advancing methylation analysis: TAPS v1.0: A fast, scalable, and non-destructive sequencing method
Authors: Haimes Josh , Marshall Craig , Sanders Travis , Vogel Sam , Ranik Martin , Casas Eduard , Wendel Doug , Karamanof Leo , Faurholme Bjarne , de Beer Abre , French Lee , Wadsworth Ross , Giordia Kristina , van der Walt Eric , Kudlow Brian 
Published: March 2024

Abstract
In the pursuit of advancing multi-cancer early detection, the exploration of cell-free DNA (cfDNA) through methylation profiling has emerged as a promising avenue. However, the realization of its full potential is impeded by limitations inherent in conventional methodologies, notably the 'gold standard' bisulfite conversion methods. These approaches pose challenges such as DNA destruction and the generation of low-complexity sequences resulting from the conversion of unmethylated cytosines to thymine. TET Assisted Pyridine-Borane Sequencing (TAPS) holds the potential as a non-destructive, rapid, and scalable alternative for base-level methylation analysis.
In this context, we introduce TET Assisted Pyridine-Borane Sequencing version 1.0 (TAPS v1.0), showcasing advancements to the technology originally introduced by Schuster-Böckler, Song, and their collaborators. TAPS v1.0 transforms 5mC into dihydrouracil (DHU) through a series of oxidation and reduction reactions. Ultimately, DHU is recognized as dU during PCR resulting in C-to-T conversions at 5mC sites, leaving unmethylated cytosines, the majority of cytosines, unchanged. The nondestructive nature of 5mC conversion yields significantly higher library yield and complexity compared to BS-seq. By leveraging Watchmaker's proprietary polymerase evolution platform, a DNA polymerase tolerant to DHU was selected for library amplification post DHU conversion, enabling unimpeded detection of 5mC, particularly in densely packed CpG repeats. Coupled with an optimized End Repair and A-tailing chemistry preceding TAPS v1.0, clinically relevant cfDNA samples of low quality and/or quantity can be analyzed in methylation detection pipelines.
To evaluate the performance of TAPS v1.0, human genomic DNA with control spike-ins featuring varying methylation statuses were employed. TAPS v1.0 exhibited significantly higher final library yield and greater complexity compared to BS-seq. Similar outcomes were observed in clinically relevant cfDNA samples.
Citation Format: Josh Haimes, Craig Marshall, Travis Sanders, Sam Vogel, Martin Ranik, Eduard Casas, Doug Wendel, Leo Karamanof, Bjarne Faurholme, Abre de Beer, Lee French, Ross Wadsworth, Kristina Giordia, Eric van der Walt, Brian Kudlow. Advancing methylation analysis: TAPS v1.0: A fast, scalable, and non-destructive sequencing method [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 7025.
Abstract 7042: Enhancing TCR T cell function in solid tumors through in vivo combinatorial screens and single-cell analysis
Authors: Polyak Dina , Fuhriman Jessica , Susanto Josephine , Merrell Allyson , Simon Mandi , Oh Catherine , Cordazo Andrew , DeTomasso David , Tocchini Carla , Sail Vibhavari , Cui Eric , Milush Jeff , Gray-Rupp Levi , Galvin Brendan , Murriel Christopher , Zheng Grace , Boroughs Angela C. , Thakore Pratiksha , Oh Soyoung , Freimer Jake , Chen Bob , Eidenschenk Celine , Wheeler Emily , Levine Jacob , Huetter Jan-Christian , Schartner Jill , Geiger-Schuller Katie , Rozenblatt-Rosen Orit , Rutz Sascha , Mellman Ira , Haining W. Nicholas 
Published: March 2024

Abstract
The therapeutic potential of T cell therapies for treating solid tumors can be limited by intrinsic T cell exhaustion mechanisms and the suppressive tumor microenvironment. To better understand these challenges and identify genetic perturbations to enhance T cell functions, we developed in vivo exhaustion models and performed pooled CRISPR/Cas9-based screens with detailed characterization of T cell states through single cell RNA-sequencing (scRNA-seq). In vivo Xenograft exhaustion models were developed in the format of T cell receptor (TCR) T cells, with tumor cell lines expressing TCR-specific antigen (NY-ESO-1) respectively. Individual perturbations were introduced into T cells via non-viral editing and pooled before transferred into mice with established tumors of various sizes that provided continuous antigen exposure to drive exhaustion, while providing sufficient number of T cells from tumor and spleen tissues for scRNA-seq. The pooled CRISPR in vivo screens in human TCR T cells enabled us to evaluate T cell phenotypes resulting from gain-of-function, loss-of-function, or combinations of these modifications across a wide array of target genes. We identified known and previously uncharacterized combinatorial perturbations that were enriched or depleted and were associated with distinct transcriptional phenotypes over the course of chronic stimulation. This approach allows us to bridge the gaps in our understanding of how T cells can be reprogrammed to overcome exhaustion and function more effectively in the challenging environment of solid tumors.
Citation Format: Dina Polyak, Jessica Fuhriman, Josephine Susanto, Allyson Merrell, Mandi Simon, Catherine Oh, Andrew Cordazo, David DeTomasso, Carla Tocchini, Vibhavari Sail, Eric Cui, Jeff Milush, Levi Gray-Rupp, Brendan Galvin, Christopher Murriel, Grace Zheng, Angela C. Boroughs, Pratiksha Thakore, Soyoung Oh, Jake Freimer, Bob Chen, Celine Eidenschenk, Emily Wheeler, Jacob Levine, Jan-Christian Huetter, Jill Schartner, Katie Geiger-Schuller, Orit Rozenblatt-Rosen, Sascha Rutz, Ira Mellman, W. Nicholas Haining. Enhancing TCR T cell function in solid tumors through in vivo combinatorial screens and single-cell analysis [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 7042.
Abstract 7110: Characterizing pY240-PTEN:Ki-67 interactions and development of a PPI disrupting peptide
Authors: Jones Brandon , Patel Sejal , Furnari Frank 
Published: March 2024

Abstract
Glioblastoma (GBM) is the most aggressive and common malignant primary brain tumor. Standard of care for GBM patients involves chemotherapy and ionizing radiation which induce DNA damage to kill tumor cells; however resistance to these treatment modalities commonly develop through various mechanisms. One novel mechanism of radioresistance is through enhanced homologous recombination (HR) DNA damage response (DDR) mediated by nuclear-localized tyrosine-phosphorylated PTEN (pY240-PTEN) recruited to chromatin through interaction with the PP1 Binding Domain (PP1BD) of Ki-67. PTEN is known to play an important tumor-suppressive role and is found to be mutated in approximately 40% of GBMs. A Y240F-PTEN knock-in mouse model has shown that loss of Y240 phosphorylation results in IR sensitivity. Ki-67 dependent, pY240-PTEN facilitated DDR may be regulated by currently uncharacterized interactions within the Ki-67 PP1BD and determination of these interactions may enable development of complex-disrupting peptides capable of radiosensitizing glioma cells. To this end, I have identified residues in the Ki-67 PP1BD that are essential for pY240-PTEN interaction via streptavidin pulldown of N-terminal biotinylated peptides synthesized with alanine mutations at all residues spanning the Ki-67 PP1BD. Orthogonally, glioma cell lines have been engineered that stably express Ki-67 minigene constructs harboring mutation of the identified PP1BD residues. The effects of these mutations on PTEN:Ki-67 interaction, as well as DDR, HR, chromatin accessibility, and colony formation efficiency are currently being interrogated. Competitor peptides have been designed based on candidate Ki-67 residues and evaluated for their ability to bind PTEN. Further optimization of these peptides has led to candidates that are being assessed for stability and potential to radiosensitize glioma cells. In addition, regulation of pY240-PTEN:Ki-67 interaction by posttranslational modification of the Ki-67 PP1BD by aurora B kinase and cyclin dependent kinase 1 has been investigated through pulldown of biotinylated peptides harboring phosphorylated candidate residues. Lastly, Ki-67 has been knocked out in U87 glioma cells, as well as TS528 glioma stem like cells, and the resulting effect on IR sensitivity and DDR is being investigated in the absence, or presence of PTEN. Overall, this project has begun to characterize the regulation and critical molecular interactions between pY240-PTEN and Ki-67, elucidating potential strategies that could disrupt these interactions to enhance the efficacy of radiotherapy.
Citation Format: Brandon Jones, Sejal Patel, Frank Furnari. Characterizing pY240-PTEN:Ki-67 interactions and development of a PPI disrupting peptide [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 7110.
Abstract 7132: Preclinical characterization of LAE119, a novel PARP1 selective inhibitor and trapper
Authors: Li Ming , Chen Yan , Chen Junyan , Jiang Ling , Lin Xiaofen , Gu Justin 
Published: March 2024

Abstract
Current PARP inhibitors primarily target PARP1/2 and demonstrate high efficacy against tumors with deficiencies in homologous recombination repair, such as those with BRCA mutations. However, these inhibitors are also associated with significant hematological toxicities. Studies have indicated that the synthetic lethality observed with BRCA mutations is mainly driven by PARP1, while PARP2 is not essential in this context. PARP2 has been shown to be crucial for the survival of hematopoietic stem/progenitor cells in animal models. Therefore, selective inhibition of PARP1 could potentially reduce toxicity and improve therapeutic outcomes. Here we introduce LAE119, a potent and selective PARP1 inhibitor and PARP1-DNA trapper. It demonstrates more than a 1000-fold selectivity for PARP1 DNA trapping compared to PARP2. In comparison to most PARP inhibitors including AZD5305, LAE119 exhibits extremely long residence time on PARP1 in both biochemical and cellular assays. It demonstrates robust anti-proliferation activity against BRCA2−/− DLD-1 cells and MDA-MB-436 cells, with IC50 value of 0.6 nM in both cell lines. In CAL51 cells, which has a BRCA2 mutation but with low PARP1 expression level and are much less sensitive to AZD5305, LAE119 demonstrates much better activity than AZD5305, particularly when PARP1 level is increased with transgene expression. LAE119 demonstrated substantial tumor inhibition in MDA-MB-436 and Capan-1 xenograft models. LAE119 also displays favorable ADME properties and PK profiles. It has high tumor/plasma ratio which is beneficial for sustainable anti-tumor effect and reduction of off-target effects. In rat hematologic toxicity study, LAE119 at 10 mpk QD dose was well tolerated and had minimal effects on hematologic parameters. Both in vitro and in vivo data strongly support the further clinical investigation of LAE119.
Citation Format: Ming Li, Yan Chen, Junyan Chen, Ling Jiang, Xiaofen Lin, Justin Gu. Preclinical characterization of LAE119, a novel PARP1 selective inhibitor and trapper [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 7132.
Abstract 7134: Treatment of pancreatic cancer cells with tumor treating fields (TTFields) and PARP inhibitors
Authors: Ene Hila , Meir Kerem Ben , Martinez-Conde Antonia , Frechtel-Gerzi Roni , Gabay Hila , Gerasimova Daria , Engelman Rotem , Dor-On Eyal , Haber Adi , Giladi Moshe , Palti Yoram 
Published: March 2024

Abstract
Background: Therapeutic options for advanced stage pancreatic cancer are limited. Patients harboring germline BRCA mutations benefit from PARP inhibitors (PARPi); unfortunately, such mutations are rare in pancreatic cancer. Tumor Treating Fields (TTFields), electric fields that disrupt cellular processes crucial for cancer cell viability, have shown effectiveness against pancreatic cancer cells, and are currently under clinical investigation for the treatment of patients with pancreatic cancer. The mechanism of action of TTFields in various cancer types has suggested involvement of BRCA downregulation. The current study examined the potential sensitization of BRCA wild-type pancreatic cancer cell lines to PARPi with TTFields application.
Methods: BxPC3 and AsPC1 human pancreatic BRCA wild-type cancer cells were treated for 72 h with TTFields (frequency of 150 kHz; intensity of 1 and 0.5 V/cm RMS, respectively), using the inovitro device. The PARPi niraparib and olaparib were each administered to the cells at various concentrations, with or without co-application of TTFields. At treatment cessation, cell count, colony formation, and apoptosis were measured.
Results: Applying PARPi to pancreatic cell lines yielded a dose-dependent cytotoxic and anti-clonogenic effects, and induced apoptosis. TTFields application also induced such effects when applied alone, while delivery of TTFields together with PARPi amplified the effects demonstrated by PARPi alone.
Conclusions: Concomitant application of TTFields and PARPi in BRCA wild type pancreatic cancer cells exhibits a potential improvement relative to the mono-therapies. This could be rationalized based on the previously demonstrated ability of TTFields to induce a state of BRCAness in cancer cells, and suggests benefit for TTFields and PARPi co-treatment in the absence of background BRCA mutations.
Citation Format: Hila Ene, Kerem Ben Meir, Antonia Martinez-Conde, Roni Frechtel-Gerzi, Hila Gabay, Daria Gerasimova, Rotem Engelman, Eyal Dor-On, Adi Haber, Moshe Giladi, Yoram Palti. Treatment of pancreatic cancer cells with tumor treating fields (TTFields) and PARP inhibitors [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 7134.
Abstract 7147: ASN-3186 is a potent and selective inhibitor of USP1 for the treatment of BRCA1/2 mut and HRD+ cancers
Authors: Sun Qiaoling , Chen Yunfei , Wu Maojiang , Lv Jing , Jin Hongyue , Zeng Peng , Song Xia , Hou Wenfeng , Huang Qi , Niu Wei , Zhang Mengyao , Wang Tie-Lin , Chen Alice 
Published: March 2024

Abstract
Ubiquitin-specific protease 1 (USP1), a well-characterized member of the deubiquitinating enzyme family, selectively cleaves ubiquitin from various target proteins, including DNA repair protein PCNA. USP1 contributes to oncogenesis by playing critical roles in DNA damage repair processes including translesion synthesis and the Fanconi anemia pathway. Despite the clinical benefit achieved with PARP inhibitors (PARPi) in BRCA-mutated (BRCAm) or homologous recombination deficient (HRD+) populations, some patients either do not respond to therapy or develop resistance. USP1 inhibitors may have the potential to address this unmet clinical need as USP1 functions in distinct DNA damage repair pathway as compared to PARP. ASN-3186 is a novel, potent, and selective USP1 inhibitor with enzyme IC50 value of single digit nanomolar and selectivity &gt;1000-fold against other family members. ASN-3186 demonstrated potent anti-proliferative activity in the BRCA1m triple negative breast cancer (TNBC) cell line, MDA-MB-436 (IC50 &lt;30 nM). MDA-MB-436 CDX mouse model confirmed dose-dependent, single-agent inhibitory activity of ASN-3186 in vivo with higher potency than KSQ4279, possibly due to ASN-3186’s higher oral bioavailability. Efficacy is consistent with increase of pharmacodynamic biomarker ub-PCNA. The combination of ASN-3186 and PARPi Olaparib yielded a more robust and durable anti-tumor response, with near-complete tumor regression demonstrated at higher combination dose. Moreover, addition of ASN-3186 significantly sensitized Olaparib’s minimal anti-tumor activity in CAOV3 (ovarian, HRD high) and MX-1 (TNBC, BCRA1/2 mut) models, which are resistant to PAPRi, indicating that it has the potential to overcome PARPi resistance. Synthetic lethal activity was also observed when ASN-3186 was combined with DNA damage drug Gemcitabine. Furthermore, ASN-3186 displayed desirable ADME and PK profiles with high oral bioavailabilities (&gt;75%) across species. These data support further clinical development of ASN-3186 as a potential best-in-class USP1 inhibitor, both as a single agent as well as in combination with PARPi, for treatment of BRCA1/2 mut and HRD+ cancers.
Citation Format: Qiaoling Sun, Yunfei Chen, Maojiang Wu, Jing Lv, Hongyue Jin, Peng Zeng, Xia Song, Wenfeng Hou, Qi Huang, Wei Niu, Mengyao Zhang, Tie-Lin Wang, Alice Chen. ASN-3186 is a potent and selective inhibitor of USP1 for the treatment of BRCA1/2 mut and HRD+ 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 7147.
Abstract 7184: Simulating extended dosing intervals for atezolizumab: A comparative analysis between NONMEM and Pumas
Authors: Bateman Francis , Arisa Oluwatobi , Cabanas Natalia Corvalan , Zeng Yi , Peer Cody , Schmidt Keith , Figg William Douglas 
Published: March 2024

Abstract
The initially approved dosage regimens of 840 mg every 2 weeks, 1200 mg every 3 weeks, and 1680 mg every 4 weeks are considered excessive concerning the specified minimum effective concentration of 6 ug/mL and the significant exposure-response relationship with Adverse Events of Special Interest (AESI). Our previous research, demonstrated through simulation, indicated that an extended-interval dosing regimen (840 mg every 6 weeks) after two standard loading doses maintained efficacy with a nonsignificant exposure-response relationship with AESI.In alignment with the FDA's initiative "Project Optimus," which aims to optimize drug dosing for improved therapeutic outcomes, we explore alternative dosage regimens for atezolizumab. Through a comparison of the traditional 30-year-old industry standard NONMEM software and the recently developed PumasAI software, we simulate these regimens, utilizing our previously published article as a benchmark. Given the rapid evolution of artificial intelligence (AI) and machine learning, it is crucial for pharmacokinetic modeling to adapt and leverage these advancements. We anticipate that this paper will contribute to the integration of AI and machine learning software in pharmacokinetic analysis, aligning with the goals of "Project Optimus" to ensure that drug concentrations are optimized for efficacy and safety.
Table 1: Comparative Summary of Simulated Pharmacokinetic Parameters: Pumas vs. NONMEM Pumas NONMEM Regimen Cycle Week Cmax (ug/mL) Cmax (ug/mL) Cmax (ug/mL) Cmax (ug/mL) Cmin (ug/mL) Weekly AUC (ug*day/mL) 1200 mg q3w 1st 3 384(278-533) 64.1(31.4-112) 919(640-1290) 394 (278-559) 75.6 (44.5-121) 1003 (755-1342) 7th 21 541(371-795) 146(53.8-349) 1750(977-3210) 583 (414-847) 180 (75.9-396) 2014 (1169-3535) 840 mg q2w x2, 840 mg q6w 1st 2 270(195-379) 61.6(35.5-100) 775(570-1085) 275 (184-397) 71.2 (46.4-108) 834 (620-1131) 7th 38 314(221-448) 33.6(8.8-127) 650(357-1375) 336 (235-487) 46.9 (13.5-150) 774 (441-1562) 1200 mg q3w x2, 840 mg q6w 1st 3 384(278-533) 64.1(31.4-112) 919(640-1290) 394 (278-559) 75.6 (44.5-121) 1003(755-1342) 7th 39 316(224-459) 36.0(8.4-129) 670(340-1406) 327 (217-492) 46.6 (13.4-157) 763 (411-1594) 1680 mg q4w x2, 840 mg q6w 1st 4 545(380-779) 63.1(26.9-122) 1096(735-1555) 552 (375-793) 78.1 (40.7-135) 1203(869-1651) 7th 40 318(222-469) 33.9(7.7-126) 657(343-1385) 332 (227-491) 46.5 (13.6-140) 771 (436-1464)
Citation Format: Francis Bateman, Oluwatobi Arisa, Natalia Corvalan Cabanas, Yi Zeng, Cody Peer, Keith Schmidt, William Douglas Figg. Simulating extended dosing intervals for atezolizumab: A comparative analysis between NONMEM and Pumas [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 7184.